X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=2970000e2c20609df97f15d90b839caf82a509f0;hb=ee44d3091d42315924bf9844c12d0a1eb0db229e;hp=5a03ade4c6de57e2632361183f1aebe2a53d22ef;hpb=ab62b1a706df8e2ab1fbf26fa5037d6c22293655;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 5a03ade4..2970000e 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,7 +1,24 @@ -// vtkGdcmReader.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: vtkGdcmReader.cxx,v $ + Language: C++ + Date: $Date: 2005/07/17 04:34:20 $ + Version: $Revision: 1.73 $ + + Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de + l'Image). All rights reserved. See Doc/License.txt or + http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + //----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// -// WARNING TODO CLENAME +// WARNING TODO CLEANME // Actual limitations of this code: // // /////// Redundant and unnecessary header parsing @@ -9,12 +26,19 @@ // 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 +// 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: +// 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 @@ -23,21 +47,21 @@ // 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 gdcmHeader in the constructor) in order to access +// 2b/ the core of ExecuteData then needs gdcm::File (which in turns +// initialises gdcm::File 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: +// maintain a list of gdcm::Files (created by say ExecuteInformation) created +// once and for all accross the life of vtkGdcmFile (it would only load +// new gdcm::File if the user changes the list). ExecuteData would then use +// those gdcm::File 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... +// a vtkGdcmFile) the gdcm::File structure is loaded in memory. +// The average size of a gdcm::File being of 100Ko, +// if oneloads 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 @@ -46,11 +70,21 @@ // This data is never "freed" neither in the destructor nor when the // filename list is extended, ExecuteData is called a second (or third) // time... +// +// +//===> Since many users expect from vtkGdcmReader it 'orders' the images +// (that's the job of gdcm::SerieHelper), user may now call +// vtkGdcmReader::SetCoherentFileList() to pass a 'Coherent File List' +// as produced by gdcm::SerieHelper +// See the limitations of gdcm::SerieHelper before ... // ////////////////////////////////////////////////////////////// +#include "gdcmFileHelper.h" #include "gdcmFile.h" -#include "gdcmHeaderHelper.h" +#include "gdcmDocument.h" // for NO_SEQ + #include "vtkGdcmReader.h" +#include "gdcmDebug.h" //#include #include @@ -58,7 +92,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.48 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.73 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -67,6 +101,10 @@ vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; this->AllowLookupTable = 0; + this->LightChecking = false; + this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW, + // NO_SHADOWSEQ) + this->CoherentFileList = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -79,16 +117,16 @@ vtkGdcmReader::~vtkGdcmReader() //----------------------------------------------------------------------------- // Print -void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) +void vtkGdcmReader::PrintSelf(ostream &os, vtkIndent indent) { - vtkImageReader::PrintSelf(os,indent); + this->Superclass::PrintSelf(os,indent); os << indent << "Filenames : " << endl; vtkIndent nextIndent = indent.GetNextIndent(); - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) + for (std::list::iterator it = FileNameList.begin(); + it != FileNameList.end(); + ++it) { - os << nextIndent << FileName->c_str() << endl ; + os << nextIndent << it->c_str() << endl ; } } @@ -110,7 +148,7 @@ 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]; + char *LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->FileNameList.push_back(LocalName); delete[] LocalName; @@ -126,11 +164,20 @@ void vtkGdcmReader::SetFileName(const char *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. - vtkDebugMacro("Clearing all files given with AddFileName"); + vtkDebugMacro(<< "Clearing all files given with AddFileName"); this->FileNameList.clear(); 