From: jpr Date: Sun, 17 Jul 2005 04:34:20 +0000 (+0000) Subject: Add SetCoherentFileList() method, to use the 'file ordering' of X-Git-Tag: Version1.2.bp~301 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=9cfc0e09d292826980e3d63728d46b5c6b185bf4;p=gdcm.git Add SetCoherentFileList() method, to use the 'file ordering' of gdcm::SerieHelper (and save some CPU time, avoding parsing twice all the file headers) --- diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 8b215718..2970000e 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.cxx,v $ Language: C++ - Date: $Date: 2005/06/29 16:12:43 $ - Version: $Revision: 1.72 $ + 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 @@ -47,20 +47,19 @@ // 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 gdcmFile 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 +// 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 gdcmFile if the user changes the list). ExecuteData would then use -// those gdcmFile and hence avoid calling the construtor: +// 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 vtkGdcmFile) the gdcmFile structure is loaded in memory. +// a vtkGdcmFile) the gdcm::File structure is loaded in memory. // The average size of a gdcm::File being of 100Ko, -// - 100 Ko ? Better say 1 Mo; we are in 2005 ! - // if oneloads 10 stacks of images with say 200 images each, // you end-up with a loss of 200Mo... // @@ -71,6 +70,13 @@ // 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" @@ -86,7 +92,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.72 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.73 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -96,8 +102,9 @@ vtkGdcmReader::vtkGdcmReader() this->LookupTable = NULL; this->AllowLookupTable = 0; this->LightChecking = false; - this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW + this->LoadMode = 0; // Load everything (possible values : NO_SEQ, NO_SHADOW, // NO_SHADOWSEQ) + this->CoherentFileList = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -180,7 +187,9 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - if ( this->LightChecking ) + if ( this->CoherentFileList != 0 ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceAlreadyDone(); + else if ( this->LightChecking ) this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); else this->TotalNumberOfPlanes = this->CheckFileCoherence(); @@ -222,7 +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; @@ -230,7 +239,7 @@ 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: @@ -278,7 +287,7 @@ void vtkGdcmReader::ExecuteInformation() this->Superclass::ExecuteInformation(); } - + /* * Update => ouput->Update => UpdateData => Execute => ExecuteData * (see vtkSource.cxx for last step). @@ -288,7 +297,15 @@ void vtkGdcmReader::ExecuteInformation() */ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - if (this->InternalFileNameList.empty()) + if ( CoherentFileList != 0 ) // When a list of names is passed + { + 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; @@ -322,39 +339,69 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) unsigned long UpdateProgressCount = 0; // Filling the allocated memory space with each image/volume: + unsigned char *Dest = (unsigned char *)data->GetScalarPointer(); - 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 ( 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") { - if (!(UpdateProgressCount%UpdateProgressTarget)) + // 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) { - 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 + + } } } @@ -494,6 +541,7 @@ int vtkGdcmReader::CheckFileCoherence() // Stage 1.2: check for Gdcm parsability //gdcm::File GdcmFile( filename->c_str() ); + // to save some parsing time. gdcm::File GdcmFile; GdcmFile.SetLoadMode( LoadMode ); @@ -647,9 +695,27 @@ void vtkGdcmReader::AddInternalFileName(const char *name) } /* - * 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( + 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, @@ -657,12 +723,29 @@ size_t vtkGdcmReader::LoadImageInMemory( unsigned long &updateProgressCount) { vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); + gdcm::File *f; f = new gdcm::File(); f->SetLoadMode( LoadMode ); - f->Load( fileName.c_str() ); + f->SetFileName( fileName.c_str() ); + f->Load( ); + + return DoTheLoadingJob (f, + dest, + updateProgressTarget, + updateProgressCount); + delete f; +} - gdcm::FileHelper fileH( 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 @@ -672,19 +755,19 @@ 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 = fileH.GetFile()->GetXSize(); - int numLines = fileH.GetFile()->GetYSize(); - int numPlanes = fileH.GetFile()->GetZSize(); - int lineSize = NumComponents * numColumns * fileH.GetFile()->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 *src; - if( fileH.GetFile()->HasLUT() && AllowLookupTable ) + if( fileH->GetFile()->HasLUT() && AllowLookupTable ) { - size = fileH.GetImageDataSize(); - src = (unsigned char*) fileH.GetImageDataRaw(); - unsigned char *lut = (unsigned char*) fileH.GetLutRGBA(); + size = fileH->GetImageDataSize(); + src = (unsigned char*) fileH->GetImageDataRaw(); + unsigned char *lut = (unsigned char*) fileH->GetLutRGBA(); if(!this->LookupTable) { @@ -707,8 +790,8 @@ size_t vtkGdcmReader::LoadImageInMemory( } else { - size = fileH.GetImageDataSize(); - src = (unsigned char*)fileH.GetImageData(); + size = fileH->GetImageDataSize(); + src = (unsigned char*)fileH->GetImageData(); } unsigned char *dst = dest + planeSize - lineSize; @@ -729,7 +812,7 @@ size_t vtkGdcmReader::LoadImageInMemory( } dst += 2 * planeSize; } - delete f; + delete fileH; return size; } @@ -746,12 +829,14 @@ int vtkGdcmReader::CheckFileCoherenceLight() gdcm::File GdcmFile; GdcmFile.SetLoadMode( LoadMode ); - GdcmFile.Load(filename->c_str() ); + 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 try vtkGdcmReader::CheckFileCoherenceLight"); + << "instead of vtkGdcmReader::CheckFileCoherenceLight"); return 0; } int NX = GdcmFile.GetXSize(); @@ -789,4 +874,56 @@ int vtkGdcmReader::CheckFileCoherenceLight() 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; +} //----------------------------------------------------------------------------- diff --git a/vtk/vtkGdcmReader.h b/vtk/vtkGdcmReader.h index e419490d..fd30e58b 100644 --- a/vtk/vtkGdcmReader.h +++ b/vtk/vtkGdcmReader.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.h,v $ Language: C++ - Date: $Date: 2005/06/29 16:12:43 $ - Version: $Revision: 1.22 $ + Date: $Date: 2005/07/17 04:34:20 $ + Version: $Revision: 1.23 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -20,10 +20,12 @@ #define __vtkGdcmReader_h #include "gdcmCommon.h" // To avoid warnings concerning the std +#include "gdcmFile.h" #include #include #include +#include //----------------------------------------------------------------------------- class vtkLookupTable; @@ -39,7 +41,8 @@ public: virtual void RemoveAllFileName(void); virtual void AddFileName(const char *name); virtual void SetFileName(const char *name); - + void SetCoherentFileList( std::vector *cfl) { + CoherentFileList = cfl; }; void SetCheckFileCoherenceLight(); // Description: @@ -54,7 +57,7 @@ public: /** * \brief Sets the LoadMode as a boolean string. - * NO_SEQ, NO_SHADOW, ... (nothing more, right now) + * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ... (nothing more, right now) * WARNING : before using NO_SHADOW, be sure *all* your files * contain accurate values in the 0x0000 element (if any) * of *each* Shadow Group. The parser will fail if the size is wrong ! @@ -71,15 +74,24 @@ protected: virtual void BuildFileListFromPattern(); virtual int CheckFileCoherence(); virtual int CheckFileCoherenceLight(); - + virtual int CheckFileCoherenceAlreadyDone(); private: void RemoveAllInternalFileName(void); void AddInternalFileName(const char* name); //BTX - size_t LoadImageInMemory(std::string FileName, unsigned char *Dest, - const unsigned long UpdateProgressTarget, - unsigned long & UpdateProgressCount); + size_t LoadImageInMemory(std::string fileName, unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount); + + size_t LoadImageInMemory(gdcm::File *f, unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount); + + size_t DoTheLoadingJob (gdcm::File *f, + unsigned char *dest, + const unsigned long updateProgressTarget, + unsigned long &updateProgressCount); //ETX // Variables @@ -112,13 +124,17 @@ private: // Otherwise, InternalFileNameList correspond to the list of // files patterned std::list InternalFileNameList; + std::vector *CoherentFileList; + //ETX /// \brief Bit string integer (each one considered as a boolean) /// Bit 0 : Skip Sequences, if possible /// Bit 1 : Skip Shadow Groups if possible - /// Probabely, some more to add + /// Bit 2 : Skip Sequences inside a Shadow Group, if possible + /// Probabely (?), some more to add int LoadMode; + }; //-----------------------------------------------------------------------------