diff --git a/Core/Code/IO/mitkDicomSeriesReader.cpp b/Core/Code/IO/mitkDicomSeriesReader.cpp index b38fb6c561..c69c8626a2 100644 --- a/Core/Code/IO/mitkDicomSeriesReader.cpp +++ b/Core/Code/IO/mitkDicomSeriesReader.cpp @@ -1,882 +1,926 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // uncomment for learning more about the internal sorting mechanisms //#define MBILOG_ENABLE_DEBUG #include #include #include #include #include #include #include #include "mitkProperties.h" namespace mitk { typedef itk::GDCMSeriesFileNames DcmFileNamesGeneratorType; DataNode::Pointer DicomSeriesReader::LoadDicomSeries(const StringContainer &filenames, bool sort, bool check_4d, UpdateCallBackMethod callback) { DataNode::Pointer node = DataNode::New(); if (DicomSeriesReader::LoadDicomSeries(filenames, *node, sort, check_4d, callback)) { if( filenames.empty() ) { return NULL; } return node; } else { return NULL; } } bool DicomSeriesReader::LoadDicomSeries(const StringContainer &filenames, DataNode &node, bool sort, bool check_4d, UpdateCallBackMethod callback) { if( filenames.empty() ) { MITK_WARN << "Calling LoadDicomSeries with empty filename string container. Probably invalid application logic."; node.SetData(NULL); return true; // this is not actually an error but the result is very simple } DcmIoType::Pointer io = DcmIoType::New(); try { if (io->CanReadFile(filenames.front().c_str())) { io->SetFileName(filenames.front().c_str()); io->ReadImageInformation(); switch (io->GetComponentType()) { case DcmIoType::UCHAR: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::CHAR: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::USHORT: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::SHORT: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::UINT: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::INT: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::ULONG: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::LONG: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::FLOAT: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; case DcmIoType::DOUBLE: DicomSeriesReader::LoadDicom(filenames, node, sort, check_4d, callback); return true; default: MITK_ERROR << "Found unsupported DICOM pixel type: (enum value) " << io->GetComponentType(); } } } catch(itk::MemoryAllocationError& e) { MITK_ERROR << "Out of memory. Cannot load DICOM series: " << e.what(); } catch(std::exception& e) { MITK_ERROR << "Error encountered when loading DICOM series:" << e.what(); } catch(...) { MITK_ERROR << "Unspecified error encountered when loading DICOM series."; } return false; } bool DicomSeriesReader::IsDicom(const std::string &filename) { DcmIoType::Pointer io = DcmIoType::New(); return io->CanReadFile(filename.c_str()); } bool DicomSeriesReader::IsPhilips3DDicom(const std::string &filename) { DcmIoType::Pointer io = DcmIoType::New(); if (io->CanReadFile(filename.c_str())) { //Look at header Tag 3001,0010 if it is "Philips3D" gdcm::Reader reader; reader.SetFileName(filename.c_str()); reader.Read(); gdcm::DataSet &data_set = reader.GetFile().GetDataSet(); gdcm::StringFilter sf; sf.SetFile(reader.GetFile()); if (data_set.FindDataElement(gdcm::Tag(0x3001, 0x0010)) && (sf.ToString(gdcm::Tag(0x3001, 0x0010)) == "Philips3D ")) { return true; } } return false; } bool DicomSeriesReader::ReadPhilips3DDicom(const std::string &filename, mitk::Image::Pointer output_image) { // Now get PhilipsSpecific Tags gdcm::PixmapReader reader; reader.SetFileName(filename.c_str()); reader.Read(); gdcm::DataSet &data_set = reader.GetFile().GetDataSet(); gdcm::StringFilter sf; sf.SetFile(reader.GetFile()); gdcm::Attribute<0x0028,0x0011> dimTagX; // coloumns || sagittal gdcm::Attribute<0x3001,0x1001, gdcm::VR::UL, gdcm::VM::VM1> dimTagZ; //I