bug fixed: lmrc2Dto3D

diff --git a/Integration/2DClustering/Makefile b/Integration/2DClustering/Makefile
index 9805424..4ae6574 100644 (file)
--- a/Integration/2DClustering/Makefile
+++ b/Integration/2DClustering/Makefile
@@ -8,6 +8,7 @@
 #    xxxx.roi
 #    Makefile.config
 #
+
 include Makefile.config
 
 .SUFFIXES: .roi .preshrink .pad .padlst .log .logIn
@@ -16,7 +17,7 @@ include Makefile.config
 
 #
 Menu::
-       @echo "------------ How to use this Makefile-------------------"
+       @echo "------------ How to use this Makefile -------------------"
        @echo "make Init"
        @echo "make ALLROIS"
        @echo "make Pad"

diff --git a/include/eosBayes.h b/include/eosBayes.h
index 868174e..17e6798 100644 (file)
--- a/include/eosBayes.h
+++ b/include/eosBayes.h
@@ -19,5 +19,10 @@ typedef struct eosBayes {
        eosBayesDistribution* likelihood;
 } eosBayes;
 
+extern void eosBayesInit(eosBayes* b, int numDistribution, int numLikelihood, int mode);
+extern void eosBayesDistributionInit(eosBayes* b, int mode);
+extern void eosBayesDistributionInit0(eosBayesDistribution* d, int mode);
+extern void eosBayesEstimation(eosBayesDistribution* d, int mode);
+extern void eosBayesWrite(FILE* fpt, eosBayesDistribution* d, int mode);
 
 #endif /* EOS_BAYES_H */

diff --git a/src/Objects/DataManip/transform/doc/transform.html b/src/Objects/DataManip/transform/doc/transform.html
index 053b4bf..0096d71 100644 (file)
--- a/src/Objects/DataManip/transform/doc/transform.html
+++ b/src/Objects/DataManip/transform/doc/transform.html
@@ -3,67 +3,6 @@
 <H2>Information from source codes</H2>
 </A>
 <PRE>
-../src/lAllCommonLineCalculation.c:
-
-../src/lAngularWeightCalculation.c:
-
-../src/lCommonLineCalculation.c:
-
-../src/lCommonLineDataSetInPlaneRotation.c:
-
-../src/lCommonLinesDataSet.c:
-
-../src/lDescartesIntoPolar.c:
-
-../src/lEvaluateCorrelationMapwithCommonLine.c:
-
-../src/lFETOrientationSearchByAnnealing.c:
-
-../src/lFETOrientationSearchByFeatureAlignment.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentInitSet.c:
-
-../src/lFETOrientationSearchByFeatureAlignmentSphere.c:
-
-../src/lFETmapOrientationSearchBySimultaneousFitting.c:
-
-../src/lFETsmallMapSetCreate_forSimultaneousMinimization.c:
-
-../src/lInitialDataFileRead.c:
-
-../src/lJcalulation.c:
-
-../src/lLcalculation.c:
-
-../src/lPlaneRotationAngleSet.c:
-
-../src/lllDataSeparationInfoPrint.c:
-
-../src/lllDataSeparationInfoRead.c:
-
-../src/lllDataSeparationInfoSet.c:
-
-../src/lllDatarMaxLimitForSeparation.c:
-
-../src/lllExtract.c:
-
-../src/lllExtractCtfinfFileCreate.c:
-
-../src/lllExtractWithSeparation.c:
-
-../src/lllExtractdYEstimate.c:
-
-../src/lmrc2Dto3D.c:
-
-../src/lmrc2Dto3DSIRT.c:
-
-../src/lmrc3Dto2D.c:
-
-../src/lmrcImageFileListAndEulerAngleDataRead.c:
-
-../src/lmrcImageOneLineGet.c:
-
-../src/lmrcImageSinogramCorrelationAdditionalWeight.c:
 </PRE>
 <HR>
 <A NAME="include">

diff --git a/src/Objects/DataManip/transform/src/lmrc2Dto3D.c b/src/Objects/DataManip/transform/src/lmrc2Dto3D.c
index efaa6ad..a586339 100755 (executable)
--- a/src/Objects/DataManip/transform/src/lmrc2Dto3D.c
+++ b/src/Objects/DataManip/transform/src/lmrc2Dto3D.c
@@ -235,6 +235,7 @@ lmrcImage2Dto3DSingle(mrcImage* out, mrcImage* counter, int counterNum, mrcImage
 
