From: Eduardo DAVILA Date: Mon, 4 Dec 2017 21:33:32 +0000 (+0100) Subject: #2711 creaVtk Feature New Normal - new Box ReadMHDPlane X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?p=creaVtk.git;a=commitdiff_plain;h=2be75c89f7e0723283b34e40008536172861dd82 #2711 creaVtk Feature New Normal - new Box ReadMHDPlane --- diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx index 223fe7e..4364ec6 100644 --- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx +++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx @@ -59,7 +59,7 @@ vtkImageData* ReadMHDPlane::CreateDefaultImage() return newImage; } - +/* EED Borrame void ReadMHDPlane::ReadNormalMHD() { // THE MAIN PROCESSING METHOD BODY @@ -82,13 +82,11 @@ void ReadMHDPlane::ReadNormalMHD() int width; long long dataSize; - if (bbGetInputDirectionPlane()=="XY") { inputfilename=bbGetInputFileName(); } // if XY - if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX")) { //-- Split FileName @@ -129,7 +127,6 @@ void ReadMHDPlane::ReadNormalMHD() if (ffIn!=NULL) { FILE *ffOut = fopen(newFileName.c_str(),"w"); - while(!feof(ffIn)) { strcpy(mystring,"\n"); @@ -146,14 +143,12 @@ void ReadMHDPlane::ReadNormalMHD() 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 @@ -176,7 +171,6 @@ void ReadMHDPlane::ReadNormalMHD() 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) @@ -187,7 +181,6 @@ void ReadMHDPlane::ReadNormalMHD() } // while fclose(ffIn); fclose(ffOut); - if (ok==true) { vtkMetaImageReader * reader = vtkMetaImageReader::New(); @@ -198,31 +191,81 @@ void ReadMHDPlane::ReadNormalMHD() } 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) ); } +*/ +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; + } // XY + if (bbGetInputDirectionPlane()=="YZ") + { + sizeX = 1; + sizeY = ext[1]-ext[0]+1; + sizeZ = ext[3]-ext[2]+1; + sizeLine = sizeY; + } // YZ + if (bbGetInputDirectionPlane()=="ZX") + { + sizeX = ext[1]-ext[0]+1; + sizeY = 1; + sizeZ = ext[3]-ext[2]+1; + sizeLine = sizeX; + } // 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(); + 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(); + void *ptrDst=newImageOrinted->GetScalarPointer() + sizeByte*dimY; + void *ptrOrg=img->GetScalarPointer(); + for (yy=0 ; yySetScalarTypeToChar(); 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); } @@ -274,13 +312,9 @@ void ReadMHDPlane::Read64lseek() 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; @@ -288,17 +322,12 @@ void ReadMHDPlane::Read64lseek() 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"); @@ -306,8 +335,6 @@ void ReadMHDPlane::Read64lseek() newImage=CreateDefaultImage(); // exit(1); } - - if ((bbGetInputDirectionPlane()=="XY") && (fd>=0)) { newImage->SetSpacing( spcX,spcY,spcZ ); @@ -328,15 +355,13 @@ 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 ((bbGetInputDirectionPlane()=="ZX") && (fd>=0)) { newImage->SetSpacing( spcX,spcZ,spcY ); newImage->SetDimensions( dimX,dimZ,width ); @@ -348,10 +373,9 @@ void ReadMHDPlane::Read64lseek() int iWidth; for (iWidth=0;iWidth=0)) { newImage->SetSpacing( spcY,spcZ,spcX ); @@ -366,7 +390,6 @@ void ReadMHDPlane::Read64lseek() { copy_YZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize); } - } // if PLANE YZ #if defined(_WIN32) _close (fd); @@ -376,8 +399,154 @@ void ReadMHDPlane::Read64lseek() } else { newImage=CreateDefaultImage(); } // if ffIn + bbSetOutputOut( newImage ); + bbSetOutputOut2( ChangeOrientation(newImage) ); +} +*/ +void ReadMHDPlane::Read64lseek(std::string fileNameIn, std::string plane) +{ + 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( 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,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 = 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"); + fprintf(stderr, "%s\n", strerror(errno)); + newImage=CreateDefaultImage(); +// exit(1); + } + 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 ); + 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) + { + printf("EED ReadMHDPlane::Read64lseek \n"); + 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 ((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 ); + 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;iWidth