X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=db2e605d7a2938250a3fb881c0094a0f5edc2abf;hb=40ab72c408a2ff2631b66c7bd46593358b7e064f;hp=ae0c80999afeb23db64cc783415d4e224c74b52e;hpb=75fe55c7b72932dac378a24e7315071bc0ac9af6;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index ae0c8099..db2e605d 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,4 +1,21 @@ -// vtkGdcmReader.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: vtkGdcmReader.cxx,v $ + Language: C++ + Date: $Date: 2005/04/28 09:29:05 $ + Version: $Revision: 1.69 $ + + 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 CLEANME @@ -9,12 +26,19 @@ // header of a file before the corresponding image gets loaded in the // ad-hoc vtkData ! // Here is the process: -// 1/ First loading happens in ExecuteInformation which in order to -// positionate the vtk extents calls CheckFileCoherence. The purpose +// 1/ First loading happens in ExecuteInformation which, in order to +// positionate the vtk extents, calls CheckFileCoherence. The purpose // of CheckFileCoherence is to make sure all the images in the future -// stack are "homogenous" (same size, same representation...). This -// can only be achieved by parsing all the Dicom headers... -// 2/ ExecuteData is then responsible for the next two loadings: +// stack are "homogenous" (same size, same representation...). +// This can only be achieved by parsing all the Dicom headers... +// --> to avoid loosing too much time : +// If user is 150% sure *all* the files are coherent, that is to say : +// they may be open, they are gdcm-readable, they have the same sizes, +// they have the same 'pixel' type, they are single frame, +// they have the same color convention ... +// he may use SetCheckFileCoherenceLight() to request a 'light' coherence +// checking +// 2/ ExecuteData is then responsible for the next two loadings - 2 ?!?-: // 2a/ ExecuteData calls AllocateOutputData that in turn seems to // (indirectely call) ExecuteInformation which ends up in a second // header parsing @@ -24,20 +48,21 @@ // is compared to this new value to find a modification in the class // parameters // 2b/ the core of ExecuteData then needs gdcmFile (which in turns -// initialises gdcmHeader in the constructor) in order to access +// initialises gdcmFile in the constructor) in order to access // the data-image. // // Possible solution: // maintain a list of gdcmFiles (created by say ExecuteInformation) created -// once and for all accross the life of vtkGdcmHeader (it would only load +// once and for all accross the life of vtkGdcmFile (it would only load // new gdcmFile if the user changes the list). ExecuteData would then use // those gdcmFile and hence avoid calling the construtor: // - advantage: the header of the files would only be parser once. // - drawback: once execute information is called (i.e. on creation of -// a vtkGdcmHeader) the gdcmFile structure is loaded in memory. -// The average size of a gdcmHeader being of 100Ko, is one -// loads 10 stacks of images with say 200 images each, you -// end-up with a loss of 200Mo... +// a vtkGdcmFile) the gdcmFile structure is loaded in memory. +// The average size of a gdcm::File being of 100Ko, +// - 100 Ko ? Better say 1 Mo; we are in 2005 ! - +// if oneloads 10 stacks of images with say 200 images each, +// you end-up with a loss of 200Mo... // // /////// Never unallocated memory: // ExecuteData allocates space for the pixel data [which will get pointed @@ -48,8 +73,8 @@ // time... // ////////////////////////////////////////////////////////////// +#include "gdcmFileHelper.h" #include "gdcmFile.h" -#include "gdcmHeader.h" #include "vtkGdcmReader.h" //#include @@ -58,7 +83,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.59 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.69 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -67,6 +92,7 @@ vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; this->AllowLookupTable = 0; + this->LightChecking = false; } vtkGdcmReader::~vtkGdcmReader() @@ -110,7 +136,7 @@ void vtkGdcmReader::AddFileName(const char* name) { // We need to bypass the const pointer [since list<>.push_bash() only // takes a char* (but not a const char*)] by making a local copy: - char * LocalName = new char[strlen(name) + 1]; + char *LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->FileNameList.push_back(LocalName); delete[] LocalName; @@ -131,6 +157,15 @@ void vtkGdcmReader::SetFileName(const char *name) this->Modified(); } +/* + * Ask for a 'light' checking - actually : just initializing- + *if you are 150% sure *all* the files are coherent + */ +void vtkGdcmReader::SetCheckFileCoherenceLight() +{ + LightChecking = true; +} + //----------------------------------------------------------------------------- // Protected /* @@ -140,7 +175,11 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->LightChecking ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); + else + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) { vtkErrorMacro(<< "File set is not coherent. Exiting..."); @@ -209,7 +248,6 @@ void vtkGdcmReader::ExecuteInformation() { vtkDebugMacro(<< "16 bits signed image"); this->SetDataScalarTypeToShort(); - //vtkErrorMacro(<< "Cannot handle 16 bit signed files"); } else if ( ImageType == "32U" ) { @@ -240,7 +278,7 @@ void vtkGdcmReader::ExecuteInformation() * Update => ouput->Update => UpdateData => Execute => ExecuteData * (see vtkSource.cxx for last step). * This function (redefinition of vtkImageReader::ExecuteData, see - * VTK/IO/vtkImageReader.cxx) reads a data from a file. The datas + * VTK/IO/vtkImageReader.cxx) reads a data from a file. The data * extent/axes are assumed to be the same as the file extent/order. */ void vtkGdcmReader::ExecuteData(vtkDataObject *output) @@ -252,6 +290,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) } // FIXME : extraneous parsing of header is made when allocating OuputData + // --> ?!? vtkImageData *data = this->AllocateOutputData(output); data->SetExtent(this->DataExtent); data->GetPointData()->GetScalars()->SetName("DicomImage-Volume"); @@ -277,7 +316,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) // The actual advance measure: unsigned long UpdateProgressCount = 0; - // Feeling the allocated memory space with each image/volume: + // Filling the allocated memory space with each image/volume: unsigned char *Dest = (unsigned char *)data->GetScalarPointer(); for (std::list::iterator filename = InternalFileNameList.begin(); filename != InternalFileNameList.end(); @@ -426,6 +465,10 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += 1; /////// Stage 0: check for file name: + + // fixme : how can the filename be equal to "GDCM_UNREADABLE" + // right now ?!? + if(*filename == std::string("GDCM_UNREADABLE")) continue; @@ -436,7 +479,7 @@ int vtkGdcmReader::CheckFileCoherence() if (!fp) { vtkErrorMacro(<< "Unable to open file " << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from read files: " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -444,34 +487,39 @@ int vtkGdcmReader::CheckFileCoherence() fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcm::Header GdcmHeader(filename->c_str() ); - if (!GdcmHeader.IsReadable()) + + //gdcm::File GdcmFile( filename->c_str() ); + // to save some parsing time. + gdcm::File GdcmFile; + GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); + GdcmFile.Load(filename->c_str() ); + if (!GdcmFile.IsReadable()) { vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from read files: " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; } // Stage 1.3: further gdcm compatibility on PixelType - std::string type = GdcmHeader.GetPixelType(); + std::string type = GdcmFile.GetPixelType(); if ( (type != "8U") && (type != "8S") && (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; } // Stage 2: check coherence of the set of files - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - int NZ = GdcmHeader.GetZSize(); + int NX = GdcmFile.GetXSize(); + int NY = GdcmFile.GetYSize(); + int NZ = GdcmFile.GetZSize(); if (FoundReferenceFile) { // Stage 2.1: mandatory coherence stage: @@ -479,9 +527,9 @@ 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; @@ -490,20 +538,19 @@ 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()); } - // Stage 2.3: when the file contains a volume (as opposed to an image), - // notify the caller. + // Stage 2.3: when the file is 'multiframe', notify the caller. if (NZ > 1) { - vtkErrorMacro(<< "This file contains multiple planes (images)" + vtkErrorMacro(<< "This file is a 'Multiframe' one: " << filename->c_str()); } @@ -516,13 +563,13 @@ int vtkGdcmReader::CheckFileCoherence() } else { - // We didn't have a workable reference file yet. Set this one - // as the reference. + // We didn't have a workable reference file yet. + // Set this one as the reference. FoundReferenceFile = true; vtkDebugMacro(<< "This file taken as coherence reference:" - << filename->c_str()); - vtkDebugMacro(<< "Image dimension of reference file as read from Gdcm:" - << NX << " " << NY << " " << NZ); + << filename->c_str()); + vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:" + << NX << " " << NY << " " << NZ); vtkDebugMacro(<< "Number of planes added to the stack: " << NZ); // Set aside the size of the image this->NumColumns = NX; @@ -530,28 +577,21 @@ int vtkGdcmReader::CheckFileCoherence() ReferenceNZ = NZ; ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added this->ImageType = type; - this->PixelSize = GdcmHeader.GetPixelSize(); + this->PixelSize = GdcmFile.GetPixelSize(); - if( GdcmHeader.HasLUT() && this->AllowLookupTable ) + if( GdcmFile.HasLUT() && this->AllowLookupTable ) { // I could raise an error is AllowLookupTable is on and