X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=1e0852bdbab52c64923cf2d9c62321b20455b80e;hb=659604feaaaf9519d03d59d66711f6b4b8290804;hp=4a18c5ac1cbd56a76ffe16987b3231e950434952;hpb=9d4af637535366b0741e3315b83b6b50582d46d6;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 4a18c5ac..1e0852bd 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,21 +1,76 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.11 2003/06/12 16:58:31 malaterre Exp $ -//CLEANME#include -#include +// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.29 2003/12/22 12:46:19 regrain Exp $ +// ////////////////////////////////////////////////////////////// +// WARNING TODO CLENAME +// 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... +// 2/ ExecuteData is then responsible for the next two loadings: +// 2a/ ExecuteData calls AllocateOutputData that in turn seems to +// (indirectely call) ExecuteInformation which ends up in a second +// header parsing +// 2b/ the core of ExecuteData then needs gdcmFile (which in turns +// initialises gdcmHeader 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 +// 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... +// +// /////// 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 "gdcmFile.h" +#include "gdcmHeaderHelper.h" +#include "vtkGdcmReader.h" + +//#include #include #include #include -#include "vtkGdcmReader.h" -#include "gdcm.h" +#include + vtkGdcmReader::vtkGdcmReader() { // Constructor + this->LookupTable = NULL; } //---------------------------------------------------------------------------- vtkGdcmReader::~vtkGdcmReader() { - // FIXME free memory + this->RemoveAllFileName(); + this->InternalFileNameList.clear(); + if(this->LookupTable) this->LookupTable->Delete(); +} + +//---------------------------------------------------------------------------- +// Remove all files from the list of images to read. +void vtkGdcmReader::RemoveAllFileName(void) +{ this->FileNameList.clear(); } @@ -38,11 +93,28 @@ void vtkGdcmReader::SetFileName(const char *name) { vtkImageReader2::SetFileName(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: + // this list when we manually positionate the filename. this->FileNameList.clear(); this->Modified(); } +//---------------------------------------------------------------------------- +// Adds a file name to the internal list of images to read. +void vtkGdcmReader::RemoveAllInternalFileName(void) +{ + this->InternalFileNameList.clear(); +} + +//---------------------------------------------------------------------------- +// Adds a file name to the internal list of images to read. +void vtkGdcmReader::AddInternalFileName(const char* name) +{ + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->InternalFileNameList.push_back(LocalName); + delete[] LocalName; +} + //---------------------------------------------------------------------------- // vtkGdcmReader can have the file names specified through two ways: // (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and @@ -62,6 +134,7 @@ void vtkGdcmReader::BuildFileListFromPattern() if (! this->FileNameList.empty() ) { vtkDebugMacro("Using the AddFileName specified files"); + this->InternalFileNameList=this->FileNameList; return; } @@ -72,12 +145,24 @@ void vtkGdcmReader::BuildFileListFromPattern() return; } - for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) + this->RemoveAllInternalFileName(); + if( this->FileNameList.empty() ) { - this->ComputeInternalFileName(idx); + //Multiframe case: + this->ComputeInternalFileName(this->DataExtent[4]); vtkDebugMacro("Adding file " << this->InternalFileName); - this->AddFileName(this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); } + else + { + //stack of 2D dicom case: + for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) + { + this->ComputeInternalFileName(idx); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } + } } //---------------------------------------------------------------------------- @@ -100,7 +185,7 @@ int vtkGdcmReader::CheckFileCoherence() int ReturnedTotalNumberOfPlanes = 0; // The returned value. this->BuildFileListFromPattern(); - if (this->FileNameList.empty()) + if (this->InternalFileNameList.empty()) { vtkErrorMacro("FileNames are not set."); return 0; @@ -110,12 +195,23 @@ int vtkGdcmReader::CheckFileCoherence() int ReferenceNZ = 0; // Loop on the filenames: - // - check for their existence and gdcm "parasability" + // - check for their existence and gdcm "parsability" // - get the coherence check done: - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); + 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: + if(*FileName==std::string("GDCM_UNREADABLE")) + continue; + /////// Stage 1: check for file readability: // Stage 1.1: check for file existence. FILE *fp; @@ -131,7 +227,7 @@ int vtkGdcmReader::CheckFileCoherence() fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcmHeader GdcmHeader(FileName->c_str()); + gdcmHeaderHelper GdcmHeader(FileName->c_str()); if (!GdcmHeader.IsReadable()) { vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); @@ -148,6 +244,7 @@ int vtkGdcmReader::CheckFileCoherence() && (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()); *FileName = "GDCM_UNREADABLE"; @@ -192,14 +289,12 @@ int vtkGdcmReader::CheckFileCoherence() { vtkErrorMacro("This file contains multiple planes (images)" << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << 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; + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added continue; } else { @@ -215,20 +310,40 @@ int vtkGdcmReader::CheckFileCoherence() this->NumColumns = NX; this->NumLines = NY; ReferenceNZ = NZ; - ReturnedTotalNumberOfPlanes += NZ; + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added this->ImageType = type; this->PixelSize = GdcmHeader.GetPixelSize(); + + if( GdcmHeader.HasLUT() ) + { + this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + } + else + { + this->NumComponents = GdcmHeader.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(); + } } // End of loop on FileName ///////// The files we CANNOT load are flaged. On debugging purposes - // count the loadable number of files and display thir number: + // count the loadable number of files and display their number: int NumberCoherentFiles = 0; - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) + for (std::list::iterator Filename = InternalFileNameList.begin(); + Filename != InternalFileNameList.end(); + ++Filename) { - if (*FileName != "GDCM_UNREADABLE") + if (*Filename != "GDCM_UNREADABLE") NumberCoherentFiles++; } vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); @@ -240,14 +355,14 @@ int vtkGdcmReader::CheckFileCoherence() vtkDebugMacro("Total number of planes on the stack: " << ReturnedTotalNumberOfPlanes); - return ReturnedTotalNumberOfPlanes; + + return ReturnedTotalNumberOfPlanes; } //---------------------------------------------------------------------------- // Configure the output e.g. WholeExtent, spacing, origin, scalar type... void vtkGdcmReader::ExecuteInformation() { - //FIXME free any old memory this->TotalNumberOfPlanes = this->CheckFileCoherence(); if ( this->TotalNumberOfPlanes == 0) { @@ -256,7 +371,7 @@ void vtkGdcmReader::ExecuteInformation() } // if the user has not set the extent, but has set the VOI - // set the zaxis extent to the VOI z axis + // 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])) { @@ -291,11 +406,8 @@ void vtkGdcmReader::ExecuteInformation() this->DataExtent[1] = this->NumColumns - 1; this->DataExtent[2] = 0; this->DataExtent[3] = this->NumLines - 1; - if(this->FileNameList.size() > 1) - { - this->DataExtent[4] = 0; - this->DataExtent[5] = this->TotalNumberOfPlanes - 1; - } + this->DataExtent[4] = 0; + this->DataExtent[5] = this->TotalNumberOfPlanes - 1; // We don't need to positionate the Endian related stuff (by using // this->SetDataByteOrderToBigEndian() or SetDataByteOrderToLittleEndian() @@ -334,6 +446,9 @@ void vtkGdcmReader::ExecuteInformation() this->SetDataScalarTypeToInt(); } + //Set number of scalar components: + this->SetNumberOfScalarComponents(this->NumComponents); + vtkImageReader::ExecuteInformation(); } @@ -346,21 +461,49 @@ size_t vtkGdcmReader::LoadImageInMemory( const unsigned long UpdateProgressTarget, unsigned long & UpdateProgressCount) { - vtkDebugMacro("Copying to memmory image" << FileName.c_str()); + vtkDebugMacro("Copying to memory image" << FileName.c_str()); gdcmFile GdcmFile(FileName.c_str()); - size_t size = GdcmFile.GetImageDataSize(); + size_t size; // If the data structure of vtk for image/volume representation // were straigthforwards the following would suffice: // GdcmFile.GetImageDataIntoVector((void*)Dest, size); - // But vtk chose to invert the lines of an image, that is the last + // But vtk chooses to invert the lines of an image, that is the last // line comes first (for some axis related reasons?). Hence we need - // to load the image line by line, starting from the end: - int NumColumns = GdcmFile.GetXSize(); - int NumLines = GdcmFile.GetYSize(); - int NumPlanes = GdcmFile.GetZSize(); - int LineSize = NumColumns * GdcmFile.GetPixelSize(); - unsigned char * Source = (unsigned char*)GdcmFile.GetImageData(); + // to load the image line by line, starting from the end. + int NumColumns = GdcmFile.GetHeader()->GetXSize(); + int NumLines = GdcmFile.GetHeader()->GetYSize(); + int NumPlanes = GdcmFile.GetHeader()->GetZSize(); + int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize(); + + unsigned char * Source; + if( GdcmFile.GetHeader()->HasLUT() ) + { + size = GdcmFile.GetImageDataSizeRaw(); + Source = (unsigned char*) GdcmFile.GetImageDataRaw(); + unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); + + if(!this->LookupTable) this->LookupTable = vtkLookupTable::New(); + this->LookupTable->SetNumberOfTableValues(256); + for (int tmp=0; tmp<256; tmp++) + { + this->LookupTable->SetTableValue(tmp, + (float)Lut[4*tmp+0]/255.0, + (float)Lut[4*tmp+1]/255.0, + (float)Lut[4*tmp+2]/255.0, + 1); + } + this->LookupTable->SetRange(0,255); + vtkDataSetAttributes *a=this->GetOutput()->GetPointData(); + a->GetScalars()->SetLookupTable(this->LookupTable); + free(Lut); + } + else + { + size = GdcmFile.GetImageDataSize(); + Source = (unsigned char*)GdcmFile.GetImageData(); + } + unsigned char * pSource = Source; //pointer for later deletion unsigned char * Destination = Dest + size - LineSize; for (int plane = 0; plane < NumPlanes; plane++) @@ -379,76 +522,92 @@ size_t vtkGdcmReader::LoadImageInMemory( UpdateProgressCount++; } } + //GetImageData allocate a (void*)malloc, remove it: + free(pSource); + return size; } //---------------------------------------------------------------------------- -// Update -> UpdateData -> Execute -> ExecuteData (see vtkSource.cxx for -// last step. +// 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 -// extent/axes are assumed to be the -// same as the file extent/order. +// extent/axes are assumed to be the same as the file extent/order. void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (this->FileNameList.empty()) + if (this->InternalFileNameList.empty()) { vtkErrorMacro("A least a valid FileName must be specified."); return; } + // 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"); - // The memory size for a full stack of images of course depends - // on the number of planes and the size of each image: - size_t StackNumPixels = this->NumColumns * this->NumLines - * this->TotalNumberOfPlanes; - size_t stack_size = StackNumPixels * this->PixelSize; - // Allocate pixel data space itself. - unsigned char *mem = new unsigned char [stack_size]; - - // Variables for the UpdateProgress. We shall use 50 steps to signify - // the advance of the process: - unsigned long UpdateProgressTarget = (unsigned long) this->NumLines - * this->TotalNumberOfPlanes - / 50.0; - // The actual advance measure: - unsigned long UpdateProgressCount = 0; - - // Feeling the allocated memory space with each image/volume: - unsigned char * Dest = mem; - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.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") - { - 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: - UpdateProgressCount += this->NumLines; - if (!(UpdateProgressCount%UpdateProgressTarget)) + // Test if output has valid extent + // Prevent memory errors + if((this->DataExtent[1]-this->DataExtent[0]>=0) && + (this->DataExtent[3]-this->DataExtent[2]>=0) && + (this->DataExtent[5]-this->DataExtent[4]>=0)) + { + // The memory size for a full stack of images of course depends + // on the number of planes and the size of each image: + size_t StackNumPixels = this->NumColumns * this->NumLines + * this->TotalNumberOfPlanes * this->NumComponents; + size_t stack_size = StackNumPixels * this->PixelSize; + // Allocate pixel data space itself. + unsigned char *mem = new unsigned char [stack_size]; + + // Variables for the UpdateProgress. We shall use 50 steps to signify + // the advance of the process: + unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines + * this->TotalNumberOfPlanes + / 50.0); + // The actual advance measure: + unsigned long UpdateProgressCount = 0; + + // Feeling the allocated memory space with each image/volume: + unsigned char * Dest = mem; + 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") { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - } // Else, file not loadable - } // Loop on files - - // The "size" of the vtkScalars data is expressed in number of points, - // and is not the memory size representing those points: - data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); - this->Modified(); + // 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 + + // The "size" of the vtkScalars data is expressed in number of points, + // and is not the memory size representing those points: + data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); + //don't know why it's here, it's calling one more time ExecuteInformation: + //this->Modified(); + } } //----------------------------------------------------------------------------