new file: Display2/

	new file:   mrc2png/
	new file:   mrcFFTCentralSectionCompare/
	new file:   mrcImageDistanceConversion/
	modified:   mrcImageFeatureCalc/
	new file:   mrcImageHoleFilling/
	new file:   mrcImageMeanFreePathCalc/
	modified:   mrcImageROIs/
	new file:   mrcImageShapePCA/

diff --git a/Display2/test2-0000.roi b/Display2/test2-0000.roi
new file mode 100644 (file)
index 0000000..2f373fa
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diff --git a/Display2/test2-0001.roi b/Display2/test2-0001.roi
new file mode 100644 (file)
index 0000000..62b3434
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diff --git a/Display2/test2-0002.roi b/Display2/test2-0002.roi
new file mode 100644 (file)
index 0000000..e9e4c07
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diff --git a/Display2/test2-0003.roi b/Display2/test2-0003.roi
new file mode 100644 (file)
index 0000000..15c2202
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diff --git a/Display2/test2-0004.roi b/Display2/test2-0004.roi
new file mode 100644 (file)
index 0000000..7eb263c
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diff --git a/Display2/test2-0005.roi b/Display2/test2-0005.roi
new file mode 100644 (file)
index 0000000..6d3f4ee
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diff --git a/Display2/test2-0006.roi b/Display2/test2-0006.roi
new file mode 100644 (file)
index 0000000..b56c23f
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diff --git a/Display2/test2-0007.roi b/Display2/test2-0007.roi
new file mode 100644 (file)
index 0000000..e8e8126
Binary files /dev/null and b/Display2/test2-0007.roi differ

diff --git a/Display2/test2-0008.roi b/Display2/test2-0008.roi
new file mode 100644 (file)
index 0000000..f4e16d5
Binary files /dev/null and b/Display2/test2-0008.roi differ

diff --git a/Display2/test2-0009.roi b/Display2/test2-0009.roi
new file mode 100644 (file)
index 0000000..9210e55
Binary files /dev/null and b/Display2/test2-0009.roi differ

diff --git a/Display2/test2-0010.roi b/Display2/test2-0010.roi
new file mode 100644 (file)
index 0000000..68f23f0
Binary files /dev/null and b/Display2/test2-0010.roi differ

diff --git a/Display2/test2.mon b/Display2/test2.mon
new file mode 100644 (file)
index 0000000..143adb8
Binary files /dev/null and b/Display2/test2.mon differ

diff --git a/Display2/test2.mrc b/Display2/test2.mrc
new file mode 100644 (file)
index 0000000..458a08b
Binary files /dev/null and b/Display2/test2.mrc differ

diff --git a/Display2/test2.roiinfo b/Display2/test2.roiinfo
new file mode 100644 (file)
index 0000000..46bbfd2
--- /dev/null
+++ b/Display2/test2.roiinfo
@@ -0,0 +1,2 @@
+test/data/test2-0000.roi TiltRect      179.545015     1441.365373      497.000000     1119.000000      813.454985     1430.634627      496.000000     1753.000000
+test/data/test2-0001.roi TiltRect      813.846527     1402.603829      516.867507     1743.925617      181.803661     1452.391540      478.782681     1111.069752

diff --git a/mrc2png/test2.byte b/mrc2png/test2.byte
new file mode 100644 (file)
index 0000000..da3970b
Binary files /dev/null and b/mrc2png/test2.byte differ

diff --git a/mrc2png/test2.byte.png b/mrc2png/test2.byte.png
new file mode 100644 (file)
index 0000000..f3f8312
Binary files /dev/null and b/mrc2png/test2.byte.png differ

diff --git a/mrc2png/test2.mrc b/mrc2png/test2.mrc
new file mode 100644 (file)
index 0000000..458a08b
Binary files /dev/null and b/mrc2png/test2.mrc differ

diff --git a/mrc2png/test2.shrink b/mrc2png/test2.shrink
new file mode 100644 (file)
index 0000000..8b13216
Binary files /dev/null and b/mrc2png/test2.shrink differ

diff --git a/mrc2png/test2.shrink.png b/mrc2png/test2.shrink.png
new file mode 100644 (file)
index 0000000..f3f8312
Binary files /dev/null and b/mrc2png/test2.shrink.png differ

diff --git a/mrcFFTCentralSectionCompare/Out.txt b/mrcFFTCentralSectionCompare/Out.txt
new file mode 100755 (executable)
index 0000000..719161b
--- /dev/null
+++ b/mrcFFTCentralSectionCompare/Out.txt
@@ -0,0 +1 @@
+0.159154

diff --git a/mrcFFTCentralSectionCompare/Out2.txt b/mrcFFTCentralSectionCompare/Out2.txt
new file mode 100755 (executable)
index 0000000..e69de29

diff --git a/mrcFFTCentralSectionCompare/Out3.txt b/mrcFFTCentralSectionCompare/Out3.txt
new file mode 100755 (executable)
index 0000000..e69de29

diff --git a/mrcFFTCentralSectionCompare/Out4.txt b/mrcFFTCentralSectionCompare/Out4.txt
new file mode 100755 (executable)
index 0000000..e69de29

diff --git a/mrcFFTCentralSectionCompare/Out5.txt b/mrcFFTCentralSectionCompare/Out5.txt
new file mode 100755 (executable)
index 0000000..e69de29

diff --git a/mrcImageDistanceConversion/121p-move-2d.bin b/mrcImageDistanceConversion/121p-move-2d.bin
new file mode 100644 (file)
index 0000000..40d3f03
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move-2d.bin differ

diff --git a/mrcImageDistanceConversion/121p-move-2d.distance b/mrcImageDistanceConversion/121p-move-2d.distance
new file mode 100644 (file)
index 0000000..c0ac8cc
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move-2d.distance differ

