mrcImageBinarization: version up : density band extraction

	modified:   include/lmrcImageBinarization.h
	modified:   src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.c
	modified:   src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.h
	modified:   src/Tools/mrcImage/mrcImageBinalization/Config/OptionControlFile
	modified:   src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.c

diff --git a/include/lmrcImageBinarization.h b/include/lmrcImageBinarization.h
index 5f72856..b7daba2 100644 (file)
--- a/include/lmrcImageBinarization.h
+++ b/include/lmrcImageBinarization.h
@@ -29,6 +29,7 @@ typedef struct lmrcImageBinarizationInfo {
        
        int flagDeltaThreshold;
        double deltaThreshold;
+       double sigmaThreshold;
 }lmrcImageBinarizationInfo;
 
 /* struct end */

diff --git a/include/lmrcImageFeatureCalc.h b/include/lmrcImageFeatureCalc.h
new file mode 100644 (file)
index 0000000..bc0f501
--- /dev/null
+++ b/include/lmrcImageFeatureCalc.h
@@ -0,0 +1,57 @@
+/*
+# lmrcImageFeatureCalc.h : $Revision$  
+# $Date$ 
+# Created by $Author$
+# Usage : lmrcImageFeatureCalc.h 
+# Attention
+#   $Loccker$
+#      $State$ 
+#
+*/
+/* $Log$ */
+#ifndef LMRC_IMAGE_FEATURE_CALC 
+#define        LMRC_IMAGE_FEATURE_CALC 
+
+#include <stdio.h>
+#include "./lmrcImageCalcArea.h"
+
+/* constant begin */
+
+
+/* constant end */
+
+/* struct begin */
+ 
+struct lmrcImagePerimeterCalcInfo {
+       int flagArea;
+       mrcImage* Area;
+       mrcImage* Label;
+
+       //
+       mrcImage* ChainCode;
+} lmrcImagePerimeterCalcInfo; 
+
+struct lmrcImageCircularityCalcInfo {
+       
+} lmrcImageCircularityCalcInfo; 
+
+
+/* struct end */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* prototype begin */
+
+void lmrcImagePerimeterCalc(mrcImage* out, mrcImage* in, lmrcImagePerimeterCalcInfo* linfo, int mode);
+void lmrcImageCircularityCalc(mrcImage* out, mrcImage* in, lmrcImageCircularityCalc* linfo, int mode);
+
+
+/* prototype end */
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif  /* LMRC_IMAGE_FEATURE_CALC */ 

