From 844285f083c7bb09584e1875d5acf00fb08c22a0 Mon Sep 17 00:00:00 2001 From: regrain Date: Tue, 13 Jan 2004 15:49:29 +0000 Subject: [PATCH] * vtk/*.[h|cxx] : coding style -- BeNours --- ChangeLog | 1 + vtk/vtkGdcmReader.cxx | 970 ++++++++++++++++++++++-------------------- vtk/vtkGdcmReader.h | 99 +++-- 3 files changed, 553 insertions(+), 517 deletions(-) diff --git a/ChangeLog b/ChangeLog index 64caba12..9b180ef0 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,5 +1,6 @@ 2004-01-13 Benoit Regrain * src/*.[h|cxx] : coding style + * vtk/*.[h|cxx] : coding style 2004-01-13 Benoit Regrain * gdcmPython/testSuite.py : test the readable flag of file for tests diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index d10df40d..61989684 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,4 +1,5 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.30 2004/01/13 11:32:31 jpr Exp $ +// vtkGdcmReader.cxx +//----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// // WARNING TODO CLENAME // Actual limitations of this code: @@ -52,144 +53,331 @@ #include #include - +//----------------------------------------------------------------------------- +// Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { - // Constructor - this->LookupTable = NULL; + this->LookupTable = NULL; } -//---------------------------------------------------------------------------- vtkGdcmReader::~vtkGdcmReader() { - this->RemoveAllFileName(); - this->InternalFileNameList.clear(); - if(this->LookupTable) this->LookupTable->Delete(); + this->RemoveAllFileName(); + this->InternalFileNameList.clear(); + if(this->LookupTable) + this->LookupTable->Delete(); } -//---------------------------------------------------------------------------- -// Remove all files from the list of images to read. +//----------------------------------------------------------------------------- +// Print +void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) +{ + vtkImageReader::PrintSelf(os,indent); + os << indent << "Filenames : " << endl; + vtkIndent nextIndent = indent.GetNextIndent(); + for (std::list::iterator FileName = FileNameList.begin(); + FileName != FileNameList.end(); + ++FileName) + { + os << nextIndent << FileName->c_str() << endl ; + } +} + +//----------------------------------------------------------------------------- +// Public +/* + * Remove all files from the list of images to read. + */ void vtkGdcmReader::RemoveAllFileName(void) { - this->FileNameList.clear(); + this->FileNameList.clear(); } -//---------------------------------------------------------------------------- -// Adds a file name to the list of images to read. +/* + * Adds a file name to the list of images to read. + */ 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]; - strcpy(LocalName, name); - this->FileNameList.push_back(LocalName); - this->Modified(); - delete[] LocalName; + // 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]; + strcpy(LocalName, name); + this->FileNameList.push_back(LocalName); + this->Modified(); + delete[] LocalName; } -//---------------------------------------------------------------------------- -// Sets up a filename to be read. -void vtkGdcmReader::SetFileName(const char *name) { - vtkImageReader2::SetFileName(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. - this->FileNameList.clear(); - this->Modified(); +/* + * Sets up a filename to be read. + */ +void vtkGdcmReader::SetFileName(const char *name) +{ + vtkImageReader2::SetFileName(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. + this->FileNameList.clear(); + this->Modified(); } -//---------------------------------------------------------------------------- -// Adds a file name to the internal list of images to read. -void vtkGdcmReader::RemoveAllInternalFileName(void) +//----------------------------------------------------------------------------- +// Protected +/* + * Configure the output e.g. WholeExtent, spacing, origin, scalar type... + */ +void vtkGdcmReader::ExecuteInformation() { - this->InternalFileNameList.clear(); + 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 )) + { + 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; + + // 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(); + } + + //Set number of scalar components: + this->SetNumberOfScalarComponents(this->NumComponents); + + vtkImageReader::ExecuteInformation(); } -//---------------------------------------------------------------------------- -// Adds a file name to the internal list of images to read. -void vtkGdcmReader::AddInternalFileName(const char* name) +/* + * 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 + * extent/axes are assumed to be the same as the file extent/order. + */ +void vtkGdcmReader::ExecuteData(vtkDataObject *output) { - char * LocalName = new char[strlen(name) + 1]; - strcpy(LocalName, name); - this->InternalFileNameList.push_back(LocalName); - delete[] LocalName; + if (this->InternalFileNameList.empty()) + { + vtkErrorMacro("A least a valid FileName must be specified."); + return; + } + + // 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"); + + // Test if output has valid extent + // Prevent memory errors + if((this->DataExtent[1]-this->DataExtent[0]>=0) && + (this->DataExtent[3]-this->DataExtent[2]>=0) && + (this->DataExtent[5]-this->DataExtent[4]>=0)) + { + // 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; + // Allocate pixel data space itself. + unsigned char *mem = new unsigned char [stack_size]; + + // Variables for the UpdateProgress. We shall use 50 steps to signify + // the advance of the process: + unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines + * this->TotalNumberOfPlanes + / 50.0); + // The actual advance measure: + unsigned long UpdateProgressCount = 0; + + // Feeling the allocated memory space with each image/volume: + unsigned char * Dest = mem; + 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 (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + } + } // Else, file not loadable + } // Loop on files + + // The "size" of the vtkScalars data is expressed in number of points, + // and is not the memory size representing those points: + data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); + //don't know why it's here, it's calling one more time ExecuteInformation: + //this->Modified(); + } } -//---------------------------------------------------------------------------- -// vtkGdcmReader can have the file names specified through two ways: -// (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and -// SetFilePattern() -// (2) By successive calls to vtkGdcmReader::AddFileName() -// When the first method was used by caller we need to update the local -// filename list +/* + * vtkGdcmReader can have the file names specified through two ways: + * (1) by calling the vtkImageReader2::SetFileName(), SetFilePrefix() and + * SetFilePattern() + * (2) By successive calls to vtkGdcmReader::AddFileName() + * When the first method was used by caller we need to update the local + * filename list + */ void vtkGdcmReader::BuildFileListFromPattern() { 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"); - return; - } + { + vtkErrorMacro("Both file patterns and AddFileName schemes were used"); + vtkErrorMacro("Only the files specified with AddFileName shall be used"); + return; + } if (! this->FileNameList.empty() ) - { - vtkDebugMacro("Using the AddFileName specified files"); - this->InternalFileNameList=this->FileNameList; - return; - } + { + vtkDebugMacro("Using the AddFileName specified files"); + this->InternalFileNameList=this->FileNameList; + return; + } if (!this->FileName && !this->FilePattern) - { - vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); - vtkErrorMacro("specify a FileName or FilePattern."); - return; - } + { + vtkErrorMacro("FileNames are not set. Either use AddFileName() or"); + vtkErrorMacro("specify a FileName or FilePattern."); + return; + } this->RemoveAllInternalFileName(); if( this->FileNameList.empty() ) - { - //Multiframe case: - this->ComputeInternalFileName(this->DataExtent[4]); - vtkDebugMacro("Adding file " << this->InternalFileName); - this->AddInternalFileName(this->InternalFileName); - } + { + //Multiframe case: + this->ComputeInternalFileName(this->DataExtent[4]); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } else - { - //stack of 2D dicom case: - for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) - { - this->ComputeInternalFileName(idx); - vtkDebugMacro("Adding file " << this->InternalFileName); - this->AddInternalFileName(this->InternalFileName); - } - } + { + //stack of 2D dicom case: + for (int idx = this->DataExtent[4]; idx <= this->DataExtent[5]; ++idx) + { + this->ComputeInternalFileName(idx); + vtkDebugMacro("Adding