diff --git a/mrcImageDistanceConversion/121p-move-2d.distance4 b/mrcImageDistanceConversion/121p-move-2d.distance4
new file mode 100644 (file)
index 0000000..c0ac8cc
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move-2d.distance4 differ

diff --git a/mrcImageDistanceConversion/121p-move-2d.distance8 b/mrcImageDistanceConversion/121p-move-2d.distance8
new file mode 100644 (file)
index 0000000..4e2db48
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move-2d.distance8 differ

diff --git a/mrcImageDistanceConversion/121p-move-2d.mrc b/mrcImageDistanceConversion/121p-move-2d.mrc
new file mode 100644 (file)
index 0000000..a39a3d0
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move-2d.mrc differ

diff --git a/mrcImageDistanceConversion/121p-move.bin b/mrcImageDistanceConversion/121p-move.bin
new file mode 100644 (file)
index 0000000..b49d3d6
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.bin differ

diff --git a/mrcImageDistanceConversion/121p-move.distance18 b/mrcImageDistanceConversion/121p-move.distance18
new file mode 100644 (file)
index 0000000..128c03c
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.distance18 differ

diff --git a/mrcImageDistanceConversion/121p-move.distance26 b/mrcImageDistanceConversion/121p-move.distance26
new file mode 100644 (file)
index 0000000..128c03c
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.distance26 differ

diff --git a/mrcImageDistanceConversion/121p-move.distance4 b/mrcImageDistanceConversion/121p-move.distance4
new file mode 100644 (file)
index 0000000..6c14e89
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.distance4 differ

diff --git a/mrcImageDistanceConversion/121p-move.distance6 b/mrcImageDistanceConversion/121p-move.distance6
new file mode 100644 (file)
index 0000000..128c03c
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.distance6 differ

diff --git a/mrcImageDistanceConversion/121p-move.distance8 b/mrcImageDistanceConversion/121p-move.distance8
new file mode 100644 (file)
index 0000000..e39b8bb
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.distance8 differ

diff --git a/mrcImageDistanceConversion/121p-move.mrc b/mrcImageDistanceConversion/121p-move.mrc
new file mode 100644 (file)
index 0000000..73d8447
Binary files /dev/null and b/mrcImageDistanceConversion/121p-move.mrc differ

diff --git a/mrcImageFeatureCalc/test.info b/mrcImageFeatureCalc/test.info
index d4767a5..55a6278 100644 (file)
--- a/mrcImageFeatureCalc/test.info
+++ b/mrcImageFeatureCalc/test.info
@@ -1,4 +1,4 @@
-    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity     diameter
+    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity       radius
 000000    34.4354    34.4132    47.8910  428697.0000      0      0      0     0.0000   10000.0000   10000.0000   10000.0000
 000001    46.7244    21.8306    52.1859   21705.0000     40      9      0  9337.0000       0.0655    1727.8359      17.3044
 000002    20.2446    18.4345     5.6273     695.0000     20     18      0   475.0000       0.5097     221.8765       5.4950

diff --git a/mrcImageFeatureCalc/test.info18 b/mrcImageFeatureCalc/test.info18
index 6dc2a22..33de370 100644 (file)
--- a/mrcImageFeatureCalc/test.info18
+++ b/mrcImageFeatureCalc/test.info18
@@ -1,4 +1,4 @@
-    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity     diameter
+    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity       radius
 000000    34.4354    34.4132    47.8910  428697.0000      0      0      0     0.0000   10000.0000   10000.0000   10000.0000
 000001    46.7237    21.8319    52.1874   21707.0000     40      9      0  9314.0000       0.0660    1714.7827      17.3050
 000002    20.2446    18.4345     5.6273     695.0000     20     18      0   472.0000       0.5195     217.6990       5.4950

diff --git a/mrcImageFeatureCalc/test.info26 b/mrcImageFeatureCalc/test.info26
index a1d0b25..28c9098 100644 (file)
--- a/mrcImageFeatureCalc/test.info26
+++ b/mrcImageFeatureCalc/test.info26
@@ -1,4 +1,4 @@
-    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity     diameter
+    id        gcx        gcy        gcz         area startx starty startz   surfArea  circularity   complexity       radius
 000000    34.4354    34.4132    47.8910  428697.0000      0      0      0     0.0000   10000.0000   10000.0000   10000.0000
 000001    46.7237    21.8319    52.1874   21707.0000     40      9      0  6002.0000       0.2465     458.8686      17.3050
 000002    20.2446    18.4345     5.6273     695.0000     20     18      0   333.0000       1.4794      76.4475       5.4950

diff --git a/mrcImageFeatureCalc/test2D.info b/mrcImageFeatureCalc/test2D.info
index e21bd88..65bb700 100644 (file)
--- a/mrcImageFeatureCalc/test2D.info
+++ b/mrcImageFeatureCalc/test2D.info
@@ -1,4 +1,4 @@
-    id        gcx        gcy        gcz         area startx starty startz  perimeter  circularity   complexity     diameter
+    id        gcx        gcy        gcz         area startx starty startz  perimeter  circularity   complexity       radius
 000000    33.9348    34.7792     0.0000    4338.0000      0      0      0    -1.0000   10000.0000   10000.0000   10000.0000
 000001    48.8459    20.7803     0.0000     305.0000     46     13      0    75.0000       0.6814      18.4426       9.8531
 000002    28.5500    24.7000     0.0000      20.0000     27     21      0    23.0000       0.4751      26.4500       2.5231

diff --git a/mrcImageFeatureCalc/test2D.info8 b/mrcImageFeatureCalc/test2D.info8
index 2118343..eb03dbe 100644 (file)
--- a/mrcImageFeatureCalc/test2D.info8
+++ b/mrcImageFeatureCalc/test2D.info8
@@ -1,4 +1,4 @@
-    id        gcx        gcy        gcz         area startx starty startz  perimeter  circularity   complexity     diameter
+    id        gcx        gcy        gcz         area startx starty startz  perimeter  circularity   complexity       radius
 000000    33.9348    34.7792     0.0000    4338.0000      0      0      0    -1.0000   10000.0000   10000.0000   10000.0000
 000001    48.8459    20.7803     0.0000     305.0000     46     13      0    65.0416       0.9060      13.8702       9.8531
 000002    26.2821    24.8718     0.0000      39.0000     27     21      0    39.2132       0.3187      39.4276       3.5234

