X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vtk%2FvtkGdcmReader.cxx;h=3a3de007a9d5b7eb1568a6123dd94f45767463f0;hb=0ffb612fa350791ea6de473a5c5a1fd965f80227;hp=619896842d27832903bd5ec5ea83dc4d5c6b8452;hpb=844285f083c7bb09584e1875d5acf00fb08c22a0;p=gdcm.git diff --git a/vtk/vtkGdcmReader.cxx b/vtk/vtkGdcmReader.cxx index 61989684..3a3de007 100644 --- a/vtk/vtkGdcmReader.cxx +++ b/vtk/vtkGdcmReader.cxx @@ -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. @@ -61,7 +66,7 @@ vtkGdcmReader::vtkGdcmReader() } vtkGdcmReader::~vtkGdcmReader() -{ +{ this->RemoveAllFileName(); this->InternalFileNameList.clear(); if(this->LookupTable) @@ -72,15 +77,15 @@ vtkGdcmReader::~vtkGdcmReader() // 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 ; - } + 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 ; + } } //----------------------------------------------------------------------------- @@ -91,6 +96,7 @@ void vtkGdcmReader::PrintSelf(ostream& os, vtkIndent indent) void vtkGdcmReader::RemoveAllFileName(void) { this->FileNameList.clear(); + this->Modified(); } /* @@ -103,8 +109,8 @@ 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 +122,7 @@ 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(); } @@ -127,93 +134,102 @@ 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(); - } + // 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); - //Set number of scalar components: - this->SetNumberOfScalarComponents(this->NumComponents); + this->fileTime=this->MTime; + } - vtkImageReader::ExecuteInformation(); + this->Superclass::ExecuteInformation(); } /* @@ -248,7 +264,6 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) * 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: @@ -259,7 +274,7 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) unsigned long UpdateProgressCount = 0; // Feeling the allocated memory space with each image/volume: - unsigned char * Dest = mem; + unsigned char *Dest = (unsigned char *)data->GetPointData()->GetScalars()->GetVoidPointer(0); for (std::list::iterator FileName = InternalFileNameList.begin(); FileName != InternalFileNameList.end(); ++FileName) @@ -292,12 +307,6 @@ void vtkGdcmReader::ExecuteData(vtkDataObject *output) } } // 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(); } } @@ -311,10 +320,26 @@ 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; } @@ -325,24 +350,24 @@ 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); @@ -413,9 +438,10 @@ int vtkGdcmReader::CheckFileCoherence() continue; } fclose(fp); - + // Stage 1.2: check for Gdcm parsability - gdcmHeaderHelper GdcmHeader(FileName->c_str()); + gdcmHeaderHelper GdcmHeader(FileName->c_str(), false, true); + // true : for enableSequences if (!GdcmHeader.IsReadable()) { vtkErrorMacro("Gdcm cannot parse file " << FileName->c_str()); @@ -579,12 +605,13 @@ size_t vtkGdcmReader::LoadImageInMemory( 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() << "]"); + gdcmFile GdcmFile(FileName.c_str(),false,true); + // true : to enable SeQuences 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 @@ -596,6 +623,7 @@ size_t vtkGdcmReader::LoadImageInMemory( int LineSize = NumComponents * NumColumns * GdcmFile.GetHeader()->GetPixelSize(); unsigned char * Source; + if( GdcmFile.GetHeader()->HasLUT() ) { size = GdcmFile.GetImageDataSizeRaw(); @@ -623,7 +651,8 @@ size_t vtkGdcmReader::LoadImageInMemory( { size = GdcmFile.GetImageDataSize(); Source = (unsigned char*)GdcmFile.GetImageData(); - } + } + unsigned char * pSource = Source; //pointer for later deletion unsigned char * Destination = Dest + size - LineSize; @@ -643,9 +672,18 @@ size_t vtkGdcmReader::LoadImageInMemory( 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); - return size; }