Rebuild for X86LINUX:

	modified:   hostdepend/X86LINUX64/bin/X86LINUX64/*

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/Display2 b/hostdepend/X86LINUX64/bin/X86LINUX64/Display2
index 34d793a..066a860 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/StereoDisplay b/hostdepend/X86LINUX64/bin/X86LINUX64/StereoDisplay
new file mode 100755 (executable)
index 0000000..74e210d
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/array2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/array2mrc
index 554567d..c26963c 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/bin2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/bin2mrc
index 3246033..66d86d2 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/clusterLog2ToLog b/hostdepend/X86LINUX64/bin/X86LINUX64/clusterLog2ToLog
index 96489cc..9664841 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/clusterLogASCII2Binary b/hostdepend/X86LINUX64/bin/X86LINUX64/clusterLogASCII2Binary
index 80d55bc..2134e0b 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/clusterShow b/hostdepend/X86LINUX64/bin/X86LINUX64/clusterShow
index 6264497..e19957c 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDeterminationFromThonRing b/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDeterminationFromThonRing
index 2e56811..4677b61 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDetermine b/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDetermine
index d942961..42b8296 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDisplay b/hostdepend/X86LINUX64/bin/X86LINUX64/ctfDisplay
index fe3393c..429050c 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/ctfWeightMapCreation b/hostdepend/X86LINUX64/bin/X86LINUX64/ctfWeightMapCreation
index 36470ab..f842af0 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdAtomChangeDistanceFromAtom b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdAtomChangeDistanceFromAtom
index 56c047f..987bebc 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdAtomDistanceDistribution b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdAtomDistanceDistribution
index 5772a43..cf19490 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdFilePrint b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdFilePrint
index 8d86592..41f410b 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdInfo
index d18ef57..39ae3b6 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdSelectAtoms b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdSelectAtoms
index dea6330..55ce2c4 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdSerectAtom b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdSerectAtom
index 1416ae6..a90c6fd 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/dcdTimeSeriesBehavior b/hostdepend/X86LINUX64/bin/X86LINUX64/dcdTimeSeriesBehavior
index 5e23206..9cb57d0 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/defocusDeterminationFromThonRing b/hostdepend/X86LINUX64/bin/X86LINUX64/defocusDeterminationFromThonRing
index c59d24e..70106d9 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/emData2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/emData2mrc
index cd6e2fc..d69bb89 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/imagesView b/hostdepend/X86LINUX64/bin/X86LINUX64/imagesView
index a77d55b..0f8f0d8 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/imodst2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/imodst2mrc
index 850da1a..25682e5 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/ip2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/ip2mrc
index aca47ad..c8203ab 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/llDataAverage b/hostdepend/X86LINUX64/bin/X86LINUX64/llDataAverage
index 4059f4b..b91d7b1 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/llDataAxisSearch b/hostdepend/X86LINUX64/bin/X86LINUX64/llDataAxisSearch
index 1185b49..6f4dd86 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/llDataMultiCTFCompensation b/hostdepend/X86LINUX64/bin/X86LINUX64/llDataMultiCTFCompensation
index 643969a..17696f9 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/moi2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/moi2mrc
index e3d4b3e..886cf8f 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2fld b/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2fld
index f4781f9..8b38e65 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2gif b/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2gif
index 64d9d0b..6ce4507 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2mrc b/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2mrc
index 2dbac3d..704efd8 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2tiff b/hostdepend/X86LINUX64/bin/X86LINUX64/mrc2tiff
index 3620d98..143fd5a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrc3DExtractZ b/hostdepend/X86LINUX64/bin/X86LINUX64/mrc3DExtractZ
index 6413e65..ffe0cf1 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFETnormalizeBySD b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFETnormalizeBySD
index 8595e3e..9040cf9 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTCTFCompensation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTCTFCompensation
index 8d20384..db72503 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTDigitize b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTDigitize
index 3232ee8..ad1f30d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTExpression b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTExpression
index ee321ec..a20d2a0 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTFibreDiagram b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTFibreDiagram
index ce571a1..e535ecf 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTFiltering b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTFiltering
index a4f5aa1..92fee4d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTIQEstimation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTIQEstimation
index 63b3982..2977db2 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTInfo
index e966179..ac774ec 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTLayerLineCheck b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTLayerLineCheck
index de36408..5ac6616 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTMedianFilter b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTMedianFilter
index 4bb9389..bbbc6cc 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTProjection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTProjection
index e69f245..0a64c1a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTResampling b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTResampling
index 580f440..bf79829 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTShellInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTShellInfo
index f919411..68a61b3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTSizeChange b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTSizeChange
index 0e608f1..d2d8c79 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTSpectrum b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTSpectrum
index e220456..e24357e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTXFiltering b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTXFiltering
index 783ef50..7ead713 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTplainreduce b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFFTplainreduce
index fe49754..4988f49 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFTMeridianEquatorRedece b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcFTMeridianEquatorRedece
index 831a835..60aeff3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1DProjectionfrom2D b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1DProjectionfrom2D
index 653efff..ee4109f 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dAverageByCorrelation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dAverageByCorrelation
index 744c703..c9c65eb 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dShiftAverageByAnnealing b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dShiftAverageByAnnealing
index f227a96..2e1bfe9 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dShiftByCorrelation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage1dShiftByCorrelation
index b8f6703..418ceaa 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2DBackProjection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2DBackProjection
index 664e17e..aeadaf0 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2DProjection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2DProjection
index bec2dcf..4aefe61 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2pdb b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage2pdb
index 6da46e0..509fafa 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DHighResoEmphasis b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DHighResoEmphasis
index 4200f6c..68f4e02 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DPad b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DPad
index b1fe891..c75092b 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DPad2 b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DPad2
index efcf5a2..d84c5c2 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DWindowing b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImage3DWindowing
index 5c9d322..8dac0c5 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAbnormalValueRemove b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAbnormalValueRemove
index fb56b03..a105a1f 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAdaptiveBinalization b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAdaptiveBinalization
index 64073cb..5564c8b 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAdd b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAdd
index 1d4cecd..14ce454 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAreaCalc b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAreaCalc
index eb75ee0..8489b19 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAsProbability b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAsProbability
index c5d6ba6..1959b24 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAssignedToTFofPDB b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAssignedToTFofPDB
index d836693..a6c52bc 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAssignedToTFofPDB and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAssignedToTFofPDB differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoCorrelationWithWindowing b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoCorrelationWithWindowing
index a1bf230..7c1ce1f 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtract b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtract
index aa8ec4e..908ea37 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis
index a9d5119..5f28354 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation
index 328a400..1f5acae 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D
index eb5ce7d..5f93904 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAverage b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAverage
index 768ba5c..1b9be78 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBandPassFilter b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBandPassFilter
index 80efcc5..d4eb70d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBilateralFilter b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBilateralFilter
index 1045de6..00221ac 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBinalization b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBinalization
index 8f21343..27f88d0 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBlockMerge b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageBlockMerge
index 3281b6c..555af6e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCCDNoiseRemove b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCCDNoiseRemove
index 36005fe..f990956 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensation
index a2aec99..835845e 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensation and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensation differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensationForTiltImage b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensationForTiltImage
index 546c4c7..0a774e4 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensationForTiltImage and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFCompensationForTiltImage differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFDetermination b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFDetermination
index 868fcf1..372c0d8 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFObservation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFObservation
index ce88a72..89ed2aa 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFObservation and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFObservation differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFSN b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCTFSN
index 8810170..100bee5 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCVE b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCVE
index 39114d6..d1996dd 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterDensityChange b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterDensityChange
index fd2b7b7..7d53ade 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterGet b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterGet
index 9ac01be..6649ed3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterOfMassCalculate b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCenterOfMassCalculate
index 02ef98a..7a0fa9e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCircumferentialProjection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCircumferentialProjection
index 25104ce..c60a0b3 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCircumferentialProjection and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCircumferentialProjection differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClosing b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClosing
index ebc4033..a36141e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageClusterAnalysis
index 73d4c86..c9ca11e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageColoring b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageColoring
index 1c8acb9..8294803 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnection
index 644d8e5..e6875e7 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnectivityNumberCalc b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnectivityNumberCalc
index 1d1b71a..33d7385 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnectivityNumberCalc and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConnectivityNumberCalc differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageContourSurfaceCreate b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageContourSurfaceCreate
index 1bfced5..866a9de 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageContourSurfaceCreate and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageContourSurfaceCreate differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConvolution b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageConvolution
index 94a6aae..5241a56 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoordinateChange b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoordinateChange
index 5519bfa..3fc99bb 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoreImageCalc b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoreImageCalc
index 6562cd9..1ac85c3 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoreImageCalc and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCoreImageCalc differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCorrelationInFourierSpace b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCorrelationInFourierSpace
index caeef9c..2ec3418 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCrystalCreate b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCrystalCreate
index 2189a17..51d8d4d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCylinderSection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageCylinderSection
index a575f3b..229b5f3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDeadPixelCorrection b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDeadPixelCorrection
index a8ea3ba..eb20b5e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityChangeEstimation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityChangeEstimation
index dbbea4d..03ac94e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityInfo b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityInfo
index 9333ec8..10c75aa 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityNormalization b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityNormalization
index 6af40f1..c648938 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityNormalizationByImage b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDensityNormalizationByImage
index cf005dc..3fb1955 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDilation
index 24aaf75..6e88a7a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDisplayDensityAsTempFactor b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDisplayDensityAsTempFactor
index c1197ad..2b2c38c 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDistanceConversion b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDistanceConversion
index b940e89..7ed0023 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideInfoForTomography b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideInfoForTomography
index b2062be..f07999a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideIntoTwoImages b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideIntoTwoImages
index 2a71ac1..6ae1208 100755 (executable)
Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideIntoTwoImages and b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDivideIntoTwoImages differ

diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDividedByFile b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageDividedByFile
new file mode 100755 (executable)
index 0000000..381e405
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEdgeEnhancement b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEdgeEnhancement
new file mode 100755 (executable)
index 0000000..fd1bc65
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEdgeImageGet b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEdgeImageGet
index d25c104..9899c1d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageErosion b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageErosion
index 9c24ea6..70027de 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEstimateTiltImage b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageEstimateTiltImage
index 0954149..d9bedcb 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageExpression b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageExpression
index 5c0a2c5..41b45bd 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFFT b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFFT
index d72d42d..61970e3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFFTLayerLineExtraction b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFFTLayerLineExtraction
index 7b2d5a8..3715591 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFOMCalc b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFOMCalc
index 1410310..cf65698 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFeatureExtraction b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFeatureExtraction
index 5c6b283..1a4bfdc 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilterCreate b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilterCreate
index 01344c7..7783d5c 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilteringbyFile b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilteringbyFile
index ab7e043..75b600a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilteringbyFileForVariance b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFilteringbyFileForVariance
index c4cb782..fca5485 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierShellCorrelation b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageFourierShellCorrelation
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index f21de0e..3541a9a 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/ctfInfo/src/X86LINUX64/libctfInfo.a and b/hostdepend/X86LINUX64/src/Objects/DataManip/ctfInfo/src/X86LINUX64/libctfInfo.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/llData/src/X86LINUX64/libllData.a b/hostdepend/X86LINUX64/src/Objects/DataManip/llData/src/X86LINUX64/libllData.a
index 09cbf77..ba01bc4 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/llData/src/X86LINUX64/libllData.a and b/hostdepend/X86LINUX64/src/Objects/DataManip/llData/src/X86LINUX64/libllData.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/ltlgData/src/X86LINUX64/libltlgData.a b/hostdepend/X86LINUX64/src/Objects/DataManip/ltlgData/src/X86LINUX64/libltlgData.a
index 2ae216d..34ef55a 100644 (file)
Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/ltlgData/src/X86LINUX64/libltlgData.a and b/hostdepend/X86LINUX64/src/Objects/DataManip/ltlgData/src/X86LINUX64/libltlgData.a differ

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
index 4e46051..2b957bb 100644 (file)
--- a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
@@ -12,6 +12,7 @@ X86LINUX64/lmrcImageAverage.o:lmrcImageAverage.o
 X86LINUX64/lmrcImageBandPassFilter.o:lmrcImageBandPassFilter.o
 X86LINUX64/lmrcImageBilateralFilter.o:lmrcImageBilateralFilter.o
 X86LINUX64/lmrcImageBinarization.o:lmrcImageBinarization.o
+X86LINUX64/lmrcImageBottomHatTransform.o:lmrcImageBottomHatTransform.o
 X86LINUX64/lmrcImageBoundaryInfo.o:lmrcImageBoundaryInfo.o
 X86LINUX64/lmrcImageCTFCompensation.o:lmrcImageCTFCompensation.o
 X86LINUX64/lmrcImageCTFDetermination.o:lmrcImageCTFDetermination.o
@@ -43,6 +44,7 @@ X86LINUX64/lmrcImageDilation.o:lmrcImageDilation.o
 X86LINUX64/lmrcImageDistanceConversion.o:lmrcImageDistanceConversion.o
 X86LINUX64/lmrcImageEdge.o:lmrcImageEdge.o
 X86LINUX64/lmrcImageEdgeAverage.o:lmrcImageEdgeAverage.o
+X86LINUX64/lmrcImageEdgeEnhancement.o:lmrcImageEdgeEnhancement.o
 X86LINUX64/lmrcImageErosion.o:lmrcImageErosion.o
 X86LINUX64/lmrcImageFFT.o:lmrcImageFFT.o
 X86LINUX64/lmrcImageFOMCalc.o:lmrcImageFOMCalc.o
@@ -56,6 +58,7 @@ X86LINUX64/lmrcImageFourierShellCorrelation.o:lmrcImageFourierShellCorrelation.o
 X86LINUX64/lmrcImageHighPassFilter.o:lmrcImageHighPassFilter.o
 X86LINUX64/lmrcImageHighlighting.o:lmrcImageHighlighting.o
 X86LINUX64/lmrcImageLabeling.o:lmrcImageLabeling.o
+X86LINUX64/lmrcImageLogicalOperation.o:lmrcImageLogicalOperation.o
 X86LINUX64/lmrcImageLowPassFilter.o:lmrcImageLowPassFilter.o
 X86LINUX64/lmrcImageMasking.o:lmrcImageMasking.o
 X86LINUX64/lmrcImageMaxDataGet.o:lmrcImageMaxDataGet.o
@@ -74,6 +77,7 @@ X86LINUX64/lmrcImagePad.o:lmrcImagePad.o
 X86LINUX64/lmrcImagePartImageSegmentation.o:lmrcImagePartImageSegmentation.o
 X86LINUX64/lmrcImagePixelSummationOfProbabilityGetByImage.o:lmrcImagePixelSummationOfProbabilityGetByImage.o
 X86LINUX64/lmrcImagePosterization.o:lmrcImagePosterization.o
+X86LINUX64/lmrcImagePrevitt.o:lmrcImagePrevitt.o
 X86LINUX64/lmrcImageProjection.o:lmrcImageProjection.o
 X86LINUX64/lmrcImageProportionalDensityLevelSetByImage.o:lmrcImageProportionalDensityLevelSetByImage.o
 X86LINUX64/lmrcImageROI2D.o:lmrcImageROI2D.o
@@ -81,6 +85,7 @@ X86LINUX64/lmrcImageROI3D.o:lmrcImageROI3D.o
 X86LINUX64/lmrcImageROInotChangeHeaderLength.o:lmrcImageROInotChangeHeaderLength.o
 X86LINUX64/lmrcImageRadialDistribution.o:lmrcImageRadialDistribution.o
 X86LINUX64/lmrcImageRhoFiltering.o:lmrcImageRhoFiltering.o
+X86LINUX64/lmrcImageRoberts.o:lmrcImageRoberts.o
 X86LINUX64/lmrcImageRotation.o:lmrcImageRotation.o
 X86LINUX64/lmrcImageSSDA.o:lmrcImageSSDA.o
 X86LINUX64/lmrcImageSamplingUnitChange.o:lmrcImageSamplingUnitChange.o
@@ -98,6 +103,7 @@ X86LINUX64/lmrcImageSinogram.o:lmrcImageSinogram.o
 X86LINUX64/lmrcImageSinogramCorrelation.o:lmrcImageSinogramCorrelation.o
 X86LINUX64/lmrcImageSinogramFFT.o:lmrcImageSinogramFFT.o
 X86LINUX64/lmrcImageSmoothing.o:lmrcImageSmoothing.o
+X86LINUX64/lmrcImageSobel.o:lmrcImageSobel.o
 X86LINUX64/lmrcImageSolventFlattening.o:lmrcImageSolventFlattening.o
 X86LINUX64/lmrcImageSphere.o:lmrcImageSphere.o
 X86LINUX64/lmrcImageSplit.o:lmrcImageSplit.o
@@ -106,6 +112,7 @@ X86LINUX64/lmrcImageSubtractionCalc.o:lmrcImageSubtractionCalc.o
 X86LINUX64/lmrcImageSummationCalculate.o:lmrcImageSummationCalculate.o
 X86LINUX64/lmrcImageSymmetryFind.o:lmrcImageSymmetryFind.o
 X86LINUX64/lmrcImageTfunction.o:lmrcImageTfunction.o
+X86LINUX64/lmrcImageTopHatTransform.o:lmrcImageTopHatTransform.o
 X86LINUX64/lmrcImageTrans.o:lmrcImageTrans.o
 X86LINUX64/lmrcImageTransformDescartesIntoPolar.o:lmrcImageTransformDescartesIntoPolar.o
 X86LINUX64/lmrcImageTriming.o:lmrcImageTriming.o
@@ -600,6 +607,40 @@ lmrcImageBinarization.o: lmrcImageBinarization.c /usr/include/stdio.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h lmrcImageBinarization.h \
  ../inc/mrcImage.h
+lmrcImageBottomHatTransform.o: lmrcImageBottomHatTransform.c \
+ lmrcImageSubtractionCalc.h ../inc/mrcImage.h /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h lmrcImageMorphology.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h
 lmrcImageBoundaryInfo.o: lmrcImageBoundaryInfo.c lmrcImageBoundaryInfo.h
 lmrcImageCTFCompensation.o: lmrcImageCTFCompensation.c \
  /usr/include/stdlib.h /usr/include/features.h /usr/include/sys/cdefs.h \
@@ -1543,6 +1584,40 @@ lmrcImageEdgeAverage.o: lmrcImageEdgeAverage.c \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h
+lmrcImageEdgeEnhancement.o: lmrcImageEdgeEnhancement.c \
+ /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /home/people/tacyas/Eos/include/Memory.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h lmrcImageEdgeEnhancement.h \
+ ../inc/mrcImage.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h
 lmrcImageErosion.o: lmrcImageErosion.c \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
@@ -1615,8 +1690,7 @@ lmrcImageFFT.o: lmrcImageFFT.c /home/people/tacyas/Eos/include/genUtil.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
- /home/people/tacyas/Eos/include/Array.h \
- /home/people/tacyas/Eos/util/X86LINUX64/cuda/include/cuda.h fftn.h
+ /home/people/tacyas/Eos/include/Array.h fftn.h
 lmrcImageFOMCalc.o: lmrcImageFOMCalc.c \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
@@ -1987,6 +2061,39 @@ lmrcImageLabeling.o: lmrcImageLabeling.c \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h
+lmrcImageLogicalOperation.o: lmrcImageLogicalOperation.c \
+ /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h lmrcImageLogic.h \
+ ../inc/mrcImage.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h
 lmrcImageLowPassFilter.o: lmrcImageLowPassFilter.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
@@ -2570,6 +2677,39 @@ lmrcImagePosterization.o: lmrcImagePosterization.c \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
  /home/people/tacyas/Eos/include/Memory.h ../inc/mrcImage.h
+lmrcImagePrevitt.o: lmrcImagePrevitt.c /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ lmrcImageEdgeEnhancement.h ../inc/mrcImage.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /home/people/tacyas/Eos/include/genUtil.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h
 lmrcImageProjection.o: lmrcImageProjection.c lmrcImageProjection.h \
  /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
@@ -2796,6 +2936,40 @@ lmrcImageRhoFiltering.o: lmrcImageRhoFiltering.c /usr/include/math.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h lmrcImageRhoFiltering.h \
  ../inc/mrcImage.h
+lmrcImageRoberts.o: lmrcImageRoberts.c \
+ /home/people/tacyas/Eos/include/Memory.h /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h lmrcImageEdgeEnhancement.h ../inc/mrcImage.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h
 lmrcImageRotation.o: lmrcImageRotation.c /usr/include/math.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
@@ -3327,6 +3501,39 @@ lmrcImageSmoothing.o: lmrcImageSmoothing.c /usr/include/stdio.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h
+lmrcImageSobel.o: lmrcImageSobel.c /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h lmrcImageEdgeEnhancement.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ ../inc/mrcImage.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h
 lmrcImageSolventFlattening.o: lmrcImageSolventFlattening.c \
  ../inc/mrcImage.h /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
@@ -3580,6 +3787,40 @@ lmrcImageTfunction.o: lmrcImageTfunction.c /usr/include/stdio.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h \
  /home/people/tacyas/Eos/include/Memory.h
+lmrcImageTopHatTransform.o: lmrcImageTopHatTransform.c \
+ lmrcImageSubtractionCalc.h ../inc/mrcImage.h /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Array.h lmrcImageMorphology.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h
 lmrcImageTrans.o: lmrcImageTrans.c ../inc/mrcImage.h /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
index 376274d..422f61c 100644 (file)
--- a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
+++ b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
@@ -13,6 +13,7 @@ lmrcImageAverage.c \
 lmrcImageBandPassFilter.c \
 lmrcImageBilateralFilter.c \
 lmrcImageBinarization.c \
+lmrcImageBottomHatTransform.c \
 lmrcImageBoundaryInfo.c \
 lmrcImageCTFCompensation.c \
 lmrcImageCTFDetermination.c \
@@ -44,6 +45,7 @@ lmrcImageDilation.c \
 lmrcImageDistanceConversion.c \
 lmrcImageEdge.c \
 lmrcImageEdgeAverage.c \
+lmrcImageEdgeEnhancement.c \
 lmrcImageErosion.c \
 lmrcImageFFT.c \
 lmrcImageFOMCalc.c \
@@ -57,6 +59,7 @@ lmrcImageFourierShellCorrelation.c \
 lmrcImageHighPassFilter.c \
 lmrcImageHighlighting.c \
 lmrcImageLabeling.c \
+lmrcImageLogicalOperation.c \
 lmrcImageLowPassFilter.c \
 lmrcImageMasking.c \
 lmrcImageMaxDataGet.c \
@@ -75,6 +78,7 @@ lmrcImagePad.c \
 lmrcImagePartImageSegmentation.c \
 lmrcImagePixelSummationOfProbabilityGetByImage.c \
 lmrcImagePosterization.c \
+lmrcImagePrevitt.c \
 lmrcImageProjection.c \
 lmrcImageProportionalDensityLevelSetByImage.c \
 lmrcImageROI2D.c \
@@ -82,6 +86,7 @@ lmrcImageROI3D.c \
 lmrcImageROInotChangeHeaderLength.c \
 lmrcImageRadialDistribution.c \
 lmrcImageRhoFiltering.c \
+lmrcImageRoberts.c \
 lmrcImageRotation.c \
 lmrcImageSSDA.c \
 lmrcImageSamplingUnitChange.c \
@@ -99,6 +104,7 @@ lmrcImageSinogram.c \
 lmrcImageSinogramCorrelation.c \
 lmrcImageSinogramFFT.c \
 lmrcImageSmoothing.c \
+lmrcImageSobel.c \
 lmrcImageSolventFlattening.c \
 lmrcImageSphere.c \
 lmrcImageSplit.c \
@@ -107,6 +113,7 @@ lmrcImageSubtractionCalc.c \
 lmrcImageSummationCalculate.c \
 lmrcImageSymmetryFind.c \
 lmrcImageTfunction.c \
+lmrcImageTopHatTransform.c \
 lmrcImageTrans.c \
 lmrcImageTransformDescartesIntoPolar.c \
 lmrcImageTriming.c \
@@ -165,6 +172,7 @@ lmrcImageAverage.o \
 lmrcImageBandPassFilter.o \
 lmrcImageBilateralFilter.o \
 lmrcImageBinarization.o \
+lmrcImageBottomHatTransform.o \
 lmrcImageBoundaryInfo.o \
 lmrcImageCTFCompensation.o \
 lmrcImageCTFDetermination.o \
@@ -196,6 +204,7 @@ lmrcImageDilation.o \
 lmrcImageDistanceConversion.o \
 lmrcImageEdge.o \
 lmrcImageEdgeAverage.o \
+lmrcImageEdgeEnhancement.o \
 lmrcImageErosion.o \
 lmrcImageFFT.o \
 lmrcImageFOMCalc.o \
@@ -209,6 +218,7 @@ lmrcImageFourierShellCorrelation.o \
 lmrcImageHighPassFilter.o \
 lmrcImageHighlighting.o \
 lmrcImageLabeling.o \
+lmrcImageLogicalOperation.o \
 lmrcImageLowPassFilter.o \
 lmrcImageMasking.o \
 lmrcImageMaxDataGet.o \
@@ -227,6 +237,7 @@ lmrcImagePad.o \
 lmrcImagePartImageSegmentation.o \
 lmrcImagePixelSummationOfProbabilityGetByImage.o \
 lmrcImagePosterization.o \
+lmrcImagePrevitt.o \
 lmrcImageProjection.o \
 lmrcImageProportionalDensityLevelSetByImage.o \
 lmrcImageROI2D.o \
@@ -234,6 +245,7 @@ lmrcImageROI3D.o \
 lmrcImageROInotChangeHeaderLength.o \
 lmrcImageRadialDistribution.o \
 lmrcImageRhoFiltering.o \
+lmrcImageRoberts.o \
 lmrcImageRotation.o \
 lmrcImageSSDA.o \
 lmrcImageSamplingUnitChange.o \
@@ -251,6 +263,7 @@ lmrcImageSinogram.o \
 lmrcImageSinogramCorrelation.o \
 lmrcImageSinogramFFT.o \
 lmrcImageSmoothing.o \
+lmrcImageSobel.o \
 lmrcImageSolventFlattening.o \
 lmrcImageSphere.o \
 lmrcImageSplit.o \
@@ -259,6 +272,7 @@ lmrcImageSubtractionCalc.o \
 lmrcImageSummationCalculate.o \
 lmrcImageSymmetryFind.o \
 lmrcImageTfunction.o \
+lmrcImageTopHatTransform.o \
 lmrcImageTrans.o \
 lmrcImageTransformDescartesIntoPolar.o \
 lmrcImageTriming.o \
@@ -317,6 +331,7 @@ lmrcImageAverage.sharedo \
 lmrcImageBandPassFilter.sharedo \
 lmrcImageBilateralFilter.sharedo \
 lmrcImageBinarization.sharedo \
+lmrcImageBottomHatTransform.sharedo \
 lmrcImageBoundaryInfo.sharedo \
 lmrcImageCTFCompensation.sharedo \
 lmrcImageCTFDetermination.sharedo \
@@ -348,6 +363,7 @@ lmrcImageDilation.sharedo \
 lmrcImageDistanceConversion.sharedo \
 lmrcImageEdge.sharedo \
 lmrcImageEdgeAverage.sharedo \
+lmrcImageEdgeEnhancement.sharedo \
 lmrcImageErosion.sharedo \
 lmrcImageFFT.sharedo \
 lmrcImageFOMCalc.sharedo \
@@ -361,6 +377,7 @@ lmrcImageFourierShellCorrelation.sharedo \
 lmrcImageHighPassFilter.sharedo \
 lmrcImageHighlighting.sharedo \
 lmrcImageLabeling.sharedo \
+lmrcImageLogicalOperation.sharedo \
 lmrcImageLowPassFilter.sharedo \
 lmrcImageMasking.sharedo \
 lmrcImageMaxDataGet.sharedo \
@@ -379,6 +396,7 @@ lmrcImagePad.sharedo \
 lmrcImagePartImageSegmentation.sharedo \
 lmrcImagePixelSummationOfProbabilityGetByImage.sharedo \
 lmrcImagePosterization.sharedo \
+lmrcImagePrevitt.sharedo \
 lmrcImageProjection.sharedo \
 lmrcImageProportionalDensityLevelSetByImage.sharedo \
 lmrcImageROI2D.sharedo \
@@ -386,6 +404,7 @@ lmrcImageROI3D.sharedo \
 lmrcImageROInotChangeHeaderLength.sharedo \
 lmrcImageRadialDistribution.sharedo \
 lmrcImageRhoFiltering.sharedo \
+lmrcImageRoberts.sharedo \
 lmrcImageRotation.sharedo \
 lmrcImageSSDA.sharedo \
 lmrcImageSamplingUnitChange.sharedo \
@@ -403,6 +422,7 @@ lmrcImageSinogram.sharedo \
 lmrcImageSinogramCorrelation.sharedo \
 lmrcImageSinogramFFT.sharedo \
 lmrcImageSmoothing.sharedo \
+lmrcImageSobel.sharedo \
 lmrcImageSolventFlattening.sharedo \
 lmrcImageSphere.sharedo \
 lmrcImageSplit.sharedo \
@@ -411,6 +431,7 @@ lmrcImageSubtractionCalc.sharedo \
 lmrcImageSummationCalculate.sharedo \
 lmrcImageSymmetryFind.sharedo \
 lmrcImageTfunction.sharedo \
+lmrcImageTopHatTransform.sharedo \
 lmrcImageTrans.sharedo \
 lmrcImageTransformDescartesIntoPolar.sharedo \
 lmrcImageTriming.sharedo \
@@ -469,6 +490,7 @@ X86LINUX64/lmrcImageAverage.o \
 X86LINUX64/lmrcImageBandPassFilter.o \
 X86LINUX64/lmrcImageBilateralFilter.o \
 X86LINUX64/lmrcImageBinarization.o \
+X86LINUX64/lmrcImageBottomHatTransform.o \
 X86LINUX64/lmrcImageBoundaryInfo.o \
 X86LINUX64/lmrcImageCTFCompensation.o \
 X86LINUX64/lmrcImageCTFDetermination.o \
@@ -500,6 +522,7 @@ X86LINUX64/lmrcImageDilation.o \
 X86LINUX64/lmrcImageDistanceConversion.o \
 X86LINUX64/lmrcImageEdge.o \
 X86LINUX64/lmrcImageEdgeAverage.o \
+X86LINUX64/lmrcImageEdgeEnhancement.o \
 X86LINUX64/lmrcImageErosion.o \
 X86LINUX64/lmrcImageFFT.o \
 X86LINUX64/lmrcImageFOMCalc.o \
@@ -513,6 +536,7 @@ X86LINUX64/lmrcImageFourierShellCorrelation.o \
 X86LINUX64/lmrcImageHighPassFilter.o \
 X86LINUX64/lmrcImageHighlighting.o \
 X86LINUX64/lmrcImageLabeling.o \
+X86LINUX64/lmrcImageLogicalOperation.o \
 X86LINUX64/lmrcImageLowPassFilter.o \
 X86LINUX64/lmrcImageMasking.o \
 X86LINUX64/lmrcImageMaxDataGet.o \
@@ -531,6 +555,7 @@ X86LINUX64/lmrcImagePad.o \
 X86LINUX64/lmrcImagePartImageSegmentation.o \
 X86LINUX64/lmrcImagePixelSummationOfProbabilityGetByImage.o \
 X86LINUX64/lmrcImagePosterization.o \
+X86LINUX64/lmrcImagePrevitt.o \
 X86LINUX64/lmrcImageProjection.o \
 X86LINUX64/lmrcImageProportionalDensityLevelSetByImage.o \
 X86LINUX64/lmrcImageROI2D.o \
@@ -538,6 +563,7 @@ X86LINUX64/lmrcImageROI3D.o \
 X86LINUX64/lmrcImageROInotChangeHeaderLength.o \
 X86LINUX64/lmrcImageRadialDistribution.o \
 X86LINUX64/lmrcImageRhoFiltering.o \
+X86LINUX64/lmrcImageRoberts.o \
 X86LINUX64/lmrcImageRotation.o \
 X86LINUX64/lmrcImageSSDA.o \
 X86LINUX64/lmrcImageSamplingUnitChange.o \
@@ -555,6 +581,7 @@ X86LINUX64/lmrcImageSinogram.o \
 X86LINUX64/lmrcImageSinogramCorrelation.o \
 X86LINUX64/lmrcImageSinogramFFT.o \
 X86LINUX64/lmrcImageSmoothing.o \
+X86LINUX64/lmrcImageSobel.o \
 X86LINUX64/lmrcImageSolventFlattening.o \
 X86LINUX64/lmrcImageSphere.o \
 X86LINUX64/lmrcImageSplit.o \
@@ -563,6 +590,7 @@ X86LINUX64/lmrcImageSubtractionCalc.o \
 X86LINUX64/lmrcImageSummationCalculate.o \
 X86LINUX64/lmrcImageSymmetryFind.o \
 X86LINUX64/lmrcImageTfunction.o \
+X86LINUX64/lmrcImageTopHatTransform.o \
 X86LINUX64/lmrcImageTrans.o \
 X86LINUX64/lmrcImageTransformDescartesIntoPolar.o \
 X86LINUX64/lmrcImageTriming.o \
@@ -621,6 +649,7 @@ X86LINUX64/lmrcImageAverage.sharedo \
 X86LINUX64/lmrcImageBandPassFilter.sharedo \
 X86LINUX64/lmrcImageBilateralFilter.sharedo \
 X86LINUX64/lmrcImageBinarization.sharedo \
+X86LINUX64/lmrcImageBottomHatTransform.sharedo \
 X86LINUX64/lmrcImageBoundaryInfo.sharedo \
 X86LINUX64/lmrcImageCTFCompensation.sharedo \
 X86LINUX64/lmrcImageCTFDetermination.sharedo \
@@ -652,6 +681,7 @@ X86LINUX64/lmrcImageDilation.sharedo \
 X86LINUX64/lmrcImageDistanceConversion.sharedo \
 X86LINUX64/lmrcImageEdge.sharedo \
 X86LINUX64/lmrcImageEdgeAverage.sharedo \
+X86LINUX64/lmrcImageEdgeEnhancement.sharedo \
 X86LINUX64/lmrcImageErosion.sharedo \
 X86LINUX64/lmrcImageFFT.sharedo \
 X86LINUX64/lmrcImageFOMCalc.sharedo \
@@ -665,6 +695,7 @@ X86LINUX64/lmrcImageFourierShellCorrelation.sharedo \
 X86LINUX64/lmrcImageHighPassFilter.sharedo \
 X86LINUX64/lmrcImageHighlighting.sharedo \
 X86LINUX64/lmrcImageLabeling.sharedo \
+X86LINUX64/lmrcImageLogicalOperation.sharedo \
 X86LINUX64/lmrcImageLowPassFilter.sharedo \
 X86LINUX64/lmrcImageMasking.sharedo \
 X86LINUX64/lmrcImageMaxDataGet.sharedo \
@@ -683,6 +714,7 @@ X86LINUX64/lmrcImagePad.sharedo \
 X86LINUX64/lmrcImagePartImageSegmentation.sharedo \
 X86LINUX64/lmrcImagePixelSummationOfProbabilityGetByImage.sharedo \
 X86LINUX64/lmrcImagePosterization.sharedo \
+X86LINUX64/lmrcImagePrevitt.sharedo \
 X86LINUX64/lmrcImageProjection.sharedo \
 X86LINUX64/lmrcImageProportionalDensityLevelSetByImage.sharedo \
 X86LINUX64/lmrcImageROI2D.sharedo \
@@ -690,6 +722,7 @@ X86LINUX64/lmrcImageROI3D.sharedo \
 X86LINUX64/lmrcImageROInotChangeHeaderLength.sharedo \
 X86LINUX64/lmrcImageRadialDistribution.sharedo \
 X86LINUX64/lmrcImageRhoFiltering.sharedo \
+X86LINUX64/lmrcImageRoberts.sharedo \
 X86LINUX64/lmrcImageRotation.sharedo \
 X86LINUX64/lmrcImageSSDA.sharedo \
 X86LINUX64/lmrcImageSamplingUnitChange.sharedo \
@@ -707,6 +740,7 @@ X86LINUX64/lmrcImageSinogram.sharedo \
 X86LINUX64/lmrcImageSinogramCorrelation.sharedo \
 X86LINUX64/lmrcImageSinogramFFT.sharedo \
 X86LINUX64/lmrcImageSmoothing.sharedo \
+X86LINUX64/lmrcImageSobel.sharedo \
 X86LINUX64/lmrcImageSolventFlattening.sharedo \
 X86LINUX64/lmrcImageSphere.sharedo \
 X86LINUX64/lmrcImageSplit.sharedo \
@@ -715,6 +749,7 @@ X86LINUX64/lmrcImageSubtractionCalc.sharedo \
 X86LINUX64/lmrcImageSummationCalculate.sharedo \
 X86LINUX64/lmrcImageSymmetryFind.sharedo \
 X86LINUX64/lmrcImageTfunction.sharedo \
+X86LINUX64/lmrcImageTopHatTransform.sharedo \
 X86LINUX64/lmrcImageTrans.sharedo \
 X86LINUX64/lmrcImageTransformDescartesIntoPolar.sharedo \
 X86LINUX64/lmrcImageTriming.sharedo \
@@ -773,6 +808,7 @@ lmrcImageAverage.debugo \
 lmrcImageBandPassFilter.debugo \
 lmrcImageBilateralFilter.debugo \
 lmrcImageBinarization.debugo \
+lmrcImageBottomHatTransform.debugo \
 lmrcImageBoundaryInfo.debugo \
 lmrcImageCTFCompensation.debugo \
 lmrcImageCTFDetermination.debugo \
@@ -804,6 +840,7 @@ lmrcImageDilation.debugo \
 lmrcImageDistanceConversion.debugo \
 lmrcImageEdge.debugo \
 lmrcImageEdgeAverage.debugo \
+lmrcImageEdgeEnhancement.debugo \
 lmrcImageErosion.debugo \
 lmrcImageFFT.debugo \
 lmrcImageFOMCalc.debugo \
@@ -817,6 +854,7 @@ lmrcImageFourierShellCorrelation.debugo \
 lmrcImageHighPassFilter.debugo \
 lmrcImageHighlighting.debugo \
 lmrcImageLabeling.debugo \
+lmrcImageLogicalOperation.debugo \
 lmrcImageLowPassFilter.debugo \
 lmrcImageMasking.debugo \
 lmrcImageMaxDataGet.debugo \
@@ -835,6 +873,7 @@ lmrcImagePad.debugo \
 lmrcImagePartImageSegmentation.debugo \
 lmrcImagePixelSummationOfProbabilityGetByImage.debugo \
 lmrcImagePosterization.debugo \
+lmrcImagePrevitt.debugo \
 lmrcImageProjection.debugo \
 lmrcImageProportionalDensityLevelSetByImage.debugo \
 lmrcImageROI2D.debugo \
@@ -842,6 +881,7 @@ lmrcImageROI3D.debugo \
 lmrcImageROInotChangeHeaderLength.debugo \
 lmrcImageRadialDistribution.debugo \
 lmrcImageRhoFiltering.debugo \
+lmrcImageRoberts.debugo \
 lmrcImageRotation.debugo \
 lmrcImageSSDA.debugo \
 lmrcImageSamplingUnitChange.debugo \
@@ -859,6 +899,7 @@ lmrcImageSinogram.debugo \
 lmrcImageSinogramCorrelation.debugo \
 lmrcImageSinogramFFT.debugo \
 lmrcImageSmoothing.debugo \
+lmrcImageSobel.debugo \
 lmrcImageSolventFlattening.debugo \
 lmrcImageSphere.debugo \
 lmrcImageSplit.debugo \
@@ -867,6 +908,7 @@ lmrcImageSubtractionCalc.debugo \
 lmrcImageSummationCalculate.debugo \
 lmrcImageSymmetryFind.debugo \
 lmrcImageTfunction.debugo \
+lmrcImageTopHatTransform.debugo \
 lmrcImageTrans.debugo \
 lmrcImageTransformDescartesIntoPolar.debugo \
 lmrcImageTriming.debugo \
@@ -923,6 +965,7 @@ X86LINUX64/lmrcImageAverage.debugo \
 X86LINUX64/lmrcImageBandPassFilter.debugo \
 X86LINUX64/lmrcImageBilateralFilter.debugo \
 X86LINUX64/lmrcImageBinarization.debugo \
+X86LINUX64/lmrcImageBottomHatTransform.debugo \
 X86LINUX64/lmrcImageBoundaryInfo.debugo \
 X86LINUX64/lmrcImageCTFCompensation.debugo \
 X86LINUX64/lmrcImageCTFDetermination.debugo \
@@ -954,6 +997,7 @@ X86LINUX64/lmrcImageDilation.debugo \
 X86LINUX64/lmrcImageDistanceConversion.debugo \
 X86LINUX64/lmrcImageEdge.debugo \
 X86LINUX64/lmrcImageEdgeAverage.debugo \
+X86LINUX64/lmrcImageEdgeEnhancement.debugo \
 X86LINUX64/lmrcImageErosion.debugo \
 X86LINUX64/lmrcImageFFT.debugo \
 X86LINUX64/lmrcImageFOMCalc.debugo \
@@ -967,6 +1011,7 @@ X86LINUX64/lmrcImageFourierShellCorrelation.debugo \
 X86LINUX64/lmrcImageHighPassFilter.debugo \
 X86LINUX64/lmrcImageHighlighting.debugo \
 X86LINUX64/lmrcImageLabeling.debugo \
+X86LINUX64/lmrcImageLogicalOperation.debugo \
 X86LINUX64/lmrcImageLowPassFilter.debugo \
 X86LINUX64/lmrcImageMasking.debugo \
 X86LINUX64/lmrcImageMaxDataGet.debugo \
@@ -985,6 +1030,7 @@ X86LINUX64/lmrcImagePad.debugo \
 X86LINUX64/lmrcImagePartImageSegmentation.debugo \
 X86LINUX64/lmrcImagePixelSummationOfProbabilityGetByImage.debugo \
 X86LINUX64/lmrcImagePosterization.debugo \
+X86LINUX64/lmrcImagePrevitt.debugo \
 X86LINUX64/lmrcImageProjection.debugo \
 X86LINUX64/lmrcImageProportionalDensityLevelSetByImage.debugo \
 X86LINUX64/lmrcImageROI2D.debugo \
@@ -992,6 +1038,7 @@ X86LINUX64/lmrcImageROI3D.debugo \
 X86LINUX64/lmrcImageROInotChangeHeaderLength.debugo \
 X86LINUX64/lmrcImageRadialDistribution.debugo \
 X86LINUX64/lmrcImageRhoFiltering.debugo \
+X86LINUX64/lmrcImageRoberts.debugo \
 X86LINUX64/lmrcImageRotation.debugo \
 X86LINUX64/lmrcImageSSDA.debugo \
 X86LINUX64/lmrcImageSamplingUnitChange.debugo \
@@ -1009,6 +1056,7 @@ X86LINUX64/lmrcImageSinogram.debugo \
 X86LINUX64/lmrcImageSinogramCorrelation.debugo \
 X86LINUX64/lmrcImageSinogramFFT.debugo \
 X86LINUX64/lmrcImageSmoothing.debugo \
+X86LINUX64/lmrcImageSobel.debugo \
 X86LINUX64/lmrcImageSolventFlattening.debugo \
 X86LINUX64/lmrcImageSphere.debugo \
 X86LINUX64/lmrcImageSplit.debugo \
@@ -1017,6 +1065,7 @@ X86LINUX64/lmrcImageSubtractionCalc.debugo \
 X86LINUX64/lmrcImageSummationCalculate.debugo \
 X86LINUX64/lmrcImageSymmetryFind.debugo \
 X86LINUX64/lmrcImageTfunction.debugo \
+X86LINUX64/lmrcImageTopHatTransform.debugo \
 X86LINUX64/lmrcImageTrans.debugo \
 X86LINUX64/lmrcImageTransformDescartesIntoPolar.debugo \
 X86LINUX64/lmrcImageTriming.debugo \
@@ -1075,6 +1124,7 @@ lmrcImageAverage.cudagdb.o \
 lmrcImageBandPassFilter.cudagdb.o \
 lmrcImageBilateralFilter.cudagdb.o \
 lmrcImageBinarization.cudagdb.o \
+lmrcImageBottomHatTransform.cudagdb.o \
 lmrcImageBoundaryInfo.cudagdb.o \
 lmrcImageCTFCompensation.cudagdb.o \
 lmrcImageCTFDetermination.cudagdb.o \
@@ -1106,6 +1156,7 @@ lmrcImageDilation.cudagdb.o \
 lmrcImageDistanceConversion.cudagdb.o \
 lmrcImageEdge.cudagdb.o \
 lmrcImageEdgeAverage.cudagdb.o \
+lmrcImageEdgeEnhancement.cudagdb.o \
 lmrcImageErosion.cudagdb.o \
 lmrcImageFFT.cudagdb.o \
 lmrcImageFOMCalc.cudagdb.o \
@@ -1119,6 +1170,7 @@ lmrcImageFourierShellCorrelation.cudagdb.o \
 lmrcImageHighPassFilter.cudagdb.o \
 lmrcImageHighlighting.cudagdb.o \
 lmrcImageLabeling.cudagdb.o \
+lmrcImageLogicalOperation.cudagdb.o \
 lmrcImageLowPassFilter.cudagdb.o \
 lmrcImageMasking.cudagdb.o \
 lmrcImageMaxDataGet.cudagdb.o \
@@ -1137,6 +1189,7 @@ lmrcImagePad.cudagdb.o \
 lmrcImagePartImageSegmentation.cudagdb.o \
 lmrcImagePixelSummationOfProbabilityGetByImage.cudagdb.o \
 lmrcImagePosterization.cudagdb.o \
+lmrcImagePrevitt.cudagdb.o \
 lmrcImageProjection.cudagdb.o \
 lmrcImageProportionalDensityLevelSetByImage.cudagdb.o \
 lmrcImageROI2D.cudagdb.o \
@@ -1144,6 +1197,7 @@ lmrcImageROI3D.cudagdb.o \
 lmrcImageROInotChangeHeaderLength.cudagdb.o \
 lmrcImageRadialDistribution.cudagdb.o \
 lmrcImageRhoFiltering.cudagdb.o \
+lmrcImageRoberts.cudagdb.o \
 lmrcImageRotation.cudagdb.o \
 lmrcImageSSDA.cudagdb.o \
 lmrcImageSamplingUnitChange.cudagdb.o \
@@ -1161,6 +1215,7 @@ lmrcImageSinogram.cudagdb.o \
 lmrcImageSinogramCorrelation.cudagdb.o \
 lmrcImageSinogramFFT.cudagdb.o \
 lmrcImageSmoothing.cudagdb.o \
+lmrcImageSobel.cudagdb.o \
 lmrcImageSolventFlattening.cudagdb.o \
 lmrcImageSphere.cudagdb.o \
 lmrcImageSplit.cudagdb.o \
@@ -1169,6 +1224,7 @@ lmrcImageSubtractionCalc.cudagdb.o \
 lmrcImageSummationCalculate.cudagdb.o \
 lmrcImageSymmetryFind.cudagdb.o \
 lmrcImageTfunction.cudagdb.o \
+lmrcImageTopHatTransform.cudagdb.o \
 lmrcImageTrans.cudagdb.o \
 lmrcImageTransformDescartesIntoPolar.cudagdb.o \
 lmrcImageTriming.cudagdb.o \
@@ -1227,6 +1283,7 @@ X86LINUX64/lmrcImageAverage.cudagdb.o \
 X86LINUX64/lmrcImageBandPassFilter.cudagdb.o \
 X86LINUX64/lmrcImageBilateralFilter.cudagdb.o \
 X86LINUX64/lmrcImageBinarization.cudagdb.o \
+X86LINUX64/lmrcImageBottomHatTransform.cudagdb.o \
 X86LINUX64/lmrcImageBoundaryInfo.cudagdb.o \
 X86LINUX64/lmrcImageCTFCompensation.cudagdb.o \
 X86LINUX64/lmrcImageCTFDetermination.cudagdb.o \
@@ -1258,6 +1315,7 @@ X86LINUX64/lmrcImageDilation.cudagdb.o \
 X86LINUX64/lmrcImageDistanceConversion.cudagdb.o \
 X86LINUX64/lmrcImageEdge.cudagdb.o \
 X86LINUX64/lmrcImageEdgeAverage.cudagdb.o \
+X86LINUX64/lmrcImageEdgeEnhancement.cudagdb.o \
 X86LINUX64/lmrcImageErosion.cudagdb.o \
 X86LINUX64/lmrcImageFFT.cudagdb.o \
 X86LINUX64/lmrcImageFOMCalc.cudagdb.o \
@@ -1271,6 +1329,7 @@ X86LINUX64/lmrcImageFourierShellCorrelation.cudagdb.o \
 X86LINUX64/lmrcImageHighPassFilter.cudagdb.o \
 X86LINUX64/lmrcImageHighlighting.cudagdb.o \
 X86LINUX64/lmrcImageLabeling.cudagdb.o \
+X86LINUX64/lmrcImageLogicalOperation.cudagdb.o \
 X86LINUX64/lmrcImageLowPassFilter.cudagdb.o \
 X86LINUX64/lmrcImageMasking.cudagdb.o \
 X86LINUX64/lmrcImageMaxDataGet.cudagdb.o \
@@ -1289,6 +1348,7 @@ X86LINUX64/lmrcImagePad.cudagdb.o \
 X86LINUX64/lmrcImagePartImageSegmentation.cudagdb.o \
 X86LINUX64/lmrcImagePixelSummationOfProbabilityGetByImage.cudagdb.o \
 X86LINUX64/lmrcImagePosterization.cudagdb.o \
+X86LINUX64/lmrcImagePrevitt.cudagdb.o \
 X86LINUX64/lmrcImageProjection.cudagdb.o \
 X86LINUX64/lmrcImageProportionalDensityLevelSetByImage.cudagdb.o \
 X86LINUX64/lmrcImageROI2D.cudagdb.o \
@@ -1296,6 +1356,7 @@ X86LINUX64/lmrcImageROI3D.cudagdb.o \
 X86LINUX64/lmrcImageROInotChangeHeaderLength.cudagdb.o \
 X86LINUX64/lmrcImageRadialDistribution.cudagdb.o \
 X86LINUX64/lmrcImageRhoFiltering.cudagdb.o \
+X86LINUX64/lmrcImageRoberts.cudagdb.o \
 X86LINUX64/lmrcImageRotation.cudagdb.o \
 X86LINUX64/lmrcImageSSDA.cudagdb.o \
 X86LINUX64/lmrcImageSamplingUnitChange.cudagdb.o \
@@ -1313,6 +1374,7 @@ X86LINUX64/lmrcImageSinogram.cudagdb.o \
 X86LINUX64/lmrcImageSinogramCorrelation.cudagdb.o \
 X86LINUX64/lmrcImageSinogramFFT.cudagdb.o \
 X86LINUX64/lmrcImageSmoothing.cudagdb.o \
+X86LINUX64/lmrcImageSobel.cudagdb.o \
 X86LINUX64/lmrcImageSolventFlattening.cudagdb.o \
 X86LINUX64/lmrcImageSphere.cudagdb.o \
 X86LINUX64/lmrcImageSplit.cudagdb.o \
@@ -1321,6 +1383,7 @@ X86LINUX64/lmrcImageSubtractionCalc.cudagdb.o \
 X86LINUX64/lmrcImageSummationCalculate.cudagdb.o \
 X86LINUX64/lmrcImageSymmetryFind.cudagdb.o \
 X86LINUX64/lmrcImageTfunction.cudagdb.o \
+X86LINUX64/lmrcImageTopHatTransform.cudagdb.o \
 X86LINUX64/lmrcImageTrans.cudagdb.o \
 X86LINUX64/lmrcImageTransformDescartesIntoPolar.cudagdb.o \
 X86LINUX64/lmrcImageTriming.cudagdb.o \

diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a
index 824a8f3..c6c37c5 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a
index 2b9fbaf..8c9664c 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo
index 2e65591..f626193 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAverage.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAverage.sharedo
index 0c5f0fa..5911ed1 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageBottomHatTransform.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageBottomHatTransform.sharedo
new file mode 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageEdgeEnhancement.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageEdgeEnhancement.sharedo
new file mode 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageFFT.sharedo
index 9cf8a58..7b724d9 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageLogicalOperation.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageLogicalOperation.sharedo
new file mode 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageMontageCreate.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageMontageCreate.sharedo
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImagePrevitt.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImagePrevitt.sharedo
new file mode 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageRoberts.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageRoberts.sharedo
new file mode 100644 (file)
index 0000000..9d5f910
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new file mode 100644 (file)
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new file mode 100644 (file)
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a b/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a b/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo b/hostdepend/X86LINUX64/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/simulation/src/X86LINUX64/libsimulation.a b/hostdepend/X86LINUX64/src/Objects/DataManip/simulation/src/X86LINUX64/libsimulation.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/DataManip/transform/src/X86LINUX64/libtransform.a b/hostdepend/X86LINUX64/src/Objects/DataManip/transform/src/X86LINUX64/libtransform.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/General/AI/src/X86LINUX64/libAI.a b/hostdepend/X86LINUX64/src/Objects/General/AI/src/X86LINUX64/libAI.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/General/Array/src/X86LINUX64/libArray.a b/hostdepend/X86LINUX64/src/Objects/General/Array/src/X86LINUX64/libArray.a
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diff --git a/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a b/hostdepend/X86LINUX64/src/Objects/General/Cluster/src/X86LINUX64/libCluster.a
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diff --git a/hostdepend/X86LINUX64/src/Tools/Cluster/clusterLog2ToLog/src/X86LINUX64/clusterLog2ToLog b/hostdepend/X86LINUX64/src/Tools/Cluster/clusterLog2ToLog/src/X86LINUX64/clusterLog2ToLog
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diff --git a/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdFilePrint/src/X86LINUX64/dcdFilePrint b/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdFilePrint/src/X86LINUX64/dcdFilePrint
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diff --git a/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdInfo/src/X86LINUX64/dcdInfo b/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdInfo/src/X86LINUX64/dcdInfo
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diff --git a/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdSelectAtoms/src/X86LINUX64/dcdSelectAtoms b/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdSelectAtoms/src/X86LINUX64/dcdSelectAtoms
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diff --git a/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdSerectAtom/src/X86LINUX64/dcdSerectAtom b/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdSerectAtom/src/X86LINUX64/dcdSerectAtom
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diff --git a/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86LINUX64/dcdTimeSeriesBehavior b/hostdepend/X86LINUX64/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/X86LINUX64/dcdTimeSeriesBehavior
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diff --git a/hostdepend/X86LINUX64/src/Tools/Integration/Display2/src/X86LINUX64/Display2 b/hostdepend/X86LINUX64/src/Tools/Integration/Display2/src/X86LINUX64/Display2
index 34d793a..066a860 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/Integration/StereoDisplay/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/Integration/StereoDisplay/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..c9bf52c
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/Integration/StereoDisplay/src/X86LINUX64/.Depend
@@ -0,0 +1,130 @@
+StereoDisplay.o: StereoDisplay.c /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/GL/gl.h \
+ /usr/include/GL/glext.h /usr/include/inttypes.h /usr/include/stdint.h \
+ /usr/include/bits/wchar.h /usr/include/GL/glu.h /usr/include/GL/glut.h \
+ /usr/include/GL/freeglut_std.h ../inc/config.h \
+ ../inc/../inc/StereoDisplay.h /home/people/tacyas/Eos/include/genUtil.h \
+ /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/Memory.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/tgaFile.h
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/StereoDisplay.h /home/people/tacyas/Eos/include/genUtil.h \
+ /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/StereoDisplay.h /home/people/tacyas/Eos/include/genUtil.h \
+ /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/StereoDisplay.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/StereoDisplay.h

diff --git a/hostdepend/X86LINUX64/src/Tools/Integration/StereoDisplay/src/X86LINUX64/StereoDisplay b/hostdepend/X86LINUX64/src/Tools/Integration/StereoDisplay/src/X86LINUX64/StereoDisplay
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diff --git a/hostdepend/X86LINUX64/src/Tools/Integration/ctfDisplay/src/X86LINUX64/ctfDisplay b/hostdepend/X86LINUX64/src/Tools/Integration/ctfDisplay/src/X86LINUX64/ctfDisplay
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diff --git a/hostdepend/X86LINUX64/src/Tools/Integration/imagesView/src/X86LINUX64/imagesView b/hostdepend/X86LINUX64/src/Tools/Integration/imagesView/src/X86LINUX64/imagesView
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diff --git a/hostdepend/X86LINUX64/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86LINUX64/ctfDeterminationFromThonRing b/hostdepend/X86LINUX64/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/X86LINUX64/ctfDeterminationFromThonRing
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diff --git a/hostdepend/X86LINUX64/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86LINUX64/ctfWeightMapCreation b/hostdepend/X86LINUX64/src/Tools/ctfInfo/ctfWeightMapCreation/src/X86LINUX64/ctfWeightMapCreation
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diff --git a/hostdepend/X86LINUX64/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86LINUX64/defocusDeterminationFromThonRing b/hostdepend/X86LINUX64/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/X86LINUX64/defocusDeterminationFromThonRing
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diff --git a/hostdepend/X86LINUX64/src/Tools/ctfInfo/tiltInfoDetermine/src/X86LINUX64/tiltInfoDetermine b/hostdepend/X86LINUX64/src/Tools/ctfInfo/tiltInfoDetermine/src/X86LINUX64/tiltInfoDetermine
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diff --git a/hostdepend/X86LINUX64/src/Tools/filter/array2mrc/src/X86LINUX64/array2mrc b/hostdepend/X86LINUX64/src/Tools/filter/array2mrc/src/X86LINUX64/array2mrc
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diff --git a/hostdepend/X86LINUX64/src/Tools/filter/bin2mrc/src/X86LINUX64/bin2mrc b/hostdepend/X86LINUX64/src/Tools/filter/bin2mrc/src/X86LINUX64/bin2mrc
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diff --git a/hostdepend/X86LINUX64/src/Tools/filter/emData2mrc/src/X86LINUX64/emData2mrc b/hostdepend/X86LINUX64/src/Tools/filter/emData2mrc/src/X86LINUX64/emData2mrc
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diff --git a/hostdepend/X86LINUX64/src/Tools/filter/imodst2mrc/src/X86LINUX64/imodst2mrc b/hostdepend/X86LINUX64/src/Tools/filter/imodst2mrc/src/X86LINUX64/imodst2mrc
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diff --git a/hostdepend/X86LINUX64/src/Tools/filter/ip2mrc/src/X86LINUX64/ip2mrc b/hostdepend/X86LINUX64/src/Tools/filter/ip2mrc/src/X86LINUX64/ip2mrc
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diff --git a/hostdepend/X86LINUX64/src/Tools/llData/llDataAverage/src/X86LINUX64/llDataAverage b/hostdepend/X86LINUX64/src/Tools/llData/llDataAverage/src/X86LINUX64/llDataAverage
index 4059f4b..b91d7b1 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/llData/llDataAverage/src/X86LINUX64/llDataAverage and b/hostdepend/X86LINUX64/src/Tools/llData/llDataAverage/src/X86LINUX64/llDataAverage differ

diff --git a/hostdepend/X86LINUX64/src/Tools/llData/llDataAxisSearch/src/X86LINUX64/llDataAxisSearch b/hostdepend/X86LINUX64/src/Tools/llData/llDataAxisSearch/src/X86LINUX64/llDataAxisSearch
index 1185b49..6f4dd86 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/llData/llDataAxisSearch/src/X86LINUX64/llDataAxisSearch and b/hostdepend/X86LINUX64/src/Tools/llData/llDataAxisSearch/src/X86LINUX64/llDataAxisSearch differ

diff --git a/hostdepend/X86LINUX64/src/Tools/llData/llDataMultiCTFCompensation/src/X86LINUX64/llDataMultiCTFCompensation b/hostdepend/X86LINUX64/src/Tools/llData/llDataMultiCTFCompensation/src/X86LINUX64/llDataMultiCTFCompensation
index 643969a..17696f9 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/llData/llDataMultiCTFCompensation/src/X86LINUX64/llDataMultiCTFCompensation and b/hostdepend/X86LINUX64/src/Tools/llData/llDataMultiCTFCompensation/src/X86LINUX64/llDataMultiCTFCompensation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..0726606
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/.Depend
@@ -0,0 +1,92 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h ../inc/../inc/mrc2hdf.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h ../inc/../inc/mrc2hdf.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrc2hdf.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrc2hdf.h

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/Makefile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/X86LINUX64 b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/X86LINUX64
new file mode 120000 (symlink)
index 0000000..2fba5ac
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrc2hdf/src/X86LINUX64
\ No newline at end of file

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc3DExtractZ/src/X86LINUX64/mrc3DExtractZ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc3DExtractZ/src/X86LINUX64/mrc3DExtractZ
index 6413e65..ffe0cf1 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc3DExtractZ/src/X86LINUX64/mrc3DExtractZ and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrc3DExtractZ/src/X86LINUX64/mrc3DExtractZ differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86LINUX64/mrcFETnormalizeBySD b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86LINUX64/mrcFETnormalizeBySD
index 8595e3e..9040cf9 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86LINUX64/mrcFETnormalizeBySD and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFETnormalizeBySD/src/X86LINUX64/mrcFETnormalizeBySD differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86LINUX64/mrcFFTCTFCompensation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTCTFCompensation/src/X86LINUX64/mrcFFTCTFCompensation
index 8d20384..db72503 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTDigitize/src/X86LINUX64/mrcFFTDigitize b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTDigitize/src/X86LINUX64/mrcFFTDigitize
index 3232ee8..ad1f30d 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTExpression/src/X86LINUX64/mrcFFTExpression b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTExpression/src/X86LINUX64/mrcFFTExpression
index ee321ec..a20d2a0 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTExpression/src/X86LINUX64/mrcFFTExpression and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTExpression/src/X86LINUX64/mrcFFTExpression differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86LINUX64/mrcFFTFibreDiagram b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFibreDiagram/src/X86LINUX64/mrcFFTFibreDiagram
index ce571a1..e535ecf 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFiltering/src/X86LINUX64/mrcFFTFiltering b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFiltering/src/X86LINUX64/mrcFFTFiltering
index a4f5aa1..92fee4d 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFiltering/src/X86LINUX64/mrcFFTFiltering and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTFiltering/src/X86LINUX64/mrcFFTFiltering differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86LINUX64/mrcFFTIQEstimation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTIQEstimation/src/X86LINUX64/mrcFFTIQEstimation
index 63b3982..2977db2 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTInfo/src/X86LINUX64/mrcFFTInfo b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTInfo/src/X86LINUX64/mrcFFTInfo
index e966179..ac774ec 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86LINUX64/mrcFFTLayerLineCheck b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/X86LINUX64/mrcFFTLayerLineCheck
index de36408..5ac6616 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86LINUX64/mrcFFTMedianFilter b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTMedianFilter/src/X86LINUX64/mrcFFTMedianFilter
index 4bb9389..bbbc6cc 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTProjection/src/X86LINUX64/mrcFFTProjection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTProjection/src/X86LINUX64/mrcFFTProjection
index e69f245..0a64c1a 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTResampling/src/X86LINUX64/mrcFFTResampling b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTResampling/src/X86LINUX64/mrcFFTResampling
index 580f440..bf79829 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTShellInfo/src/X86LINUX64/mrcFFTShellInfo b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTShellInfo/src/X86LINUX64/mrcFFTShellInfo
index f919411..68a61b3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTSizeChange/src/X86LINUX64/mrcFFTSizeChange b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTSizeChange/src/X86LINUX64/mrcFFTSizeChange
index 0e608f1..d2d8c79 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTSpectrum/src/X86LINUX64/mrcFFTSpectrum b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTSpectrum/src/X86LINUX64/mrcFFTSpectrum
index e220456..e24357e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTXFiltering/src/X86LINUX64/mrcFFTXFiltering b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTXFiltering/src/X86LINUX64/mrcFFTXFiltering
index 783ef50..7ead713 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTplainreduce/src/X86LINUX64/mrcFFTplainreduce b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFFTplainreduce/src/X86LINUX64/mrcFFTplainreduce
index fe49754..4988f49 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86LINUX64/mrcFTMeridianEquatorRedece b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/X86LINUX64/mrcFTMeridianEquatorRedece
index 831a835..60aeff3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86LINUX64/mrcImage1DProjectionfrom2D b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/X86LINUX64/mrcImage1DProjectionfrom2D
index 653efff..ee4109f 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86LINUX64/mrcImage1dAverageByCorrelation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/X86LINUX64/mrcImage1dAverageByCorrelation
index 744c703..c9c65eb 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86LINUX64/mrcImage1dShiftAverageByAnnealing b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86LINUX64/mrcImage1dShiftAverageByAnnealing
index f227a96..2e1bfe9 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86LINUX64/mrcImage1dShiftAverageByAnnealing and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/X86LINUX64/mrcImage1dShiftAverageByAnnealing differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86LINUX64/mrcImage1dShiftByCorrelation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86LINUX64/mrcImage1dShiftByCorrelation
index b8f6703..418ceaa 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86LINUX64/mrcImage1dShiftByCorrelation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/X86LINUX64/mrcImage1dShiftByCorrelation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86LINUX64/mrcImage2DBackProjection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86LINUX64/mrcImage2DBackProjection
index 664e17e..aeadaf0 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86LINUX64/mrcImage2DBackProjection and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DBackProjection/src/X86LINUX64/mrcImage2DBackProjection differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DProjection/src/X86LINUX64/mrcImage2DProjection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DProjection/src/X86LINUX64/mrcImage2DProjection
index bec2dcf..4aefe61 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DProjection/src/X86LINUX64/mrcImage2DProjection and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2DProjection/src/X86LINUX64/mrcImage2DProjection differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2pdb/src/X86LINUX64/mrcImage2pdb b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage2pdb/src/X86LINUX64/mrcImage2pdb
index 6da46e0..509fafa 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86LINUX64/mrcImage3DHighResoEmphasis b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86LINUX64/mrcImage3DHighResoEmphasis
index 4200f6c..68f4e02 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86LINUX64/mrcImage3DHighResoEmphasis and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/X86LINUX64/mrcImage3DHighResoEmphasis differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad/src/X86LINUX64/mrcImage3DPad b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad/src/X86LINUX64/mrcImage3DPad
index b1fe891..c75092b 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad/src/X86LINUX64/mrcImage3DPad and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad/src/X86LINUX64/mrcImage3DPad differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad2/src/X86LINUX64/mrcImage3DPad2 b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DPad2/src/X86LINUX64/mrcImage3DPad2
index efcf5a2..d84c5c2 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DWindowing/src/X86LINUX64/mrcImage3DWindowing b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DWindowing/src/X86LINUX64/mrcImage3DWindowing
index 5c9d322..8dac0c5 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DWindowing/src/X86LINUX64/mrcImage3DWindowing and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImage3DWindowing/src/X86LINUX64/mrcImage3DWindowing differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86LINUX64/mrcImageAbnormalValueRemove b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86LINUX64/mrcImageAbnormalValueRemove
index fb56b03..a105a1f 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86LINUX64/mrcImageAbnormalValueRemove and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/X86LINUX64/mrcImageAbnormalValueRemove differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86LINUX64/mrcImageAdaptiveBinalization b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86LINUX64/mrcImageAdaptiveBinalization
index 64073cb..5564c8b 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86LINUX64/mrcImageAdaptiveBinalization and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/X86LINUX64/mrcImageAdaptiveBinalization differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdd/src/X86LINUX64/mrcImageAdd b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdd/src/X86LINUX64/mrcImageAdd
index 1d4cecd..14ce454 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdd/src/X86LINUX64/mrcImageAdd and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAdd/src/X86LINUX64/mrcImageAdd differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
index abe9a39..4290ea8 100644 (file)
--- a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAddValue/src/X86LINUX64/.Depend
@@ -96,8 +96,7 @@ mrcImageAddValue.o: mrcImageAddValue.c /usr/include/stdio.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Array.h \
  /home/people/tacyas/Eos/include/lmrcImageAddValue.h \
- /home/people/tacyas/Eos/include/mrcImage.h \
- /home/people/tacyas/Eos/include/eosCuda.h
+ /home/people/tacyas/Eos/include/mrcImage.h
 usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAreaCalc/src/X86LINUX64/mrcImageAreaCalc b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAreaCalc/src/X86LINUX64/mrcImageAreaCalc
index eb75ee0..8489b19 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAreaCalc/src/X86LINUX64/mrcImageAreaCalc and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAreaCalc/src/X86LINUX64/mrcImageAreaCalc differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAsProbability/src/X86LINUX64/mrcImageAsProbability b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAsProbability/src/X86LINUX64/mrcImageAsProbability
index c5d6ba6..1959b24 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAsProbability/src/X86LINUX64/mrcImageAsProbability and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAsProbability/src/X86LINUX64/mrcImageAsProbability differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86LINUX64/mrcImageAssignedToTFofPDB b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86LINUX64/mrcImageAssignedToTFofPDB
index d836693..a6c52bc 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86LINUX64/mrcImageAssignedToTFofPDB and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/X86LINUX64/mrcImageAssignedToTFofPDB differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86LINUX64/mrcImageAutoCorrelationWithWindowing b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86LINUX64/mrcImageAutoCorrelationWithWindowing
index a1bf230..7c1ce1f 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86LINUX64/mrcImageAutoCorrelationWithWindowing and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/X86LINUX64/mrcImageAutoCorrelationWithWindowing differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract
index aa8ec4e..908ea37 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/X86LINUX64/mrcImageAutoFilamentExtract differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis
index a9d5119..5f28354 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/X86LINUX64/mrcImageAutoFilamentExtractResultAnalysis differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86LINUX64/mrcImageAutoRotationCorrelation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86LINUX64/mrcImageAutoRotationCorrelation
index 328a400..1f5acae 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86LINUX64/mrcImageAutoRotationCorrelation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/X86LINUX64/mrcImageAutoRotationCorrelation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D
index eb5ce7d..5f93904 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAverage/src/X86LINUX64/mrcImageAverage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAverage/src/X86LINUX64/mrcImageAverage
index 768ba5c..1b9be78 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAverage/src/X86LINUX64/mrcImageAverage and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAverage/src/X86LINUX64/mrcImageAverage differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86LINUX64/mrcImageBandPassFilter b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86LINUX64/mrcImageBandPassFilter
index 80efcc5..d4eb70d 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86LINUX64/mrcImageBandPassFilter and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBandPassFilter/src/X86LINUX64/mrcImageBandPassFilter differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86LINUX64/mrcImageBilateralFilter b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBilateralFilter/src/X86LINUX64/mrcImageBilateralFilter
index 1045de6..00221ac 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBinalization/src/X86LINUX64/mrcImageBinalization b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBinalization/src/X86LINUX64/mrcImageBinalization
index 8f21343..27f88d0 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBinalization/src/X86LINUX64/mrcImageBinalization and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBinalization/src/X86LINUX64/mrcImageBinalization differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBlockMerge/src/X86LINUX64/mrcImageBlockMerge b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBlockMerge/src/X86LINUX64/mrcImageBlockMerge
index 3281b6c..555af6e 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBlockMerge/src/X86LINUX64/mrcImageBlockMerge and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBlockMerge/src/X86LINUX64/mrcImageBlockMerge differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..d099477
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/.Depend
@@ -0,0 +1,130 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageBottomHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageBottomHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+mrcImageBottomHatTransform.o: mrcImageBottomHatTransform.c \
+ /usr/include/stdio.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageBottomHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/lmrcImageMorphology.h \
+ /home/people/tacyas/Eos/include/mrcImage.h \
+ /home/people/tacyas/Eos/include/genUtil.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageBottomHatTransform.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageBottomHatTransform.h