diff --git a/mrcImageHoleFilling/test2.NoHole4 b/mrcImageHoleFilling/test2.NoHole4
new file mode 100644 (file)
index 0000000..371af36
Binary files /dev/null and b/mrcImageHoleFilling/test2.NoHole4 differ

diff --git a/mrcImageHoleFilling/test2.NoHole4.png b/mrcImageHoleFilling/test2.NoHole4.png
new file mode 100644 (file)
index 0000000..e69de29

diff --git a/mrcImageHoleFilling/test2.NoHole8 b/mrcImageHoleFilling/test2.NoHole8
new file mode 100644 (file)
index 0000000..1279993
Binary files /dev/null and b/mrcImageHoleFilling/test2.NoHole8 differ

diff --git a/mrcImageHoleFilling/test2.area4 b/mrcImageHoleFilling/test2.area4
new file mode 100644 (file)
index 0000000..3329dd1
Binary files /dev/null and b/mrcImageHoleFilling/test2.area4 differ

diff --git a/mrcImageHoleFilling/test2.area8 b/mrcImageHoleFilling/test2.area8
new file mode 100644 (file)
index 0000000..9da6d1a
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diff --git a/mrcImageHoleFilling/test2.bin b/mrcImageHoleFilling/test2.bin
new file mode 100644 (file)
index 0000000..a062d13
Binary files /dev/null and b/mrcImageHoleFilling/test2.bin differ

diff --git a/mrcImageHoleFilling/test2.bin.gif b/mrcImageHoleFilling/test2.bin.gif
new file mode 100644 (file)
index 0000000..a298f11
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diff --git a/mrcImageHoleFilling/test2.black4 b/mrcImageHoleFilling/test2.black4
new file mode 100644 (file)
index 0000000..d08b74e
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diff --git a/mrcImageHoleFilling/test2.black8 b/mrcImageHoleFilling/test2.black8
new file mode 100644 (file)
index 0000000..d08b74e
Binary files /dev/null and b/mrcImageHoleFilling/test2.black8 differ

diff --git a/mrcImageHoleFilling/test2.label4 b/mrcImageHoleFilling/test2.label4
new file mode 100644 (file)
index 0000000..18727f1
Binary files /dev/null and b/mrcImageHoleFilling/test2.label4 differ

diff --git a/mrcImageHoleFilling/test2.label8 b/mrcImageHoleFilling/test2.label8
new file mode 100644 (file)
index 0000000..e04af2d
Binary files /dev/null and b/mrcImageHoleFilling/test2.label8 differ

diff --git a/mrcImageHoleFilling/test2.mrc b/mrcImageHoleFilling/test2.mrc
new file mode 100644 (file)
index 0000000..458a08b
Binary files /dev/null and b/mrcImageHoleFilling/test2.mrc differ

diff --git a/mrcImageHoleFilling/test2.nohole.4.gif b/mrcImageHoleFilling/test2.nohole.4.gif
new file mode 100644 (file)
index 0000000..f18b5ea
Binary files /dev/null and b/mrcImageHoleFilling/test2.nohole.4.gif differ

diff --git a/mrcImageHoleFilling/test2.nohole.8.gif b/mrcImageHoleFilling/test2.nohole.8.gif
new file mode 100644 (file)
index 0000000..8b74a5a
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diff --git a/mrcImageHoleFilling/test2.open b/mrcImageHoleFilling/test2.open
new file mode 100644 (file)
index 0000000..88944ec
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diff --git a/mrcImageHoleFilling/test2.tst b/mrcImageHoleFilling/test2.tst
new file mode 120000 (symlink)
index 0000000..0c59d44
--- /dev/null
+++ b/mrcImageHoleFilling/test2.tst
@@ -0,0 +1 @@
+test2.open
\ No newline at end of file

diff --git a/mrcImageHoleFilling/test3.NoHole6 b/mrcImageHoleFilling/test3.NoHole6
new file mode 100644 (file)
index 0000000..cefa9f0
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diff --git a/mrcImageHoleFilling/test3.area6 b/mrcImageHoleFilling/test3.area6
new file mode 100644 (file)
index 0000000..30f83fd
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diff --git a/mrcImageHoleFilling/test3.bin b/mrcImageHoleFilling/test3.bin
new file mode 100644 (file)
index 0000000..4db3c76
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diff --git a/mrcImageHoleFilling/test3.black6 b/mrcImageHoleFilling/test3.black6
new file mode 100644 (file)
index 0000000..7d7d50b
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diff --git a/mrcImageHoleFilling/test3.label6 b/mrcImageHoleFilling/test3.label6
new file mode 100644 (file)
index 0000000..93cd297
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diff --git a/mrcImageHoleFilling/test3.mrc b/mrcImageHoleFilling/test3.mrc
new file mode 100644 (file)
index 0000000..889158b
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diff --git a/mrcImageHoleFilling/test3.tst b/mrcImageHoleFilling/test3.tst
new file mode 120000 (symlink)
index 0000000..4d32c92
--- /dev/null
+++ b/mrcImageHoleFilling/test3.tst
@@ -0,0 +1 @@
+test3.bin
\ No newline at end of file