have no idea what is VM1. // (Philips specific) // transversal gdcm::Attribute<0x0028,0x0010> dimTagY; // rows || coronal gdcm::Attribute<0x0028,0x0008> dimTagT; // how many frames gdcm::Attribute<0x0018,0x602c> spaceTagX; // Spacing in X , unit is "physicalTagx" (usually centimeter) gdcm::Attribute<0x0018,0x602e> spaceTagY; gdcm::Attribute<0x3001,0x1003, gdcm::VR::FD, gdcm::VM::VM1> spaceTagZ; // (Philips specific) gdcm::Attribute<0x0018,0x6024> physicalTagX; // if 3, then spacing params are centimeter gdcm::Attribute<0x0018,0x6026> physicalTagY; gdcm::Attribute<0x3001,0x1002, gdcm::VR::US, gdcm::VM::VM1> physicalTagZ; // (Philips specific) dimTagX.Set(data_set); dimTagY.Set(data_set); dimTagZ.Set(data_set); dimTagT.Set(data_set); spaceTagX.Set(data_set); spaceTagY.Set(data_set); spaceTagZ.Set(data_set); physicalTagX.Set(data_set); physicalTagY.Set(data_set); physicalTagZ.Set(data_set); unsigned int dimX = dimTagX.GetValue(), dimY = dimTagY.GetValue(), dimZ = dimTagZ.GetValue(), dimT = dimTagT.GetValue(), physicalX = physicalTagX.GetValue(), physicalY = physicalTagY.GetValue(), physicalZ = physicalTagZ.GetValue(); float spaceX = spaceTagX.GetValue(), spaceY = spaceTagY.GetValue(), spaceZ = spaceTagZ.GetValue(); if (physicalX == 3) // spacing parameter in cm, have to convert it to mm. spaceX = spaceX * 10; if (physicalY == 3) // spacing parameter in cm, have to convert it to mm. spaceY = spaceY * 10; if (physicalZ == 3) // spacing parameter in cm, have to convert it to mm. spaceZ = spaceZ * 10; // Ok, got all necessary Tags! // Now read Pixeldata (7fe0,0010) X x Y x Z x T Elements const gdcm::Pixmap &pixels = reader.GetPixmap(); gdcm::RAWCodec codec; codec.SetPhotometricInterpretation(gdcm::PhotometricInterpretation::MONOCHROME2); codec.SetPixelFormat(pixels.GetPixelFormat()); codec.SetPlanarConfiguration(0); gdcm::DataElement out; codec.Decode(data_set.GetDataElement(gdcm::Tag(0x7fe0, 0x0010)), out); const gdcm::ByteValue *bv = out.GetByteValue(); const char *new_pixels = bv->GetPointer(); // Create MITK Image + Geometry typedef itk::Image ImageType; //Pixeltype might be different sometimes? Maybe read it out from header ImageType::RegionType myRegion; ImageType::SizeType mySize; ImageType::IndexType myIndex; ImageType::SpacingType mySpacing; ImageType::Pointer imageItk = ImageType::New(); mySpacing[0] = spaceX; mySpacing[1] = spaceY; mySpacing[2] = spaceZ; mySpacing[3] = 1; myIndex[0] = 0; myIndex[1] = 0; myIndex[2] = 0; myIndex[3] = 0; mySize[0] = dimX; mySize[1] = dimY; mySize[2] = dimZ; mySize[3] = dimT; myRegion.SetSize( mySize); myRegion.SetIndex( myIndex ); imageItk->SetSpacing(mySpacing); imageItk->SetRegions( myRegion); imageItk->Allocate(); imageItk->FillBuffer(0); itk::ImageRegionIterator iterator(imageItk, imageItk->GetLargestPossibleRegion()); iterator.GoToBegin(); unsigned long pixCount = 0; unsigned long planeSize = dimX*dimY; unsigned long planeCount = 0; unsigned long timeCount = 0; unsigned long numberOfSlices = dimZ; while (!iterator.IsAtEnd()) { unsigned long adressedPixel = pixCount + (numberOfSlices-1-planeCount)*planeSize // add offset to adress the first pixel of current plane + timeCount*numberOfSlices*planeSize; // add time offset iterator.Set( new_pixels[ adressedPixel ] ); pixCount++; ++iterator; if (pixCount == planeSize) { pixCount = 0; planeCount++; } if (planeCount == numberOfSlices) { planeCount = 0; timeCount++; } if (timeCount == dimT) { break; } } mitk::CastToMitkImage(imageItk, output_image); return true; // actually never returns false yet.. but exception possible } DicomSeriesReader::TwoStringContainers DicomSeriesReader::AnalyzeFileForITKImageSeriesReaderSpacingAssumption( const StringContainer& files, const