From f5e3c1a0829440b3ab3f47d870ff770f3e108158 Mon Sep 17 00:00:00 2001 From: Eduardo DAVILA Date: Wed, 6 Dec 2017 19:55:41 +0100 Subject: [PATCH] #2711 creaVtk Feature New Normal - new Box ReadMHDPlane --- .../src/bbcreaVtkReadMHDPlane.cxx | 479 +++++------------- bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h | 6 +- 2 files changed, 121 insertions(+), 364 deletions(-) diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx index 48b1603..800b0be 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx @@ -59,350 +59,113 @@ vtkImageData* ReadMHDPlane::CreateDefaultImage() return newImage; } -/* EED Borrame -void ReadMHDPlane::ReadNormalMHD() +vtkImageData* ReadMHDPlane::ChangeOrientation(vtkImageData* imgOrg) { -// THE MAIN PROCESSING METHOD BODY -// Here we simply set the input 'In' value to the output 'Out' -// And print out the output value -// INPUT/OUTPUT ACCESSORS ARE OF THE FORM : -// void bbSet{Input|Output}NAME(const TYPE&) -// const TYPE& bbGet{Input|Output}NAME() const -// Where : -// * NAME is the name of the input/output -// (the one provided in the attribute 'name' of the tag 'input') -// * TYPE is the C++ type of the input/output -// (the one provided in the attribute 'type' of the tag 'input') - -// bbSetOutputOut( bbGetInputIn() ); -// std::cout << "Output value = " <=sz) {ok=false;} - } // if - if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { dataSize=sizeof(char); } - if (strncmp("ElementType = VTK_CHAR",mystring,22)==0) { dataSize=sizeof(char); } - if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { dataSize=sizeof(unsigned char); } - if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0) { dataSize=sizeof(unsigned char); } - if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { dataSize=sizeof(unsigned short); } - if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { dataSize=sizeof(unsigned short); } - if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { dataSize=sizeof(short); } - if (strncmp("ElementType = VTK_SHORT",mystring,23)==0) { dataSize=sizeof(short); } - if (strncmp("ElementType = MET_UINT",mystring,22)==0) { dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,30)==0) { dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = MET_INT",mystring,21)==0) { dataSize=sizeof(int); } - if (strncmp("ElementType = VTK_INT",mystring,21)==0) { dataSize=sizeof(int); } - if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { dataSize=sizeof(float); } - if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { dataSize=sizeof(float); } - if (strncmp("ElementType = MET_LONG",mystring,22)==0) { dataSize=sizeof(long); } - if (strncmp("ElementType = VTK_LONG",mystring,22)==0) { dataSize=sizeof(long); } - if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { dataSize=sizeof(double); } - if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { dataSize=sizeof(double); } - newHeaderSize=newHeaderSize*dataSize; - if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");} - if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");} - if (strncmp("ElementDataFile",mystring,15)==0) - { - fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize ); - } // if - fprintf(ffOut,mystring); - } // while - fclose(ffIn); - fclose(ffOut); - if (ok==true) - { - vtkMetaImageReader * reader = vtkMetaImageReader::New(); - reader->SetFileName( newFileName.c_str() ); - reader->Update(); - newImage = reader->GetOutput(); - } // if ok - } else { - ok=false; - printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() ); - }// if ffIn - if (ok==false) - { - newImage=CreateDefaultImage(); - } // if ok - - bbSetOutputOut( newImage ); - bbSetOutputOut2( ChangeOrientation(newImage) ); -} -*/ + int width = bbGetInputWidth(); + int ext[6]; + int sizeXOrg, sizeYOrg,sizeZOrg; + int sizeXDst, sizeYDst,sizeZDst; + imgOrg->GetWholeExtent(ext); + int sizeLine; + + sizeXOrg = ext[1]-ext[0]+1; + sizeYOrg = ext[3]-ext[2]+1; + sizeZOrg = ext[5]-ext[4]+1; -vtkImageData* ReadMHDPlane::ChangeOrientation(vtkImageData* img) -{ - int ext[6]; - int sizeX, sizeY,sizeZ; - img->GetWholeExtent(ext); - int sizeLine; if (bbGetInputDirectionPlane()=="XY") { - sizeX = ext[1]-ext[0]+1; - sizeY = ext[3]-ext[2]+1; - sizeZ = 1; + sizeXDst = ext[1]-ext[0]+1; + sizeYDst = ext[3]-ext[2]+1; + sizeZDst = width; } // XY if (bbGetInputDirectionPlane()=="YZ") { - sizeX = 1; - sizeY = ext[1]-ext[0]+1; - sizeZ = ext[3]-ext[2]+1; - sizeLine = sizeY; + sizeXDst = width; + sizeYDst = ext[1]-ext[0]+1; + sizeZDst = ext[3]-ext[2]+1; + sizeLine = sizeYDst; } // YZ if (bbGetInputDirectionPlane()=="ZX") { - sizeX = ext[1]-ext[0]+1; - sizeY = 1; - sizeZ = ext[3]-ext[2]+1; - sizeLine = sizeX; + sizeXDst = ext[1]-ext[0]+1; + sizeYDst = width; + sizeZDst = ext[3]-ext[2]+1; + sizeLine = sizeXDst; } // ZX - vtkImageData *newImageOrinted = vtkImageData::New(); - newImageOrinted->Initialize(); - newImageOrinted->SetScalarType( img->GetScalarType() ); - newImageOrinted->SetSpacing( img->GetSpacing() ); - newImageOrinted->SetDimensions( sizeX,sizeY,sizeZ ); - newImageOrinted->SetWholeExtent(0,sizeX-1,0,sizeY-1,0,sizeZ-1 ); - newImageOrinted->SetExtent(0,sizeX-1,0,sizeY-1,0,sizeZ-1 ); - newImageOrinted->SetNumberOfScalarComponents(1); - newImageOrinted->AllocateScalars(); - newImageOrinted->Update(); + vtkImageData *imgDst = vtkImageData::New(); + imgDst->Initialize(); + imgDst->SetScalarType( imgOrg->GetScalarType() ); + imgDst->SetSpacing( imgOrg->GetSpacing() ); + imgDst->SetDimensions( sizeXDst,sizeYDst,sizeZDst ); + imgDst->SetWholeExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 ); + imgDst->SetExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 ); + imgDst->SetNumberOfScalarComponents(1); + imgDst->AllocateScalars(); + imgDst->Update(); + + char *ptrDst,*ptrOrg; + int sizeBytes = imgOrg->GetScalarSize(); + int sizeLineBytes = sizeLine*imgOrg->GetScalarSize(); + int xx,yy,zz; + + long int sizeXDstBytes = sizeXDst*sizeBytes; + long int sizeXYDstBytes = sizeXDst*sizeYDst*sizeBytes; + long int sizeXYDstBytes2 = sizeXDst*sizeYDst*sizeBytes*2; + long int sizeXYZDstBytes = sizeXDst*sizeYDst*sizeZDst*sizeBytes; + long int sizeXYZDstBytes1 = sizeXDst*sizeYDst*(sizeZDst-1)*sizeBytes; + + ptrOrg = (char*)( imgOrg->GetScalarPointer() ); + if (bbGetInputDirectionPlane()=="XY") { - memcpy ( newImageOrinted->GetScalarPointer(), img->GetScalarPointer(), sizeX*sizeY*sizeZ*img->GetScalarSize() ); - } else { - int yy; - int dimY=ext[3]-ext[2]+1; - int sizeByte=sizeLine*img->GetScalarSize(); - char *ptrDst=(char*)(newImageOrinted->GetScalarPointer()) + sizeByte*dimY; - char *ptrOrg=(char*)(img->GetScalarPointer()); - for (yy=0 ; yyGetScalarPointer(), ptrOrg , sizeXDst*sizeYDst*sizeZDst*(imgOrg->GetScalarSize()) ); + } // if XY -/* EED Borrame -void ReadMHDPlane::Read64lseek() -{ - int slice; - int width; - width = bbGetInputWidth(); - if (width<=0 ) { width=1; } - slice = bbGetInputSlice(); - if (slice<0 ) { slice=0; } - int dimX=-1,dimY=-1,dimZ=-1; - int dim=-1; - std::string formattype("VOID"); - std::string elementdatafile("VOID"); - float spcX=-1,spcY=-1,spcZ=-1; - float ox=-1,oy=-1,oz=-1; - long int headersize=0; - vtkImageData *newImage=NULL; - char mystring[250]; - char strTmp[30]; - char strTmp2[30]; - FILE *ffIn = fopen(bbGetInputFileName().c_str(),"r"); - long long dataSize; - if (ffIn!=NULL) + if (bbGetInputDirectionPlane()=="ZX") { - newImage = vtkImageData::New(); - while(!feof(ffIn)) + ptrDst = (char*)( imgDst->GetScalarPointer(0,0,sizeYOrg-00-1) ); + for( zz=0 ; zzSetScalarTypeToChar(); dataSize=sizeof(char); } - if (strncmp("ElementType = VTK_CHAR",mystring,22)==0) { newImage->SetScalarTypeToChar(); dataSize=sizeof(char); } - if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { newImage->SetScalarTypeToUnsignedChar(); dataSize=sizeof(unsigned char); } - if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0) { newImage->SetScalarTypeToUnsignedChar(); dataSize=sizeof(unsigned char); } - if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newImage->SetScalarTypeToUnsignedShort(); dataSize=sizeof(unsigned short);} - if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort(); dataSize=sizeof(unsigned short);} - if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newImage->SetScalarTypeToShort(); dataSize=sizeof(short); } - if (strncmp("ElementType = VTK_SHORT",mystring,23)==0) { newImage->SetScalarTypeToShort(); dataSize=sizeof(short); } - if (strncmp("ElementType = MET_UINT",mystring,22)==0) { newImage->SetScalarTypeToUnsignedInt(); dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,30)==0) { newImage->SetScalarTypeToUnsignedInt(); dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = MET_INT",mystring,21)==0) { newImage->SetScalarTypeToInt(); dataSize=sizeof(int); } - if (strncmp("ElementType = VTK_INT",mystring,21)==0) { newImage->SetScalarTypeToInt(); dataSize=sizeof(int); } - if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newImage->SetScalarTypeToFloat(); dataSize=sizeof(float); } - if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { newImage->SetScalarTypeToFloat(); dataSize=sizeof(float); } - if (strncmp("ElementType = MET_LONG",mystring,22)==0) { newImage->SetScalarTypeToLong(); dataSize=sizeof(long); } - if (strncmp("ElementType = VTK_LONG",mystring,22)==0) { newImage->SetScalarTypeToLong(); dataSize=sizeof(long); } - if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble(); dataSize=sizeof(double); } - if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble(); dataSize=sizeof(double); } - } // while - fclose(ffIn); - newImage->Initialize(); - int fd; - long long ret; - std::size_t found; - std::string filename; - found = bbGetInputFileName().find_last_of("/\\"); - filename = bbGetInputFileName().substr(0,found+1) + elementdatafile ; - long long pos; - long long lsize = dimX*dimY*width *dataSize; -#if defined(_WIN32) - _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 ); -#else - fd = open ( filename.c_str() , O_RDONLY|O_LARGEFILE ); -#endif // defined(_WIN32) - if (fd < 0) - { - printf("EED ReadMHDPlane::Read64lseek WARNNING! raw file not exist\n"); - fprintf(stderr, "%s\n", strerror(errno)); - newImage=CreateDefaultImage(); -// exit(1); - } - if ((bbGetInputDirectionPlane()=="XY") && (fd>=0)) - { - newImage->SetSpacing( spcX,spcY,spcZ ); - newImage->SetDimensions( dimX,dimY,width ); - newImage->SetWholeExtent(0, dimX-1,0,dimY-1,0,width-1 ); - newImage->SetExtent(0, dimX-1,0,dimY-1,0,width-1 ); - newImage->SetNumberOfScalarComponents(1); - newImage->AllocateScalars(); - newImage->Update(); - pos = dimX*dimY*(long long)slice*dataSize; -#if defined(_WIN32) - if (_lseeki64( fd, pos, SEEK_SET ) < 0) -#else - if (lseek64(fd, pos, SEEK_SET) < 0) -#endif // defined(_WIN32) +// ptrDst=(char*)( imgDst->GetScalarPointer(0,zz,sizeYOrg-00-1) ); + for( yy=0 ; yyGetScalarPointer() , lsize)) < 0) - { - fprintf(stderr, "Failed reading: %s\n", strerror(errno)); - exit(1); - } - } // if PLANE XY - if ((bbGetInputDirectionPlane()=="ZX") && (fd>=0)) - { - newImage->SetSpacing( spcX,spcZ,spcY ); - newImage->SetDimensions( dimX,dimZ,width ); - newImage->SetWholeExtent(0, dimX-1,0,dimZ-1,0,width-1 ); - newImage->SetExtent(0, dimX-1,0,dimZ-1,0,width-1 ); - newImage->SetNumberOfScalarComponents(1); - newImage->AllocateScalars(); - newImage->Update(); - int iWidth; - for (iWidth=0;iWidth=0)) - { - newImage->SetSpacing( spcY,spcZ,spcX ); - newImage->SetDimensions( dimY,dimZ,width ); - newImage->SetWholeExtent(0, dimY-1,0,dimZ-1,0,width-1 ); - newImage->SetExtent(0, dimY-1,0,dimZ-1,0,width-1 ); - newImage->SetNumberOfScalarComponents(1); - newImage->AllocateScalars(); - newImage->Update(); - int iWidth; - for (iWidth=0;iWidthGetScalarPointer(0,yy,zz) ); +// ptrDst=(char*)( imgDst->GetScalarPointer(0,zz,sizeYOrg-yy-1) ); + memcpy ( ptrDst, ptrOrg , sizeLineBytes ); + ptrOrg = ptrOrg + sizeLineBytes; + ptrDst = ptrDst - sizeXYDstBytes; + } // for yy + ptrDst = ptrDst + sizeXDstBytes; + ptrDst = ptrDst + sizeXYZDstBytes; + } // for zz + } // ZX + + if (bbGetInputDirectionPlane()=="YZ") + { + ptrDst = (char*)( imgDst->GetScalarPointer(0,0,sizeYOrg-0-1) ); + for( zz=0 ; zzGetScalarPointer(zz,0,sizeYOrg-0-1) ); + for( yy=0 ; yyGetScalarPointer(zz,0,sizeYOrg-yy-1) ); + for( xx=0 ; xxGetScalarPointer(xx,yy,zz) ); +// ptrDst=(char*)( imgDst->GetScalarPointer(zz,xx,sizeYOrg-yy-1) ); + memcpy ( ptrDst, ptrOrg , sizeBytes ); + ptrOrg+= sizeBytes; + ptrDst+= sizeXDstBytes; + } /// for xx + ptrDst = ptrDst - sizeXYDstBytes2; + } // for yy + ptrDst = ptrDst + sizeXYZDstBytes; +// ptrDst++; + } // for zz + } // ZX + + return imgDst; } -*/ void ReadMHDPlane::Read64lseek(std::string fileNameIn, std::string plane) { @@ -605,7 +368,6 @@ void ReadMHDPlane::copy_ZX_plane(int fd,vtkImageData *newImage,int slice,int iWi fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno)); exit(1); } - if ((ret = read(fd, pImage , dimX*dataSize)) < 0) { fprintf(stderr, "Failed reading: %s\n", strerror(errno)); @@ -615,75 +377,72 @@ void ReadMHDPlane::copy_ZX_plane(int fd,vtkImageData *newImage,int slice,int iWi } // for j } - - void ReadMHDPlane::Process() { - if (bbGetInputType()==0) + if (bbGetInputActive()==true) { - //-- Split FileName - std::string inputfilename; - std::size_t found = bbGetInputFileName().find_last_of("/\\"); - std::string path = bbGetInputFileName().substr(0,found+1); - std::string