X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=dc8662708c825f645b121456b40ceed821f1ccc1;hb=05a31743c6545f03a9841531f2d54b7b1552e681;hp=139623d32626e1a09105180b35f8011271df8928;hpb=a70d6842239569070ae649d20e2db2beb7685bc2;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 139623d3..dc866270 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -1,7 +1,7 @@ // vtkGdcmReader.cxx //----------------------------------------------------------------------------- // ////////////////////////////////////////////////////////////// -// WARNING TODO CLENAME +// WARNING TODO CLEANME // Actual limitations of this code: // // /////// Redundant and unnecessary header parsing @@ -18,6 +18,11 @@ // 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 // the data-image. @@ -53,11 +58,15 @@ #include #include +vtkCxxRevisionMacro(vtkGdcmReader, "$Revision: 1.51 $"); +vtkStandardNewMacro(vtkGdcmReader); + //----------------------------------------------------------------------------- // Constructor / Destructor vtkGdcmReader::vtkGdcmReader() { this->LookupTable = NULL; + this->AllowLookupTable = 0; } vtkGdcmReader::~vtkGdcmReader() @@ -72,14 +81,14 @@ 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 +100,7 @@ void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) void vtkGdcmReader::RemoveAllFileName(void) { this->FileNameList.clear(); + this->Modified(); } /* @@ -103,8 +113,8 @@ 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 +126,7 @@ 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 +138,100 @@ 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]; } - } - // 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; + // 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(); - } - 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(); } @@ -248,9 +264,9 @@ 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 @@ -263,17 +279,17 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) // 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) + 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); } @@ -308,10 +324,26 @@ 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; } @@ -322,24 +354,24 @@ void vtkGdcmReader::BuildFileListFromPattern() 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("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); 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); @@ -382,9 +414,9 @@ 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 @@ -394,45 +426,45 @@ 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("Unable to open file " << filename->c_str()); vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } fclose(fp); - + // Stage 1.2: check for Gdcm parsability - gdcmHeaderHelper GdcmHeader(FileName->c_str()); + gdcm::Header GdcmHeader(filename->c_str() ); if (!GdcmHeader.IsReadable()) { - vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); + vtkErrorMacro("Gdcm cannot parse file " << filename->c_str()); vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; + << 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") ) + && (type != "16U") && (type != "16S") + && (type != "32U") && (type != "32S") ) { - vtkErrorMacro("Bad File Type for file" << FileName->c_str()); + 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"; + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } @@ -444,14 +476,14 @@ int vtkGdcmReader::CheckFileCoherence() { // 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()); + << filename->c_str()); vtkErrorMacro("Removing this file from readed files " - << FileName->c_str()); - *FileName = "GDCM_UNREADABLE"; + << filename->c_str()); + *filename = "GDCM_UNREADABLE"; continue; } @@ -459,12 +491,12 @@ int vtkGdcmReader::CheckFileCoherence() if ( NZ != ReferenceNZ ) { vtkErrorMacro("File is not coherent in Z with previous ones" - << FileName->c_str()); + << filename->c_str()); } else { vtkDebugMacro("File is coherent with previous ones" - << FileName->c_str()); + << filename->c_str()); } // Stage 2.3: when the file contains a volume (as opposed to an image), @@ -472,7 +504,7 @@ int vtkGdcmReader::CheckFileCoherence() if (NZ > 1) { vtkErrorMacro("This file contains multiple planes (images)" - << FileName->c_str()); + << filename->c_str()); } // Eventually, this file can be added on the stack. Update the @@ -488,7 +520,7 @@ int vtkGdcmReader::CheckFileCoherence() // as the reference. FoundReferenceFile = true; vtkDebugMacro("This file taken as coherence reference:" - << FileName->c_str()); + << 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); @@ -500,8 +532,9 @@ int vtkGdcmReader::CheckFileCoherence() this->ImageType = type; this->PixelSize = GdcmHeader.GetPixelSize(); - if( GdcmHeader.HasLUT() ) + if( GdcmHeader.HasLUT() && this->AllowLookupTable ) { + // I could raise an error is AllowLookupTable is on and HasLUT() off this->NumComponents = GdcmHeader.GetNumberOfScalarComponentsRaw(); } else @@ -520,17 +553,19 @@ int vtkGdcmReader::CheckFileCoherence() this->DataOrigin[2] = GdcmHeader.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); @@ -571,78 +606,91 @@ 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::File 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.GetHeader()->GetXSize(); + int numLines = file.GetHeader()->GetYSize(); + int numPlanes = file.GetHeader()->GetZSize(); + int lineSize = NumComponents * numColumns * file.GetHeader()->GetPixelSize(); - unsigned char * Source; - if( GdcmFile.GetHeader()->HasLUT() ) + unsigned char * source; + + if( file.GetHeader()->HasLUT() && AllowLookupTable ) { - size = GdcmFile.GetImageDataSizeRaw(); - Source = (unsigned char*) GdcmFile.GetImageDataRaw(); - unsigned char *Lut = GdcmFile.GetHeader()->GetLUTRGBA(); + size = file.GetImageDataSizeRaw(); + source = (unsigned char*) file.GetImageDataRaw(); + unsigned char *lut = file.GetHeader()->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(); + source = (unsigned char*)file.GetImageData(); + } + + unsigned char * pSource = source; //pointer for later deletion + unsigned char * destination = dest + size - lineSize; - for (int plane = 0; plane < NumPlanes; plane++) + 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*)destination, (void*)source, lineSize); + source += lineSize; + destination -= lineSize; // Update progress related: - if (!(UpdateProgressCount%UpdateProgressTarget)) + if (!(updateProgressCount%updateProgressTarget)) { - this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget)); + this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget)); } - UpdateProgressCount++; + updateProgressCount++; } } + +// 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: - free(pSource); - + delete[] pSource; return size; }