X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=2970000e2c20609df97f15d90b839caf82a509f0;hb=d1a38a4f0d357d1d8079eacf4de5e0aeb3eff973;hp=db2e605d7a2938250a3fb881c0094a0f5edc2abf;hpb=40ab72c408a2ff2631b66c7bd46593358b7e064f;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index db2e605d..2970000e 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.cxx,v $ Language: C++ - Date: $Date: 2005/04/28 09:29:05 $ - Version: $Revision: 1.69 $ + Date: $Date: 2005/07/17 04:34:20 $ + Version: $Revision: 1.73 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -47,20 +47,19 @@ // made (method Modified() ), the MTime value is increased. The fileTime // 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 gdcmFile in the constructor) in order to access +// 2b/ the core of ExecuteData then needs gdcm::File (which in turns +// initialises gdcm::File in the constructor) in order to access // the data-image. // // Possible solution: -// maintain a list of gdcmFiles (created by say ExecuteInformation) created +// maintain a list of gdcm::Files (created by say ExecuteInformation) created // 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: +// new gdcm::File if the user changes the list). ExecuteData would then use +// those gdcm::File 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 vtkGdcmFile) the gdcmFile structure is loaded in memory. +// a vtkGdcmFile) the gdcm::File 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... // @@ -71,11 +70,21 @@ // This data is never "freed" neither in the destructor nor when the // filename list is extended, ExecuteData is called a second (or third) // time... +// +// +//===> Since many users expect from vtkGdcmReader it 'orders' the images +// (that's the job of gdcm::SerieHelper), user may now call +// vtkGdcmReader::SetCoherentFileList() to pass a 'Coherent File List' +// as produced by gdcm::SerieHelper +// See the limitations of gdcm::SerieHelper before ... // ////////////////////////////////////////////////////////////// #include "gdcmFileHelper.h" #include "gdcmFile.h" +#include "gdcmDocument.h" // for NO_SEQ + #include "vtkGdcmReader.h" +#include "gdcmDebug.h" //#include #include @@ -83,7 +92,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.69 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.73 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -93,6 +102,9 @@ vtkGdcmReader::vtkGdcmReader() this->LookupTable = NULL; this->AllowLookupTable = 0; this->LightChecking = false; + this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW, + // NO_SHADOWSEQ) + this->CoherentFileList = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -105,7 +117,7 @@ vtkGdcmReader::~vtkGdcmReader() //----------------------------------------------------------------------------- // Print -void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) +void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent) { this->Superclass::PrintSelf(os,indent); os << indent << "Filenames : " << endl; @@ -158,7 +170,7 @@ void vtkGdcmReader::SetFileName(const char *name) } /* - * Ask for a 'light' checking - actually : just initializing- + * Ask for a 'light' checking -actually : just initializing- *if you are 150% sure *all* the files are coherent */ void vtkGdcmReader::SetCheckFileCoherenceLight() @@ -175,7 +187,9 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - if ( this->LightChecking ) + if ( this->CoherentFileList != 0 ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceAlreadyDone(); + else if ( this->LightChecking ) this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); else this->TotalNumberOfPlanes = this->CheckFileCoherence(); @@ -217,7 +231,7 @@ void vtkGdcmReader::ExecuteInformation() } } - // Positionate the Extent. + // Set the Extents. this->DataExtent[0] = 0; this->DataExtent[1] = this->NumColumns - 1; this->DataExtent[2] = 0; @@ -225,7 +239,7 @@ void vtkGdcmReader::ExecuteInformation() this->DataExtent[4] = 0; this->DataExtent[5] = this->TotalNumberOfPlanes - 1; - // We don't need to positionate the Endian related stuff (by using + // We don't need to set the Endian related stuff (by using // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian() // since the reading of the file is done by gdcm. // But we do need to set up the data type