X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=a387d6119ece21a049cfce3d75a9f2bb314e2ad3;hb=f2dd700472606cce1b889e6527ca7ed68a6bbde6;hp=cad97d6873565ba9e835a8b765f3b2ed0ff2d7bc;hpb=1ec0287059d80bb579efc2b1aa4378e509eae4c9;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index cad97d68..a387d611 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: 2007/12/13 16:18:13 $ + Version: $Revision: 1.94 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -18,81 +18,101 @@ //----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// -// WARNING TODO CLEANME -// Actual limitations of this code: // -// /////// Redundant and unnecessary header parsing -// In it's current state this code actually parses three times the Dicom -// 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 -// 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... -// --> 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 -// This is fixed by adding a test at the beginning of ExecuteInformation -// on the modification of the object instance. If a modification have been -// 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 -// the data-image. +//===> Many users expect from vtkGdcmReader it 'orders' the images +// (that's the job of GDCM_NAME_SPACE::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_NAME_SPACE::SerieHelper *sh= new GDCM_NAME_SPACE::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 'Serie' is of interest +// // it's up to the user to decide ! +// GDCM_NAME_SPACE::FileList *l = sh->GetFirstSingleSerieUIDFileSet(); +// +// // 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 +// +// // WARNING : all that follows works only with 'bona fide' Series +// // (In some Series; there are more than one 'orientation' +// // Don't expected to build a 'volume' with that! +// // +// // -> use sh->SplitOnOrientation(l) +// // - or sh->SplitOnPosition(l), or SplitOnTagValue(l, gr, el) - +// // depending on what you want to do +// // and iterate on the various 'X Coherent File Sets' // -// Possible solution: -// maintain a list of gdcmFiles (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. -// - drawback: once execute information is called (i.e. on creation of -// 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... +// // if user *knows* he has to drop the 'duplicates' images +// // (same Position) +// sh->SetDropDuplicatePositions(true); +// +// // Sorting the list is mandatory +// // a side effect is to compute ZSpacing for the fle set +// 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_NAME_SPACE::SerieHelper +// reader->SetCoherentFileList(l); +// reader->Update(); +// +// WARNING TODO CLEANME +// Actual limitations of this code +// when a Coherent File List from SerieHelper is not used (bad idea :-( // -// /////// Never unallocated memory: -// ExecuteData allocates space for the pixel data [which will get pointed -// by the vtkPointData() through the call -// data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0);] -// 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 "gdcmSerieHelper.h" // for ImagePositionPatientOrdering() + #include "vtkGdcmReader.h" +#include "gdcmDebug.h" +#include "gdcmCommon.h" -//#include #include #include #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.71 $"); -vtkStandardNewMacro(vtkGdcmReader); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.94 $") +vtkStandardNewMacro(vtkGdcmReader) //----------------------------------------------------------------------------- // Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; - this->AllowLookupTable = 0; - this->LightChecking = false; + this->AllowLookupTable = false; + //this->AllowLightChecking = false; + this->LoadMode = GDCM_NAME_SPACE::LD_ALL; // Load everything (possible values : + // - LD_NOSEQ, + // - LD_NOSHADOW, + // - LD_NOSHADOWSEQ) + this->CoherentFileList = 0; + this->UserFunction = 0; + + this->OwnFile=true; + // this->Execution=false; // For VTK5.0 + + this->KeepOverlays = false; } vtkGdcmReader::~vtkGdcmReader() @@ -105,7 +125,7 @@ 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; @@ -136,10 +156,7 @@ 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]; - strcpy(LocalName, name); - this->FileNameList.push_back(LocalName); - delete[] LocalName; + this->FileNameList.push_back(name); this->Modified(); } @@ -157,15 +174,6 @@ 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 /* @@ -173,23 +181,35 @@ void vtkGdcmReader::SetCheckFileCoherenceLight() */ void vtkGdcmReader::ExecuteInformation() { +// if(this->Execution) // For VTK5.0 +// return; +// +// this->Execution=true; // end For VTK5.0 + this->RemoveAllInternalFile(); if(this->MTime>this->fileTime) { - if ( this->LightChecking ) - this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); + this->TotalNumberOfPlanes = 0; + + if ( this->CoherentFileList != 0 ) + { + this->UpdateFileInformation(); + } else - this->TotalNumberOfPlanes = this->CheckFileCoherence(); + { + this->BuildFileListFromPattern(); + this->LoadFileInformation(); + } if ( this->TotalNumberOfPlanes == 0) { vtkErrorMacro(<< "File set is not coherent. Exiting..."); return; } - + // if the user has not set the extent, but has set the VOI // set the z axis extent to the VOI z axis if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && - (this->DataVOI[4] || this->DataVOI[5])) + (this->DataVOI[4] || this->DataVOI[5])) { this->DataExtent[4] = this->DataVOI[4]; this->DataExtent[5] = this->DataVOI[5]; @@ -217,7 +237,7 @@ 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 +245,7 @@ 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: @@ -271,9 +291,15 @@ void vtkGdcmReader::ExecuteInformation() this->fileTime=this->MTime; } - this->Superclass::ExecuteInformation(); -} + this->Superclass::ExecuteInformation(); + + //this->GetOutput()->SetUpdateExtentToWholeExtent();// For VTK5.0 + //this->BuildData(this->GetOutput()); + //this->Execution=false; + //this->RemoveAllInternalFile(); // End For VTK5.0 +} + /* * Update => ouput->Update => UpdateData => Execute => ExecuteData * (see vtkSource.cxx for last step). @@ -283,16 +309,41 @@ void vtkGdcmReader::ExecuteInformation() */ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (this->InternalFileNameList.empty()) + vtkImageData *data=vtkImageData::SafeDownCast(output); + data->SetExtent(this->DataExtent); + +/* 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; } +*/ + + // data->AllocateScalars(); // For VTK5.0 + // if (this->UpdateExtentIsEmpty(output)) + // { + // return; + // } +//} // end For VTK5.0 + + data->AllocateScalars(); // For VTK5.0 + +#if (VTK_MAJOR_VERSION >= 5) || ( VTK_MAJOR_VERSION == 4 && VTK_MINOR_VERSION > 2 ) +//#if (VTK_MAJOR_VERSION >= 5) + if (this->UpdateExtentIsEmpty(output)) + { + return; + } +#endif - // 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"); // Test if output has valid extent @@ -317,40 +368,21 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) unsigned long UpdateProgressCount = 0; // Filling the allocated memory space with each image/volume: + + size_t size = this->NumColumns * this->NumLines * this->NumPlanes + * data->GetScalarSize() * this->NumComponents; 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 (!(UpdateProgressCount%UpdateProgressTarget)) - { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - } - } // Else, file not loadable - } // Loop on files + for (std::vector::iterator it = InternalFileList.begin(); + it != InternalFileList.end(); + ++it) + { + this->LoadImageInMemory(*it, Dest, + UpdateProgressTarget, + UpdateProgressCount); + Dest += size; + } } + this->RemoveAllInternalFile(); // For VTK5.0 } /* @@ -365,6 +397,7 @@ void vtkGdcmReader::BuildFileListFromPattern() { this->RemoveAllInternalFileName(); + // Test miscellanous cases if ((! this->FileNameList.empty()) && this->FileName ) { vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used"); @@ -386,6 +419,7 @@ void vtkGdcmReader::BuildFileListFromPattern() return; } + // Create the InternalFileNameList if (! this->FileNameList.empty() ) { vtkDebugMacro(<< "Using the AddFileName specified files"); @@ -420,93 +454,61 @@ void vtkGdcmReader::BuildFileListFromPattern() } } -/* - * When more than one filename is specified (i.e. we expect loading - * a stack or volume) we need to check that the corresponding images/volumes - * to be loaded are coherent i.e. to make sure: - * - they all share the same X dimensions - * - they all share the same Y dimensions - * - they all share the same ImageType ( 8 bit signed, or unsigned...) +/** + * Load all the files and set it in the InternalFileList + * For each file, the readability and the coherence of image caracteristics + * are tested. If an image doesn't agree the required specifications, it + * isn't considered and no data will be set for the planes corresponding + * to this image * - * Eventually, we emit a warning when all the files do NOT share the - * Z dimension, since we can still build a stack but the - * files are not coherent in Z, which is probably a source a trouble... - * When files are not readable (either the file cannot be opened or - * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". - * This method returns the total number of planar images to be loaded - * (i.e. an image represents one plane, but a volume represents many planes) + * The source of this work is the list of file name