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ticket #35034 v2.2.20p0134
authorTakuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Wed, 1 Apr 2015 19:39:17 +0000 (04:39 +0900)
committerTakuo Yasunaga <yasunaga@bio.kyutech.ac.jp>
Wed, 1 Apr 2015 19:39:17 +0000 (04:39 +0900)
Sphere index, Disk index, Cylinder index
Larger values indicate its shape.

src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c patch | blob | history
src/Tools/Config/Define.inc patch | blob | history
src/Tools/Makefile [changed from file to symlink] patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/init.c patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile patch | blob | history
src/Tools/mrcImage/mrcImageShapePCA/src/usage.c patch | blob | history

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c b/src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c
index 9f6b6ba..e70c5ab 100644 (file)
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageShapePCA.c
@@ -66,7 +66,7 @@ lmrcImageShapePCA(mrcImage* in, lmrcImageShapePCAInfo* linfo, int mode)
 int
 lmrcImageShapePCAResultsPrint(FILE* fpt, lmrcImageShapePCAInfo* linfo, int mode)
 {
-       double sum;
+       double sum, sum2;
        double lambda[3];
        int i;
 
@@ -88,18 +88,42 @@ lmrcImageShapePCAResultsPrint(FILE* fpt, lmrcImageShapePCAInfo* linfo, int mode)
        for(i=0; i<3; i++) {
                sum += lambda[i];
        }
+       sum2 = 0;
        for(i=0; i<3; i++) {
                lambda[i] /= sum;
+               sum2 += SQR(lambda[i]);
        }
        for(i=0; i<3; i++) {
        fprintf(fpt, "%15.6f ", lambda[i]);
        }
        fprintf(fpt, "\n");
 
-       fprintf(fpt, "logS(SphereIndex) : %15.6f\n", log10(1/(lambda[0]*lambda[1] + lambda[1]*lambda[2] +lambda[2]*lambda[0] )));
-       fprintf(fpt, "exp(S-1)(SphereIndex) : %15.6f\n", exp(1/(lambda[0]*lambda[1] + lambda[1]*lambda[2] +lambda[2]*lambda[0] )-1));
-       fprintf(fpt, "SphereIndex : %15.6f\n", SQR(lambda[0] - lambda[1])  + SQR(lambda[1]-lambda[2]) + SQR(lambda[2]-lambda[0]));
-       fprintf(fpt, "Log(SphereIndex) : %15.6f\n", log10(SQR(lambda[0] - lambda[1])  + SQR(lambda[1]-lambda[2]) + SQR(lambda[2]-lambda[0])));
+       if(mode&0x1) {
+               fprintf(fpt, "logS(SphereIndex): %15.6f\n", -log10(1/(lambda[0]*lambda[1] + lambda[1]*lambda[2] +lambda[2]*lambda[0] )));
+               fprintf(fpt, "exp(S-1)(SphereIndex): %15.6f\n", 1.0/exp(1/(lambda[0]*lambda[1] + lambda[1]*lambda[2] +lambda[2]*lambda[0] )-1));
+               fprintf(fpt, "SphereIndex(var): %15.6f\n", 1.0/(SQR(lambda[0] - lambda[1])  + SQR(lambda[1]-lambda[2]) + SQR(lambda[2]-lambda[0])));
+               fprintf(fpt, "Log(SphereIndex(var)): %15.6f\n", -log10(SQR(lambda[0] - lambda[1])  + SQR(lambda[1]-lambda[2]) + SQR(lambda[2]-lambda[0])));
+               fprintf(fpt, "SphereIndex(var): %15.6f\n", 1.0/(SQR(lambda[0] - lambda[1])  + SQR(lambda[1]-lambda[2]) + SQR(lambda[2]-lambda[0])));
+               fprintf(fpt, "SphereIndex(0.33): %15.6f\n", 1.0/(SQR(lambda[0] - 1.0/3)  + SQR(lambda[1]-1.0/3) + SQR(lambda[2]-1.0/3)));
+               fprintf(fpt, "Log(SphereIndex(0.33)): %15.6f\n", -log10(SQR(lambda[0] - 1.0/3)  + SQR(lambda[1]-1.0/3) + SQR(lambda[2]-1.0/3)));
+       }
+       if(mode&0x2) {
+               fprintf(fpt, "DiskIndex: %15.6f\n", 1.0/(lambda[2]/lambda[0]*lambda[2]/lambda[1]));
+               fprintf(fpt, "logD(DiskIndex): %15.6f\n", -log10(lambda[2]/lambda[0]*lambda[2]/lambda[1]));
+               fprintf(fpt, "DiskIndex(var): %15.6f\n", 1.0/(SQR(lambda[0]-lambda[1]) + SQR(lambda[2] )));
+               fprintf(fpt, "Log(DiskIndex(var)): %15.6f\n", -log10(SQR(lambda[0]-lambda[1]) + SQR(lambda[2] )));
+               fprintf(fpt, "DiskIndex(0.5): %15.6f\n", 1.0/(SQR(lambda[0]-0.5) + SQR(lambda[1]-0.5) + SQR(lambda[2] )));
+               fprintf(fpt, "Log(DiskIndex(0.5)): %15.6f\n", -log10(SQR(lambda[0]-0.5) + SQR(lambda[1]-0.5) + SQR(lambda[2] )));
+       }
+       if(mode&0x4) {
+               fprintf(fpt, "CylinderIndex: %15.6f\n", 1.0/(lambda[1]/lambda[0]*lambda[2]/lambda[0]));
+               fprintf(fpt, "logC(CylinderIndex): %15.6f\n", -log10(lambda[1]/lambda[0]*lambda[2]/lambda[0]));
+               fprintf(fpt, "CylinderIndex(var) : %15.6f\n", 1.0/(SQR(lambda[0] -1) + SQR(lambda[1] - lambda[2])));
+               fprintf(fpt, "Log(CylinderIndex(var) : %15.6f\n", -log10(SQR(lambda[0] -1) +SQR(lambda[1] - lambda[2])));
+               fprintf(fpt, "CylinderIndex(1.0) : %15.6f\n", 1.0/(SQR(lambda[0] -1) + SQR(lambda[1]) + SQR(lambda[2])));
+               fprintf(fpt, "Log(CylinderIndex(1.0)) : %15.6f\n", -log10(SQR(lambda[0] -1) +SQR(lambda[1]) + SQR(lambda[2])));
+       }
+
 