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/Makefile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86LINUX64/mrcImageCCDNoiseRemove b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86LINUX64/mrcImageCCDNoiseRemove
index 36005fe..f990956 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86LINUX64/mrcImageCCDNoiseRemove and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/X86LINUX64/mrcImageCCDNoiseRemove differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86LINUX64/mrcImageCTFCompensation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86LINUX64/mrcImageCTFCompensation
index a2aec99..835845e 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86LINUX64/mrcImageCTFCompensation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensation/src/X86LINUX64/mrcImageCTFCompensation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86LINUX64/mrcImageCTFCompensationForTiltImage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86LINUX64/mrcImageCTFCompensationForTiltImage
index 546c4c7..0a774e4 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86LINUX64/mrcImageCTFCompensationForTiltImage and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/X86LINUX64/mrcImageCTFCompensationForTiltImage differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86LINUX64/mrcImageCTFDetermination b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86LINUX64/mrcImageCTFDetermination
index 868fcf1..372c0d8 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86LINUX64/mrcImageCTFDetermination and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFDetermination/src/X86LINUX64/mrcImageCTFDetermination differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFObservation/src/X86LINUX64/mrcImageCTFObservation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFObservation/src/X86LINUX64/mrcImageCTFObservation
index ce88a72..89ed2aa 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFObservation/src/X86LINUX64/mrcImageCTFObservation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFObservation/src/X86LINUX64/mrcImageCTFObservation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFSN/src/X86LINUX64/mrcImageCTFSN b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCTFSN/src/X86LINUX64/mrcImageCTFSN
index 8810170..100bee5 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCVE/src/X86LINUX64/mrcImageCVE b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCVE/src/X86LINUX64/mrcImageCVE
index 39114d6..d1996dd 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86LINUX64/mrcImageCenterDensityChange b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterDensityChange/src/X86LINUX64/mrcImageCenterDensityChange
index fd2b7b7..7d53ade 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterGet/src/X86LINUX64/mrcImageCenterGet b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterGet/src/X86LINUX64/mrcImageCenterGet
index 9ac01be..6649ed3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86LINUX64/mrcImageCenterOfMassCalculate b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/X86LINUX64/mrcImageCenterOfMassCalculate
index 02ef98a..7a0fa9e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86LINUX64/mrcImageCircumferentialProjection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/X86LINUX64/mrcImageCircumferentialProjection
index 25104ce..c60a0b3 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClosing/src/X86LINUX64/mrcImageClosing b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClosing/src/X86LINUX64/mrcImageClosing
index ebc4033..a36141e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageClusterAnalysis/src/X86LINUX64/mrcImageClusterAnalysis
index 73d4c86..c9ca11e 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageColoring/src/X86LINUX64/mrcImageColoring b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageColoring/src/X86LINUX64/mrcImageColoring
index 1c8acb9..8294803 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnection/src/X86LINUX64/mrcImageConnection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnection/src/X86LINUX64/mrcImageConnection
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86LINUX64/mrcImageConnectivityNumberCalc b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86LINUX64/mrcImageConnectivityNumberCalc
index 1d1b71a..33d7385 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86LINUX64/mrcImageConnectivityNumberCalc and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/X86LINUX64/mrcImageConnectivityNumberCalc differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86LINUX64/mrcImageContourSurfaceCreate b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86LINUX64/mrcImageContourSurfaceCreate
index 1bfced5..866a9de 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86LINUX64/mrcImageContourSurfaceCreate and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/X86LINUX64/mrcImageContourSurfaceCreate differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConvolution/src/X86LINUX64/mrcImageConvolution b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConvolution/src/X86LINUX64/mrcImageConvolution
index 94a6aae..5241a56 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConvolution/src/X86LINUX64/mrcImageConvolution and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageConvolution/src/X86LINUX64/mrcImageConvolution differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86LINUX64/mrcImageCoordinateChange b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86LINUX64/mrcImageCoordinateChange
index 5519bfa..3fc99bb 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86LINUX64/mrcImageCoordinateChange and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoordinateChange/src/X86LINUX64/mrcImageCoordinateChange differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86LINUX64/mrcImageCoreImageCalc b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86LINUX64/mrcImageCoreImageCalc
index 6562cd9..1ac85c3 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86LINUX64/mrcImageCoreImageCalc and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCoreImageCalc/src/X86LINUX64/mrcImageCoreImageCalc differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86LINUX64/mrcImageCorrelationInFourierSpace b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86LINUX64/mrcImageCorrelationInFourierSpace
index caeef9c..2ec3418 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86LINUX64/mrcImageCorrelationInFourierSpace and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/X86LINUX64/mrcImageCorrelationInFourierSpace differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86LINUX64/mrcImageCrystalCreate b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86LINUX64/mrcImageCrystalCreate
index 2189a17..51d8d4d 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86LINUX64/mrcImageCrystalCreate and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCrystalCreate/src/X86LINUX64/mrcImageCrystalCreate differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCylinderSection/src/X86LINUX64/mrcImageCylinderSection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCylinderSection/src/X86LINUX64/mrcImageCylinderSection
index a575f3b..229b5f3 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCylinderSection/src/X86LINUX64/mrcImageCylinderSection and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageCylinderSection/src/X86LINUX64/mrcImageCylinderSection differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86LINUX64/mrcImageDeadPixelCorrection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86LINUX64/mrcImageDeadPixelCorrection
index a8ea3ba..eb20b5e 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86LINUX64/mrcImageDeadPixelCorrection and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/X86LINUX64/mrcImageDeadPixelCorrection differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86LINUX64/mrcImageDensityChangeEstimation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86LINUX64/mrcImageDensityChangeEstimation
index dbbea4d..03ac94e 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86LINUX64/mrcImageDensityChangeEstimation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/X86LINUX64/mrcImageDensityChangeEstimation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityInfo/src/X86LINUX64/mrcImageDensityInfo b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityInfo/src/X86LINUX64/mrcImageDensityInfo
index 9333ec8..10c75aa 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityInfo/src/X86LINUX64/mrcImageDensityInfo and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityInfo/src/X86LINUX64/mrcImageDensityInfo differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86LINUX64/mrcImageDensityNormalization b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86LINUX64/mrcImageDensityNormalization
index 6af40f1..c648938 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86LINUX64/mrcImageDensityNormalization and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalization/src/X86LINUX64/mrcImageDensityNormalization differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86LINUX64/mrcImageDensityNormalizationByImage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86LINUX64/mrcImageDensityNormalizationByImage
index cf005dc..3fb1955 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86LINUX64/mrcImageDensityNormalizationByImage and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/X86LINUX64/mrcImageDensityNormalizationByImage differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation
index 24aaf75..6e88a7a 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDilation/src/X86LINUX64/mrcImageDilation differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86LINUX64/mrcImageDisplayDensityAsTempFactor b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86LINUX64/mrcImageDisplayDensityAsTempFactor
index c1197ad..2b2c38c 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86LINUX64/mrcImageDisplayDensityAsTempFactor and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/X86LINUX64/mrcImageDisplayDensityAsTempFactor differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86LINUX64/mrcImageDistanceConversion b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86LINUX64/mrcImageDistanceConversion
index b940e89..7ed0023 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86LINUX64/mrcImageDistanceConversion and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDistanceConversion/src/X86LINUX64/mrcImageDistanceConversion differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86LINUX64/mrcImageDivideInfoForTomography b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86LINUX64/mrcImageDivideInfoForTomography
index b2062be..f07999a 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86LINUX64/mrcImageDivideInfoForTomography and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/X86LINUX64/mrcImageDivideInfoForTomography differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86LINUX64/mrcImageDivideIntoTwoImages b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86LINUX64/mrcImageDivideIntoTwoImages
index 2a71ac1..6ae1208 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86LINUX64/mrcImageDivideIntoTwoImages and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/X86LINUX64/mrcImageDivideIntoTwoImages differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..22e7327
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/.Depend
@@ -0,0 +1,129 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageDividedByFile.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageDividedByFile.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+mrcImageDividedByFile.o: mrcImageDividedByFile.c /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageDividedByFile.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/mrcImage.h \
+ /home/people/tacyas/Eos/include/genUtil.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageDividedByFile.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageDividedByFile.h

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/Makefile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/mrcImageDividedByFile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/mrcImageDividedByFile
new file mode 100755 (executable)
index 0000000..381e405
Binary files /dev/null and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64/mrcImageDividedByFile differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..311372c
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/.Depend
@@ -0,0 +1,131 @@
+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageEdgeEnhancement.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageEdgeEnhancement.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+mrcImageEdgeEnhancement.o: mrcImageEdgeEnhancement.c /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageEdgeEnhancement.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/mrcImage.h \
+ /home/people/tacyas/Eos/include/genUtil.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Array.h \
+ /home/people/tacyas/Eos/include/lmrcImageEdgeEnhancement.h \
+ /home/people/tacyas/Eos/include/mrcImage.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageEdgeEnhancement.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageEdgeEnhancement.h

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/Makefile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/Makefile
new file mode 100755 (executable)
index 0000000..ec61247
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/Makefile
@@ -0,0 +1,114 @@
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
+include $(EOS_HOME)/src/Config/DefineTool.inc
+
+LIBFILES   = \
+                       $(LIBPREFIX)EosObjects$(LIBSUFFIX) 
+
+LIBFILESDEBUG   = \
+                       $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) 
+
+SRCC  = \
+                       $(OBJECTNAME).c \
+                       init.c \
+                       argCheck.c \
+                       usage.c  \
+                       util.c 
+
+SRCCXX  = \
+                       $(OBJECTNAME).cc \
+                       init.cc \
+                       argCheck.cc \
+                       usage.cc  \
+                       util.cc 
+
+MODULES    = \
+                       $(OBJECTNAME).o \
+                       init.o \
+                       argCheck.o \
+                       usage.o  \
+                       util.o 
+
+REALMODULES    = \
+                       $(OSTYPE)/$(OBJECTNAME).o \
+                       $(OSTYPE)/init.o \
+                       $(OSTYPE)/argCheck.o \
+                       $(OSTYPE)/usage.o \
+                       $(OSTYPE)/util.o 
+
+MODULESDEBUG    = \
+                       $(OBJECTNAME).debugo \
+                       init.debugo \
+                       argCheck.debugo \
+                       usage.debugo  \
+                       util.debugo 
+
+MODULESCUDAGDB    = \
+                       $(OBJECTNAME).cudagdb.o \
+                       init.cudagdb.o \
+                       argCheck.cudagdb.o \
+                       usage.cudagdb.o  \
+                       util.cudagdb.o 
+
+REALMODULESDEBUG    = \
+                       $(OSTYPE)/$(OBJECTNAME).debugo \
+                       $(OSTYPE)/init.debugo \
+                       $(OSTYPE)/argCheck.debugo \
+                       $(OSTYPE)/usage.debugo \
+                       $(OSTYPE)/util.debugo 
+
+
+$(OBJECTNAME): $(MODULES) $(LIBFILES)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+               $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ;  \
+       fi
+
+
+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
+       @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
+       then \
+               echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
+       then \
+               echo "MICO"; \
+               echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+               $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@  ; \
+       fi
+       @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
+       then \
+               echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+               $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ;  \
+       fi
+
+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
+       echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
+       $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
+
+include ./.Depend
+include  $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/mrcImageEdgeEnhancement b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/mrcImageEdgeEnhancement
new file mode 100755 (executable)
index 0000000..fd1bc65
Binary files /dev/null and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64/mrcImageEdgeEnhancement differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86LINUX64/mrcImageEdgeImageGet b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86LINUX64/mrcImageEdgeImageGet
index d25c104..9899c1d 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86LINUX64/mrcImageEdgeImageGet and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeImageGet/src/X86LINUX64/mrcImageEdgeImageGet differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageErosion/src/X86LINUX64/mrcImageErosion b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageErosion/src/X86LINUX64/mrcImageErosion
index 9c24ea6..70027de 100755 (executable)
Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageErosion/src/X86LINUX64/mrcImageErosion and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageErosion/src/X86LINUX64/mrcImageErosion differ

diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86LINUX64/mrcImageEstimateTiltImage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/X86LINUX64/mrcImageEstimateTiltImage
index 0954149..d9bedcb 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageExpression/src/X86LINUX64/mrcImageExpression b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageExpression/src/X86LINUX64/mrcImageExpression
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFFT/src/X86LINUX64/mrcImageFFT b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFFT/src/X86LINUX64/mrcImageFFT
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86LINUX64/mrcImageFFTLayerLineExtraction b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/X86LINUX64/mrcImageFFTLayerLineExtraction
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86LINUX64/mrcImageFOMCalc b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFOMCalc.org/src/X86LINUX64/mrcImageFOMCalc
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86LINUX64/mrcImageFeatureExtraction b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFeatureExtraction/src/X86LINUX64/mrcImageFeatureExtraction
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilterCreate/src/X86LINUX64/mrcImageFilterCreate b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilterCreate/src/X86LINUX64/mrcImageFilterCreate
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86LINUX64/mrcImageFilteringbyFile b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilteringbyFile/src/X86LINUX64/mrcImageFilteringbyFile
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86LINUX64/mrcImageFilteringbyFileForVariance b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/X86LINUX64/mrcImageFilteringbyFileForVariance
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86LINUX64/mrcImageFourierShellCorrelation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/X86LINUX64/mrcImageFourierShellCorrelation
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86LINUX64/mrcImageFractalFourierShellCorrelation b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/X86LINUX64/mrcImageFractalFourierShellCorrelation
index 39e571b..6a8410b 100755 (executable)
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageGaussDisc/src/X86LINUX64/mrcImageGaussDisc b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageGaussDisc/src/X86LINUX64/mrcImageGaussDisc
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageGaussSphere/src/X86LINUX64/mrcImageGaussSphere b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageGaussSphere/src/X86LINUX64/mrcImageGaussSphere
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHeaderChange/src/X86LINUX64/mrcImageHeaderChange b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHeaderChange/src/X86LINUX64/mrcImageHeaderChange
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86LINUX64/mrcImageHelicalAveraging b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalAveraging/src/X86LINUX64/mrcImageHelicalAveraging
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86LINUX64/mrcImageHelicalMappingFrom2DImage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/X86LINUX64/mrcImageHelicalMappingFrom2DImage
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86LINUX64/mrcImageHelicalMasking b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMasking/src/X86LINUX64/mrcImageHelicalMasking
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86LINUX64/mrcImageHelicalMaskingBy2DImage b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/X86LINUX64/mrcImageHelicalMaskingBy2DImage
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86LINUX64/mrcImageHelicalProjection b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHelicalProjection/src/X86LINUX64/mrcImageHelicalProjection
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86LINUX64/mrcImageHighPassFilter b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageHighPassFilter/src/X86LINUX64/mrcImageHighPassFilter
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..0ec75f1
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64/.Depend
@@ -0,0 +1,130 @@
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+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageLogicalOperation.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
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diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64/.Depend b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64/.Depend
new file mode 100644 (file)
index 0000000..70cf5a9
--- /dev/null
+++ b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64/.Depend
@@ -0,0 +1,130 @@
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+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageTopHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+init.o: init.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageTopHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/File.h \
+ /home/people/tacyas/Eos/include/Memory.h
+mrcImageTopHatTransform.o: mrcImageTopHatTransform.c /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h ../inc/config.h \
+ ../inc/../inc/mrcImageTopHatTransform.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
+ /home/people/tacyas/Eos/include/lmrcImageMorphology.h \
+ /home/people/tacyas/Eos/include/mrcImage.h \
+ /home/people/tacyas/Eos/include/genUtil.h \
+ /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Matrix3D.h \
+ /home/people/tacyas/Eos/include/Array.h
+usage.o: usage.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageTopHatTransform.h
+util.o: util.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/config.h \
+ ../inc/../inc/mrcImageTopHatTransform.h

diff --git a/src/Objects/DataExpress/.Source b/src/Objects/DataExpress/.Source
index 926a3bc..3f6de90 100644 (file)
--- a/src/Objects/DataExpress/.Source
+++ b/src/Objects/DataExpress/.Source
@@ -1,10 +1,10 @@
 SOURCE=\
+Contour \
+TclTk \
 alsa \
 avsFile \
-Contour \
 eosRuby \
 gifFile \
 openGL \
 psFile \
-TclTk \
 #LastSource

diff --git a/src/Objects/DataExpress/.Source.org b/src/Objects/DataExpress/.Source.org
index 926a3bc..3f6de90 100644 (file)
--- a/src/Objects/DataExpress/.Source.org
+++ b/src/Objects/DataExpress/.Source.org
@@ -1,10 +1,10 @@
 SOURCE=\
+Contour \
+TclTk \
 alsa \
 avsFile \
-Contour \
 eosRuby \
 gifFile \
 openGL \
 psFile \
-TclTk \
 #LastSource

diff --git a/src/Objects/DataExpress/gifFile/doc/gifFile.html b/src/Objects/DataExpress/gifFile/doc/gifFile.html
index 2dbc0f7..8ede649 100755 (executable)
--- a/src/Objects/DataExpress/gifFile/doc/gifFile.html
+++ b/src/Objects/DataExpress/gifFile/doc/gifFile.html
@@ -5,26 +5,16 @@
 <PRE>
 ../src/decoder.c:
 
-<<<<<<< HEAD
-=======
-../src/gifcompr.c:
-
-../src/gifencod.c:
-
->>>>>>> FETCH_HEAD
 ../src/gifFileInit.c:
 
 ../src/gifFileWrite.c:
 
 ../src/gifUtil.c:
 
-<<<<<<< HEAD
 ../src/gifcompr.c:
 
 ../src/gifencod.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lmrc2gif.c:
 </PRE>
 <HR>

diff --git a/src/Objects/DataExpress/openGL/doc/openGL.html b/src/Objects/DataExpress/openGL/doc/openGL.html
index 5aeeff5..102066c 100644 (file)
--- a/src/Objects/DataExpress/openGL/doc/openGL.html
+++ b/src/Objects/DataExpress/openGL/doc/openGL.html
@@ -47,11 +47,8 @@
 
 ../src/lmolvieLight.c:
 
-<<<<<<< HEAD
 ../src/lmolvieMRCread.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lmolvieMouse.c:
 
 ../src/lmolvieMouseDrive.c:
@@ -62,11 +59,6 @@
 
 ../src/lmolvieMouseParallel.c:
 
-<<<<<<< HEAD
-=======
-../src/lmolvieMRCread.c:
-
->>>>>>> FETCH_HEAD
 ../src/lmolvieMrcViewerDisplay.c:
 
 ../src/lmolvieMrcViewerKeyboard.c:

diff --git a/src/Objects/DataExpress/psFile/doc/psFile.html b/src/Objects/DataExpress/psFile/doc/psFile.html
index 98160bb..136ec81 100755 (executable)
--- a/src/Objects/DataExpress/psFile/doc/psFile.html
+++ b/src/Objects/DataExpress/psFile/doc/psFile.html
@@ -5,17 +5,10 @@
 <PRE>
 ../src/psFileCircle.c:
 
-<<<<<<< HEAD
 ../src/psFileContour.c:
 
 ../src/psFileContour3D.c:
 
-=======
-../src/psFileContour3D.c:
-
-../src/psFileContour.c:
-
->>>>>>> FETCH_HEAD
 ../src/psFileEnd.c:
 
 ../src/psFileImage.c:

diff --git a/src/Objects/DataManip/.Source b/src/Objects/DataManip/.Source
index 046ab7e..19c24fd 100644 (file)
--- a/src/Objects/DataManip/.Source
+++ b/src/Objects/DataManip/.Source
@@ -1,15 +1,15 @@
 SOURCE=\
-ctfInfo \
 DCDFile \
+IMAGIC \
+MATH \
+ctfInfo \
 dsn6File \
 emData \
-IMAGIC \
 khorosData \
 largeIP \
 llData \
 ltlgData \
 mapFile \
-MATH \
 mrcImage \
 pdbFile \
 simulation \

diff --git a/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html b/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
index 40e4a56..149c6a6 100755 (executable)
--- a/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
+++ b/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
@@ -22,17 +22,10 @@ ctfInfo
 
 ../src/ctfInfoRead.c:
 
-<<<<<<< HEAD
 ../src/ctfInfoWrite.c:
 
 ../src/ctfInfoWrite2.c:
 
-=======
-../src/ctfInfoWrite2.c:
-
-../src/ctfInfoWrite.c:
-
->>>>>>> FETCH_HEAD
 ../src/ctfWeight.c:
 
 ../src/ctfZeroPoint.c:

diff --git a/src/Objects/DataManip/llData/doc/llData.html b/src/Objects/DataManip/llData/doc/llData.html
index 7c0efb1..c8cd425 100755 (executable)
--- a/src/Objects/DataManip/llData/doc/llData.html
+++ b/src/Objects/DataManip/llData/doc/llData.html
@@ -21,17 +21,10 @@
 <PRE>
 ../src/llDataCheck.c:
 
-<<<<<<< HEAD
 ../src/llDataETC.c:
 
 ../src/llDataError.c:
 
-=======
-../src/llDataError.c:
-
-../src/llDataETC.c:
-
->>>>>>> FETCH_HEAD
 ../src/llDataGet.c:
 
 ../src/llDataInfo.c:
@@ -58,54 +51,32 @@
 
 ../src/lllDataAvgTo.c:
 
-<<<<<<< HEAD
 ../src/lllDataAxisSearch.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lllDataAxisSearch2.c:
 
 ../src/lllDataAxisSearchAndAverage.c:
 
-<<<<<<< HEAD
 ../src/lllDataCTFCompensate.c:
 
 ../src/lllDataCTFObservation.c:
-=======
-../src/lllDataAxisSearch.c:
->>>>>>> FETCH_HEAD
 
 ../src/lllDataCompare.c:
 
 ../src/lllDataContributionCalcDifferentN.c:
 
-<<<<<<< HEAD
-=======
-../src/lllDataCTFCompensate.c:
-
-../src/lllDataCTFObservation.c:
-
->>>>>>> FETCH_HEAD
 ../src/lllDataDifferenceCalc.c:
 
 ../src/lllDataEquatorAdd.c:
 
 ../src/lllDataExtract.c:
 
-<<<<<<< HEAD
 ../src/lllDataFit.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lllDataFit2.c:
 
 ../src/lllDataFitAndAverage.c:
 
-<<<<<<< HEAD
-=======
-../src/lllDataFit.c:
-
->>>>>>> FETCH_HEAD
 ../src/lllDataFitMergedLL.c:
 
 ../src/lllDataFitOut.c:
@@ -130,19 +101,11 @@
 
 ../src/lllDataRescaling.c:
 
-<<<<<<< HEAD
 ../src/lllDataSingleCTFCompensation.c:
 
 ../src/lllDataWeightSet.c:
 
 ../src/lllDatarMaxLimit.c:
-=======
-../src/lllDatarMaxLimit.c:
-
-../src/lllDataSingleCTFCompensation.c:
-
-../src/lllDataWeightSet.c:
->>>>>>> FETCH_HEAD
 </PRE>
 <HR>
 <A NAME="include">

diff --git a/src/Objects/DataManip/mrcImage/doc/mrcImage.html b/src/Objects/DataManip/mrcImage/doc/mrcImage.html
index 89be30f..7414b2e 100755 (executable)
--- a/src/Objects/DataManip/mrcImage/doc/mrcImage.html
+++ b/src/Objects/DataManip/mrcImage/doc/mrcImage.html
@@ -131,6 +131,8 @@
 
 ../src/lmrcImageBinarization.c:
 
+../src/lmrcImageBottomHatTransform.c:
+
 ../src/lmrcImageBoundaryInfo.c:
 
 ../src/lmrcImageCTFCompensation.c:
@@ -200,6 +202,8 @@
 
 ../src/lmrcImageEdgeAverage.c:
 
+../src/lmrcImageEdgeEnhancement.c:
+
 ../src/lmrcImageErosion.c:
 
 ../src/lmrcImageFFT.c:
@@ -226,6 +230,8 @@
 
 ../src/lmrcImageLabeling.c:
 
+../src/lmrcImageLogicalOperation.c:
+
 ../src/lmrcImageLowPassFilter.c:
 
 ../src/lmrcImageMasking.c:
@@ -263,6 +269,8 @@
 
 ../src/lmrcImagePosterization.c:
 
+../src/lmrcImagePrevitt.c:
+
 ../src/lmrcImageProjection.c:
 
 ../src/lmrcImageProportionalDensityLevelSetByImage.c:
@@ -277,6 +285,8 @@
 
 ../src/lmrcImageRhoFiltering.c:
 
+../src/lmrcImageRoberts.c:
+
 ../src/lmrcImageRotation.c:
 
 ../src/lmrcImageSSDA.c:
@@ -311,6 +321,8 @@
 
 ../src/lmrcImageSmoothing.c:
 
+../src/lmrcImageSobel.c:
+
 ../src/lmrcImageSolventFlattening.c:
 
 ../src/lmrcImageSphere.c:
@@ -327,6 +339,8 @@
 
 ../src/lmrcImageTfunction.c:
 
+../src/lmrcImageTopHatTransform.c:
+
 ../src/lmrcImageTrans.c:
 
 ../src/lmrcImageTransformDescartesIntoPolar.c:

diff --git a/src/Objects/DataManip/transform/doc/transform.html b/src/Objects/DataManip/transform/doc/transform.html
index c63e980..053b4bf 100644 (file)
--- a/src/Objects/DataManip/transform/doc/transform.html
+++ b/src/Objects/DataManip/transform/doc/transform.html
@@ -17,11 +17,6 @@
 
 ../src/lEvaluateCorrelationMapwithCommonLine.c:
 
-<<<<<<< HEAD
-=======
-../src/lFETmapOrientationSearchBySimultaneousFitting.c:
-
->>>>>>> FETCH_HEAD
 ../src/lFETOrientationSearchByAnnealing.c:
 
 ../src/lFETOrientationSearchByFeatureAlignment.c:
@@ -30,11 +25,8 @@
 
 ../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
 
-<<<<<<< HEAD
 ../src/lFETmapOrientationSearchBySimultaneousFitting.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
 
 ../src/lInitialDataFileRead.c:
@@ -43,11 +35,7 @@
 
 ../src/lLcalculation.c:
 
-<<<<<<< HEAD
 ../src/lPlaneRotationAngleSet.c:
-=======
-../src/lllDatarMaxLimitForSeparation.c:
->>>>>>> FETCH_HEAD
 
 ../src/lllDataSeparationInfoPrint.c:
 
@@ -55,26 +43,16 @@
 
 ../src/lllDataSeparationInfoSet.c:
 
-<<<<<<< HEAD
 ../src/lllDatarMaxLimitForSeparation.c:
 
-=======
->>>>>>> FETCH_HEAD
 ../src/lllExtract.c:
 
 ../src/lllExtractCtfinfFileCreate.c:
 
-<<<<<<< HEAD
 ../src/lllExtractWithSeparation.c:
 
 ../src/lllExtractdYEstimate.c:
 
-=======
-../src/lllExtractdYEstimate.c:
-
-../src/lllExtractWithSeparation.c:
-
->>>>>>> FETCH_HEAD
 ../src/lmrc2Dto3D.c:
 
 ../src/lmrc2Dto3DSIRT.c:
@@ -86,11 +64,6 @@
 ../src/lmrcImageOneLineGet.c:
 
 ../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
-<<<<<<< HEAD
-=======
-
-../src/lPlaneRotationAngleSet.c:
->>>>>>> FETCH_HEAD
 </PRE>
 <HR>
 <A NAME="include">

diff --git a/src/Objects/General/.Source b/src/Objects/General/.Source
index 49f7a7f..566c712 100644 (file)
--- a/src/Objects/General/.Source
+++ b/src/Objects/General/.Source
@@ -4,15 +4,8 @@ Array \
 Cluster \
 Crystal \
 DataBase \
-dummy \
 Eos \
-eosCuda \
-eosFunc \
-eosList \
-eosPoint \
-eosPThread \
 File \
-genUtil \
 Map2D \
 Matrix3D \
 Memory \
@@ -23,4 +16,11 @@ Socket \
 SpecialNumber \
 String \
 Vector \
+dummy \
+eosCuda \
+eosFunc \
+eosList \
+eosPThread \
+eosPoint \
+genUtil \
 #LastSource

diff --git a/src/Objects/General/Matrix3D/doc/Matrix3D.html b/src/Objects/General/Matrix3D/doc/Matrix3D.html
index 7f61fc0..699f5b0 100755 (executable)
--- a/src/Objects/General/Matrix3D/doc/Matrix3D.html
+++ b/src/Objects/General/Matrix3D/doc/Matrix3D.html
@@ -5,17 +5,10 @@
 <PRE>
 ../src/matrix3DEulerAngleGet.c:
 
-<<<<<<< HEAD
 ../src/matrix3DEulerAngleSet.c:
 
 ../src/matrix3DEulerAngles.c:
 
-=======
-../src/matrix3DEulerAngles.c:
-
-../src/matrix3DEulerAngleSet.c:
-
->>>>>>> FETCH_HEAD
 ../src/matrix3DFile.c:
 
 ../src/matrix3DInit.c:

diff --git a/src/Objects/General/Vector/doc/Vector.html b/src/Objects/General/Vector/doc/Vector.html
index 03bd822..09a1a28 100755 (executable)
--- a/src/Objects/General/Vector/doc/Vector.html
+++ b/src/Objects/General/Vector/doc/Vector.html
@@ -10,21 +10,13 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-<<<<<<< HEAD
-=======
-../src/lVectorSpline2D.c:
-
->>>>>>> FETCH_HEAD
 ../src/Vector.c:
 
 ../src/VectorRead.c:
 
 ../src/VectorScalarProduct.c:
-<<<<<<< HEAD
 
 ../src/lVectorSpline2D.c:
-=======
->>>>>>> FETCH_HEAD
 </PRE>
 <HR>
 <A NAME="include">

diff --git a/src/Tools/Cluster/clusterLog2ToLog/src/clusterLog2ToLog.html b/src/Tools/Cluster/clusterLog2ToLog/src/clusterLog2ToLog.html
index e842e0b..cda9680 100755 (executable)
--- a/src/Tools/Cluster/clusterLog2ToLog/src/clusterLog2ToLog.html
+++ b/src/Tools/Cluster/clusterLog2ToLog/src/clusterLog2ToLog.html
@@ -1 +1,19 @@
-/bin/bash: clusterLog2ToLog: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>clusterLog2ToLog</TITLE>
+</HEAD>
+<BODY>
+<H1>clusterLog2ToLog</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: clusterLog2ToLog
+Options:
+    [-i[nput]            In                  (stdin     )] :Optional  :Input: Log2
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Log
+    [-lastNum            lastNum             (1         )] :Optional  :lastClusterNumber
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/Cluster/clusterLogASCII2Binary/src/clusterLogASCII2Binary.html b/src/Tools/Cluster/clusterLogASCII2Binary/src/clusterLogASCII2Binary.html
index ef20586..81a32ea 100755 (executable)
--- a/src/Tools/Cluster/clusterLogASCII2Binary/src/clusterLogASCII2Binary.html
+++ b/src/Tools/Cluster/clusterLogASCII2Binary/src/clusterLogASCII2Binary.html
@@ -1 +1,18 @@
-/bin/bash: clusterLogASCII2Binary: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>clusterLogASCII2Binary</TITLE>
+</HEAD>
+<BODY>
+<H1>clusterLogASCII2Binary</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: clusterLogASCII2Binary
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/Cluster/clusterShow/src/clusterShow.html b/src/Tools/Cluster/clusterShow/src/clusterShow.html
index 34fb3f4..8d8956e 100755 (executable)
--- a/src/Tools/Cluster/clusterShow/src/clusterShow.html
+++ b/src/Tools/Cluster/clusterShow/src/clusterShow.html
@@ -1 +1,32 @@
-/bin/bash: clusterShow: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>clusterShow</TITLE>
+</HEAD>
+<BODY>
+<H1>clusterShow</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: clusterShow
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :InputData: ASCII Log: Need -i, -i2, or -ib
+    [-i[nput]2           In2                 (NULL      )] :Optional  :InputData: ASCII Log2
+    [-i[nput]b[inary]    InB                 (NULL      )] :Optional  :InputData: BinaryLog: basename
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: All
+    [-O[utput]           Out2                (stdout    )] :Optional  :Output: ClusterOnly
+    [-PS[output]         OutPS               (stdout    )] :Optional  :Output: ClusterForPS: Need -I
+    [-O[utput]L[ist]     OutOL               (stdout    )] :Optional  :Output: ClusterList 
+    [-O[utput]T[reeInfo] TreeInfo            (NULL      )] :Optional  :Output: TreeInfo
+    [-A[verage]L[ist]    OutAL               (stdout    )OutALRange          (0         )OutALSuffix         (avg       )] :Optional  :Output: ClusterList range
+    [-Last[ClusterNumber]LastNum             (1         )] :Optional  :Last: Num
+    [-S[cale]            ShoulderScale       (1         )ArmScale            (1         )] :Optional  :Scale: Shoulder Arm
+    [-P[osition]         PosX                (0         )PosY                (0         )] :Optional  :Position: X Y
+    [-Offset             Offset              (1         )] :Optional  :Offset: Arm
+    [-I[nfileList]       InList              (NULL      )] :Optional  :FileList
+    [-Log                ] :Optional  :Arm: Log Scale
+    [-Scaling            ] :Optional  :with Scaling
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/Coord/pointsSetToPDB/src/pointsSetToPDB.html b/src/Tools/Coord/pointsSetToPDB/src/pointsSetToPDB.html
index 77bbedc..3b652c9 100644 (file)
--- a/src/Tools/Coord/pointsSetToPDB/src/pointsSetToPDB.html
+++ b/src/Tools/Coord/pointsSetToPDB/src/pointsSetToPDB.html
@@ -1 +1 @@
-/bin/bash: pointsSetToPDB: そのようなファイルやディレクトリはありません
+/bin/bash: pointsSetToPDB: No such file or directory

diff --git a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html
index db595e4..5fc26b8 100755 (executable)
--- a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html
+++ b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdAtomChangeDistanceFromAtom: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdAtomChangeDistanceFromAtom</TITLE>
@@ -19,4 +16,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html
index 11c72ae..c2042b2 100755 (executable)
--- a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html
+++ b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdAtomDistanceDistribution: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdAtomDistanceDistribution</TITLE>
@@ -20,4 +17,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdCompareCA/src/dcdCompareCA.html b/src/Tools/DCDFile/dcdCompareCA/src/dcdCompareCA.html
index 1d30ca3..050ab05 100644 (file)
--- a/src/Tools/DCDFile/dcdCompareCA/src/dcdCompareCA.html
+++ b/src/Tools/DCDFile/dcdCompareCA/src/dcdCompareCA.html
@@ -1 +1 @@
-/bin/bash: dcdCompareCA: そのようなファイルやディレクトリはありません
+/bin/bash: dcdCompareCA: No such file or directory

diff --git a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/dcdDistanceAtomBetweenAtom.html b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/dcdDistanceAtomBetweenAtom.html
index 73fb85d..d72a437 100755 (executable)
--- a/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/dcdDistanceAtomBetweenAtom.html
+++ b/src/Tools/DCDFile/dcdDistanceAtomBetweenAtom/src/dcdDistanceAtomBetweenAtom.html
@@ -1 +1 @@
-/bin/bash: dcdDistanceAtomBetweenAtom: そのようなファイルやディレクトリはありません
+/bin/bash: dcdDistanceAtomBetweenAtom: No such file or directory

diff --git a/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html b/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html
index d9d666e..e85357e 100755 (executable)
--- a/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html
+++ b/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdFilePrint: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdFilePrint</TITLE>
@@ -25,4 +22,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html b/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html
index d6d1984..79234f5 100755 (executable)
--- a/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html
+++ b/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdInfo: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdInfo</TITLE>
@@ -21,4 +18,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html b/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html
index b39a522..a6fd128 100755 (executable)
--- a/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html
+++ b/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdSelectAtoms: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdSelectAtoms</TITLE>
@@ -19,4 +16,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html b/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html
index 409fff3..13fb11b 100755 (executable)
--- a/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html
+++ b/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdSerectAtom: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdSerectAtom</TITLE>
@@ -19,4 +16,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html
index 6924f00..a5d6293 100755 (executable)
--- a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html
+++ b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: dcdTimeSeriesBehavior: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>dcdTimeSeriesBehavior</TITLE>
@@ -19,4 +16,3 @@ Options:
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/Integration/.Source b/src/Tools/Integration/.Source
index d7ac761..f6c928a 100644 (file)
--- a/src/Tools/Integration/.Source
+++ b/src/Tools/Integration/.Source
@@ -1,12 +1,12 @@
 SOURCE=\
-ctfDisplay \
 Display2 \
 Display3 \
 Eos \
+StereoDisplay \
+Visualmake \
+ctfDisplay \
 imagesClustering \
 imagesView \
 obj3Don2DImageView \
 smolet \
-StereoDisplay \
-Visualmake \
 #LastSource

diff --git a/src/Tools/Integration/Display2/src/Display2.html b/src/Tools/Integration/Display2/src/Display2.html
index f58c5e8..b4e11a4 100644 (file)
--- a/src/Tools/Integration/Display2/src/Display2.html
+++ b/src/Tools/Integration/Display2/src/Display2.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: Display2: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>Display2</TITLE>
@@ -12,11 +9,7 @@
 Usage: Display2
 Options:
     [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-<<<<<<< HEAD
     [-t[epmlate]         Template            (85.roi    )] :Optional  :Template for InputFile 
-=======
-    [-t[epmlate]         Template            (2100635408.roi    )] :Optional  :Template for InputFile 
->>>>>>> FETCH_HEAD
     [-H[ighForThres]     ThresHigh           (0.0       )] :Optional  :Template for InputFile 
     [-L[owForThres]      ThresLow            (0.0       )] :Optional  :Template for InputFile 
     [-Zoom               Zoom                (1.0       )] :Optional  :Zoom for InputFile 
@@ -33,4 +26,3 @@ mrcInfoGet [Nx|Ny|Nz|Max|Min|Mean|Hist]
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/Integration/Display3/src/Display3.html b/src/Tools/Integration/Display3/src/Display3.html
index 3d25872..4346669 100755 (executable)
--- a/src/Tools/Integration/Display3/src/Display3.html
+++ b/src/Tools/Integration/Display3/src/Display3.html
@@ -1 +1 @@
-/bin/bash: Display3: そのようなファイルやディレクトリはありません
+/bin/bash: Display3: No such file or directory

diff --git a/src/Tools/Integration/Eos/src/Eos.html b/src/Tools/Integration/Eos/src/Eos.html
index 0a42df1..0a2b06d 100755 (executable)
--- a/src/Tools/Integration/Eos/src/Eos.html
+++ b/src/Tools/Integration/Eos/src/Eos.html
@@ -1 +1 @@
-/bin/bash: Eos: そのようなファイルやディレクトリはありません
+/bin/bash: Eos: No such file or directory

diff --git a/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html b/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html
index c2680f1..9f672fc 100644 (file)
--- a/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html
+++ b/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>StereoDisplay</TITLE>
@@ -25,4 +22,3 @@ Left2 Right2
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/Integration/Visualmake/src/Visualmake.html b/src/Tools/Integration/Visualmake/src/Visualmake.html
index 81236bf..f152e8e 100755 (executable)
--- a/src/Tools/Integration/Visualmake/src/Visualmake.html
+++ b/src/Tools/Integration/Visualmake/src/Visualmake.html
@@ -1 +1 @@
-/bin/bash: Visualmake: そのようなファイルやディレクトリはありません
+/bin/bash: Visualmake: No such file or directory

diff --git a/src/Tools/Integration/ctfDisplay/src/ctfDisplay.html b/src/Tools/Integration/ctfDisplay/src/ctfDisplay.html
index d3eab47..f1cef89 100755 (executable)
--- a/src/Tools/Integration/ctfDisplay/src/ctfDisplay.html
+++ b/src/Tools/Integration/ctfDisplay/src/ctfDisplay.html
@@ -1 +1,23 @@
-/bin/bash: ctfDisplay: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfDisplay</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfDisplay</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfDisplay
+Options:
+    [-i[nput]            inMRC               (NULL      )] :Optional  :Input:MRC(FFT)
+    [-o[utput]           outCTF              (stdout    )] :Optional  :Input/Output: ctfinfo
+    [-Rmax               Rmax                (0.2       )] :Optional  :Rmax [A-1] 
+    [-Imax               Imax                (0.2       )] :Optional  :Intensity: min-max
+    [-Imin               Imin                (0.02      )] :Optional  :Intensity: min-max
+    [-AutoRange          ] :Optional  :Intensity: min-max
+    [-Log                ] :Optional  :Log of Intensity
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/Integration/imagesClustering/src/imagesClustering.html b/src/Tools/Integration/imagesClustering/src/imagesClustering.html
index 64e3b5f..4037769 100644 (file)
--- a/src/Tools/Integration/imagesClustering/src/imagesClustering.html
+++ b/src/Tools/Integration/imagesClustering/src/imagesClustering.html
@@ -1 +1 @@
-/bin/bash: imagesClustering: そのようなファイルやディレクトリはありません
+/bin/bash: imagesClustering: No such file or directory

diff --git a/src/Tools/Integration/imagesView/src/imagesView.html b/src/Tools/Integration/imagesView/src/imagesView.html
index 378721e..29186a7 100755 (executable)
--- a/src/Tools/Integration/imagesView/src/imagesView.html
+++ b/src/Tools/Integration/imagesView/src/imagesView.html
@@ -1 +1,19 @@
-/bin/bash: imagesView: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>imagesView</TITLE>
+</HEAD>
+<BODY>
+<H1>imagesView</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: imagesView
+Options:
+    [-i[nput]            In                  (stdin     )] :Optional  :Input: FileList
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: FileViewCondition
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+Additional Usage
+This command for viewing images with a suffix
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/Integration/obj3Don2DImageView/src/obj3Don2DImageView.html b/src/Tools/Integration/obj3Don2DImageView/src/obj3Don2DImageView.html
index f75764b..47d9835 100644 (file)
--- a/src/Tools/Integration/obj3Don2DImageView/src/obj3Don2DImageView.html
+++ b/src/Tools/Integration/obj3Don2DImageView/src/obj3Don2DImageView.html
@@ -1 +1 @@
-/bin/bash: obj3Don2DImageView: そのようなファイルやディレクトリはありません
+/bin/bash: obj3Don2DImageView: No such file or directory

diff --git a/src/Tools/Integration/smolet/src/smolet.html b/src/Tools/Integration/smolet/src/smolet.html
index 604f304..a220d8c 100755 (executable)
--- a/src/Tools/Integration/smolet/src/smolet.html
+++ b/src/Tools/Integration/smolet/src/smolet.html
@@ -1 +1 @@
-/bin/bash: smolet: そのようなファイルやディレクトリはありません
+/bin/bash: smolet: No such file or directory

diff --git a/src/Tools/admin/mallocCheck/src/mallocCheck.html b/src/Tools/admin/mallocCheck/src/mallocCheck.html
index 5f456a7..27fc63b 100644 (file)
--- a/src/Tools/admin/mallocCheck/src/mallocCheck.html
+++ b/src/Tools/admin/mallocCheck/src/mallocCheck.html
@@ -1 +1 @@
-/bin/bash: mallocCheck: そのようなファイルやディレクトリはありません
+/bin/bash: mallocCheck: No such file or directory

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/ctfDeterminationFromPhaseComparison.html b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/ctfDeterminationFromPhaseComparison.html
index b2a25f9..6979a31 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/ctfDeterminationFromPhaseComparison.html
+++ b/src/Tools/ctfInfo/ctfDeterminationFromPhaseComparison/src/ctfDeterminationFromPhaseComparison.html
@@ -1 +1 @@
-/bin/bash: ctfDeterminationFromPhaseComparison: そのようなファイルやディレクトリはありません
+/bin/bash: ctfDeterminationFromPhaseComparison: No such file or directory

diff --git a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/ctfDeterminationFromThonRing.html b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/ctfDeterminationFromThonRing.html
index 5c8a660..daa955c 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/ctfDeterminationFromThonRing.html
+++ b/src/Tools/ctfInfo/ctfDeterminationFromThonRing/src/ctfDeterminationFromThonRing.html
@@ -1 +1,24 @@
-/bin/bash: ctfDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfDeterminationFromThonRing</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfDeterminationFromThonRing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfDeterminationFromThonRing
+Options:
+    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-oP[utput]          Out2                (NULL      )] :Optional  :OutputParameter
+    [-kV                 kV                  (200       )] :Optional  :kV
+    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
+    [-Def                minDef              (0.0       )maxDef              (200000.0  )delDef              (1000.0    )] :Optional  :Def[A]
+    [-Amp                minAmp              (0.0       )maxAmp              (0.4       )delAmp              (0.005     )] :Optional  :AmpToPhase
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-R[/A]              R                   (NULL      )... ] :Variable  :ThonRing[/A]
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/ctfInfo/ctfDetermine/src/ctfDetermine.html b/src/Tools/ctfInfo/ctfDetermine/src/ctfDetermine.html
index 82732af..79e0c79 100755 (executable)
--- a/src/Tools/ctfInfo/ctfDetermine/src/ctfDetermine.html
+++ b/src/Tools/ctfInfo/ctfDetermine/src/ctfDetermine.html
@@ -1 +1,50 @@
-/bin/bash: ctfDetermine: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfDetermine</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfDetermine</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfDetermine
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile:  mrcImage
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile: Parameters
+    [-D[efocus]          Defocus             (0.0       )] :Optional  :InitialDefocus[A]
+    [-Cs                 Cs                  (1.7       )] :Optional  :InitialCs[mm]
+    [-Cc                 Cc                  (1.2       )] :Optional  :InitialCs[mm]
+    [-dE                 dE                  (0.2       )] :Optional  :InitialCs[mm]
+    [-Ac[cerratedVoltage]Ac                  (200       )] :Optional  :Ac[kV]
+    [-CutLow             CutLow              (0.05      )] :Optional  :CutOffLowFrequncy[/A]
+    [-CutHigh            CutHigh             (0.5       )] :Optional  :CutOffHighFrequncy[/A]
+    [-I0                 I0                  (1.0       )] :Optional  :I0
+    [-ratio              ratioOfAmpToPhase   (0.1       )] :Optional  :ratioOfAmpToPhase
+    [-Ai                 Ai                  (0.03      )] :Optional  :IlluminationAngle[mrad]
+    [-BofMTF             BofMTF              (15.0      )] :Optional  :B of MTF [A]
+    [-BofV[ibration]     BofVibration        (3.0       )] :Optional  :B of Vibration [A]
+    [-Mag[nification]    Magnification       (1.0       )] :Optional  :Magnification
+    [-[White]Noise       WhiteNoise          (0.0       )] :Optional  :Signal/Noise Ratio
+    [-[White]Noise2      WhiteNoise2         (0.0       )] :Optional  :Signal/Noise Ratio
+    [-MolcEnv            MolcEnv             (0.0       )] :Optional  :Gaussian: Molcular Envelop [A]
+    [-MolcEnv2           MolcEnvTable        (NULL      )] :Optional  :Table: Molcular Envelop
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-min                min                 (-10       )] :Optional  :min of coefficient area
+    [-max                max                 (10        )] :Optional  :max of coefficient area
+    [-s[tep]             step                (0.01      )] :Optional  :step of coefficient
+    [-d[egree]           degree              (6         )] :Optional  :agree of function
+    [-S[ection]          section             (4         )] :Optional  :section number of fft
+>>> Mode <<< 
+         0 : MinMax Methods (Henderson-like CTF determination) 
+         16: Fitting Methods 
+         32: Differential Methods 
+         64: Covariance Methods 
+         96: Differential & covariance  Methods 
+        128: MinSquare Methods 
+        160: Differential+MinSquare Methods by Imamura 
+        161: Differential+MinSquare Methods+NoiseRemoval(+1) 
+        163: Differential+MinSquare Methods+NoiseRemoval(+1)+EnvelopeFromLocalMaxima(+2) 
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/ctfInfo/ctfFunctionServer/src/ctfFunctionServer.html b/src/Tools/ctfInfo/ctfFunctionServer/src/ctfFunctionServer.html
index af1a077..6724c14 100755 (executable)
--- a/src/Tools/ctfInfo/ctfFunctionServer/src/ctfFunctionServer.html
+++ b/src/Tools/ctfInfo/ctfFunctionServer/src/ctfFunctionServer.html
@@ -1 +1 @@
-/bin/bash: ctfFunctionServer: そのようなファイルやディレクトリはありません
+/bin/bash: ctfFunctionServer: No such file or directory

diff --git a/src/Tools/ctfInfo/ctfWeightMapCreation/src/ctfWeightMapCreation.html b/src/Tools/ctfInfo/ctfWeightMapCreation/src/ctfWeightMapCreation.html
index ce920f6..23d3392 100755 (executable)
--- a/src/Tools/ctfInfo/ctfWeightMapCreation/src/ctfWeightMapCreation.html
+++ b/src/Tools/ctfInfo/ctfWeightMapCreation/src/ctfWeightMapCreation.html
@@ -1 +1,32 @@
-/bin/bash: ctfWeightMapCreation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ctfWeightMapCreation</TITLE>
+</HEAD>
+<BODY>
+<H1>ctfWeightMapCreation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ctfWeightMapCreation
+Options:
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
+    [-df                 Defocus             (2.7       )] :Essential :Defocus[A]:under(+)
+    [-white              WhiteNoise          (1.0       )] :Optional  :WhiteNoise(N/S)
+    [-noise              Noise               (NULL      )] :Optional  :Noise Power Spectrum
+    [-splusn             SplusN              (NULL      )] :Optional  :Signal+Noise Power Spectrum
+    [-dRinv              dRinv               (1024*5/3  )] :Essential :dRinv[A]
+    [-dRmaxInv           dRmaxInv            (10.0      )] :Essential :dRmaxInv[A]
+    [-SinWin             SinWinRminInv       (20.0      )SinWinRmaxInv       (10.0      )] :Optional  :RminInv[A] RmaxInv[A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+Mode:
+      0: No correction  : F = G
+      1: Phase contrast : F = G*(H/abs(H))(Only 1 or -1)
+      2: Phase contrast : F = G*H (Winer filter (S/N << 1))
+      3: Phase contrast : F = G/H (Inverse filter)
+      4: Phase contrast : F = G*(H/(H*H + N*N)) (Winer filter (white noise : Required Option -white))
+      5: Phase contrast : F = G*(H/abs(H)*abs(G*G-N*N)/(G*G)) (Winer filter: Required Option -noise, -splusn))
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/ctfInfo/ctfZeroPoint/src/ctfZeroPoint.html b/src/Tools/ctfInfo/ctfZeroPoint/src/ctfZeroPoint.html
index e33196d..5641dee 100755 (executable)
--- a/src/Tools/ctfInfo/ctfZeroPoint/src/ctfZeroPoint.html
+++ b/src/Tools/ctfInfo/ctfZeroPoint/src/ctfZeroPoint.html
@@ -1 +1 @@
-/bin/bash: ctfZeroPoint: そのようなファイルやディレクトリはありません
+/bin/bash: ctfZeroPoint: No such file or directory

diff --git a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/defocusDeterminationFromThonRing.html b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/defocusDeterminationFromThonRing.html
index 44e4dc4..ae8bf0e 100755 (executable)
--- a/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/defocusDeterminationFromThonRing.html
+++ b/src/Tools/ctfInfo/defocusDeterminationFromThonRing/src/defocusDeterminationFromThonRing.html
@@ -1 +1,43 @@
-/bin/bash: defocusDeterminationFromThonRing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>defocusDeterminationFromThonRing</TITLE>
+</HEAD>
+<BODY>
+<H1>defocusDeterminationFromThonRing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: defocusDeterminationFromThonRing
+Options:
+    [-i[nput]            In                  (stdin     )] :Optional  :InputDataFile
+    [-i[nput] N[ame]     InN                 (stdin     )] :Optional  :InputNameInInformationFile
+    [-i[nput] R[eference]InR                 (stdin     )] :Optional  :InputReferenceForLength
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-o[utput] I[nformation]OutI                (stdout    )] :Optional  :OutputInformationFile
+    [-o[utput] I[nformation]OutI2               (stdout    )] :Optional  :OutputInformationFile
+    [-o[utput] I[nformation]OutI3               (stdout    )] :Optional  :OutputInformationFile
+    [-kV                 kV                  (200       )] :Optional  :kV
+    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
+    [-A[mplitude contrast]AoverP              (0.05      )] :Optional  :The ratio of amplitude contrast to phase contrast
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-ctfMode            ctfMode             (0         )] :Optional  :CTFMode
+    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.
+    [-R[/A]              R                   (NULL      )... ] :Variable  :ThonRing[/A]
+----- Additional Usage ----- 
+>>>> o[uput] I[nformation] <<<<
+This file is used for [mrcImageMultiCTFCompensation and mrcImageCTFCompensation] 
+>>>> o[uput] I[nformation] 2<<<<
+This file is used for [llDataCTFCompensate -I2] 
+>>>> o[uput] I[nformation] 3<<<<
+This file is used for [llExtractWithLayerSeparation] 
+Options: -truePitch, -PixelSize, -deltadY and -ctfMode
+>>>> ctfMode <<<< 
+ 0: Phase CTF 
+ 1: PhaseCTF + ratio*AmpCTF 
+>>>> mode <<<< 
+No action
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/ctfInfo/tiltInfoDetermine/src/tiltInfoDetermine.html b/src/Tools/ctfInfo/tiltInfoDetermine/src/tiltInfoDetermine.html
index bde86d9..00d3e50 100755 (executable)
--- a/src/Tools/ctfInfo/tiltInfoDetermine/src/tiltInfoDetermine.html
+++ b/src/Tools/ctfInfo/tiltInfoDetermine/src/tiltInfoDetermine.html
@@ -1 +1,20 @@
-/bin/bash: tiltInfoDetermine: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>tiltInfoDetermine</TITLE>
+</HEAD>
+<BODY>
+<H1>tiltInfoDetermine</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: tiltInfoDetermine
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-defocusIn[put]     defocus             (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ag]              mag                 (2.4       )] :Optional  :Mag
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/database/homology2PG/src/homology2PG.html b/src/Tools/database/homology2PG/src/homology2PG.html
index 4858f04..bd82fcc 100755 (executable)
--- a/src/Tools/database/homology2PG/src/homology2PG.html
+++ b/src/Tools/database/homology2PG/src/homology2PG.html
@@ -1,26 +1 @@
-<<<<<<< HEAD
-/bin/bash: homology2PG: そのようなファイルやディレクトリはありません
-=======
-<HTML>
-<HEAD>
-<TITLE>homology2PG</TITLE>
-</HEAD>
-<BODY>
-<H1>homology2PG</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: homology2PG
-Options:
-    [-i[nput]            In                  (stdin     )] :Essential :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-skip               Skip                (0         )] :Optional  :SkipResidueNumber
-    [-H[ost]             Host                (pc00      )] :Optional  :HostName
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-P[ort]             Port                (5432      )] :Optional  :Port
-    [-d[atabase]         database            (test      )] :Optional  :database
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
->>>>>>> FETCH_HEAD
+/bin/bash: homology2PG: No such file or directory

diff --git a/src/Tools/database/pgDataBaseSelectServer/src/pgDataBaseSelectServer.html b/src/Tools/database/pgDataBaseSelectServer/src/pgDataBaseSelectServer.html
index 720f03a..59e1ede 100755 (executable)
--- a/src/Tools/database/pgDataBaseSelectServer/src/pgDataBaseSelectServer.html
+++ b/src/Tools/database/pgDataBaseSelectServer/src/pgDataBaseSelectServer.html
@@ -1 +1 @@
-/bin/bash: pgDataBaseSelectServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgDataBaseSelectServer: No such file or directory

diff --git a/src/Tools/database/pgJournalSelect/src/pgJournalSelect.html b/src/Tools/database/pgJournalSelect/src/pgJournalSelect.html
index cb1c30e..a4e41b6 100755 (executable)
--- a/src/Tools/database/pgJournalSelect/src/pgJournalSelect.html
+++ b/src/Tools/database/pgJournalSelect/src/pgJournalSelect.html
@@ -1,24 +1 @@
-<<<<<<< HEAD
-/bin/bash: pgJournalSelect: そのようなファイルやディレクトリはありません
-=======
-<HTML>
-<HEAD>
-<TITLE>pgJournalSelect</TITLE>
-</HEAD>
-<BODY>
-<H1>pgJournalSelect</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pgJournalSelect
-Options:
-    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
-    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-H[ost]             Host                (pc00      )] :Optional  :HostName
-    [-P[ort]             Port                (5432      )] :Optional  :Port
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
->>>>>>> FETCH_HEAD
+/bin/bash: pgJournalSelect: No such file or directory

diff --git a/src/Tools/database/pgJournalSelectCORBAClient/src/pgJournalSelectCORBAClient.html b/src/Tools/database/pgJournalSelectCORBAClient/src/pgJournalSelectCORBAClient.html
index c333623..06bf88f 100755 (executable)
--- a/src/Tools/database/pgJournalSelectCORBAClient/src/pgJournalSelectCORBAClient.html
+++ b/src/Tools/database/pgJournalSelectCORBAClient/src/pgJournalSelectCORBAClient.html
@@ -1 +1 @@
-/bin/bash: pgJournalSelectCORBAClient: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAClient: No such file or directory

diff --git a/src/Tools/database/pgJournalSelectCORBAServer/src/pgJournalSelectCORBAServer.html b/src/Tools/database/pgJournalSelectCORBAServer/src/pgJournalSelectCORBAServer.html
index f02c9f4..1e1e220 100755 (executable)
--- a/src/Tools/database/pgJournalSelectCORBAServer/src/pgJournalSelectCORBAServer.html
+++ b/src/Tools/database/pgJournalSelectCORBAServer/src/pgJournalSelectCORBAServer.html
@@ -1 +1 @@
-/bin/bash: pgJournalSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgJournalSelectCORBAServer: No such file or directory

diff --git a/src/Tools/database/pgMemoSelectCORBAServer/src/pgMemoSelectCORBAServer.html b/src/Tools/database/pgMemoSelectCORBAServer/src/pgMemoSelectCORBAServer.html
index 1933db7..d4d7722 100755 (executable)
--- a/src/Tools/database/pgMemoSelectCORBAServer/src/pgMemoSelectCORBAServer.html
+++ b/src/Tools/database/pgMemoSelectCORBAServer/src/pgMemoSelectCORBAServer.html
@@ -1 +1 @@
-/bin/bash: pgMemoSelectCORBAServer: そのようなファイルやディレクトリはありません
+/bin/bash: pgMemoSelectCORBAServer: No such file or directory

diff --git a/src/Tools/database/pgSelect/src/pgSelect.html b/src/Tools/database/pgSelect/src/pgSelect.html
index 3bf4bb2..2568842 100755 (executable)
--- a/src/Tools/database/pgSelect/src/pgSelect.html
+++ b/src/Tools/database/pgSelect/src/pgSelect.html
@@ -1,24 +1 @@
-<<<<<<< HEAD
-/bin/bash: pgSelect: そのようなファイルやディレクトリはありません
-=======
-<HTML>
-<HEAD>
-<TITLE>pgSelect</TITLE>
-</HEAD>
-<BODY>
-<H1>pgSelect</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: pgSelect
-Options:
-    [-H[ostname]         hostname            (pc17      )] :Optional  :hostname
-    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
-    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         )] :Optional  :Mode
-    [-P[ortNumber]       port                (7777      )] :Optional  :port
-    [-D[ataBaseName]     dbName              (test      )] :Optional  :dbName
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
->>>>>>> FETCH_HEAD
+/bin/bash: pgSelect: No such file or directory

diff --git a/src/Tools/filter/array2mrc/src/array2mrc.html b/src/Tools/filter/array2mrc/src/array2mrc.html
index 3da72a8..c6464e0 100755 (executable)
--- a/src/Tools/filter/array2mrc/src/array2mrc.html
+++ b/src/Tools/filter/array2mrc/src/array2mrc.html
@@ -1 +1,33 @@
-/bin/bash: array2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>array2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>array2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: array2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-m[ode]m[rcimage]   mm                  (2         )] :Optional  :Mode of mrcImage
+    [-l[ength]m[rcimage] lm                  (0         )] :Optional  :Length of mrcImage
+----- Additional Usage -----
+-- Attension --
+Array format : left-hand
+mrc   format : right-hand
+---------------
+>>> Array Format under Eos <<<<
+ndim N0 N1 N2 ...
+data(0,   0,   0,...,        0) data(1,   0,   0,...,        0) data(2,   0,   0,...,        0) ... data(N0-1,   0,   0,...,        0)
+data(0,   1,   0,...,        0) data(1,   1,   0,...,        0) data(2,   1,   0,...,        0) ... data(N0-1,   1,   0,...,        0)
+..............................................................
+data(0,N1-1,   0,...,        0) data(1,N1-1,   0,...,        0) data(2,N1-1,   0,...,        0) ... data(N0-1,N1-1,   0,...,        0)
+data(0,   0,   1,...,        0) data(1,   0,   1,...,        0) data(2,   0,   1,...,        0) ... data(N0-1,   0,   1,...,        0)
+..............................................................
+data(0,N1-1,N2-1,...,Nndim-1-1) data(1,N1-1,N2-1,...,Nndim-1-1) data(2,N1-1,N2-1,...,Nndim-1-1) ... data(N0-1,N1-1,N2-1,...,Nndim-1-1)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/bin2mrc/src/bin2mrc.html b/src/Tools/filter/bin2mrc/src/bin2mrc.html
index 926f2e3..922b969 100644 (file)
--- a/src/Tools/filter/bin2mrc/src/bin2mrc.html
+++ b/src/Tools/filter/bin2mrc/src/bin2mrc.html
@@ -1 +1,18 @@
-/bin/bash: bin2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>bin2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>bin2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: bin2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/emData2mrc/src/emData2mrc.html b/src/Tools/filter/emData2mrc/src/emData2mrc.html
index 4d70b55..eeeee53 100755 (executable)
--- a/src/Tools/filter/emData2mrc/src/emData2mrc.html
+++ b/src/Tools/filter/emData2mrc/src/emData2mrc.html
@@ -1 +1,19 @@
-/bin/bash: emData2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>emData2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>emData2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: emData2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-m[agCorrection]    magCorrection       (1.0       )] :Optional  :MagCorrection: 
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/imodst2mrc/src/imodst2mrc.html b/src/Tools/filter/imodst2mrc/src/imodst2mrc.html
index 1f5c53c..2e12630 100755 (executable)
--- a/src/Tools/filter/imodst2mrc/src/imodst2mrc.html
+++ b/src/Tools/filter/imodst2mrc/src/imodst2mrc.html
@@ -1 +1,19 @@
-/bin/bash: imodst2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>imodst2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>imodst2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: imodst2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: Imod Store 
+    [-o[utput]           Out                 (NULL      )] :Optional  :Output: MRC 
+    [-O[utput]           ] :Optional  :Output: MRC LIST
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/ip2mrc/src/ip2mrc.html b/src/Tools/filter/ip2mrc/src/ip2mrc.html
index 7ea92cc..df96cc2 100755 (executable)
--- a/src/Tools/filter/ip2mrc/src/ip2mrc.html
+++ b/src/Tools/filter/ip2mrc/src/ip2mrc.html
@@ -1 +1,26 @@
-/bin/bash: ip2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>ip2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>ip2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: ip2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile[.img]
+    [-i2[nput]           InTem               (NULL      )] :Optional  :InputDataFile[.tem]
+    [-i3[nput]           InInf               (NULL      )] :Optional  :InputDataFile[.inf]
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-o2[utput]          Out2                (NULL      )] :Optional  :OutputDataFile[1/4]
+    [-Mag                Mag                 (40000     )] :Optional  :Magnification
+    [-SE                 SE                  (200       )] :Optional  :SE
+    [-OutMode            OutMode             (1         )] :Optional  :OutPutMode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+mode: 0: No Skip
+mode: 1: Skip(128 byte)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/moi2mrc/src/moi2mrc.html b/src/Tools/filter/moi2mrc/src/moi2mrc.html
index d70e306..411b77e 100755 (executable)
--- a/src/Tools/filter/moi2mrc/src/moi2mrc.html
+++ b/src/Tools/filter/moi2mrc/src/moi2mrc.html
@@ -1 +1,24 @@
-/bin/bash: moi2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>moi2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>moi2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: moi2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
+    [-Mag[nification]    Mag                 (150       )] :Optional  :Magnification[xk]:
+    [-Mag2[nification]   Mag2                (1.64      )] :Optional  :Magnification[CCD/Film]
+    [-ADUperE            ADUperE             (20        )] :Optional  :[ADU/electron]
+    [-info               Info                (1         )] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         )] :Optional  :Mode: 0:char(mean+-3sd) 1:short(direct) 2:float(e-)
+----- Additional Usage -----
+>>>> -info Integer
+ 1: All Header Info List 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/mrc2fld/src/mrc2fld.html b/src/Tools/filter/mrc2fld/src/mrc2fld.html
index 93a06c7..63c8b2d 100755 (executable)
--- a/src/Tools/filter/mrc2fld/src/mrc2fld.html
+++ b/src/Tools/filter/mrc2fld/src/mrc2fld.html
@@ -1 +1,28 @@
-/bin/bash: mrc2fld: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc2fld</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2fld</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2fld
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-shiftx             shiftx              (0.0       )] :Optional  :shiftx[A]
+    [-shifty             shifty              (0.0       )] :Optional  :shifty[A]
+    [-shiftz             shiftz              (0.0       )] :Optional  :shiftz[A]
+    [-I                  ] :Optional  :Inverse
+    [-R[adius]C[ylindrical]] :Optional  :Radius: Cylindrical
+    [-M[ag]              Mag                 (1.0       )] :Optional  :density x mag
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+mode 0:Char(Byte) Image 
+       If you want to use volume rendering, you must select Char.
+mode 2:Float Image 
+mode 102:Double Image 
+       If you want to use for contour image, you should select Float/Double.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/mrc2gif/src/mrc2gif.html b/src/Tools/filter/mrc2gif/src/mrc2gif.html
index 88332df..f4a4e3d 100755 (executable)
--- a/src/Tools/filter/mrc2gif/src/mrc2gif.html
+++ b/src/Tools/filter/mrc2gif/src/mrc2gif.html
@@ -1 +1,22 @@
-/bin/bash: mrc2gif: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc2gif</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2gif</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2gif
+Options:
+    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
+    [-H[igh]             High                (0         )] :Optional  :HighThreshold
+    [-L[ow]              Low                 (0         )] :Optional  :LowThreshold
+    [-I[nverse]          ] :Optional  :Inverse(Black is white)
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode: 
+                       0 (8bits), 1(16bits)
+                       
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/mrc2lattice/src/mrc2lattice.html b/src/Tools/filter/mrc2lattice/src/mrc2lattice.html
index c6d41f7..ab26b17 100755 (executable)
--- a/src/Tools/filter/mrc2lattice/src/mrc2lattice.html
+++ b/src/Tools/filter/mrc2lattice/src/mrc2lattice.html
@@ -1 +1 @@
-/bin/bash: mrc2lattice: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2lattice: No such file or directory

diff --git a/src/Tools/filter/mrc2mrc/src/mrc2mrc.html b/src/Tools/filter/mrc2mrc/src/mrc2mrc.html
index c7fa497..9b8dfbf 100755 (executable)
--- a/src/Tools/filter/mrc2mrc/src/mrc2mrc.html
+++ b/src/Tools/filter/mrc2mrc/src/mrc2mrc.html
@@ -1 +1,26 @@
-/bin/bash: mrc2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2mrc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: 
+    [-i[nput]t[ype]      InType              (FEIextendedMRC)] :Optional  :InputDataType
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-o[utput]t[ype]     OutType             (Eos       )] :Optional  :OutputDataType
+    [-Length             LenX                (1.0       )LenY                (1.0       )LenZ                (1.0       )] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+>> To be suppoerted (Not all)
+Eos
+CCP4-2000
+IMODextendedMRC
+FEIextendedMRC
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/mrc2pov/src/mrc2pov.html b/src/Tools/filter/mrc2pov/src/mrc2pov.html
index 6449e6b..9c70bfc 100755 (executable)
--- a/src/Tools/filter/mrc2pov/src/mrc2pov.html
+++ b/src/Tools/filter/mrc2pov/src/mrc2pov.html
@@ -1 +1 @@
-/bin/bash: mrc2pov: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2pov: No such file or directory

diff --git a/src/Tools/filter/mrc2tiff/src/mrc2tiff.html b/src/Tools/filter/mrc2tiff/src/mrc2tiff.html
index 6019f67..fae55b0 100755 (executable)
--- a/src/Tools/filter/mrc2tiff/src/mrc2tiff.html
+++ b/src/Tools/filter/mrc2tiff/src/mrc2tiff.html
@@ -1 +1,24 @@
-/bin/bash: mrc2tiff: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc2tiff</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc2tiff</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc2tiff
+Options:
+    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
+    [-H[igh]             High                (0         )] :Optional  :HighThreshold
+    [-L[ow]              Low                 (0         )] :Optional  :LowThreshold
+    [-I[nverse]          ] :Optional  :Inverse(Black is white)
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode: 
+                       0 (8bits), 1(16bits)
+                       
+--- Attention ---
+Previously, the black and white were inter-changed between mrc and tiff.  Now they are not changed
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/filter/mrc2viff/src/mrc2viff.html b/src/Tools/filter/mrc2viff/src/mrc2viff.html
index fff63e8..c2a1c1e 100755 (executable)
--- a/src/Tools/filter/mrc2viff/src/mrc2viff.html
+++ b/src/Tools/filter/mrc2viff/src/mrc2viff.html
@@ -1 +1 @@
-/bin/bash: mrc2viff: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2viff: No such file or directory

diff --git a/src/Tools/filter/test2/src/test.html b/src/Tools/filter/test2/src/test.html
index c0cd035..b0c1ef6 100755 (executable)
--- a/src/Tools/filter/test2/src/test.html
+++ b/src/Tools/filter/test2/src/test.html
@@ -1 +1 @@
-/bin/bash: test: そのようなファイルやディレクトリはありません
+/bin/bash: test: No such file or directory

diff --git a/src/Tools/filter/tiff2mrc/src/tiff2mrc.html b/src/Tools/filter/tiff2mrc/src/tiff2mrc.html
index b0919a3..7e09f0f 100755 (executable)
--- a/src/Tools/filter/tiff2mrc/src/tiff2mrc.html
+++ b/src/Tools/filter/tiff2mrc/src/tiff2mrc.html
@@ -1 +1,37 @@
-/bin/bash: tiff2mrc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>tiff2mrc</TITLE>
+</HEAD>
+<BODY>
+<H1>tiff2mrc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: tiff2mrc
+Options:
+    [-i[nput]            inFile              (NULL      )] :Essential :InputDataFile
+    [-o[utput]           outFile             (NULL      )] :Essential :OutputDataFile
+    [-r[esolution]       Resolution          (2.5       )] :Optional  :Resolution[A]
+    [-t[ime]             time                (1.0       )] :Optional  :x OptimalTime
+    [-d[irnum]           dirnum              (0         )] :Optional  :tiffDirectoryNumber
+    [-I[nverse]          ] :Optional  :Black<->White
+    [-Signed             ] :Optional  :Original image is Signed or Not: Default unsigned
+    [-Offset             Offset              (0.0       )] :Optional  :OffsetValue
+    [-Max                Max                 (16        )] :Optional  :MaxValue:2^Max
+    [-Min                Min                 (1         )] :Optional  :MinValue:2^Min: without 0
+    [-realMin            realMin             (0.0       )] :Optional  :Real MinValue
+    [-realMax            realMax             (0.0       )] :Optional  :Real MaxValue
+    [-realMaxBit         realMaxBit          (14        )] :Optional  :Real MaxValue Bit
+    [-sin                sinFile             (NULL      )] :Optional  :sin file from Zeiss
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-S[hrink]           Shrink              (8         )] :Optional  :ShrinkMode
+    [-M[ode]             Mode                (0         )] :Optional  :Mode: mrcMode: Def: if -m 0, -M 0. if -m 1 -M 2
+    [-m[ode]             mode                (0         )] :Optional  :Mode: 0 (Direct), 1(Log10(65535/data))
+---- mode ----
+0x0000000f bits: Direct or Log
+0x000000f0 bits: Which Color
+                 R: 00
+                 G: 10
+                 B: 20
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/hf2000/hf2000Init/src/hf2000Init.html b/src/Tools/hf2000/hf2000Init/src/hf2000Init.html
index 990c140..cfe38eb 100755 (executable)
--- a/src/Tools/hf2000/hf2000Init/src/hf2000Init.html
+++ b/src/Tools/hf2000/hf2000Init/src/hf2000Init.html
@@ -1 +1,19 @@
-/bin/bash: hf2000Init: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>hf2000Init</TITLE>
+</HEAD>
+<BODY>
+<H1>hf2000Init</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: hf2000Init
+Options:
+    [-tty                tty                 (/dev/ttyS1)] :Optional  :DeviceFile
+    [-speed              speed               (4800      )] :Optional  :SerialPort Speed
+    [-S[erver]           Host                (tkyemg-pc06)Server              (6000      )] :Optional  :host port: As Server: Default Shell mode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/hf2000/hf2000LenzCurrent/src/hf2000LenzCurrent.html b/src/Tools/hf2000/hf2000LenzCurrent/src/hf2000LenzCurrent.html
index 7f106b7..60361f4 100755 (executable)
--- a/src/Tools/hf2000/hf2000LenzCurrent/src/hf2000LenzCurrent.html
+++ b/src/Tools/hf2000/hf2000LenzCurrent/src/hf2000LenzCurrent.html
@@ -1 +1,22 @@
-/bin/bash: hf2000LenzCurrent: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>hf2000LenzCurrent</TITLE>
+</HEAD>
+<BODY>
+<H1>hf2000LenzCurrent</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: hf2000LenzCurrent
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-tty                tty                 (/dev/ttyS1)] :Optional  :TTY
+    [-speed              speed               (4800      )] :Optional  :TTY
+    [-which[Lenz]        which               (OBJ       )] :Optional  :Lenz:C1/C2/C3/OBJ/I1/I2/P1/P2
+    [-I[nteractive]      Interactive         (5         )] :Optional  :[sec]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/hf2000/hf2000SpecimenPosition/src/hf2000SpecimenPosition.html b/src/Tools/hf2000/hf2000SpecimenPosition/src/hf2000SpecimenPosition.html
index 670d13e..5b975cc 100755 (executable)
--- a/src/Tools/hf2000/hf2000SpecimenPosition/src/hf2000SpecimenPosition.html
+++ b/src/Tools/hf2000/hf2000SpecimenPosition/src/hf2000SpecimenPosition.html
@@ -1 +1,23 @@
-/bin/bash: hf2000SpecimenPosition: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>hf2000SpecimenPosition</TITLE>
+</HEAD>
+<BODY>
+<H1>hf2000SpecimenPosition</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: hf2000SpecimenPosition
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-tty                tty                 (/dev/ttyS1)] :Optional  :TTY
+    [-speed              Speed               (4800      )] :Optional  :Speed
+    [-p[osition]         posX                (0.0       )posY                (0.0       )] :Optional  :Set Position[um,um]
+    [-I[nteractive]      Interactive         (5         )] :Optional  :Interactive[sec]
+    [-S[erver]           Host                (tkyemg-pc06)Port                (6000      )] :Optional  :Host port Server[sec]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/khorosTool/khorosFilterGenerate/src/khorosFilterGenerate.html b/src/Tools/khorosTool/khorosFilterGenerate/src/khorosFilterGenerate.html
index a7e6e5f..3c0fe4f 100755 (executable)
--- a/src/Tools/khorosTool/khorosFilterGenerate/src/khorosFilterGenerate.html
+++ b/src/Tools/khorosTool/khorosFilterGenerate/src/khorosFilterGenerate.html
@@ -1 +1 @@
-/bin/bash: khorosFilterGenerate: そのようなファイルやディレクトリはありません
+/bin/bash: khorosFilterGenerate: No such file or directory

diff --git a/src/Tools/llData/.Source b/src/Tools/llData/.Source
index 5d0d829..cfead12 100644 (file)
--- a/src/Tools/llData/.Source
+++ b/src/Tools/llData/.Source
@@ -1,9 +1,9 @@
 SOURCE=\
 llDataAverage \
 llDataAxisSearch \
+llDataCTFCompensate \
 llDataCompare \
 llDataContributionCalcDifferentN \
-llDataCTFCompensate \
 llDataDump \
 llDataEquatorAdd \
 llDataExtract \
@@ -17,9 +17,9 @@ llDataNormalization \
 llDataPrint \
 llDataRescaling \
 llDataResolutionCheck \
-llDatarMaxLimit \
 llDataRotation \
 llDataSelectionEstimation \
 llDataSeparate \
 llDataWeightSet \
+llDatarMaxLimit \
 #LastSource

diff --git a/src/Tools/llData/llDataAverage/src/llDataAverage.html b/src/Tools/llData/llDataAverage/src/llDataAverage.html
index 974910b..9079897 100755 (executable)
--- a/src/Tools/llData/llDataAverage/src/llDataAverage.html
+++ b/src/Tools/llData/llDataAverage/src/llDataAverage.html
@@ -1 +1,33 @@
-/bin/bash: llDataAverage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataAverage</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataAverage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataAverage
+Options:
+    [-M[odel]            Model               (NULL      )] :Essential :Input: ModelFileName(llData)
+    [-i[nput]            In                  (NULL      )] :Essential :Input: InputDataFile
+    [-l[ayer]            llInfo              (NULL      )] :Essential :Input: Layer Line Information
+    [-A[verage]          Ave                 (NULL      )] :Essential :Output: Averaged File Name
+    [-o[utput]           OutParam            (stdout    )] :Optional  :Output: FittedParameter
+    [-o2[utput]          OutParam2           (NULL      )] :Optional  :Output: FittedParameter(phi, z)
+    [-O[utput]           Out                 (NULL      )] :Optional  :Output: FittedData
+    [-P2[plot]           P2                  (NULL      )] :Optional  :Output: P2PlotData
+    [-t[ruePitch]        truePitch           (1.0       )] :Optional  :True Pitch
+    [-d[eltaR]           dR                  (1.0       )] :Optional  :deltaR
+    [-r[adial]           rmin                (1.0       )rmax                (1.0       )dr                  (1.0       )] :Optional  :Radial[Ratio]
+    [-p[hi]              phimin              (0.0       )phimax              (180.0     )dphi                (5.0       )] :Optional  :Phi [degree]
+    [-z[shift]           zmin                (0.0       )zmax                (60.0      )dz                  (5.0       )] :Optional  :z [A]
+    [-withoutAntiPole    ] :Optional  :Not Allow Antipole
+    [-C[utValue]         CutValue            (1.0       )] :Optional  :CutValue
+    [-pvm                pvm                 (0         )] :Optional  :PVM: 
+    [-pvmList            pvmList             (stdin     )] :Optional  :PVM: HostList
+    [-pvmList            Log                 (stdout    )] :Optional  :PVM: HostList
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/llData/llDataAxisSearch/src/llDataAxisSearch.html b/src/Tools/llData/llDataAxisSearch/src/llDataAxisSearch.html
index 8410b65..95b12ff 100755 (executable)
--- a/src/Tools/llData/llDataAxisSearch/src/llDataAxisSearch.html
+++ b/src/Tools/llData/llDataAxisSearch/src/llDataAxisSearch.html
@@ -1 +1,46 @@
-/bin/bash: llDataAxisSearch: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataAxisSearch</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataAxisSearch</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataAxisSearch
+Options:
+    [-i1[nput]           In1                 (NULL      )] :Optional  :In: NearSide
+    [-i2[nput]           In2                 (NULL      )] :Optional  :In: FarSide
+    [-o1[utput]          Out1                (NULL      )] :Optional  :Out: NearSide
+    [-o2[utput]          Out2                (NULL      )] :Optional  :Out: FarSide
+    [-a[verage]          Avg                 (NULL      )] :Optional  :Out: Average
+    [-o[utput]           Out                 (NULL      )] :Optional  :Out: FitParam
+    [-op2[utput]         OutP2               (NULL      )] :Optional  :OutParam2: FitParam Distribution [mrcImage]
+    [-t[ruePitch]        truePitch           (0.0       )] :Optional  :TruePitch[A]
+    [-l[ayer]            L                   (NULL      )] :Optional  :LayerInfo
+    [-O[mega]            Omin                (0.0       )Omax                (0.0       )Odelta              (1.0       )] :Optional  :Omega[degree]
+    [-x[shift]           xmin                (-10.0     )xmax                (10.0      )xdelta              (0.1       )] :Optional  :shiftx[A]
+    [-R                  R                   (10.0      )] :Optional  :Resolution[A]
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+----- Layer Line Information File ----- 
+L N Weight
+..........
+
+----- Control File -----
+In1[inFile:NULL]                               #In: NearSide
+In2[inFile:NULL]                               #In: FarSide
+Out1[outFile:NULL]                             #Out: NearSide
+Out2[outFile:NULL]                             #Out: FarSide
+Avg[outFile:NULL]                              #Out: Average
+Out[outFile:NULL]                              #Out: FitParam
+truePitch[Real:NULL]                           #TruePitch[A]
+L[inFile:NULL]                         #LayerInfo
+Omin[Real:0.0] Omax[Real:0.0]  Odelta[Real:1.0]                                #Omega[degree]
+xmin[Real:-10.0]       xmax[Real:10.0] xdelta[Real:0.1]                                #shiftx[A]
+R[Real:10.0]                           #Resolution[A]
+mode[Integer:0]                                #Mode
+----- Inside Axis Search Parameter File -----
+info.In1, info.In2, paraFit.Para.R*DEGREE, paraFit.Para.x.Value, paraFit.Para.Omega.Value
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/llData/llDataFitServer/src/llDataFitServer.html b/src/Tools/llData/llDataFitServer/src/llDataFitServer.html
index f747b3a..395cdc4 100755 (executable)
--- a/src/Tools/llData/llDataFitServer/src/llDataFitServer.html
+++ b/src/Tools/llData/llDataFitServer/src/llDataFitServer.html
@@ -1 +1 @@
-/bin/bash: llDataFitServer: そのようなファイルやディレクトリはありません
+/bin/bash: llDataFitServer: No such file or directory

diff --git a/src/Tools/llData/llDataMultiCTFCompensation/src/llDataMultiCTFCompensation.html b/src/Tools/llData/llDataMultiCTFCompensation/src/llDataMultiCTFCompensation.html
index 17ee693..68bd2a9 100755 (executable)
--- a/src/Tools/llData/llDataMultiCTFCompensation/src/llDataMultiCTFCompensation.html
+++ b/src/Tools/llData/llDataMultiCTFCompensation/src/llDataMultiCTFCompensation.html
@@ -1 +1,36 @@
-/bin/bash: llDataMultiCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataMultiCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataMultiCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataMultiCTFCompensation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: FileList
+    [-M[odel]            Ref                 (NULL      )] :Essential :Input: Model Data
+    [-l[ayerLine]        llInfo              (NULL      )] :Essential :Input: Layer Line Information
+    [-A[verageFile]      Ave                 (NULL      )] :Essential :Output: AverageFile
+    [-o[utput]           OutParam            (NULL      )] :Optional  :Output: FittedParameter
+    [-O[utput]           Out                 (NULL      )] :Optional  :Output: FileList:  PhaseShift of Each Filament
+    [-o2[utput]          OutParam2           (NULL      )] :Optional  :Output: [phi, z] map
+    [-P2[output]         OutParamP2          (NULL      )] :Optional  :Output: For P-P' 
+    [-N[oise]            Noise               (0.0       )] :Optional  :Noise Ratio
+    [-t[ruePitch]        truePitch           (761.4     )] :Essential :truePitch[A]
+    [-d[eltaR]           deltaR              (1.0       )] :Optional  :deltaR[A]
+    [-r[adial]           rmin                (1.0       )rmax                (1.0       )dr                  (1.0       )] :Optional  :Radial[Ratio]
+    [-p[hi]              phimin              (0.0       )phimax              (180.0     )dphi                (1.0       )] :Optional  :Phi [degree]
+    [-z[shift]           zmin                (0.0       )zmax                (180.0     )dz                  (1.0       )] :Optional  :z [A]
+    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax [/A]
+    [-MaxIter[ation]     MaxIter             (1         )] :Optional  :MaxIteration
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+---- InputFileFormat ----
+filename weight(NumberOfAveragedFile) deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
+----- Mode -----
+    0: |CTFi|/Sigma(SQR(CTFi))
+    1:  CTFi /Sigma(SQR(CTFi))
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/llData/llDataPrint/src/llDataPrint.html b/src/Tools/llData/llDataPrint/src/llDataPrint.html
index 881d1b2..20d97af 100755 (executable)
--- a/src/Tools/llData/llDataPrint/src/llDataPrint.html
+++ b/src/Tools/llData/llDataPrint/src/llDataPrint.html
@@ -1 +1,21 @@
-/bin/bash: llDataPrint: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>llDataPrint</TITLE>
+</HEAD>
+<BODY>
+<H1>llDataPrint</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: llDataPrint
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
+    [-i[nput]s           Ins                 (NULL      )] :Optional  :InputDataFileList
+    [-i2[nput]           Nea                 (NULL      )Far                 (NULL      )] :Optional  :InputDataFile(nea and far)
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-Rmax               Rmax                (0.1       )] :Optional  :Input: Rmax [/A]
+    [-I[nteractive]      ] :Optional  :Interactive
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/llData/llDataRotation/src/llDataRotation.html b/src/Tools/llData/llDataRotation/src/llDataRotation.html
index 9e8216c..198afb7 100755 (executable)
--- a/src/Tools/llData/llDataRotation/src/llDataRotation.html
+++ b/src/Tools/llData/llDataRotation/src/llDataRotation.html
@@ -1 +1 @@
-/bin/bash: llDataRotation: そのようなファイルやディレクトリはありません
+/bin/bash: llDataRotation: No such file or directory

diff --git a/src/Tools/llData/llDataSeparate/src/llDataSeparate.html b/src/Tools/llData/llDataSeparate/src/llDataSeparate.html
index 04b51e4..04ba39e 100755 (executable)
--- a/src/Tools/llData/llDataSeparate/src/llDataSeparate.html
+++ b/src/Tools/llData/llDataSeparate/src/llDataSeparate.html
@@ -1 +1 @@
-/bin/bash: llDataSeparate: そのようなファイルやディレクトリはありません
+/bin/bash: llDataSeparate: No such file or directory

diff --git a/src/Tools/mrcImage/.Source.org b/src/Tools/mrcImage/.Source.org
index 7030321..275eca2 100644 (file)
--- a/src/Tools/mrcImage/.Source.org
+++ b/src/Tools/mrcImage/.Source.org
@@ -95,6 +95,7 @@ mrcImageDisplayDensityAsTempFactor \
 mrcImageDistanceConversion \
 mrcImageDivideInfoForTomography \
 mrcImageDivideIntoTwoImages \
+mrcImageDividedByFile \
 mrcImageEdgeEnhancement \
 mrcImageEdgeImageGet \
 mrcImageEnhancementWithFuzzySets \

diff --git a/src/Tools/mrcImage/fft2d/src/fft2d.html b/src/Tools/mrcImage/fft2d/src/fft2d.html
index e339a9d..333b8ab 100755 (executable)
--- a/src/Tools/mrcImage/fft2d/src/fft2d.html
+++ b/src/Tools/mrcImage/fft2d/src/fft2d.html
@@ -1 +1 @@
-/bin/bash: fft2d: そのようなファイルやディレクトリはありません
+/bin/bash: fft2d: No such file or directory

diff --git a/src/Tools/mrcImage/mrc2dsn6/src/mrc2dsn6.html b/src/Tools/mrcImage/mrc2dsn6/src/mrc2dsn6.html
index 5344eb9..f4ace0b 100755 (executable)
--- a/src/Tools/mrcImage/mrc2dsn6/src/mrc2dsn6.html
+++ b/src/Tools/mrcImage/mrc2dsn6/src/mrc2dsn6.html
@@ -1 +1 @@
-/bin/bash: mrc2dsn6: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2dsn6: No such file or directory

diff --git a/src/Tools/mrcImage/mrc2map/src/mrc2map.html b/src/Tools/mrcImage/mrc2map/src/mrc2map.html
index ebd2b9f..2a6e59e 100755 (executable)
--- a/src/Tools/mrcImage/mrc2map/src/mrc2map.html
+++ b/src/Tools/mrcImage/mrc2map/src/mrc2map.html
@@ -1 +1 @@
-/bin/bash: mrc2map: そのようなファイルやディレクトリはありません
+/bin/bash: mrc2map: No such file or directory