generated by the + * BuildFileListFromPattern method */ -int vtkGdcmReader::CheckFileCoherence() +void vtkGdcmReader::LoadFileInformation() { - int ReturnedTotalNumberOfPlanes = 0; // The returned value. - - this->BuildFileListFromPattern(); - if (this->InternalFileNameList.empty()) - { - vtkErrorMacro(<< "FileNames are not set."); - return 0; - } - - bool FoundReferenceFile = false; - int ReferenceNZ = 0; + GDCM_NAME_SPACE::File *file; + bool foundReference=false; + std::string type; - // Loop on the filenames: - // - check for their existence and gdcm "parsability" - // - get the coherence check done: + this->OwnFile=true; for (std::list::iterator filename = InternalFileNameList.begin(); filename != InternalFileNameList.end(); ++filename) { - // The file is always added in the number of planes - // - If file doesn't exist, it will be replaced by a black plane in the - // ExecuteData method - // - If file has more than 1 plane, other planes will be added later to - // to the ReturnedTotalNumberOfPlanes variable counter - 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; - - /////// Stage 1: check for file readability: - // Stage 1.1: check for file existence. + // check for file readability FILE *fp; fp = fopen(filename->c_str(),"rb"); if (!fp) { vtkErrorMacro(<< "Unable to open file " << filename->c_str()); vtkErrorMacro(<< "Removing this file from read files: " - << filename->c_str()); - *filename = "GDCM_UNREADABLE"; + << filename->c_str()); + file = NULL; + InternalFileList.push_back(file); continue; } fclose(fp); - // 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() ); - if (!GdcmFile.IsReadable()) + // Read the file + file=GDCM_NAME_SPACE::File::New(); + file->SetLoadMode( LoadMode ); + file->SetFileName(filename->c_str() ); + file->Load(); + + // Test the Dicom file readability + if(!file->IsReadable()) { vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); vtkErrorMacro(<< "Removing this file from read files: " << filename->c_str()); - *filename = "GDCM_UNREADABLE"; + file->Delete(); + file=NULL; + InternalFileList.push_back(file); continue; } - // Stage 1.3: further gdcm compatibility on PixelType - std::string type = GdcmFile.GetPixelType(); + // Test the Pixel Type recognition + type = file->GetPixelType(); if ( (type != "8U") && (type != "8S") && (type != "16U") && (type != "16S") && (type != "32U") && (type != "32S") ) @@ -514,113 +516,190 @@ 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"); - *filename = "GDCM_UNREADABLE"; + << " Removing this file from read files"); + file->Delete(); + file=NULL; + InternalFileList.push_back(file); continue; } - // Stage 2: check coherence of the set of files - int NX = GdcmFile.GetXSize(); - int NY = GdcmFile.GetYSize(); - int NZ = GdcmFile.GetZSize(); - if (FoundReferenceFile) + // Test the image informations + if(!foundReference) { - // Stage 2.1: mandatory coherence stage: - if ( ( NX != this->NumColumns ) - || ( NY != this->NumLines ) - || ( 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 = "GDCM_UNREADABLE"; - continue; - } - - // Stage 2.2: optional coherence stage - if ( NZ != ReferenceNZ ) - { - vtkErrorMacro(<< "File is not coherent in Z with previous ones: " - << filename->c_str()); - } - else - { - vtkDebugMacro(<< "File is coherent with previous ones: " - << 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()); - } - - // Eventually, this file can be added on the stack. Update the - // full size of the stack - vtkDebugMacro("Number of planes added to the stack: " << NZ); - ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added - continue; + foundReference = true; + GetFileInformation(file); - } - else - { - // 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()); + << 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; - ReferenceNZ = NZ; - ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added - 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(); + << this->NumColumns << " " << this->NumLines << " " + << this->NumPlanes); + } + else if(!TestFileInformation(file)) + { + file->Delete(); + file=NULL; } - } // End of loop on filename - ///////// The files we CANNOT load are flaged. On debugging purposes - // count the loadable number of files and display their number: - int NumberCoherentFiles = 0; - for (std::list::iterator it = InternalFileNameList.begin(); - it != InternalFileNameList.end(); - ++it) + InternalFileList.push_back(file); + } +} + +/** + * Update the file informations. + * This works exactly like LoadFileInformation, but the source of work + * is the list of coherent files + */ +void vtkGdcmReader::UpdateFileInformation() +{ + this->InternalFileList=*(this->CoherentFileList); + this->OwnFile=false; + + for(gdcmFileList::iterator it=InternalFileList.begin(); + it!