diff --git a/mrcImageMeanFreePathCalc/test.black.all b/mrcImageMeanFreePathCalc/test.black.all
new file mode 100644 (file)
index 0000000..9efb5cd
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diff --git a/mrcImageMeanFreePathCalc/test.black.any b/mrcImageMeanFreePathCalc/test.black.any
new file mode 100644 (file)
index 0000000..f2a14bc
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diff --git a/mrcImageMeanFreePathCalc/test.blackEdge.any b/mrcImageMeanFreePathCalc/test.blackEdge.any
new file mode 100644 (file)
index 0000000..985acd3
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diff --git a/mrcImageMeanFreePathCalc/test.mfp.any b/mrcImageMeanFreePathCalc/test.mfp.any
new file mode 100644 (file)
index 0000000..87a856b
--- /dev/null
+++ b/mrcImageMeanFreePathCalc/test.mfp.any
@@ -0,0 +1,94 @@
+ANALYSIS Average HowManyLines HowManyVoxels
+White:        0.000000 3222 0
+Black:      125.000000 21 1
+WhiteEdge:        0.000000 0 0
+BlackEdge:        0.000000 95060 0
+
+DATA: 
+length      White      Black  WhiteEdge  BlackEdge       rateWhite       rateBlack   rateWhiteEdge   rateBlackEdge        aveWhite        aveBlack    aveWhiteEdge    aveBlackEdge      realLength
+     1          0          6          0          0        0.000000      600.000000        0.000000        0.000000        0.000000       28.571429        0.000000        0.000000        2.000000
+     2          0          6          0          0        0.000000      600.000000        0.000000        0.000000        0.000000       28.571429        0.000000        0.000000        4.000000
+     3          0          7          0          0        0.000000      700.000000        0.000000        0.000000        0.000000       33.333333        0.000000        0.000000        6.000000
+     4          0          2          0          0        0.000000      200.000000        0.000000        0.000000        0.000000        9.523810        0.000000        0.000000        8.000000
+     5          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       10.000000
+     6          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       12.000000
+     7          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       14.000000
+     8          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       16.000000
+     9          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       18.000000
+    10          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       20.000000
+    11          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       22.000000
+    12          4          0          0          0        0.000000        0.000000        0.000000        0.000000        0.124146        0.000000        0.000000        0.000000       24.000000
+    13         66          0          0          0        0.000000        0.000000        0.000000        0.000000        2.048417        0.000000        0.000000        0.000000       26.000000
+    14        143          0          0          0        0.000000        0.000000        0.000000        0.000000        4.438237        0.000000        0.000000        0.000000       28.000000
+    15        271          0          0          0        0.000000        0.000000        0.000000        0.000000        8.410925        0.000000        0.000000        0.000000       30.000000
+    16        425          0          0          0        0.000000        0.000000        0.000000        0.000000       13.190565        0.000000        0.000000        0.000000       32.000000
+    17        619          0          0          1        0.000000        0.000000        0.000000        0.000000       19.211670        0.000000        0.000000        0.001052       34.000000
+    18        499          0          0          0        0.000000        0.000000        0.000000        0.000000       15.487275        0.000000        0.000000        0.000000       36.000000
+    19        606          0          0          0        0.000000        0.000000        0.000000        0.000000       18.808194        0.000000        0.000000        0.000000       38.000000
+    20        362          0          0          0        0.000000        0.000000        0.000000        0.000000       11.235258        0.000000        0.000000        0.000000       40.000000
+    21        201          0          0          0        0.000000        0.000000        0.000000        0.000000        6.238361        0.000000        0.000000        0.000000       42.000000
+    22         26          0          0          0        0.000000        0.000000        0.000000        0.000000        0.806952        0.000000        0.000000        0.000000       44.000000
+    23          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       46.000000
+    24          0          0          0          1        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.001052       48.000000
+    25          0          0          0          1        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.001052       50.000000
+    26          0          0          0          1        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.001052       52.000000
+    27          0          0          0          1        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.001052       54.000000
+    28          0          0          0          2        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.002104       56.000000
+    29          0          0          0          2        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.002104       58.000000
+    30          0          0          0          4        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.004208       60.000000
+    31          0          0          0         12        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.012624       62.000000
+    32          0          0          0         20        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.021039       64.000000
+    33          0          0          0         48        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.050494       66.000000
+    34          0          0          0         47        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.049442       68.000000
+    35          0          0          0        203        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.213549       70.000000
+    36          0          0          0        283        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.297707       72.000000
+    37          0          0          0        239        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.251420       74.000000
+    38          0          0          0        381        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.400799       76.000000
+    39          0          0          0        453        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.476541       78.000000
+    40          0          0          0        389        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.409215       80.000000
+    41          0          0          0        432        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.454450       82.000000
+    42          0          0          0        696        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.732169       84.000000
+    43          0          0          0       1247        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.311803       86.000000
+    44          0          0          0       1008        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.060383       88.000000
+    45          0          0          0       1921        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.020829       90.000000
+    46          0          0          0        994        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.045655       92.000000
+    47          0          0          0       2282        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.400589       94.000000
+    48          0          0          0       3501        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.682937       96.000000
+    49          0          0          0       2874        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.023354       98.000000
+    50          0          0          0       2535        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.666737      100.000000
+    51          0          0          0       3425        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.602988      102.000000
+    52          0          0          0       4097        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.309910      104.000000
+    53          0          0          0       3653        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.842836      106.000000
+    54          0          0          0       4699        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.943194      108.000000
+    55          0          0          0       3693        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.884915      110.000000
+    56          0          0          0       4185        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.402483      112.000000
+    57          0          0          0       4370        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.597097      114.000000
+    58          0          0          0       4608        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.847465      116.000000
+    59          0          0          0       4303        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.526615      118.000000
+    60          0          0          0       4682        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.925310      120.000000
+    61          0          0          0       3832        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.031138      122.000000
+    62          0          0          0       4907        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        5.162003      124.000000
+    63          0          0          0       3726        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.919630      126.000000
+    64          0          0          0       3016        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.172733      128.000000
+    65          0          0          0       3703        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        3.895434      130.000000
+    66          0          0          0       3905        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.107932      132.000000
+    67          0          0          0       2675        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.814012      134.000000
+    68          0          0          0       2596        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.730907      136.000000
+    69          0          0          0       1342        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.411740      138.000000
+    70          0          0          0        973        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.023564      140.000000
+    71          0          0          0        958        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.007785      142.000000
+    72          0          0          0       1063        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.118241      144.000000
+    73          0          0          0        958        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        1.007785      146.000000
+    74          0          0          0         87        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.091521      148.000000
+    75          0          0          0         26        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.027351      150.000000
+    76          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      152.000000
+    77          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      154.000000
+    78          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      156.000000
+    79          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      158.000000
+    80          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      160.000000
+    81          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      162.000000
+    82          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      164.000000
+    83          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      166.000000
+    84          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      168.000000
+    85          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      170.000000
+    86          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      172.000000

