From: Takuo Yasunaga Date: Mon, 23 Nov 2020 04:36:23 +0000 (+0900) Subject: Add mrcImageDensityWeightedAreaCalc: X-Git-Tag: v2.3.72p0309 X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=52f9a2f0752fad300172893877546d9c2ad39611;p=eos%2Fbase.git Add mrcImageDensityWeightedAreaCalc: Please enter the commit message for your changes. Lines starting with '#' will be ignored, and an empty message aborts the commit. On branch master Your branch is up to date with 'origin/master'. Changes to be committed: new file: bin/mrcImageDensityWeightedAreaCalc modified: include/lmrcImageCalcArea.h modified: include/lmrcImageFeatureCalc.h modified: include/lmrcImageNormalizing.h modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h modified: src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h modified: src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c modified: src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h modified: src/Objects/DataManip/mrcImage/src/mrcImageInfo.c modified: src/Tools/Config/Define.inc modified: src/Tools/mrcImage/.Source modified: src/Tools/mrcImage/.Source.org new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Define.inc new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/OptionControlFile new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Target.inc new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Makefile new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/doc/Makefile new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/config.h new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/mrcImageDensityWeightedAreaCalc.h new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Depend new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Source new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/Makefile new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/X86MAC64 new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/argCheck.c new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/init.c new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.c new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.html new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.pane new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/Makefile new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/data new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/usage.c new file: src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/util.c modified: src/Tools/mrcImage/mrcImageFeatureCalc/Config/OptionControlFile modified: src/Tools/mrcImage/mrcImageFeatureCalc/inc/mrcImageFeatureCalc.h modified: src/Tools/mrcImage/mrcImageFeatureCalc/src/argCheck.c modified: src/Tools/mrcImage/mrcImageFeatureCalc/src/init.c modified: src/Tools/mrcImage/mrcImageFeatureCalc/src/mrcImageFeatureCalc.pane modified: src/Tools/mrcImage/mrcImageFeatureCalc/src/usage.c --- diff --git a/bin/mrcImageDensityWeightedAreaCalc b/bin/mrcImageDensityWeightedAreaCalc new file mode 120000 index 0000000000..eddb95508d --- /dev/null +++ b/bin/mrcImageDensityWeightedAreaCalc @@ -0,0 +1 @@ +../sbin/MachineIndependent \ No newline at end of file diff --git a/include/lmrcImageCalcArea.h b/include/lmrcImageCalcArea.h index 0e0375bab5..412bd7e496 100644 --- a/include/lmrcImageCalcArea.h +++ b/include/lmrcImageCalcArea.h @@ -9,5 +9,13 @@ # */ +#ifndef __LMRC_IMAGE_CALC_AREA_H +#define __LMRC_IMAGE_CALC_AREA_H + #include "mrcImage.h" void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, int mode); + +void lmrcImageCalcDensityWeightedArea(mrcImage* densityWeightedArea, mrcImage* label, mrcImage* in, mrcImage* inDensity, int neighbor, int mode); + + +#endif // __LMRC_IMAGE_CALC_AREA_H diff --git a/include/lmrcImageFeatureCalc.h b/include/lmrcImageFeatureCalc.h index 46cc9a0bc4..dce148da2b 100644 --- a/include/lmrcImageFeatureCalc.h +++ b/include/lmrcImageFeatureCalc.h @@ -122,7 +122,6 @@ extern void lmrcImageSurfaceAreaCalc(mrcImage* out, mrcImage* in, lmrcImageSurfa extern void lmrcImageSurfaceAreaCalcPrint(FILE* fpt, lmrcImageSurfaceAreaCalcInfo linfo, int mode); extern void lmrcImageSurfaceAreaCalcUsage(FILE* fpt); - extern void lmrcImageCircularityCalc(lmrcImageFeatureList* linfo, int mode); extern void lmrcImageComplexityCalc(lmrcImageFeatureList* linfo, int mode); extern void lmrcImageRadiusCalc(lmrcImageFeatureList* linfo, int mode); diff --git a/include/lmrcImageNormalizing.h b/include/lmrcImageNormalizing.h index f34f145b33..58c83e0e52 100644 --- a/include/lmrcImageNormalizing.h +++ b/include/lmrcImageNormalizing.h @@ -26,7 +26,8 @@ typedef enum lmrcImageNormalizingMode { lmrcImageNormalizingModeUsingContour=2, lmrcImageNormalizingModeUsingContourWithSolventFlattening=3, lmrcImageNormalizingModeNoEstimation=4, - lmrcImageNormalizingModeAssumeGaussian=5 + lmrcImageNormalizingModeAssumeGaussian=5, + lmrcImageNormalizingModeMin75percent=6 } lmrcImageNormalizingMode ; typedef struct lmrcImageNormalizingInfo { diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c index de083758ca..76e82c3d67 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c @@ -12,6 +12,7 @@ #undef DEBUG #include "genUtil.h" #include "Memory.h" +#include "./lmrcImageDensity.h" #include "./lmrcImageLabeling.h" #include "./lmrcImageCalcArea.h" @@ -63,3 +64,83 @@ lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, i mrcStatDataSet(area, 0); } + +void +lmrcImageCalcDensityWeightedArea(mrcImage* area, mrcImage* label, mrcImage* in, mrcImage* inDensity, int neighbor, int mode) +{ + mrcImageParaTypeReal x, y, z; + double data, data0, data1; + int maxLabel, i, inde; + double* sum; + int total; + lmrcImageDensityInfoInfo linfo; + + DEBUGPRINT("lmrcImageCalcArea Start\n"); + lmrcImageLabeling(label, in, neighbor, 0); + mrcStatDataSet(label, 0); + + maxLabel = (int)(label->HeaderAMax+0.5); + sum = (double*)memoryAllocate(sizeof(double)*(maxLabel+1), "in lmrcImageCalcArea"); + + for(i=0; iHeaderN.x; x++) { + for(y=0; yHeaderN.y; y++) { + for(z=0; zHeaderN.z; z++) { + mrcPixelDataGet(label, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest); + mrcPixelDataGet(inDensity, x, y, z, &data1, mrcPixelRePart, mrcPixelHowNearest); + i = (int)(data+0.5); + sum[i]+=data1; + } + } + } + + area->Header = in->Header; + mrcInit(area, NULL); + + for(x=0; xHeaderN.x; x++) { + for(y=0; yHeaderN.y; y++) { + for(z=0; zHeaderN.z; z++) { + mrcPixelDataGet(label, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest); + if(fabs(data)<1e-6) { + mrcPixelDataSet(area, x, y, z, 0, mrcPixelRePart); + } else { + mrcPixelDataSet(area, x, y, z, sum[(int)(data+0.5)], mrcPixelRePart); + } + } + } + } + + linfo.deltaVolume = 0.25; + lmrcImageDensityInfo(&linfo, area, mrcImageDensityInfoPercentageVolume); + + switch(mode) { + case 0: + break; + case 1: // 75% + for(x=0; xHeaderN.x; x++) { + for(y=0; yHeaderN.y; y++) { + for(z=0; zHeaderN.z; z++) { + mrcPixelDataGet(label, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest); + mrcPixelDataGet(area, x, y, z, &data1, mrcPixelRePart, mrcPixelHowNearest); + if(fabs(data)<1e-6) { + mrcPixelDataSet(area, x, y, z, 0, mrcPixelRePart); + } else { + data0 = data1/linfo.percentageVolume.data[1]*0.75; + mrcPixelDataSet(area, x, y, z, data0, mrcPixelRePart); + } + } + } + } + break; + default: { + fprintf(stderr, "Not supported mode in lmrcImageCalcDensityWeightedArea: %d\n", mode); + exit(EXIT_FAILURE); + break; + } + } + mrcStatDataSet(area, 0); +} + + diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h index 0e0375bab5..412bd7e496 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h @@ -9,5 +9,13 @@ # */ +#ifndef __LMRC_IMAGE_CALC_AREA_H +#define __LMRC_IMAGE_CALC_AREA_H + #include "mrcImage.h" void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, int mode); + +void lmrcImageCalcDensityWeightedArea(mrcImage* densityWeightedArea, mrcImage* label, mrcImage* in, mrcImage* inDensity, int neighbor, int mode); + + +#endif // __LMRC_IMAGE_CALC_AREA_H diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h b/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h index 46cc9a0bc4..dce148da2b 100644 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h @@ -122,7 +122,6 @@ extern void lmrcImageSurfaceAreaCalc(mrcImage* out, mrcImage* in, lmrcImageSurfa extern void lmrcImageSurfaceAreaCalcPrint(FILE* fpt, lmrcImageSurfaceAreaCalcInfo linfo, int mode); extern void lmrcImageSurfaceAreaCalcUsage(FILE* fpt); - extern void lmrcImageCircularityCalc(lmrcImageFeatureList* linfo, int mode); extern void lmrcImageComplexityCalc(lmrcImageFeatureList* linfo, int mode); extern void lmrcImageRadiusCalc(lmrcImageFeatureList* linfo, int mode); diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c b/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c index b8329f922f..641d37e9da 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.c @@ -1,13 +1,4 @@ -/* -# %M% %Y% %I% -# The latest update : %G% at %U% -#%Z% lmrcImageNormalizing ver %I% -#%Z% Created by tacyas -#%Z% -#%Z% Usage : lmrcImageNormalizing -#%Z% Attention -#%Z% -*/ +/* # %M% %Y% %I% # The latest update : %G% at %U% #%Z% lmrcImageNormalizing ver %I% #%Z% Created by tacyas #%Z% #%Z% Usage : lmrcImageNormalizing #%Z% Attention #%Z% */ #include #include static char __sccs_id[] = "%Z%lmrcImageNormalizing ver%I%; Date:%D% %Z%"; @@ -55,6 +46,8 @@ lmrcImageNormalizingModePrint(FILE* fpt, int mode) fprintf(fpt, " data = A*data + B \n"); fprintf(fpt, "%3d: Assume the density as gaussion.\n", lmrcImageNormalizingModeAssumeGaussian); fprintf(fpt, " data = A*Normalized(data) + B , where normalized means (average=0, SD=1)\n"); + fprintf(fpt, "%3d: Min-75percent: Background and Object(75)\n", lmrcImageNormalizingModeMin75percent); + fprintf(fpt, " data = A*(data-Min)/(75percent-Min)x0.75 + B \n"); } void @@ -155,6 +148,18 @@ lmrcImageNormalizing(mrcImage* out, mrcImage* in, lmrcImageNormalizingInfo* linf } break; } + case lmrcImageNormalizingModeMin75percent: { + for(x=0; xHeaderN.x; x++) { + for(y=0; yHeaderN.y; y++) { + for(z=0; zHeaderN.z; z++) { + mrcPixelDataGet(in, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest); + data = linfo->A*(data - in->HeaderAMin)/(in->HeaderAMax - in->HeaderAMax)*0.75 + linfo->B; + mrcPixelDataSet(out, x, y, z, data, mrcPixelRePart); + } + } + } + break; + } case lmrcImageNormalizingModeUsingContour: { for(x=0; xHeaderN.x; x++) { for(y=0; yHeaderN.y; y++) { diff --git a/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h b/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h index f34f145b33..58c83e0e52 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h +++ b/src/Objects/DataManip/mrcImage/src/lmrcImageNormalizing.h @@ -26,7 +26,8 @@ typedef enum lmrcImageNormalizingMode { lmrcImageNormalizingModeUsingContour=2, lmrcImageNormalizingModeUsingContourWithSolventFlattening=3, lmrcImageNormalizingModeNoEstimation=4, - lmrcImageNormalizingModeAssumeGaussian=5 + lmrcImageNormalizingModeAssumeGaussian=5, + lmrcImageNormalizingModeMin75percent=6 } lmrcImageNormalizingMode ; typedef struct lmrcImageNormalizingInfo { diff --git a/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c b/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c index 255f91657b..8995b8635a 100755 --- a/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c +++ b/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c @@ -1002,6 +1002,5 @@ lmrcImageInformation(mrcImageInformation* info, mrcImage* img) exit(EXIT_FAILURE); } } - } diff --git a/src/Tools/Config/Define.inc b/src/Tools/Config/Define.inc index 1f12516874..165c17dc76 100644 --- a/src/Tools/Config/Define.inc +++ b/src/Tools/Config/Define.inc @@ -29,3 +29,10 @@ WORLDNAME=Tools WORLDNAME=Tools WORLDNAME=Tools WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools +WORLDNAME=Tools diff --git a/src/Tools/mrcImage/.Source b/src/Tools/mrcImage/.Source index 6545c9cb5a..67d45743cc 100644 --- a/src/Tools/mrcImage/.Source +++ b/src/Tools/mrcImage/.Source @@ -97,6 +97,7 @@ mrcImageDensityChangeEstimation \ mrcImageDensityInfo \ mrcImageDensityNormalization \ mrcImageDensityNormalizationByImage \ +mrcImageDensityWeightedAreaCalc \ mrcImageDilation \ mrcImageDisplayDensityAsTempFactor \ mrcImageDistanceConversion \ diff --git a/src/Tools/mrcImage/.Source.org b/src/Tools/mrcImage/.Source.org index c02c7fe500..6545c9cb5a 100644 --- a/src/Tools/mrcImage/.Source.org +++ b/src/Tools/mrcImage/.Source.org @@ -122,6 +122,7 @@ mrcImageFilamentSearchResultShow \ mrcImageFilterCreate \ mrcImageFilteringbyFile \ mrcImageFilteringbyFileForVariance \ +mrcImageFlatFieldCorrection \ mrcImageFloating \ mrcImageFourierNeighborCorrelation \ mrcImageFourierPowerSpectrum \ diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Define.inc b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Define.inc new file mode 100755 index 0000000000..ec581b332e --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Define.inc @@ -0,0 +1,4 @@ +OBJECTNAME = mrcImageDensityWeightedAreaCalc +EXTRA_LIB = +EXTRA_CCOPTS = +EXTRA_INC = diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/OptionControlFile new file mode 100755 index 0000000000..86f9e01789 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/OptionControlFile @@ -0,0 +1,9 @@ +# OptionControlFile +# FileFormat +"-i","-i[nput]","Input:binary","Essential","1","1","In","inFile::mrcImage","NULL" +"-d","-d[ensity]","Input:density","Essential","1","1","InDensity","inFile::mrcImage","NULL" +"-o","-o[utput]","Output:weightedArea","Essential","1","1","Out","outFile::mrcImage","NULL" +"-oL","-o[utput]L[abel]","Output:Label","Optional","1","1","OutLabel","outFile::mrcImage","NULL" +"-n","-n[eighbor]","Neighbor:[6|8]","Optional","1","1","Neighbor","Integer","8" +"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL" +"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0" diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Target.inc b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Config/Target.inc new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Makefile b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Makefile new file mode 100755 index 0000000000..3d1cbd98da --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/Makefile @@ -0,0 +1,115 @@ +include ../../../Config/Define.inc +include ../../Config/Define.inc +include ../Config/Define.inc +include Config/Define.inc + +all: + cd src; make all; cd .. + +install: + cd src; make install; cd .. + + +putSF: + if [ -f private ] ; \ + then \ + echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \ + else \ + cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit || cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \ + fi + +put: + cd src; make put; cd .. + +clean: + cd src; make clean; cd .. + +depend: + cd src; make depend; cd .. + +check: + @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \ + echo making directory; \ + mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \ + fi + ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); + @$(RM) src/Makefile + @echo "New src/Makefile" + @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile + @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; make depend + +update: + @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \ + echo making directory; \ + mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \ + fi + ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE); + @$(RM) src/Makefile + @echo "New src/Makefile" + @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile + @cd src; rm -f $(OSTYPE)/.Depend; touch $(OSTYPE)/.Depend; echo "Y" | make update + +cvsupdate:: + cvs -d $(EOS_CVSROOT) update -d + +cvscommit:: + cvs -d $(EOS_CVSROOT) commit + +backup: + @cd ../../../..; \ + echo $(OBJECTNAME) ; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \ + tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile + +backup-all: + @cd ../../../..; \ + echo $(OBJECTNAME) ; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \ + tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile + +distribute: + cd ../../../..; \ + echo $(OBJECTNAME) ; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \ + tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) + +distribute-all: + @cd ../../../..; \ + echo $(OBJECTNAME) ; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z]*.[A-z]*; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \ + tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) + +eosintroduce: + ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./ + +include Config/Target.inc diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/doc/Makefile b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/doc/Makefile new file mode 100755 index 0000000000..8215199e1b --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/doc/Makefile @@ -0,0 +1,2 @@ +install: + cd ../src; make install-doc; cd ../doc diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/config.h b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/config.h new file mode 100755 index 0000000000..7c883e70b2 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/config.h @@ -0,0 +1,6 @@ +#ifndef CONFIG_H +#define CONFIG_H + +#include "../inc/mrcImageDensityWeightedAreaCalc.h" + +#endif /* CONFIG_H */ diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/mrcImageDensityWeightedAreaCalc.h b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/mrcImageDensityWeightedAreaCalc.h new file mode 100755 index 0000000000..2a2083adef --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/inc/mrcImageDensityWeightedAreaCalc.h @@ -0,0 +1,57 @@ +#ifndef MRCIMAGEDENSITYWEIGHTEDAREACALC_H +#define MRCIMAGEDENSITYWEIGHTEDAREACALC_H +#include +#include + +#define OPTION_FLAG '-' +#define OPTION_FLAG_POS (0) +#define OPTION_POS (1) + + + + +typedef struct mrcImageDensityWeightedAreaCalcInfo { + long flagRedirect; + + long flagIn; + char* In; + FILE* fptIn; + + long flagInDensity; + char* InDensity; + FILE* fptInDensity; + + long flagOut; + char* Out; + FILE* fptOut; + + long flagOutLabel; + char* OutLabel; + FILE* fptOutLabel; + + long flagNeighbor; + long Neighbor; + + long flagconfigFile; + char* configFile; + FILE* fptconfigFile; + + long flagmode; + long mode; + +} mrcImageDensityWeightedAreaCalcInfo; +#ifdef __cplusplus +extern "C" { +#endif +extern void argCheck(mrcImageDensityWeightedAreaCalcInfo* info, int argc, char* avgv[]); +extern void khorosInit(int argc, char* avgv[]); +extern void init0(mrcImageDensityWeightedAreaCalcInfo* info); +extern void init1(mrcImageDensityWeightedAreaCalcInfo* info); +extern void usage(char* usage); +extern void additionalUsage(void); +extern void htmlBeforeUsage(char* usage); +extern void htmlAfterUsage(char* usage); +#ifdef __cplusplus +}; +#endif +#endif /* MRCIMAGEDENSITYWEIGHTEDAREACALC_H */ diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Depend b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Depend new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Source b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/.Source new file mode 100755 index 0000000000..e69de29bb2 diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/Makefile b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/Makefile new file mode 100755 index 0000000000..a360703891 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/Makefile @@ -0,0 +1,430 @@ +include ../Config/Define.inc +include ../../Config/Define.inc +include ../../../Config/Define.inc +include ../../../../Config/Define.inc + +EOSHOME=../../../../../ +DSTDIR=$(EOSHOME)/bin +DSTDOC=$(EOSHOME)/doc +DSTTAR=$(EOSHOME)/tar + +INCFILES = + +LIBFILES = \ + $(LIBPREFIX)EosObjects$(LIBSUFFIX) + +LIBFILESDEBUG = \ + $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX) + +SRCC = \ + $(OBJECTNAME).c \ + init.c \ + argCheck.c \ + usage.c \ + util.c \ + +SRCCXX = \ + $(OBJECTNAME).cc \ + init.cc \ + argCheck.cc \ + usage.cc \ + util.cc \ + +MODULES = \ + $(OBJECTNAME).o \ + init.o \ + argCheck.o \ + usage.o \ + util.o \ + +REALMODULES = \ + $(OSTYPE)/$(OBJECTNAME).o \ + $(OSTYPE)/init.o \ + $(OSTYPE)/argCheck.o \ + $(OSTYPE)/usage.o \ + $(OSTYPE)/util.o + +MODULESDEBUG = \ + $(OBJECTNAME).debugo \ + init.debugo \ + argCheck.debugo \ + usage.debugo \ + util.debugo \ + +REALMODULESDEBUG = \ + $(OSTYPE)/$(OBJECTNAME).debugo \ + $(OSTYPE)/init.debugo \ + $(OSTYPE)/argCheck.debugo \ + $(OSTYPE)/usage.debugo \ + $(OSTYPE)/util.debugo + + +all: $(OSTYPE)/$(OBJECTNAME) + if [ ! -L $(OSTYPE) ] ; then \ + moveHostdependent; \ + fi + +debug: $(OSTYPE)/$(OBJECTNAME).debug + +cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb + + +$(OSTYPE)/$(OBJECTNAME):: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +$(OSTYPE)/$(OBJECTNAME).debug:: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +$(OSTYPE)/$(OBJECTNAME).cudagdb:: + @$(RM) -f $(OSTYPE)/Makefile ; \ + $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \ + cd $(OSTYPE); \ + $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME) + +cvsupdate:: + cvs -d $(EOS_CVSROOT) update -d + +cvscommit:: + cvs -d $(EOS_CVSROOT) commit + +edit: + @if [ -r $(OBJECTNAME).c ]; \ + then \ + sccsEdit $(OBJECTNAME).c; \ + else \ + echo "Source files are already editable"; \ + fi + @if [ -r wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsEdit $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are already editable."; \ + fi + @if [ -r ruby/$(OBJECTNAME).rb ]; \ + then \ + cd ruby; sccsEdit $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are already editable."; \ + fi + @if [ -r perl/$(OBJECTNAME).pl ]; \ + then \ + cd perl; sccsEdit $(OBJECTNAME).pl ; \ + else \ + echo "Source files (perl) are already editable."; \ + fi + @if [ -r ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsEdit OptionControlFile; \ + else \ + echo "OptionControlFile are already editable."; \ + fi + +unedit: + @if [ -w $(OBJECTNAME).c ]; \ + then \ + sccsUnedit $(OBJECTNAME).c; \ + else \ + echo "Source files are not editable"; \ + fi + @if [ -w wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsUnedit $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are not editable."; \ + fi + @if [ -w ruby/$(OBJECTNAME).rb]; \ + then \ + cd ruby; sccsUnedit $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are not editable."; \ + fi + @if [ -w perl/$(OBJECTNAME).pl ]; \ + then \ + cd perl; sccsUnedit $(OBJECTNAME).pl ; \ + else \ + echo "Source files (ruby) are not editable."; \ + fi + @if [ -w ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsUnedit OptionControlFile; \ + else \ + echo "OptionControlFile are not editable."; \ + fi + +report: + @if [ -r $(OBJECTNAME).c ]; \ + then \ + sccsReport $(OBJECTNAME).c; \ + else \ + echo "Source files are already editable"; \ + fi + @if [ -r wish/$(OBJECTNAME).wish ]; \ + then \ + cd wish; sccsReport $(OBJECTNAME).wish; \ + else \ + echo "Source files (wish) are already editable."; \ + fi + @if [ -r ruby/$(OBJECTNAME).rb ]; \ + then \ + cd ruby; sccsReport $(OBJECTNAME).rb; \ + else \ + echo "Source files (ruby) are already editable."; \ + fi + @if [ -r perl/$(OBJECTNAME).pl ] ; \ + then \ + cd perl; sccsReport $(OBJECTNAME).pl ; \ + else \ + echo "Source files (perl) are already editable."; \ + fi + @if [ -r ../Config/OptionControlFile ]; \ + then \ + cd ../Config; sccsReport OptionControlFile; \ + else \ + echo "OptionControlFile are already editable."; \ + fi + +clean : + rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \ + $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \ + $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \ + $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \ + $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \ + *.bak *.$(OSTYPE) core + +install: install-bin install-doc install-wish install-ruby install-shell install-perl + @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \ + then \ + if [ -x $(KHOROS_KGENOBJ) ] ; \ + then \ + make install-khoros ; \ + fi; \ + fi + +install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) + +$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME) + @echo ---- Installing to bin + @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME) + @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \ + then \ + mkdir $(DSTDIR)/$(OSTYPE); \ + fi + @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \ + then \ + echo "Compilation is complete"; \ + $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \ + $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \ + $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \ + else \ + echo "Compilation is incomplete. $(OBJECTNAME)"; \ + fi + @echo ---- end of bin + +install-wish: + @if [ -d wish ]; \ + then \ + echo "---- Tcl/Tk file Install"; \ + if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\ + touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\ + $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\ + echo "---- Tcl/Tk file Installed";\ + fi + +install-ruby: + @if [ -d ruby ]; \ + then \ + echo "---- Ruby/Tk file Install"; \ + if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \ + echo "---- Ruby/Tk file Installed"; \ + fi + +install-perl: + @if [ -d perl ]; \ + then \ + echo "---- Perl/Tk file Install"; \ + if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \ + fi; \ + $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \ + echo "---- Perl/Tk file Installed"; \ + fi + +install-shell: + @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \ + fi + @if [ -d shell ]; \ + then \ + echo "---- Shell file Install"; \ + if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \ + then \ + mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \ + fi ; \ + $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \ + $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \ + echo "---- Shell file Installed"; \ + fi + +install-khoros: + @echo Installing to khoros + @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \ + then \ + echo kgenobj;\ + $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \ + fi + @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \ + then \ + $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \ + fi + @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \ + then \ + $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \ + if [ $? ] ; \ + then \ + echo "-- setting khoros ---" ; \ + if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \ + then \ + $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \ + $(RM) -f $(OBJECTNAME).pane ; \ + $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \ + $(CD) ../../ ; \ + $(CHMOD) -R 555 $(OBJECTNAME); \ + else \ + echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \ + fi ; \ + else \ + echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \ + fi ; \ + echo "-- end of khoros-installing"; \ + fi + +install-doc: html + @if [ ! -d $(DSTDOC)/SmallTools ]; \ + then \ + mkdir $(DSTDOC)/SmallTools ;\ + fi + @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \ + then \ + $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\ + fi + @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @if [ -f ../doc/*.html ]; \ + then \ + $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\ + fi + @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html + @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \ + then \ + cd $(DSTDOC)/SmallTools; $(MAKE); \ + fi + +html: $(OBJECTNAME).html + +configFileRead: + @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile + +$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME) + @echo creating html + @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp + @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html + @$(RM) $(OBJECTNAME).html.tmp + +$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME) + @ln -s -f ../sbin/MachineIndependent $@ + +depend:: + @echo dependency checking now + @if [ ! -L $(OSTYPE) ] ; then \ + moveHostdependent; \ + fi + rm -f $(OSTYPE)/.Depend + #echo C + @if [ -f $(OBJECTNAME).c ] ; \ + then \ + echo "dependency: *.c"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \ + fi + #echo CC + @if [ -f $(OBJECTNAME).cc ] ; \ + then \ + echo "dependency: *.cc"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \ + fi + @if [ -f $(OBJECTNAME).ccm ] ; \ + then \ + echo "dependency: *.ccm"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \ + fi + @if [ -f $(OBJECTNAME).cu ] ; \ + then \ + echo "dependency: *.cu"; \ + echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \ + $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \ + fi + +update:../Config/OptionControlFile + maketool $(CLASSNAME) $(OBJECTNAME) update + +updateNoAns:../Config/OptionControlFile + maketool $(CLASSNAME) $(OBJECTNAME) update N + +changeName:: + +Test:$(OSTYPE)/$(OBJECTNAME) TestDir + @if [ -f test/Makefile ] ; \ + then \ + cd test; make ; \ + else \ + echo "No test Makefile"; \ + fi + +TestDir:: + @if [ ! -d test ] ; \ + then \ + echo "Creating test dir"; \ + mkdir test; \ + fi + @if [ ! -f test/Makefile ] ; \ + then \ + echo "Creating Makefile"; \ + cd test; \ + protoTestMakefileCreate; \ + fi + @if [ ! -d test/data ]; \ + then \ + mkdir $(EOSHOME)/data/$(OBJECTNAME); \ + cd test; \ + ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \ + fi + +tar:: + cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \ + ../bin/*/$(OBJECTNAME).* \ + ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \ + ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar + +-include $(OSTYPE)/.Depend +-include ../Config/Target.inc diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/X86MAC64 b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/X86MAC64 new file mode 120000 index 0000000000..2d488ec31e --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/X86MAC64 @@ -0,0 +1 @@ +../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/X86MAC64 \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/argCheck.c b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/argCheck.c new file mode 100755 index 0000000000..9a0c4a89e2 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/argCheck.c @@ -0,0 +1,129 @@ +#include +#include +#include +#include +#include "../inc/config.h" +#include "genUtil.h" +#include "eosString.h" +#include "File.h" +#include "Memory.h" + + +void +argCheck(mrcImageDensityWeightedAreaCalcInfo* info, int argc, char* argv[]) +{ + long i; + char s[1024]; + FILE* fpt; + + if(NULL==(fpt=fopen(".EosLog", "a+"))) { + + } else { + for(i=0; iIn = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagIn++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("d") { + if(i+1InDensity = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagInDensity++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("o") { + if(i+1Out = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagOut++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("oL") { + if(i+1OutLabel = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagOutLabel++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("n") { + if(i+1Neighbor = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagNeighbor++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("c") { + if(i+1configFile = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagconfigFile++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("m") { + if(i+1mode = stringGetNthIntegerData(argv[i+1], 1, " ,"); + i++; + info->flagmode++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("h") { + usage(argv[0]); + exit(EXIT_SUCCESS); + break; + } + SCASE("html") { + htmlBeforeUsage(argv[0]); + usage(argv[0]); + htmlAfterUsage(argv[0]); + exit(EXIT_SUCCESS); + break; + } + SDEFAULT { + fprintf(stderr, "Not Supported Options: :%s\n", argv[i]); + usage(argv[0]); + exit(EXIT_FAILURE); + break; + } + SSWITCHEND; + } + } +} diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/init.c b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/init.c new file mode 100755 index 0000000000..41cb124c29 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/init.c @@ -0,0 +1,110 @@ +#include +#include +#include +#include +#include "../inc/config.h" +#include "genUtil.h" +#include "eosString.h" +#include "File.h" +#include "Memory.h" + + +void +init0(mrcImageDensityWeightedAreaCalcInfo* info) +{ + info->fptIn = NULL; info->flagIn = 0; + info->fptInDensity = NULL; info->flagInDensity = 0; + info->fptOut = NULL; info->flagOut = 0; + info->fptOutLabel = NULL; info->flagOutLabel = 0; + info->Neighbor = 8; info->flagNeighbor = 0; + info->fptconfigFile = NULL; info->flagconfigFile = 0; + info->mode = 0; info->flagmode = 0; +} + +void +init1(mrcImageDensityWeightedAreaCalcInfo* info) +{ + char s[1024]; + int i; + if(!info->flagIn) { + stringGetFromFile(s, "In", stdin, stdout, 0); + info->In = stringGetNthWord(s, 1, " ,\t"); + info->flagIn++; + } + if(info->flagIn) { + info->fptIn = fileOpen(info->In, "r"); + } + + if(!info->flagInDensity) { + stringGetFromFile(s, "InDensity", stdin, stdout, 0); + info->InDensity = stringGetNthWord(s, 1, " ,\t"); + info->flagInDensity++; + } + if(info->flagInDensity) { + info->fptInDensity = fileOpen(info->InDensity, "r"); + } + + if(!info->flagOut) { + stringGetFromFile(s, "Out", stdin, stdout, 0); + info->Out = stringGetNthWord(s, 1, " ,\t"); + info->flagOut++; + } + if(info->flagOut) { + info->fptOut = fileOpen(info->Out, "w"); + } + + if(info->flagOutLabel) { + info->fptOutLabel = fileOpen(info->OutLabel, "w"); + } + + if(info->flagNeighbor) { + } + + if(info->flagconfigFile) { + info->fptconfigFile = fileOpen(info->configFile, "r"); + } + + if(info->flagmode) { + } + +} +#ifdef KHOROS +#include +#include "bootstrap.h" +#include "dataserv.h" +#include "datamanip.h" +extern void func_usage_additions(void); +extern void func_free_args(kexit_status status, kaddr client_data); +extern void func_get_args(kform* pane); + +void +func_usage_additions(void) +{ +} +void +func_free_args(kexit_status status, kaddr client_data) +{ +} +void +func_get_args(kform* pane) +{ +} +void +khorosInit(int argc, char* argv[]) +{ + char* eospath; + char panepath[1024]; + FILE* fpt; + + eospath = getenv("EOS_HOME"); + sprintf(panepath, "%s/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.pane", eospath); + khoros_initialize(argc, argv, "EOS"); + fpt = fopen(panepath, "r"); if(NULL!=fpt) { + fclose(fpt); + kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImageDensityWeightedAreaCalc", + func_usage_additions, + func_get_args, + func_free_args); + } +} +#endif /* KHOROS */ diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.c b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.c new file mode 100755 index 0000000000..8e87dad321 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.c @@ -0,0 +1,71 @@ +/* +# mrcImageDensityWeightedAreaCalc : $Revision$ +# $Date$ +# Created by $Author$ +# Usage : mrcImageDensityWeightedAreaCalc +# Attention +# $Loccker$ +# $State$ +# +*/ +#include +#include +#include +#include +#define GLOBAL_DECLARATION +#include "../inc/config.h" + +#define DEBUG +#include "genUtil.h" +#include "mrcImage.h" +#include "lmrcImageCalcArea.h" + +/* +Example: +typedef struct lmrcImageDensityWeightedAreaCalcInfo { + float a; + int b; +} lmrcImageDensityWeightedAreaCalcInfo; + +typedef enum lmrcImageDensityWeightedAreaCalcMode { + a=0, + b=1 +} lmrcImageDensityWeightedAreaCalcMode; +*/ + +int +main(int argc, char* argv[]) +{ + mrcImage in; + mrcImage inDens; + mrcImage out; + mrcImage label; + + mrcImageDensityWeightedAreaCalcInfo info; + + init0(&info); + argCheck(&info, argc, argv); + init1(&info); + + DEBUGPRINT("Program Start\n"); + + mrcFileRead(&in, info.In, "in main", 0); + mrcFileRead(&inDens, info.InDensity, "in main", 0); + + lmrcImageCalcDensityWeightedArea(&out, &label, &in, &inDens, info.Neighbor, info.mode); + + if(info.flagOutLabel) { + mrcFileWrite(&label, info.OutLabel, "in main", 0); + } + mrcFileWrite(&out, info.Out, "in main", 0); + exit(EXIT_SUCCESS); +} + +void +additionalUsage() +{ + fprintf(stderr, "----- Additional Usage -----\n"); + fprintf(stderr, "-m \n"); + fprintf(stderr, " 0: Sum of density\n"); + fprintf(stderr, " 1: Transform top of 75 pecents of sum of density to 0.75\n"); +} diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.html b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.html new file mode 100755 index 0000000000..6322399c6a --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.html @@ -0,0 +1,24 @@ + + +mrcImageDensityWeightedAreaCalc + + +

mrcImageDensityWeightedAreaCalc

+

Usage

+
+Usage: mrcImageDensityWeightedAreaCalc
+Options:
+    [-i[nput]            In                  (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:binary
+    [-d[ensity]          InDensity           (NULL      ).as(inFile::mrcImage    ) ] :Essential :Input:density
+    [-o[utput]           Out                 (NULL      ).as(outFile::mrcImage   ) ] :Essential :Output:weightedArea
+    [-o[utput]L[abel]    OutLabel            (NULL      ).as(outFile::mrcImage   ) ] :Optional  :Output:Label
+    [-n[eighbor]         Neighbor            (8         ).as(Integer             ) ] :Optional  :Neighbor:[6|8]
+    [-c[onfig]           configFile          (NULL      ).as(inFile              ) ] :Optional  :ConfigurationFile
+    [-m[ode]             mode                (0         ).as(Integer             ) ] :Optional  :Mode
+----- Additional Usage -----
+-m 
+    0: Sum of density
+    1: Transform top of 75 pecents of sum of density to 0.75
+
+ + diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.pane b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.pane new file mode 100755 index 0000000000..148eaf9584 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/mrcImageDensityWeightedAreaCalc.pane @@ -0,0 +1,19 @@ +-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata + -M 1 1 52x1+0+0 +1+0 ' ' subform + -P 1 0 52x1+0+1 +0+0 ' ' mrcImageDensityWeightedAreaCalc + -D 1 0 9x1+0+0 'Options' _gui_options + -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license + -E + -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageDensityWeightedAreaCalc + -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/doc/mrcImageDensityWeightedAreaCalc.doc help + -Q 1 0 5.25x1+47+0 'Close' + -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:binary' i + -I 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'InDensity' 'Input:density' d + -O 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'Out' 'Output:weightedArea' o + -O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'OutLabel' 'Output:Label' oL + -i 1 0 1 0 0 -1x1+1+7.500000 0 0 8 0 0 'Neighbor' 'Neighbor:[6|8]' n + -I 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'configFile' 'ConfigurationFile' c + -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'mode' 'Mode' m + -E + -E +-E diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/Makefile b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/Makefile new file mode 100755 index 0000000000..e4091569d7 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/Makefile @@ -0,0 +1,26 @@ +include ../../Config/Define.inc +include ../../../Config/Define.inc +include ../../../../Config/Define.inc +include ../../../../../Config/Define.inc + +DATA=data/TEM_filter_sample + +all: help exec exec1 + +help: + @echo "----- Help Message Check -----" + @../$(OSTYPE)/$(OBJECTNAME) -h + +exec: + @echo "----- Execution Check -----" + ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).bin3 -d $(DATA).mrc3 -o $(DATA)-8.densWA -oL $(DATA)-8.label -n 8 -m 0 + ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).bin3 -d $(DATA).mrc3 -o $(DATA)-4.densWA -oL $(DATA)-4.label -n 4 -m 0 + @echo "----- Calc check -----" + +exec1: + @echo "----- Execution Check -----" + ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).bin3 -d $(DATA).mrc3 -o $(DATA)-8-1.densWA -oL $(DATA)-8-1.label -n 8 -m 1 + ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).bin3 -d $(DATA).mrc3 -o $(DATA)-4-1.densWA -oL $(DATA)-4-1.label -n 4 -m 1 + @echo "----- Calc check -----" + +clean: diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/data b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/data new file mode 120000 index 0000000000..80a2e2789f --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/test/data @@ -0,0 +1 @@ +../../../../../..//data/mrcImageDensityWeightedAreaCalc \ No newline at end of file diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/usage.c b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/usage.c new file mode 100755 index 0000000000..85482e6fe0 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/usage.c @@ -0,0 +1,39 @@ +#include +#include +#include "../inc/config.h" + +void +usage(char* thisProgram) +{ + fprintf(stderr, "Usage: %s\n", thisProgram); + fprintf(stderr, "Options:\n"); + fprintf(stderr, " [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:binary\n"); + fprintf(stderr, " [-d[ensity] InDensity (NULL ).as(inFile::mrcImage ) ] :Essential :Input:density\n"); + fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:weightedArea\n"); + fprintf(stderr, " [-o[utput]L[abel] OutLabel (NULL ).as(outFile::mrcImage ) ] :Optional :Output:Label\n"); + fprintf(stderr, " [-n[eighbor] Neighbor (8 ).as(Integer ) ] :Optional :Neighbor:[6|8]\n"); + fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n"); + fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n"); + additionalUsage(); +} + +void +htmlBeforeUsage(char* thisProgram) +{ + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "%s\n", thisProgram); + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "

%s

\n", thisProgram); + fprintf(stderr, "

Usage

\n"); + fprintf(stderr, "
\n");
+}
+
+void
+htmlAfterUsage(char* thisProgram)
+{
+    fprintf(stderr, "
\n"); + fprintf(stderr, "\n"); + fprintf(stderr, "\n"); +} diff --git a/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/util.c b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/util.c new file mode 100755 index 0000000000..ee5e5f2324 --- /dev/null +++ b/src/Tools/mrcImage/mrcImageDensityWeightedAreaCalc/src/util.c @@ -0,0 +1,4 @@ +#include +#include +#include "../inc/config.h" + diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/Config/OptionControlFile b/src/Tools/mrcImage/mrcImageFeatureCalc/Config/OptionControlFile index 4a45855ed2..d33f48c19a 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/Config/OptionControlFile +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/Config/OptionControlFile @@ -8,5 +8,6 @@ "-oC","-o[utput]C[hainID]","Output:ChainID","Optional","1","1","OutChain","outFile::mrcImage","NULL" "-oS","-o[utput]S[urfaceArea]","Output:SurfaceArea","Optional","1","1","OutSurfaceArea","outFile::mrcImage","NULL" "-n","-n[eighbor]","Neighbor: [4(0)|8 or 6(0)|18|26]","Optional","1","1","neighbor","Integer","0" +"-d","-d[ensity]","Input:binary","Optional","1","1","InDensity","inFile::mrcImage","NULL" "-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL" "-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0" diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/inc/mrcImageFeatureCalc.h b/src/Tools/mrcImage/mrcImageFeatureCalc/inc/mrcImageFeatureCalc.h index c98eb42532..57f097bb7d 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/inc/mrcImageFeatureCalc.h +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/inc/mrcImageFeatureCalc.h @@ -44,6 +44,10 @@ typedef struct mrcImageFeatureCalcInfo { long flagneighbor; long neighbor; + long flagInDensity; + char* InDensity; + FILE* fptInDensity; + long flagconfigFile; char* configFile; FILE* fptconfigFile; diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/src/argCheck.c b/src/Tools/mrcImage/mrcImageFeatureCalc/src/argCheck.c index 51829bbf67..95dd29fb85 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/src/argCheck.c +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/src/argCheck.c @@ -116,6 +116,17 @@ argCheck(mrcImageFeatureCalcInfo* info, int argc, char* argv[]) } SBREAK; } + SCASE("d") { + if(i+1InDensity = stringGetNthWord(argv[i+1], 1, " ,"); + i++; + info->flagInDensity++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } SCASE("c") { if(i+1configFile = stringGetNthWord(argv[i+1], 1, " ,"); diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/src/init.c b/src/Tools/mrcImage/mrcImageFeatureCalc/src/init.c index fd549e8925..ec66e67652 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/src/init.c +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/src/init.c @@ -20,6 +20,7 @@ init0(mrcImageFeatureCalcInfo* info) info->fptOutChain = NULL; info->flagOutChain = 0; info->fptOutSurfaceArea = NULL; info->flagOutSurfaceArea = 0; info->neighbor = 0; info->flagneighbor = 0; + info->fptInDensity = NULL; info->flagInDensity = 0; info->fptconfigFile = NULL; info->flagconfigFile = 0; info->mode = 0; info->flagmode = 0; } @@ -65,6 +66,10 @@ init1(mrcImageFeatureCalcInfo* info) if(info->flagneighbor) { } + if(info->flagInDensity) { + info->fptInDensity = fileOpen(info->InDensity, "r"); + } + if(info->flagconfigFile) { info->fptconfigFile = fileOpen(info->configFile, "r"); } diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/src/mrcImageFeatureCalc.pane b/src/Tools/mrcImage/mrcImageFeatureCalc/src/mrcImageFeatureCalc.pane index 82bd268f5f..acf873bd59 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/src/mrcImageFeatureCalc.pane +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/src/mrcImageFeatureCalc.pane @@ -15,8 +15,9 @@ -O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'OutChain' 'Output:ChainID' oC -O 1 0 1 0 0 1 -1x1+1+10.500000 ' ' 'OutSurfaceArea' 'Output:SurfaceArea' oS -i 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'neighbor' 'Neighbor: [4(0)|8 or 6(0)|18|26]' n - -I 1 0 1 0 0 1 -1x1+1+13.500000 ' ' 'configFile' 'ConfigurationFile' c - -i 1 0 1 0 0 -1x1+1+15.000000 0 0 0 0 0 'mode' 'Mode' m + -I 1 0 1 0 0 1 -1x1+1+13.500000 ' ' 'InDensity' 'Input:binary' d + -I 1 0 1 0 0 1 -1x1+1+15.000000 ' ' 'configFile' 'ConfigurationFile' c + -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'mode' 'Mode' m -E -E -E diff --git a/src/Tools/mrcImage/mrcImageFeatureCalc/src/usage.c b/src/Tools/mrcImage/mrcImageFeatureCalc/src/usage.c index 30c9f70d21..4a3b1cab00 100755 --- a/src/Tools/mrcImage/mrcImageFeatureCalc/src/usage.c +++ b/src/Tools/mrcImage/mrcImageFeatureCalc/src/usage.c @@ -15,6 +15,7 @@ usage(char* thisProgram) fprintf(stderr, " [-o[utput]C[hainID] OutChain (NULL ).as(outFile::mrcImage ) ] :Optional :Output:ChainID\n"); fprintf(stderr, " [-o[utput]S[urfaceArea]OutSurfaceArea (NULL ).as(outFile::mrcImage ) ] :Optional :Output:SurfaceArea\n"); fprintf(stderr, " [-n[eighbor] neighbor (0 ).as(Integer ) ] :Optional :Neighbor: [4(0)|8 or 6(0)|18|26]\n"); + fprintf(stderr, " [-d[ensity] InDensity (NULL ).as(inFile::mrcImage ) ] :Optional :Input:binary\n"); fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n"); fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n"); additionalUsage();