+ if ( CoherentFileList != 0 ) // When a list of names is passed
+ {
+ if (this->CoherentFileList->empty())
+ {
+ vtkErrorMacro(<< "Coherent File List must have at least a valid File*.");
+ return;
+ }
+ }
+ else 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; //not used
+ // Allocate pixel data space itself.
+
+ // 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;
+
+ // Filling the allocated memory space with each image/volume:
+
+ unsigned char *Dest = (unsigned char *)data->GetScalarPointer();
+
+ if ( CoherentFileList == 0 ) // When a list of names is passed
+ {
+ for (std::list<std::string>::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
+
+ }
+ else // when a Coherent File List is passed
+ {
+ for (std::vector<gdcm::File* >::iterator it = CoherentFileList->begin();
+ it != CoherentFileList->end();
+ ++it)
+ {
+
+ //std::cout <<"----------------- " << (*it)->GetFileName() << std::endl;
+
+ Dest += this->LoadImageInMemory(*it, Dest,
+ UpdateProgressTarget,
+ UpdateProgressCount);
+ // Update progress related for bad files:
+ UpdateProgressCount += this->NumLines;
+ if (UpdateProgressTarget > 0)
+ {
+ if (!(UpdateProgressCount%UpdateProgressTarget))
+ {
+ this->UpdateProgress(UpdateProgressCount/(50.0*UpdateProgressTarget));
+ }
+ }
+ } // Loop on files
+
+ }
+ }
+}
+
+/*
+ * 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()
+{
+ this->RemoveAllInternalFileName();
+
+ if ((! this->FileNameList.empty()) && this->FileName )
+ {
+ 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");
+ this->InternalFileNameList=this->FileNameList;
+ return;
+ }
+
+ if (!this->FileName && !this->FilePrefix)
+ {
+ vtkErrorMacro(<< "FileNames are not set. Either use AddFileName() or");
+ vtkErrorMacro(<< "specify a FileName or FilePrefix.");
+ return;
+ }
+
+ if( this->FileName )
+ {
+ // 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
+ {
+ // 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);
+ 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)
+ */
+int vtkGdcmReader::CheckFileCoherence()
+{
+ int ReturnedTotalNumberOfPlanes = 0; // The returned value.
+
+ this->BuildFileListFromPattern();
+ if (this->InternalFileNameList.empty())
+ {
+ vtkErrorMacro(<< "FileNames are not set.");
+ return 0;
+ }
+
+ bool FoundReferenceFile = false;
+ int ReferenceNZ = 0;
+
+ // Loop on the filenames:
+ // - check for their existence and gdcm "parsability"
+ // - get the coherence check done:
+ for (std::list<std::string>::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:
+
+ // fixme : how can the filename be equal to "GDCM_UNREADABLE"
+ // right now ?!?
+
+ 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 read files: "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
+ continue;
+ }
+ fclose(fp);
+
+ // Stage 1.2: check for Gdcm parsability
+
+ //gdcm::File GdcmFile( filename->c_str() );
+
+ // to save some parsing time.
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "Removing this file from read files: "
+ << filename->c_str());
+ *filename = "GDCM_UNREADABLE";
+ continue;
+ }
+
+ // Stage 1.3: further gdcm compatibility on PixelType
+ std::string type = GdcmFile.GetPixelType();
+ if ( (type != "8U") && (type != "8S")
+ && (type != "16U") && (type != "16S")
+ && (type != "32U") && (type != "32S") )
+ {
+ vtkErrorMacro(<< "Bad File Type for file " << filename->c_str() << "\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 = 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 ) )
+ {
+ 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());
+ }
+ else
+ {
+ vtkDebugMacro(<< "File is coherent with previous ones: "
+ << filename->c_str());
+ }
+
+ // Stage 2.3: when the file is 'multiframe', notify the caller.