=InternalFileList.end(); + ++it) { - if (*it != "GDCM_UNREADABLE") + if( *it != NULL) { - NumberCoherentFiles++; + GetFileInformation(*it); + break; } } - vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles); +} + +/** + * Get the informations from a file. + * These informations are required to specify the output image + * caracteristics + */ +void vtkGdcmReader::GetFileInformation(GDCM_NAME_SPACE::File *file) +{ + // Get the image caracteristics + this->NumColumns = file->GetXSize(); + this->NumLines = file->GetYSize(); + this->NumPlanes = file->GetZSize(); - if (ReturnedTotalNumberOfPlanes == 0) + if (CoherentFileList == 0) + this->TotalNumberOfPlanes = this->NumPlanes*InternalFileNameList.size(); + else + this->TotalNumberOfPlanes = this->NumPlanes*CoherentFileList->size(); + + this->ImageType = file->GetPixelType(); + this->PixelSize = file->GetPixelSize(); + + this->DataSpacing[0] = file->GetXSpacing(); + this->DataSpacing[1] = file->GetYSpacing(); + + // Most of the file headers have NO z spacing + // It must be calculated from the whole GDCM_NAME_SPACE::Serie (if any) + // using Jolinda Smith's algoritm. + // see GDCM_NAME_SPACE::SerieHelper::ImagePositionPatientOrdering() + if (CoherentFileList == 0) + this->DataSpacing[2] = file->GetZSpacing(); + else { - vtkErrorMacro(<< "No loadable file."); + // Just because OrderFileList() is a member of GDCM_NAME_SPACE::SerieHelper + // we need to instanciate sh. + GDCM_NAME_SPACE::SerieHelper *sh = GDCM_NAME_SPACE::SerieHelper::New(); + sh->OrderFileList(CoherentFileList); // calls ImagePositionPatientOrdering() + this->DataSpacing[2] = sh->GetZSpacing(); + sh->Delete(); + } + + // Get the image data caracteristics + if( file->HasLUT() && this->AllowLookupTable ) + { + // I could raise an error is AllowLookupTable is on and HasLUT() off + this->NumComponents = file->GetNumberOfScalarComponentsRaw(); + } + else + { + this->NumComponents = file->GetNumberOfScalarComponents(); //rgb or mono } +} - vtkDebugMacro(<< "Total number of planes on the stack: " - << ReturnedTotalNumberOfPlanes); - - return ReturnedTotalNumberOfPlanes; +/* + * When more than one filename is specified (i.e. we expect loading + * a stack or volume) we need to check that the corresponding images/volumes + * to be loaded are coherent i.e. to make sure: + * - they all share the same X dimensions + * - they all share the same Y dimensions + * - they all share the same ImageType ( 8 bit signed, or unsigned...) + * + * Eventually, we emit a warning when all the files do NOT share the + * Z dimension, since we can still build a stack but the + * files are not coherent in Z, which is probably a source a trouble... + * When files are not readable (either the file cannot be opened or + * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". + * This method returns the total number of planar images to be loaded + * (i.e. an image represents one plane, but a volume represents many planes) + */ +/** + * Test the coherent informations of the file with the reference informations + * used as image caracteristics. The tested informations are : + * - they all share the same X dimensions + * - they all share the same Y dimensions + * - they all share the same Z dimensions + * - they all share the same number of components + * - they all share the same ImageType ( 8 bit signed, or unsigned...) + * + * \return True if the file match, False otherwise + */ +bool vtkGdcmReader::TestFileInformation(GDCM_NAME_SPACE::File *file) +{ + int numColumns = file->GetXSize(); + int numLines = file->GetYSize(); + int numPlanes = file->GetZSize(); + int numComponents; + unsigned int pixelSize = file->GetPixelSize(); + + if( file->HasLUT() && this->AllowLookupTable ) + numComponents = file->GetNumberOfScalarComponentsRaw(); + else + numComponents = file->GetNumberOfScalarComponents(); //rgb or mono + + if( numColumns != this->NumColumns ) + { + vtkErrorMacro(<< "File X value doesn't match with the previous ones: " + << file->GetFileName().c_str() + << ". Found " << numColumns << ", must be " + << this->NumColumns); + return false; + } + if( numLines != this->NumLines ) + { + vtkErrorMacro(<< "File Y value doesn't match with the previous ones: " + << file->GetFileName().c_str() + << ". Found " << numLines << ", must be " + << this->NumLines); + return false; + } + if( numPlanes != this->NumPlanes ) + { + vtkErrorMacro(<< "File Z value doesn't match with the previous ones: " + << file->GetFileName().c_str() + << ". Found " << numPlanes << ", must be " + << this->NumPlanes); + return false; + } + if( numComponents != this->NumComponents ) + { + vtkErrorMacro(<< "File Components count doesn't match with the previous ones: " + << file->GetFileName().c_str() + << ". Found " << numComponents << ", must be " + << this->NumComponents); + return false; + } + if( pixelSize != this->PixelSize ) + { + vtkErrorMacro(<< "File pixel size doesn't match with the previous ones: " + << file->GetFileName().c_str() + << ". Found " << pixelSize << ", must be " + << this->PixelSize); + return false; + } + + return true; } //----------------------------------------------------------------------------- @@ -645,18 +724,94 @@ void vtkGdcmReader::AddInternalFileName(const char *name) } /* - * Loads the contents of the image/volume contained by Filename at - * the Dest memory address. Returns the size of the data loaded. + * Remove all file names to the internal list of images to read. */ -size_t vtkGdcmReader::LoadImageInMemory( +void vtkGdcmReader::RemoveAllInternalFile(void) +{ + if(this->OwnFile) + { + for(gdcmFileList::iterator it=InternalFileList.begin(); + it!=InternalFileList.end(); + ++it) + { + (*it)->Delete(); + } + } + this->InternalFileList.clear(); +} + +void vtkGdcmReader::IncrementProgress(const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + // Update progress related for bad files: + updateProgressCount += this->NumLines; + if (updateProgressTarget > 0) + { + if (!(updateProgressCount%updateProgressTarget)) + { + this->UpdateProgress( + updateProgressCount/(50.0*updateProgressTarget)); + } + } +} + +/* + * Loads the contents of the image/volume contained by char *fileName at + * the dest memory address. Returns the size of the data loaded. + */ +/*void 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() ); - size_t size; + + GDCM_NAME_SPACE::File *f; + f = new GDCM_NAME_SPACE::File(); + f->SetLoadMode( LoadMode ); + f->SetFileName( fileName.c_str() ); + f->Load( ); + + LoadImageInMemory(f,dest, + updateProgressTarget, + updateProgressCount); + delete f; +}*/ + +/* + * Loads the contents of the image/volume contained by GDCM_NAME_SPACE::File* f at + * the Dest memory address. Returns the size of the data loaded. + * \ param f File to consider. NULL if the file must be skiped + * \remarks Assume that if (f != NULL) then its caracteristics match + * with the previous ones + */ +void vtkGdcmReader::LoadImageInMemory( + GDCM_NAME_SPACE::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + if(!f) + return; + + GDCM_NAME_SPACE::FileHelper *fileH = GDCM_NAME_SPACE::FileHelper::New( f ); + fileH->SetUserFunction( UserFunction ); + + fileH->SetKeepOverlays ( this->KeepOverlays); + + int numColumns = f->GetXSize(); + int numLines = f->GetYSize(); + int numPlanes = f->GetZSize(); + int numComponents; + + if( f->HasLUT() && this->AllowLookupTable ) + numComponents = f->GetNumberOfScalarComponentsRaw(); + else + numComponents = f->GetNumberOfScalarComponents(); //rgb or mono + vtkDebugMacro(<< "numComponents:" << numComponents); + vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName().c_str() << "]"); + //size_t size; // If the data structure of vtk for image/volume representation // were straigthforwards the following would be enough: @@ -665,19 +820,17 @@ 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 lineSize = NumComponents * numColumns * f->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(); + // to avoid bcc 5.5 w + /*size = */ fileH->GetImageDataSize(); + src = (unsigned char*) fileH->GetImageDataRaw(); + unsigned char *lut = (unsigned char*) fileH->GetLutRGBA(); if(!this->LookupTable) { @@ -696,12 +849,13 @@ size_t vtkGdcmReader::LoadImageInMemory( this->LookupTable->SetRange(0,255); vtkDataSetAttributes *a = this->GetOutput()->GetPointData(); a->GetScalars()->SetLookupTable(this->LookupTable); - free(lut); + delete[] lut; } else { - size = file.GetImageDataSize(); - src = (unsigned char*)file.GetImageData(); + //size = fileH->GetImageDataSize(); + // useless - just an accessor; 'size' unused + src = (unsigned char*)fileH->GetImageData(); } unsigned char *dst = dest + planeSize - lineSize; @@ -716,69 +870,15 @@ size_t vtkGdcmReader::LoadImageInMemory( // Update progress related: if (!(updateProgressCount%updateProgressTarget)) { - this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget)); + this->UpdateProgress( + updateProgressCount/(50.0*updateProgressTarget)); } updateProgressCount++; } 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(); - // 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()); - 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(); + fileH->Delete(); } + //-----------------------------------------------------------------------------