From 40ab72c408a2ff2631b66c7bd46593358b7e064f Mon Sep 17 00:00:00 2001 From: jpr Date: Thu, 28 Apr 2005 09:29:05 +0000 Subject: [PATCH] Aware user (who *does* know all the files whose names are in InternalFileNameList are 'coherent', that is to say : - 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 ? is now allowed to ask for a 'light' checking (actualy : initialization, from the first file characteristics), using vtkGdcmReader::SetCheckFileCoherenceLight() --- vtk/vtkGdcmReader.cxx | 152 +++++++++++++++++++++++++++++++----------- vtk/vtkGdcmReader.h | 20 +++--- 2 files changed, 126 insertions(+), 46 deletions(-) diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 110b0904..db2e605d 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.cxx,v $ Language: C++ - Date: $Date: 2005/04/22 12:07:39 $ - Version: $Revision: 1.68 $ + Date: $Date: 2005/04/28 09:29:05 $ + Version: $Revision: 1.69 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -26,12 +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 @@ -52,9 +59,10 @@ // - 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. -// The average size of a gdcmFile being of 100Ko, is one -// loads 10 stacks of images with say 200 images each, you -// end-up with a loss of 200Mo... +// 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... // // /////// Never unallocated memory: // ExecuteData allocates space for the pixel data [which will get pointed @@ -75,7 +83,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.68 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.69 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -84,6 +92,7 @@ vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; this->AllowLookupTable = 0; + this->LightChecking = false; } vtkGdcmReader::~vtkGdcmReader() @@ -127,7 +136,7 @@ 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; @@ -148,6 +157,15 @@ void vtkGdcmReader::SetFileName(const char *name) 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 /* @@ -157,7 +175,11 @@ void vtkGdcmReader::ExecuteInformation() { if(this->MTime>this->fileTime) { - this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->LightChecking ) + this->TotalNumberOfPlanes = this->CheckFileCoherenceLight(); + else + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) { vtkErrorMacro(<< "File set is not coherent. Exiting..."); @@ -268,6 +290,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) } // 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"); @@ -442,6 +465,10 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += 1; /////// Stage 0: check for file name: + + // fixme : how can the filename be equal to "GDCM_UNREADABLE" + // right now ?!? + if(*filename == std::string("GDCM_UNREADABLE")) continue; @@ -452,7 +479,7 @@ int vtkGdcmReader::CheckFileCoherence() if (!fp) { vtkErrorMacro(<< "Unable to open file " << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from read files: " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -460,11 +487,16 @@ int vtkGdcmReader::CheckFileCoherence() fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcm::File GdcmFile(filename->c_str() ); + + //gdcm::File GdcmFile( filename->c_str() ); + // to save some parsing time. + gdcm::File GdcmFile; + GdcmFile.SetLoadMode( NO_SEQ | NO_SHADOW ); + GdcmFile.Load(filename->c_str() ); if (!GdcmFile.IsReadable()) { vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from read files: " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -495,9 +527,9 @@ int vtkGdcmReader::CheckFileCoherence() || ( NY != this->NumLines ) || ( type != this->ImageType ) ) { - vtkErrorMacro(<< "This file is not coherent with previous ones" + vtkErrorMacro(<< "This file is not coherent with previous ones: " << filename->c_str()); - vtkErrorMacro(<< "Removing this file from readed files " + vtkErrorMacro(<< "Removing this file from readed files: " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -506,20 +538,19 @@ int vtkGdcmReader::CheckFileCoherence() // Stage 2.2: optional coherence stage if ( NZ != ReferenceNZ ) { - vtkErrorMacro(<< "File is not coherent in Z with previous ones" + vtkErrorMacro(<< "File is not coherent in Z with previous ones: " << filename->c_str()); } else { - vtkDebugMacro(<< "File is coherent with previous ones" + 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)" + vtkErrorMacro(<< "This file is a 'Multiframe' one: " << filename->c_str()); } @@ -536,9 +567,9 @@ int vtkGdcmReader::CheckFileCoherence() // 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); + << 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; @@ -556,18 +587,11 @@ int vtkGdcmReader::CheckFileCoherence() 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(); - - //Set image origin - //this->DataOrigin[0] = GdcmFile.GetXOrigin(); - //this->DataOrigin[1] = GdcmFile.GetYOrigin(); - //this->DataOrigin[2] = GdcmFile.GetZOrigin(); - } } // End of loop on filename @@ -609,9 +633,9 @@ 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; @@ -694,9 +718,61 @@ size_t vtkGdcmReader::LoadImageInMemory( updateProgressCount++; } dst += 2 * planeSize; - } - + } 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( NO_SEQ | NO_SHADOW ); + GdcmFile.Load(filename->c_str() ); + if (!GdcmFile.IsReadable()) + { + vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str()); + vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence " + << "instead of try vtkGdcmReader::CheckFileCoherenceLight"); + return 0; + } + int NX = GdcmFile.GetXSize(); + int NY = GdcmFile.GetYSize(); + int NZ = GdcmFile.GetZSize(); + 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(); +} //----------------------------------------------------------------------------- diff --git a/vtk/vtkGdcmReader.h b/vtk/vtkGdcmReader.h index b04b56d9..801df340 100644 --- a/vtk/vtkGdcmReader.h +++ b/vtk/vtkGdcmReader.h @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.h,v $ Language: C++ - Date: $Date: 2004/12/09 10:59:59 $ - Version: $Revision: 1.20 $ + Date: $Date: 2005/04/28 09:29:05 $ + Version: $Revision: 1.21 $ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de l'Image). All rights reserved. See Doc/License.txt or @@ -37,18 +37,20 @@ public: void PrintSelf(ostream& os, vtkIndent indent); virtual void RemoveAllFileName(void); - virtual void AddFileName(const char* name); + virtual void AddFileName(const char *name); virtual void SetFileName(const char *name); + + void SetCheckFileCoherenceLight(); // Description: // If this flag is set and the DICOM reader encounters a dicom file with // lookup table the data will be kept as unsigned chars and a lookuptable // will be exported and accessible through GetLookupTable() - vtkSetMacro(AllowLookupTable,int); - vtkGetMacro(AllowLookupTable,int); - vtkBooleanMacro(AllowLookupTable,int); + vtkSetMacro(AllowLookupTable, int); + vtkGetMacro(AllowLookupTable, int); + vtkBooleanMacro(AllowLookupTable, int); - vtkGetObjectMacro(LookupTable,vtkLookupTable); + vtkGetObjectMacro(LookupTable, vtkLookupTable); protected: vtkGdcmReader(); @@ -58,13 +60,14 @@ protected: virtual void ExecuteData(vtkDataObject *output); virtual void BuildFileListFromPattern(); virtual int CheckFileCoherence(); + virtual int CheckFileCoherenceLight(); private: void RemoveAllInternalFileName(void); void AddInternalFileName(const char* name); //BTX - size_t LoadImageInMemory(std::string FileName, unsigned char * Dest, + size_t LoadImageInMemory(std::string FileName, unsigned char *Dest, const unsigned long UpdateProgressTarget, unsigned long & UpdateProgressCount); //ETX @@ -73,6 +76,7 @@ private: vtkLookupTable *LookupTable; vtkTimeStamp fileTime; int AllowLookupTable; + bool LightChecking; //BTX // Number of columns of the image/volume to be loaded -- 2.46.1