+ if (NZ > 1)
+ {
+ vtkErrorMacro(<< "This file is a 'Multiframe' one: "
+ << 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 dimensions 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 = GdcmFile.GetPixelSize();
+
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono
+ }
+ //Set image spacing
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
+ }
+ } // 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<std::string>::iterator it = InternalFileNameList.begin();
+ it != InternalFileNameList.end();
+ ++it)
+ {
+ if (*it != "GDCM_UNREADABLE")
+ {
+ NumberCoherentFiles++;
+ }
+ }
+ vtkDebugMacro(<< "Number of coherent files: " << NumberCoherentFiles);
+
+ if (ReturnedTotalNumberOfPlanes == 0)
+ {
+ vtkErrorMacro(<< "No loadable file.");
+ }
+
+ vtkDebugMacro(<< "Total number of planes on the stack: "
+ << ReturnedTotalNumberOfPlanes);
+
+ return ReturnedTotalNumberOfPlanes;
+}
+
+//-----------------------------------------------------------------------------
+// Private
+/*
+ * Remove all file names to the internal list of images to read.
+ */
+void vtkGdcmReader::RemoveAllInternalFileName(void)
+{
+ this->InternalFileNameList.clear();
+}
+
+/*
+ * 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 gdcm::File* f at
+ * the Dest memory address. Returns the size of the data loaded.
+ */
+size_t vtkGdcmReader::LoadImageInMemory(
+ gdcm::File *f,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ // vtkDebugMacro(<< "Copying to memory image [" << f->GetFileName() << "]");
+
+ return DoTheLoadingJob (f,
+ dest,
+ updateProgressTarget,
+ updateProgressCount);
+}
+
+/*
+ * Loads the contents of the image/volume contained by char *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() << "]");
+
+ gdcm::File *f;
+ f = new gdcm::File();
+ f->SetLoadMode( LoadMode );
+ f->SetFileName( fileName.c_str() );
+ f->Load( );
+
+ return DoTheLoadingJob (f,
+ dest,
+ updateProgressTarget,
+ updateProgressCount);
+ delete f;
+}
+
+/*
+ * Service method for LoadImageInMemory
+*/
+size_t vtkGdcmReader::DoTheLoadingJob (gdcm::File *f,
+ unsigned char *dest,
+ const unsigned long updateProgressTarget,
+ unsigned long &updateProgressCount)
+{
+ gdcm::FileHelper *fileH = new gdcm::FileHelper( f );
+ size_t size;
+
+ // If the data structure of vtk for image/volume representation
+ // 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 = fileH->GetFile()->GetXSize();
+ int numLines = fileH->GetFile()->GetYSize();
+ int numPlanes = fileH->GetFile()->GetZSize();
+ int lineSize = NumComponents * numColumns * fileH->GetFile()->GetPixelSize();
+ int planeSize = lineSize * numLines;
+
+ unsigned char *src;
+
+ if( fileH->GetFile()->HasLUT() && AllowLookupTable )
+ {
+ size = fileH->GetImageDataSize();
+ src = (unsigned char*) fileH->GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) fileH->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->SetRange(0,255);
+ vtkDataSetAttributes *a = this->GetOutput()->GetPointData();
+ a->GetScalars()->SetLookupTable(this->LookupTable);
+ free(lut);
+ }
+ else
+ {
+ size = fileH->GetImageDataSize();
+ src = (unsigned char*)fileH->GetImageData();
+ }
+
+ unsigned char *dst = dest + planeSize - lineSize;
+ for (int plane = 0; plane < numPlanes; plane++)
+ {
+ for (int line = 0; line < numLines; line++)
+ {
+ // Copy one line at proper destination:
+ memcpy((void*)dst, (void*)src, lineSize);
+ src += lineSize;
+ dst -= lineSize;
+ // Update progress related:
+ if (!(updateProgressCount%updateProgressTarget))
+ {
+ this->UpdateProgress(updateProgressCount/(50.0*updateProgressTarget));
+ }
+ updateProgressCount++;
+ }
+ dst += 2 * planeSize;
+ }
+ delete fileH;
+ return size;
+}
+
+// -------------------------------------------------------------------------
+
+// We assume the use *does* know all the files whose names
+// are in InternalFileNameList exist, may be open, are gdcm-readable
+// have the same sizes, have the same 'pixel' type, are single frame
+// have the same color convention, ..., anything else ?