        return 0;
 }
diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 07ded41..3870150 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -580,3 +580,5 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools
+WORLDNAME=Tools
diff --git a/src/Tools/Makefile b/src/Tools/Makefile
deleted file mode 100755 (executable)
index ad841104b1b4aa83ce554496adb2d2476544f988..0000000000000000000000000000000000000000
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1,5 +0,0 @@
-include ../Config/Define.inc
-include Config/Define.inc
-include .Source
-
-include Config/Target.inc
diff --git a/src/Tools/Makefile b/src/Tools/Makefile
new file mode 120000 (symlink)
index 0000000000000000000000000000000000000000..80a2401a7dc3d8e1cdc121c22208bd28b6887cf3
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1 @@
+/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
index a64a77e..99cf312 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageShapePCA/Config/OptionControlFile
@@ -3,5 +3,5 @@
 "-i","-i[nput]","Input: mrcImage","Essential","1","1","In","inFile::mrcImage","NULL"
 "-o","-o[utput]","Output: ASCII","Optional","1","1","Out","outFile::ASCII","stdout"
 "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
-"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","1"
 "-C","-C[ontour]","Contour","Variable","1","1","Contour","Real","1.0"
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/init.c b/src/Tools/mrcImage/mrcImageShapePCA/src/init.c
index fb4b92b..3e48ebf 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/init.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/init.c
@@ -15,7 +15,7 @@ init0(mrcImageShapePCAInfo* info)
     info->fptIn = NULL;    info->flagIn = 0;
     info->fptOut = stdout;    info->flagOut = 0;
     info->fptconfigFile = NULL;    info->flagconfigFile = 0;
-    info->mode = 0;    info->flagmode = 0;
+    info->mode = 1;    info->flagmode = 0;
     info->Contour = NULL;    info->flagContour = 0;
 }
 
