X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=vtk%2FvtkGdcmReader.cxx;h=e46553e72108d440bd70a930a17dff63cb9f93ce;hb=e4be15de84d96cad6e70e5b043c1bfdd37a18bcf;hp=cad97d6873565ba9e835a8b765f3b2ed0ff2d7bc;hpb=1ec0287059d80bb579efc2b1aa4378e509eae4c9;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index cad97d68..e46553e7 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.cxx,v $ Language: C++ - Date: $Date: 2005/06/06 08:38:29 $ - Version: $Revision: 1.71 $ + Date: $Date: 2005/08/22 12:30:36 $ + Version: $Revision: 1.76 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,8 +18,42 @@ //----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// +// +//===> Many users expect from vtkGdcmReader it 'orders' the images +// (that's the job of gdcm::SerieHelper ...) +// When user *knows* the files with same Serie UID +// have same sizes, same 'pixel' type, same color convention, ... +// the right way to proceed is as follow : +// +// gdcm::SerieHelper *sh= new gdcm::SerieHelper(); +// // if user wants *not* to load some parts of the file headers +// sh->SetLoadMode(loadMode); +// // if user wants *not* to load some files +// sh->AddRestriction(group, element, value, operator); +// sh->AddRestriction( ... +// sh->SetDirectory(directoryWithImages); +// +// // if user wants to sort reverse order +// sh->SetSortOrderToReverse(); +// // here, we suppose only the first Coherent File List is of interest +// gdcm::FileList *l = sh->GetFirstCoherentFileList(); +// // if user is doesn't trust too much the files with same Serie UID +// if ( !sh->IsCoherent(l) ) +// return; // not same sizes, same 'pixel' type -> stop +// sh->OrderFileList(l); // sort the list +// +// vtkGdcmReader *reader = vtkGdcmReader::New(); +// // if user wants to modify pixel order (Mirror, TopDown, 90°Rotate, ...) +// // he has to supply the function that does the job +// // (a *very* simple example is given in vtkgdcmSerieViewer.cxx) +// reader->SetUserFunction (userSuppliedFunction); +// // to pass a 'Coherent File List' as produced by gdcm::SerieHelper +// reader->SetCoherentFileList(l); +// reader->Update(); + // WARNING TODO CLEANME -// Actual limitations of this code: +// Actual limitations of this code +// when a Coherent File List from SerieHelper is not used (bad idea :-( // // /////// Redundant and unnecessary header parsing // In it's current state this code actually parses three times the Dicom @@ -47,20 +81,19 @@ // 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 +// initializes 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: -// - advantage: the header of the files would only be parser once. +// new gdcm::File if the user changes the list). ExecuteData would then use +// those gdcm::File and hence avoid calling the constructor: +// - advantage: the header of the files would only be parsed 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 +104,17 @@ // This data is never "freed" neither in the destructor nor when the // filename list is extended, ExecuteData is called a second (or third) // time... +// +// + // ////////////////////////////////////////////////////////////// #include "gdcmFileHelper.h" #include "gdcmFile.h" +#include "gdcmDocument.h" // for NO_SEQ + #include "vtkGdcmReader.h" +#include "gdcmDebug.h" //#include #include @@ -83,8 +122,8 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.71 $"); -vtkStandardNewMacro(vtkGdcmReader); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.76 $") +vtkStandardNewMacro(vtkGdcmReader) //----------------------------------------------------------------------------- // Constructor / Destructor @@ -92,7 +131,11 @@ vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; this->AllowLookupTable = 0; - this->LightChecking = false; + this->AllowLightChecking = 0; + this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW, + // NO_SHADOWSEQ) + this->CoherentFileList = 0; + this->UserFunction = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -105,7 +148,7 @@ 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; @@ -158,13 +201,13 @@ 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() -{ - LightChecking = true; -} +//void vtkGdcmReader::SetCheckFileCoherenceLight() +//{ +// LightChecking = true; +//} //----------------------------------------------------------------------------- // Protected @@ -175,7 +218,9 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - if ( this->LightChecking ) + if ( this->CoherentFileList != 0 ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceAlreadyDone(); + else if ( this->AllowLightChecking ) this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); else this->TotalNumberOfPlanes = this->CheckFileCoherence(); @@ -217,7 +262,7 @@ 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 +270,7 @@ 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 +318,7 @@ void vtkGdcmReader::ExecuteInformation() this->Superclass::ExecuteInformation(); } - + /* * Update => ouput->Update => UpdateData => Execute => ExecuteData * (see vtkSource.cxx for last step). @@ -283,7 +328,15 @@ 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 +370,69 @@ 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") + { + // Update progress related for good files is made in LoadImageInMemory + Dest += this->LoadImageInMemory(*filename, Dest, + UpdateProgressTarget, + UpdateProgressCount); + } + else { - if (!(UpdateProgressCount%UpdateProgressTarget)) + // 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 + + } } } @@ -480,7 +563,7 @@ int vtkGdcmReader::CheckFileCoherence() { vtkErrorMacro(<< "Unable to open file " << filename->c_str()); vtkErrorMacro(<< "Removing this file from read files: " - << filename->c_str()); + << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; } @@ -488,14 +571,11 @@ int vtkGdcmReader::CheckFileCoherence() // Stage 1.2: check for Gdcm parsability - //gdcm::File GdcmFile( filename->c_str() ); // to save some parsing time. gdcm::File GdcmFile; - // Some images have a wrong length for 0x0000 element of private groups - // Better we don't use NO_SHADOW as a default option - //GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); - GdcmFile.SetLoadMode( NO_SEQ ); - 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()); @@ -514,7 +594,7 @@ int vtkGdcmReader::CheckFileCoherence() 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"); + << " Removing this file from read files"); *filename = "GDCM_UNREADABLE"; continue; } @@ -531,9 +611,9 @@ int vtkGdcmReader::CheckFileCoherence() || ( type != this->ImageType ) ) { vtkErrorMacro(<< "This file is not coherent with previous ones: " - << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files: " - << filename->c_str()); + << filename->c_str()); + vtkErrorMacro(<< "Removing this file from read files: " + << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; } @@ -542,19 +622,19 @@ int vtkGdcmReader::CheckFileCoherence() if ( NZ != ReferenceNZ ) { vtkErrorMacro(<< "File is not coherent in Z with previous ones: " - << filename->c_str()); + << filename->c_str()); } else { vtkDebugMacro(<< "File is coherent with previous ones: " - << filename->c_str()); + << filename->c_str()); } // Stage 2.3: when the file is 'multiframe', notify the caller. if (NZ > 1) { vtkErrorMacro(<< "This file is a 'Multiframe' one: " - << filename->c_str()); + << filename->c_str()); } // Eventually, this file can be added on the stack. Update the @@ -645,17 +725,59 @@ 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 ); + fileH->SetUserFunction( UserFunction ); + size_t size; // If the data structure of vtk for image/volume representation @@ -665,19 +787,19 @@ 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) { @@ -700,8 +822,8 @@ 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; @@ -721,7 +843,8 @@ size_t vtkGdcmReader::LoadImageInMemory( updateProgressCount++; } dst += 2 * planeSize; - } + } + delete fileH; return size; } @@ -737,13 +860,15 @@ 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(); @@ -781,4 +906,56 @@ 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; +} //-----------------------------------------------------------------------------