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.c b/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.c
index 114c4be..9ff5269 100755 (executable)
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.c
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.c
@@ -119,6 +119,20 @@ lmrcImageBinarization0(mrcImage* out, mrcImage* in, lmrcImageBinarizationInfo li
                                                        }
                                                        break;
                                                }
+                                               case 4: 
+                                               case 6: {
+                                                       if(t - linfo.sigmaThreshold <= data0  && data0 <= t + linfo.sigmaThreshold ) { /* Near */
+                                                               flagNear = 1;
+                                                       }
+                                                       break;
+                                               }
+                                               case 5: 
+                                               case 7: {
+                                                       if(data0 < t - linfo.sigmaThreshold || t + linfo.sigmaThreshold < data0 ) { /* Near */
+                                                               flagNear = 1;
+                                                       }
+                                                       break;
+                                               }
                                                default: {
                                                        fprintf(stderr, "Not supported mode in lmrcImageBinarization : %d", mode);
                                                        break;
@@ -136,7 +150,7 @@ lmrcImageBinarization0(mrcImage* out, mrcImage* in, lmrcImageBinarizationInfo li
                                if(0<flagNear) {
                                        break;
                                }
-                       }       
+                       }
                }       
                switch(mode) {
                        case 0: {
@@ -192,6 +206,58 @@ lmrcImageBinarization0(mrcImage* out, mrcImage* in, lmrcImageBinarizationInfo li
                                }
                                break;
                        }
+               case 4: {
+                               if(data < t - linfo.sigmaThreshold || t + linfo.sigmaThreshold < data){
+                                       if(0<linfo.flagNear && 0<flagNear) {
+                                               data = 1;
+                                       } else {
+                                               data = 0;
+                                       }
+                               } else {
+                                       data = 1;
+                                       n++;
+                               }        
+                               break;
+                       }
+               case 5: {
+                               if(t - linfo.sigmaThreshold <= data && data <= t + linfo.sigmaThreshold){
+                                       if(0<linfo.flagNear && 0<flagNear) {
+                                               data = 1;
+                                       } else {
+                                               data = 0;
+                                       }
+                               } else {
+                                       data = 1;
+                                       n++;
+                               }        
+                               break;
+                       }
+               case 6: {
+                               if(data < t - linfo.sigmaThreshold || t + linfo.sigmaThreshold < data){
+                                       if(0<linfo.flagNear && 0<flagNear) {
+                                               data = data;
+                                       } else {
+                                               data = v;
+                                       }
+                               } else {
+                                       data = data;
+                                       n++;
+                               }        
+                               break;
+                       }
+               case 7: {
+                               if(t - linfo.sigmaThreshold <= data && data <= t + linfo.sigmaThreshold){
+                                       if(0<linfo.flagNear && 0<flagNear) {
+                                               data = data;
+                                       } else {
+                                               data = v;
+                                       }
+                               } else {
+                                       data = data;
+                                       n++;
+                               }        
+                               break;
+                       }
                        default: {
                                fprintf(stderr, "Not supported mode in lmrcImageBinarization : %d", mode);
                                break;
@@ -214,12 +280,16 @@ lmrcImageBinarizationUsage(FILE* fpt)
        fprintf(fpt, "     1: Above thresHold, 0.     Under thresHold, 1.\n");
        fprintf(fpt, "     2: Under thresHold, value. Above thresHold, unchanged.\n");
        fprintf(fpt, "     3: Above thresHold, value. Under thresHold, unchanged.\n");
-       fprintf(fpt, "     16: Automatically Determine threshold by Kittler Method\n");
-       fprintf(fpt, "     32: Automatically Determine threshold by Ohtsu Method\n");
-       fprintf(fpt, "     48: Automatically Determine threshold by p-tile Method\n");
+       fprintf(fpt, "     4: thresHold +- sigma, 1.     Others 0.\n");
+       fprintf(fpt, "     5: thresHold +- sigma, 0.     Others 1.\n");
+       fprintf(fpt, "     6: thresHold +- sigma, unchanged. Others value.\n");
+       fprintf(fpt, "     7: thresHold +- sigma, value.     Others unchanged.\n");
+       fprintf(fpt, "     +16: Automatically Determine threshold by Kittler Method\n");
+       fprintf(fpt, "     +32: Automatically Determine threshold by Ohtsu Method\n");
+       fprintf(fpt, "     +48: Automatically Determine threshold by p-tile Method\n");
        fprintf(fpt, "          p range: 0.0 - 1.0\n"); 
-       fprintf(fpt, "     64: Automatically Determine threshold by Differential-Histogram Method\n");
-       fprintf(fpt, "     80: Automatically Determine threshold by Laplacian-Histogram Method\n");
+       fprintf(fpt, "     +64: Automatically Determine threshold by Differential-Histogram Method\n");
+       fprintf(fpt, "     +80: Automatically Determine threshold by Laplacian-Histogram Method\n");
 }
 
 double

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.h b/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.h
index 5f72856..b7daba2 100755 (executable)
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.h
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageBinarization.h
@@ -29,6 +29,7 @@ typedef struct lmrcImageBinarizationInfo {
        
        int flagDeltaThreshold;
        double deltaThreshold;
+       double sigmaThreshold;
 }lmrcImageBinarizationInfo;
 
 /* struct end */

diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h b/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h
index 7536b33..bc0f501 100644 (file)
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h
@@ -13,7 +13,7 @@
 #define        LMRC_IMAGE_FEATURE_CALC 
 
 #include <stdio.h>
-#include "lmrcImageAreaCalc.h"
+#include "./lmrcImageCalcArea.h"
 
 /* constant begin */
 

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index 6dc46fd..0e2c87b 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -620,3 +620,4 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/mrcImage/mrcImageBinalization/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageBinalization/Config/OptionControlFile
index 8012ae0..91934ec 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/Config/OptionControlFile
+++ b/src/Tools/mrcImage/mrcImageBinalization/Config/OptionControlFile
@@ -5,6 +5,7 @@
 "-O","-O[utput]","Output:Parameters","Optional","1","1","OutParam","outFile::ASCII","stdout"
 "-t","-t[hreshold]","Value of threshold","Optional","1","1","t","Real","0"
 "-dt","-d[elta]t[hreshold]","Difference threshold","Optional","1","1","deltaThreshold","Real","0"
+"-st","-s[igma]t[hreshold]","Sigma threshold(BandPath)","Optional","1","1","sigmaThreshold","Real","0.5"
 "-v","-v[alue]","Value","Optional","1","1","v","Real","0"
 "-near","-near","Near[pixel]: Near-area also binary","Optional","1","1","near","Real","0"
 "-nLevel","-nLevel","nLevel: For creating histgram by Kittler and Ohtsu ","Optional","1","1","nLevel","Integer","256"