for downstream filters: @@ -273,7 +287,7 @@ void vtkGdcmReader::ExecuteInformation() this->Superclass::ExecuteInformation(); } - + /* * Update => ouput->Update => UpdateData => Execute => ExecuteData * (see vtkSource.cxx for last step). @@ -283,7 +297,15 @@ void vtkGdcmReader::ExecuteInformation() */ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (this->InternalFileNameList.empty()) + if ( CoherentFileList != 0 ) // When a list of names is passed + { + if (this->CoherentFileList->empty()) + { + vtkErrorMacro(<< "Coherent File List must have at least a valid File*."); + return; + } + } + else if (this->InternalFileNameList.empty()) { vtkErrorMacro(<< "A least a valid FileName must be specified."); return; @@ -317,39 +339,69 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) unsigned long UpdateProgressCount = 0; // 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(); - ++filename) - { - // Images that were tagged as unreadable in CheckFileCoherence() - // are substituted with a black image to let the caller visually - // notice something wrong is going on: - if (*filename != "GDCM_UNREADABLE") - { - // Update progress related for good files is made in LoadImageInMemory - Dest += this->LoadImageInMemory(*filename, Dest, - UpdateProgressTarget, - UpdateProgressCount); - } - else - { - // We insert a black image in the stack for the user to be aware that - // this image/volume couldn't be loaded. We simply skip one image - // size: - Dest += this->NumColumns * this->NumLines * this->PixelSize; - - // Update progress related for bad files: - UpdateProgressCount += this->NumLines; - if (UpdateProgressTarget > 0) + + if ( CoherentFileList == 0 ) // When a list of names is passed + { + for (std::list::iterator filename = InternalFileNameList.begin(); + filename != InternalFileNameList.end(); + ++filename) + { + // Images that were tagged as unreadable in CheckFileCoherence() + // are substituted with a black image to let the caller visually + // notice something wrong is going on: + if (*filename != "GDCM_UNREADABLE") { - if (!(UpdateProgressCount%UpdateProgressTarget)) + // Update progress related for good files is made in LoadImageInMemory + Dest += this->LoadImageInMemory(*filename, Dest, + UpdateProgressTarget, + UpdateProgressCount); + } + else + { + // We insert a black image in the stack for the user to be aware that + // this image/volume couldn't be loaded. We simply skip one image + // size: + Dest += this->NumColumns * this->NumLines * this->PixelSize; + + // Update progress related for bad files: + UpdateProgressCount += this->NumLines; + if (UpdateProgressTarget > 0) { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } } - } - } // Else, file not loadable - } // Loop on files + } // Else, file not loadable + } // Loop on files + + } + else // when a Coherent File List is passed + { + for (std::vector::iterator it = CoherentFileList->begin(); + it != CoherentFileList->end(); + ++it) + { + + //std::cout <<"----------------- " << (*it)->GetFileName() << std::endl; + + Dest += this->LoadImageInMemory(*it, Dest, + UpdateProgressTarget, + UpdateProgressCount); + // Update progress related for bad files: + UpdateProgressCount += this->NumLines; + if (UpdateProgressTarget > 0) + { + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + } + } // Loop on files + + } } } @@ -489,9 +541,10 @@ int vtkGdcmReader::CheckFileCoherence() // Stage 1.2: check for Gdcm parsability //gdcm::File GdcmFile( filename->c_str() ); + // to save some parsing time. gdcm::File GdcmFile; - GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); + GdcmFile.SetLoadMode( LoadMode ); GdcmFile.Load(filename->c_str() ); if (!GdcmFile.IsReadable()) { @@ -642,17 +695,57 @@ void vtkGdcmReader::AddInternalFileName(const char *name) } /* - * Loads the contents of the image/volume contained by Filename at + * Loads the contents of the image/volume contained by gdcm::File* f at * the Dest memory address. Returns the size of the data loaded. */ +size_t vtkGdcmReader::LoadImageInMemory( + gdcm::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + // vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName() << "]"); + + return DoTheLoadingJob (f, + dest, + updateProgressTarget, + updateProgressCount); +} + +/* + * Loads