gdcm::Scanner::MappingType& tagValueMappings_) { // result.first = files that fit ITK's assumption // result.second = files that do not fit, should be run through AnalyzeFileForITKImageSeriesReaderSpacingAssumption() again TwoStringContainers result; // we const_cast here, because I could not use a map.at(), which would make the code much more readable gdcm::Scanner::MappingType& tagValueMappings = const_cast(tagValueMappings_); const gdcm::Tag tagImagePositionPatient(0x0020,0x0032); // Image Position (Patient) const gdcm::Tag tagImageOrientation(0x0020, 0x0037); // Image Orientation Vector3D fromFirstToSecondOrigin; fromFirstToSecondOrigin.Fill(0.0); bool fromFirstToSecondOriginInitialized(false); Point3D thisOrigin; Point3D lastOrigin; Point3D lastDifferentOrigin; bool lastOriginInitialized(false); + MITK_DEBUG << "--------------------------------------------------------------------------------"; MITK_DEBUG << "Analyzing files for z-spacing assumption of ITK's ImageSeriesReader "; unsigned int fileIndex(0); for (StringContainer::const_iterator fileIter = files.begin(); fileIter != files.end(); ++fileIter, ++fileIndex) { + bool fileFitsIntoPattern(false); + // Read tag value into point3D. PLEASE replace this by appropriate GDCM code if you figure out how to do that std::string thisOriginString = tagValueMappings[fileIter->c_str()][tagImagePositionPatient]; std::istringstream originReader(thisOriginString); std::string coordinate; unsigned int dim(0); while( std::getline( originReader, coordinate, '\\' ) ) thisOrigin[dim++] = atof(coordinate.c_str()); if (dim != 3) { MITK_ERROR << "Reader implementation made wrong assumption on tag (0020,0032). Found " << dim << "instead of 3 values."; } MITK_DEBUG << " " << fileIndex << " " << *fileIter << " at " << thisOriginString << "(" << thisOrigin[0] << "," << thisOrigin[1] << "," << thisOrigin[2] << ")"; if ( lastOriginInitialized && (thisOrigin == lastOrigin) ) { - MITK_DEBUG << "Sort away " << *fileIter << " for separate time step"; // we already have one occupying this position + MITK_DEBUG << " ==> Sort away " << *fileIter << " for separate time step"; // we already have one occupying this position result.second.push_back( *fileIter ); + fileFitsIntoPattern = false; } else { if (!fromFirstToSecondOriginInitialized && lastOriginInitialized) // calculate vector as soon as possible when we get a new position { fromFirstToSecondOrigin = thisOrigin - lastDifferentOrigin; fromFirstToSecondOriginInitialized = true; // Now make sure this direction is along the normal vector of the first slice // If this is NOT the case, then we have a data set with a TILTED GANTRY geometry, // which cannot be loaded into a single mitk::Image at the moment // Again ugly code to read tag Image Orientation into two vEctors Vector3D right; right.Fill(0.0); Vector3D up; right.Fill(0.0); // might be down as well, but it is just a name at this point std::string thisOrientationString = tagValueMappings[fileIter->c_str()][tagImageOrientation]; std::istringstream orientationReader(thisOrientationString); std::string coordinate; unsigned int dim(0); while( std::getline( orientationReader, coordinate, '\\' ) ) if (dim<3) right[dim++] = atof(coordinate.c_str()); else up[dim++ - 3] = atof(coordinate.c_str()); if (dim != 6) { MITK_ERROR << "Reader implementation made wrong assumption on tag (0020,0037). Found " << dim << "instead of 6 values."; } - MITK_DEBUG << "Tilt check: right vector (" << right[0] << "," << right[1] << "," << right[2] << "), " - "up vector (" << up[0] << "," << up[1] << "," << up[2] << ")"; /* Determine if line (thisOrigin + l * normal) contains lastDifferentOrigin. Done by calculating the distance of lastDifferentOrigin from line (thisOrigin + l *normal) E.g. http://mathworld.wolfram.com/Point-LineDistance3-Dimensional.html squared distance = | (pointAlongNormal - thisOrign) x (thisOrigin - lastDifferentOrigin) | ^ 2 / |pointAlongNormal - thisOrigin| ^ 2 ( x meaning the cross product ) + + MITK_DEBUG << "Tilt check: right vector (" << right[0] << "," << right[1] << "," << right[2] << "), " + "up vector (" << up[0] << "," << up[1] << "," << up[2] << ")"; */ Vector3D normal = itk::CrossProduct(right, up); Point3D pointAlongNormal = thisOrigin + normal; double numerator = itk::CrossProduct( pointAlongNormal - thisOrigin , thisOrigin - lastDifferentOrigin ).GetSquaredNorm(); double denominator = (pointAlongNormal - thisOrigin).GetSquaredNorm(); double distance = sqrt(numerator / denominator); if (distance > 0.001) // mitk::eps is too small; 1/1000 of a mm should be enough to detect tilt { - MITK_WARN << "Series seems to contain a tilted geometry. Will load series as many single slices."; - MITK_WARN << "Distance of expected slice origin from actual slice origin: " << distance; + MITK_DEBUG << " Series might contain a tilted geometry"; + MITK_DEBUG << " Distance of expected slice origin from actual slice origin: " << distance; + MITK_DEBUG << " ==> Sort away " << *fileIter << " for later analysis"; + + /* Pessimistic approach: split block right here result.first.assign( files.begin(), fileIter ); result.second.insert( result.second.end(), fileIter, files.end() ); return result; // stop processing with first split + */ + + /* optimistic approach: save file for later, check all further files */ + + result.second.push_back(*fileIter); + fileFitsIntoPattern = false; + } + else + { + result.first.push_back(*fileIter); // this file is good for current block + fileFitsIntoPattern = true; } } else if (fromFirstToSecondOriginInitialized) // we already know the offset between slices { Point3D assumedOrigin = lastDifferentOrigin + fromFirstToSecondOrigin; Vector3D originError = assumedOrigin - thisOrigin; double norm = originError.GetNorm(); double toleratedError(0.005); // max. 1/10mm error when measurement crosses 20 slices in z direction if (norm > toleratedError) { - MITK_WARN << "File " << *fileIter << " breaks the inter-slice distance pattern (diff = " + MITK_DEBUG << " File does not fit into the inter-slice distance pattern (diff = " << norm << ", allowed " << toleratedError << ")."; - MITK_WARN << "Expected position (" << assumedOrigin[0] << "," + MITK_DEBUG << " Expected position (" << assumedOrigin[0] << "," << assumedOrigin[1] << "," << assumedOrigin[2] << "), got position (" << thisOrigin[0] << "," << thisOrigin[1] << "," << thisOrigin[2] << ")"; + MITK_DEBUG << " ==> Sort away " << *fileIter << " for later analysis"; // At this point we know we deviated from the expectation of ITK's ImageSeriesReader // We split the input file list at this point, i.e. all files up to this one (excluding it) // are returned as group 1, the remaining files (including the faulty one) are group 2 + /* + Pessimistic approach: split right here: + result.first.assign( files.begin(), fileIter ); result.second.insert( result.second.end(), fileIter, files.end() ); return result; // stop processing with first split + */ + + /* Optimistic approach: check if any of the remaining slices fits in */ + result.second.push_back( *fileIter ); // sort away for further analysis + fileFitsIntoPattern = false; + } + else + { + result.first.push_back(*fileIter); // this file is good for current block + fileFitsIntoPattern = true; } } - - result.first.push_back(*fileIter); + else // this should be the very first slice + { + result.first.push_back(*fileIter); // this file is good for current block + fileFitsIntoPattern = true; + } } // recored current origin for reference in later iterations - if ( !lastOriginInitialized || thisOrigin != lastOrigin ) + if ( !lastOriginInitialized || fileFitsIntoPattern && (thisOrigin != lastOrigin) ) { lastDifferentOrigin = thisOrigin; } lastOrigin = thisOrigin; lastOriginInitialized = true; } return result; } DicomSeriesReader::UidFileNamesMap DicomSeriesReader::GetSeries(const StringContainer& files, const StringContainer &restrictions) { return GetSeries(files, true, restrictions); } DicomSeriesReader::UidFileNamesMap DicomSeriesReader::GetSeries(const StringContainer& files, bool sortTo3DPlust, const StringContainer &restrictions) { /** assumption about this method: returns a map of uid-like-key --> list(filename) each entry should contain filenames that have images of same - series instance uid (automatically done by GDCMSeriesFileNames - 0020,0037 image orientation (patient) - 0028,0030 pixel spacing (x,y) - 0018,0050 slice thickness */ UidFileNamesMap groupsOfSimilarImages; // preliminary result, refined into the final result mapOf3DPlusTBlocks // use GDCM directly, itk::GDCMSeriesFileNames does not work with GDCM 2 // PART I: scan files for sorting relevant DICOM tags, // separate images that differ in any of those // attributes (they cannot possibly form a 3D block) // scan for relevant tags in dicom files gdcm::Scanner scanner; const gdcm::Tag tagSeriesInstanceUID(0x0020,0x000e); // Series Instance UID scanner.AddTag( tagSeriesInstanceUID ); const gdcm::Tag tagImageOrientation(0x0020, 0x0037); // image orientation scanner.AddTag( tagImageOrientation ); const gdcm::Tag tagPixelSpacing(0x0028, 0x0030); // pixel spacing scanner.AddTag( tagPixelSpacing ); const gdcm::Tag tagSliceThickness(0x0018, 0x0050); // slice thickness scanner.AddTag( tagSliceThickness ); const gdcm::Tag tagNumberOfRows(0x0028, 0x0010); // number rows scanner.AddTag( tagNumberOfRows ); const gdcm::Tag tagNumberOfColumns(0x0028, 0x0011); // number cols scanner.AddTag( tagNumberOfColumns ); // additional tags read in this scan to allow later analysis // THESE tag are not used for initial separating of files const gdcm::Tag tagImagePositionPatient(0x0020,0x0032); // Image Position (Patient) scanner.AddTag( tagImagePositionPatient ); // TODO add further restrictions from arguments // let GDCM scan files if ( !scanner.Scan( files ) ) { MITK_ERROR << "gdcm::Scanner failed when scanning " << files.size() << " input files."; return groupsOfSimilarImages; } // assign files IDs that will separate them for loading into image blocks for (gdcm::Scanner::ConstIterator fileIter = scanner.Begin(); fileIter != scanner.End(); ++fileIter) { - MITK_DEBUG << "Read file " << fileIter->first << std::endl; + //MITK_DEBUG << "Scan file " << fileIter->first << std::endl; if ( std::string(fileIter->first).empty() ) continue; // TODO understand why Scanner has empty string entries // we const_cast here, because I could not use a map.at() function in CreateMoreUniqueSeriesIdentifier. // doing the same thing with find would make the code less readable. Since we forget the Scanner results // anyway after this function, we can simply tolerate empty map entries introduced by bad operator[] access std::string moreUniqueSeriesId = CreateMoreUniqueSeriesIdentifier( const_cast(fileIter->second) ); groupsOfSimilarImages [ moreUniqueSeriesId ].push_back( fileIter->first ); } // PART III: sort slices spatially for ( UidFileNamesMap::const_iterator groupIter = groupsOfSimilarImages.begin(); groupIter != groupsOfSimilarImages.end(); ++groupIter ) { groupsOfSimilarImages[ groupIter->first ] = SortSeriesSlices( groupIter->second ); // sort each slice group spatially } // PART II: analyze pre-sorted images for valid blocks (i.e. blocks of equal z-spacing), // separate into multiple blocks if necessary. // // Analysis