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 /* @@ -140,10 +187,16 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->CoherentFileList != 0 ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceAlreadyDone(); + else if ( this->LightChecking ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); + else + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) { - vtkErrorMacro("File set is not coherent. Exiting..."); + vtkErrorMacro(<< "File set is not coherent. Exiting..."); return; } @@ -168,7 +221,7 @@ void vtkGdcmReader::ExecuteInformation() (this->DataVOI[4] < 0) || (this->DataVOI[5] >= this->TotalNumberOfPlanes )) { - vtkWarningMacro("The requested VOI is larger than expected extent."); + vtkWarningMacro(<< "The requested VOI is larger than expected extent."); this->DataVOI[0] = 0; this->DataVOI[1] = this->NumColumns - 1; this->DataVOI[2] = 0; @@ -178,7 +231,7 @@ void vtkGdcmReader::ExecuteInformation() } } - // Positionate the Extent. + // Set the Extents. this->DataExtent[0] = 0; this->DataExtent[1] = this->NumColumns - 1; this->DataExtent[2] = 0; @@ -186,45 +239,44 @@ 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: if ( ImageType == "8U" ) { - vtkDebugMacro("8 bits unsigned image"); + vtkDebugMacro(<< "8 bits unsigned image"); this->SetDataScalarTypeToUnsignedChar(); } else if ( ImageType == "8S" ) { - vtkErrorMacro("Cannot handle 8 bit signed files"); + vtkErrorMacro(<< "Cannot handle 8 bit signed files"); return; } else if ( ImageType == "16U" ) { - vtkDebugMacro("16 bits unsigned image"); + vtkDebugMacro(<< "16 bits unsigned image"); this->SetDataScalarTypeToUnsignedShort(); } else if ( ImageType == "16S" ) { - vtkDebugMacro("16 bits signed image"); + 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 !"); + vtkDebugMacro(<< "32 bits unsigned image"); + vtkDebugMacro(<< "WARNING: forced to signed int !"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "32S" ) { - vtkDebugMacro("32 bits signed image"); + vtkDebugMacro(<< "32 bits signed image"); this->SetDataScalarTypeToInt(); } else if ( ImageType == "FD" ) { - vtkDebugMacro("64 bits Double image"); + vtkDebugMacro(<< "64 bits Double image"); this->SetDataScalarTypeToDouble(); } //Set number of scalar components: @@ -235,23 +287,32 @@ void vtkGdcmReader::ExecuteInformation() this->Superclass::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 + * VTK/IO/vtkImageReader.cxx) reads a data from a file. The data * extent/axes are assumed to be the same as the file extent/order. */ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (this->InternalFileNameList.empty()) + if ( CoherentFileList != 0 ) // When a list of names is passed { - vtkErrorMacro("A least a valid FileName must be specified."); + 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; } // 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"); @@ -277,40 +338,70 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) // The actual advance measure: unsigned long UpdateProgressCount = 0; - // Feeling the allocated memory space with each image/volume: - unsigned char *Dest = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0); - 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) + // Filling the allocated memory space with each image/volume: + + unsigned char *Dest = (unsigned char *)data->GetScalarPointer(); + + if ( CoherentFileList == 0 ) // When a list of names is passed + { + 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 { - if (!(UpdateProgressCount%UpdateProgressTarget)) + // 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) { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } } - } - } // Else, file not loadable - } // Loop on files + } // Else, file not loadable + } // Loop on files + + } + else // when a Coherent File List is passed + { + for (std::vector::iterator it = CoherentFileList->begin(); + it != CoherentFileList->end(); + ++it) + { + + //std::cout <<"----------------- " << (*it)->GetFileName() << std::endl; + + Dest += this->LoadImageInMemory(*it, Dest, + UpdateProgressTarget, + UpdateProgressCount); + // Update progress related for bad files: + UpdateProgressCount += this->NumLines; + if (UpdateProgressTarget > 0) + { + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + } + } // Loop on files + + } } } @@ -328,36 +419,36 @@ void vtkGdcmReader::BuildFileListFromPattern() if ((! this->FileNameList.empty()) && this->FileName ) { - vtkErrorMacro("Both AddFileName and SetFileName schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both AddFileName and SetFileName schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if ((! this->FileNameList.empty()) && this->FilePrefix ) { - vtkErrorMacro("Both AddFileName and SetFilePrefix schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both AddFileName and SetFilePrefix schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if (this->FileName && this->FilePrefix) { - vtkErrorMacro("Both SetFileName and SetFilePrefix schemes were used"); - vtkErrorMacro("No images loaded ! "); + vtkErrorMacro(<< "Both SetFileName and SetFilePrefix schemes were used"); + vtkErrorMacro(<< "No images loaded ! "); return; } if (! this->FileNameList.empty() ) { - vtkDebugMacro("Using the AddFileName specified files"); + vtkDebugMacro(<< "Using the AddFileName specified files"); this->InternalFileNameList=this->FileNameList; return; } if (!this->FileName && !this->FilePrefix) { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePrefix."); + vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro(<< "specify a FileName or FilePrefix."); return; } @@ -366,7 +457,7 @@ void vtkGdcmReader::BuildFileListFromPattern() // Single file loading (as given with ::SetFileName()): // Case of multi-frame file considered here this->ComputeInternalFileName(this->DataExtent[4]); - vtkDebugMacro("Adding file " << this->InternalFileName); + vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } else @@ -375,7 +466,7 @@ void vtkGdcmReader::BuildFileListFromPattern() for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) { this->ComputeInternalFileName(idx); - vtkDebugMacro("Adding file " << this->InternalFileName); + vtkDebugMacro(<< "Adding file " << this->InternalFileName); this->AddInternalFileName(this->InternalFileName); } } @@ -404,7 +495,7 @@ int vtkGdcmReader::CheckFileCoherence() this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) { - vtkErrorMacro("FileNames are not set."); + vtkErrorMacro(<< "FileNames are not set."); return 0; } @@ -414,9 +505,9 @@ int vtkGdcmReader::CheckFileCoherence() // Loop on the filenames: // - check for their existence and gdcm "parsability" // - get the coherence check done: - for (std::list::iterator FileName = InternalFileNameList.begin(); - FileName != InternalFileNameList.end(); - ++FileName) + 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 @@ -426,85 +517,94 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += 1; /////// Stage 0: check for file name: - if(*FileName==std::string("GDCM_UNREADABLE")) + + // 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. FILE *fp; - fp = fopen(FileName->c_str(),"rb"); + 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"; + vtkErrorMacro(<< "Unable to open file " << filename->c_str()); + vtkErrorMacro(<< "Removing this file from read files: " + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcmHeader GdcmHeader(FileName->c_str() ); - if (!GdcmHeader.IsReadable()) + + //gdcm::File GdcmFile( filename->c_str() ); + + // to save some parsing time. + gdcm::File GdcmFile; + GdcmFile.SetLoadMode( LoadMode ); + GdcmFile.Load(filename->c_str() ); + if (!GdcmFile.IsReadable()) { - vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; + vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); + vtkErrorMacro(<< "Removing this file from read files: " + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } // Stage 1.3: further gdcm compatibility on PixelType - std::string type = GdcmHeader.GetPixelType(); + std::string type = GdcmFile.GetPixelType(); if ( (type != "8U") && (type != "8S") - && (type != "16U") && (type != "16S") - && (type != "32U") && (type != "32S") ) + && (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"; + 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"; continue; } // Stage 2: check coherence of the set of files - int NX = GdcmHeader.GetXSize(); - int NY = GdcmHeader.GetYSize(); - int NZ = GdcmHeader.GetZSize(); + int NX = GdcmFile.GetXSize(); + int NY = GdcmFile.GetYSize(); + int NZ = GdcmFile.GetZSize(); if (FoundReferenceFile) { // Stage 2.1: mandatory coherence stage: if ( ( NX != this->NumColumns ) - || ( NY != this->NumLines ) - || ( type != this->ImageType ) ) + || ( 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"; + 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()); + vtkErrorMacro(<< "File is not coherent in Z with previous ones: " + << filename->c_str()); } else { - vtkDebugMacro("File is coherent with previous ones" - << FileName->c_str()); + vtkDebugMacro(<< "File is coherent with previous ones: " + << filename->c_str()); } - // Stage 2.3: when the file contains a volume (as opposed to an image), - // notify the caller. + // Stage 2.3: when the file is 'multiframe', notify the caller. if (NZ > 1) { - vtkErrorMacro("This file contains multiple planes (images)" - << FileName->c_str()); + vtkErrorMacro(<< "This file is a 'Multiframe' one: " + << filename->c_str()); } // Eventually, this file can be added on the stack. Update the @@ -516,63 +616,58 @@ int vtkGdcmReader::CheckFileCoherence() } else { - // We didn't have a workable reference file yet. Set this one - // as the reference. + // 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()); - vtkDebugMacro("Image dimension of reference file as read from Gdcm:" - << NX << " " << NY << " " << NZ); - vtkDebugMacro("Number of planes added to the stack: " << NZ); + vtkDebugMacro(<< "This file taken as coherence 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; ReferenceNZ = NZ; ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added this->ImageType = type; - this->PixelSize = GdcmHeader.GetPixelSize(); + this->PixelSize = GdcmFile.GetPixelSize(); - if( GdcmHeader.HasLUT() && this->AllowLookupTable ) + if( GdcmFile.HasLUT() && this->AllowLookupTable ) { // I could raise an error is AllowLookupTable is on and HasLUT() off - this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw(); } else { - this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono - } - + this->NumComponents = GdcmFile.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(); - + this->DataSpacing[0] = GdcmFile.GetXSpacing(); + this->DataSpacing[1] = GdcmFile.GetYSpacing(); + this->DataSpacing[2] = GdcmFile.GetZSpacing(); } - } // End of loop on FileName + } // 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 Filename = InternalFileNameList.begin(); - Filename != InternalFileNameList.end(); - ++Filename) + for (std::list::iterator it = InternalFileNameList.begin(); + it != InternalFileNameList.end(); + ++it) { - if (*Filename != "GDCM_UNREADABLE") - NumberCoherentFiles++; + if (*it != "GDCM_UNREADABLE") + { + NumberCoherentFiles++; + } } - vtkDebugMacro("Number of coherent files: " << NumberCoherentFiles); + vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles); if (ReturnedTotalNumberOfPlanes == 0) { - vtkErrorMacro("No loadable file."); + vtkErrorMacro(<< "No loadable file."); } - vtkDebugMacro("Total number of planes on the stack: " + vtkDebugMacro(<< "Total number of planes on the stack: " << ReturnedTotalNumberOfPlanes); return ReturnedTotalNumberOfPlanes; @@ -591,26 +686,66 @@ void vtkGdcmReader::RemoveAllInternalFileName(void) /* * Adds a file name to the internal list of images to read. */ -void vtkGdcmReader::AddInternalFileName(const char* name) +void vtkGdcmReader::AddInternalFileName(const char *name) { - char * LocalName = new char[strlen(name) + 1]; + char *LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->InternalFileNameList.push_back(LocalName); delete[] LocalName; } /* - * Loads the contents of the image/volume contained by Filename at + * Loads the contents of the image/volume contained by gdcm::File* f 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) + gdcm::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + // vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName() << "]"); + + return DoTheLoadingJob (f, + dest, + updateProgressTarget, + updateProgressCount); +} + +/* + * Loads the contents of the image/volume contained by char *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) { - vtkDebugMacro("Copying to memory image [" << FileName.c_str() << "]"); - gdcmFile GdcmFile( FileName.c_str() ); + vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); + + gdcm::File *f; + f = new gdcm::File(); + f->SetLoadMode( LoadMode ); + f->SetFileName( fileName.c_str() ); + f->Load( ); + + return DoTheLoadingJob (f, + dest, + updateProgressTarget, + updateProgressCount); + delete f; +} + +/* + * Service method for LoadImageInMemory +*/ +size_t vtkGdcmReader::DoTheLoadingJob (gdcm::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount) +{ + gdcm::FileHelper *fileH = new gdcm::FileHelper( f ); size_t size; // If the data structure of vtk for image/volume representation @@ -620,74 +755,175 @@ 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 = GdcmFile.GetHeader()->GetXSize(); - int NumLines = GdcmFile.GetHeader()->GetYSize(); - int NumPlanes = GdcmFile.GetHeader()->GetZSize(); - int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize(); + int numColumns = fileH->GetFile()->GetXSize(); + int numLines = fileH->GetFile()->GetYSize(); + int numPlanes = fileH->GetFile()->GetZSize(); + int lineSize = NumComponents * numColumns * fileH->GetFile()->GetPixelSize(); + int planeSize = lineSize * numLines; - unsigned char * Source; + unsigned char *src; - if( GdcmFile.GetHeader()->HasLUT() && this->AllowLookupTable ) + if( fileH->GetFile()->HasLUT() && AllowLookupTable ) { - size = GdcmFile.GetImageDataSizeRaw(); - Source = (unsigned char*) GdcmFile.GetImageDataRaw(); - unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); + size = fileH->GetImageDataSize(); + src = (unsigned char*) fileH->GetImageDataRaw(); + unsigned char *lut = (unsigned char*) fileH->GetLutRGBA(); - if(!this->LookupTable) + 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, + (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(); + vtkDataSetAttributes *a = this->GetOutput()->GetPointData(); a->GetScalars()->SetLookupTable(this->LookupTable); - free(Lut); + free(lut); } else { - size = GdcmFile.GetImageDataSize(); - Source = (unsigned char*)GdcmFile.GetImageData(); + size = fileH->GetImageDataSize(); + src = (unsigned char*)fileH->GetImageData(); } - - unsigned char * pSource = Source; //pointer for later deletion - unsigned char * Destination = Dest + size - LineSize; - for (int plane = 0; plane < NumPlanes; plane++) + unsigned char *dst = dest + planeSize - lineSize; + for (int plane = 0; plane < numPlanes; plane++) { - for (int line = 0; line < NumLines; line++) + for (int line = 0; line < numLines; line++) { // Copy one line at proper destination: - memcpy((void*)Destination, (void*)Source, LineSize); - Source += LineSize; - Destination -= LineSize; + memcpy((void*)dst, (void*)src, lineSize); + src += lineSize; + dst -= lineSize; // Update progress related: - if (!(UpdateProgressCount%UpdateProgressTarget)) + if (!(updateProgressCount%updateProgressTarget)) { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget)); } - UpdateProgressCount++; + updateProgressCount++; } + dst += 2 * planeSize; } - -// DO NOT remove this commented out code . -// Nobody knows what's expecting you ... -// Just to 'see' what was actually read on disk :-( - -// FILE * f2; -// f2 = fopen("SpuriousFile.RAW","wb"); -// fwrite(Dest,size,1,f2); -// fclose(f2); - - //GetImageData allocate a (void*)malloc, remove it: - delete[] pSource; + delete fileH; 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( LoadMode ); + GdcmFile.SetFileName(filename->c_str() ); + GdcmFile.Load( ); + + if (!GdcmFile.IsReadable()) + { + vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); + vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence " + << "instead of 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(); +} + +// 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::CheckFileCoherenceAlreadyDone() +{ + if ( CoherentFileList->empty() ) + { + vtkErrorMacro(<< "Coherent File List is empty "); + return 0; + } + + gdcm::File *gdcmFile = (*CoherentFileList)[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. + // --> TODO : loop on the File* to get NZ of each one ! + int NZ = CoherentFileList->size(); + std::string type = gdcmFile->GetPixelType(); + //vtkDebugMacro(<< "The first file is taken as reference: " + // << (*CoherentFileList)[0]->GetFileName() ); + 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 NZ; +} //-----------------------------------------------------------------------------