X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=b9aa0732117d1438b2f337e5138c71cf2fb19a26;hb=f94f85b5578c5a8575f9cadc3702766defd9d707;hp=b8464b40b1d1271f6ea84da2622e7ef03dfdb732;hpb=49236d643fd420ddc5787a6cab3bbc0a45729fd0;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index b8464b40..b9aa0732 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,15 +1,15 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.21 2003/10/24 15:38:56 malaterre Exp $ +// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.28 2003/11/13 10:23:41 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 +// 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 purpous +// 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... @@ -18,17 +18,17 @@ // (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 +// 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 consctutor: +// 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 sctructue is loaded in memory. +// 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... @@ -37,22 +37,26 @@ // 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 +// 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 +#include "gdcmFile.h" +#include "gdcmHeaderHelper.h" +#include "vtkGdcmReader.h" + +//#include #include #include #include -#include "vtkGdcmReader.h" -#include "gdcm.h" -#include "gdcmHeaderHelper.h" +#include + vtkGdcmReader::vtkGdcmReader() { // Constructor + this->LookupTable = NULL; } //---------------------------------------------------------------------------- @@ -60,6 +64,7 @@ vtkGdcmReader::~vtkGdcmReader() { this->RemoveAllFileName(); this->InternalFileNameList.clear(); + if(this->LookupTable) this->LookupTable->Delete(); } //---------------------------------------------------------------------------- @@ -177,7 +182,7 @@ void vtkGdcmReader::BuildFileListFromPattern() // (i.e. an image represents one plane, but a volume represents many planes) int vtkGdcmReader::CheckFileCoherence() { - int ReturnedTotalNumberOfPlanes = 0; // The returned value. + int ReturnedTotalNumberOfPlanes = 0; // The returned value. this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) @@ -190,14 +195,14 @@ 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 = 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 place in the + // - 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 @@ -239,6 +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"; @@ -307,7 +313,15 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added this->ImageType = type; this->PixelSize = GdcmHeader.GetPixelSize(); - this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono + + if( GdcmHeader.HasLUT() ) + { + this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + } + else + { + this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono + } //Set image spacing this->DataSpacing[0] = GdcmHeader.GetXSpacing(); @@ -323,7 +337,7 @@ int vtkGdcmReader::CheckFileCoherence() } // 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 = InternalFileNameList.begin(); Filename != InternalFileNameList.end(); @@ -357,7 +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])) { @@ -449,19 +463,46 @@ size_t vtkGdcmReader::LoadImageInMemory( { 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: + // 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 = NumComponents * NumColumns * GdcmFile.GetPixelSize(); - unsigned char * Source = (unsigned char*)GdcmFile.GetImageData(); + + unsigned char * Source; + if( GdcmFile.HasLUT() ) + { + size = GdcmFile.GetImageDataSizeRaw(); + Source = (unsigned char*) GdcmFile.GetImageDataRaw(); + unsigned char *Lut = GdcmFile.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;