X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=110b090460aa935808667bdce599792aad0408b8;hb=750a99fba37bba2b57708a54047c10a054809b77;hp=4922c856c0b799c2cd7aa99945479ed0690c0c46;hpb=b083a867887309f4cefa627a0e7dd960bd26be36;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 4922c856..110b0904 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,4 +1,21 @@ -// vtkGdcmReader.cxx +/*========================================================================= + + Program: gdcm + Module: $RCSfile: vtkGdcmReader.cxx,v $ + Language: C++ + Date: $Date: 2005/04/22 12:07:39 $ + Version: $Revision: 1.68 $ + + 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 CLEANME @@ -24,18 +41,18 @@ // 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 +// initialises gdcmFile 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 +// 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: // - 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 +// 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... // @@ -48,8 +65,8 @@ // time... // ////////////////////////////////////////////////////////////// +#include "gdcmFileHelper.h" #include "gdcmFile.h" -#include "gdcmHeader.h" #include "vtkGdcmReader.h" //#include @@ -58,7 +75,7 @@ #include #include -vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.56 $"); +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.68 $"); vtkStandardNewMacro(vtkGdcmReader); //----------------------------------------------------------------------------- @@ -126,7 +143,7 @@ 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(); } @@ -143,7 +160,7 @@ void vtkGdcmReader::ExecuteInformation() 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 +185,7 @@ 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; @@ -192,39 +209,38 @@ void vtkGdcmReader::ExecuteInformation() // 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: @@ -240,14 +256,14 @@ 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) { if (this->InternalFileNameList.empty()) { - vtkErrorMacro("A least a valid FileName must be specified."); + vtkErrorMacro(<< "A least a valid FileName must be specified."); return; } @@ -277,8 +293,8 @@ 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); + // 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) @@ -328,36 +344,36 @@ 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 +382,7 @@ 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 +391,7 @@ 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 +420,7 @@ int vtkGdcmReader::CheckFileCoherence() this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) { - vtkErrorMacro("FileNames are not set."); + vtkErrorMacro(<< "FileNames are not set."); return 0; } @@ -435,8 +451,8 @@ int vtkGdcmReader::CheckFileCoherence() fp = fopen(filename->c_str(),"rb"); if (!fp) { - vtkErrorMacro("Unable to open file " << filename->c_str()); - vtkErrorMacro("Removing this file from readed files " + vtkErrorMacro(<< "Unable to open file " << filename->c_str()); + vtkErrorMacro(<< "Removing this file from readed files " << filename->c_str()); *filename = "GDCM_UNREADABLE"; continue; @@ -444,34 +460,34 @@ int vtkGdcmReader::CheckFileCoherence() fclose(fp); // Stage 1.2: check for Gdcm parsability - gdcm::Header GdcmHeader(filename->c_str() ); - if (!GdcmHeader.IsReadable()) + gdcm::File GdcmFile(filename->c_str() ); + if (!GdcmFile.IsReadable()) { - vtkErrorMacro("Gdcm cannot parse file " << filename->c_str()); - vtkErrorMacro("Removing this file from readed files " + 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(); + std::string type = GdcmFile.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()); + 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: @@ -479,9 +495,9 @@ 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; @@ -490,12 +506,12 @@ 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()); } @@ -503,7 +519,7 @@ int vtkGdcmReader::CheckFileCoherence() // notify the caller. if (NZ > 1) { - vtkErrorMacro("This file contains multiple planes (images)" + vtkErrorMacro(<< "This file contains multiple planes (images)" << filename->c_str()); } @@ -516,41 +532,41 @@ 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:" + vtkDebugMacro(<< "This file taken as coherence reference:" << filename->c_str()); - vtkDebugMacro("Image dimension of reference file as read from Gdcm:" + vtkDebugMacro(<< "Image dimension of reference file as read from Gdcm:" << NX << " " << NY << " " << NZ); - vtkDebugMacro("Number of planes added to the stack: " << 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(); + this->DataSpacing[0] = GdcmFile.GetXSpacing(); + this->DataSpacing[1] = GdcmFile.GetYSpacing(); + this->DataSpacing[2] = GdcmFile.GetZSpacing(); //Set image origin - this->DataOrigin[0] = GdcmHeader.GetXOrigin(); - this->DataOrigin[1] = GdcmHeader.GetYOrigin(); - this->DataOrigin[2] = GdcmHeader.GetZOrigin(); + //this->DataOrigin[0] = GdcmFile.GetXOrigin(); + //this->DataOrigin[1] = GdcmFile.GetYOrigin(); + //this->DataOrigin[2] = GdcmFile.GetZOrigin(); } } // End of loop on filename @@ -567,14 +583,14 @@ int vtkGdcmReader::CheckFileCoherence() 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; @@ -607,12 +623,12 @@ void vtkGdcmReader::AddInternalFileName(const char* name) */ size_t vtkGdcmReader::LoadImageInMemory( std::string fileName, - unsigned char * dest, + unsigned char *dest, const unsigned long updateProgressTarget, unsigned long & updateProgressCount) { - vtkDebugMacro("Copying to memory image [" << fileName.c_str() << "]"); - gdcm::File file( fileName.c_str() ); + vtkDebugMacro(<< "Copying to memory image [" << fileName.c_str() << "]"); + gdcm::FileHelper file( fileName.c_str() ); size_t size; // If the data structure of vtk for image/volume representation @@ -622,17 +638,18 @@ 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 = file.GetHeader()->GetXSize(); - int numLines = file.GetHeader()->GetYSize(); - int numPlanes = file.GetHeader()->GetZSize(); - int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize(); + int numColumns = file.GetFile()->GetXSize(); + int numLines = file.GetFile()->GetYSize(); + int numPlanes = file.GetFile()->GetZSize(); + int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize(); + int planeSize = lineSize * numLines; - unsigned char * source; + unsigned char *src; - if( file.GetHeader()->HasLUT() && AllowLookupTable ) + if( file.GetFile()->HasLUT() && AllowLookupTable ) { size = file.GetImageDataSize(); - source = (unsigned char*) file.GetImageDataRaw(); + src = (unsigned char*) file.GetImageDataRaw(); unsigned char *lut = (unsigned char*) file.GetLutRGBA(); if(!this->LookupTable) @@ -656,20 +673,19 @@ size_t vtkGdcmReader::LoadImageInMemory( } else { - size = file.GetImageDataSize(); - source = (unsigned char*)file.GetImageData(); + size = file.GetImageDataSize(); + src = (unsigned char*)file.GetImageData(); } - - unsigned char * destination = dest + size - lineSize; + unsigned char *dst = dest + planeSize - 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; + memcpy((void*)dst, (void*)src, lineSize); + src += lineSize; + dst -= lineSize; // Update progress related: if (!(updateProgressCount%updateProgressTarget)) { @@ -677,25 +693,9 @@ size_t vtkGdcmReader::LoadImageInMemory( } 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: - - // CLEANME - // Now, the delete on values keep from GetImageData is useless (made in - // the PixelConvert class) - -// unsigned char * pSource = source; //pointer for later deletion -// delete[] pSource; return size; }