diff --git a/mrcImageMeanFreePathCalc/test.mfp.x b/mrcImageMeanFreePathCalc/test.mfp.x
index ac26ae6..8301e42 100644 (file)
--- a/mrcImageMeanFreePathCalc/test.mfp.x
+++ b/mrcImageMeanFreePathCalc/test.mfp.x
@@ -1,46 +1,46 @@
 ANALYSIS Average HowManyLines HowManyVoxels
-White:       12.170701 387 3222
-Black:        0.042106 65 8526
-WhiteEdge:        0.000000 0 0
-BlackEdge:       62.878980 1858 86556
+White:        0.000000 2 3222
+Black:        0.000000 0 95082
+WhiteEdge:        0.000000 16 0
+BlackEdge:        0.000000 0 0
 
 DATA: 
 length      White      Black  WhiteEdge  BlackEdge       rateWhite       rateBlack   rateWhiteEdge   rateBlackEdge        aveWhite        aveBlack    aveWhiteEdge    aveBlackEdge      realLength
-     1         33         35          0          0        1.024209        0.410509        0.000000        0.000000        8.527132       53.846154        0.000000        0.000000        2.000000
-     2         44         12          0          0        1.365611        0.140746        0.000000        0.000000       11.369509       18.461538        0.000000        0.000000        4.000000
-     3         30          9          0          0        0.931099        0.105559        0.000000        0.000000        7.751938       13.846154        0.000000        0.000000        6.000000
-     4         24          6          0          0        0.744879        0.070373        0.000000        0.000000        6.201550        9.230769        0.000000        0.000000        8.000000
-     5         28          2          0          0        0.869025        0.023458        0.000000        0.000000        7.235142        3.076923        0.000000        0.000000       10.000000
-     6         10          0          0          0        0.310366        0.000000        0.000000        0.000000        2.583979        0.000000        0.000000        0.000000       12.000000
-     7         29          1          0          0        0.900062        0.011729        0.000000        0.000000        7.493540        1.538462        0.000000        0.000000       14.000000
-     8         19          0          0          0        0.589696        0.000000        0.000000        0.000000        4.909561        0.000000        0.000000        0.000000       16.000000
-     9         19          0          0          0        0.589696        0.000000        0.000000        0.000000        4.909561        0.000000        0.000000        0.000000       18.000000
-    10         14          0          0          0        0.434513        0.000000        0.000000        0.000000        3.617571        0.000000        0.000000        0.000000       20.000000
-    11         21          0          0          0        0.651769        0.000000        0.000000        0.000000        5.426357        0.000000        0.000000        0.000000       22.000000
-    12         16          0          0          0        0.496586        0.000000        0.000000        0.000000        4.134367        0.000000        0.000000        0.000000       24.000000
-    13         11          0          0          0        0.341403        0.000000        0.000000        0.000000        2.842377        0.000000        0.000000        0.000000       26.000000
-    14         13          0          0          0        0.403476        0.000000        0.000000        0.000000        3.359173        0.000000        0.000000        0.000000       28.000000
-    15         16          0          0          0        0.496586        0.000000        0.000000        0.000000        4.134367        0.000000        0.000000        0.000000       30.000000
-    16         15          0          0          0        0.465549        0.000000        0.000000        0.000000        3.875969        0.000000        0.000000        0.000000       32.000000
-    17         14          0          0          0        0.434513        0.000000        0.000000        0.000000        3.617571        0.000000        0.000000        0.000000       34.000000
-    18         10          0          0          0        0.310366        0.000000        0.000000        0.000000        2.583979        0.000000        0.000000        0.000000       36.000000
-    19         17          0          0          0        0.527623        0.000000        0.000000        0.000000        4.392765        0.000000        0.000000        0.000000       38.000000
-    20          4          0          0          1        0.124146        0.000000        0.000000        0.001155        1.033592        0.000000        0.000000        0.053821       40.000000
-    21          0          0          0         14        0.000000        0.000000        0.000000        0.016174        0.000000        0.000000        0.000000        0.753498       42.000000
-    22          0          0          0         47        0.000000        0.000000        0.000000        0.054300        0.000000        0.000000        0.000000        2.529602       44.000000
-    23          0          0          0         54        0.000000        0.000000        0.000000        0.062387        0.000000        0.000000        0.000000        2.906351       46.000000
-    24          0          0          0         63        0.000000        0.000000        0.000000        0.072785        0.000000        0.000000        0.000000        3.390743       48.000000
-    25          0          0          0         60        0.000000        0.000000        0.000000        0.069319        0.000000        0.000000        0.000000        3.229279       50.000000
-    26          0          0          0         94        0.000000        0.000000        0.000000        0.108600        0.000000        0.000000        0.000000        5.059203       52.000000
-    27          0          0          0         75        0.000000        0.000000        0.000000        0.086649        0.000000        0.000000        0.000000        4.036598       54.000000
-    28          0          0          0         65        0.000000        0.000000        0.000000        0.075096        0.000000        0.000000        0.000000        3.498385       56.000000
-    29          0          0          0         38        0.000000        0.000000        0.000000        0.043902        0.000000        0.000000        0.000000        2.045210       58.000000
-    30          0          0          0         28        0.000000        0.000000        0.000000        0.032349        0.000000        0.000000        0.000000        1.506997       60.000000
-    31          0          0          0         32        0.000000        0.000000        0.000000        0.036970        0.000000        0.000000        0.000000        1.722282       62.000000
-    32          0          0          0         24        0.000000        0.000000        0.000000        0.027728        0.000000        0.000000        0.000000        1.291712       64.000000
-    33          0          0          0         12        0.000000        0.000000        0.000000        0.013864        0.000000        0.000000        0.000000        0.645856       66.000000
-    34          0          0          0         25        0.000000        0.000000        0.000000        0.028883        0.000000        0.000000        0.000000        1.345533       68.000000
-    35          0          0          0         12        0.000000        0.000000        0.000000        0.013864        0.000000        0.000000        0.000000        0.645856       70.000000
+     1          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        2.000000
+     2          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        4.000000
+     3          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        6.000000
+     4          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        8.000000
+     5          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       10.000000
+     6          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       12.000000
+     7          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       14.000000
+     8          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       16.000000
+     9          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       18.000000
+    10          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       20.000000
+    11          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       22.000000
+    12          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       24.000000
+    13          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       26.000000
+    14          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       28.000000
+    15          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       30.000000
+    16          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       32.000000
+    17          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       34.000000
+    18          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       36.000000
+    19          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       38.000000
+    20          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       40.000000
+    21          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       42.000000
+    22          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       44.000000
+    23          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       46.000000
+    24          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       48.000000
+    25          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       50.000000
+    26          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       52.000000
+    27          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       54.000000
+    28          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       56.000000
+    29          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       58.000000
+    30          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       60.000000
+    31          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       62.000000
+    32          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       64.000000
+    33          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       66.000000
+    34          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       68.000000
+    35          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       70.000000
     36          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       72.000000
     37          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       74.000000
     38          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000       76.000000
@@ -69,4 +69,26 @@ length      White      Black  WhiteEdge  BlackEdge       rateWhite       rateBla
     61          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      122.000000
     62          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      124.000000
     63          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      126.000000
-    64          0          0          0       1214        0.000000        0.000000        0.000000        1.402560        0.000000        0.000000        0.000000       65.339074      128.000000
+    64          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      128.000000
+    65          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      130.000000
+    66          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      132.000000
+    67          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      134.000000
+    68          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      136.000000
+    69          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      138.000000
+    70          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      140.000000
+    71          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      142.000000
+    72          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      144.000000
+    73          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      146.000000
+    74          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      148.000000
+    75          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      150.000000
+    76          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      152.000000
+    77          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      154.000000
+    78          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      156.000000
+    79          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      158.000000
+    80          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      160.000000
+    81          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      162.000000
+    82          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      164.000000
+    83          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      166.000000
+    84          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      168.000000
+    85          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      170.000000
+    86          0          0          0          0        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000        0.000000      172.000000