the contents of the image/volume contained by char *fileName at + * the dest memory address. Returns the size of the data loaded. + */ size_t vtkGdcmReader::LoadImageInMemory( std::string fileName, unsigned char *dest, const unsigned long updateProgressTarget, - unsigned long & updateProgressCount) + unsigned long &updateProgressCount) { vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); - gdcm::FileHelper file( fileName.c_str() ); + + gdcm::File *f; + f = new gdcm::File(); + f->SetLoadMode( LoadMode ); + f->SetFileName( fileName.c_str() ); + f->Load( ); + + return DoTheLoadingJob (f, + dest, + updateProgressTarget, + updateProgressCount); + delete f; +} + +/* + * Service method for LoadImageInMemory +*/ +size_t vtkGdcmReader::DoTheLoadingJob (gdcm::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + gdcm::FileHelper *fileH = new gdcm::FileHelper( f ); size_t size; // If the data structure of vtk for image/volume representation @@ -662,19 +755,19 @@ 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.GetFile()->GetXSize(); - int numLines = file.GetFile()->GetYSize(); - int numPlanes = file.GetFile()->GetZSize(); - int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize(); + int numColumns = fileH->GetFile()->GetXSize(); + int numLines = fileH->GetFile()->GetYSize(); + int numPlanes = fileH->GetFile()->GetZSize(); + int lineSize = NumComponents * numColumns * fileH->GetFile()->GetPixelSize(); int planeSize = lineSize * numLines; unsigned char *src; - if( file.GetFile()->HasLUT() && AllowLookupTable ) + if( fileH->GetFile()->HasLUT() && AllowLookupTable ) { - size = file.GetImageDataSize(); - src = (unsigned char*) file.GetImageDataRaw(); - unsigned char *lut = (unsigned char*) file.GetLutRGBA(); + size = fileH->GetImageDataSize(); + src = (unsigned char*) fileH->GetImageDataRaw(); + unsigned char *lut = (unsigned char*) fileH->GetLutRGBA(); if(!this->LookupTable) { @@ -697,8 +790,8 @@ size_t vtkGdcmReader::LoadImageInMemory( } else { - size = file.GetImageDataSize(); - src = (unsigned char*)file.GetImageData(); + size = fileH->GetImageDataSize(); + src = (unsigned char*)fileH->GetImageData(); } unsigned char *dst = dest + planeSize - lineSize; @@ -718,7 +811,8 @@ size_t vtkGdcmReader::LoadImageInMemory( updateProgressCount++; } dst += 2 * planeSize; - } + } + delete fileH; return size; } @@ -734,18 +828,23 @@ int vtkGdcmReader::CheckFileCoherenceLight() std::list::iterator filename = InternalFileNameList.begin(); gdcm::File GdcmFile; - GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); - GdcmFile.Load(filename->c_str() ); + GdcmFile.SetLoadMode( LoadMode ); + GdcmFile.SetFileName(filename->c_str() ); + GdcmFile.Load( ); + if (!GdcmFile.IsReadable()) { vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence " - << "instead of try vtkGdcmReader::CheckFileCoherenceLight"); + << "instead of vtkGdcmReader::CheckFileCoherenceLight"); return 0; } int NX = GdcmFile.GetXSize(); int NY = GdcmFile.GetYSize(); - int NZ = GdcmFile.GetZSize(); + // CheckFileCoherenceLight should be called *only* when user knows + // he deals with single frames files. + // Z size is then the number of files. + int NZ = InternalFileNameList.size(); std::string type = GdcmFile.GetPixelType(); vtkDebugMacro(<< "The first file is taken as reference: " << filename->c_str()); @@ -775,4 +874,56 @@ int vtkGdcmReader::CheckFileCoherenceLight() return InternalFileNameList.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::CheckFileCoherenceAlreadyDone() +{ + if ( CoherentFileList->empty() ) + { + vtkErrorMacro(<< "Coherent File List is empty "); + return 0; + } + + gdcm::File *gdcmFile = (*CoherentFileList)[0]; + + int NX = gdcmFile->GetXSize(); + int NY = gdcmFile->GetYSize(); + // CheckFileCoherenceLight should be called *only* when user knows + // he deals with single frames files. + // Z size is then the number of files. + // --> TODO : loop on the File* to get NZ of each one ! + int NZ = CoherentFileList->size(); + std::string type = gdcmFile->GetPixelType(); + //vtkDebugMacro(<< "The first file is taken as reference: " + // << (*CoherentFileList)[0]->GetFileName() ); + 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 NZ; +} //-----------------------------------------------------------------------------