diff --git a/src/Tools/mrcImage/mrc3DExtractZ/src/mrc3DExtractZ.html b/src/Tools/mrcImage/mrc3DExtractZ/src/mrc3DExtractZ.html
index 167c421..6e6d45a 100755 (executable)
--- a/src/Tools/mrcImage/mrc3DExtractZ/src/mrc3DExtractZ.html
+++ b/src/Tools/mrcImage/mrc3DExtractZ/src/mrc3DExtractZ.html
@@ -1 +1,19 @@
-/bin/bash: mrc3DExtractZ: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrc3DExtractZ</TITLE>
+</HEAD>
+<BODY>
+<H1>mrc3DExtractZ</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrc3DExtractZ
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-b[ottom]           ZB                  (0         )] :Optional  :Bottom of output data
+    [-t[op]              ZT                  (-1        )] :Optional  :Top of output data. Default:top of input data
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/mrcFETnormalizeBySD.html b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/mrcFETnormalizeBySD.html
index 8df6381..69ec4ae 100755 (executable)
--- a/src/Tools/mrcImage/mrcFETnormalizeBySD/src/mrcFETnormalizeBySD.html
+++ b/src/Tools/mrcImage/mrcFETnormalizeBySD/src/mrcFETnormalizeBySD.html
@@ -1 +1,30 @@
-/bin/bash: mrcFETnormalizeBySD: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFETnormalizeBySD</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFETnormalizeBySD</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFETnormalizeBySD
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputFileList
+    [-i[nput]s[ample]    InSample            (NULL      )] :Optional  :FileListforSDcalc
+    [-r[ead]SD           readSD              (NULL      )] :Optional  :readFETSDfile
+    [-w[rite]SD          writeSD             (NULL      )] :Optional  :writeFETSDfile
+    [-o[utput]           Out                 (NULL      )] :Optional  :OutputASmrcImage
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+
+----- Additional Usage -----
+-is  :[inputsample] is FileList for SDcalculation.
+           use when the inputFileList is large
+-rSD : to use SDdata(without calculate) mrc format
+-wSD : write out the SDdata as mrc format
+       this file can be used next normalize with "-rSD"command.
+-o   : save all normalized data into one mrcImage.
+       do not use when the inputFileList is large
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/mrcFFTCTFCompensation.html b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/mrcFFTCTFCompensation.html
index 2ab5ff1..48c2f1e 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTCTFCompensation/src/mrcFFTCTFCompensation.html
+++ b/src/Tools/mrcImage/mrcFFTCTFCompensation/src/mrcFFTCTFCompensation.html
@@ -1 +1,23 @@
-/bin/bash: mrcFFTCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTCTFCompensation
+Options:
+    [-i[nput]            In                  ] :Essential :InputDataFile
+    [-o[utput]           Out                 ] :Essential :OutputDataFile
+    [-I[nputWeight]      CTFIn               ] :Essential :InputWeightFile
+    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                ] :Optional  :Mode
+>>> CTFWeigting File
+RR0 F0 : If R<RR0, Weight=0. If RR0<=R<RR1,  Weight={(RR1-R)*F0+(R-RR0)*F1}/(RR1-RR0), i.e., Linear Interpolation
+RR1 F1 : 
+...................................
+RRn Fn : If RRn<=R, Fn
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTDigitize/src/mrcFFTDigitize.html b/src/Tools/mrcImage/mrcFFTDigitize/src/mrcFFTDigitize.html
index f732271..8ee5702 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTDigitize/src/mrcFFTDigitize.html
+++ b/src/Tools/mrcImage/mrcFFTDigitize/src/mrcFFTDigitize.html
@@ -1 +1,21 @@
-/bin/bash: mrcFFTDigitize: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTDigitize</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTDigitize</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTDigitize
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-l[evel]            Level               (2.0       )] :Optional  :Level
+    [-min[imum]          Min                 (0.0       )] :Essential :Minimum
+    [-max[imum]          Max                 (0.0       )] :Essential :Maximum
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTExpression/src/mrcFFTExpression.html b/src/Tools/mrcImage/mrcFFTExpression/src/mrcFFTExpression.html
index e49234d..a4d5f53 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTExpression/src/mrcFFTExpression.html
+++ b/src/Tools/mrcImage/mrcFFTExpression/src/mrcFFTExpression.html
@@ -1 +1,26 @@
-/bin/bash: mrcFFTExpression: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTExpression</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTExpression</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTExpression
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-T[hreshold]        Thres               (1e-16     )] :Optional  :Threshold to calculate.For mode 1 and 3.
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- FFT Expression MOde -----
+0:Amplitude
+1:LogAmplitude
+2:Power
+3:LogPower
+4:Phase
+5:Real
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/mrcFFTFibreDiagram.html b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/mrcFFTFibreDiagram.html
index 947f69e..b3669ed 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTFibreDiagram/src/mrcFFTFibreDiagram.html
+++ b/src/Tools/mrcImage/mrcFFTFibreDiagram/src/mrcFFTFibreDiagram.html
@@ -1 +1,19 @@
-/bin/bash: mrcFFTFibreDiagram: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTFibreDiagram</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTFibreDiagram</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTFibreDiagram
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: HelicalObject/FFT3D or Image3D
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: 2D mrcImage
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+  -mode 0 : average PHI-axis to express RZ space
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTFiltering/src/mrcFFTFiltering.html b/src/Tools/mrcImage/mrcFFTFiltering/src/mrcFFTFiltering.html
index fe88113..49cc48b 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTFiltering/src/mrcFFTFiltering.html
+++ b/src/Tools/mrcImage/mrcFFTFiltering/src/mrcFFTFiltering.html
@@ -1 +1,25 @@
-/bin/bash: mrcFFTFiltering: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTFiltering</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTFiltering</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTFiltering
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: Filtered Image
+    [-IQ                 IQ                  (NULL      )] :Optional  :Output: IQ Map
+    [-vx                 vx                  (0         )] :Optional  :Vector(x)
+    [-vy                 vy                  (0         )] :Optional  :Vector(y)
+    [-v1                 v1x                 (0         )v1y                 (0         )] :Optional  :Vector(v1)
+    [-v2                 v2x                 (0         )v2y                 (0         )] :Optional  :Vector(v2)
+    [-sx                 sx                  (1         )] :Optional  :Size(x)
+    [-sy                 sy                  (1         )] :Optional  :Size(y)
+    [-neg[lect]F00       ] :Optional  :Neglect F00
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTIQEstimation/src/mrcFFTIQEstimation.html b/src/Tools/mrcImage/mrcFFTIQEstimation/src/mrcFFTIQEstimation.html
index 11ccdd9..baf89ff 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTIQEstimation/src/mrcFFTIQEstimation.html
+++ b/src/Tools/mrcImage/mrcFFTIQEstimation/src/mrcFFTIQEstimation.html
@@ -1 +1,20 @@
-/bin/bash: mrcFFTIQEstimation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTIQEstimation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTIQEstimation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTIQEstimation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
+    [-sp[otList]         SpotList            (stdin     )] :Essential :Input: SpotList: X Y Z
+    [-radius             radius              (3         )] :Optional  :Input: [pixel]
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: ASCII
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.html b/src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.html
index cf78640..b16b6e0 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.html
+++ b/src/Tools/mrcImage/mrcFFTInfo/src/mrcFFTInfo.html
@@ -1 +1,25 @@
-/bin/bash: mrcFFTInfo: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTInfo
+Options:
+    [-i[nput]            In                  ] :Essential :InputDataFile
+    [-o[utput]           Out                 ] :Essential :OutputDataFile
+    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                ] :Optional  :Mode
+Mode: 
+        1 :Scattering Angular Distribution(Sum)
+        2 :X-axis (OutPut: Mag, Phase)
+        4 :Y-axis (OutPut: Mag, Phase)
+        5 :Y-axis (Average:Along X-axis)(OutPut: Mag, Phase)
+        8 :Scattering Angular Distribution(Average)
+       16 :with spacing 
+       32 :with Angular Distribution(SD)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/mrcFFTLayerLineCheck.html b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/mrcFFTLayerLineCheck.html
index eccb702..dc76786 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/mrcFFTLayerLineCheck.html
+++ b/src/Tools/mrcImage/mrcFFTLayerLineCheck/src/mrcFFTLayerLineCheck.html
@@ -1 +1,20 @@
-/bin/bash: mrcFFTLayerLineCheck: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTLayerLineCheck</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTLayerLineCheck</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTLayerLineCheck
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc(FT)
+    [-L[ayer]            L                   (2         )] :Optional  :Input: Layer(pixel)
+    [-NoEq               ] :Optional  :Input: No l=0
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTMedianFilter/src/mrcFFTMedianFilter.html b/src/Tools/mrcImage/mrcFFTMedianFilter/src/mrcFFTMedianFilter.html
index 5c2e620..2ac577e 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTMedianFilter/src/mrcFFTMedianFilter.html
+++ b/src/Tools/mrcImage/mrcFFTMedianFilter/src/mrcFFTMedianFilter.html
@@ -1 +1,22 @@
-/bin/bash: mrcFFTMedianFilter: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTMedianFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTMedianFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTMedianFilter
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-r                  r                   (1         )] :Optional  :Radius of Kernel Size (Pixel)
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Calculation is performed on amplitude only.
+Output: Real part is amplitude and imaginary part is zero.
+Use this program only for CTF determination.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTProjection/src/mrcFFTProjection.html b/src/Tools/mrcImage/mrcFFTProjection/src/mrcFFTProjection.html
index d4b3479..64ffbcc 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTProjection/src/mrcFFTProjection.html
+++ b/src/Tools/mrcImage/mrcFFTProjection/src/mrcFFTProjection.html
@@ -1 +1,21 @@
-/bin/bash: mrcFFTProjection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTProjection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+The 2D FFT Image projects to Y-axis
+This image is not true.
+Because the real part is buried with mag and the imaginary part is buried with zero.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTResampling/src/mrcFFTResampling.html b/src/Tools/mrcImage/mrcFFTResampling/src/mrcFFTResampling.html
index fca6e57..698f792 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTResampling/src/mrcFFTResampling.html
+++ b/src/Tools/mrcImage/mrcFFTResampling/src/mrcFFTResampling.html
@@ -1 +1,20 @@
-/bin/bash: mrcFFTResampling: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTResampling</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTResampling</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTResampling
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-nx[umber]          Nx                  (64.0      )] :Optional  :NumberX
+    [-ny[umber]          Ny                  (64.0      )] :Optional  :NumberY
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTShellInfo/src/mrcFFTShellInfo.html b/src/Tools/mrcImage/mrcFFTShellInfo/src/mrcFFTShellInfo.html
index f13ac49..a00d2a0 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTShellInfo/src/mrcFFTShellInfo.html
+++ b/src/Tools/mrcImage/mrcFFTShellInfo/src/mrcFFTShellInfo.html
@@ -1 +1,21 @@
-/bin/bash: mrcFFTShellInfo: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTShellInfo</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTShellInfo</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTShellInfo
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc/FFT
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: 
+    [-R[angeOfShell]     minR                (0         )maxR                (0.1       )] :Optional  :minR/maxR[/A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (1         )] :Optional  :Mode
+----- Additional Usage -----
+-mode 1 : AveragedMagnitute
+-mode 2 : AveragedPower
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTSizeChange/src/mrcFFTSizeChange.html b/src/Tools/mrcImage/mrcFFTSizeChange/src/mrcFFTSizeChange.html
index a595476..d7e464c 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTSizeChange/src/mrcFFTSizeChange.html
+++ b/src/Tools/mrcImage/mrcFFTSizeChange/src/mrcFFTSizeChange.html
@@ -1 +1,20 @@
-/bin/bash: mrcFFTSizeChange: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTSizeChange</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTSizeChange</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTSizeChange
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-x[length]          Nx                  (1.0       )] :Optional  :Pixel size 
+    [-y[length]          Ny                  (1.0       )] :Optional  :Pixel size 
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTSpectrum/src/mrcFFTSpectrum.html b/src/Tools/mrcImage/mrcFFTSpectrum/src/mrcFFTSpectrum.html
index 38e5536..9f9575b 100644 (file)
--- a/src/Tools/mrcImage/mrcFFTSpectrum/src/mrcFFTSpectrum.html
+++ b/src/Tools/mrcImage/mrcFFTSpectrum/src/mrcFFTSpectrum.html
@@ -1 +1,20 @@
-/bin/bash: mrcFFTSpectrum: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTSpectrum</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTSpectrum</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTSpectrum
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input:fft
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output:spectrum
+    [-n                  N                   (1         )] :Optional  :n-division: 2PI/n
+    [-axis               Axis                (0.0       )] :Optional  :axis: 0
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTXFiltering/src/mrcFFTXFiltering.html b/src/Tools/mrcImage/mrcFFTXFiltering/src/mrcFFTXFiltering.html
index b83d4d3..ac6d98a 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTXFiltering/src/mrcFFTXFiltering.html
+++ b/src/Tools/mrcImage/mrcFFTXFiltering/src/mrcFFTXFiltering.html
@@ -1 +1,21 @@
-/bin/bash: mrcFFTXFiltering: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTXFiltering</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTXFiltering</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTXFiltering
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-RMaxX              RMaxX               (0         )] :Optional  :RMax value of X [1/A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+This filter cuts high resolution information only X direction.
+RMaxX [1/A] is maximum resolution
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFFTplainreduce/src/mrcFFTplainreduce.html b/src/Tools/mrcImage/mrcFFTplainreduce/src/mrcFFTplainreduce.html
index 0721da8..a9b9a09 100755 (executable)
--- a/src/Tools/mrcImage/mrcFFTplainreduce/src/mrcFFTplainreduce.html
+++ b/src/Tools/mrcImage/mrcFFTplainreduce/src/mrcFFTplainreduce.html
@@ -1 +1,23 @@
-/bin/bash: mrcFFTplainreduce: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFFTplainreduce</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFFTplainreduce</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFFTplainreduce
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-p[osition]         Pos                 (0         )] :Optional  :Position of reduced plain
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-v[alue]            Value               (0         )] :Optional  :Value to multiply
+----- Additional Usage -----
+mode 0:pos=z.
+mode 1:pos=x.
+mode 2:pos=y.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/mrcFTMeridianEquatorRedece.html b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/mrcFTMeridianEquatorRedece.html
index 08e602f..fd05de8 100755 (executable)
--- a/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/mrcFTMeridianEquatorRedece.html
+++ b/src/Tools/mrcImage/mrcFTMeridianEquatorRedece/src/mrcFTMeridianEquatorRedece.html
@@ -1 +1,20 @@
-/bin/bash: mrcFTMeridianEquatorRedece: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcFTMeridianEquatorRedece</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcFTMeridianEquatorRedece</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcFTMeridianEquatorRedece
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-X                  MaxX                (-1        )] :Optional  :Max X to put zero (pixel).  Default is no operation.
+    [-Y                  MaxY                (-1        )] :Optional  :Max Y to put zero (pixel).  Default is no operation.
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/mrcImage1DProjectionfrom2D.html b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/mrcImage1DProjectionfrom2D.html
index 3067ef6..42d4331 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/mrcImage1DProjectionfrom2D.html
+++ b/src/Tools/mrcImage/mrcImage1DProjectionfrom2D/src/mrcImage1DProjectionfrom2D.html
@@ -1 +1,18 @@
-/bin/bash: mrcImage1DProjectionfrom2D: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage1DProjectionfrom2D</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage1DProjectionfrom2D</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage1DProjectionfrom2D
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-d[egree]           phi                 (0         )] :Optional  :Degree of the line to project
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/mrcImage1dAverageByCorrelation.html b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/mrcImage1dAverageByCorrelation.html
index 3616fb9..8ecf312 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/mrcImage1dAverageByCorrelation.html
+++ b/src/Tools/mrcImage/mrcImage1dAverageByCorrelation/src/mrcImage1dAverageByCorrelation.html
@@ -1 +1,18 @@
-/bin/bash: mrcImage1dAverageByCorrelation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage1dAverageByCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage1dAverageByCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage1dAverageByCorrelation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-r[ange]            range               (0         )] :Optional  :Search range of shift.Default:Nx
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage1dCutAverage/src/mrcImage1dCutAverage.html b/src/Tools/mrcImage/mrcImage1dCutAverage/src/mrcImage1dCutAverage.html
index 44cd939..94cae65 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dCutAverage/src/mrcImage1dCutAverage.html
+++ b/src/Tools/mrcImage/mrcImage1dCutAverage/src/mrcImage1dCutAverage.html
@@ -1 +1 @@
-/bin/bash: mrcImage1dCutAverage: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage1dCutAverage: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/mrcImage1dShiftAverageByAnnealing.html b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/mrcImage1dShiftAverageByAnnealing.html
index 0c25cc0..2e19fca 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/mrcImage1dShiftAverageByAnnealing.html
+++ b/src/Tools/mrcImage/mrcImage1dShiftAverageByAnnealing/src/mrcImage1dShiftAverageByAnnealing.html
@@ -1 +1,37 @@
-/bin/bash: mrcImage1dShiftAverageByAnnealing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage1dShiftAverageByAnnealing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage1dShiftAverageByAnnealing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage1dShiftAverageByAnnealing
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-s[ignal position]  Signal              (NULL      )] :Essential :File to define position of signal
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-r[ange]            range               (0         )] :Optional  :Search range of shift.Default:Nx
+    [-d[elta]            delta               (1.0       )] :Optional  :Spacing of molecule(Pixel).
+    [-T[eperature]       temperature         (1.0       )] :Optional  :Initial temperature.
+    [-iter[ation]        iter                (1000      )] :Optional  :Number of iteration before reducing temperature.
+    [-eps[ilon]          eps                 (0.001     )] :Optional  :Temperature(T) reduced to (1-epsilon)T.
+    [-tol                tol                 (1e-2      )] :Optional  :Number to identify convergence
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+----- mode -----
+0:All search 
+1:annealing method 
+2:mode 1 and refine by powel.
+3:mode 1 and refine by annealing.
+----- mode2 -----
+0:by amplitude 
+1:by power 
+2:by amplitude using only phase 
+3:by power using only phase 
+4:by amplitude using S/sqrt(S) 
+5:by power using only  S/sqrt(S) 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/mrcImage1dShiftByCorrelation.html b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/mrcImage1dShiftByCorrelation.html
index 2d884e4..61b99ab 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/mrcImage1dShiftByCorrelation.html
+++ b/src/Tools/mrcImage/mrcImage1dShiftByCorrelation/src/mrcImage1dShiftByCorrelation.html
@@ -1 +1,25 @@
-/bin/bash: mrcImage1dShiftByCorrelation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage1dShiftByCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage1dShiftByCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage1dShiftByCorrelation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
+    [-range              range               (0         )] :Optional  :Search range of shift.Default:Nx
+    [-s[ignal position]  Signal              (NULL      )] :Essential :File to define position of signal
+    [-d[elta]            delta               (1.0       )] :Optional  :Spacing of molecule(Pixel).
+    [-norm[alize]        ] :Optional  :Normalize before correlation
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+-----  mode -----
+0:Phase residual
+1:Normal correlation
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage2DBackProjection/src/mrcImage2DBackProjection.html b/src/Tools/mrcImage/mrcImage2DBackProjection/src/mrcImage2DBackProjection.html
index e44ca0a..bc6e75e 100644 (file)
--- a/src/Tools/mrcImage/mrcImage2DBackProjection/src/mrcImage2DBackProjection.html
+++ b/src/Tools/mrcImage/mrcImage2DBackProjection/src/mrcImage2DBackProjection.html
@@ -1 +1,19 @@
-/bin/bash: mrcImage2DBackProjection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage2DBackProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage2DBackProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage2DBackProjection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-z                  NumZ                (10        )] :Optional  :Z: pixel  
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage2DProjection/src/mrcImage2DProjection.html b/src/Tools/mrcImage/mrcImage2DProjection/src/mrcImage2DProjection.html
index 0574e44..cfe9420 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage2DProjection/src/mrcImage2DProjection.html
+++ b/src/Tools/mrcImage/mrcImage2DProjection/src/mrcImage2DProjection.html
@@ -1 +1,20 @@
-/bin/bash: mrcImage2DProjection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage2DProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage2DProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage2DProjection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-w[omega]           Omega               (0         )] :Optional  :Omega
+    [-p[hi]              Phi                 (0         )] :Optional  :Phi
+    [-a[lpha]            Alpha               (0         )] :Optional  :Alpha
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage2pdb/src/mrcImage2pdb.html b/src/Tools/mrcImage/mrcImage2pdb/src/mrcImage2pdb.html
index 893f1fd..173019c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage2pdb/src/mrcImage2pdb.html
+++ b/src/Tools/mrcImage/mrcImage2pdb/src/mrcImage2pdb.html
@@ -1 +1,30 @@
-/bin/bash: mrcImage2pdb: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage2pdb</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage2pdb</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage2pdb
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (5         )] :Optional  :Mode
+    [-hi[gh]             h                   (0         )] :Optional  :Value of high threshold. Default is the MAX.
+    [-lo[w]              l                   (0         )] :Optional  :Value of low threshold. Default is the MIN.
+    [-L[attice]          ] :Optional  :Atoms are on lattice points
+    [-Skip               Skip                (1         )] :Optional  :Skip atoms.
+    [-R[andom]           Random              (0         )] :Optional  :Random
+    [-d[elta]            delta               (0.1       )] :Optional  :Delta to select atoms to avoid too much concentration. Requiers 0-0.5 value. For mode2-4.
+----- Additional Usage -----
+mode0: One atom for one boxel.
+mode1: Eight atoms for one boxel.
+mode2: On the surface of high threshold. Atoms few.
+mode3: On the surface of high threshold. Atoms medium.
+mode4: On the surface of high threshold. Atoms many
+mode5 (Default) : On the surface of high threshold. Mesh mode.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/mrcImage3DHighResoEmphasis.html b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/mrcImage3DHighResoEmphasis.html
index 172027f..697ca6c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/mrcImage3DHighResoEmphasis.html
+++ b/src/Tools/mrcImage/mrcImage3DHighResoEmphasis/src/mrcImage3DHighResoEmphasis.html
@@ -1 +1,25 @@
-/bin/bash: mrcImage3DHighResoEmphasis: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage3DHighResoEmphasis</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage3DHighResoEmphasis</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage3DHighResoEmphasis
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-L[owThreshold]     L                   (0         )] :Optional  :Low threshold to modify
+    [-H[ighThreshold]    H                   (0         )] :Optional  :High threshold to modify
+    [-A[value]           A                   (0         )] :Optional  :A value
+    [-B[value]           B                   (0         )] :Optional  :B value
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- algorithm -----
+R<L data*exp(A*L+B*L*L)
+L<R<H data*exp(A*R+B*R*R) 
+R>H data*exp(A*H+B*H*H) 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage3DPad/src/mrcImage3DPad.html b/src/Tools/mrcImage/mrcImage3DPad/src/mrcImage3DPad.html
index 5ab4537..e89d3a2 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DPad/src/mrcImage3DPad.html
+++ b/src/Tools/mrcImage/mrcImage3DPad/src/mrcImage3DPad.html
@@ -1 +1,31 @@
-/bin/bash: mrcImage3DPad: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage3DPad</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage3DPad</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage3DPad
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-r[max]             r                   (0         )] :Optional  :Threshold radius of signal.Default is Nx.
+    [-w[idth]            w                   (1         )] :Optional  :Width of slope. For mode 1.
+    [-v[alue]            v                   (0         )] :Optional  :Value of out of threshold.
+    [-Nx                 Nx                  (0         )] :Optional  :Number of x.Default is inputfile.
+    [-Ny                 Ny                  (0         )] :Optional  :Number of y.Default is inputfile.
+    [-Nz                 Nz                  (0         )] :Optional  :Number of z.Default is inputfile.
+    [-Floating           ] :Optional  :Floating
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode2]            mode2               (0         )] :Optional  :Mode
+----- mode -----
+0:Default: Out of threshold is avrage of threshold plain.
+1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
+----- mode2 -----
+0:For filaments.  R is calculated from its axis.
+1:For particles.  R is calculated from its center.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage3DPad2/src/mrcImage3DPad2.html b/src/Tools/mrcImage/mrcImage3DPad2/src/mrcImage3DPad2.html
index 1970110..a3553eb 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DPad2/src/mrcImage3DPad2.html
+++ b/src/Tools/mrcImage/mrcImage3DPad2/src/mrcImage3DPad2.html
@@ -1 +1,31 @@
-/bin/bash: mrcImage3DPad2: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage3DPad2</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage3DPad2</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage3DPad2
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-r[max]             r                   (0         )] :Optional  :Threshold radius of signal.Default is Nx.
+    [-w[idth]            w                   (1         )] :Optional  :Width of slope. For mode 1.
+    [-v[alue]            v                   (0         )] :Optional  :Value of out of threshold.
+    [-Nx                 Nx                  (0         )] :Optional  :Number of x.Default is inputfile.
+    [-Ny                 Ny                  (0         )] :Optional  :Number of y.Default is inputfile.
+    [-Nz                 Nz                  (0         )] :Optional  :Number of z.Default is inputfile.
+    [-Floating           ] :Optional  :Floating
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode2]            mode2               (0         )] :Optional  :Mode
+----- mode -----
+0:Default: Out of threshold is avrage of threshold plain.
+1:Mulplying cos function. Default: Out of threshold is avrage of threshold plain.
+----- mode2 -----
+0:For filaments.  R is calculated from its axis.
+1:For particles.  R is calculated from its center.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/mrcImage3DSymmetryFind.html b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/mrcImage3DSymmetryFind.html
index c663730..70d61f2 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/mrcImage3DSymmetryFind.html
+++ b/src/Tools/mrcImage/mrcImage3DSymmetryFind/src/mrcImage3DSymmetryFind.html
@@ -1 +1 @@
-/bin/bash: mrcImage3DSymmetryFind: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImage3DSymmetryFind: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImage3DWindowing/src/mrcImage3DWindowing.html b/src/Tools/mrcImage/mrcImage3DWindowing/src/mrcImage3DWindowing.html
index 102020c..440441f 100755 (executable)
--- a/src/Tools/mrcImage/mrcImage3DWindowing/src/mrcImage3DWindowing.html
+++ b/src/Tools/mrcImage/mrcImage3DWindowing/src/mrcImage3DWindowing.html
@@ -1 +1,27 @@
-/bin/bash: mrcImage3DWindowing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImage3DWindowing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImage3DWindowing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImage3DWindowing
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrcImage
+    [-center             cx                  (0         )cy                  (0         )cz                  (0         )] :Optional  :Center:
+    [-w[idth]            wx                  (0         )wy                  (0         )wz                  (0         )] :Optional  :Width
+    [-r[dius]            r                   (0         )] :Optional  :Radius
+    [-w[idth]r[dius]     w                   (0         )] :Optional  :Width for R
+    [-w[idth]z           widthz              (0         )] :Optional  :Width for z
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+0: GaussianRectangularSolid
+1: CosCylindar(+Offset)
+2: CosSphere
+3: CosSphere(+Offset)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.html b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.html
index 22e6f97..aa4a52e 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.html
+++ b/src/Tools/mrcImage/mrcImageAbnormalValueRemove/src/mrcImageAbnormalValueRemove.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageAbnormalValueRemove: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAbnormalValueRemove</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAbnormalValueRemove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAbnormalValueRemove
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
+    [-v[alueForCut]      cutValue            (3.0       )] :Optional  :CutValue/Sigma
+    [-u[nsigned]         UnsignedMax         (65535     )UnsignedHalf        (16384     )] :Optional  :Unsigned to Signed: Need Max
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Mode: 
+    0: Random Value 
+    1: Near Value 
+    2: Random Value using SD and mean within Normal Area
+    3: Mean Value using SD and mean within Normal Area
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/mrcImageAdaptiveBinalization.html b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/mrcImageAdaptiveBinalization.html
index 1803d13..ff2a470 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/mrcImageAdaptiveBinalization.html
+++ b/src/Tools/mrcImage/mrcImageAdaptiveBinalization/src/mrcImageAdaptiveBinalization.html
@@ -1 +1,18 @@
-/bin/bash: mrcImageAdaptiveBinalization: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAdaptiveBinalization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAdaptiveBinalization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAdaptiveBinalization
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-s[ize]             Size                (10        )] :Optional  :Size of area to average
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAdd/src/mrcImageAdd.html b/src/Tools/mrcImage/mrcImageAdd/src/mrcImageAdd.html
index 3d235b4..2a2c751 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAdd/src/mrcImageAdd.html
+++ b/src/Tools/mrcImage/mrcImageAdd/src/mrcImageAdd.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageAdd: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAdd</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAdd</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAdd
+Options:
+    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile1
+    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile2
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-I[nput array of file]In                  (stdin     )] :Optional  :InputDataFiles
+----- Additional Usage -----
+mode 0:Add 
+mode 1:Add / (Number of Pictures)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAddValue/src/mrcImageAddValue.html b/src/Tools/mrcImage/mrcImageAddValue/src/mrcImageAddValue.html
index 99bfc4e..5a2375b 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAddValue/src/mrcImageAddValue.html
+++ b/src/Tools/mrcImage/mrcImageAddValue/src/mrcImageAddValue.html
@@ -1,20 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageAddValue</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageAddValue</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageAddValue
-Options:
-    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :Input: mrc
-    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :Output: mrc
-    [-v[alue]            Value               (0.0       ).as(Real                ) ] :Optional  :Value: o=i+v
-    [-cuda               cudaDeviceID        (0         ).as(Integer             ) ] :Optional  :UseCuda
-    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageAddValue: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html b/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html
index a02698d..33d5adf 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html
+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageAreaCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAreaCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAreaCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAreaCalc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrcImage:area
+    [-O[utput]           OutInfo             (stdout    )] :Optional  :Output: ASCII: area info
+    [-l[abel]            Label               (NULL      )] :Optional  :Output: mrcImage:labeling
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAsProbability/src/mrcImageAsProbability.html b/src/Tools/mrcImage/mrcImageAsProbability/src/mrcImageAsProbability.html
index d506be8..3958a27 100644 (file)
--- a/src/Tools/mrcImage/mrcImageAsProbability/src/mrcImageAsProbability.html
+++ b/src/Tools/mrcImage/mrcImageAsProbability/src/mrcImageAsProbability.html
@@ -1 +1,18 @@
-/bin/bash: mrcImageAsProbability: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAsProbability</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAsProbability</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAsProbability
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/mrcImageAssignedToTFofPDB.html b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/mrcImageAssignedToTFofPDB.html
index c5792d9..8b30423 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/mrcImageAssignedToTFofPDB.html
+++ b/src/Tools/mrcImage/mrcImageAssignedToTFofPDB/src/mrcImageAssignedToTFofPDB.html
@@ -1 +1,24 @@
-/bin/bash: mrcImageAssignedToTFofPDB: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAssignedToTFofPDB</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAssignedToTFofPDB</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAssignedToTFofPDB
+Options:
+    [-i[nput]            In                  ] :Essential :InputDataFile(mrcImage)
+    [-p[dbFile]          InPDB               ] :Essential :InputDataFile(pdbFile)
+    [-o[utput]           Out                 ] :Essential :OutputDataFile(pdbFile)
+    [-H[igh]             HighLevel           ] :Optional  :HighLevel
+    [-L[ow]              LowLevel            ] :Optional  :LowLevel
+    [-c[onfig]           configFile          ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                ] :Optional  :Mode
+>>> Mode:      
+       0: Default.
+       1 : Origin is Center  (1) or BottomLeft (0).
+       2 : Posi-Nega Reverse (2) or Direct     (0).
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
index 38aa625..d17af3a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
+++ b/src/Tools/mrcImage/mrcImageAutoCorrelationWithWindowing/src/mrcImageAutoCorrelationWithWindowing.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageAutoCorrelationWithWindowing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoCorrelationWithWindowing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoCorrelationWithWindowing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoCorrelationWithWindowing
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-O[utput]           OutWin              (NULL      )] :Optional  :Output WindowedFile
+    [-W[indowing]y       Wy                  (6         )] :Optional  :Window Height: N.y * 1/Wy
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.html b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.html
index 4554948..e4525d3 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.html
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtract/src/mrcImageAutoFilamentExtract.html
@@ -1 +1,49 @@
-/bin/bash: mrcImageAutoFilamentExtract: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoFilamentExtract</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoFilamentExtract</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoFilamentExtract
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-i[nput]S[ource]fileInS                 (NULL      )] :Essential :InputSourceFile
+    [-o[utput]E[xtract]  OutE                (NULL      )] :Essential :OutputFileForExtraction
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output Log File
+    [-o[utput]F[inal]    OutF                (stdout    )] :Optional  :OutputFinalFile
+    [-r[oi]ROI           blx                 (0.0       )bly                 (0.0       )brx                 (0.0       )bry                 (0.0       )trx                 (0.0       )try                 (0.0       )tlx                 (0.0       )tly                 (0.0       )] :Optional  :Rectangle ROI 
+    [-r[oi]Unbent        roiLine             (0.0       )... ] :Variable  :
+    [-x                  x                   (120       )] :Optional  :x range for ROI or Unbent
+    [-d[elta]dYmax       ddYmax              (0.9       )] :Optional  :delta dY max
+    [-d[elta]dYmin       ddYmin              (0.2       )] :Optional  :delta dY mim
+    [-T[ransepose]       T                   (0         )] :Optional  :corresponding to mrcImageTransepose mode
+    [-maxd[elta]Y        maxdY               (12        )] :Optional  :Maximum number of layer line
+    [-H[eight] R[ange]   HeightRange         (0         )] :Optional  :Height Range [Pixel]
+    [-RMaxX              RMaxX               (0.05      )] :Optional  :RMaxX [1/A] (supported mode 1)
+    [-mag                mag                 (1.1       )] :Optional  :magnification ratio
+    [-truePitch          truePitch           (430       )] :Optional  :True Pitch [A]
+    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
+    [-finaly             finaly              (0         )] :Optional  :final y [pixel] for extraction
+    [-Ignore             Ignore              (0         )] :Optional  :Ignore the final y 
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- mode -----
+0 : Meridian Reflection 
+1 : All layer-lines
+----- NOTE for Heigth Range-----
+HR option is stranger than caliculated HR
+----- NOTE for ROI-----
+-rROI, -rUnbent, -iS, -ddYmax, -ddYmin and -T options are for ROI
+----- NOTE for File for Extraction-----
+-oE file use as extraction file.
+----- NOTE for FINAL-----
+-finaly and -oF is for final extraction
+-truePitch, -Ly and -dY are for magnification change
+-Ignore option ignore finaly
+This extract do with magnification and header change
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/mrcImageAutoFilamentExtractResultAnalysis.html b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/mrcImageAutoFilamentExtractResultAnalysis.html
index a5dc250..89fb6fd 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/mrcImageAutoFilamentExtractResultAnalysis.html
+++ b/src/Tools/mrcImage/mrcImageAutoFilamentExtractResultAnalysis/src/mrcImageAutoFilamentExtractResultAnalysis.html
@@ -1 +1,23 @@
-/bin/bash: mrcImageAutoFilamentExtractResultAnalysis: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoFilamentExtractResultAnalysis</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoFilamentExtractResultAnalysis</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoFilamentExtractResultAnalysis
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-truePitch          truePitch           (430       )] :Optional  :True Pitch
+    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
+    [-deltadY            deltadY             (0.5       )] :Optional  :A range of deltadY to determine dY.
+    [-y                  y                   (0         )] :Optional  :y [pixel] for final extraction
+    [-Mag                mag                 (1.1       )] :Optional  :magnification ratio
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/mrcImageAutoRotationCorrelation.html b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/mrcImageAutoRotationCorrelation.html
index e748a02..592e7cc 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/mrcImageAutoRotationCorrelation.html
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation/src/mrcImageAutoRotationCorrelation.html
@@ -1 +1,111 @@
-/bin/bash: mrcImageAutoRotationCorrelation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoRotationCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoRotationCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoRotationCorrelation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: testImage [mrcImage]
+    [-r[eference]        Ref                 (NULL      )] :Essential :Input: refImage [mrcImage]
+    [-nRot1              nRot1               (1         )] :Optional  :Rotation number of Ref for Rot1: Def 1
+    [-nRot2              nRot2               (1         )] :Optional  :Rotation number of Ref for Rot2: Def 1
+    [-nRot3              nRot3               (1         )] :Optional  :Rotation number of Ref for Rot3: Def 1
+    [-dRot1              dRot1               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot1; Def.: 360/nRot1
+    [-dRot2              dRot2               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot2; Def.: 360/nRot2
+    [-dRot3              dRot3               (1.0       )] :Optional  :Delta Angle [Degree] of Ref for Rot3; Def.: 360/nRot3
+    [-startRot1          startRot1           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot1; Def.: 0
+    [-startRot2          startRot2           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot2; Def.: 0
+    [-startRot3          startRot3           (0.0       )] :Optional  :Start Angle [Degree] of Ref for Rot3; Def.: 0
+    [-StackOrder         StackOrder          (0         )] :Optional  :Stack Order for Stacked 2D of references, refer to attention
+    [-o[utput]           Out                 (NULL      )] :Optional  :Output: Parameter [mrcImage-format]
+    [-O[utput]           OutASC              (stdout    )] :Optional  :Output: Parameter [ASCII] 
+    [-cor[relation]      corFile             (NULL      )] :Optional  :Correation Map at Maximum (Linear) [mrcImage-format]
+    [-cor[relation]2     corFile2            (NULL      )] :Optional  :Correation Map2 at Maximum (Set Mode Correlation)[mrcImage-format]
+    [-cor[relation]All   corAllFile          (NULL      )] :Optional  :Correation Map with All Rotation [mrcImage-format]
+    [-fit[tedToRef]      fitFile             (NULL      )] :Optional  :Output: rotatedImage at Maximum(Linear Correlation) [mrcImage]
+    [-fit[tedToRef]2     fitFile2            (NULL      )] :Optional  :Output: rotatedImage at Maximum(Set Correlation mode) [mrcImage]
+    [-RefineMode         RefineMode          (0         )] :Optional  :RefinementStep: Linear:0 or SetMode:1
+    [-n[umber]           Rot                 (36        )] :Optional  :Input: Rotation around the vertical axis against image plane: dRot = 360/n [degree]
+    [-range              minAngle            (-5.0      )maxAngle            (5.0       )] :Optional  :Input: SearchRange: Rotation around the vertical axis against image plane 
+    [-refStep1           refStep1            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot1
+    [-refStep2           refStep2            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot2
+    [-refStep3           refStep3            (1         )] :Optional  :SearchStep for Ref: Each Image along Rot3
+    [-nRot1Area          nRot1AreaMin        (-360      )nRot1AreaMax        (360       )nRot1AreaStep       (25        )] :Optional  :number of Ref for Rot1
+    [-nRot2Area          nRot2AreaMin        (-360      )nRot2AreaMax        (360       )nRot2AreaStep       (25        )] :Optional  :number of Ref for Rot2
+    [-nRot3Area          nRot3AreaMin        (-360      )nRot3AreaMax        (360       )nRot3AreaStep       (25        )] :Optional  :number of Ref for Rot3
+    [-Iter[ation]        Iter                (1         )] :Optional  :Iteration for Rotation around the vertical axis against image plane
+    [-Method             Method              (0         )] :Optional  :0: Correlation, 1: SSDA
+    [-s[earchRegion]     sminx               (0         )sminy               (0         )smaxx               (0/*N.x-1*/)smaxy               (0/*N.y-1*/)] :Optional  :SearchRegion [pixel]: used in lmrcImageAutoRotationCorrelation 
+    [-Shift              ] :Optional  :Image Shift, when in > ref
+    [-RepeatX            RepeatX             (27.3      )] :Optional  :RepeatX[A]
+    [-RepeatXDelta       RepeatXDelta        (5         )] :Optional  :RepeatXDelta[A]
+    [-RepeatY            RepeatY             (27.3      )] :Optional  :RepeatY[A]
+    [-RepeatYDelta       RepeatYDelta        (5         )] :Optional  :RepeatYDelta[A]
+    [-Xshift             ] :Optional  :X-Shift Only
+    [-NoShift            ] :Optional  :No-Shift
+    [-Log                Log                 (stdout    )] :Optional  :Output: LogFile
+    [-pvm                pvm                 (1         )] :Optional  :Task Number
+    [-pvmList            pvmList             (NULL      )] :Optional  :ConfigurationFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Mode -----
+When, -Method 0(Default:Correlation)
+0: Normal Correlation FxG*
+1: Phase  Correlation FxG*/     |FxG*|
+2: Phase  Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0 
+Refinement Correlation Map
+0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
+1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|  
+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
+      ----- Attention -----
+      You must not set bit 16: bit 16 is set in this program as default.
+When, -Method 1 (SSDA:Sequential Similarity Detection Algorithm)
+When, -Method 2 (Rotational Cross-Correlation Function)
+-m NotSupported
+
+>>>>>>>> Attention 1 -----
+You should set -n or -range. These parameters are used for reference image rotation
+
+>>>>>>>> Attention 2 -----
+You must set -nRot1/2/3.
+-nRot[1|2|3]     Number of Reference Images: 
+You should set -dRot1/2/3.
+-dRot[1|2|3]     Delta Angle [degree] of Reference Images: 
+You should set -startRot1/2/3.
+-startRot[1|2|3] Start Angle [degree] of Reference Images: 
+
+  e.g.) If mrc3Dto2D -Rot1 89 91 1 -Rot2 0 359 2 -Rot3 3 12 3, 
+           -nRot1 3   -dRot1 1 -startRot1 89 
+           -nRot2 180 -dRot2 2 -startRot2  0 
+           -nRot3 4   -dRot1 3 -startRot1  3 
+
+>>>>>>>> Attention 3 : the relation between dRot1 and nRotArea ----
+-nRot[1|2|3]Area Min[degree] Max[degree] Step[degree]
+If not -dRot[1|2|3], we cannot estimate nStep, which is the number of skip step using referencefiles .
+
+>>>>>>>> Attention 4 : Stack order of ref-image -----
+-StackOrder
+    0: for pdb2mrc2d : default
+    1: for mrc3Dto2D 
+If not -dRot[1|2|3], we cannot estimate nStep, which is the number of skip step using referencefiles .
+
+>>>>>>>> Attention 5 : Refinement Mode -----
+-RefineMode 
+    0: for LinearCorrelation;  default
+    1: for SetModeCorrelation 
+
+>>>>>>>> Attention 6 : Search Area -----
+-refStep[1|2|3] 
+     Skip image number: Just skip ref-images 
+ or 
+-nRot[1|2|3]Area 
+     Set the search area. You finally can refine parameters by each ref-image following -RefineMode. 
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html
index 103c076..9d06763 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html
@@ -1 +1,45 @@
-/bin/bash: mrcImageAutoRotationCorrelation3D: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAutoRotationCorrelation3D</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAutoRotationCorrelation3D</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAutoRotationCorrelation3D
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc[test]
+    [-r[ef]              Ref                 (NULL      )] :Essential :Input: mrc[ref]
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: Parameter
+    [-cor                Cor                 (NULL      )] :Optional  :Output: CorMap
+    [-fit                Fit                 (stdout    )] :Optional  :Output: Best Fit
+    [-E[uler]A[ngle]     EulerAngle          (YOYS      )] :Optional  :Input: EulerAngle
+    [-Rot1               Rot1Min             (0.0       )Rot1Max             (360.0     )Rot1Delta           (5.0       )] :Optional  :Rot1
+    [-Rot2               Rot2Min             (0.0       )Rot2Max             (180.0     )Rot2Delta           (5.0       )] :Optional  :Rot2
+    [-Rot3               Rot3Min             (0.0       )Rot3Max             (360.0     )Rot3Delta           (5.0       )] :Optional  :Rot3
+    [-Xrange             XrangeMin           (0         )XrangeMax           (0         )] :Optional  :Xrange[pixel]: Not set, all space search
+    [-Yrange             YrangeMin           (0         )YrangeMax           (0         )] :Optional  :Yrange[pixel]: Not set, all space search
+    [-Zrange             ZrangeMin           (0         )ZrangeMax           (0         )] :Optional  :Zrange[pixel]: Not set, all space search
+    [-M[ode]             Mode                (0         )] :Optional  :Mode: Correlation Mode
+    [-M[ode]R[otation]   ModeRotation        (0         )] :Optional  :Mode: Rotation3D Mode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode: InterpolationMode
+----- Additional Usage -----
+----- -M  CorrelationMode -----
+0: Normal Correlation FxG*
+1: Phase  Correlation FxG*/     |FxG*|
+2: Phase  Correlation FxG*/sqrt(|FxG*|)
+3: Normalized Normal Correlation FxG*/|F||G|)
+16: (0,0) = 0 
+Refinement Correlation Map
+0: sqrt(Sum |Fi-Gi|^2                 / Sum |Gi|^2)
+1:      Sum |Gi||phaseFi - phaseGi|   / Sum |Gi|  
+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi|  )
+----- -MR RotationMode -----
+ 0: padding 0 
+ 1: padding average 
+ +0:  within ellipsoidal area.
+ +16: within square area.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/mrcImageAutoRotationCorrelationResultPrint.html b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/mrcImageAutoRotationCorrelationResultPrint.html
index 1eee1c7..e40c07b 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/mrcImageAutoRotationCorrelationResultPrint.html
+++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelationResultPrint/src/mrcImageAutoRotationCorrelationResultPrint.html
@@ -1 +1 @@
-/bin/bash: mrcImageAutoRotationCorrelationResultPrint: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageAutoRotationCorrelationResultPrint: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageAverage/src/mrcImageAverage.html b/src/Tools/mrcImage/mrcImageAverage/src/mrcImageAverage.html
index 8981bc7..a6b858f 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageAverage/src/mrcImageAverage.html
+++ b/src/Tools/mrcImage/mrcImageAverage/src/mrcImageAverage.html
@@ -1 +1,19 @@
-/bin/bash: mrcImageAverage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageAverage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageAverage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageAverage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: Image File List
+    [-w[eight]           InWeight            (NULL      )] :Optional  :Input: Weight File List
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: Average
+    [-o[utput]W[eight]   OutWeight           (NULL      )] :Optional  :Output: Weight
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageBandPassFilter/src/mrcImageBandPassFilter.html b/src/Tools/mrcImage/mrcImageBandPassFilter/src/mrcImageBandPassFilter.html
index 658345f..c037f8f 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBandPassFilter/src/mrcImageBandPassFilter.html
+++ b/src/Tools/mrcImage/mrcImageBandPassFilter/src/mrcImageBandPassFilter.html
@@ -1 +1,28 @@
-/bin/bash: mrcImageBandPassFilter: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageBandPassFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBandPassFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBandPassFilter
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-h[alf]v[aluepoint]l[ow]hvl                 (1.0       )] :Optional  :HalfValuePointLow
+    [-h[alf]v[aluepoint]h[igh]hvh                 (1.0       )] :Optional  :HalfValuePointHigh
+    [-w[idth]l[ow]       wl                  (1.0       )] :Optional  :WidthOfDumpingLow
+    [-w[idth]h[igh]      wh                  (1.0       )] :Optional  :WidthOfDumpingHigh
+    [-lowweight          lowWeight           (0.0       )] :Optional  :Weight of Low Freq.
+>>> Mode <<<< 
+    1: Step filter : required argumnent: -hvl -hvh
+    2: Cos filter  : required argumnent: -hvl -hvh -wl -wh
+    3: Exp filter  : required argumnent: -hvl -hvh -wl -wh
+>>> -lowweight <<<< 
+Weight of Low Freq.  
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageBilateralFilter/src/mrcImageBilateralFilter.html b/src/Tools/mrcImage/mrcImageBilateralFilter/src/mrcImageBilateralFilter.html
index 5a89b13..a68e566 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBilateralFilter/src/mrcImageBilateralFilter.html
+++ b/src/Tools/mrcImage/mrcImageBilateralFilter/src/mrcImageBilateralFilter.html
@@ -1 +1,36 @@
-/bin/bash: mrcImageBilateralFilter: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageBilateralFilter</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBilateralFilter</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBilateralFilter
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-s[igma]D[ensity]   SigmaDensity        (2.0       )] :Optional  :SigmaDensity
+    [-k[ernal]T[type]D[ensity]KernelTypeDensity   (0         )] :Optional  :KernelTypeForDensity
+    [-s[igma]S[pace]     SigmaSpace          (1.0       )] :Optional  :SigmaSpace
+    [-s[igma]S[pace]3    SigmaSpaceX         (1.0       )SigmaSpaceY         (1.0       )SigmaSpaceZ         (1.0       )] :Optional  :SigmaSpace(3D)
+    [-k[ernel]T[ype]S[pace]KernelTypeSpace     (0         )] :Optional  :KernelTypeForSpace
+    [-k[ernel]S[ize]     KernelSize          (5         )] :Optional  :KernelSize
+    [-k[ernel]S[ize]3    KernelSizeX         (5         )KernelSizeY         (5         )KernelSizeZ         (5         )] :Optional  :KernelSize(3D)
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Bilateral Filter
+    by Tomashi and Manduchi
+    C. Tomasi and R. Manduchi, Bilateral Filtering for Gray and Color Images, Proceedings of the 1998 IEEE International Conference on Computer Vision, Bombay, India
+ fi = Sigma_j(W(i,j)*Ij)/ Sigma_j(Wj)   
+   ,where W(i,j)=W_x(xi,xj)*W_I(Ii,Ij)    
+------- linfo.mode : 0 
+                 W_x(xi,xj) = exp(-|xi-xj|^2/2 sigmaSpace^2  )
+                 W_I(Ii,Ij) = exp(-|Ii-Ij|^2/2 sigmaDensity^2)
+------- linfo.mode : 1 
+                 W_x(xi,xj) = 1/(1+|xi-xj|^2/sigmaSpace^2  )   
+                 W_I(Ii,Ij) = 1/(1+|Ii-Ij|^2/sigmaDensity^2)   
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
index e2f98b6..2aba805 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
@@ -1 +1,34 @@
-/bin/bash: mrcImageBinalization: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageBinalization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBinalization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBinalization
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-t[hreshold]        t                   (0         )] :Optional  :Value of threshold
+    [-v[alue]            v                   (0         )] :Optional  :Value
+    [-near               near                (0         )] :Optional  :Near[pixel]: Near-area also binary
+    [-nLevel             nLevel              (256       )] :Optional  :nLevel: For creating histgram by Kittler and Ohtsu 
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-p[tile]            p                   (0.5       )] :Optional  :p
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Additional Usage -----
+mode 0: Under thresHold, 0.     Above thresHold, 1.
+     1: Above thresHold, 0.     Under thresHold, 1.
+     2: Under thresHold, value. Above thresHold, unchanged.
+     3: Above thresHold, value. Under thresHold, unchanged.
+     16: Automatically Determine threshold by Kittler Method
+     32: Automatically Determine threshold by Ohtsu Method
+     48: Automatically Determine threshold by p-tile Method
+          p range: 0.0 - 1.0
+     64: Automatically Determine threshold by Differential-Histogram Method
+     80: Automatically Determine threshold by Laplacian-Histogram Method
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageBlockMerge/src/mrcImageBlockMerge.html b/src/Tools/mrcImage/mrcImageBlockMerge/src/mrcImageBlockMerge.html
index 49cfec7..bd846ea 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBlockMerge/src/mrcImageBlockMerge.html
+++ b/src/Tools/mrcImage/mrcImageBlockMerge/src/mrcImageBlockMerge.html
@@ -1 +1,18 @@
-/bin/bash: mrcImageBlockMerge: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageBlockMerge</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageBlockMerge</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageBlockMerge
+Options:
+    [-I[nput array of file]In                  (stdin     )] :Essential :InputDataFiles
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile b/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile
deleted file mode 120000 (symlink)
index ef1f6300ba0b84da4931ed574ccec31fc5b88177..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile b/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageBottomHatTransform/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64 b/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64
new file mode 120000 (symlink)
index 0000000..e249902
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageBottomHatTransform/src/X86LINUX64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageBottomHatTransform/src/mrcImageBottomHatTransform.html b/src/Tools/mrcImage/mrcImageBottomHatTransform/src/mrcImageBottomHatTransform.html
index 073a813..4cfbee8 100644 (file)
--- a/src/Tools/mrcImage/mrcImageBottomHatTransform/src/mrcImageBottomHatTransform.html
+++ b/src/Tools/mrcImage/mrcImageBottomHatTransform/src/mrcImageBottomHatTransform.html
@@ -1,23 +1 @@
-<HTML>
-<HEAD>
-<TITLE>mrcImageBottomHatTransform</TITLE>
-</HEAD>
-<BODY>
-<H1>mrcImageBottomHatTransform</H1>
-<H2>Usage</H2>
-<PRE>
-Usage: mrcImageBottomHatTransform
-Options:
-    [-i[nput]            In                  (NULL      ).as(inFile              ) ] :Essential :InputDataFile
-    [-o[utput]           Out                 (NULL      ).as(outFile             ) ] :Essential :OutputDataFile
-    [-times              times               (1         ).as(Integer             ) ] :Optional  :Times: erosion*times -> dilation*times
-    [-o[utput]SE         OutSE               (NULL      ).as(outFile             ) ] :Optional  :Output: MRC(SE)
-    [-S[tructuring]E[lement]SEmode              (0         ).as(Integer             ) ] :Optional  :StructuringElement
-    [-r[adius]           radius              (2         ).as(Integer             ) ] :Optional  :Radius
-    [-n                  n                   (5         ).as(Integer             ) ] :Optional  :size
-    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
------ Additional Usage -----
-</PRE>
-</BODY>
-</HTML>
+/bin/bash: mrcImageBottomHatTransform: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/mrcImageCCDNoiseRemove.html b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/mrcImageCCDNoiseRemove.html
index 7cf68c5..3cf625c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/mrcImageCCDNoiseRemove.html
+++ b/src/Tools/mrcImage/mrcImageCCDNoiseRemove/src/mrcImageCCDNoiseRemove.html
@@ -1 +1,24 @@
-/bin/bash: mrcImageCCDNoiseRemove: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCCDNoiseRemove</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCCDNoiseRemove</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCCDNoiseRemove
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
+    [-N[oise]            InNoise             (NULL      )] :Essential :Input: noise information
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+mode: 0        random values
+mode: 1        neighbor point's values
+>>>>> CCD Noise Remove Format
+VLine  x y height width     ; Vertical Line Noise Remove[pixel]
+Square x y height width     ; Square Noise Remove[pixel] 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensation/src/mrcImageCTFCompensation.html b/src/Tools/mrcImage/mrcImageCTFCompensation/src/mrcImageCTFCompensation.html
index 86248a8..3e169c9 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFCompensation/src/mrcImageCTFCompensation.html
+++ b/src/Tools/mrcImage/mrcImageCTFCompensation/src/mrcImageCTFCompensation.html
@@ -1 +1,44 @@
-/bin/bash: mrcImageCTFCompensation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFCompensation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFCompensation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFCompensation
+Options:
+    [-i[nput]            In                  (stdin     )] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
+    [-info[mation]       Info                (NULL      )] :Optional  :InformationFile(Essense only)
+    [-info[mation]2      Info2               (NULL      )] :Optional  :InformationFile2(Display2 ctfinfo format)
+    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     )] :Optional  :Defocus[A]:under(+)
+    [-white              WhiteNoise          (0.1       )] :Optional  :WhiteNoise(N/S)
+    [-SinWin             SinWinRmin          (0.1       )SinWinRmax          (1.0       )] :Optional  :Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.
+    [-A[mplitude contrast]Amp                 (0.1       )] :Optional  :The ratio of amplitude contrast to phase contrast
+    [-Astig[matism]      dfMin               (0         )dfMax               (0         )asAxis              (0         )] :Optional  :With Astigmatism
+    [-NoAstig[matism]    ] :Optional  :Without Astigmatism
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- mode -----
+mode 0: No Correction
+mode 1: x ctf/|ctf|, phase flipping
+mode 2: x ctf,       phase flipping and ctf-multiplying
+mode 3: x 1/ctf    (0.1<|ctf|       phase flipping and ctf-divided
+mode 4: x ctf/(SQR(ctf)+SQR(NS))    phase-flipping + Winner Filtering 
+mode 5: x SQR(ctf) x ctf/|ctf|      phase-flipping + ctf-Weighted
+mode 6: x 1/|ctf|  (0.1<|ctf|)      No phase-flipping + ctf-divided
+mode 7: x |ctf|/(SQR(ctf)+SQR(NS))  No phase flipping + Winner Filtering 
+mode 8: x  ctf /(SQR(ctf)+SQR(NS*exp(a*R)))  phase flipping + Winner Filtering + NS-raising 
+mode 9: x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R)))  No phase flipping + Winner Filtering + NS-raising 
+----- Note -----
+You can enter information from -info
+Info file was made by llExtractWithLayerSeparationFilamentInfo -oI 
+defocus Cs kV AmplitudeContrast
+----- Note1 -----
+-NoStig is the highest priority and so -Astig and parameters in -info2 are ignored.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/mrcImageCTFCompensationForTiltImage.html b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/mrcImageCTFCompensationForTiltImage.html
index e443751..760f7ad 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/mrcImageCTFCompensationForTiltImage.html
+++ b/src/Tools/mrcImage/mrcImageCTFCompensationForTiltImage/src/mrcImageCTFCompensationForTiltImage.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageCTFCompensationForTiltImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFCompensationForTiltImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFCompensationForTiltImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFCompensationForTiltImage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-I[nformation]      Info                (NULL      )] :Essential :Infomation
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [cut[Back]           cut                 (6         )] :Optional  :Cut
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCTFDetermination/src/mrcImageCTFDetermination.html b/src/Tools/mrcImage/mrcImageCTFDetermination/src/mrcImageCTFDetermination.html
index 1ee6096..3f14adf 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFDetermination/src/mrcImageCTFDetermination.html
+++ b/src/Tools/mrcImage/mrcImageCTFDetermination/src/mrcImageCTFDetermination.html
@@ -1 +1,74 @@
-/bin/bash: mrcImageCTFDetermination: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFDetermination</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFDetermination</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFDetermination
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-r[eference]        Ref                 (NULL      )] :Essential :ReferenceDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output Optimum [text]
+    [-oP[utput]          Out2                (NULL      )] :Optional  :Output Distribution [mrc image]
+    [-oC[utput]          OutC                (NULL      )] :Optional  :Output CTF Information file
+    [-oF[utput]          OutF                (NULL      )] :Optional  :Output Result FFT[mrc image]
+    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
+    [-Ain                Ain                 (0.02      )] :Optional  :IlluminationAperture[mrad]
+    [-W[hiteNoise]       WhiteNoise          (1.0       )] :Optional  :
+    [-df                 mindf               (0.0       )maxdf               (200000    )deldf               (1000      )] :Optional  :df[A] for in
+    [-AoverP             minAoverP           (0.0       )maxAoverP           (1.0       )delAoverP           (0.01      )] :Optional  :AoverP[A] for in
+    [-Rmin               Rmin                (0.0       )] :Optional  :Rmin[/A]
+    [-Rmax               Rmax                (0.1       )] :Optional  :Rmax[/A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]F[ilter type]mF                  (1         )] :Optional  :Filter Type
+    [-m[ode]W[ight type] mW                  (0         )] :Optional  :Wight Type
+    [-m[ode]S[um type]   mS                  (0         )] :Optional  :Sum Type
+    [-m[ode]C[TF Info type]mC                  (0         )] :Optional  :CTF Information Type
+    [-M[ode]             M                   (0         )] :Optional  :ref Type
+    [-PixelSize          PixelSize           (5         )] :Optional  :Pixel Size [A]
+    [-Width              Width               (120       )] :Optional  :Pad Width [pixel]
+    [-truePitch          truePitch           (430       )] :Optional  :True Pitch [A]
+    [-dfRef              firstDf             (70000     )withinDf            (1000      )] :Optional  :dfRef for ref
+    [-AoverPRef          firstAoverP         (0.05      )withinAoverP        (0.01      )] :Optional  :A over P Ref for ref
+    [-MaxIter            maxiter             (10        )] :Optional  :MaxIteration for ref
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- mrcFile -----
+in  <- Original Image 
+ref <- CTF Compensated Image
+----- in <- Fiter Type (-mF) -----
+               0: No CTF compensation
+               1: Phase only: W = CTF/|CTF|
+               2: Multiply  : W = CTF
+               3: Multiply  : W = 1/CTF
+               4: Wiener filter (constant noise): W = CTF/(|CTF|^2+N^2)
+               5: Multiply  : W = CTF^2
+----- in <- Wight Type (-mW) -----
+               0: Weight = 1
+               1: Weight = (|in| + |ref|)/2
+----- in <- Sum Type (-mS) -----
+               0: Sigma[Phase(i)]
+               1: Sigma[Phase(i)*Weight(i)] / Sigma[Weight(i)]
+----- ref <- Type (-M) -----
+               0: CTF compensated single image
+               1: Three-dimentional reconstruction images that were made by 
+                  nea and far Bessel separation.
+                  CTF compensatation were done between min defocus to max defocus.
+                  This mode is for myosin filaments.
+                  (Options) -PixelSize -Width -truePitch
+                            -dfRef -AoverPRef -MaxIter
+               2: Result FFT
+                  (Options) -oF, -dfRef, -AoverPRef
+----- OutPut File-----
+                 -o : defocus and amlitude-contrast at minimum point
+                 -oP: mrc file
+                 -oC: ctf information file for ctf compensation
+                       Type (-mC)
+                               0: lllExtractCtfinfFileCreate (mode 0) 
+                               1: lllExtractCtfinfFileCreate (mode 1) 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html b/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html
index 6c4f21f..c7e6184 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html
+++ b/src/Tools/mrcImage/mrcImageCTFObservation/src/mrcImageCTFObservation.html
@@ -1 +1,31 @@
-/bin/bash: mrcImageCTFObservation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFObservation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFObservation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFObservation
+Options:
+    [-i[nput]            In                  (stdin     )] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
+    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (2.1       )] :Optional  :Cs[mm]
+    [-df                 Defocus             (27000     )] :Optional  :Defocus [A]:under(+)
+    [-A                  AoverP              (0.0       )] :Optional  :AmplitudeContrast/PhaseContrast
+    [-Ain                Ain                 (0.0       )] :Optional  :IlluminationAperture[mrad]
+    [-white              WhiteNoise          (1.0       )] :Optional  :WhiteNoise(N/S)
+    [-SinWin             SinWinRmin          (0.1       )SinWinRmax          (1.0       )] :Optional  :Windowing by sine function from Rmin[A] to Rmax[A]
+    [-ctfMode            ctfMode             (0         )] :Optional  :CTFMode
+    [-Astig[matism]      dfMin               (0         )dfMax               (0         )asAxis              (0         )] :Optional  :With Atigmatism
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- ctfMode -----
+-ctfMode 0  : Phase Only
+-ctfMode 1  : Phase and Amplitude 
+-ctfMode 32  : With Illumination Angle
+-ctfMode 256  : As Absolute Value
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCTFSN/src/mrcImageCTFSN.html b/src/Tools/mrcImage/mrcImageCTFSN/src/mrcImageCTFSN.html
index d9b96b1..a98b231 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCTFSN/src/mrcImageCTFSN.html
+++ b/src/Tools/mrcImage/mrcImageCTFSN/src/mrcImageCTFSN.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageCTFSN: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCTFSN</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCTFSN</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCTFSN
+Options:
+    [-i[nput]            In                  (stdin     )] :Essential :InputFile
+    [-o[utput]           Out                 (stdout    )] :Essential :OutputDataFile
+    [-kV                 kV                  (200       )] :Optional  :AccVol[kV]
+    [-Cs                 Cs                  (1.7       )] :Optional  :Cs[mm]
+    [-df                 Defocus             (2.7       )] :Essential :Defocus[A]:under(+)
+    [-n1                 deg1                (2         )] :Optional  :Degree of zero point minimum
+    [-n2                 deg2                (4         )] :Optional  :Degree of zero point maximum
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCVE/src/mrcImageCVE.html b/src/Tools/mrcImage/mrcImageCVE/src/mrcImageCVE.html
index ed6df09..ed5cd8d 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCVE/src/mrcImageCVE.html
+++ b/src/Tools/mrcImage/mrcImageCVE/src/mrcImageCVE.html
@@ -1 +1,19 @@
-/bin/bash: mrcImageCVE: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCVE</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCVE</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCVE
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-sx                 sx                  (25        )] :Optional  :x of Kernel Size
+    [-sy                 sy                  (25        )] :Optional  :y of Kernel Size
+    [-sz                 sz                  (1         )] :Optional  :z of Kernel Size
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/mrcImageCenterDensityChange.html b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/mrcImageCenterDensityChange.html
index 2628aba..65c3b83 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterDensityChange/src/mrcImageCenterDensityChange.html
+++ b/src/Tools/mrcImage/mrcImageCenterDensityChange/src/mrcImageCenterDensityChange.html
@@ -1 +1,31 @@
-/bin/bash: mrcImageCenterDensityChange: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCenterDensityChange</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCenterDensityChange</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCenterDensityChange
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-r[adius]min        rmin                (0         )] :Optional  :min radius[A]
+    [-r[adius]max        rmax                (90        )] :Optional  :max radius[A]
+    [-ratio              ratio               (0         )] :Optional  :ratio
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode]             radiusMode          (0         )] :Optional  :radiusMode
+----- Additional Usage -----
+----- radiusMode -----
+0: 
+change density from r=0 to r=rmin 
+then connect density gradually from rmin to rmax 
+1: 
+connect density gradually from rmin to rmax 
+change density more than rmax 
+----- mode -----
+0: multiply
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCenterGet/src/mrcImageCenterGet.html b/src/Tools/mrcImage/mrcImageCenterGet/src/mrcImageCenterGet.html
index 4e266f7..6e9e837 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterGet/src/mrcImageCenterGet.html
+++ b/src/Tools/mrcImage/mrcImageCenterGet/src/mrcImageCenterGet.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageCenterGet: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCenterGet</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCenterGet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCenterGet
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-Nx[Number of x]    Nx                  (0         )] :Optional  :Nx:Default Nx of inputfile
+    [-Ny[Number of y]    Ny                  (0         )] :Optional  :Ny:Default Ny of inputfile
+    [-Nz[Number of z]    Nz                  (0         )] :Optional  :Nz:Default Nz of inputfile
+    [-Cx[Center x]       Cx                  (0         )] :Optional  :Cetnter x position of extracted image.Default is center of iuput image.
+    [-Cy[Center y]       Cy                  (0         )] :Optional  :Cetnter y position of extracted image.Default is center of iuput image.
+    [-Cz[Center z]       Cz                  (0         )] :Optional  :Cetnter z position of extracted image.Default is center of iuput image.
+    [-even               ] :Optional  :all dimensions of N are even. 
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/mrcImageCenterOfMassCalculate.html b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/mrcImageCenterOfMassCalculate.html
index 9c54656..5cb7a1c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/mrcImageCenterOfMassCalculate.html
+++ b/src/Tools/mrcImage/mrcImageCenterOfMassCalculate/src/mrcImageCenterOfMassCalculate.html
@@ -1 +1,18 @@
-/bin/bash: mrcImageCenterOfMassCalculate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCenterOfMassCalculate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCenterOfMassCalculate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCenterOfMassCalculate
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (stdout    )] :Optional  :InputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/mrcImageCircumferentialProjection.html b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/mrcImageCircumferentialProjection.html
index 9dbed01..d40f02b 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/mrcImageCircumferentialProjection.html
+++ b/src/Tools/mrcImage/mrcImageCircumferentialProjection/src/mrcImageCircumferentialProjection.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageCircumferentialProjection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCircumferentialProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCircumferentialProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCircumferentialProjection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-dang               dang                (10        )] :Optional  :Delta Angle[degree]
+    [-zmin               zmin                (0         )] :Optional  :Z Minimum[A]
+    [-zmax               zmax                (100       )] :Optional  :Z Maximum[A]
+    [-dz                 dz                  (10        )] :Optional  :Delta Z[A]
+    [-rmin               rmin                (0         )] :Optional  :Radius Minimum[A]
+    [-rmax               rmax                (200       )] :Optional  :Radius Maximum[A]
+    [-threshold          threshold           (0         )] :Optional  :Set threshold value.  Averaged density is more than threshold value
+    [-dr                 dr                  (10        )] :Optional  :Delta Radius[A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+x --> r
+y --> z
+--------- mode ---------
+0: Out Put Averaged Density (dataSum = dataSum / nang)
+1: Out Put Added    Density (dataSum = dataSum / nang *(2*PI*r))
+2: Out Put Averaged Density more than threshold (dataSum = dataSum / [nang number more than threshold value] *(2*PI*r))
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageClosing/src/mrcImageClosing.html b/src/Tools/mrcImage/mrcImageClosing/src/mrcImageClosing.html
index d7dcb14..39073ad 100644 (file)
--- a/src/Tools/mrcImage/mrcImageClosing/src/mrcImageClosing.html
+++ b/src/Tools/mrcImage/mrcImageClosing/src/mrcImageClosing.html
@@ -1 +1,33 @@
-/bin/bash: mrcImageClosing: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageClosing</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageClosing</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageClosing
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
+    [-times              times               (1         )] :Optional  :Times: erosion*times -> dilation*times
+    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         )] :Optional  :Radius
+    [-n                  n                   (5         )] :Optional  :size
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
index 3c004ec..00f921a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
+++ b/src/Tools/mrcImage/mrcImageClusterAnalysis/src/mrcImageClusterAnalysis.html
@@ -1 +1,39 @@
-/bin/bash: mrcImageClusterAnalysis: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageClusterAnalysis</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageClusterAnalysis</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageClusterAnalysis
+Options:
+    [-I[nput array of file]In                  (NULL      )] :Essential :InputDataFiles
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-O[utput]           ] :Optional  :Output: averaged images: filename is xxxx.avg: xxxx is input filename.
+    [-N[umberOfClusters] N                   (1         )] :Optional  :Number of clusters
+    [-Min[imumCorrelation]Min                 (0.0       )] :Optional  :Minimum: Correlation: Conditions for ending
+    [-Iter[ation]        ] :Optional  :IterationFlag
+    [-A[uto]R[otation]   AutoRotation        (72        )] :Optional  :AutoRotation: rotation divided by this value
+    [-A[utoRot]Range     ARMin               (0         )ARMax               (360       )] :Optional  :AutoRotationRange
+    [-A[uto]R[otation]iter[ation]AutoRotationIteration(2         )] :Optional  :AutoRotationIteration
+    [-A[uto]R[otation]MethodAutoRotationMethod  (0         )] :Optional  :Method for Correlation for Auto Rotation
+    [-M[odeForCorrelation]correlationMode     (19        )] :Optional  :Correlation Mode for AutoRotation
+    [-pvm                ] :Optional  :Parallel Analysis by PVM
+    [-pvmList            pvmList             (NULL      )] :Optional  :pvmList: Input
+    [-Log                Log                 (stdout    )] :Optional  :Log: Output
+    [-Log2               Log2                (NULL      )] :Optional  :Log2: Output: ClusterNode Only
+    [-LogIn              LogIn               (NULL      )] :Optional  :previousLog: Input
+    [-prevF[ileNum]      prevFileNum         (0         )] :Optional  :previousLogFileNum: Input
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         )] :Optional  :Mode
+----- Additional Usage -----
+Distance between clusters: mode
+       mode 0: By Correlation
+       mode 1: By Euclid Distance
+       mode 2: By Ward Method (default) : Euclid Length (no rotation) or its square (rotation)
+       mode 3: By Ward Method using Linear Correlation : (1 - Correlation)/(1 + Correlation)
+       mode 4: By Linear Correlation :                   (1 - Correlation)/(1 + Correlation)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html b/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html
index e00803c..647bfea 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html
+++ b/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageColoring: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageColoring</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageColoring</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageColoring
+Options:
+    [-r[ed]              rIn                 (NULL      )] :Optional  :Red:InputDataFile
+    [-g[reen]            gIn                 (NULL      )] :Optional  :Green:InputDataFile
+    [-b[lue]             bIn                 (NULL      )] :Optional  :Blue:InputDataFile
+    [-rH[ight]           rHigh               (1         )] :Optional  :Red:HighThres
+    [-rL[ow]             rLow                (0         )] :Optional  :Red:LowThres
+    [-gH[ight]           gHigh               (1         )] :Optional  :Green:HighThres
+    [-gL[ow]             gLow                (0         )] :Optional  :Green:LowThres
+    [-bH[ibht]           bHigh               (1         )] :Optional  :Blue:HibhThres
+    [-bL[ow]             bLow                (0         )] :Optional  :BLue:LowThres
+    [-o[utput]           Out                 (NULL      )] :Optional  :gif:OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageConnection/src/mrcImageConnection.html b/src/Tools/mrcImage/mrcImageConnection/src/mrcImageConnection.html
index 6c13602..784b263 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConnection/src/mrcImageConnection.html
+++ b/src/Tools/mrcImage/mrcImageConnection/src/mrcImageConnection.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageConnection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageConnection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageConnection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageConnection
+Options:
+    [-i[nput]1           In1                 (NULL      )] :Essential :InputDataFile
+    [-i[nput]2           In2                 (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+-m 0: z connection
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/mrcImageConnectivityNumberCalc.html b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/mrcImageConnectivityNumberCalc.html
index 4e5aec2..4808f98 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/mrcImageConnectivityNumberCalc.html
+++ b/src/Tools/mrcImage/mrcImageConnectivityNumberCalc/src/mrcImageConnectivityNumberCalc.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageConnectivityNumberCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageConnectivityNumberCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageConnectivityNumberCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageConnectivityNumberCalc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-f[orm]             form                (0         )] :Optional  :Form
+    [-I[nvers]           invers              (0         )] :Optional  :Invers
+----- Additional Usage -----
+mode   0 : Four Neighborhood. [default] : For 2 Dimension. 
+       1 : Eight Nieghborhood.          : 
+       2 : Eighteen Neighborhood.       : For 3 Dimension. 
+
+form   0 : No change. [default]      
+       1 : Spread of pixel data 1.   
+       2 : Thin of pixel data 1.     
+       3 : Frame of image by data 1. 
+
+invers 0 : The object is 1 value. [default] 
+       1 : The background is 1 value.       
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/mrcImageContourSurfaceCreate.html b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/mrcImageContourSurfaceCreate.html
index 78eb5d8..86bc892 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/mrcImageContourSurfaceCreate.html
+++ b/src/Tools/mrcImage/mrcImageContourSurfaceCreate/src/mrcImageContourSurfaceCreate.html
@@ -1 +1,23 @@
-/bin/bash: mrcImageContourSurfaceCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageContourSurfaceCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageContourSurfaceCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageContourSurfaceCreate
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
+    [-C[ontour]          Contour             (0.0       )] :Essential :Input: Contour Value
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+    -m 0 : SimpleMethod
+              When a point has contour surfaces between six voxels (Upper-Downward Right-Left For-Back) and the point,
+              the point is defined as ContourSurface
+              -C option are required 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageConvolution/src/mrcImageConvolution.html b/src/Tools/mrcImage/mrcImageConvolution/src/mrcImageConvolution.html
index 66d3381..9c890d4 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageConvolution/src/mrcImageConvolution.html
+++ b/src/Tools/mrcImage/mrcImageConvolution/src/mrcImageConvolution.html
@@ -1 +1,30 @@
-/bin/bash: mrcImageConvolution: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageConvolution</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageConvolution</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageConvolution
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
+    [-i[nput]k[ernal]a[rray]InKernelArray       (NULL      )] :Optional  :Input: Array
+    [-i[nput]k[ernal]m[rc]InKernelMRC         (NULL      )] :Optional  :Input: mrcImage
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-times              times               (1         )] :Optional  :Repeat time
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+>>> Array Format under Eos <<<<
+ndim N0 N1 N2 ...
+data(0,   0,   0,...,        0) data(1,   0,   0,...,        0) data(2,   0,   0,...,        0) ... data(N0-1,   0,   0,...,        0)
+data(0,   1,   0,...,        0) data(1,   1,   0,...,        0) data(2,   1,   0,...,        0) ... data(N0-1,   1,   0,...,        0)
+..............................................................
+data(0,N1-1,   0,...,        0) data(1,N1-1,   0,...,        0) data(2,N1-1,   0,...,        0) ... data(N0-1,N1-1,   0,...,        0)
+data(0,   0,   1,...,        0) data(1,   0,   1,...,        0) data(2,   0,   1,...,        0) ... data(N0-1,   0,   1,...,        0)
+..............................................................
+data(0,N1-1,N2-1,...,Nndim-1-1) data(1,N1-1,N2-1,...,Nndim-1-1) data(2,N1-1,N2-1,...,Nndim-1-1) ... data(N0-1,N1-1,N2-1,...,Nndim-1-1)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCoordinateChange/src/mrcImageCoordinateChange.html b/src/Tools/mrcImage/mrcImageCoordinateChange/src/mrcImageCoordinateChange.html
index 9ec1650..b71fe3e 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCoordinateChange/src/mrcImageCoordinateChange.html
+++ b/src/Tools/mrcImage/mrcImageCoordinateChange/src/mrcImageCoordinateChange.html
@@ -1 +1,17 @@
-/bin/bash: mrcImageCoordinateChange: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCoordinateChange</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCoordinateChange</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCoordinateChange
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/mrcImageCoreImageCalc.html b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/mrcImageCoreImageCalc.html
index 58ccbbd..a89141f 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCoreImageCalc/src/mrcImageCoreImageCalc.html
+++ b/src/Tools/mrcImage/mrcImageCoreImageCalc/src/mrcImageCoreImageCalc.html
@@ -1 +1,33 @@
-/bin/bash: mrcImageCoreImageCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCoreImageCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCoreImageCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCoreImageCalc
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: Pretreated Core-loss Image
+    [-e[neryg]l[oss]     EL                  (180       )] :Essential :Input: EnergyLoss
+    [-bg[List]           BG                  (NULL      )] :Essential :Input: Bg File List
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: Core-Loss Image
+    [-O[utputBG]         OutBG               (NULL      )] :Optional  :Output: BG-Image
+    [-Chi[sq]            OutChi              (NULL      )] :Optional  :Output: Chi-Image
+    [-initial[Value]     A1                  (5040      )A2                  (500       )A3                  (-12       )] :Optional  :Input: A1 + A2*EELS^A3
+    [-limitA3            LimitA3Min          (-16       )LimitA3Max          (-5        )] :Optional  :Input: limit A3
+    [-baseEELS           BaseEELS            (160.0     )] :Optional  :Input: BaseEELS as 1.0
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+>>> BGFile List 
+FileName1 EEL
+FileName2 EEL
+AAA       160
+BBB       170
+>>> Mode 
+Mode 0: Multi Window Method 
+        Need more than three pre- and post- edge images to calculate background
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCorrelation/src/mrcImageCorrelation.html b/src/Tools/mrcImage/mrcImageCorrelation/src/mrcImageCorrelation.html
index 5a9a547..06a1cac 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelation/src/mrcImageCorrelation.html
+++ b/src/Tools/mrcImage/mrcImageCorrelation/src/mrcImageCorrelation.html
@@ -1 +1 @@
-/bin/bash: mrcImageCorrelation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelation: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/mrcImageCorrelationInFourierSpace.html b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/mrcImageCorrelationInFourierSpace.html
index bedf4fb..f5b1e5c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/mrcImageCorrelationInFourierSpace.html
+++ b/src/Tools/mrcImage/mrcImageCorrelationInFourierSpace/src/mrcImageCorrelationInFourierSpace.html
@@ -1 +1,21 @@
-/bin/bash: mrcImageCorrelationInFourierSpace: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCorrelationInFourierSpace</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCorrelationInFourierSpace</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCorrelationInFourierSpace
+Options:
+    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile
+    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Mode 0: (FxG*)/(|FG|) 
+Mode 1: Phase residual 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCorrelationServer/src/mrcImageCorrelationServer.html b/src/Tools/mrcImage/mrcImageCorrelationServer/src/mrcImageCorrelationServer.html
index ab293c0..669d0fa 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationServer/src/mrcImageCorrelationServer.html
+++ b/src/Tools/mrcImage/mrcImageCorrelationServer/src/mrcImageCorrelationServer.html
@@ -1 +1 @@
-/bin/bash: mrcImageCorrelationServer: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationServer: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/mrcImageCorrelationWithCTFCompensation.html b/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/mrcImageCorrelationWithCTFCompensation.html
index 2db7171..af00726 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/mrcImageCorrelationWithCTFCompensation.html
+++ b/src/Tools/mrcImage/mrcImageCorrelationWithCTFCompensation/src/mrcImageCorrelationWithCTFCompensation.html
@@ -1 +1 @@
-/bin/bash: mrcImageCorrelationWithCTFCompensation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCorrelationWithCTFCompensation: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageCrystalCreate/src/mrcImageCrystalCreate.html b/src/Tools/mrcImage/mrcImageCrystalCreate/src/mrcImageCrystalCreate.html
index f871214..ad07e0f 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCrystalCreate/src/mrcImageCrystalCreate.html
+++ b/src/Tools/mrcImage/mrcImageCrystalCreate/src/mrcImageCrystalCreate.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageCrystalCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCrystalCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCrystalCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCrystalCreate
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-nx                 nx                  (1         )] :Optional  :Number:x-axis
+    [-ny                 ny                  (1         )] :Optional  :Number:y-axis
+    [-nz                 nz                  (1         )] :Optional  :Number:z-axis
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/mrcImageCutAndSetInArray.html b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/mrcImageCutAndSetInArray.html
index debce9b..c183353 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/mrcImageCutAndSetInArray.html
+++ b/src/Tools/mrcImage/mrcImageCutAndSetInArray/src/mrcImageCutAndSetInArray.html
@@ -1 +1 @@
-/bin/bash: mrcImageCutAndSetInArray: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageCutAndSetInArray: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageCylinderSection/src/mrcImageCylinderSection.html b/src/Tools/mrcImage/mrcImageCylinderSection/src/mrcImageCylinderSection.html
index f036354..00f7701 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageCylinderSection/src/mrcImageCylinderSection.html
+++ b/src/Tools/mrcImage/mrcImageCylinderSection/src/mrcImageCylinderSection.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageCylinderSection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageCylinderSection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageCylinderSection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageCylinderSection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-angmin             angmin              (0         )] :Optional  :Angle Minimum[degree]
+    [-angmax             angmax              (360       )] :Optional  :Angle Maximum[degree]
+    [-dang               dang                (10        )] :Optional  :Delta Angle[degree]
+    [-zmin               zmin                (0         )] :Optional  :Z Minimum[A]
+    [-zmax               zmax                (100       )] :Optional  :Z Maximum[A]
+    [-dz                 dz                  (10        )] :Optional  :Delta Z[A]
+    [-rmin               rmin                (0         )] :Optional  :Radius Minimum[A]
+    [-rmax               rmax                (250       )] :Optional  :Radius Maximum[A]
+    [-dr                 dr                  (10        )] :Optional  :Delta Radius[A]
+    [-W[eight]           ] :Optional  :Data are weithed by r
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Format Change
+x --> ang
+y --> z
+z --> r
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/mrcImageDeadPixelCorrection.html b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/mrcImageDeadPixelCorrection.html
index 870ad7a..1ba82f0 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/mrcImageDeadPixelCorrection.html
+++ b/src/Tools/mrcImage/mrcImageDeadPixelCorrection/src/mrcImageDeadPixelCorrection.html
@@ -1 +1,19 @@
-/bin/bash: mrcImageDeadPixelCorrection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDeadPixelCorrection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDeadPixelCorrection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDeadPixelCorrection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-dp[dead point]     Dp                  (NULL      )] :Essential :DeadPointPositionFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDeconvolution/src/mrcImageDeconvolution.html b/src/Tools/mrcImage/mrcImageDeconvolution/src/mrcImageDeconvolution.html
index 0a73b3d..3d5aedc 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDeconvolution/src/mrcImageDeconvolution.html
+++ b/src/Tools/mrcImage/mrcImageDeconvolution/src/mrcImageDeconvolution.html
@@ -1 +1 @@
-/bin/bash: mrcImageDeconvolution: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageDeconvolution: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/mrcImageDensityChangeEstimation.html b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/mrcImageDensityChangeEstimation.html
index 422fe58..ffba89c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/mrcImageDensityChangeEstimation.html
+++ b/src/Tools/mrcImage/mrcImageDensityChangeEstimation/src/mrcImageDensityChangeEstimation.html
@@ -1 +1,26 @@
-/bin/bash: mrcImageDensityChangeEstimation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDensityChangeEstimation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDensityChangeEstimation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDensityChangeEstimation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
+    [-i[nput]2           In2                 (NULL      )] :Essential :Input: mrcImage2
+    [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Attention !!!-----
+In Eos system, positive values are regarded as density.
+If a pixel has a negative value, the value of the pixel is regarded as zero.lmrcImageDensityChangeEstimation Mode: 
+2: CentreOfGravity 
+4: Max             
+8: SD around CentreOfGravity 
+16: SD around Max             
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html b/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
index e6ee2aa..91c6b17 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
+++ b/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
@@ -1,6 +1,3 @@
-<<<<<<< HEAD
-/bin/bash: mrcImageDensityInfo: そのようなファイルやディレクトリはありません
-=======
 <HTML>
 <HEAD>
 <TITLE>mrcImageDensityInfo</TITLE>
@@ -13,7 +10,7 @@ Usage: mrcImageDensityInfo
 Options:
     [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
     [-o[utput]           Out                 (stdout    )] :Optional  :OutputDataFile
-    [-C[ontour]          Contour             (10        )] :Optional  :ContourLevel: 10 2.901940e-307ach
+    [-C[ontour]          Contour             (10        )] :Optional  :ContourLevel: 10 1.235076e-312ach
     [-log                Log                 (NULL      )] :Optional  :OutputDataFile
     [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
     [-m[ode]             mode                (0         )] :Optional  :Mode
@@ -28,4 +25,3 @@ If a pixel has a negative value, the value of the pixel is regarded as zero.lmrc
 </PRE>
 </BODY>
 </HTML>
->>>>>>> FETCH_HEAD

