X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=898245c60c79a90bbdd7873cec5b2855da783bd6;hb=4ea1fcd3d772209d51220b85a60900500f9525ff;hp=02f05672b4f7c49687c54acba1ff250152386a69;hpb=c34ecaa3bf4a10a611d4324686a8c25e93d805b8;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 02f05672..898245c6 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,10 +1,54 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.15 2003/07/07 09:10:33 regrain Exp $ +// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.19 2003/09/10 09:31:55 malaterre 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 corrersponding 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 purpous +// 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 +// initialiszes 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 consctutor: +// - 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 sctructue 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 desctutor nor when the +// filename list is extended, ExecuteData is called a second (or third) +// time... +// ////////////////////////////////////////////////////////////// + #include #include #include #include #include "vtkGdcmReader.h" #include "gdcm.h" +#include "gdcmHeaderHelper.h" vtkGdcmReader::vtkGdcmReader() { @@ -14,7 +58,6 @@ vtkGdcmReader::vtkGdcmReader() //---------------------------------------------------------------------------- vtkGdcmReader::~vtkGdcmReader() { - // FIXME free memory this->RemoveAllFileName(); this->InternalFileNameList.clear(); } @@ -97,7 +140,7 @@ void vtkGdcmReader::BuildFileListFromPattern() return; } - this->RemoveAllInternalFileName(); + this->RemoveAllInternalFileName(); for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) { this->ComputeInternalFileName(idx); @@ -168,7 +211,7 @@ 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()); @@ -253,6 +296,17 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added this->ImageType = type; this->PixelSize = GdcmHeader.GetPixelSize(); + + //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 @@ -283,7 +337,6 @@ int vtkGdcmReader::CheckFileCoherence() // 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) { @@ -382,7 +435,7 @@ 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(); @@ -397,6 +450,7 @@ size_t vtkGdcmReader::LoadImageInMemory( int NumPlanes = GdcmFile.GetZSize(); int LineSize = NumColumns * GdcmFile.GetPixelSize(); unsigned char * 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++) @@ -415,6 +469,9 @@ size_t vtkGdcmReader::LoadImageInMemory( UpdateProgressCount++; } } + //GetImageData allocate a (void*)malloc, remove it: + free(pSource); + return size; } @@ -423,8 +480,7 @@ size_t vtkGdcmReader::LoadImageInMemory( // (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->InternalFileNameList.empty()) @@ -433,16 +489,16 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) return; } - // FIXME : the bad parse of header is made when allocating OuputData + // 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 // 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)) + 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: @@ -491,7 +547,6 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) } } } // Else, file not loadable - } // Loop on files // The "size" of the vtkScalars data is expressed in number of points,