diff --git a/src/Tools/mrcImage/mrcImageBinalization/inc/mrcImageBinalization.h b/src/Tools/mrcImage/mrcImageBinalization/inc/mrcImageBinalization.h
index 36189cb..de6a715 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/inc/mrcImageBinalization.h
+++ b/src/Tools/mrcImage/mrcImageBinalization/inc/mrcImageBinalization.h
@@ -31,6 +31,9 @@ typedef struct mrcImageBinalizationInfo {
     long flagdeltaThreshold;
     float deltaThreshold;
     
+    long flagsigmaThreshold;
+    float sigmaThreshold;
+    
     long flagv;
     float v;
     

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/argCheck.c b/src/Tools/mrcImage/mrcImageBinalization/src/argCheck.c
index 4742e52..1c10432 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/argCheck.c
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/argCheck.c
@@ -83,6 +83,17 @@ argCheck(mrcImageBinalizationInfo* info, int argc, char* argv[])
                     }
                     SBREAK;
                 }
+                SCASE("st") {
+                    if(i+1<argc) {
+                        info->sigmaThreshold = stringGetNthRealData(argv[i+1], 1, " ,");
+                        i++;
+                        info->flagsigmaThreshold++;
+                    } else {
+                        usage(argv[0]);
+                        exit(EXIT_FAILURE);
+                    }
+                    SBREAK;
+                }
                 SCASE("v") {
                     if(i+1<argc) {
                         info->v = stringGetNthRealData(argv[i+1], 1, " ,");

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/init.c b/src/Tools/mrcImage/mrcImageBinalization/src/init.c
index a76ca3e..b9aa1d6 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/init.c
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/init.c
@@ -17,6 +17,7 @@ init0(mrcImageBinalizationInfo* info)
     info->fptOutParam = stdout;    info->flagOutParam = 0;
     info->t = 0;    info->flagt = 0;
     info->deltaThreshold = 0;    info->flagdeltaThreshold = 0;
+    info->sigmaThreshold = 0.5;    info->flagsigmaThreshold = 0;
     info->v = 0;    info->flagv = 0;
     info->near = 0;    info->flagnear = 0;
     info->nLevel = 256;    info->flagnLevel = 0;
@@ -58,6 +59,9 @@ init1(mrcImageBinalizationInfo* info)
     if(info->flagdeltaThreshold) {
     }
     
+    if(info->flagsigmaThreshold) {
+    }
+    
     if(info->flagv) {
     }
     

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.c b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.c
index 0ccbc58..1cfad20 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.c
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.c
@@ -52,8 +52,9 @@ main(int argc, char* argv[])
 
        linfo.flagDeltaThreshold = info.flagdeltaThreshold;
        linfo.deltaThreshold = info.deltaThreshold;
+       linfo.sigmaThreshold = info.sigmaThreshold;
 
-       DEBUGPRINT1("mode: %d\n", info.mode);
+       DEBUGPRINT1("mode: %ld\n", info.mode);
        threshold = lmrcImageBinarization(&out, &in, linfo, info.mode);
 
        mrcFileWrite(&out, info.Out ,"in main" ,0);

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
index 5052a21..2735fa9 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.html
@@ -13,6 +13,7 @@ Options:
     [-O[utput]           OutParam            (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:Parameters
     [-t[hreshold]        t                   (0         ).as(Real                ) ] :Optional  :Value of threshold
     [-d[elta]t[hreshold] deltaThreshold      (0         ).as(Real                ) ] :Optional  :Difference threshold
+    [-s[igma]t[hreshold] sigmaThreshold      (0.5       ).as(Real                ) ] :Optional  :Sigma threshold(BandPath)
     [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value
     [-near               near                (0         ).as(Real                ) ] :Optional  :Near[pixel]: Near-area also binary
     [-nLevel             nLevel              (256       ).as(Integer             ) ] :Optional  :nLevel: For creating histgram by Kittler and Ohtsu 
@@ -25,12 +26,16 @@ mode 0: Under thresHold, 0.     Above thresHold, 1.
      1: Above thresHold, 0.     Under thresHold, 1.
      2: Under thresHold, value. Above thresHold, unchanged.
      3: Above thresHold, value. Under thresHold, unchanged.
-     16: Automatically Determine threshold by Kittler Method
-     32: Automatically Determine threshold by Ohtsu Method
-     48: Automatically Determine threshold by p-tile Method
+     4: thresHold +- sigma, 1.     Others 0.
+     5: thresHold +- sigma, 0.     Others 1.
+     6: thresHold +- sigma, unchanged. Others value.
+     7: thresHold +- sigma, value.     Others unchanged.
+     +16: Automatically Determine threshold by Kittler Method
+     +32: Automatically Determine threshold by Ohtsu Method
+     +48: Automatically Determine threshold by p-tile Method
           p range: 0.0 - 1.0
-     64: Automatically Determine threshold by Differential-Histogram Method
-     80: Automatically Determine threshold by Laplacian-Histogram Method
+     +64: Automatically Determine threshold by Differential-Histogram Method
+     +80: Automatically Determine threshold by Laplacian-Histogram Method
 </PRE>
 </BODY>
 </HTML>