HasLUT() off - this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw(); } else { - this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono - } - + this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono + } //Set image spacing - this->DataSpacing[0] = GdcmHeader.GetXSpacing(); - this->DataSpacing[1] = GdcmHeader.GetYSpacing(); - this->DataSpacing[2] = GdcmHeader.GetZSpacing(); - - //Set image origin - this->DataOrigin[0] = GdcmHeader.GetXOrigin(); - this->DataOrigin[1] = GdcmHeader.GetYOrigin(); - this->DataOrigin[2] = GdcmHeader.GetZOrigin(); - + this->DataSpacing[0] = GdcmFile.GetXSpacing(); + this->DataSpacing[1] = GdcmFile.GetYSpacing(); + this->DataSpacing[2] = GdcmFile.GetZSpacing(); } } // End of loop on filename @@ -593,9 +633,9 @@ void vtkGdcmReader::RemoveAllInternalFileName(void) /* * Adds a file name to the internal list of images to read. */ -void vtkGdcmReader::AddInternalFileName(const char* name) +void vtkGdcmReader::AddInternalFileName(const char *name) { - char * LocalName = new char[strlen(name) + 1]; + char *LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->InternalFileNameList.push_back(LocalName); delete[] LocalName; @@ -607,12 +647,12 @@ 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() << "]"); - gdcm::File file( fileName.c_str() ); + gdcm::FileHelper file( fileName.c_str() ); size_t size; // If the data structure of vtk for image/volume representation @@ -622,17 +662,18 @@ size_t vtkGdcmReader::LoadImageInMemory( // line comes first (for some axis related reasons?). Hence we need // to load the image line by line, starting from the end. - int numColumns = file.GetHeader()->GetXSize(); - int numLines = file.GetHeader()->GetYSize(); - int numPlanes = file.GetHeader()->GetZSize(); - int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize(); + int numColumns = file.GetFile()->GetXSize(); + int numLines = file.GetFile()->GetYSize(); + int numPlanes = file.GetFile()->GetZSize(); + int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize(); + int planeSize = lineSize * numLines; - unsigned char * source; + unsigned char *src; - if( file.GetHeader()->HasLUT() && AllowLookupTable ) + if( file.GetFile()->HasLUT() && AllowLookupTable ) { size = file.GetImageDataSize(); - source = (unsigned char*) file.GetImageDataRaw(); + src = (unsigned char*) file.GetImageDataRaw(); unsigned char *lut = (unsigned char*) file.GetLutRGBA(); if(!this->LookupTable) @@ -656,20 +697,19 @@ size_t vtkGdcmReader::LoadImageInMemory( } else { - size = file.GetImageDataSize(); - source = (unsigned char*)file.GetImageData(); + size = file.GetImageDataSize(); + src = (unsigned char*)file.GetImageData(); } - - 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)) { @@ -677,18 +717,62 @@ size_t vtkGdcmReader::LoadImageInMemory( } updateProgressCount++; } - } - -// 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); - + dst += 2 * planeSize; + } return size; } +// ------------------------------------------------------------------------- + +// We assume the use *does* know all the files whose names +// are in InternalFileNameList exist, may be open, are gdcm-readable +// have the same sizes, have the same 'pixel' type, are single frame +// have the same color convention, ..., anything else ? + +int vtkGdcmReader::CheckFileCoherenceLight() +{ + std::list::iterator filename = InternalFileNameList.begin(); + + gdcm::File GdcmFile; + GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); + GdcmFile.Load(filename->c_str() ); + if (!GdcmFile.IsReadable()) + { + vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); + vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence " + << "instead of try vtkGdcmReader::CheckFileCoherenceLight"); + return 0; + } + int NX = GdcmFile.GetXSize(); + int NY = GdcmFile.GetYSize(); + int NZ = GdcmFile.GetZSize(); + std::string type = GdcmFile.GetPixelType(); + vtkDebugMacro(<< "The first file is taken as reference: " + << filename->c_str()); + vtkDebugMacro(<< "Image dimensions of reference file as read from Gdcm:" + << NX << " " << NY << " " << NZ); + vtkDebugMacro(<< "Number of planes added to the stack: " << NZ); + // Set aside the size of the image + this->NumColumns = NX; + this->NumLines = NY; + this->ImageType = type; + this->PixelSize = GdcmFile.GetPixelSize(); + + if( GdcmFile.HasLUT() && this->AllowLookupTable ) + { + // I could raise an error is AllowLookupTable is on and HasLUT() off + this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw(); + } + else + { + this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono + } + + //Set image spacing + this->DataSpacing[0] = GdcmFile.GetXSpacing(); + this->DataSpacing[1] = GdcmFile.GetYSpacing(); + this->DataSpacing[2] = GdcmFile.GetZSpacing(); + + return InternalFileNameList.size(); +} //-----------------------------------------------------------------------------