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
index e7415af..cb31d52 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.c
@@ -64,7 +64,11 @@ additionalUsage()
        fprintf(stderr, "           100%% 60%% 40%%\n");
        fprintf(stderr, "----- Objectives -----\n");
        fprintf(stderr, "Determine the orientations/molecular axis by PCA alogrism\n");
-       fprintf(stderr, "  $ mrcImagePCA -i mrc -o parameter -C C1 C2 C3 ...\n");
+       fprintf(stderr, "  $ mrcImageShapePCA -i mrc -o parameter -C C1 C2 C3 ...\n");
+       fprintf(stderr, "-m \n");
+       fprintf(stderr, "  +1: Sphere (default)\n");
+       fprintf(stderr, "  +2: Disk\n");
+       fprintf(stderr, "  +4: Cylinder\n");
        fprintf(stderr, "\n");
 
 }
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
index 3bd6a0e..2384338 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.html
@@ -11,7 +11,7 @@ Options:
     [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage
     [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII
     [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
-    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode
     [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour
 ----- Additional Usage -----
 -C : ContourLevels
@@ -19,7 +19,11 @@ Options:
            100% 60% 40%
 ----- Objectives -----
 Determine the orientations/molecular axis by PCA alogrism
-  $ mrcImagePCA -i mrc -o parameter -C C1 C2 C3 ...
+  $ mrcImageShapePCA -i mrc -o parameter -C C1 C2 C3 ...
+-m 
+  +1: Sphere (default)
+  +2: Disk
+  +4: Cylinder
 
 </PRE>
 </BODY>
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
index 3a3e0e7..f8dc1ca 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/mrcImageShapePCA.pane
@@ -10,7 +10,7 @@
         -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input: mrcImage' i
         -O 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output: ASCII' o
         -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -i 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'mode' 'Mode' m
+        -i 1 0 1 0 0 -1x1+1+6.000000 0 0 1 0 0 'mode' 'Mode' m
         -f 1 0 1 0 0 -1x1+1+7.500000 0 0 1.000000 0 0 0 'Contour' 'Contour' C
     -E
   -E
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile b/src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile
index e212e9e..7cf731a 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/test/Makefile
@@ -11,13 +11,13 @@ help:
 
 exec: exec2
        @echo "----- Execution Check -----"
-       ../$(OSTYPE)/$(OBJECTNAME) -i data/121p-move.mrc -o data/121p-move.mrc.PCA -C 23696.7 
+       ../$(OSTYPE)/$(OBJECTNAME) -i data/121p-move.mrc -o data/121p-move.mrc.PCA -C 23696.7 -m 7
        pdbPCA -i data/121p-move.pdb -o data/121p-move.pdb.PCA
        @echo "----- Calc check -----"          
 
 exec2:
        @echo "----- Execution Check -----"
-       ../$(OSTYPE)/$(OBJECTNAME) -i data/myosinSwissModRefine2.mrc -o data/myosinSwissModRefine2.mrc.PCA -C 3.11319
+       ../$(OSTYPE)/$(OBJECTNAME) -i data/myosinSwissModRefine2.mrc -o data/myosinSwissModRefine2.mrc.PCA -C 3.11319 -m 7
        pdbPCA -i data/myosinSwissModRefine2.pdb -o data/myosinSwissModRefine2.pdb.PCA
        @echo "----- Calc check -----"          
 
diff --git a/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c b/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
index b6a5b59..7b4104c 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageShapePCA/src/usage.c
@@ -10,7 +10,7 @@ usage(char* thisProgram)
     fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input: mrcImage\n");
     fprintf(stderr, "    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output: ASCII\n");
     fprintf(stderr, "    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile\n");
-    fprintf(stderr, "    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode\n");
+    fprintf(stderr, "    [-m[ode]             mode                (1         ).as(Integer             ) ] :Optional  :Mode\n");
     fprintf(stderr, "    [-C[ontour]          Contour             (1.0       ).as(Real                ) ... ] :Variable  :Contour\n");
     additionalUsage();
 }
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