+
+int vtkGdcmReader::CheckFileCoherenceLight()
+{
+ std::list<std::string>::iterator filename = InternalFileNameList.begin();
+
+ gdcm::File GdcmFile;
+ GdcmFile.SetLoadMode( LoadMode );
+ GdcmFile.SetFileName(filename->c_str() );
+ GdcmFile.Load( );
+
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence "
+ << "instead of vtkGdcmReader::CheckFileCoherenceLight");
+ return 0;
+ }
+ int NX = GdcmFile.GetXSize();
+ int NY = GdcmFile.GetYSize();
+ // CheckFileCoherenceLight should be called *only* when user knows
+ // he deals with single frames files.
+ // Z size is then the number of files.
+ int NZ = InternalFileNameList.size();
+ std::string type = GdcmFile.GetPixelType();
+ vtkDebugMacro(<< "The first file is taken as reference: "
+ << filename->c_str());
+ vtkDebugMacro(<< "Image dimensions 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;
+ this->ImageType = type;
+ this->PixelSize = GdcmFile.GetPixelSize();
+
+ if( GdcmFile.HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = GdcmFile.GetNumberOfScalarComponents(); //rgb or mono
+ }
+
+ //Set image spacing
+ this->DataSpacing[0] = GdcmFile.GetXSpacing();
+ this->DataSpacing[1] = GdcmFile.GetYSpacing();
+ this->DataSpacing[2] = GdcmFile.GetZSpacing();
+
+ return InternalFileNameList.size();
+}
+
+// We assume the use *does* know all the files whose names
+// are in InternalFileNameList exist, may be open, are gdcm-readable
+// have the same sizes, have the same 'pixel' type, are single frame
+// have the same color convention, ..., anything else ?
+
+int vtkGdcmReader::CheckFileCoherenceAlreadyDone()
+{
+ if ( CoherentFileList->empty() )
+ {
+ vtkErrorMacro(<< "Coherent File List is empty ");
+ return 0;
+ }
+
+ gdcm::File *gdcmFile = (*CoherentFileList)[0];
+
+ int NX = gdcmFile->GetXSize();
+ int NY = gdcmFile->GetYSize();
+ // CheckFileCoherenceLight should be called *only* when user knows
+ // he deals with single frames files.
+ // Z size is then the number of files.
+ // --> TODO : loop on the File* to get NZ of each one !
+ int NZ = CoherentFileList->size();
+ std::string type = gdcmFile->GetPixelType();
+ //vtkDebugMacro(<< "The first file is taken as reference: "
+ // << (*CoherentFileList)[0]->GetFileName() );
+ vtkDebugMacro(<< "Image dimensions 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;
+ this->ImageType = type;
+ this->PixelSize = gdcmFile->GetPixelSize();
+
+ if( gdcmFile->HasLUT() && this->AllowLookupTable )
+ {
+ // I could raise an error is AllowLookupTable is on and HasLUT() off
+ this->NumComponents = gdcmFile->GetNumberOfScalarComponentsRaw();
+ }
+ else
+ {
+ this->NumComponents = gdcmFile->GetNumberOfScalarComponents(); //rgb or mono
+ }
+
+ //Set image spacing
+ this->DataSpacing[0] = gdcmFile->GetXSpacing();
+ this->DataSpacing[1] = gdcmFile->GetYSpacing();
+ this->DataSpacing[2] = gdcmFile->GetZSpacing();
+
+ return NZ;