        /* */
        DEBUGPRINT("Backprojection Start\n");
+       DEBUGPRINT1("prj: %f\n", prj.ImageFloatImage[prj.HeaderN.x/2 + prj.HeaderN.y/2*prj.HeaderN.x]);
        switch(linfo->mode) {
                case mrc2Dto3DModeSimpleBackProjection: { /* Backprojection */
                        lmrc2Dto3DSimpleBackProjectionForEach(out, &prj, linfo, Matrix, mode);
@@ -258,6 +259,7 @@ lmrcImage2Dto3DSingle(mrcImage* out, mrcImage* counter, int counterNum, mrcImage
                        break;
                }
        }
+       DEBUGPRINT1("out: %f\n", out->ImageFloatImage[out->HeaderN.x/2 + out->HeaderN.y/2*out->HeaderN.x + out->HeaderN.z/2*out->HeaderN.x*out->HeaderN.y]);
 
        DEBUGPRINT("Backprojection End\n");
        mrcImageFree(&prj, "in lmrc2Dto3DSingle");
@@ -366,7 +368,9 @@ lmrc2Dto3D(mrcImage* out, mrcImage* in, lmrc2Dto3DInfo* linfo, long mode)
                        eosPThreadCreate(&pthread, iThread, (void*)lmrcImage2Dto3DSingleForPThread, &(pthreadArg[iThread]), 0);
                        //lmrcImage2Dto3DSingleForPThread(&(pthreadArg[iThread]));
                } else {
+                       DEBUGPRINT("No threading: lmrcImage2Dto3DSingle\n");
                        lmrcImage2Dto3DSingle(out, &(counter[iThread]), threadCounter[iThread], in, i, linfo, mode);
+                       DEBUGPRINT1("out before filter: %f\n", out->ImageFloatImage[out->HeaderN.x/2 + out->HeaderN.y/2*out->HeaderN.x + out->HeaderN.z/2*out->HeaderN.x*out->HeaderN.y]);
                }
                threadCounter[iThread]++;
                
@@ -385,7 +389,7 @@ lmrc2Dto3D(mrcImage* out, mrcImage* in, lmrc2Dto3DInfo* linfo, long mode)
        if(linfo->flagDouble && linfo->mode==mrc2Dto3DModeFilteredBackProjection) {
                /* Perform RhoFiltering */
 #ifdef DEBUG
-               //mrcFileWrite(out, "/tmp/RawDataforDebug.mrc3d", "in main", 0);
+               mrcFileWrite(out, "/tmp/RawDataforDebug.mrc3d", "in main", 0);
                mrcFileWrite(&(counter[0]), "/tmp/counter0", "in main", 0);
 #endif
                for(i=0, j=0; i<threadNum; i++) {
@@ -400,6 +404,7 @@ lmrc2Dto3D(mrcImage* out, mrcImage* in, lmrc2Dto3DInfo* linfo, long mode)
                }
                // Perform Filtering 
                lmrcImageRhoFiltering2(out, linfo->CounterForWeight, threadNum, Matrix, &linfo->rhoInfo, 1);
+               DEBUGPRINT1("out after filter: %f\n", out->ImageFloatImage[out->HeaderN.x/2 + out->HeaderN.y/2*out->HeaderN.x + out->HeaderN.z/2*out->HeaderN.x*out->HeaderN.y]);
        } else {
                lmrcImageDividedByReal(out, numProjection);
        }
@@ -482,7 +487,8 @@ lmrc2Dto3DFilteredBackProjectionForEach(mrcImage* out, mrcImage* prj, lmrc2Dto3D
        mrcImageParaTypeReal    gx, gy, gz;
        mrcImageParaTypeReal    g3x, g3y, g3z;
        floatVector v; 
-       int index;
+       int index3d;
+       int index2d;
 
        floatVectorInit(&v, 4);
        v.data[3] = 1.0;
@@ -507,7 +513,7 @@ lmrc2Dto3DFilteredBackProjectionForEach(mrcImage* out, mrcImage* prj, lmrc2Dto3D
                tmpzy = Matrix[1][2]*v.data[1]; 
 