diff --git a/mrcImageMeanFreePathCalc/test.mode3.dir.0 b/mrcImageMeanFreePathCalc/test.mode3.dir.0
new file mode 100644 (file)
index 0000000..1639819
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.mode3.dir.0 differ

diff --git a/mrcImageMeanFreePathCalc/test.mode3.dir.1 b/mrcImageMeanFreePathCalc/test.mode3.dir.1
new file mode 100644 (file)
index 0000000..048ba6f
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.mode3.dir.1 differ

diff --git a/mrcImageMeanFreePathCalc/test.mode3.dir.2 b/mrcImageMeanFreePathCalc/test.mode3.dir.2
new file mode 100644 (file)
index 0000000..1297055
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.mode3.dir.2 differ

diff --git a/mrcImageMeanFreePathCalc/test.white.all b/mrcImageMeanFreePathCalc/test.white.all
new file mode 100644 (file)
index 0000000..4dba527
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.white.all differ

diff --git a/mrcImageMeanFreePathCalc/test.white.any b/mrcImageMeanFreePathCalc/test.white.any
new file mode 100644 (file)
index 0000000..4dba527
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.white.any differ

diff --git a/mrcImageMeanFreePathCalc/test.whiteEdge.any b/mrcImageMeanFreePathCalc/test.whiteEdge.any
new file mode 100644 (file)
index 0000000..c24d923
Binary files /dev/null and b/mrcImageMeanFreePathCalc/test.whiteEdge.any differ

diff --git a/mrcImageROIs/test-0000.roi b/mrcImageROIs/test-0000.roi
index ab0331a..ede72e6 100755 (executable)
Binary files a/mrcImageROIs/test-0000.roi and b/mrcImageROIs/test-0000.roi differ

diff --git a/mrcImageROIs/test-0001.roi b/mrcImageROIs/test-0001.roi
index a09c1b9..edd3772 100755 (executable)
Binary files a/mrcImageROIs/test-0001.roi and b/mrcImageROIs/test-0001.roi differ

diff --git a/mrcImageROIs/test-0002.roi b/mrcImageROIs/test-0002.roi
index d6daeb8..a21ae1c 100755 (executable)
Binary files a/mrcImageROIs/test-0002.roi and b/mrcImageROIs/test-0002.roi differ

diff --git a/mrcImageROIs/test-0003.roi b/mrcImageROIs/test-0003.roi
index b0fd334..d3a495e 100755 (executable)
Binary files a/mrcImageROIs/test-0003.roi and b/mrcImageROIs/test-0003.roi differ

diff --git a/mrcImageROIs/test-0004.roi b/mrcImageROIs/test-0004.roi
index d5c3fc4..ccf3b51 100755 (executable)
Binary files a/mrcImageROIs/test-0004.roi and b/mrcImageROIs/test-0004.roi differ

diff --git a/mrcImageROIs/test-0005.roi b/mrcImageROIs/test-0005.roi
index 4c06f19..3093c1e 100755 (executable)
Binary files a/mrcImageROIs/test-0005.roi and b/mrcImageROIs/test-0005.roi differ