file " << this->InternalFileName); + this->AddInternalFileName(this->InternalFileName); + } + } } -//---------------------------------------------------------------------------- -// When more than one filename is specified (i.e. we expect loading -// a stack or volume) we need to check that the corresponding images/volumes -// to be loaded are coherent i.e. to make sure: -// - they all share the same X dimensions -// - they all share the same Y dimensions -// - they all share the same ImageType ( 8 bit signed, or unsigned...) -// -// Eventually, we emit a warning when all the files do NOT share the -// Z dimension, since we can still build a stack but the -// files are not coherent in Z, which is probably a source a trouble... -// When files are not readable (either the file cannot be opened or -// because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". -// This method returns the total number of planar images to be loaded -// (i.e. an image represents one plane, but a volume represents many planes) +/* + * When more than one filename is specified (i.e. we expect loading + * a stack or volume) we need to check that the corresponding images/volumes + * to be loaded are coherent i.e. to make sure: + * - they all share the same X dimensions + * - they all share the same Y dimensions + * - they all share the same ImageType ( 8 bit signed, or unsigned...) + * + * Eventually, we emit a warning when all the files do NOT share the + * Z dimension, since we can still build a stack but the + * files are not coherent in Z, which is probably a source a trouble... + * When files are not readable (either the file cannot be opened or + * because gdcm cannot parse it), they are flagged as "GDCM_UNREADABLE". + * This method returns the total number of planar images to be loaded + * (i.e. an image represents one plane, but a volume represents many planes) + */ int vtkGdcmReader::CheckFileCoherence() { int ReturnedTotalNumberOfPlanes = 0; // The returned value. this->BuildFileListFromPattern(); if (this->InternalFileNameList.empty()) - { - vtkErrorMacro("FileNames are not set."); - return 0; - } + { + vtkErrorMacro("FileNames are not set."); + return 0; + } bool FoundReferenceFile = false; int ReferenceNZ = 0; @@ -197,430 +385,268 @@ 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) - { - // 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 - // ExecuteData method - // - If file has more than 1 plane, other planes will be added later to - // to the ReturnedTotalNumberOfPlanes variable counter - ReturnedTotalNumberOfPlanes += 1; - - /////// Stage 0: check for file name: - 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"); - if (!fp) - { - vtkErrorMacro("Unable to open file " << FileName->c_str()); - vtkErrorMacro("Removing this file from readed files " + 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 + // ExecuteData method + // - If file has more than 1 plane, other planes will be added later to + // to the ReturnedTotalNumberOfPlanes variable counter + ReturnedTotalNumberOfPlanes += 1; + + /////// Stage 0: check for file name: + 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"); + if (!fp) + { + vtkErrorMacro("Unable to open file " << FileName->c_str()); + vtkErrorMacro("Removing this file from readed files " << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; - continue; - } - fclose(fp); + *FileName = "GDCM_UNREADABLE"; + continue; + } + fclose(fp); - // Stage 1.2: check for Gdcm parsability - gdcmHeaderHelper GdcmHeader(FileName->c_str()); - if (!GdcmHeader.IsReadable()) - { - 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(); - 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()); - *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(); - if (FoundReferenceFile) - { - - // Stage 2.1: mandatory coherence stage: - if ( ( NX != this->NumColumns ) - || ( NY != this->NumLines ) - || ( type != this->ImageType ) ) - { - vtkErrorMacro("This file is not coherent with previous ones" - << FileName->c_str()); + // Stage 1.2: check for Gdcm parsability + gdcmHeaderHelper GdcmHeader(FileName->c_str()); + if (!GdcmHeader.IsReadable()) + { + vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); + << FileName->c_str()); *FileName = "GDCM_UNREADABLE"; continue; + } + + // Stage 1.3: further gdcm compatibility on PixelType + std::string type = GdcmHeader.