        for(x=0; x<out->HeaderN.x; x++) {
-               index = x + y*out->HeaderN.x + z*out->HeaderN.x*out->HeaderN.y; 
+               index3d = x + y*out->HeaderN.x + z*out->HeaderN.x*out->HeaderN.y; 
                v.data[0] = x-g3x; 
                tmpxx = Matrix[0][0]*v.data[0]; 
                tmpyx = Matrix[0][1]*v.data[0]; 
@@ -527,8 +533,8 @@ lmrc2Dto3DFilteredBackProjectionForEach(mrcImage* out, mrcImage* prj, lmrc2Dto3D
                        //mrcPixelDataGet(out, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
                        if( -0.5<=prjx && prjx<prj->HeaderN.x-0.5
                          &&-0.5<=prjy && prjy<prj->HeaderN.y-0.5) {
-                               data = out->ImageFloatImage[index];
-                               //mrcPixelDataGet(prj, prjx, prjy, 0.0, &projdata, mrcPixelRePart, linfo->InterpolationMode);
+                               data = out->ImageFloatImage[index3d];
+                               mrcPixelDataGet(prj, prjx, prjy, 0.0, &projdata, mrcPixelRePart, linfo->InterpolationMode);
                                if(linfo->flagDouble && linfo->rhoInfo.flagThicknessWeight) {
                                        normz = fabs(tmpz/g3z); 
                                        if(normz < 0.9) {
@@ -540,7 +546,7 @@ lmrc2Dto3DFilteredBackProjectionForEach(mrcImage* out, mrcImage* prj, lmrc2Dto3D
                                        }
                                } 
                        //      mrcPixelDataSet(out, x, y, z, data + projdata, mrcPixelRePart);
-                               out->ImageFloatImage[index] = data + projdata;
+                               out->ImageFloatImage[index3d] = data + projdata;
                        }
                }
        }

diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc
index cec3e03..c5f25d3 100755 (executable)
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -600,3 +600,4 @@ WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
 WORLDNAME=Tools
+WORLDNAME=Tools

diff --git a/src/Tools/Makefile b/src/Tools/Makefile
deleted file mode 120000 (symlink)
index 80a2401a7dc3d8e1cdc121c22208bd28b6887cf3..0000000000000000000000000000000000000000
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1 +0,0 @@
-/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file

diff --git a/src/Tools/Makefile b/src/Tools/Makefile
new file mode 100755 (executable)
index 0000000000000000000000000000000000000000..ad841104b1b4aa83ce554496adb2d2476544f988
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1,5 @@
+include ../Config/Define.inc
+include Config/Define.inc
+include .Source
+
+include Config/Target.inc

diff --git a/src/Tools/mrcImage/mrcImageUnsharpening/src/mrcImageUnsharpening.c b/src/Tools/mrcImage/mrcImageUnsharpening/src/mrcImageUnsharpening.c
index cf98495..54594f7 100755 (executable)
--- a/src/Tools/mrcImage/mrcImageUnsharpening/src/mrcImageUnsharpening.c
+++ b/src/Tools/mrcImage/mrcImageUnsharpening/src/mrcImageUnsharpening.c
@@ -15,7 +15,7 @@
 #define GLOBAL_DECLARATION
 #include "../inc/config.h"
 
-#define DEBUG
+#undef DEBUG
 #include "genUtil.h"
 #include "mrcImage.h"
 

diff --git a/src/Tools/mrcImage/mrcImageUnsharpening/src/test/Makefile b/src/Tools/mrcImage/mrcImageUnsharpening/src/test/Makefile
old mode 100644 (file)
new mode 100755 (executable)

diff --git a/src/Tools/rec3d/mrc2Dto3D/src/test/Makefile b/src/Tools/rec3d/mrc2Dto3D/src/test/Makefile
index b9f558b..9e5e8a4 100755 (executable)
--- a/src/Tools/rec3d/mrc2Dto3D/src/test/Makefile
+++ b/src/Tools/rec3d/mrc2Dto3D/src/test/Makefile
@@ -11,12 +11,12 @@ help:
 
 exec:
        @echo "----- Execution Check -----"
-       time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc2d3d -o data/test.mrc2d3d.mrc3d -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test.mrc2d3d.mrc3d.counter 2> /dev/null
+       time ../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc2d3d -o data/test.mrc2d3d.mrc3d.1 -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test.mrc2d3d.mrc3d.counter.1 2> /dev/null
        time ~/Eos/bin/$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc2d3d -o data/test.mrc2d3d.mrc3d -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test.mrc2d3d.mrc3d.counter 2> /dev/null
 
 exec2:
        @echo "----- Execution Check 2-----"
-       time ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.mrc2d3d -o data/test2.mrc2d3d.mrc3d -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test2.mrc2d3d.mrc3d.counter 2> /dev/null
+       time ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.mrc2d3d -o data/test2.mrc2d3d.mrc3d.2 -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test2.mrc2d3d.mrc3d.counter.2 2> /dev/null
        time ~/Eos/bin/$(OSTYPE)/$(OBJECTNAME) -i data/test2.mrc2d3d -o data/test2.mrc2d3d.mrc3d -Double -CounterThreshold 1 -WeightMode 3 -m 1 -InterpolationMode 2 -DoubleCounter data/test2.mrc2d3d.mrc3d.counter 2> /dev/null
 
 exec-pthread: