From: Takuo Yasunaga Date: Tue, 25 Jun 2013 21:58:27 +0000 (+0900) Subject: modified: src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/ X-Git-Url: http://git.osdn.net/view?a=commitdiff_plain;h=bc864cd5e1295da56ebe04968aaf91aadec55c7f;p=eos%2FhostdependX86LINUX64.git modified: src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/ Add the function of range restriction related: modified: src/Objects/DataManip/mrcImage/inc/mrcImage.h related: modified: src/Objects/DataManip/mrcImage/src/mrcImageInfo.c modified: src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h modified: src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c related: previous modification for arrayPCA(add average argument); --- diff --git a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D b/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D index e3b322d202..57c616647a 100755 Binary files a/hostdepend/X86LINUX64/bin/X86LINUX64/mrcImageAutoRotationCorrelation3D and 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100644 Binary files a/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/mrcImageInfo.sharedo and b/hostdepend/X86LINUX64/src/Objects/DataManip/mrcImage/src/X86LINUX64/mrcImageInfo.sharedo differ diff --git a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D index e3b322d202..57c616647a 100755 Binary files a/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D and b/hostdepend/X86LINUX64/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/X86LINUX64/mrcImageAutoRotationCorrelation3D differ diff --git a/include/lmrcSinogramFET.h b/include/lmrcSinogramFET.h index 316d7148ad..91145e2c6c 100644 --- a/include/lmrcSinogramFET.h +++ b/include/lmrcSinogramFET.h @@ -34,6 +34,7 @@ typedef struct lmrcSinogramFETPCAInfo{ int flagInImage; mrcImage* inImage; Array X; + Array Ave; Array C; Array u; Array lambda; diff --git a/include/mrcImage.h b/include/mrcImage.h index 7365369c4d..68f472e2ca 100644 --- a/include/mrcImage.h +++ b/include/mrcImage.h @@ -318,6 +318,22 @@ typedef struct mrcImageInformation { long flagrmax; double RMS; /* Root mean square */ int mode; + + /* For Search Area */ + int flagXrange; + int flagYrange; + int flagZrange; + double XrangeMin; + double XrangeMax; + double YrangeMin; + double YrangeMax; + double ZrangeMin; + double ZrangeMax; + + int flagCentre; + double CentreX; + double CentreY; + double CentreZ; } mrcImageInformation; /* struct end */ diff --git a/src/Objects/DataManip/mrcImage/doc/mrcImage.html b/src/Objects/DataManip/mrcImage/doc/mrcImage.html index 858c2ed7ec..e80febf09e 100755 --- a/src/Objects/DataManip/mrcImage/doc/mrcImage.html +++ b/src/Objects/DataManip/mrcImage/doc/mrcImage.html @@ -4,7 +4,7 @@

mrcImage

-

Update Time 06/24/13---09:37:26

+

Update Time 06/24/13---21:41:38

Concept

mrcImage.h

Data Structure

@@ -729,6 +729,22 @@ typedef struct mrcImageInformation { long flagrmax; double RMS; /* Root mean square */ int mode; + + /* For Search Area */ + int flagXrange; + int flagYrange; + int flagZrange; + double XrangeMin; + double XrangeMax; + double YrangeMin; + double YrangeMax; + double ZrangeMin; + double ZrangeMax; + + int flagCentre; + double CentreX; + double CentreY; + double CentreZ; } mrcImageInformation; /* struct end */ diff --git a/src/Objects/DataManip/mrcImage/inc/mrcImage.h b/src/Objects/DataManip/mrcImage/inc/mrcImage.h index 7365369c4d..68f472e2ca 100755 --- a/src/Objects/DataManip/mrcImage/inc/mrcImage.h +++ b/src/Objects/DataManip/mrcImage/inc/mrcImage.h @@ -318,6 +318,22 @@ typedef struct mrcImageInformation { long flagrmax; double RMS; /* Root mean square */ int mode; + + /* For Search Area */ + int flagXrange; + int flagYrange; + int flagZrange; + double XrangeMin; + double XrangeMax; + double YrangeMin; + double YrangeMax; + double ZrangeMin; + double ZrangeMax; + + int flagCentre; + double CentreX; + double CentreY; + double CentreZ; } mrcImageInformation; /* struct end */ diff --git a/src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h b/src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h index 316d7148ad..91145e2c6c 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h +++ b/src/Objects/DataManip/mrcImage/src/lmrcSinogramFET.h @@ -34,6 +34,7 @@ typedef struct lmrcSinogramFETPCAInfo{ int flagInImage; mrcImage* inImage; Array X; + Array Ave; Array C; Array u; Array lambda; diff --git a/src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c b/src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c index 59c70ae45b..f52a853cc8 100755 --- a/src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c +++ b/src/Objects/DataManip/mrcImage/src/lmrcSinogramFETPCA.c @@ -31,13 +31,16 @@ lmrcSinogramFETPCA(lmrcSinogramFETPCAInfo in, int mode){ double data, data1, data2; char s[256]; mrcImage temp; - y = in.inImage->HeaderN.y; in.X.dim = 2; in.X.n[0] = in.inImage->HeaderN.x; in.X.n[1] = y * in.inImage->HeaderN.z; arrayInit(&(in.X), "X in lmrcSinogramFETPCA"); + in.Ave.dim = 2; + in.Ave.n[0] = in.inImage->HeaderN.x; + in.Ave.n[1] = y * in.inImage->HeaderN.z; + arrayInit(&(in.Ave), "Ave in lmrcSinogramFETPCA"); for(k=0; kHeaderN.z; k++){ for(j=0; jHeaderN.y; j++){ @@ -48,7 +51,7 @@ lmrcSinogramFETPCA(lmrcSinogramFETPCAInfo in, int mode){ } } //fprintf(stderr,"before arrayPCA\n"); - arrayPCA(&(in.u), &(in.C), &(in.lambda), &(in.X), 0); + arrayPCA(&(in.u), &(in.C), &(in.lambda), &(in.X), &(in.Ave), 0); //fprintf(stderr,"after arrayPCA\n"); //arrayWriteToFile(in.Out, &(in.X), "in main"); diff --git a/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c b/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c index 7405e4805d..2bfbff888f 100755 --- a/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c +++ b/src/Objects/DataManip/mrcImage/src/mrcImageInfo.c @@ -583,11 +583,19 @@ lmrcImageInformation(mrcImageInformation* info, mrcImage* img) int cy; int cz; int count; + int xmin, ymin, zmin; + int xmax, ymax, zmax; DEBUGPRINT("meanOfAll\n"); - - cx = img->HeaderN.x/2; - cy = img->HeaderN.y/2; - cz = img->HeaderN.z/2; + + if(info->flagCentre) { + cx = info->CentreX; + cy = info->CentreY; + cz = info->CentreZ; + } else { + cx = img->HeaderN.x/2; + cy = img->HeaderN.y/2; + cz = img->HeaderN.z/2; + } mrcPixelDataGet(img, (mrcImageParaTypeReal)cx, (mrcImageParaTypeReal)cy, @@ -601,10 +609,35 @@ lmrcImageInformation(mrcImageInformation* info, mrcImage* img) info->maxCoord.y = cy; info->maxCoord.z = cz; sumForMean = sumForSd = 0; + + if(info->flagXrange) { + xmin = info->XrangeMin; + xmax = info->XrangeMax; + } else { + xmin = -32; + xmax = +32; + } + + if(info->flagYrange) { + ymin = info->YrangeMin; + ymax = info->YrangeMax; + } else { + ymin = -32; + ymax = +32; + } + + if(info->flagZrange) { + zmin = info->ZrangeMin; + zmax = info->ZrangeMax; + } else { + zmin = -32; + zmax = +32; + } + count=0; - for(iz=MAX(0,cz-32); izHeaderN.z); iz++) { - for(iy=MAX(0,cy-32); iyHeaderN.y); iy++) { - for(ix=MAX(0,cx-32); ixHeaderN.x); ix++) { + for(iz=cz+zmin; izXrangeMin = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagXrangeMin++; + info->XrangeMax = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagXrangeMax++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("Yrange") { + if(i+2YrangeMin = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagYrangeMin++; + info->YrangeMax = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagYrangeMax++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } + SCASE("Zrange") { + if(i+2ZrangeMin = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagZrangeMin++; + info->ZrangeMax = stringGetNthRealData(argv[i+1], 1, " ,"); + i++; + info->flagZrangeMax++; + } else { + usage(argv[0]); + exit(EXIT_FAILURE); + } + SBREAK; + } SCASE("M") { if(i+1Mode = stringGetNthIntegerData(argv[i+1], 1, " ,"); diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/init.c b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/init.c index 04739ce361..b300565993 100755 --- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/init.c +++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/init.c @@ -27,6 +27,12 @@ init0(mrcImageAutoRotationCorrelation3DInfo* info) info->Rot3Min = 0.0; info->flagRot3Min = 0; info->Rot3Max = 360.0; info->flagRot3Max = 0; info->Rot3Delta = 5.0; info->flagRot3Delta = 0; + info->XrangeMin = 0; info->flagXrangeMin = 0; + info->XrangeMax = 0; info->flagXrangeMax = 0; + info->YrangeMin = 0; info->flagYrangeMin = 0; + info->YrangeMax = 0; info->flagYrangeMax = 0; + info->ZrangeMin = 0; info->flagZrangeMin = 0; + info->ZrangeMax = 0; info->flagZrangeMax = 0; info->Mode = 0; info->flagMode = 0; info->ModeRotation = 0; info->flagModeRotation = 0; info->fptconfigFile = NULL; info->flagconfigFile = 0; @@ -98,6 +104,24 @@ init1(mrcImageAutoRotationCorrelation3DInfo* info) if(info->flagRot3Delta) { } + if(info->flagXrangeMin) { + } + + if(info->flagXrangeMax) { + } + + if(info->flagYrangeMin) { + } + + if(info->flagYrangeMax) { + } + + if(info->flagZrangeMin) { + } + + if(info->flagZrangeMax) { + } + if(info->flagMode) { } diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.c b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.c index 717ed9ed36..ed1f556cf4 100755 --- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.c +++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.c @@ -33,6 +33,13 @@ typedef struct lmrcImageAutoRotationCorrelation3DInfo { lmrcImageAutoRotationCorrelation3DRange Rot3; char* EulerAngle; + int flagXrange; + int flagYrange; + int flagZrange; + lmrcImageAutoRotationCorrelation3DRange Xrange; + lmrcImageAutoRotationCorrelation3DRange Yrange; + lmrcImageAutoRotationCorrelation3DRange Zrange; + long CorrelationMode; mrcImage CorMap; mrcImage LinearCorMap; @@ -90,6 +97,17 @@ main(int argc, char* argv[]) linfo.CorrelationMode = info.Mode; linfo.RotationMode = info.ModeRotation; + linfo.flagXrange = info.flagXrangeMin; + linfo.flagYrange = info.flagYrangeMin; + linfo.flagZrange = info.flagZrangeMin; + + linfo.Xrange.Min = info.XrangeMin; + linfo.Xrange.Max = info.XrangeMax; + linfo.Yrange.Min = info.YrangeMin; + linfo.Yrange.Max = info.YrangeMax; + linfo.Zrange.Min = info.ZrangeMin; + linfo.Zrange.Max = info.ZrangeMax; + mrcFileRead(&in, info.In, "in main", 0); mrcFileRead(&ref, info.Ref, "in main", 0); @@ -158,8 +176,28 @@ void lmrcImageAutoRotationCorrelation3D( mrcImageInformation info; double max=-1; - info.mode = meanOfAll; - + + if(info.flagXrange || info.flagYrange || info.flagZrange) { + info.mode = meanOfCentre; + + info.flagXrange = linfo->flagXrange; + info.XrangeMin = linfo->Xrange.Min; + info.XrangeMax = linfo->Xrange.Max; + info.flagYrange = linfo->flagYrange; + info.YrangeMin = linfo->Yrange.Min; + info.YrangeMax = linfo->Yrange.Max; + info.flagZrange = linfo->flagZrange; + info.ZrangeMin = linfo->Zrange.Min; + info.ZrangeMax = linfo->Zrange.Max; + + info.flagCentre = 1; + info.CentreX = 0; + info.CentreY = 0; + info.CentreZ = 0; + } else { + info.mode = meanOfAll; + } + DEBUGPRINT3("%d %d %d N for Rotation\n", linfo->Rot1.N, linfo->Rot2.N, linfo->Rot3.N); DEBUGPRINT3("Rot1 %f %f %f \n", linfo->Rot1.Min, linfo->Rot1.Max, linfo->Rot1.Delta); DEBUGPRINT3("Rot2 %f %f %f \n", linfo->Rot2.Min, linfo->Rot2.Max, linfo->Rot2.Delta); diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html index 50aef879d1..9d06763c36 100755 --- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html +++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.html @@ -17,6 +17,9 @@ Options: [-Rot1 Rot1Min (0.0 )Rot1Max (360.0 )Rot1Delta (5.0 )] :Optional :Rot1 [-Rot2 Rot2Min (0.0 )Rot2Max (180.0 )Rot2Delta (5.0 )] :Optional :Rot2 [-Rot3 Rot3Min (0.0 )Rot3Max (360.0 )Rot3Delta (5.0 )] :Optional :Rot3 + [-Xrange XrangeMin (0 )XrangeMax (0 )] :Optional :Xrange[pixel]: Not set, all space search + [-Yrange YrangeMin (0 )YrangeMax (0 )] :Optional :Yrange[pixel]: Not set, all space search + [-Zrange ZrangeMin (0 )ZrangeMax (0 )] :Optional :Zrange[pixel]: Not set, all space search [-M[ode] Mode (0 )] :Optional :Mode: Correlation Mode [-M[ode]R[otation] ModeRotation (0 )] :Optional :Mode: Rotation3D Mode [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.pane b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.pane index 39b5af0b5a..dcdeedf7f0 100755 --- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.pane +++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/mrcImageAutoRotationCorrelation3D.pane @@ -16,10 +16,13 @@ -I 1 0 0 1 0 1 -1x1+1+10 ' ' '0.0' 'Rot1Min' Rot1 -I 1 0 0 1 0 1 -1x1+1+12 ' ' '0.0' 'Rot2Min' Rot2 -I 1 0 0 1 0 1 -1x1+1+13 ' ' '0.0' 'Rot3Min' Rot3 - -i 1 0 1 0 0 -1x1+1+15.000000 0 0 0 0 0 'Mode' 'Mode: Correlation Mode' M - -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'ModeRotation' 'Mode: Rotation3D Mode' MR - -I 1 0 1 0 0 1 -1x1+1+18.000000 ' ' 'configFile' 'ConfigurationFile' c - -i 1 0 1 0 0 -1x1+1+19.500000 0 0 0 0 0 'mode' 'Mode: InterpolationMode' m + -I 1 0 0 1 0 1 -1x1+1+15 ' ' '0' 'XrangeMin' Xrange[pixel]: Not set, all space search + -I 1 0 0 1 0 1 -1x1+1+16 ' ' '0' 'YrangeMin' Yrange[pixel]: Not set, all space search + -I 1 0 0 1 0 1 -1x1+1+18 ' ' '0' 'ZrangeMin' Zrange[pixel]: Not set, all space search + -i 1 0 1 0 0 -1x1+1+19.500000 0 0 0 0 0 'Mode' 'Mode: Correlation Mode' M + -i 1 0 1 0 0 -1x1+1+21.000000 0 0 0 0 0 'ModeRotation' 'Mode: Rotation3D Mode' MR + -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: InterpolationMode' m -E -E -E diff --git a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/usage.c b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/usage.c index b446f0e1eb..ec1ddcbed6 100755 --- a/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/usage.c +++ b/src/Tools/mrcImage/mrcImageAutoRotationCorrelation3D/src/usage.c @@ -16,6 +16,9 @@ usage(char* thisProgram) fprintf(stderr, " [-Rot1 Rot1Min (0.0 )Rot1Max (360.0 )Rot1Delta (5.0 )] :Optional :Rot1\n"); fprintf(stderr, " [-Rot2 Rot2Min (0.0 )Rot2Max (180.0 )Rot2Delta (5.0 )] :Optional :Rot2\n"); fprintf(stderr, " [-Rot3 Rot3Min (0.0 )Rot3Max (360.0 )Rot3Delta (5.0 )] :Optional :Rot3\n"); + fprintf(stderr, " [-Xrange XrangeMin (0 )XrangeMax (0 )] :Optional :Xrange[pixel]: Not set, all space search\n"); + fprintf(stderr, " [-Yrange YrangeMin (0 )YrangeMax (0 )] :Optional :Yrange[pixel]: Not set, all space search\n"); + fprintf(stderr, " [-Zrange ZrangeMin (0 )ZrangeMax (0 )] :Optional :Zrange[pixel]: Not set, all space search\n"); fprintf(stderr, " [-M[ode] Mode (0 )] :Optional :Mode: Correlation Mode\n"); fprintf(stderr, " [-M[ode]R[otation] ModeRotation (0 )] :Optional :Mode: Rotation3D Mode\n"); fprintf(stderr, " [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile\n");