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 Changes to be committed:
	modified:   src/Tools/Config/Define.inc
	modified:   src/Tools/mrcImage/mrcImageOpticalFlow/Config/OptionControlFile
	modified:   src/Tools/mrcImage/mrcImageOpticalFlow/src/init.c
	modified:   src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.html
	modified:   src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.pane
	modified:   src/Tools/mrcImage/mrcImageOpticalFlow/src/usage.c

 Changes not staged for commit:
	modified:   include/eosMATH.h

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 8e67020..9367728 100644 (file)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -9,3 +9,4 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/mrcImage/mrcImageOpticalFlow/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageOpticalFlow/Config/OptionControlFile
index 1068fd8..6d014e4 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpticalFlow/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageOpticalFlow/Config/OptionControlFile
@@ -3,8 +3,8 @@
 "-i1","-i[nput]1","Input","Essential","1","1","In1","inFile::mrcImage","NULL"
 "-i2","-i[nput]2","Input","Essential","1","1","In2","inFile::mrcImage","NULL"
 "-i3","-i[nput]3","Input","Optional","1","1","In3","inFile::mrcImage","NULL"
-"-o","-o[utput]","OutputDataFile","Essential","3","1","Vx","outFile::mrcImage","NULL","2","Vy","outFile::mrcImage","NULL","3","Vz","outFile::mrcImage","NULL"
-"-oF","-o[utput]F","OutputDataFile","Essential","4","1","OutFx","outFile::mrcImage","NULL","2","OutFy","outFile::mrcImage","NULL","3","OutFz","outFile::mrcImage","NULL","4","OutDi","outFile::mrcImage","NULL" 
+"-o","-o[utput]","OutputDataFile","Optional","3","1","Vx","outFile::mrcImage","NULL","2","Vy","outFile::mrcImage","NULL","3","Vz","outFile::mrcImage","NULL"
+"-oF","-o[utput]F","OutputDataFile","Optional","4","1","OutFx","outFile::mrcImage","NULL","2","OutFy","outFile::mrcImage","NULL","3","OutFz","outFile::mrcImage","NULL","4","OutDi","outFile::mrcImage","NULL" 
 "-oSize","-o[utput]Size","Output:Chimera","Optional","1","1","Size","outFile::mrcImage","NULL"
 "-oCOMMAND","-o[utput]COMMAND","Output:Chimera","Optional","1","1","OutCOMMAND","outFile::ASCII","NULL"
 "-oBILD","-o[utput]BILD","Output:Chimera","Optional","1","1","OutBILD","outFile::ASCII","NULL"

diff --git a/src/Tools/mrcImage/mrcImageOpticalFlow/src/init.c b/src/Tools/mrcImage/mrcImageOpticalFlow/src/init.c
index 1b744dd..13adeb4 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpticalFlow/src/init.c
+++ b/src/Tools/mrcImage/mrcImageOpticalFlow/src/init.c
@@ -61,65 +61,30 @@ init1(mrcImageOpticalFlowInfo* info)
         info->fptIn3 = fileOpen(info->In3, "r");
     }
     
-    if(!info->flagVx) {
-        stringGetFromFile(s, "Vx", stdin, stdout, 0);
-        info->Vx = stringGetNthWord(s, 1, " ,\t");
-        info->flagVx++;
-    }
     if(info->flagVx) {
         info->fptVx = fileOpen(info->Vx, "w");
     }
     
-    if(!info->flagVy) {
-        stringGetFromFile(s, "Vy", stdin, stdout, 0);
-        info->Vy = stringGetNthWord(s, 1, " ,\t");
-        info->flagVy++;
-    }
     if(info->flagVy) {
         info->fptVy = fileOpen(info->Vy, "w");
     }
     
-    if(!info->flagVz) {
-        stringGetFromFile(s, "Vz", stdin, stdout, 0);
-        info->Vz = stringGetNthWord(s, 1, " ,\t");
-        info->flagVz++;
-    }
     if(info->flagVz) {
         info->fptVz = fileOpen(info->Vz, "w");
     }
     
-    if(!info->flagOutFx) {
-        stringGetFromFile(s, "OutFx", stdin, stdout, 0);
-        info->OutFx = stringGetNthWord(s, 1, " ,\t");
-        info->flagOutFx++;
-    }
     if(info->flagOutFx) {
         info->fptOutFx = fileOpen(info->OutFx, "w");
     }
     
-    if(!info->flagOutFy) {
-        stringGetFromFile(s, "OutFy", stdin, stdout, 0);
-        info->OutFy = stringGetNthWord(s, 1, " ,\t");
-        info->flagOutFy++;
-    }
     if(info->flagOutFy) {
         info->fptOutFy = fileOpen(info->OutFy, "w");
     }
     
-    if(!info->flagOutFz) {
-        stringGetFromFile(s, "OutFz", stdin, stdout, 0);
-        info->OutFz = stringGetNthWord(s, 1, " ,\t");
-        info->flagOutFz++;
-    }
     if(info->flagOutFz) {
         info->fptOutFz = fileOpen(info->OutFz, "w");
     }
     
-    if(!info->flagOutDi) {
-        stringGetFromFile(s, "OutDi", stdin, stdout, 0);
-        info->OutDi = stringGetNthWord(s, 1, " ,\t");
-        info->flagOutDi++;
-    }
     if(info->flagOutDi) {
         info->fptOutDi = fileOpen(info->OutDi, "w");
     }

diff --git a/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.html b/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.html
index a0368a3..ad22506 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.html
+++ b/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.html
@@ -13,11 +13,11 @@ Options:
     [-i[nput]3           In3                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input
     [-o[utput]           Vx                  (NULL      ).as(outFile::mrcImage   ) 
                          Vy                  (NULL      ).as(outFile::mrcImage   ) 
-                         Vz                  (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile
+                         Vz                  (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile
     [-o[utput]F          OutFx               (NULL      ).as(outFile::mrcImage   ) 
                          OutFy               (NULL      ).as(outFile::mrcImage   ) 
                          OutFz               (NULL      ).as(outFile::mrcImage   ) 
-                         OutDi               (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile
+                         OutDi               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile
     [-o[utput]Size       Size                (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Chimera
     [-o[utput]COMMAND    OutCOMMAND          (NULL      ).as(outFile::ASCII      ) ] :Optional  :Output:Chimera
     [-o[utput]BILD       OutBILD             (NULL      ).as(outFile::ASCII      ) ] :Optional  :Output:Chimera

diff --git a/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.pane b/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.pane
index 8eaa2ab..130b36b 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.pane
+++ b/src/Tools/mrcImage/mrcImageOpticalFlow/src/mrcImageOpticalFlow.pane
@@ -10,8 +10,8 @@
         -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In1' 'Input' i1
         -I 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'In2' 'Input' i2
         -I 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'In3' 'Input' i3
-        -I  1 0 1 1 0 1 -1x1+1+6 ' ' 'NULL' 'Vx' OutputDataFile
-        -I  1 0 1 1 0 1 -1x1+1+7 ' ' 'NULL' 'OutFx' OutputDataFile
+        -I  1 0 0 1 0 1 -1x1+1+6 ' ' 'NULL' 'Vx' OutputDataFile
+        -I  1 0 0 1 0 1 -1x1+1+7 ' ' 'NULL' 'OutFx' OutputDataFile
         -O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'Size' 'Output:Chimera' oSize
         -O 1 0 1 0 0 1 -1x1+1+10.500000 ' ' 'OutCOMMAND' 'Output:Chimera' oCOMMAND
         -O 1 0 1 0 0 1 -1x1+1+12.000000 ' ' 'OutBILD' 'Output:Chimera' oBILD

diff --git a/src/Tools/mrcImage/mrcImageOpticalFlow/src/usage.c b/src/Tools/mrcImage/mrcImageOpticalFlow/src/usage.c
index 71fe40e..4c56d97 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageOpticalFlow/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageOpticalFlow/src/usage.c
@@ -10,8 +10,8 @@ usage(char* thisProgram)
     fprintf(stderr, "    [-i[nput]1           In1                 (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input\n");
     fprintf(stderr, "    [-i[nput]2           In2                 (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input\n");
     fprintf(stderr, "    [-i[nput]3           In3                 (NULL      ).as(inFile::mrcImage    ) ] :Optional  :Input\n");
-    fprintf(stderr, "    [-o[utput]           Vx                  (NULL      ).as(outFile::mrcImage   ) \n                         Vy                  (NULL      ).as(outFile::mrcImage   ) \n                         Vz                  (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile\n");
-    fprintf(stderr, "    [-o[utput]F          OutFx               (NULL      ).as(outFile::mrcImage   ) \n                         OutFy               (NULL      ).as(outFile::mrcImage   ) \n                         OutFz               (NULL      ).as(outFile::mrcImage   ) \n                         OutDi               (NULL      ).as(outFile::mrcImage   ) ] :Essential :OutputDataFile\n");
+    fprintf(stderr, "    [-o[utput]           Vx                  (NULL      ).as(outFile::mrcImage   ) \n                         Vy                  (NULL      ).as(outFile::mrcImage   ) \n                         Vz                  (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile\n");
+    fprintf(stderr, "    [-o[utput]F          OutFx               (NULL      ).as(outFile::mrcImage   ) \n                         OutFy               (NULL      ).as(outFile::mrcImage   ) \n                         OutFz               (NULL      ).as(outFile::mrcImage   ) \n                         OutDi               (NULL      ).as(outFile::mrcImage   ) ] :Optional  :OutputDataFile\n");
     fprintf(stderr, "    [-o[utput]Size       Size                (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Chimera\n");
     fprintf(stderr, "    [-o[utput]COMMAND    OutCOMMAND          (NULL      ).as(outFile::ASCII      ) ] :Optional  :Output:Chimera\n");
     fprintf(stderr, "    [-o[utput]BILD       OutBILD             (NULL      ).as(outFile::ASCII      ) ] :Optional  :Output:Chimera\n");