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalization/src/mrcImageDensityNormalization.html b/src/Tools/mrcImage/mrcImageDensityNormalization/src/mrcImageDensityNormalization.html
index 9c4f7ea..2edd6db 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityNormalization/src/mrcImageDensityNormalization.html
+++ b/src/Tools/mrcImage/mrcImageDensityNormalization/src/mrcImageDensityNormalization.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageDensityNormalization: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDensityNormalization</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDensityNormalization</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDensityNormalization
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrc
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: mrc
+    [-V[alue]            Value               (100       )] :Optional  :Output: value
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Isovolume: 0 : make the sum of pixel values the input value
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/mrcImageDensityNormalizationByImage.html b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/mrcImageDensityNormalizationByImage.html
index f33d254..ebb0042 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/mrcImageDensityNormalizationByImage.html
+++ b/src/Tools/mrcImage/mrcImageDensityNormalizationByImage/src/mrcImageDensityNormalizationByImage.html
@@ -1 +1,42 @@
-/bin/bash: mrcImageDensityNormalizationByImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDensityNormalizationByImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDensityNormalizationByImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDensityNormalizationByImage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Test: Input
+    [-r[ef]              Ref                 (NULL      )] :Essential :Reference: Input
+    [-o[utput]           Out                 (NULL      )] :Essential :NormalizedImage:  Output
+    [-O[utput]           OutParam            (stdout    )] :Optional  :Parameters:       Output
+    [-D[ataForNormalizing]UsedData            (stdout    )] :Optional  :DataList to be used
+    [-Cylinder           CCenterX            (20        )CCenterY            (20        )CMinR               (10        )CMaxR               (20        )] :Optional  :Cylinder Region
+    [-testBG[Region]     tstBGMin            (-3        )tstBGMax            (3         )tstBGDelta          (0.1       )] :Optional  :SearchRegion
+    [-M[ode]             fitMode             (0         )] :Optional  :DensityFittngMethod: Mode
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Mode -----
+  1: Sigma!=1.0 
+  2: Stdout     
+  4: Reversed   
+  8: Robust Test
+Fitting Mode
+  0: Single Line
+        ref    /                      
+          ^   /   ref = A + B*tst     
+          |  /                        
+          |------> tst                
+  1: Single Line with Background
+        ref      /                              
+          ^     /   ref = A + B*tst (tst>tstBG) 
+ refBG-   | ___/          refBG     (tst<tstBG) 
+          | ------> tst                         
+               |                                
+              tstBG                             
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDilation/src/mrcImageDilation.html b/src/Tools/mrcImage/mrcImageDilation/src/mrcImageDilation.html
index cd1c00e..70fe244 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDilation/src/mrcImageDilation.html
+++ b/src/Tools/mrcImage/mrcImageDilation/src/mrcImageDilation.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageDilation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDilation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDilation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDilation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
+    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         )] :Optional  :Radius
+    [-n                  n                   (5         )] :Optional  :size
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/mrcImageDisplayDensityAsTempFactor.html b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/mrcImageDisplayDensityAsTempFactor.html
index d05ebf9..fd317af 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/mrcImageDisplayDensityAsTempFactor.html
+++ b/src/Tools/mrcImage/mrcImageDisplayDensityAsTempFactor/src/mrcImageDisplayDensityAsTempFactor.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageDisplayDensityAsTempFactor: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDisplayDensityAsTempFactor</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDisplayDensityAsTempFactor</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDisplayDensityAsTempFactor
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-p[dbfile]          Pdb                 (NULL      )] :Essential :InputPdbFile
+    [-v[alue]            Value               (1         )] :Optional  :value to multiply density
+    [-H[ighThreshold]    H                   (0.0       )] :Optional  :High Threshold
+    [-L[owThreshold]     L                   (1.0       )] :Optional  :Low Threshold
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDistanceConversion/src/mrcImageDistanceConversion.html b/src/Tools/mrcImage/mrcImageDistanceConversion/src/mrcImageDistanceConversion.html
index 9d73e7b..9172893 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDistanceConversion/src/mrcImageDistanceConversion.html
+++ b/src/Tools/mrcImage/mrcImageDistanceConversion/src/mrcImageDistanceConversion.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageDistanceConversion: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDistanceConversion</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDistanceConversion</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDistanceConversion
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-f[orm]             form                (0         )] :Optional  :Form
+----- Additional Usage -----
+mode  0 : 4 Neighborhood. [default]
+      1 : 8 Neighborhood.
+
+form  0 : Only distance conversion. [default]
+      1 : Distance conversion + Making frame.
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/mrcImageDivideInfoForTomography.html b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/mrcImageDivideInfoForTomography.html
index 25cbddd..b7775ad 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/mrcImageDivideInfoForTomography.html
+++ b/src/Tools/mrcImage/mrcImageDivideInfoForTomography/src/mrcImageDivideInfoForTomography.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageDivideInfoForTomography: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDivideInfoForTomography</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDivideInfoForTomography</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDivideInfoForTomography
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [cut[Back]           cut                 (6         )] :Optional  :Cut
+    [-d[ivide]           divide              (4         )] :Optional  :Divide
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/mrcImageDivideIntoTwoImages.html b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/mrcImageDivideIntoTwoImages.html
index fec8923..73811ba 100644 (file)
--- a/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/mrcImageDivideIntoTwoImages.html
+++ b/src/Tools/mrcImage/mrcImageDivideIntoTwoImages/src/mrcImageDivideIntoTwoImages.html
@@ -1 +1,23 @@
-/bin/bash: mrcImageDivideIntoTwoImages: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageDivideIntoTwoImages</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageDivideIntoTwoImages</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageDivideIntoTwoImages
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]1          Out1                (NULL      )] :Essential :OutputDataFile
+    [-o[utput]2          Out2                (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- mode -----
+0:Vertical to the longest axis.
+1:Vertical to x axis
+2:Vertical to y axis
+3:Vertical to z axis
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageDividedByFile/Makefile b/src/Tools/mrcImage/mrcImageDividedByFile/Makefile
deleted file mode 120000 (symlink)
index ef1f6300ba0b84da4931ed574ccec31fc5b88177..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageDividedByFile/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageDividedByFile/Makefile b/src/Tools/mrcImage/mrcImageDividedByFile/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageDividedByFile/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64 b/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64
new file mode 120000 (symlink)
index 0000000..ec1dd3d
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageDividedByFile/src/X86LINUX64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile b/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile
deleted file mode 120000 (symlink)
index ef1f6300ba0b84da4931ed574ccec31fc5b88177..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile b/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageEdgeEnhancement/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64 b/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64
new file mode 120000 (symlink)
index 0000000..74f5aa3
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageEdgeEnhancement/src/X86LINUX64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/mrcImageEdgeImageGet.html b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/mrcImageEdgeImageGet.html
index cb09c33..1b8a530 100644 (file)
--- a/src/Tools/mrcImage/mrcImageEdgeImageGet/src/mrcImageEdgeImageGet.html
+++ b/src/Tools/mrcImage/mrcImageEdgeImageGet/src/mrcImageEdgeImageGet.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageEdgeImageGet: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageEdgeImageGet</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageEdgeImageGet</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageEdgeImageGet
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage
+    [-o[utput]           Out                 (NULL      )] :Optional  :Output: mrcImage
+    [-s[ize]             Size                (64        )] :Optional  :Size: [pixel]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+mode: 
+       0: 4 Edge (x-y plane) from Image(0-3)
+       1: 8 Edge (x-y plane) + centre from Image(0-8)
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/mrcImageEnhancementWithFuzzySets.html b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/mrcImageEnhancementWithFuzzySets.html
index 310551a..6ecb123 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/mrcImageEnhancementWithFuzzySets.html
+++ b/src/Tools/mrcImage/mrcImageEnhancementWithFuzzySets/src/mrcImageEnhancementWithFuzzySets.html
@@ -1 +1 @@
-/bin/bash: mrcImageEnhancementWithFuzzySets: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageEnhancementWithFuzzySets: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageErosion/src/mrcImageErosion.html b/src/Tools/mrcImage/mrcImageErosion/src/mrcImageErosion.html
index cc0a84c..909d854 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageErosion/src/mrcImageErosion.html
+++ b/src/Tools/mrcImage/mrcImageErosion/src/mrcImageErosion.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageErosion: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageErosion</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageErosion</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageErosion
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: MRC
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: MRC
+    [-o[utput]SE         OutSE               (NULL      )] :Optional  :Output: MRC(SE)
+    [-S[tructuring]E[lement]SEmode              (0         )] :Optional  :StructuringElement
+    [-r[adius]           radius              (2         )] :Optional  :Radius
+    [-n                  n                   (5         )] :Optional  :size
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- Structuring Element : Mode 
+0: 2D Cross3x3:  4-neighbour
+1: 2D Square3x3: 8-neighbour
+2: 2D Open Disk , need (radius, n)
+3: 3D Cross3x3x3:   6-neighbour
+4: 3D Cubic3x3x3: 26-neighbour
+5: 3D Open Disk , need (radius, n)
+-----
+Dilation: Max for image : Or  for binary image 
+Erosion:  Min for image : And for binary image 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/mrcImageEstimateTiltImage.html b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/mrcImageEstimateTiltImage.html
index 7c89acf..befde18 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/mrcImageEstimateTiltImage.html
+++ b/src/Tools/mrcImage/mrcImageEstimateTiltImage/src/mrcImageEstimateTiltImage.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageEstimateTiltImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageEstimateTiltImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageEstimateTiltImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageEstimateTiltImage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-tiltAngle          TiltAngle           (0         )] :Optional  :Tilt Angle[degree]
+    [-tiltAxis           TiltAxis            (0         )] :Optional  :Tilt Axis[degree]
+    [-Inverse            ] :Optional  :To Non-tilt
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode: InterpolationMode
+----- Additional Usage -----
+-i in :2D or 3D
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageExpression/src/mrcImageExpression.html b/src/Tools/mrcImage/mrcImageExpression/src/mrcImageExpression.html
index c5a37bd..e5cb06c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageExpression/src/mrcImageExpression.html
+++ b/src/Tools/mrcImage/mrcImageExpression/src/mrcImageExpression.html
@@ -1 +1,24 @@
-/bin/bash: mrcImageExpression: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageExpression</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageExpression</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageExpression
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-T[hreshold]        Thres               (1e-16     )] :Optional  :Threshold to calculate.For mode 1 and 3.
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+----- mode -----
+0:Absolute value
+1:Log absolute value
+2:Root absolute value
+3:Square absolute value
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/mrcImageFFTLayerLineExtraction.html b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/mrcImageFFTLayerLineExtraction.html
index 61f6369..8961972 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/mrcImageFFTLayerLineExtraction.html
+++ b/src/Tools/mrcImage/mrcImageFFTLayerLineExtraction/src/mrcImageFFTLayerLineExtraction.html
@@ -1 +1,24 @@
-/bin/bash: mrcImageFFTLayerLineExtraction: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFFTLayerLineExtraction</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFFTLayerLineExtraction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFFTLayerLineExtraction
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-[input] I[nformation]InI                 (NULL      )] :Optional  :InputDataFile
+    [-truePitch          truePitch           (430       )] :Optional  :true Pitch [A]
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Input File Format
+FileName  x  z  dY 
+---------------------- 
+-I option is stronger than -dY option.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/mrcImageFOMCalc.html b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/mrcImageFOMCalc.html
index 42f0007..b3ec234 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFOMCalc.org/src/mrcImageFOMCalc.html
+++ b/src/Tools/mrcImage/mrcImageFOMCalc.org/src/mrcImageFOMCalc.html
@@ -1 +1,35 @@
-/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFOMCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFOMCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFOMCalc
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :TestData
+    [-w[eight]           Weight              (1.0       )] :Optional  :Weight
+    [-I[nput]            InList              (NULL      )] :Optional  :TestData Set
+    [-r[ef]              Ref                 (NULL      )] :Essential :Ref, Model Data
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: 
+    [-RR[ange]           Rmin                (0.0       )Rmax                (0.1       )] :Optional  :Ring Range
+    [-dR[ange]           dR                  (0.0       )] :Optional  :Ring Width
+    [-nS[ector]          nSector             (1         )] :Optional  :Sector Number
+    [-dA[lpha]           dAlpha              (5         )] :Optional  :delta Alpha
+    [-XMax               XMax                (0.0       )] :Optional  :Xmax: If not set, one calc Xmax
+    [-A[uto]S[cale]      ] :Optional  :Auto Scaling
+    [-A[llArea]A[uto]S[cale]AASRMax             (0.05      )] :Optional  :All Area Auto Scaling
+    [-RS[cale]           ] :Optional  :R Scaling
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+>> -I FileFormat 
+mrc[0]   weight[0]
+mrc[1]   weight[1]
+.....
+mrc[n-1] weight[n-1]
+This algorithm is originated from K. Yonekura for Layer Lines. Nature/SupplmentTable 2 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFOMCalc/src/mrcImageFOMCalc.html b/src/Tools/mrcImage/mrcImageFOMCalc/src/mrcImageFOMCalc.html
index 42f0007..b3ec234 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFOMCalc/src/mrcImageFOMCalc.html
+++ b/src/Tools/mrcImage/mrcImageFOMCalc/src/mrcImageFOMCalc.html
@@ -1 +1,35 @@
-/bin/bash: mrcImageFOMCalc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFOMCalc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFOMCalc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFOMCalc
+Options:
+    [-i[nput]            In                  (NULL      )] :Optional  :TestData
+    [-w[eight]           Weight              (1.0       )] :Optional  :Weight
+    [-I[nput]            InList              (NULL      )] :Optional  :TestData Set
+    [-r[ef]              Ref                 (NULL      )] :Essential :Ref, Model Data
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: 
+    [-RR[ange]           Rmin                (0.0       )Rmax                (0.1       )] :Optional  :Ring Range
+    [-dR[ange]           dR                  (0.0       )] :Optional  :Ring Width
+    [-nS[ector]          nSector             (1         )] :Optional  :Sector Number
+    [-dA[lpha]           dAlpha              (5         )] :Optional  :delta Alpha
+    [-XMax               XMax                (0.0       )] :Optional  :Xmax: If not set, one calc Xmax
+    [-A[uto]S[cale]      ] :Optional  :Auto Scaling
+    [-A[llArea]A[uto]S[cale]AASRMax             (0.05      )] :Optional  :All Area Auto Scaling
+    [-RS[cale]           ] :Optional  :R Scaling
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+>> -I FileFormat 
+mrc[0]   weight[0]
+mrc[1]   weight[1]
+.....
+mrc[n-1] weight[n-1]
+This algorithm is originated from K. Yonekura for Layer Lines. Nature/SupplmentTable 2 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/mrcImageFeatureExtraction.html b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/mrcImageFeatureExtraction.html
index fae470d..9fd19b6 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFeatureExtraction/src/mrcImageFeatureExtraction.html
+++ b/src/Tools/mrcImage/mrcImageFeatureExtraction/src/mrcImageFeatureExtraction.html
@@ -1 +1,55 @@
-/bin/bash: mrcImageFeatureExtraction: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFeatureExtraction</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFeatureExtraction</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFeatureExtraction
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[oOccurrence]r[adius]co_r                (1         )] :Optional  :Co-Occurrence radius
+    [-c[oOccurrence]t[heta]co_theta            (0         )] :Optional  :Co-Occurrence theta
+    [-r[unLength]t[heta] rl_theta            (0         )] :Optional  :RunLength theta
+    [-r[unLength]d[ev]   rl_dev              (4         )] :Optional  :RunLength devision
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+
+----- Additional Usage -----
+Feature list
+0  :densityhistgram average
+1  :densityhistgram variance
+2  :densityhistgram skewness
+3  :densityhistgram kurtosis
+4  :densityhistgram contrast
+5  :densityhistgram energy
+6  :densityhistgram entropy
+7  :co-occurrence anguler second moment
+8  :co-occurrence contrast
+9  :co-occurrence correlation
+10  :co-occurrence sum of square: variance
+11 :co-occurrence inverse difference moment
+12 :co-occurrence sum average
+13 :co-occurrence sum variance
+14 :co-occurrence sum entropy
+15 :co-occurrence entropy
+16 :co-occurrence difference variance
+17 :co-occurrence difference entropy
+18 :co-occurrence information measure of correlation 1
+19 :co-occurrence information measure of correlation 2
+20 :co-occurrence maximal correlation coefficient
+21 :difference statistics contrast
+22 :difference statistics anguler second moment
+23 :difference statistics entropy
+24 :difference statistics mean
+25 :runlength short runs emphasis
+26 :runlength long runs emphasis
+27 :runlength gray level nonuniformity
+28 :runlength run length nonuniformity
+29 :runlength run percentage
+
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFilamentSearch/src/mrcImageFilamentSearch.html b/src/Tools/mrcImage/mrcImageFilamentSearch/src/mrcImageFilamentSearch.html
index 7ed4dc2..d5f6a0a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilamentSearch/src/mrcImageFilamentSearch.html
+++ b/src/Tools/mrcImage/mrcImageFilamentSearch/src/mrcImageFilamentSearch.html
@@ -1 +1 @@
-/bin/bash: mrcImageFilamentSearch: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFilamentSearch: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageFilterCreate/src/mrcImageFilterCreate.html b/src/Tools/mrcImage/mrcImageFilterCreate/src/mrcImageFilterCreate.html
index c0a97f5..7d95a4a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilterCreate/src/mrcImageFilterCreate.html
+++ b/src/Tools/mrcImage/mrcImageFilterCreate/src/mrcImageFilterCreate.html
@@ -1 +1,29 @@
-/bin/bash: mrcImageFilterCreate: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFilterCreate</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFilterCreate</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFilterCreate
+Options:
+    [-i[nput]            In                  (stdin     )] :Optional  :Input: ASCII
+    [-o[utput]           Out                 (stdout    )] :Optional  :Output: mrcImage
+    [-nx                 Nx                  (512       )] :Essential :ImageSize: x
+    [-ny                 Ny                  (512       )] :Optional  :ImageSize: y
+    [-nz                 Nz                  (1         )] :Optional  :ImageSize: z
+    [-sx                 Sx                  (3         )] :Essential :FilterSize: x
+    [-sy                 Sy                  (3         )] :Optional  :FilterSize: y
+    [-sz                 Sz                  (1         )] :Optional  :FilterSize: z
+    [-v[erbose]          ] :Optional  :Verbose
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-M[ode]             Mode                (0         )] :Optional  :Mode: Filter shape
+    [-m[ode]             mode                (2         )] :Optional  :mode: output mrc
+----- Additional Usage -----
+>>>> Input file Format nx0 y0 z0 weight0
+x1 y1 z1 weight1
+......          
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/mrcImageFilteringbyFile.html b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/mrcImageFilteringbyFile.html
index d8f7f66..4072873 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFile/src/mrcImageFilteringbyFile.html
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFile/src/mrcImageFilteringbyFile.html
@@ -1 +1,21 @@
-/bin/bash: mrcImageFilteringbyFile: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFilteringbyFile</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFilteringbyFile</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFilteringbyFile
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-f[ilter]           Filter              (NULL      )] :Essential :FilterFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+Mode 0: Filtering input file by filter file.
+Mode 1: Output mrc fourier image of filter file.Size of filter is size of input file.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/mrcImageFilteringbyFileForVariance.html b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/mrcImageFilteringbyFileForVariance.html
index eec6a8d..b14310a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/mrcImageFilteringbyFileForVariance.html
+++ b/src/Tools/mrcImage/mrcImageFilteringbyFileForVariance/src/mrcImageFilteringbyFileForVariance.html
@@ -1 +1,19 @@
-/bin/bash: mrcImageFilteringbyFileForVariance: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFilteringbyFileForVariance</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFilteringbyFileForVariance</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFilteringbyFileForVariance
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-f[ilter]           Filter              (NULL      )] :Essential :FilterFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/mrcImageFourierPowerSpectrum.html b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/mrcImageFourierPowerSpectrum.html
index 0efd201..7f18f04 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/mrcImageFourierPowerSpectrum.html
+++ b/src/Tools/mrcImage/mrcImageFourierPowerSpectrum/src/mrcImageFourierPowerSpectrum.html
@@ -1 +1 @@
-/bin/bash: mrcImageFourierPowerSpectrum: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFourierPowerSpectrum: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/mrcImageFourierShellCorrelation.html b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/mrcImageFourierShellCorrelation.html
index 2ea93a5..2dc688d 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/mrcImageFourierShellCorrelation.html
+++ b/src/Tools/mrcImage/mrcImageFourierShellCorrelation/src/mrcImageFourierShellCorrelation.html
@@ -1 +1,32 @@
-/bin/bash: mrcImageFourierShellCorrelation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFourierShellCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFourierShellCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFourierShellCorrelation
+Options:
+    [-i1[input1]         In1                 (NULL      )] :Optional  :InputDataFile
+    [-i2[input2]         In2                 (NULL      )] :Optional  :InputDataFile
+    [-d[elta]            delta               (0         )] :Optional  :Interval of output data(1/A). Default 1/(Nx*size of pixel)
+    [-z[position]        z                   (0         )] :Optional  :z position of reference file to correlate.For mode2=1 only
+    [-L[owThreshold]     L                   (0         )] :Optional  :Low threshold for mode +2.
+    [-H[ighThreshold]    H                   (0         )] :Optional  :High threshold for mode +2.
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-M[ode2]            mode2               (0         )] :Optional  :Mode2
+    [-I1[nput array of file]In1Array            (stdin     )] :Optional  :InputDataFiles
+----- mode -----
+0: Fourier shell correlation.
+1: Fourier shell phase residual.
++2: Correlation between L and H
++4: Without equator.
+----- mode 2 -----
+0: Correlation between same size images
+1: Correlation between 2D image and image extracted from 3D image.
++2: Correlation between 2D different size images. In1 is compared with center of In2.
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/mrcImageFractalFourierShellCorrelation.html b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/mrcImageFractalFourierShellCorrelation.html
index f87359b..fcd4b18 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/mrcImageFractalFourierShellCorrelation.html
+++ b/src/Tools/mrcImage/mrcImageFractalFourierShellCorrelation/src/mrcImageFractalFourierShellCorrelation.html
@@ -1 +1,34 @@
-/bin/bash: mrcImageFractalFourierShellCorrelation: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageFractalFourierShellCorrelation</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageFractalFourierShellCorrelation</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageFractalFourierShellCorrelation
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :Input: mrcImage Input
+    [-r[eference]        Ref                 (NULL      )] :Essential :Input: mrcImage Reference
+    [-o[utput]           Out                 (NULL      )] :Essential :Output: ResolutionMap
+    [-t[hreshold]        Threshold           (0.5       )] :Optional  :Input: Threshold
+    [-s[tep]x            stepx               (1         )] :Optional  :Input: step x
+    [-s[tep]y            stepy               (1         )] :Optional  :Input: step y
+    [-s[tep]z            stepz               (1         )] :Optional  :Input: step z
+    [-maxN               maxN                (32        )] :Optional  :Input: max partIn.HeaderN
+    [-scaling[ up]       scaling             (1.25      )] :Optional  :Input: scaling up
+    [-get[ mode]         getMode             (0         )] :Optional  :Input:mrcPixelDataGetMode
+    [-Log                Log                 (NULL      )] :Optional  :Output: Log File
+    [-xmin               xmin                (0         )] :Optional  :Input: xmin
+    [-ymin               ymin                (0         )] :Optional  :Input: ymin
+    [-zmin               zmin                (0         )] :Optional  :Input: zmin
+    [-xmax               xmax                (0         )] :Optional  :Input: xmax
+    [-ymax               ymax                (0         )] :Optional  :Input: ymax
+    [-zmax               zmax                (0         )] :Optional  :Input: zmax
+    [-d[ensity]          densityThreshold    (0         )] :Optional  :Input: density threshold
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/mrcImageFractalFrourierShellCorrelation.html b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/mrcImageFractalFrourierShellCorrelation.html
index 3bcbb68..1aeea0e 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/mrcImageFractalFrourierShellCorrelation.html
+++ b/src/Tools/mrcImage/mrcImageFractalFrourierShellCorrelation/src/mrcImageFractalFrourierShellCorrelation.html
@@ -1 +1 @@
-/bin/bash: mrcImageFractalFrourierShellCorrelation: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageFractalFrourierShellCorrelation: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageGaussDisc/src/mrcImageGaussDisc.html b/src/Tools/mrcImage/mrcImageGaussDisc/src/mrcImageGaussDisc.html
index 36ab6d8..574018e 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageGaussDisc/src/mrcImageGaussDisc.html
+++ b/src/Tools/mrcImage/mrcImageGaussDisc/src/mrcImageGaussDisc.html
@@ -1 +1,33 @@
-/bin/bash: mrcImageGaussDisc: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageGaussDisc</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageGaussDisc</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageGaussDisc
+Options:
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-sigmax             sigmax              (10        )] :Optional  :sigmax[A]
+    [-sigmay             sigmay              (10        )] :Optional  :sigmay[A]
+    [-sigma_range        sigma_range         (3         )] :Optional  :sigma
+    [-weight             weight              (10        )] :Optional  :weight
+    [-size               size                (5         )] :Optional  :Pixel Size[A]
+    [-W[idth]            Width               (0         )] :Optional  :Image Width[A]
+    [-H[eight]           Height              (0         )] :Optional  :Image Height[A]
+    [-cx                 centrex             (0         )] :Optional  :x: Centre[A]
+    [-cy                 centrey             (0         )] :Optional  :y: Centre[A]
+    [-a[ngle]            Angle               (0         )] :Optional  :Angle: [degree]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         )] :Optional  :Mode
+----- Additional Usage -----
+Gauss Disc is cutted at sigma_range*sigma 
+Gauss Disc = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)) 
+mrcImageFileSize is (sigma_range*sigmax*2) x (sigma_range*sigmay*2) 
+-----------------------------------------------------------------------------------
+mode 0 char 
+mode 2 float 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageGaussSphere/src/mrcImageGaussSphere.html b/src/Tools/mrcImage/mrcImageGaussSphere/src/mrcImageGaussSphere.html
index 6b8fab9..d798bc8 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageGaussSphere/src/mrcImageGaussSphere.html
+++ b/src/Tools/mrcImage/mrcImageGaussSphere/src/mrcImageGaussSphere.html
@@ -1 +1,35 @@
-/bin/bash: mrcImageGaussSphere: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageGaussSphere</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageGaussSphere</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageGaussSphere
+Options:
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-E[uler]A[ngle]     EA                  (YOYS      )Rot1                (0.0       )Rot2                (0.0       )Rot3                (0.0       )] :Optional  :Input: Gauss Sphere: Rotation
+    [-centre             ShiftX              (0.0       )ShiftY              (0.0       )ShiftZ              (0.0       )] :Optional  :Input: Gauss Sphere: Centre
+    [-sigmax             sigmax              (10        )] :Optional  :sigmax[A]
+    [-sigmay             sigmay              (20        )] :Optional  :sigmay[A]
+    [-sigmaz             sigmaz              (30        )] :Optional  :sigmaz[A]
+    [-sigma_range        sigma_range         (3         )] :Optional  :x times
+    [-weight             weight              (10        )] :Optional  :weight
+    [-size               size                (5         )] :Optional  :Pixel Size[A]
+    [-W[idth]            Width               (0         )] :Optional  :Width[A]
+    [-H[ight]            Height              (0         )] :Optional  :Height[A]
+    [-S[ection]          Section             (0         )] :Optional  :Section[A]
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (2         )] :Optional  :Mode
+Gauss Sphere is cutted at sigma_range*sigma 
+Gauss Sphere = weight * exp ( - ((x^2 / sigmax^2)+(y^2 / sigmay^2)+(z^2 / sigmaz^2)) 
+mrcImageFileSize is (sigma_range*sigmax*2) x (sigma_range*sigmay*2) x (sigma_range*sigmaz*2) 
+-----------------------------------------------------------------------------------
+-EA: for rotation 
+-----------------------------------------------------------------------------------
+mode 0 char 
+mode 2 float 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHeaderChange/src/mrcImageHeaderChange.html b/src/Tools/mrcImage/mrcImageHeaderChange/src/mrcImageHeaderChange.html
index 623f0e7..09a5482 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHeaderChange/src/mrcImageHeaderChange.html
+++ b/src/Tools/mrcImage/mrcImageHeaderChange/src/mrcImageHeaderChange.html
@@ -1 +1,22 @@
-/bin/bash: mrcImageHeaderChange: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHeaderChange</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHeaderChange</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHeaderChange
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[output]          Out                 (NULL      )] :Essential :OutputDataFile
+    [-r[esolution]       r                   (0.0       )] :Optional  :Pixel size
+    [-x[length]          Lx                  (0.0       )] :Optional  :Pixel size along x axis(A).Default:No change
+    [-y[length]          Ly                  (0.0       )] :Optional  :Pixel size along y axis(A).Default:No change
+    [-z[length]          Lz                  (0.0       )] :Optional  :Pixel size along z axis(A).Default:No change
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+If r is defined, pixel size is r
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/mrcImageHelicalAveraging.html b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/mrcImageHelicalAveraging.html
index f3cdc15..59b50a1 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalAveraging/src/mrcImageHelicalAveraging.html
+++ b/src/Tools/mrcImage/mrcImageHelicalAveraging/src/mrcImageHelicalAveraging.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageHelicalAveraging: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHelicalAveraging</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHelicalAveraging</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHelicalAveraging
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dp                  (-167.143  )] :Optional  :deltaphi(degree)
+    [-N[umber]           N                   (1         )] :Optional  :Number of particles to average
+    [-W[indow]           W                   (1         )] :Optional  :Window size to average [pixel].
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+0: Discrete.  Parameter N is needed.  
+1: Continuous.  Parameter W is needed.  
+2: Continuous.  Parameter W is needed.  Data are weighted by exp(- (dz/W)^2) 
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/mrcImageHelicalConvolution.html b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/mrcImageHelicalConvolution.html
index 52bd310..95aa8fd 100644 (file)
--- a/src/Tools/mrcImage/mrcImageHelicalConvolution/src/mrcImageHelicalConvolution.html
+++ b/src/Tools/mrcImage/mrcImageHelicalConvolution/src/mrcImageHelicalConvolution.html
@@ -1 +1 @@
-/bin/bash: mrcImageHelicalConvolution: そのようなファイルやディレクトリはありません
+/bin/bash: mrcImageHelicalConvolution: No such file or directory

