X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=619896842d27832903bd5ec5ea83dc4d5c6b8452;hb=844285f083c7bb09584e1875d5acf00fb08c22a0;hp=1b86f6fff04b604a023ab43fd53d2c72129fe97f;hpb=7c0064682f6082ac5e91abf1b4519d891aeb6095;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 1b86f6ff..61989684 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,25 +1,101 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.9 2003/06/03 10:26:07 frog Exp $ -//CLEANME#include -#include +// vtkGdcmReader.cxx +//----------------------------------------------------------------------------- +// ////////////////////////////////////////////////////////////// +// 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 +//----------------------------------------------------------------------------- +// Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { - // Constructor + this->LookupTable = NULL; } -//---------------------------------------------------------------------------- vtkGdcmReader::~vtkGdcmReader() { - // FIXME free memory + this->RemoveAllFileName(); + this->InternalFileNameList.clear(); + if(this->LookupTable) + this->LookupTable->Delete(); +} + +//----------------------------------------------------------------------------- +// Print +void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) +{ + vtkImageReader::PrintSelf(os,indent); + os << indent << "Filenames : " << endl; + vtkIndent nextIndent = indent.GetNextIndent(); + for (std::list::iterator FileName = FileNameList.begin(); + FileName != FileNameList.end(); + ++FileName) + { + os << nextIndent << FileName->c_str() << endl ; + } } -//---------------------------------------------------------------------------- -// Adds a file name to the list of images to read. +//----------------------------------------------------------------------------- +// Public +/* + * Remove all files from the list of images to read. + */ +void vtkGdcmReader::RemoveAllFileName(void) +{ + this->FileNameList.clear(); +} + +/* + * Adds a file name to the list of images to read. + */ void vtkGdcmReader::AddFileName(const char* name) { // We need to bypass the const pointer [since list<>.push_bash() only @@ -27,380 +103,550 @@ void vtkGdcmReader::AddFileName(const char* name) char * LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->FileNameList.push_back(LocalName); - // Starting from two files we have a stack of images: - if(this->FileNameList.size() >= 2) - this->SetFileDimensionality(3); - this->Modified(); + this->Modified(); + delete[] LocalName; } -//---------------------------------------------------------------------------- -// Sets up a filename to be read. -void vtkGdcmReader::SetFileName(const char *name) { +/* + * Sets up a filename to be read. + */ +void vtkGdcmReader::SetFileName(const char *name) +{ vtkImageReader2::SetFileName(name); - // Since we maintain a list of filenames (when building a volume) - // we additionaly need to maintain this list. First we clean-up the - // list and then positionate the incoming filename: - this->FileNameList.empty(); - this->AddFileName(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->FileNameList.clear(); + this->Modified(); +} + +//----------------------------------------------------------------------------- +// Protected +/* + * Configure the output e.g. WholeExtent, spacing, origin, scalar type... + */ +void vtkGdcmReader::ExecuteInformation() +{ + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + 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->DataExtent[4] = this->DataVOI[4]; + this->DataExtent[5] = this->DataVOI[5]; + } + + // When the user has set the VOI, check it's coherence with the file content. + if (this->DataVOI[0] || this->DataVOI[1] || + this->DataVOI[2] || this->DataVOI[3] || + this->DataVOI[4] || this->DataVOI[5]) + { + if ((this->DataVOI[0] < 0) || + (this->DataVOI[1] >= this->NumColumns) || + (this->DataVOI[2] < 0) || + (this->DataVOI[3] >= this->NumLines) || + (this->DataVOI[4] < 0) || + (this->DataVOI[5] >= this->TotalNumberOfPlanes )) + { + vtkWarningMacro("The requested VOI is larger than expected extent."); + this->DataVOI[0] = 0; + this->DataVOI[1] = this->NumColumns - 1; + this->DataVOI[2] = 0; + this->DataVOI[3] = this->NumLines - 1; + this->DataVOI[4] = 