X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=91556c82e9803f3999f1f3decf2ee05f470c3d8e;hb=f04d4a677f3a7738f3d03e0783d7a38b84983a33;hp=97d0115c83fc4db6327a175eee7803ba52f3e08c;hpb=b6969c4d25a055bedc387044058beb1e4c36ee80;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 97d0115c..91556c82 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,7 +1,24 @@ -// vtkGdcmReader.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: vtkGdcmReader.cxx,v $ + Language: C++ + Date: $Date: 2004/12/09 10:59:59 $ + Version: $Revision: 1.64 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + //----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// -// WARNING TODO CLENAME +// WARNING TODO CLEANME // Actual limitations of this code: // // /////// Redundant and unnecessary header parsing @@ -49,7 +66,7 @@ // ////////////////////////////////////////////////////////////// #include "gdcmFile.h" -#include "gdcmHeaderHelper.h" +#include "gdcmHeader.h" #include "vtkGdcmReader.h" //#include @@ -58,7 +75,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.49 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.64 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -126,7 +143,7 @@ void vtkGdcmReader::SetFileName(const char *name) // Since we maintain a list of filenames, when building a volume, // (see vtkGdcmReader::AddFileName), we additionaly need to purge // this list when we manually positionate the filename. - vtkDebugMacro("Clearing all files given with AddFileName"); + vtkDebugMacro(<< "Clearing all files given with AddFileName"); this->FileNameList.clear(); this->Modified(); } @@ -143,7 +160,7 @@ void vtkGdcmReader::ExecuteInformation() this->TotalNumberOfPlanes = this->CheckFileCoherence(); if ( this->TotalNumberOfPlanes == 0) { - vtkErrorMacro("File set is not coherent. Exiting..."); + vtkErrorMacro(<< "File set is not coherent. Exiting..."); return; } @@ -168,7 +185,7 @@ void vtkGdcmReader::ExecuteInformation() (this->DataVOI[4] < 0) || (this->DataVOI[5] >= this->TotalNumberOfPlanes )) { - vtkWarningMacro("The requested VOI is larger than expected extent."); + vtkWarningMacro(<< "The requested VOI is larger than expected extent."); this->DataVOI[0] = 0; this->DataVOI[1] = this->NumColumns - 1; this->DataVOI[2] = 0; @@ -192,39 +209,39 @@ void vtkGdcmReader::ExecuteInformation() // But we do need to set up the data type for downstream filters: if ( ImageType == "8U" ) { - vtkDebugMacro("8 bits unsigned image"); + vtkDebugMacro(<< "8 bits unsigned image"); this->SetDataScalarTypeToUnsignedChar(); } else if ( ImageType == "8S" ) { - vtkErrorMacro("Cannot handle 8 bit signed files"); + vtkErrorMacro(<< "Cannot handle 8 bit signed files"); return; } else if ( ImageType == "16U" ) { - vtkDebugMacro("16 bits unsigned image"); + vtkDebugMacro(<< "16 bits unsigned image"); this->SetDataScalarTypeToUnsignedShort(); } else if ( ImageType == "16S" ) { - vtkDebugMacro("16 bits signed image"); + vtkDebugMacro(<< "16 bits signed image"); this->SetDataScalarTypeToShort(); - //vtkErrorMacro("Cannot handle 16 bit signed files"); + //vtkErrorMacro(<< "Cannot handle 16 bit signed files"); } else if ( ImageType == "32U" ) { - vtkDebugMacro("32 bits unsigned image"); - vtkDebugMacro("WARNING: forced to signed int !"); + vtkDebugMacro(<< "32 bits unsigned image"); + vtkDebugMacro(<< "WARNING: forced to signed int !"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "32S" ) { - vtkDebugMacro("32 bits signed image"); + vtkDebugMacro(<< "32 bits signed image"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "FD" ) { - vtkDebugMacro("64 bits Double image"); + vtkDebugMacro(<< "64 bits Double image"); this->SetDataScalarTypeToDouble(); } //Set number of scalar components: @@ -247,7 +264,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { if (this->InternalFileNameList.empty()) { - vtkErrorMacro("A least a valid FileName must be specified."); + vtkErrorMacro(<< "A least a valid FileName must be specified."); return; } @@ -278,7 +295,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) unsigned long UpdateProgressCount = 0; // Feeling the allocated memory space with each image/volume: - unsigned char *Dest = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0); + unsigned char *Dest = (unsigned char *)data->GetScalarPointer(); for (std::list::iterator filename = InternalFileNameList.begin(); filename != InternalFileNameList.end(); ++filename) @@ -328,36 +345,36 @@ void vtkGdcmReader::BuildFileListFromPattern() if ((! this->FileNameList.empty()) && this->FileName ) { - vtkErrorMacro("Both AddFileName and SetFileName schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if ((! this->FileNameList.empty()) && this->FilePrefix ) { - vtkErrorMacro("Both AddFileName and SetFilePrefix schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if (this->FileName && this->FilePrefix) { - vtkErrorMacro("Both SetFileName and SetFilePrefix schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if (! this->FileNameList.empty() ) { - vtkDebugMacro("Using the AddFileName specified files"); + vtkDebugMacro(<< "Using the AddFileName specified files"); this->InternalFileNameList=this->FileNameList; return; } if (!this->FileName && !this->FilePrefix) { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePrefix."); + vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro(<< "specify a FileName or FilePrefix."); return; } @@ -366,7 +383,7 @@ void vtkGdcmReader::BuildFileListFromPattern() // Single file loading (as given with ::SetFileName()): // Case of multi-frame file considered here this->ComputeInternalFileName(this->DataExtent[4]); - vtkDebugMacro("Adding file " << this->InternalFileName); + vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } else @@ -375,7 +392,7 @@ void vtkGdcmReader::BuildFileListFromPattern() for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) { this->ComputeInternalFileName(idx); - vtkDebugMacro("Adding file " << this->InternalFileName); + vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } } @@ -404,7 +421,7 @@ int vtkGdcmReader::CheckFileCoherence() this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) { - vtkErrorMacro("FileNames are not set."); + vtkErrorMacro(<< "FileNames are not set."); return 0; } @@ -435,8 +452,8 @@ int vtkGdcmReader::CheckFileCoherence() fp = fopen(filename->c_str(),"rb"); if (!fp) { - vtkErrorMacro("Unable to open file " << filename->c_str()); - vtkErrorMacro("Removing this file from readed files " + vtkErrorMacro(<< "Unable to open file " << filename->c_str()); + vtkErrorMacro(<< "Removing this file from readed files " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -444,11 +461,11 @@ int vtkGdcmReader::CheckFileCoherence() fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcmHeader GdcmHeader(filename->c_str() ); + gdcm::Header GdcmHeader(filename->c_str() ); if (!GdcmHeader.IsReadable()) { - vtkErrorMacro("Gdcm cannot parse file " << filename->c_str()); - vtkErrorMacro("Removing this file from readed files " + vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); + vtkErrorMacro(<< "Removing this file from readed files " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -460,10 +477,10 @@ int vtkGdcmReader::CheckFileCoherence() && (type != "16U") && (type != "16S") && (type != "32U") && (type != "32S") ) { - vtkErrorMacro("Bad File Type for file" << filename->c_str()); - vtkErrorMacro(" " << type.c_str()); - vtkErrorMacro("Removing this file from readed files " - << filename->c_str()); + vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\n" + << " File type found : " << type.c_str() + << " (might be 8U, 8S, 16U, 16S, 32U, 32S) \n" + << " Removing this file from readed files"); *filename = "GDCM_UNREADABLE"; continue; } @@ -479,9 +496,9 @@ int vtkGdcmReader::CheckFileCoherence() || ( NY != this->NumLines ) || ( type != this->ImageType ) ) { - vtkErrorMacro("This file is not coherent with previous ones" + vtkErrorMacro(<< "This file is not coherent with previous ones" << filename->c_str()); - vtkErrorMacro("Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from readed files " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -490,12 +507,12 @@ int vtkGdcmReader::CheckFileCoherence() // Stage 2.2: optional coherence stage if ( NZ != ReferenceNZ ) { - vtkErrorMacro("File is not coherent in Z with previous ones" + vtkErrorMacro(<< "File is not coherent in Z with previous ones" << filename->c_str()); } else { - vtkDebugMacro("File is coherent with previous ones" + vtkDebugMacro(<< "File is coherent with previous ones" << filename->c_str()); } @@ -503,7 +520,7 @@ int vtkGdcmReader::CheckFileCoherence() // notify