X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=bb13548d7d781aae6d3e864083e5c553019c5163;hb=7840ddd7d30ebe6f20959ff3ae9e0565f723c645;hp=6db14bad8d58cf810a6740d8d0a34b4e337357e9;hpb=c094e185dd6404df031524ccae8e1b51e3b84871;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 6db14bad..bb13548d 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -3,8 +3,8 @@ Program: gdcm Module: $RCSfile: vtkGdcmReader.cxx,v $ Language: C++ - Date: $Date: 2005/01/21 11:40:56 $ - Version: $Revision: 1.66 $ + Date: $Date: 2005/04/28 14:32:54 $ + Version: $Revision: 1.70 $ 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: 1.66 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.70 $"); 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..."); @@ -226,7 +248,6 @@ void vtkGdcmReader::ExecuteInformation() { vtkDebugMacro(<< "16 bits signed image"); this->SetDataScalarTypeToShort(); - //vtkErrorMacro(<< "Cannot handle 16 bit signed files"); } else if ( ImageType == "32U" ) { @@ -257,7 +278,7 @@ void vtkGdcmReader::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) @@ -269,6 +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"); @@ -294,7 +316,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) // The actual advance measure: unsigned long UpdateProgressCount = 0; - // Feeling the allocated memory space with each image/volume: + // 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(); @@ -443,6 +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; @@ -453,7 +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; @@ -461,11 +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; @@ -496,9 +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; @@ -507,20 +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()); } @@ -533,13 +563,13 @@ 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); + << 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; @@ -557,18 +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 @@ -610,9 +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; @@ -695,9 +718,64 @@ 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(); + // 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(); +} //-----------------------------------------------------------------------------