0; + this->DataVOI[5] = this->TotalNumberOfPlanes - 1; + } + } + + // Positionate the Extent. + this->DataExtent[0] = 0; + this->DataExtent[1] = this->NumColumns - 1; + this->DataExtent[2] = 0; + this->DataExtent[3] = this->NumLines - 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() + // since the reading of the file is done by gdcm. + // But we do need to set up the data type for downstream filters: + if ( ImageType == "8U" ) + { + vtkDebugMacro("8 bits unsigned image"); + this->SetDataScalarTypeToUnsignedChar(); + } + else if ( ImageType == "8S" ) + { + vtkErrorMacro("Cannot handle 8 bit signed files"); + return; + } + else if ( ImageType == "16U" ) + { + vtkDebugMacro("16 bits unsigned image"); + this->SetDataScalarTypeToUnsignedShort(); + } + else if ( ImageType == "16S" ) + { + vtkDebugMacro("16 bits signed image"); + this->SetDataScalarTypeToShort(); + //vtkErrorMacro("Cannot handle 16 bit signed files"); + } + else if ( ImageType == "32U" ) + { + vtkDebugMacro("32 bits unsigned image"); + vtkDebugMacro("WARNING: forced to signed int !"); + this->SetDataScalarTypeToInt(); + } + else if ( ImageType == "32S" ) + { + vtkDebugMacro("32 bits signed image"); + this->SetDataScalarTypeToInt(); + } + + //Set number of scalar components: + this->SetNumberOfScalarComponents(this->NumComponents); + + vtkImageReader::ExecuteInformation(); +} + +/* + * 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. + */ +void vtkGdcmReader::ExecuteData(vtkDataObject *output) +{ + 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"); + + // 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") + { + // 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(); + } } -//---------------------------------------------------------------------------- -// vtkGdcmReader can have the file names specified through two ways: -// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and -// SetFilePattern() -// (2) By successive calls to vtkGdcmReader::SetFileName() -// When the first method was used by caller we need to update the local -// filename list -void vtkGdcmReader::BuilFileListFromPattern() +/* + * vtkGdcmReader can have the file names specified through two ways: + * (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and + * SetFilePattern() + * (2) By successive calls to vtkGdcmReader::AddFileName() + * When the first method was used by caller we need to update the local + * filename list + */ +void vtkGdcmReader::BuildFileListFromPattern() { - if (! this->FileNameList.empty()) + if ((! this->FileNameList.empty()) && this->FileName ) + { + vtkErrorMacro("Both file patterns and AddFileName schemes were used"); + vtkErrorMacro("Only the files specified with AddFileName shall be used"); + return; + } + + if (! this->FileNameList.empty() ) + { + vtkDebugMacro("Using the AddFileName specified files"); + this->InternalFileNameList=this->FileNameList; return; + } + if (!this->FileName && !this->FilePattern) - { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePattern."); - return; - } - for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) - { - this->ComputeInternalFileName(idx); - vtkDebugMacro("Adding file " << this->InternalFileName); - this->AddFileName(this->InternalFileName); - } + { + vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro("specify a FileName or FilePattern."); + return; + } + + this->RemoveAllInternalFileName(); + if( this->FileNameList.empty() ) + { + //Multiframe case: + this->ComputeInternalFileName(this->DataExtent[4]); + vtkDebugMacro("Adding file " << 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); + } + } } -//---------------------------------------------------------------------------- -// When more than one filename is specified (i.e. we expect loading -// a stack or volume) we need to check the corresponding images are -// coherent: -// - they all share the same X dimensions -// - they all share the same Y dimensions -// - each file a Z dimension of 1 -// - they all share the same type ( 8 bit signed, or unsigned...) -bool vtkGdcmReader::CheckFileCoherence() +/* + * 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) + */ +int vtkGdcmReader::CheckFileCoherence() { - this->BuilFileListFromPattern(); - if (this->FileNameList.empty()) - { - vtkErrorMacro("FileNames are not set."); - return