the caller. if (NZ > 1) { - vtkErrorMacro("This file contains multiple planes (images)" + vtkErrorMacro(<< "This file contains multiple planes (images)" << filename->c_str()); } @@ -519,11 +536,11 @@ int vtkGdcmReader::CheckFileCoherence() // We didn't have a workable reference file yet. Set this one // as the reference. FoundReferenceFile = true; - vtkDebugMacro("This file taken as coherence reference:" + vtkDebugMacro(<< "This file taken as coherence reference:" << filename->c_str()); - vtkDebugMacro("Image dimension of reference file as read from Gdcm:" + vtkDebugMacro(<< "Image dimension of reference file as read from Gdcm:" << NX << " " << NY << " " << NZ); - vtkDebugMacro("Number of planes added to the stack: " << NZ); + vtkDebugMacro(<< "Number of planes added to the stack: " << NZ); // Set aside the size of the image this->NumColumns = NX; this->NumLines = NY; @@ -548,9 +565,9 @@ int vtkGdcmReader::CheckFileCoherence() this->DataSpacing[2] = GdcmHeader.GetZSpacing(); //Set image origin - this->DataOrigin[0] = GdcmHeader.GetXOrigin(); - this->DataOrigin[1] = GdcmHeader.GetYOrigin(); - this->DataOrigin[2] = GdcmHeader.GetZOrigin(); + //this->DataOrigin[0] = GdcmHeader.GetXOrigin(); + //this->DataOrigin[1] = GdcmHeader.GetYOrigin(); + //this->DataOrigin[2] = GdcmHeader.GetZOrigin(); } } // End of loop on filename @@ -567,14 +584,14 @@ int vtkGdcmReader::CheckFileCoherence() NumberCoherentFiles++; } } - vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); + vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles); if (ReturnedTotalNumberOfPlanes == 0) { - vtkErrorMacro("No loadable file."); + vtkErrorMacro(<< "No loadable file."); } - vtkDebugMacro("Total number of planes on the stack: " + vtkDebugMacro(<< "Total number of planes on the stack: " << ReturnedTotalNumberOfPlanes); return ReturnedTotalNumberOfPlanes; @@ -607,12 +624,12 @@ void vtkGdcmReader::AddInternalFileName(const char* name) */ size_t vtkGdcmReader::LoadImageInMemory( std::string fileName, - unsigned char * dest, + unsigned char *dest, const unsigned long updateProgressTarget, unsigned long & updateProgressCount) { - vtkDebugMacro("Copying to memory image [" << fileName.c_str() << "]"); - gdcmFile file( fileName.c_str() ); + vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); + gdcm::File file( fileName.c_str() ); size_t size; // If the data structure of vtk for image/volume representation @@ -626,14 +643,15 @@ size_t vtkGdcmReader::LoadImageInMemory( int numLines = file.GetHeader()->GetYSize(); int numPlanes = file.GetHeader()->GetZSize(); int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize(); + int planeSize = lineSize * numLines; - unsigned char * source; + unsigned char *src; if( file.GetHeader()->HasLUT() && AllowLookupTable ) { - size = file.GetImageDataSizeRaw(); - source = (unsigned char*) file.GetImageDataRaw(); - unsigned char *lut = file.GetHeader()->GetLUTRGBA(); + size = file.GetImageDataSize(); + src = (unsigned char*) file.GetImageDataRaw(); + unsigned char *lut = (unsigned char*) file.GetLutRGBA(); if(!this->LookupTable) { @@ -656,21 +674,19 @@ size_t vtkGdcmReader::LoadImageInMemory( } else { - size = file.GetImageDataSize(); - source = (unsigned char*)file.GetImageData(); + size = file.GetImageDataSize(); + src = (unsigned char*)file.GetImageData(); } - - unsigned char * pSource = source; //pointer for later deletion - unsigned char * destination = dest + size - lineSize; + unsigned char *dst = dest + planeSize - lineSize; for (int plane = 0; plane < numPlanes; plane++) { for (int line = 0; line < numLines; line++) { // Copy one line at proper destination: - memcpy((void*)destination, (void*)source, lineSize); - source += lineSize; - destination -= lineSize; + memcpy((void*)dst, (void*)src, lineSize); + src += lineSize; + dst -= lineSize; // Update progress related: if (!(updateProgressCount%updateProgressTarget)) { @@ -678,19 +694,9 @@ size_t vtkGdcmReader::LoadImageInMemory( } updateProgressCount++; } + dst += 2 * planeSize; } -// DO NOT remove this commented out code . -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( - -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(Dest,size,1,f2); -// fclose(f2); - - //GetImageData allocate a (void*)malloc, remove it: - delete[] pSource; return size; }