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.pane b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.pane
index 53f5151..60ecc79 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.pane
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/mrcImageBinalization.pane
@@ -12,12 +12,13 @@
         -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutParam' 'Output:Parameters' O
         -f 1 0 1 0 0 -1x1+1+6.000000 0 0 0.000000 0 0 0 't' 'Value of threshold' t
         -f 1 0 1 0 0 -1x1+1+7.500000 0 0 0.000000 0 0 0 'deltaThreshold' 'Difference threshold' dt
-        -f 1 0 1 0 0 -1x1+1+9.000000 0 0 0.000000 0 0 0 'v' 'Value' v
-        -f 1 0 1 0 0 -1x1+1+10.500000 0 0 0.000000 0 0 0 'near' 'Near[pixel]: Near-area also binary' near
-        -i 1 0 1 0 0 -1x1+1+12.000000 0 0 256 0 0 'nLevel' 'nLevel: For creating histgram by Kittler and Ohtsu ' nLevel
-        -I 1 0 1 0 0 1 -1x1+1+13.500000 ' ' 'configFile' 'ConfigurationFile' c
-        -f 1 0 1 0 0 -1x1+1+15.000000 0 0 0.500000 0 0 0 'p' 'p' p
-        -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'mode' 'Mode' m
+        -f 1 0 1 0 0 -1x1+1+9.000000 0 0 0.500000 0 0 0 'sigmaThreshold' 'Sigma threshold(BandPath)' st
+        -f 1 0 1 0 0 -1x1+1+10.500000 0 0 0.000000 0 0 0 'v' 'Value' v
+        -f 1 0 1 0 0 -1x1+1+12.000000 0 0 0.000000 0 0 0 'near' 'Near[pixel]: Near-area also binary' near
+        -i 1 0 1 0 0 -1x1+1+13.500000 0 0 256 0 0 'nLevel' 'nLevel: For creating histgram by Kittler and Ohtsu ' nLevel
+        -I 1 0 1 0 0 1 -1x1+1+15.000000 ' ' 'configFile' 'ConfigurationFile' c
+        -f 1 0 1 0 0 -1x1+1+16.500000 0 0 0.500000 0 0 0 'p' 'p' p
+        -i 1 0 1 0 0 -1x1+1+18.000000 0 0 0 0 0 'mode' 'Mode' m
     -E
   -E
 -E

diff --git a/src/Tools/mrcImage/mrcImageBinalization/src/usage.c b/src/Tools/mrcImage/mrcImageBinalization/src/usage.c
index 55bcccb..e528b17 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageBinalization/src/usage.c
+++ b/src/Tools/mrcImage/mrcImageBinalization/src/usage.c
@@ -12,6 +12,7 @@ usage(char* thisProgram)
     fprintf(stderr, "    [-O[utput]           OutParam            (stdout    ).as(outFile::ASCII      ) ] :Optional  :Output:Parameters\n");
     fprintf(stderr, "    [-t[hreshold]        t                   (0         ).as(Real                ) ] :Optional  :Value of threshold\n");
     fprintf(stderr, "    [-d[elta]t[hreshold] deltaThreshold      (0         ).as(Real                ) ] :Optional  :Difference threshold\n");
+    fprintf(stderr, "    [-s[igma]t[hreshold] sigmaThreshold      (0.5       ).as(Real                ) ] :Optional  :Sigma threshold(BandPath)\n");
     fprintf(stderr, "    [-v[alue]            v                   (0         ).as(Real                ) ] :Optional  :Value\n");
     fprintf(stderr, "    [-near               near                (0         ).as(Real                ) ] :Optional  :Near[pixel]: Near-area also binary\n");
     fprintf(stderr, "    [-nLevel             nLevel              (256       ).as(Integer             ) ] :Optional  :nLevel: For creating histgram by Kittler and Ohtsu \n");