filename = bbGetInputFileName().substr(found+1); -#ifdef _WIN32 - path=path+"YZ_ZX\\"; -#else - path=path+"YZ_ZX/"; -#endif - if (bbGetInputDirectionPlane()=="XY") { inputfilename = bbGetInputFileName(); } // if XY - if (bbGetInputDirectionPlane()=="YZ") { inputfilename = path+filename+"_YZ.mhd"; } // if YZ - if (bbGetInputDirectionPlane()=="ZX") { inputfilename = path+filename+"_ZX.mhd"; } // if XZ - Read64lseek( inputfilename ,"XY"); - } - - if (bbGetInputType()==1) - { - Read64lseek( bbGetInputFileName(), bbGetInputDirectionPlane() ); - } - +printf("EED ReadMHDPlane::Process %d \n", bbGetInputSlice() ); + if (bbGetInputType()==0) + { + //-- Split FileName + std::string inputfilename; + std::size_t found = bbGetInputFileName().find_last_of("/\\"); + std::string path = bbGetInputFileName().substr(0,found+1); + std::string filename = bbGetInputFileName().substr(found+1); + #ifdef _WIN32 + path=path+"YZ_ZX\\"; + #else + path=path+"YZ_ZX/"; + #endif + if (bbGetInputDirectionPlane()=="XY") { inputfilename = bbGetInputFileName(); } // if XY + if (bbGetInputDirectionPlane()=="YZ") { inputfilename = path+filename+"_YZ.mhd"; } // if YZ + if (bbGetInputDirectionPlane()=="ZX") { inputfilename = path+filename+"_ZX.mhd"; } // if XZ + Read64lseek( inputfilename ,"XY"); + } + if (bbGetInputType()==1) + { + Read64lseek( bbGetInputFileName(), bbGetInputDirectionPlane() ); + } + } // if active } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ReadMHDPlane::bbUserSetDefaultValues() { - // SET HERE THE DEFAULT INPUT/OUTPUT VALUES OF YOUR BOX // Here we initialize the input 'In' to 0 + bbSetInputActive(true); bbSetInputFileName(""); bbSetInputSlice(0); bbSetInputType(1); bbSetInputWidth(1); bbSetInputDirectionPlane("XY"); - } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ReadMHDPlane::bbUserInitializeProcessing() { - // THE INITIALIZATION METHOD BODY : // Here does nothing // but this is where you should allocate the internal/output pointers // if any - - } + //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== void ReadMHDPlane::bbUserFinalizeProcessing() { - // THE FINALIZATION METHOD BODY : // Here does nothing // but this is where you should desallocate the internal/output pointers -// if any - -} +// if any } -// EO namespace bbcreaVtk + +} // EO namespace bbcreaVtk diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h index fb0080a..bd80f4b 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.h @@ -5,10 +5,6 @@ #define __bbcreaVtkReadMHDPlane_h_INCLUDED__ - - - - #include "bbcreaVtk_EXPORT.h" #include "bbtkAtomicBlackBox.h" #include "iostream" @@ -27,6 +23,7 @@ class bbcreaVtk_EXPORT ReadMHDPlane //===== // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost) //===== + BBTK_DECLARE_INPUT(Active,bool); BBTK_DECLARE_INPUT(FileName,std::string); BBTK_DECLARE_INPUT(Slice,int); BBTK_DECLARE_INPUT(Width,int); @@ -56,6 +53,7 @@ BBTK_BEGIN_DESCRIBE_BLACK_BOX(ReadMHDPlane,bbtk::AtomicBlackBox); BBTK_AUTHOR("InfoDev"); BBTK_DESCRIPTION("No Description."); BBTK_CATEGORY("empty"); + BBTK_INPUT(ReadMHDPlane,Active,"true/false (default true)",bool,""); BBTK_INPUT(ReadMHDPlane,FileName,"Image file name",std::string,""); BBTK_INPUT(ReadMHDPlane,Slice,"Slice number",int,""); BBTK_INPUT(ReadMHDPlane,Width,"(1 default) Number of slices to be read",int,""); -- 2.47.1