diff --git a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/mrcImageHelicalMappingFrom2DImage.html b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/mrcImageHelicalMappingFrom2DImage.html
index e508e0c..b8fca81 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/mrcImageHelicalMappingFrom2DImage.html
+++ b/src/Tools/mrcImage/mrcImageHelicalMappingFrom2DImage/src/mrcImageHelicalMappingFrom2DImage.html
@@ -1 +1,21 @@
-/bin/bash: mrcImageHelicalMappingFrom2DImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHelicalMappingFrom2DImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHelicalMappingFrom2DImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHelicalMappingFrom2DImage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+    [-Nz                 Nz                  (1         )] :Essential :Length of output image (pixel).
+    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dp                  (-167.143  )] :Optional  :deltaphi(degree)
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHelicalMasking/src/mrcImageHelicalMasking.html b/src/Tools/mrcImage/mrcImageHelicalMasking/src/mrcImageHelicalMasking.html
index b3b4733..e89c1bb 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMasking/src/mrcImageHelicalMasking.html
+++ b/src/Tools/mrcImage/mrcImageHelicalMasking/src/mrcImageHelicalMasking.html
@@ -1 +1,25 @@
-/bin/bash: mrcImageHelicalMasking: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHelicalMasking</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHelicalMasking</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHelicalMasking
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
+    [-sz[startz]         sz                  (0         )] :Optional  :startz(pixel)
+    [-ez[startz]         ez                  (0         )] :Optional  :endz(pixel)
+    [-sphi[startphi]     sphi                (0         )] :Optional  :startphi(degree) for masking
+    [-ephi[startphi]     ephi                (90        )] :Optional  :endphi(degree) for masking
+    [-v[alue]            value               (0         )] :Optional  :value to pad
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/mrcImageHelicalMaskingBy2DImage.html b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/mrcImageHelicalMaskingBy2DImage.html
index 014e3ee..b0c4894 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/mrcImageHelicalMaskingBy2DImage.html
+++ b/src/Tools/mrcImage/mrcImageHelicalMaskingBy2DImage/src/mrcImageHelicalMaskingBy2DImage.html
@@ -1 +1,21 @@
-/bin/bash: mrcImageHelicalMaskingBy2DImage: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHelicalMaskingBy2DImage</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHelicalMaskingBy2DImage</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHelicalMaskingBy2DImage
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
+    [-M[ask]             Mask                (NULL      )] :Essential :2D Image for masking
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageHelicalProjection/src/mrcImageHelicalProjection.html b/src/Tools/mrcImage/mrcImageHelicalProjection/src/mrcImageHelicalProjection.html
index 280c834..ac847d9 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageHelicalProjection/src/mrcImageHelicalProjection.html
+++ b/src/Tools/mrcImage/mrcImageHelicalProjection/src/mrcImageHelicalProjection.html
@@ -1 +1,20 @@
-/bin/bash: mrcImageHelicalProjection: そのようなファイルやディレクトリはありません
+<HTML>
+<HEAD>
+<TITLE>mrcImageHelicalProjection</TITLE>
+</HEAD>
+<BODY>
+<H1>mrcImageHelicalProjection</H1>
+<H2>Usage</H2>
+<PRE>
+Usage: mrcImageHelicalProjection
+Options:
+    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
+    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
+    [-dz[deltaz]         dz                  (27.3      )] :Optional  :deltaz(A)
+    [-dp[deltaphi]       dphi                (13.84     )] :Optional  :deltaphi(degree)
+    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         )] :Optional  :Mode
+----- Additional Usage -----
+</PRE>
+</BODY>
+</HTML>

diff --git a/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile b/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile
deleted file mode 120000 (symlink)
index ef1f6300ba0b84da4931ed574ccec31fc5b88177..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile b/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageLogicalOperation/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64 b/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64
new file mode 120000 (symlink)
index 0000000..c93c214
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageLogicalOperation/src/X86LINUX64
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile b/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile
deleted file mode 120000 (symlink)
index ef1f6300ba0b84da4931ed574ccec31fc5b88177..0000000000000000000000000000000000000000
--- a/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile b/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageTopHatTransform/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64 b/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64
new file mode 120000 (symlink)
index 0000000..00c6f5d
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64
@@ -0,0 +1 @@
+../../../../../hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageTopHatTransform/src/X86LINUX64
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/.Source b/src/Tools/pdbUtil/.Source
index f4665f0..bbadc01 100644 (file)
--- a/src/Tools/pdbUtil/.Source
+++ b/src/Tools/pdbUtil/.Source
@@ -1,9 +1,9 @@
 SOURCE=\
+pdb2SketchMacro \
 pdb2bender \
 pdb2mrc \
 pdb2mrc2d \
 pdb2mrc2dWithCTF \
-pdb2SketchMacro \
 pdbAtomSection \
 pdbCAOnly \
 pdbChargeFit \

diff --git a/src/Tools/pdbUtil/Makefile b/src/Tools/pdbUtil/Makefile
deleted file mode 120000 (symlink)
index 2e47e5ddff98d10d147965fcdcd4993350863c2a..0000000000000000000000000000000000000000
--- a/src/Tools/pdbUtil/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/home/eos/Eos/src/Config/Template/ToolsClassTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/Makefile b/src/Tools/pdbUtil/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..dfd525eab555f9091108b34834053d364b8bf0ad
--- /dev/null
+++ b/src/Tools/pdbUtil/Makefile
@@ -0,0 +1,107 @@
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+all:
+       for dir in ${SOURCE} ; \
+       do \
+               if [ -d $${dir} ] ; then \
+                       $(CD) $${dir}; make all; $(CD) ..; \
+               fi \
+       done
+
+install:
+       for dir in ${SOURCE} ; \
+       do \
+               if [ -d $${dir} ] ; then \
+                       $(CD) $${dir}; make install; $(CD) ..; \
+               fi \
+       done
+
+put:
+       for dir in ${SOURCE} ; \
+       do \
+               if [ -d $${dir} ] ; then \
+                       $(CD) $${dir}; make put; $(CD) ..; \
+               fi \
+       done
+
+putSF:
+       if [ -f private ] ; then \
+               echo "$(WORLDNAME)/$(CLASSNAME) is private " ; \
+       else \
+               for dir in ${SOURCE} ; \
+               do \
+                       if [ -d $${dir} ] ; then \
+                               $(CD) $${dir}; make putSF; $(CD) ..; \
+                       fi \
+               done \
+       fi
+
+clean:
+       for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make clean; $(CD) ..; \
+       done
+
+check:
+       @for dir in ${SOURCE} ; do \
+               if [ -d $${dir} ] ; then \
+                       $(CD) $${dir}; \
+                       echo  $${dir}; \
+                       $(RM) Makefile; \
+                       $(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/Makefile Makefile ; \
+                       make check; \
+                       $(CD) ..; \
+               fi \
+       done
+
+depend: check
+       @for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make depend; $(CD) ..; \
+       done
+
+backup: 
+       cd ../../..; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+       tar uvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
+       @for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make backup; $(CD) ..; \
+       done
+
+backup-all: 
+       cd ../../..; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+       tar rvf ${EOS_HOME}/backup/EosBase.tar .[A-z]*
+       @for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make backup; $(CD) ..; \
+       done
+
+distribute: 
+       cd ../../..; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+       @for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make distribute; $(CD) ..; \
+       done
+
+distribute-all: 
+       cd ../../..; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Config; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/Makefile; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/.[A-z]*
+       @for dir in ${SOURCE} ; \
+       do \
+               $(CD) $${dir}; make distribute-all; $(CD) ..; \
+       done
+

diff --git a/src/Tools/pdbUtil/pdbTrans/Makefile b/src/Tools/pdbUtil/pdbTrans/Makefile
deleted file mode 120000 (symlink)
index 8735a86b444e91472ea1d2c764a74ce158b00a6c..0000000000000000000000000000000000000000
--- a/src/Tools/pdbUtil/pdbTrans/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/home/eos/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/pdbUtil/pdbTrans/Makefile b/src/Tools/pdbUtil/pdbTrans/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..4dbb018acae5475bce203b3db2365124accfa24b
--- /dev/null
+++ b/src/Tools/pdbUtil/pdbTrans/Makefile
@@ -0,0 +1,104 @@
+include ../../../Config/Define.inc
+include ../../Config/Define.inc
+include ../Config/Define.inc
+include Config/Define.inc
+
+all:
+       cd src; make all; cd ..
+
+install:
+       cd src; make install; cd ..
+
+
+putSF:
+       if [ -f private ] ; \
+       then \
+               echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
+       else \
+               cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
+       fi
+
+put:
+       cd src; make put; cd ..
+
+clean:
+       cd src; make clean; cd ..
+
+depend:
+       cd src; make depend; cd ..
+
+check:
+       @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
+               echo making directory; \
+               mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
+       fi
+       ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); 
+       @$(RM) src/Makefile
+       @echo "New src/Makefile" 
+       @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
+       @cd src; touch $(OSTYPE)/.Depend; make depend
+
+cvsupdate::
+       cvs -d $(EOS_CVSROOT) update -d 
+
+cvscommit::
+       cvs -d $(EOS_CVSROOT) commit
+
+backup:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+
+backup-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config       ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
+       
+distribute:
+       cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+       
+distribute-all:
+       @cd ../../../..;     \
+       echo $(OBJECTNAME) ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config     ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
+       tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
+
+eosintroduce:
+       ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ 
+
+include Config/Target.inc

diff --git a/src/Tools/rec3d/.Source b/src/Tools/rec3d/.Source
index e1196de..b3f8d2e 100644 (file)
--- a/src/Tools/rec3d/.Source
+++ b/src/Tools/rec3d/.Source
@@ -1,16 +1,19 @@
 SOURCE=\
-calcCommonLine \
 CheckCommonLineData \
 CheckOfOrientation \
 CheckOrientationByDegree \
 CommonLineCalculation \
-commonLinesSearchByVoting \
 EvaluateCorrelationMapwithCommonLine \
-FETmapOrientationSearchBySimultaneousFitting \
 FETOrientationSearchByAnnealing \
 FETOrientationSearchByFeatureAlignment \
+FETmapOrientationSearchBySimultaneousFitting \
 FETsmallMapSetCreate_forSimultaneousMinimization \
 LCalculationForOrientationSearch \
+ProjectionDirectionMapCreate \
+WeightCalculationOfCommonLineSearch \
+WeightCalculationOfCommonLineSearchByAllSinogram \
+calcCommonLine \
+commonLinesSearchByVoting \
 ll2ltlg \
 llExtract \
 llExtractCtfinfFileCreate \
@@ -35,7 +38,4 @@ mrcImageOrientationSearchByHybridization \
 mrcImageOrientationSearchBySimultaneousMinimization \
 mrcImageRadonTransform \
 mrcRadon2Dto3D \
-ProjectionDirectionMapCreate \
-WeightCalculationOfCommonLineSearch \
-WeightCalculationOfCommonLineSearchByAllSinogram \
 #LastSource

diff --git a/src/Tools/transform/.Source b/src/Tools/transform/.Source
index cd5caac..321ac66 100644 (file)
--- a/src/Tools/transform/.Source
+++ b/src/Tools/transform/.Source
@@ -1,5 +1,5 @@
 SOURCE=\
 Descartes2Polar \
-pointAffineTransform \
 Polar2Descartes \
+pointAffineTransform \
 #LastSource