X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=6db14bad8d58cf810a6740d8d0a34b4e337357e9;hb=8efd908ab5df098bb1a2dc8937dd3f92ad6d5154;hp=139623d32626e1a09105180b35f8011271df8928;hpb=a70d6842239569070ae649d20e2db2beb7685bc2;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 139623d3..6db14bad 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: 2005/01/21 11:40:56 $ + Version: $Revision: 1.66 $ + + 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 @@ -18,19 +35,24 @@ // 2a/ ExecuteData calls AllocateOutputData that in turn seems to // (indirectely call) ExecuteInformation which ends up in a second // header parsing +// This is fixed by adding a test at the beginning of ExecuteInformation +// on the modification of the object instance. If a modification have been +// 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 +// 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... // @@ -43,8 +65,8 @@ // time... // ////////////////////////////////////////////////////////////// +#include "gdcmFileHelper.h" #include "gdcmFile.h" -#include "gdcmHeaderHelper.h" #include "vtkGdcmReader.h" //#include @@ -53,11 +75,15 @@ #include #include +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.66 $"); +vtkStandardNewMacro(vtkGdcmReader); + //----------------------------------------------------------------------------- // Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; + this->AllowLookupTable = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -72,14 +98,14 @@ vtkGdcmReader::~vtkGdcmReader() // Print 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 ; } } @@ -91,6 +117,7 @@ void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) void vtkGdcmReader::RemoveAllFileName(void) { this->FileNameList.clear(); + this->Modified(); } /* @@ -103,8 +130,8 @@ void vtkGdcmReader::AddFileName(const char* name) char * LocalName = new char[strlen(name) + 1]; strcpy(LocalName, name); this->FileNameList.push_back(LocalName); - this->Modified(); delete[] LocalName; + this->Modified(); } /* @@ -116,6 +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"); this->FileNameList.clear(); this->Modified(); } @@ -127,95 +155,100 @@ void vtkGdcmReader::SetFileName(const char *name) */ void vtkGdcmReader::ExecuteInformation() { - this->TotalNumberOfPlanes = this->CheckFileCoherence(); - if ( this->TotalNumberOfPlanes == 0) + if(this->MTime>this->fileTime) { - vtkErrorMacro("File set is not coherent. Exiting..."); - return; - } + this->TotalNumberOfPlanes = this->CheckFileCoherence(); + if ( this->TotalNumberOfPlanes == 0) + { + vtkErrorMacro(<< "File set is not coherent. Exiting..."); + return; + } - // if the user has not set the extent, but has set the VOI - // set the z axis extent to the VOI z axis - if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && - (this->DataVOI[4] || this->DataVOI[5])) - { - this->DataExtent[4] = this->DataVOI[4]; - this->DataExtent[5] = this->DataVOI[5]; - } - - // When the user has set the VOI, check it's coherence with the file content. - if (this->DataVOI[0] || this->DataVOI[1] || - this->DataVOI[2] || this->DataVOI[3] || - this->DataVOI[4] || this->DataVOI[5]) - { - if ((this->DataVOI[0] < 0) || - (this->DataVOI[1] >= this->NumColumns) || - (this->DataVOI[2] < 0) || - (this->DataVOI[3] >= this->NumLines) || - (this->DataVOI[4] < 0) || - (this->DataVOI[5] >= this->TotalNumberOfPlanes )) + // if the user has not set the extent, but has set the VOI + // set the z axis extent to the VOI z axis + if (this->DataExtent[4]==0 && this->DataExtent[5] == 0 && + (this->DataVOI[4] || this->DataVOI[5])) { - vtkWarningMacro("The requested VOI is larger than expected extent."); - this->DataVOI[0] = 0; - this->DataVOI[1] = this->NumColumns - 1; - this->DataVOI[2] = 0; - this->DataVOI[3] = this->NumLines - 1; - this->DataVOI[4] = 0; - this->DataVOI[5] = this->TotalNumberOfPlanes - 1; + this->DataExtent[4] = this->DataVOI[4]; + this->DataExtent[5] = this->DataVOI[5]; + } + + // When the user has set the VOI, check it's coherence with the file content. + if (this->DataVOI[0] || this->DataVOI[1] || + this->DataVOI[2] || this->DataVOI[3] || + this->DataVOI[4] || this->DataVOI[5]) + { + if ((this->DataVOI[0] < 0) || + (this->DataVOI[1] >= this->NumColumns) || + (this->DataVOI[2] < 0) || + (this->DataVOI[3] >= this->NumLines) || + (this->DataVOI[4] < 0) || + (this->DataVOI[5] >= this->TotalNumberOfPlanes )) + { + vtkWarningMacro(<< "The requested VOI is larger than expected extent."); + this->DataVOI[0] = 0; + this->DataVOI[1] = this->NumColumns - 1; + this->DataVOI[2] = 0; + this->DataVOI[3] = this->NumLines - 1; + this->DataVOI[4] = 0; + this->DataVOI[5] = this->TotalNumberOfPlanes - 1; + } } - } - // Positionate the Extent. - this->DataExtent[0] = 0; - this->DataExtent[1] = this->NumColumns - 1; - this->DataExtent[2] = 0; - this->DataExtent[3] = this->NumLines - 1; - this->DataExtent[4] = 0; - this->DataExtent[5] = this->TotalNumberOfPlanes - 1; + // Positionate the Extent. + this->DataExtent[0] = 0; + this->DataExtent[1] = this->NumColumns - 1; + this->DataExtent[2] = 0; + this->DataExtent[3] = this->NumLines - 1; + this->DataExtent[4] = 0; + this->DataExtent[5] = this->TotalNumberOfPlanes - 1; - // We don't need to positionate 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"); - this->SetDataScalarTypeToUnsignedChar(); - } - else if ( ImageType == "8S" ) - { - vtkErrorMacro("Cannot handle 8 bit signed files"); - return; - } - else if ( ImageType == "16U" ) - { - vtkDebugMacro("16 bits unsigned image"); - this->SetDataScalarTypeToUnsignedShort(); - } - else if ( ImageType == "16S" ) - { - 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 !"); - this->SetDataScalarTypeToInt(); - } - else if ( ImageType == "32S" ) - { - vtkDebugMacro("32 bits signed image"); - this->SetDataScalarTypeToInt(); - } - else if ( ImageType == "FD" ) - { - vtkDebugMacro("64 bits Double image"); - this->SetDataScalarTypeToDouble(); + // We don't need to positionate 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"); + this->SetDataScalarTypeToUnsignedChar(); + } + else if ( ImageType == "8S" ) + { + vtkErrorMacro(<< "Cannot handle 8 bit signed files"); + return; + } + else if ( ImageType == "16U" ) + { + vtkDebugMacro(<< "16 bits unsigned image"); + this->SetDataScalarTypeToUnsignedShort(); + } + else if ( ImageType == "16S" ) + { + 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 !"); + this->SetDataScalarTypeToInt(); + } + else if ( ImageType == "32S" ) + { + vtkDebugMacro(<< "32 bits signed image"); + this->SetDataScalarTypeToInt(); + } + else if ( ImageType == "FD" ) + { + vtkDebugMacro(<< "64 bits Double image"); + this->SetDataScalarTypeToDouble(); + } + //Set number of scalar components: + this->SetNumberOfScalarComponents(this->NumComponents); + + this->fileTime=this->MTime; } - //Set number of scalar components: - this->SetNumberOfScalarComponents(this->NumComponents); this->Superclass::ExecuteInformation(); } @@ -231,7 +264,7 @@ 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; } @@ -248,9 +281,9 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) { // The memory size for a full stack of images of course depends // on the number of planes and the size of each image: - size_t StackNumPixels = this->NumColumns * this->NumLines - * this->TotalNumberOfPlanes * this->NumComponents; - size_t stack_size = StackNumPixels * this->PixelSize; + //size_t StackNumPixels = this->NumColumns * this->NumLines + // * this->TotalNumberOfPlanes * this->NumComponents; + //size_t stack_size = StackNumPixels * this->PixelSize; //not used // Allocate pixel data space itself. // Variables for the UpdateProgress. We shall use 50 steps to signify @@ -262,18 +295,18 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) 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) + 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") + if (*filename != "GDCM_UNREADABLE") { // Update progress related for good files is made in LoadImageInMemory - Dest += this->LoadImageInMemory(*FileName, Dest, + Dest += this->LoadImageInMemory(*filename, Dest, UpdateProgressTarget, UpdateProgressCount); } @@ -308,42 +341,58 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) */ void vtkGdcmReader::BuildFileListFromPattern() { + this->RemoveAllInternalFileName(); + if ((! this->FileNameList.empty()) && this->FileName ) { - vtkErrorMacro("Both file patterns and AddFileName schemes were used"); - vtkErrorMacro("Only the files specified with AddFileName shall be used"); + 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 ! "); + return; + } + + if (this->FileName && this->FilePrefix) + { + 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->FilePattern) + if (!this->FileName && !this->FilePrefix) { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePattern."); + vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro(<< "specify a FileName or FilePrefix."); return; } - this->RemoveAllInternalFileName(); - if( this->FileNameList.empty() ) + if( this->FileName ) { - //Multiframe case: + // 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 { - //stack of 2D dicom case: + // Multi file loading (as given with ::SetFilePattern()): 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); } } @@ -372,7 +421,7 @@ int vtkGdcmReader::CheckFileCoherence() this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) { - vtkErrorMacro("FileNames are not set."); + vtkErrorMacro(<< "FileNames are not set."); return 0; } @@ -382,9 +431,9 @@ 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 @@ -394,85 +443,85 @@ int vtkGdcmReader::CheckFileCoherence() ReturnedTotalNumberOfPlanes += 1; /////// Stage 0: check for file name: - if(*FileName==std::string("GDCM_UNREADABLE")) + 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 readed files " + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } fclose(fp); - + // Stage 1.2: check for Gdcm parsability - gdcmHeaderHelper 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 " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; + 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") ) + && (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. if (NZ > 1) { - vtkErrorMacro("This file contains multiple planes (images)" - << FileName->c_str()); + vtkErrorMacro(<< "This file contains multiple planes (images)" + << filename->c_str()); } // Eventually, this file can be added on the stack. Update the @@ -487,59 +536,62 @@ int vtkGdcmReader::CheckFileCoherence() // 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:" + 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(<< "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() ) + if( GdcmFile.HasLUT() && this->AllowLookupTable ) { - this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + // I could raise an error is AllowLookupTable is on and HasLUT() off + 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 + } // 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; @@ -571,78 +623,80 @@ void vtkGdcmReader::AddInternalFileName(const char* name) * 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) + 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::FileHelper file( fileName.c_str() ); size_t size; // If the data structure of vtk for image/volume representation - // were straigthforwards the following would suffice: + // were straigthforwards the following would be enough: // GdcmFile.GetImageDataIntoVector((void*)Dest, size); // But vtk chooses to invert the lines of an image, that is the last // 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 = 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; - if( GdcmFile.GetHeader()->HasLUT() ) + unsigned char *src; + + if( file.GetFile()->HasLUT() && AllowLookupTable ) { - size = GdcmFile.GetImageDataSizeRaw(); - Source = (unsigned char*) GdcmFile.GetImageDataRaw(); - unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); + size = file.GetImageDataSize(); + src = (unsigned char*) file.GetImageDataRaw(); + unsigned char *lut = (unsigned char*) file.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(); - } - unsigned char * pSource = Source; //pointer for later deletion - unsigned char * Destination = Dest + size - LineSize; + size = file.GetImageDataSize(); + src = (unsigned char*)file.GetImageData(); + } - 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; } - //GetImageData allocate a (void*)malloc, remove it: - free(pSource); - + return size; }