-Owall and -Oball were added: mrcImageMeanFreePathCalc

	modified:   src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile
	modified:   src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index ee2bc8b..976d158 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -7,3 +7,4 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile
index 1a43816..541b630 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile
@@ -2,7 +2,9 @@
 # FileFormat
 "-i","-i[nput]","Input:mrcImage","Essential","1","1","In","inFile::mrcImage","NULL"
 "-o","-o[utput]","Output:distribution","Optional","1","1","Out","outFile::ASCII","stdout"
+"-Owall","-O[utput]w[hite]all","Output: white+whiteEdge","Optional","1","1","OutWhiteAll","outFile::mrcImage","NULL"
 "-Ow","-O[utput]w[hite]","Output: white","Optional","1","1","OutWhite","outFile::mrcImage","NULL"
+"-Oball","-O[utput]b[lack]all","Output: black+blackEdge","Optional","1","1","OutBlackAll","outFile::mrcImage","NULL"
 "-Ob","-O[utput]b[lack]","Output: black","Optional","1","1","OutBlack","outFile::mrcImage","NULL"
 "-Owe","-O[utput]w[hite]e[dge]","Output: whiteEdge","Optional","1","1","OutWhiteEdge","outFile::mrcImage","NULL"
 "-Obe","-O[utput]b[lack]e[dge]","Output: blackEdge","Optional","1","1","OutBlackEdge","outFile::mrcImage","NULL"

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/inc/mrcImageMeanFreePathCalc.h b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/inc/mrcImageMeanFreePathCalc.h
index 29270de..c87bc04 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/inc/mrcImageMeanFreePathCalc.h
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/inc/mrcImageMeanFreePathCalc.h
@@ -21,10 +21,18 @@ typedef struct mrcImageMeanFreePathCalcInfo {
     char* Out;
     FILE* fptOut;
     
+    long flagOutWhiteAll;
+    char* OutWhiteAll;
+    FILE* fptOutWhiteAll;
+    
     long flagOutWhite;
     char* OutWhite;
     FILE* fptOutWhite;
     
+    long flagOutBlackAll;
+    char* OutBlackAll;
+    FILE* fptOutBlackAll;
+    
     long flagOutBlack;
     char* OutBlack;
     FILE* fptOutBlack;

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/argCheck.c b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/argCheck.c
index 68aef40..663afcc 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/argCheck.c
@@ -50,6 +50,17 @@ argCheck(mrcImageMeanFreePathCalcInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("Owall") {
+                    if(i+1<argc) {
+                        info->OutWhiteAll = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutWhiteAll++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("Ow") {
                     if(i+1<argc) {
                         info->OutWhite = stringGetNthWord(argv[i+1], 1, " ,");
@@ -61,6 +72,17 @@ argCheck(mrcImageMeanFreePathCalcInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("Oball") {
+                    if(i+1<argc) {
+                        info->OutBlackAll = stringGetNthWord(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagOutBlackAll++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("Ob") {
                     if(i+1<argc) {
                         info->OutBlack = stringGetNthWord(argv[i+1], 1, " ,");

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/init.c b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/init.c
index 9bc72aa..12c7382 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/init.c
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/init.c
@@ -14,7 +14,9 @@ init0(mrcImageMeanFreePathCalcInfo* info)
 {
     info->fptIn = NULL;    info->flagIn = 0;
     info->fptOut = stdout;    info->flagOut = 0;
+    info->fptOutWhiteAll = NULL;    info->flagOutWhiteAll = 0;
     info->fptOutWhite = NULL;    info->flagOutWhite = 0;
+    info->fptOutBlackAll = NULL;    info->flagOutBlackAll = 0;
     info->fptOutBlack = NULL;    info->flagOutBlack = 0;
     info->fptOutWhiteEdge = NULL;    info->flagOutWhiteEdge = 0;
     info->fptOutBlackEdge = NULL;    info->flagOutBlackEdge = 0;
@@ -47,10 +49,18 @@ init1(mrcImageMeanFreePathCalcInfo* info)
         info->fptOut = fileOpen(info->Out, "w");
     }
     
+    if(info->flagOutWhiteAll) {
+        info->fptOutWhiteAll = fileOpen(info->OutWhiteAll, "w");
+    }
+    
     if(info->flagOutWhite) {
         info->fptOutWhite = fileOpen(info->OutWhite, "w");
     }
     
+    if(info->flagOutBlackAll) {
+        info->fptOutBlackAll = fileOpen(info->OutBlackAll, "w");
+    }
+    
     if(info->flagOutBlack) {
         info->fptOutBlack = fileOpen(info->OutBlack, "w");
     }

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c
index 8f3ae10..078ee8d 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c
@@ -68,6 +68,18 @@ main(int argc, char* argv[])
                mrcFileWrite(&linfo.blackEdge, info.OutBlackEdge, "in main", 0);
        }
 
+       if(info.flagOutWhiteAll) {
+               int number = 1;
+               lmrcImageAdd(&linfo.white, &linfo.whiteEdge, &number);
+               mrcFileWrite(&linfo.white, info.OutWhiteAll, "in main", 0);
+       }
+
+       if(info.flagOutBlackAll) {
+               int number = 1;
+               lmrcImageAdd(&linfo.black, &linfo.blackEdge, &number);
+               mrcFileWrite(&linfo.black, info.OutBlackAll, "in main", 0);
+       }
+
        if(info.flagDirection && info.mode == 3) {
                char s[1024];
                for(i=0; i<3; i++) {