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()); + *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(); + if (FoundReferenceFile) + { + // Stage 2.1: mandatory coherence stage: + if ( ( NX != this->NumColumns ) + || ( 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"; + continue; } - // Stage 2.2: optional coherence stage - if ( NZ != ReferenceNZ ) + // 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 + 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) + // 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 - // full size of the stack - vtkDebugMacro("Number of planes added to the stack: " << NZ); - ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added - continue; - - } else { - // 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); - 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(); - - if( GdcmHeader.HasLUT() ) + // Eventually, this file can be added on the stack. Update the + // full size of the stack + vtkDebugMacro("Number of planes added to the stack: " << NZ); + ReturnedTotalNumberOfPlanes += NZ - 1; // First plane already added + continue; + + } + else + { + // 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); + 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(); + + if( GdcmHeader.HasLUT() ) { - this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); + this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); } - else + else { - this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono + this->NumComponents = GdcmHeader.GetNumberOfScalarComponents(); //rgb or mono } - //Set image spacing - this->DataSpacing[0] = GdcmHeader.GetXSpacing(); - this->DataSpacing[1] = GdcmHeader.GetYSpacing(); - this->DataSpacing[2] = GdcmHeader.GetZSpacing(); - - //Set image origin - this->DataOrigin[0] = GdcmHeader.GetXOrigin(); - this->DataOrigin[1] = GdcmHeader.GetYOrigin(); - this->DataOrigin[2] = GdcmHeader.GetZOrigin(); - - } - } // End of loop on FileName + //Set image spacing + this->DataSpacing[0] = GdcmHeader.GetXSpacing(); + this->DataSpacing[1] = GdcmHeader.GetYSpacing(); + this->DataSpacing[2] = GdcmHeader.GetZSpacing(); + + //Set image origin + this->DataOrigin[0] = GdcmHeader.GetXOrigin(); + this->DataOrigin[1] = GdcmHeader.GetYOrigin(); + this->DataOrigin[2] = GdcmHeader.GetZOrigin(); + + } + } // 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 Filename = InternalFileNameList.begin(); + Filename != InternalFileNameList.end(); + ++Filename) + { if (*Filename != "GDCM_UNREADABLE") 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: " - << ReturnedTotalNumberOfPlanes); + << ReturnedTotalNumberOfPlanes); - return ReturnedTotalNumberOfPlanes; + return ReturnedTotalNumberOfPlanes; } -//---------------------------------------------------------------------------- -// Configure the output e.g. WholeExtent, spacing, origin, scalar type... -void vtkGdcmReader::ExecuteInformation() +//----------------------------------------------------------------------------- +// Private +/* + * Remove all file names to the internal list of images to read. + */ +void vtkGdcmReader::RemoveAllInternalFileName(void) { - 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 )) - { - 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; - - // 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(); - } - - //Set number of scalar components: - this->SetNumberOfScalarComponents(this->NumComponents); + this->InternalFileNameList.clear(); +} - vtkImageReader::ExecuteInformation(); +/* + * Adds a file name to the internal list of images to read. + */ +void vtkGdcmReader::AddInternalFileName(const char* name) +{ + char * LocalName = new char[strlen(name) + 1]; + strcpy(LocalName, name); + this->InternalFileNameList.push_back(LocalName); + delete[] LocalName; } -//---------------------------------------------------------------------------- -// Loads the contents of the image/volume contained by Filename at -// the Dest memory address. Returns the size of the data loaded. +/* + * Loads the contents of the image/volume contained by Filename at + * 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) { - vtkDebugMacro("Copying to memory image" << FileName.c_str()); - gdcmFile GdcmFile(FileName.c_str()); - size_t size; - - // If the data structure of vtk for image/volume representation - // were