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-<TITLE>mrcImageAutoRotationCorrelation</TITLE>
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-<H1>mrcImageAutoRotationCorrelation</H1>
-<H2>Usage</H2>
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-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
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->>>>>>>> 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:
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- 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
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->>>>>>>> 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 .
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->>>>>>>> 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 .
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->>>>>>>> Attention 5 : Refinement Mode -----
--RefineMode
- 0: for LinearCorrelation; default
- 1: for SetModeCorrelation
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->>>>>>>> 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.
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