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.html b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.html
index 2325f93..58ad852 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.html
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.html
@@ -10,7 +10,9 @@ Usage: mrcImageMeanFreePathCalc
 Options:
     [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage
     [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:distribution
+    [-O[utput]w[hite]all OutWhiteAll         (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: white+whiteEdge
     [-O[utput]w[hite]    OutWhite            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: white
+    [-O[utput]b[lack]all OutBlackAll         (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: black+blackEdge
     [-O[utput]b[lack]    OutBlack            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: black
     [-O[utput]w[hite]e[dge]OutWhiteEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: whiteEdge
     [-O[utput]b[lack]e[dge]OutBlackEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: blackEdge

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.pane b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.pane
index 0e2a41c..efc6ddf 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.pane
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.pane
@@ -9,18 +9,20 @@
         -Q 1 0 5.25x1+47+0 'Close'
         -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:distribution' o
-        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutWhite' 'Output: white' Ow
-        -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'OutBlack' 'Output: black' Ob
-        -O 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'OutWhiteEdge' 'Output: whiteEdge' Owe
-        -O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'OutBlackEdge' 'Output: blackEdge' Obe
-        -s 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'Direction' 'Output: basename.[0|1|2] vector for any' Odir
-        -I  1 0 0 1 0 1 -1x1+1+12 ' ' '1' 'LineThicknessX' [pixel]
-        -i 1 0 1 0 0 -1x1+1+13.500000 0 0 0 0 0 'LineMode' 'LineMode' lm
-        -i 1 0 1 0 0 -1x1+1+15.000000 0 0 0 0 0 'LineShape' 'LineShape' ls
-        -f 1 0 1 0 0 -1x1+1+16.500000 0 0 30.000000 0 0 0 'deltaPhi' 'deltaPhi' deltaPhi
-        -f 1 0 1 0 0 -1x1+1+18.000000 0 0 30.000000 0 0 0 'deltaTheta' 'deltaTheta' deltaTheta
-        -I 1 0 1 0 0 1 -1x1+1+19.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -i 1 0 1 0 0 -1x1+1+21.000000 0 0 0 0 0 'mode' 'Mode' m
+        -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutWhiteAll' 'Output: white+whiteEdge' Owall
+        -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'OutWhite' 'Output: white' Ow
+        -O 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'OutBlackAll' 'Output: black+blackEdge' Oball
+        -O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'OutBlack' 'Output: black' Ob
+        -O 1 0 1 0 0 1 -1x1+1+10.500000 ' ' 'OutWhiteEdge' 'Output: whiteEdge' Owe
+        -O 1 0 1 0 0 1 -1x1+1+12.000000 ' ' 'OutBlackEdge' 'Output: blackEdge' Obe
+        -s 1 0 1 0 0 -1x1+1+13.500000 0 0 0 0 0 'Direction' 'Output: basename.[0|1|2] vector for any' Odir
+        -I  1 0 0 1 0 1 -1x1+1+15 ' ' '1' 'LineThicknessX' [pixel]
+        -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'LineMode' 'LineMode' lm
+        -i 1 0 1 0 0 -1x1+1+18.000000 0 0 0 0 0 'LineShape' 'LineShape' ls
+        -f 1 0 1 0 0 -1x1+1+19.500000 0 0 30.000000 0 0 0 'deltaPhi' 'deltaPhi' deltaPhi
+        -f 1 0 1 0 0 -1x1+1+21.000000 0 0 30.000000 0 0 0 'deltaTheta' 'deltaTheta' deltaTheta
+        -I 1 0 1 0 0 1 -1x1+1+22.500000 ' ' 'configFile' 'ConfigurationFile' c
+        -i 1 0 1 0 0 -1x1+1+24.000000 0 0 0 0 0 'mode' 'Mode' m
     -E
   -E
 -E

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile
index b876a6a..c97ac27 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile
@@ -38,7 +38,7 @@ exec4:
 
 exec5:
        @echo "----- Execution Check -----"
-       ../$(OSTYPE)/$(OBJECTNAME) -i data/test.bin -o data/test.mfp.any -Ow data/test.white.any -Owe data/test.whiteEdge.any -Ob data/test.black.any -Obe data/test.blackEdge.any -Odir data/test.mode3.dir -m 3 -deltaPhi 10 -deltaTheta 10
+       ../$(OSTYPE)/$(OBJECTNAME) -i data/test.bin -o data/test.mfp.any -Ow data/test.white.any -Owe data/test.whiteEdge.any -Ob data/test.black.any -Obe data/test.blackEdge.any -Odir data/test.mode3.dir -m 3 -deltaPhi 10 -deltaTheta 10 -Owall data/test.white.all -Oball data/test.black.all
 
 
 init:

diff --git a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/usage.c b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/usage.c
index f50bfe2..a85b096 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/usage.c
@@ -9,7 +9,9 @@ usage(char* thisProgram)
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:mrcImage\n");
     fprintf(stderr, "    [-o[utput]           Out                 (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:distribution\n");
+    fprintf(stderr, "    [-O[utput]w[hite]all OutWhiteAll         (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: white+whiteEdge\n");
     fprintf(stderr, "    [-O[utput]w[hite]    OutWhite            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: white\n");
+    fprintf(stderr, "    [-O[utput]b[lack]all OutBlackAll         (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: black+blackEdge\n");
     fprintf(stderr, "    [-O[utput]b[lack]    OutBlack            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: black\n");
     fprintf(stderr, "    [-O[utput]w[hite]e[dge]OutWhiteEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: whiteEdge\n");
     fprintf(stderr, "    [-O[utput]b[lack]e[dge]OutBlackEdge        (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output: blackEdge\n");