+ 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( NO_SEQ | NO_SHADOW );
+ 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 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::FileHelper file( fileName.c_str() );
+ 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 = file.GetFile()->GetXSize();
+ int numLines = file.GetFile()->GetYSize();
+ int numPlanes = file.GetFile()->GetZSize();
+ int lineSize = NumComponents * numColumns * file.GetFile()->GetPixelSize();
+ int planeSize = lineSize * numLines;
+
+ unsigned char *src;
+
+ if( file.GetFile()->HasLUT() && AllowLookupTable )
+ {
+ size = file.GetImageDataSize();
+ src = (unsigned char*) file.GetImageDataRaw();
+ unsigned char *lut = (unsigned char*) file.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 = file.GetImageDataSize();
+ src = (unsigned char*)file.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;
+ }
+ 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( NO_SEQ | NO_SHADOW );
+ GdcmFile.Load(filename->c_str() );
+ if (!GdcmFile.IsReadable())
+ {
+ vtkErrorMacro(<< "Gdcm cannot parse file " << filename->c_str());
+ vtkErrorMacro(<< "you should try vtkGdcmReader::CheckFileCoherence "
+ << "instead of try 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();