diff --git a/mrcImageROIs/test-0006.roi b/mrcImageROIs/test-0006.roi
index b645fea..ab503f0 100755 (executable)
Binary files a/mrcImageROIs/test-0006.roi and b/mrcImageROIs/test-0006.roi differ

diff --git a/mrcImageROIs/test-0007.roi b/mrcImageROIs/test-0007.roi
index 271a5eb..ab503f0 100755 (executable)
Binary files a/mrcImageROIs/test-0007.roi and b/mrcImageROIs/test-0007.roi differ

diff --git a/mrcImageROIs/test-0008.roi b/mrcImageROIs/test-0008.roi
index f447643..596c8b3 100755 (executable)
Binary files a/mrcImageROIs/test-0008.roi and b/mrcImageROIs/test-0008.roi differ

diff --git a/mrcImageROIs/test-0009.roi b/mrcImageROIs/test-0009.roi
index 8a412ef..fe083b2 100755 (executable)
Binary files a/mrcImageROIs/test-0009.roi and b/mrcImageROIs/test-0009.roi differ

diff --git a/mrcImageROIs/test.roiinfo b/mrcImageROIs/test.roiinfo
index 452e5d6..84b7abb 100755 (executable)
--- a/mrcImageROIs/test.roiinfo
+++ b/mrcImageROIs/test.roiinfo
@@ -1,7 +1,10 @@
-test-0000.roi Rect      247.000000      256.000000      287.000000      256.000000      287.000000      296.000000      247.000000      296.000000
-test-0001.roi Rect      292.000000      215.000000      332.000000      215.000000      332.000000      255.000000      292.000000      255.000000
-test-0002.roi Rect      211.000000      199.000000      251.000000      199.000000      251.000000      239.000000      211.000000      239.000000
-test-0003.roi Rect      196.000000      265.000000      236.000000      265.000000      236.000000      305.000000      196.000000      305.000000
-test-0004.roi Rect      256.000000      315.000000      296.000000      315.000000      296.000000      355.000000      256.000000      355.000000
-test-0005.roi Rect      293.000000      265.000000      333.000000      265.000000      333.000000      305.000000      293.000000      305.000000
-test-0006.roi Rect      267.000000      171.000000      307.000000      171.000000      307.000000      211.000000      267.000000      211.000000
+data/test-0000.roi Rect      247.000000      256.000000      287.000000      256.000000      287.000000      296.000000      247.000000      296.000000
+data/test-0001.roi Rect      292.000000      215.000000      332.000000      215.000000      332.000000      255.000000      292.000000      255.000000
+data/test-0002.roi Rect      211.000000      199.000000      251.000000      199.000000      251.000000      239.000000      211.000000      239.000000
+data/test-0003.roi Rect      196.000000      265.000000      236.000000      265.000000      236.000000      305.000000      196.000000      305.000000
+data/test-0004.roi Rect      256.000000      315.000000      296.000000      315.000000      296.000000      355.000000      256.000000      355.000000
+data/test-0005.roi Rect      293.000000      265.000000      333.000000      265.000000      333.000000      305.000000      293.000000      305.000000
+data/test-0006.roi Rect      267.000000      171.000000      307.000000      171.000000      307.000000      211.000000      267.000000      211.000000
+data/test-0007.roi TiltRect      267.000000      171.000000      307.000000      171.000000      307.000000      211.000000      267.000000      211.000000
+data/test-0008.roi Rect      214.147322      219.353475      249.793846      237.500797      231.646525      273.147322      196.000000      255.000000
+data/test-0009.roi TiltRect      214.147322      219.353475      249.793846      237.500797      231.646525      273.147322      196.000000      255.000000

diff --git a/mrcImageShapePCA/121p-move-2d.mrc b/mrcImageShapePCA/121p-move-2d.mrc
new file mode 100644 (file)
index 0000000..a39a3d0
Binary files /dev/null and b/mrcImageShapePCA/121p-move-2d.mrc differ

diff --git a/mrcImageShapePCA/121p-move-2d.mrc.PCA b/mrcImageShapePCA/121p-move-2d.mrc.PCA
new file mode 100644 (file)
index 0000000..f4bf3dd
--- /dev/null
+++ b/mrcImageShapePCA/121p-move-2d.mrc.PCA
@@ -0,0 +1,17 @@
+# PCA ResultsConvariace Matrix: 2 2 2 
+     146.418610       12.581398 
+      12.581398      146.418610 
+UnitVector: one unit vector per line, from 1st 2 2 2 
+       0.707107        0.707107 
+       0.707107       -0.707107 
+Lambda: 1st 2nd 1 2 
+     159.000000      133.837219 
+Average: 1 2 
+       8.116279        7.883721 
+Normalized Lambda: 1st 2nd 
+       0.542964        0.457036 
+Wcircle:       62.476421
+exp(S-1)(SphereIndex):        3.781270
+Log(SphereIndex(var)):        2.131735
+CircleIndex(0.5):      270.872725
+Log(CircleIndex(0.5)):        2.432765