straigthforwards the following would suffice: - // 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(); - - unsigned char * Source; - if( GdcmFile.GetHeader()->HasLUT() ) - { - size = GdcmFile.GetImageDataSizeRaw(); - Source = (unsigned char*) GdcmFile.GetImageDataRaw(); - unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); - - if(!this->LookupTable) this->LookupTable = vtkLookupTable::New(); - this->LookupTable->SetNumberOfTableValues(256); - for (int tmp=0; tmp<256; tmp++) + vtkDebugMacro("Copying to memory image" << FileName.c_str()); + gdcmFile GdcmFile(FileName.c_str()); + size_t size; + + // If the data structure of vtk for image/volume representation + // were straigthforwards the following would suffice: + // 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(); + + unsigned char * Source; + if( GdcmFile.GetHeader()->HasLUT() ) + { + size = GdcmFile.GetImageDataSizeRaw(); + Source = (unsigned char*) GdcmFile.GetImageDataRaw(); + unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); + + 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, - 1); + 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, + 1); } - this->LookupTable->SetRange(0,255); - vtkDataSetAttributes *a=this->GetOutput()->GetPointData(); - a->GetScalars()->SetLookupTable(this->LookupTable); - 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; - - for (int plane = 0; plane < NumPlanes; plane++) - { - for (int line = 0; line < NumLines; line++) + this->LookupTable->SetRange(0,255); + vtkDataSetAttributes *a=this->GetOutput()->GetPointData(); + a->GetScalars()->SetLookupTable(this->LookupTable); + 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; + + 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; - // Update progress related: - if (!(UpdateProgressCount%UpdateProgressTarget)) - { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - UpdateProgressCount++; + // Copy one line at proper destination: + memcpy((void*)Destination, (void*)Source, LineSize); + Source += LineSize; + Destination -= LineSize; + // Update progress related: + if (!(UpdateProgressCount%UpdateProgressTarget)) + { + this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + } + UpdateProgressCount++; } - } - //GetImageData allocate a (void*)malloc, remove it: - free(pSource); + } + //GetImageData allocate a (void*)malloc, remove it: + free(pSource); - return size; + return size; } -//---------------------------------------------------------------------------- -// 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 -// 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."); - return; - } - - // 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"); - - // Test if output has valid extent - // Prevent memory errors - if((this->DataExtent[1]-this->DataExtent[0]>=0) && - (this->DataExtent[3]-this->DataExtent[2]>=0) && - (this->DataExtent[5]-this->DataExtent[4]>=0)) - { - // 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; - // Allocate pixel data space itself. - unsigned char *mem = new unsigned char [stack_size]; - - // Variables for the UpdateProgress. We shall use 50 steps to signify - // the advance of the process: - unsigned long UpdateProgressTarget = (unsigned long) ceil (this->NumLines - * this->TotalNumberOfPlanes - / 50.0); - // The actual advance measure: - unsigned long UpdateProgressCount = 0; - - // Feeling the allocated memory space with each image/volume: - unsigned char * Dest = mem; - 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 (!(UpdateProgressCount%UpdateProgressTarget)) - { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); - } - } - } // Else, file not loadable - } // Loop on files - - // The "size" of the vtkScalars data is expressed in number of points, - // and is not the memory size representing those points: - data->GetPointData()->GetScalars()->SetVoidArray(mem, StackNumPixels, 0); - //don't know why it's here, it's calling one more time ExecuteInformation: - //this->Modified(); - } -} - -//---------------------------------------------------------------------------- -void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) -{ - vtkImageReader::PrintSelf(os,indent); - os << indent << "Filenames : " << endl; - vtkIndent nextIndent = indent.GetNextIndent(); - for (std::list::iterator FileName = FileNameList.begin(); - FileName != FileNameList.end(); - ++FileName) - { - os << nextIndent << FileName->c_str() << endl ; - } -} +//----------------------------------------------------------------------------- diff --git a/vtk/vtkGdcmReader.h b/vtk/vtkGdcmReader.h index 201eb504..84f6526d 100644 --- a/vtk/vtkGdcmReader.h +++ b/vtk/vtkGdcmReader.h @@ -1,5 +1,5 @@ -// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.h,v 1.14 2003/11/18 10:19:41 malaterre Exp $ - +// vtkGdcmReader.h +//----------------------------------------------------------------------------- #ifndef __vtkGdcmReader_h #define __vtkGdcmReader_h @@ -7,62 +7,71 @@ #include #include +//----------------------------------------------------------------------------- class vtkLookupTable; +//----------------------------------------------------------------------------- class VTK_EXPORT vtkGdcmReader : public vtkImageReader { public: - static vtkGdcmReader *New() {return new vtkGdcmReader;}; - vtkTypeMacro(vtkGdcmReader, vtkImageReader); - void PrintSelf(ostream& os, vtkIndent indent); + static vtkGdcmReader *New() {return new vtkGdcmReader;}; + vtkTypeMacro(vtkGdcmReader, vtkImageReader); + void PrintSelf(ostream& os, vtkIndent indent); - void RemoveAllFileName(void); - void AddFileName(const char* name); - void SetFileName(const char *name); - vtkGetObjectMacro(LookupTable,vtkLookupTable); + void RemoveAllFileName(void); + void AddFileName(const char* name); + void SetFileName(const char *name); + vtkGetObjectMacro(LookupTable,vtkLookupTable); protected: - vtkGdcmReader(); - ~vtkGdcmReader(); - virtual void ExecuteInformation(); - void ExecuteData(vtkDataObject *output); - void BuildFileListFromPattern(); - int CheckFileCoherence(); - -private: - void RemoveAllInternalFileName(void); - void AddInternalFileName(const char* name); - vtkLookupTable *LookupTable; + vtkGdcmReader(); + ~vtkGdcmReader(); - //BTX - // Number of columns of the image/volume to be loaded - int NumColumns; - // Number of lines of the image/volume to be loaded - int NumLines; - // Total number of planes (or images) of the stack to be build. - int TotalNumberOfPlanes; - // Number of scalar components of the image to be loaded (1=monochrome 3=rgb) - int NumComponents; - // Type of the image[s]: 8/16/32 bits, signed/unsigned: - std::string ImageType; - // Pixel size (in number of bytes): - size_t PixelSize; - // List of filenames to be read in order to build a stack of images - // or volume. The order in the list shall be the order of the images. - std::list FileNameList; + virtual void ExecuteInformation(); + void ExecuteData(vtkDataObject *output); + void BuildFileListFromPattern(); + int CheckFileCoherence(); - // List of filenames created in ExecuteInformation and used in - // ExecuteData. - // If FileNameList isn't empty, InternalFileNameList is a copy of - // FileNameList - // Otherwise, InternalFileNameList correspond to the list of - // files patterned - std::list InternalFileNameList; +private: + void RemoveAllInternalFileName(void); + void AddInternalFileName(const char* name); - size_t LoadImageInMemory(std::string FileName, unsigned char * Dest, + //BTX + size_t LoadImageInMemory(std::string FileName, unsigned char * Dest, const unsigned long UpdateProgressTarget, unsigned long & UpdateProgressCount); - //ETX + //ETX + +// Variables + vtkLookupTable *LookupTable; + + //BTX + // Number of columns of the image/volume to be loaded + int NumColumns; + // Number of lines of the image/volume to be loaded + int NumLines; + // Total number of planes (or images) of the stack to be build. + int TotalNumberOfPlanes; + // Number of scalar components of the image to be loaded (1=monochrome 3=rgb) + int NumComponents; + // Type of the image[s]: 8/16/32 bits, signed/unsigned: + std::string ImageType; + // Pixel size (in number of bytes): + size_t PixelSize; + // List of filenames to be read in order to build a stack of images + // or volume. The order in the list shall be the order of the images. + std::list FileNameList; + + // List of filenames created in ExecuteInformation and used in + // ExecuteData. + // If FileNameList isn't empty, InternalFileNameList is a copy of + // FileNameList + // Otherwise, InternalFileNameList correspond to the list of + // files patterned + std::list InternalFileNameList; + //ETX }; + +//----------------------------------------------------------------------------- #endif -- 2.45.1