false; - } - if (this->FileNameList.size() == 1) - { - vtkDebugMacro("Single file specified."); - return true; - } + 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; // Loop on the filenames: - // - check for their existence and gdcm "parasability" + // - check for their existence and gdcm "parsability" // - get the coherence check done: - bool FoundReferenceFile = false; - int ReferenceNX; - int ReferenceNY; - int ReferenceNZ; - std::string ReferenceType; - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) - { - // Check for file existence. - FILE *fp; - fp = fopen(FileName->c_str(),"rb"); - if (!fp) - { - vtkErrorMacro("Unable to open file " << *FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << *FileName->c_str()); - FileNameList.remove(*FileName); - continue; - } - fclose(fp); + 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; + fp = fopen(FileName->c_str(),"rb"); + if (!fp) + { + vtkErrorMacro("Unable to open file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + fclose(fp); - // Check for Gdcm parsability - gdcmHeader GdcmHeader(FileName->c_str()); - if (!GdcmHeader.IsReadable()) - { - vtkErrorMacro("Gdcm cannot parse file " << *FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << *FileName->c_str()); - FileNameList.remove(*FileName); - continue; - } - - // We don't know how to handle multiple images in one file yet: - int NZ = GdcmHeader.GetZSize(); - if (NZ > 1) - { - vtkErrorMacro("This file contains multiple planes (images)" - << *FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << *FileName->c_str()); - FileNameList.remove(*FileName); - continue; - } - - // Coherence stage: - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - std::string type = GdcmHeader.GetPixelType(); - if (FoundReferenceFile) - { - if ( ( NX != ReferenceNX ) - || ( NY != ReferenceNY ) - || ( NZ != ReferenceNZ ) - || ( type != ReferenceType ) ) + // Stage 1.2: check for Gdcm parsability + gdcmHeaderHelper GdcmHeader(FileName->c_str()); + if (!GdcmHeader.IsReadable()) + { + vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; + continue; + } + + // Stage 1.3: further gdcm compatibility on PixelType + std::string type = GdcmHeader.GetPixelType(); + if ( (type != "8U") && (type != "8S") + && (type != "16U") && (type != "16S") + && (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"; + continue; + } + + // Stage 2: check coherence of the set of files + int NX = GdcmHeader.GetXSize(); + int NY = GdcmHeader.GetYSize(); + int NZ = GdcmHeader.GetZSize(); + if (FoundReferenceFile) + { + // 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()); + << FileName->c_str()); vtkErrorMacro("Removing this file from readed files " - << *FileName->c_str()); - FileNameList.remove(*FileName); + << FileName->c_str()); + *FileName = "GDCM_UNREADABLE"; continue; - } else { + } + + // 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()); + << FileName->c_str()); + } + + // Stage 2.3: when the file contains a volume (as opposed to an image), + // notify the caller. + if (NZ > 1) + { + vtkErrorMacro("This file contains multiple planes (images)" + << FileName->c_str()); } - } else { - // This file shall be the reference: + + // 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; + + } + else + { + // We didn't have a workable reference file yet. Set this one + // as the reference. FoundReferenceFile = true; - ReferenceNX = NX; - ReferenceNY = NY; - ReferenceNZ = NZ; - ReferenceType = type; vtkDebugMacro("This file taken as coherence reference:" - << *FileName->c_str()); - } - } // End of loop on FileName - - if (this->FileNameList.empty()) - { - vtkDebugMacro("No gdcm parsable file."); - return false; - } - if (this->FileNameList.size() == 1) - { - vtkDebugMacro("Single parsable file left after coherence test."); - return true; - } - return true; -} + << FileName->c_str()); + vtkDebugMacro("Image dimension 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 = 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(); -//---------------------------------------------------------------------------- -// Configure the output e.g. WholeExtent, spacing, origin, scalar type... -void vtkGdcmReader::ExecuteInformation() -{ - //FIXME free any old memory - - // if the user has not set the extent, but has set the VOI - // set the zaxis extent to the VOI z axis - if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && - (this->DataVOI[4] || this->DataVOI[5])) - { - this->DataExtent[4] = this->DataVOI[4]; - this->DataExtent[5] = this->DataVOI[5]; - } - if ( ! this->CheckFileCoherence() ) - { - vtkErrorMacro("File set is not coherent. Exiting..."); - return; - } - std::string ReferenceFile = this->FileNameList.front(); - gdcmHeader GdcmHeader(ReferenceFile.c_str()); - - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - int NZ = GdcmHeader.GetZSize(); - vtkDebugMacro("Image dimension as read from Gdcm:" << - NX << " " << NY << " " << NZ); - - // When the user has set the VOI, check it's coherence with the file content. - if (this->DataVOI[0] || this->DataVOI[1] || - this->DataVOI[2] || this->DataVOI[3] || - this->DataVOI[4] || this->DataVOI[5]) - { - if ((this->DataVOI[0] < 0) || - (this->DataVOI[1] >= NX) || - (this->DataVOI[2] < 0) || - (this->DataVOI[3] >= NY) || - (this->DataVOI[4] < 0) || - (this->DataVOI[5] >= this->FileNameList.size())) - { - vtkWarningMacro("The requested VOI is larger than the file's (" - << ReferenceFile.c_str() << ") extent "); - this->DataVOI[0] = 0; - this->DataVOI[1] = NX - 1; - this->DataVOI[2] = 0; - this->DataVOI[3] = NY - 1; - this->DataVOI[4] = 0; - this->DataVOI[5] = this->FileNameList.size() - 1; } - } + } // End of loop on FileName - // Positionate the Extent. - this->DataExtent[0] = 0; - this->DataExtent[1] = NX - 1; - this->DataExtent[2] = 0; - this->DataExtent[3] = NY - 1; - if(this->FileNameList.size() > 1) - { - this->DataExtent[4] = 0; - this->DataExtent[5] = this->FileNameList.size() - 1; - } + ///////// 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 Filename = InternalFileNameList.begin(); + Filename != InternalFileNameList.end(); + ++Filename) + { + if (*Filename != "GDCM_UNREADABLE") + NumberCoherentFiles++; + } + vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); - - // We don't need to positionate 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: - std::string type = GdcmHeader.GetPixelType(); - if ( type == "8U" ) - { - vtkDebugMacro("8 bits unsigned image"); - this->SetDataScalarTypeToUnsignedChar(); - } - else if ( type == "8S" ) - { - vtkErrorMacro("Cannot handle 8 bit signed files"); - return; - } - else if ( type == "16U" ) - { - vtkDebugMacro("16 bits unsigned image"); - this->SetDataScalarTypeToUnsignedShort(); - } - else if ( type == "16S" ) - { - vtkDebugMacro("16 bits signed image"); - this->SetDataScalarTypeToShort(); - //vtkErrorMacro("Cannot handle 16 bit signed files"); - } - else if ( type == "32U" ) - { - vtkDebugMacro("32 bits unsigned image"); - vtkDebugMacro("WARNING: forced to signed int !"); - this->SetDataScalarTypeToInt(); - } - else if ( type == "32S" ) - { - vtkDebugMacro("32 bits signed image"); - this->SetDataScalarTypeToInt(); - } - else - { - vtkErrorMacro("Bad File Type " << ReferenceFile.c_str() - << "Type " << type.c_str()); - return; - } + if (ReturnedTotalNumberOfPlanes == 0) + { + vtkErrorMacro("No loadable file."); + } - vtkImageReader::ExecuteInformation(); + vtkDebugMacro("Total number of planes on the stack: " + << ReturnedTotalNumberOfPlanes); + + return ReturnedTotalNumberOfPlanes; } -//---------------------------------------------------------------------------- -void vtkGdcmReader::LoadImageInMemory(std::string FileName, - unsigned char * Dest, - size_t size) +//----------------------------------------------------------------------------- +// Private +/* + * Remove all file names to the internal list of images to read. + */ +void vtkGdcmReader::RemoveAllInternalFileName(void) { - vtkDebugMacro("Copying to memmory image" << FileName.c_str()); - gdcmFile GdcmFile(FileName.c_str()); - - if (GdcmFile.GetZSize() != 1 ) - vtkErrorMacro("Cannot handle images with multiple planes"); - - // First check the expected size of the image is the one found by gdcm. - if ( size != GdcmFile.GetImageDataSize() ) - { - vtkErrorMacro("Inconsistency with GetImageDataSize for file" - << FileName.c_str()); - vtkErrorMacro("Number of scalar components" - << this->NumberOfScalarComponents); - } + this->InternalFileNameList.clear(); +} - // 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 - // 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 LineSize = NumColumns * GdcmFile.GetPixelSize(); - unsigned char * Source = (unsigned char*)GdcmFile.GetImageData(); - unsigned char * Destination = Dest + size - LineSize; - for (int i = 0; i < NumLines; i++) - { - memcpy((void*)Destination, (void*)Source, LineSize); - Source += LineSize; - Destination -= LineSize; - } +/* + * 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; } -//---------------------------------------------------------------------------- -// 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. -void vtkGdcmReader::ExecuteData(vtkDataObject *output) +/* + * Loads the contents of the image/volume contained by 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) { - if (this->FileNameList.empty()) - { - vtkErrorMacro("A least a valid FileName must be specified."); - return; - } + vtkDebugMacro("Copying to memory image" << FileName.c_str()); + gdcmFile GdcmFile(FileName.c_str()); + size_t size; - vtkImageData *data = this->AllocateOutputData(output); - data->SetExtent(this->DataExtent); - data->GetPointData()->GetScalars()->SetName("DicomImage-Volume"); - - // First check the coherence between the DataExtent and the - // size of the pixel data as annouced by gdcm (looks a bit paranoid) - // for the reference file (i.e. the first one in the list): - std::string ReferenceFile = this->FileNameList.front(); - gdcmFile GdcmFile(ReferenceFile.c_str()); - int NumColumns = this->DataExtent[1] - this->DataExtent[0] + 1; - int NumLines = this->DataExtent[3] - this->DataExtent[2] + 1; - int NumPlanes = 1; // This has been checked in CheckFileCoherence - size_t size = NumColumns * NumLines * NumPlanes * GdcmFile.GetPixelSize(); - if ( size != GdcmFile.GetImageDataSize() ) - { - vtkDebugMacro("Inconsistency with GetImageDataSize"); - vtkDebugMacro("Number of scalar components" - << this->NumberOfScalarComponents); - } + // If the data structure of vtk for image/volume representation + // were straigthforwards the following would suffice: + // GdcmFile.GetImageDataIntoVector((void*)Dest, size); + // 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. - // The memory size for a full stack of images of course depends - // on the number of images: - size_t stack_size = size * this->FileNameList.size(); - // Allocate pixel data space itself. - unsigned char *mem = new unsigned char [stack_size]; + int NumColumns = GdcmFile.GetHeader()->GetXSize(); + int NumLines = GdcmFile.GetHeader()->GetYSize(); + int NumPlanes = GdcmFile.GetHeader()->GetZSize(); + int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize(); - unsigned char * Dest = mem; - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) - { - this->LoadImageInMemory(*FileName, Dest, size); - Dest += size; - } + unsigned char * Source; + if( GdcmFile.GetHeader()->HasLUT() ) + { + size = GdcmFile.GetImageDataSizeRaw(); + Source = (unsigned char*) GdcmFile.GetImageDataRaw(); + unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); - // The "size" of the vtkScalars data is expressed in number of points, - // and is not the memory size representing those points: - stack_size = stack_size / GdcmFile.GetPixelSize(); - data->GetPointData()->GetScalars()->SetVoidArray(mem, stack_size, 0); - this->Modified(); -} + if(!this->LookupTable) + this->LookupTable = vtkLookupTable::New(); -//---------------------------------------------------------------------------- -void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) -{ - vtkImageReader::PrintSelf(os,indent); - os << indent << "Filenames : " << endl; - vtkIndent nextIndent = indent.GetNextIndent(); - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) - { - os << nextIndent << *FileName->c_str() << endl ; - } + 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++) + { + for (int line = 0; line < NumLines; line++) + { + // Copy one line at proper destination: + memcpy((void*)Destination, (void*)Source, LineSize); + Source += LineSize; + Destination -= LineSize; + // Update progress related: + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + UpdateProgressCount++; + } + } + //GetImageData allocate a (void*)malloc, remove it: + free(pSource); + + return size; } + +//-----------------------------------------------------------------------------