diff --git a/mrcImageShapePCA/121p-move.mrc.PCA b/mrcImageShapePCA/121p-move.mrc.PCA
index 994ec02..83f2742 100644 (file)
--- a/mrcImageShapePCA/121p-move.mrc.PCA
+++ b/mrcImageShapePCA/121p-move.mrc.PCA
@@ -1,33 +1,36 @@
 # PCA ResultsConvariace Matrix: 2 3 3 
-    8100.993164     -519.232056     1449.454224 
-    -519.232056     7861.341797     -299.008453 
-    1449.454224     -299.008453     7811.953125 
+     614.608704       37.173916       67.869568 
+      37.173916      641.922668      -17.942032 
+      67.869568      -17.942032      644.956543 
 UnitVector: one unit vector per line, from 1st 2 3 3 
-       0.711418       -0.318402        0.626502 
-       0.167661        0.942631        0.288679 
-      -0.682477       -0.100331        0.723988 
+       0.655229        0.189858        0.731183 
+       0.171939        0.905019       -0.389073 
+       0.735603       -0.380651       -0.560351 
 Lambda: 1st 2nd 3rd1 3 
-    9609.826172     7677.417480     6487.043457 
+     701.117126      656.698486      543.672302 
 Average: 1 3 
-       8.095640        8.156118        8.121659 
+       8.043478        7.980676        8.014493 
 Normalized Lambda: 1st 2nd 3rd
-       0.404211        0.322929        0.272860 
-logS(SphereIndex):       -0.482885
-exp(S-1)(SphereIndex):        0.130018
-SphereIndex(var):       37.926460
-Log(SphereIndex(var)):        1.578942
-SphereIndex(var):       37.926460
-SphereIndex(0.33):      113.779380
-Log(SphereIndex(0.33)):        2.056064
-DiskIndex:        1.753223
-logD(DiskIndex):        0.243837
-DiskIndex(var):       12.336684
-Log(DiskIndex(var)):        1.091198
-DiskIndex(0.5):        8.697020
-Log(DiskIndex(0.5)):        0.939370
-CylinderIndex:        1.854253
-logC(CylinderIndex):        0.268169
-CylinderIndex(var) :        2.797425
-Log(CylinderIndex(var) :        0.446758
-CylinderIndex(1.0) :        1.873710
-Log(CylinderIndex(1.0)) :        0.272702
+       0.368720        0.345360        0.285919 
+Wsphere:       15.307695
+logS(SphereIndex):       -0.479502
+exp(S-1)(SphereIndex):        0.133122
+SphereIndex(var):       91.450388
+Log(SphereIndex(var)):        1.961186
+SphereIndex(var):       91.450388
+SphereIndex(0.33):      274.351163
+Log(SphereIndex(0.33)):        2.438307
+Wdisk:       19.495208
+DiskIndex:        1.557694
+logD(DiskIndex):        0.192482
+DiskIndex(var):       12.151319
+Log(DiskIndex(var)):        1.084623
+DiskIndex(0.5):        8.136848
+Log(DiskIndex(0.5)):        0.910456
+Wsylinder:       16.560672
+CylinderIndex:        1.376822
+logC(CylinderIndex):        0.138878
+CylinderIndex(var) :        2.487269
+Log(CylinderIndex(var) :        0.395723
+CylinderIndex(1.0) :        1.667952
+Log(CylinderIndex(1.0)) :        0.222183

diff --git a/mrcImageShapePCA/myosinSwissModRefine2.mrc.PCA b/mrcImageShapePCA/myosinSwissModRefine2.mrc.PCA
index daba612..d9eb734 100644 (file)
--- a/mrcImageShapePCA/myosinSwissModRefine2.mrc.PCA
+++ b/mrcImageShapePCA/myosinSwissModRefine2.mrc.PCA
@@ -1,33 +1,36 @@
 # PCA ResultsConvariace Matrix: 2 3 3 
-   48729.226562     1435.494995    10131.948242 
-    1435.494995    74729.234375   -21800.205078 
-   10131.948242   -21800.205078   249615.687500 
+    6126.999023      665.260681      394.832642 
+     665.260681    11164.013672    -5388.992676 
+     394.832642    -5388.992676    33041.390625 
 UnitVector: one unit vector per line, from 1st 2 3 3 
-       0.048381       -0.121010        0.991472 
-       0.109420        0.987302        0.115162 
-       0.992817       -0.102915       -0.061008 
+       0.008298       -0.226632        0.973945 
+       0.184778        0.957554        0.221243 
+       0.982745       -0.178127       -0.049823 
 Lambda: 1st 2nd 3rd1 3 
-  252770.843750    72345.484375    47957.824219 
+   34298.742188    10047.258789     5986.400391 
 Average: 1 3 
-      19.844301       19.589994       19.149263 
+      20.001015       19.739351       20.167343 
 Normalized Lambda: 1st 2nd 3rd
-       0.677535        0.193917        0.128548 
-logS(SphereIndex):       -0.613664
-exp(S-1)(SphereIndex):        0.044676
-SphereIndex(var):        1.853408
-Log(SphereIndex(var)):        0.267971
-SphereIndex(var):        1.853408
-SphereIndex(0.33):        5.560223
-Log(SphereIndex(0.33)):        0.745092
-DiskIndex:        7.950958
-logD(DiskIndex):        0.900419
-DiskIndex(var):        3.993437
-Log(DiskIndex(var)):        0.601347
-DiskIndex(0.5):        7.055673
-Log(DiskIndex(0.5)):        0.848538
-CylinderIndex:       18.415481
-logC(CylinderIndex):        1.265183
-CylinderIndex(var) :        9.237298
-Log(CylinderIndex(var) :        0.965545
-CylinderIndex(1.0) :        6.324632
-Log(CylinderIndex(1.0)) :        0.801035
+       0.681445        0.199618        0.118937 
+Wsphere:       27.212617
+logS(SphereIndex):       -0.618308
+exp(S-1)(SphereIndex):        0.042746
+SphereIndex(var):        1.801540
+Log(SphereIndex(var)):        0.255644
+SphereIndex(var):        1.801540
+SphereIndex(0.33):        5.404621
+Log(SphereIndex(0.33)):        0.732765
+Wdisk:       32.501160
+DiskIndex:        9.615996
+logD(DiskIndex):        0.982994
+DiskIndex(var):        4.060043
+Log(DiskIndex(var)):        0.608531
+DiskIndex(0.5):        7.283454
+Log(DiskIndex(0.5)):        0.862337
+Wsylinder:       51.193448
+CylinderIndex:       19.558837
+logC(CylinderIndex):        1.291343
+CylinderIndex(var) :        9.260379
+Log(CylinderIndex(var) :        0.966629
+CylinderIndex(1.0) :        6.432067
+Log(CylinderIndex(1.0)) :        0.808351