X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=bbtk_creaVtk_PKG%2Fsrc%2FbbcreaVtkReadMHDPlane.cxx;h=e9634ee8169fbe19093cf0279f4ee95048cb31c0;hb=4ae048dd3d78ddea21ded374e4bf51340df8384b;hp=f17bc9d78508517d268af61637717001ccb5cb8d;hpb=10e31d8e12d78d664924d7cb2f9cd728c7b7970f;p=creaVtk.git diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx index f17bc9d..e9634ee 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx @@ -13,8 +13,9 @@ #include #if defined(_WIN32) + #include #else -#include + #include #endif // defined(_WIN32) #include @@ -42,14 +43,19 @@ vtkImageData* ReadMHDPlane::CreateDefaultImage() sizeZ = 1; vtkImageData *newImage = vtkImageData::New(); newImage->Initialize(); - newImage->SetScalarTypeToUnsignedChar(); newImage->SetSpacing( 1,1,1 ); newImage->SetDimensions( sizeX,sizeY,sizeZ ); + newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 ); +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 newImage->SetWholeExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 ); - newImage->SetExtent(0, sizeX-1,0,sizeY-1,0,sizeZ-1 ); + newImage->SetScalarTypeToUnsignedChar(); newImage->SetNumberOfScalarComponents(1); newImage->AllocateScalars(); newImage->Update(); +#else + newImage->AllocateScalars(VTK_UNSIGNED_CHAR,1); +#endif memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 ); for (i=0; iInitialize(); + imgDst->SetSpacing( imgOrg->GetSpacing() ); + imgDst->SetDimensions( sizeXDst,sizeYDst,sizeZDst ); + imgDst->SetExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 ); + +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + imgDst->SetWholeExtent(0,sizeXDst-1,0,sizeYDst-1,0,sizeZDst-1 ); + imgDst->SetScalarType( imgOrg->GetScalarType() ); + imgDst->SetNumberOfScalarComponents(1); + imgDst->AllocateScalars(); + imgDst->Update(); #else - path=path+"YZ_ZX/"; + imgDst->AllocateScalars(imgOrg->GetScalarType(),1); #endif - - - if (bbGetInputDirectionPlane()=="YZ") - { - inputfilename = path+filename+"_YZ.mhd"; - } // if YZ - if (bbGetInputDirectionPlane()=="ZX") - { - inputfilename = path+filename+"_ZX.mhd"; - } // XZ - } // if YZ || XZ + char *ptrDst,*ptrOrg; + int sizeBytes = imgOrg->GetScalarSize(); + int sizeLineBytes = sizeLine*imgOrg->GetScalarSize(); + int xx,yy,zz; - width = bbGetInputWidth(); - if (width<=0 ) { width=1; } - - slice = bbGetInputSlice(); - if (slice<0 ) { slice=0; } + 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() ); - vtkImageData *newImage; - long long int newHeaderSize; - std::string newFileName=inputfilename+"-OneSlice"; - - int sx,sy,sz; - char mystring[250]; - char strTmp[20]; - bool ok=true; - FILE *ffIn = fopen(inputfilename.c_str(),"r"); - if (ffIn!=NULL) + if (bbGetInputDirectionPlane()=="XY") { - FILE *ffOut = fopen(newFileName.c_str(),"w"); - - while(!feof(ffIn)) - { - strcpy(mystring,"\n"); - fgets(mystring,250,ffIn); - if (strncmp("NDims",mystring,5)==0) - { - if (width==1) - { - strcpy(mystring,"NDims = 2\n"); - } else { - strcpy(mystring,"NDims = 3\n"); - } - } - if (strncmp("DimSize",mystring,6)==0) - { - sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz); - - if (width==1) - { - sprintf(mystring,"DimSize = %d %d\n",sx,sy); - } else { - sprintf(mystring,"DimSize = %d %d %d\n",sx,sy,width); - } - - newHeaderSize = (long long int)sx*(long long int)sy*(long long int)slice; - if (bbGetInputSlice()>=sz) {ok=false;} - } // if - if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { newHeaderSize=newHeaderSize*1; } - if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { newHeaderSize=newHeaderSize*1; } - if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; } - if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; } - if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*4; } - if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*4; } - 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); + memcpy ( imgDst->GetScalarPointer(), ptrOrg , sizeXDst*sizeYDst*sizeZDst*(imgOrg->GetScalarSize()) ); + } // if XY - if (ok==true) + if (bbGetInputDirectionPlane()=="ZX") + { + ptrDst = (char*)( imgDst->GetScalarPointer(0,0,sizeYOrg-00-1) ); + for( zz=0 ; zzSetFileName( newFileName.c_str() ); - reader->Update(); - newImage = reader->GetOutput(); - } // if ok - } else { - ok=false; - printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() ); - } - - if (ok==false) +// ptrDst=(char*)( imgDst->GetScalarPointer(0,zz,sizeYOrg-00-1) ); + for( yy=0 ; yyGetScalarPointer(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") { - newImage=CreateDefaultImage(); - } // if ok - - bbSetOutputOut( newImage ); + 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() +void ReadMHDPlane::Read64lseek(std::string fileNameIn, std::string plane) { + int imageType; 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"); @@ -218,75 +200,61 @@ void ReadMHDPlane::Read64lseek() 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"); + FILE *ffIn = fopen( fileNameIn.c_str() , "r"); long long dataSize; - if (ffIn!=NULL) { newImage = vtkImageData::New(); - while(!feof(ffIn)) { strcpy(mystring,"\n"); fgets(mystring,250,ffIn); - if (strncmp("NDims",mystring,5)==0) { sscanf(mystring,"%s %s %d" ,strTmp, strTmp, &dim); } - if (strncmp("DimSize",mystring,6)==0) { sscanf(mystring,"%s %s %d %d %d" ,strTmp, strTmp, &dimX, &dimY,&dimZ); } - if (strncmp("ElementType",mystring,11)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); formattype=strTmp2; } - if (strncmp("ElementSpacing",mystring,14)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &spcX,&spcY,&spcZ); } - if (strncmp("ElementSize",mystring,11)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &spcX,&spcY,&spcZ); } - if (strncmp("Offset",mystring,6)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &ox, &oy, &oz); } - if (strncmp("HeaderSize",mystring,10)==0) { sscanf(mystring,"%s %s %ld" ,strTmp, strTmp, &headersize); } - if (strncmp("ElementDataFile",mystring,15)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2; } - - if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { newImage->SetScalarTypeToChar(); 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,24)==0) { newImage->SetScalarTypeToUnsignedInt(); dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedInt(); dataSize=sizeof(unsigned int); } - if (strncmp("ElementType = MET_INT",mystring,24)==0) { newImage->SetScalarTypeToInt(); dataSize=sizeof(int); } - if (strncmp("ElementType = VTK_INT",mystring,32)==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,23)==0) { newImage->SetScalarTypeToLong(); dataSize=sizeof(long); } - if (strncmp("ElementType = VTK_LONG",mystring,23)==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); } - + if (strncmp("NDims",mystring,5)==0) { sscanf(mystring,"%s %s %d" ,strTmp, strTmp, &dim); } + if (strncmp("DimSize",mystring,6)==0) { sscanf(mystring,"%s %s %d %d %d" ,strTmp, strTmp, &dimX, &dimY,&dimZ); } + if (strncmp("ElementType",mystring,11)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); formattype=strTmp2; } + if (strncmp("ElementSpacing",mystring,14)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &spcX,&spcY,&spcZ); } + if (strncmp("ElementSize",mystring,11)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &spcX,&spcY,&spcZ); } + if (strncmp("Offset",mystring,6)==0) { sscanf(mystring,"%s %s %f %f %f" ,strTmp, strTmp, &ox, &oy, &oz); } + if (strncmp("HeaderSize",mystring,10)==0) { sscanf(mystring,"%s %s %ld" ,strTmp, strTmp, &headersize); } + if (strncmp("ElementDataFile",mystring,15)==0) { sscanf(mystring,"%s %s %s" ,strTmp, strTmp, strTmp2); elementdatafile=strTmp2; } + if (strncmp("ElementType = MET_CHAR",mystring,22)==0) { imageType=VTK_CHAR; dataSize=sizeof(char); } + if (strncmp("ElementType = VTK_CHAR",mystring,22)==0) { imageType=VTK_CHAR; dataSize=sizeof(char); } + if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) { imageType=VTK_UNSIGNED_CHAR; dataSize=sizeof(unsigned char); } + if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0) { imageType=VTK_UNSIGNED_CHAR; dataSize=sizeof(unsigned char); } + if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { imageType=VTK_UNSIGNED_SHORT; dataSize=sizeof(unsigned short);} + if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { imageType=VTK_UNSIGNED_SHORT; dataSize=sizeof(unsigned short);} + if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { imageType=VTK_SHORT; dataSize=sizeof(short); } + if (strncmp("ElementType = VTK_SHORT",mystring,23)==0) { imageType=VTK_SHORT; dataSize=sizeof(short); } + if (strncmp("ElementType = MET_UINT",mystring,22)==0) { imageType=VTK_UNSIGNED_INT; dataSize=sizeof(unsigned int); } + if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,30)==0) { imageType=VTK_UNSIGNED_INT; dataSize=sizeof(unsigned int); } + if (strncmp("ElementType = MET_INT",mystring,21)==0) { imageType=VTK_INT; dataSize=sizeof(int); } + if (strncmp("ElementType = VTK_INT",mystring,21)==0) { imageType=VTK_INT; dataSize=sizeof(int); } + if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { imageType=VTK_FLOAT; dataSize=sizeof(float); } + if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) { imageType=VTK_FLOAT; dataSize=sizeof(float); } + if (strncmp("ElementType = MET_LONG",mystring,22)==0) { imageType=VTK_LONG; dataSize=sizeof(long); } + if (strncmp("ElementType = VTK_LONG",mystring,22)==0) { imageType=VTK_LONG; dataSize=sizeof(long); } + if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { imageType=VTK_DOUBLE; dataSize=sizeof(double); } + if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { imageType=VTK_DOUBLE; 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 ; + found = fileNameIn.find_last_of("/\\"); + filename = fileNameIn.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"); @@ -294,17 +262,25 @@ void ReadMHDPlane::Read64lseek() newImage=CreateDefaultImage(); // exit(1); } - - - if ((bbGetInputDirectionPlane()=="XY") && (fd>=0)) + if ((plane=="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 ); + + + +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + newImage->SetScalarType( imageType ); + newImage->SetWholeExtent(0, dimX-1,0,dimY-1,0,width-1 ); newImage->SetNumberOfScalarComponents(1); newImage->AllocateScalars(); newImage->Update(); +#else + newImage->AllocateScalars(imageType,1); +#endif + pos = dimX*dimY*(long long)slice*dataSize; #if defined(_WIN32) if (_lseeki64( fd, pos, SEEK_SET ) < 0) @@ -316,45 +292,58 @@ void ReadMHDPlane::Read64lseek() fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno)); exit(1); } - if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0) { fprintf(stderr, "Failed reading: %s\n", strerror(errno)); exit(1); } } // if PLANE XY - - if ((bbGetInputDirectionPlane()=="XZ") && (fd>=0)) + if ((plane=="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 ); + + +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + newImage->SetScalarType( imageType ); + newImage->SetWholeExtent(0, dimX-1,0,dimZ-1,0,width-1 ); newImage->SetNumberOfScalarComponents(1); newImage->AllocateScalars(); newImage->Update(); +#else + newImage->AllocateScalars(imageType,1); +#endif + int iWidth; for (iWidth=0;iWidth=0)) + if ((plane=="YZ") && (fd>=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 ); + +//EED 2017-01-01 Migration VTK7 +#if VTK_MAJOR_VERSION <= 5 + newImage->SetScalarType( imageType ); + newImage->SetWholeExtent(0, dimY-1,0,dimZ-1,0,width-1 ); newImage->SetNumberOfScalarComponents(1); newImage->AllocateScalars(); newImage->Update(); +#else + newImage->AllocateScalars(imageType,1); +#endif + int iWidth; for (iWidth=0;iWidth