performs the following steps: // * imitate itk::ImageSeriesReader: use the distance between the first two images as z-spacing // * check what images actually fulfill ITK's z-spacing assumption // * separate all images that fail the test into new blocks, re-iterate analysis for these blocks UidFileNamesMap mapOf3DPlusTBlocks; // final result of this function for ( UidFileNamesMap::const_iterator groupIter = groupsOfSimilarImages.begin(); groupIter != groupsOfSimilarImages.end(); ++groupIter ) { UidFileNamesMap mapOf3DBlocks; // intermediate result for only this group(!) StringContainer filesStillToAnalyze = groupIter->second; std::string groupUID = groupIter->first; unsigned int subgroup(0); MITK_DEBUG << "Analyze group " << groupUID; while (!filesStillToAnalyze.empty()) // repeat until all files are grouped somehow { TwoStringContainers analysisResult = AnalyzeFileForITKImageSeriesReaderSpacingAssumption( filesStillToAnalyze, scanner.GetMappings() ); // enhance the UID for additional groups std::stringstream newGroupUID; newGroupUID << groupUID << '.' << subgroup; mapOf3DBlocks[ newGroupUID.str() ] = analysisResult.first; - MITK_DEBUG << "Sorted 3D group " << newGroupUID.str() << " with " << mapOf3DBlocks[ newGroupUID.str() ].size() << " files"; + MITK_DEBUG << "Result: sorted 3D group " << newGroupUID.str() << " with " << mapOf3DBlocks[ newGroupUID.str() ].size() << " files"; ++subgroup; filesStillToAnalyze = analysisResult.second; // remember what needs further analysis } // end of grouping, now post-process groups // PART IV: attempt to group blocks to 3D+t blocks if requested // inspect entries of mapOf3DBlocks // - if number of files is identical to previous entry, collect for 3D+t block // - as soon as number of files changes from previous entry, record collected blocks as 3D+t block, start a new one, continue // decide whether or not to group 3D blocks into 3D+t blocks where possible if ( !sortTo3DPlust ) { // copy 3D blocks to output // TODO avoid collisions (or prove impossibility) mapOf3DPlusTBlocks.insert( mapOf3DBlocks.begin(), mapOf3DBlocks.end() ); } else { // sort 3D+t (as described in "PART IV") + + MITK_DEBUG << "================================================================================"; + MITK_DEBUG << "3D+t analysis:"; unsigned int numberOfFilesInPreviousBlock(0); std::string previousBlockKey; for ( UidFileNamesMap::const_iterator block3DIter = mapOf3DBlocks.begin(); block3DIter != mapOf3DBlocks.end(); ++block3DIter ) { unsigned int numberOfFilesInThisBlock = block3DIter->second.size(); std::string thisBlockKey = block3DIter->first; if (numberOfFilesInPreviousBlock == 0) { numberOfFilesInPreviousBlock = numberOfFilesInThisBlock; mapOf3DPlusTBlocks[thisBlockKey].insert( mapOf3DPlusTBlocks[thisBlockKey].end(), block3DIter->second.begin(), block3DIter->second.end() ); - MITK_DEBUG << "3D+t group " << thisBlockKey << " started"; + MITK_DEBUG << " 3D+t group " << thisBlockKey << " started"; previousBlockKey = thisBlockKey; } else { // check whether this and the previous block share a comon origin // TODO should be safe, but a little try/catch or other error handling wouldn't hurt std::string thisOriginString = scanner.GetValue( mapOf3DBlocks[thisBlockKey].front().c_str(), tagImagePositionPatient ); std::string previousOriginString = scanner.GetValue( mapOf3DBlocks[previousBlockKey].front().c_str(), tagImagePositionPatient ); // also compare last origin, because this might differ if z-spacing is different std::string thisDestinationString = scanner.GetValue( mapOf3DBlocks[thisBlockKey].back().c_str(), tagImagePositionPatient ); std::string previousDestinationString = scanner.GetValue( mapOf3DBlocks[previousBlockKey].back().c_str(), tagImagePositionPatient ); bool identicalOrigins( (thisOriginString == previousOriginString) && (thisDestinationString == previousDestinationString) ); if (identicalOrigins && (numberOfFilesInPreviousBlock == numberOfFilesInThisBlock)) { // group with previous block mapOf3DPlusTBlocks[previousBlockKey].insert( mapOf3DPlusTBlocks[previousBlockKey].end(), block3DIter->second.begin(), block3DIter->second.end() ); - MITK_DEBUG << "3D+t group " << previousBlockKey << " enhanced with another timestep"; + MITK_DEBUG << " --> group enhanced with another timestep"; } else { // start a new block mapOf3DPlusTBlocks[thisBlockKey].insert( mapOf3DPlusTBlocks[thisBlockKey].end(), block3DIter->second.begin(), block3DIter->second.end() ); - MITK_DEBUG << "3D+t group " << thisBlockKey << " started"; + MITK_DEBUG << " ==> group closed with " << mapOf3DPlusTBlocks[previousBlockKey].size() / numberOfFilesInPreviousBlock << " time steps"; previousBlockKey = thisBlockKey; + MITK_DEBUG << " 3D+t group " << thisBlockKey << " started"; } } numberOfFilesInPreviousBlock = numberOfFilesInThisBlock; } } } - for ( UidFileNamesMap::const_iterator groupIter = groupsOfSimilarImages.begin(); groupIter != groupsOfSimilarImages.end(); ++groupIter ) + MITK_DEBUG << "================================================================================"; + MITK_DEBUG << "Summary: "; + for ( UidFileNamesMap::const_iterator groupIter = mapOf3DPlusTBlocks.begin(); groupIter != mapOf3DPlusTBlocks.end(); ++groupIter ) { - MITK_DEBUG << "Slice group " << groupIter->first << " with " << groupIter->second.size() << " files"; + MITK_DEBUG << " Image volume " << groupIter->first << " with " << groupIter->second.size() << " files"; } + MITK_DEBUG << "Done. "; + MITK_DEBUG << "================================================================================"; return mapOf3DPlusTBlocks; } DicomSeriesReader::UidFileNamesMap DicomSeriesReader::GetSeries(const std::string &dir, const StringContainer &restrictions) { gdcm::Directory directoryLister; directoryLister.Load( dir.c_str(), false ); // non-recursive return GetSeries(directoryLister.GetFilenames(), restrictions); } std::string DicomSeriesReader::CreateSeriesIdentifierPart( gdcm::Scanner::TagToValue& tagValueMap, const gdcm::Tag& tag ) { std::string result; try { result = IDifyTagValue( tagValueMap[ tag ] ? tagValueMap[ tag ] : std::string("") ); } catch (std::exception& e) { MITK_WARN << "Could not access tag " << tag << ": " << e.what(); } return result; } std::string DicomSeriesReader::CreateMoreUniqueSeriesIdentifier( gdcm::Scanner::TagToValue& tagValueMap ) { const gdcm::Tag tagSeriesInstanceUID(0x0020,0x000e); // Series Instance UID const gdcm::Tag tagImageOrientation(0x0020, 0x0037); // image orientation const gdcm::Tag tagPixelSpacing(0x0028, 0x0030); // pixel spacing const gdcm::Tag tagSliceThickness(0x0018, 0x0050); // slice thickness const gdcm::Tag tagNumberOfRows(0x0028, 0x0010); // number rows const gdcm::Tag tagNumberOfColumns(0x0028, 0x0011); // number cols std::string constructedID; try { constructedID = tagValueMap[ tagSeriesInstanceUID ]; } catch (std::exception& e) { MITK_ERROR << "CreateMoreUniqueSeriesIdentifier() could not access series instance UID. Something is seriously wrong with this image."; MITK_ERROR << "Error from exception: " << e.what(); } constructedID += CreateSeriesIdentifierPart( tagValueMap, tagNumberOfRows ); constructedID += CreateSeriesIdentifierPart( tagValueMap, tagNumberOfColumns ); constructedID += CreateSeriesIdentifierPart( tagValueMap, tagPixelSpacing ); constructedID += CreateSeriesIdentifierPart( tagValueMap, tagSliceThickness ); constructedID += CreateSeriesIdentifierPart( tagValueMap, tagImageOrientation ); constructedID.resize( constructedID.length() - 1 ); // cut of trailing '.' return constructedID; } std::string DicomSeriesReader::IDifyTagValue(const std::string& value) { std::string IDifiedValue( value ); if (value.empty()) throw std::logic_error("IDifyTagValue() illegaly called with empty tag value"); // Eliminate non-alnum characters, including whitespace... // that may have been introduced by concats. for(std::size_t i=0; i= 'a' && IDifiedValue[i] <= 'z') || (IDifiedValue[i] >= '0' && IDifiedValue[i] <= '9') || (IDifiedValue[i] >= 'A' && IDifiedValue[i] <= 'Z'))) { IDifiedValue.erase(i, 1); } } IDifiedValue += "."; return IDifiedValue; } DicomSeriesReader::StringContainer DicomSeriesReader::GetSeries(const std::string &dir, const std::string &series_uid, const StringContainer &restrictions) { UidFileNamesMap allSeries = GetSeries(dir, restrictions); StringContainer resultingFileList; for ( UidFileNamesMap::const_iterator idIter = allSeries.begin(); idIter != allSeries.end(); ++idIter ) { if ( idIter->first.find( series_uid ) == 0 ) // this ID starts with given series_uid { resultingFileList.insert( resultingFileList.end(), idIter->second.begin(), idIter->second.end() ); // append } } return resultingFileList; } DicomSeriesReader::StringContainer DicomSeriesReader::SortSeriesSlices(const StringContainer &unsortedFilenames) { gdcm::Sorter sorter; sorter.SetSortFunction(DicomSeriesReader::GdcmSortFunction); sorter.Sort(unsortedFilenames); return sorter.GetFilenames(); } bool DicomSeriesReader::GdcmSortFunction(const gdcm::DataSet &ds1, const gdcm::DataSet &ds2) { gdcm::Attribute<0x0020,0x0032> image_pos1; // Image Position (Patient) gdcm::Attribute<0x0020,0x0037> image_orientation1; // Image Orientation (Patient) image_pos1.Set(ds1); image_orientation1.Set(ds1); gdcm::Attribute<0x0020,0x0032> image_pos2; gdcm::Attribute<0x0020,0x0037> image_orientation2; image_pos2.Set(ds2); image_orientation2.Set(ds2); if (image_orientation1 != image_orientation2) { MITK_ERROR << "Dicom images have different orientations."; throw std::logic_error("Dicom images have different orientations. Call GetSeries() first to separate images."); } double normal[3]; normal[0] = image_orientation1[1] * image_orientation1[5] - image_orientation1[2] * image_orientation1[4]; normal[1] = image_orientation1[2] * image_orientation1[3] - image_orientation1[0] * image_orientation1[5]; normal[2] = image_orientation1[0] * image_orientation1[4] - image_orientation1[1] * image_orientation1[3]; double dist1 = 0.0, dist2 = 0.0; for (unsigned char i = 0u; i < 3u; ++i) { dist1 += normal[i] * image_pos1[i]; dist2 += normal[i] * image_pos2[i]; } if ( fabs(dist1 - dist2) < mitk::eps) { gdcm::Attribute<0x0008,0x0032> acq_time1; // Acquisition time (may be missing, so we check existence first) gdcm::Attribute<0x0008,0x0032> acq_time2; if (ds1.FindDataElement(gdcm::Tag(0x0008,0x0032))) acq_time1.Set(ds1); if (ds2.FindDataElement(gdcm::Tag(0x0008,0x0032))) acq_time2.Set(ds2); // TODO this could lead to comparison of unset times (does Attribute initialize to good defaults?) // exception: same position: compare by acquisition time return acq_time1 < acq_time2; } else { // default: compare position return dist1 < dist2; } } std::string DicomSeriesReader::GetConfigurationString() { std::stringstream configuration; configuration << "MITK_USE_GDCMIO: "; configuration << "true"; configuration << "\n"; configuration << "GDCM_VERSION: "; #ifdef GDCM_MAJOR_VERSION configuration << GDCM_VERSION; #endif //configuration << "\n"; return configuration.str(); } void DicomSeriesReader::CopyMetaDataToImageProperties( const StringContainer& files, DcmIoType* io, Image* image ) { if (!io || !image) return; StringLookupTable filesForSlices; unsigned int slice(0); for ( StringContainer::const_iterator fIter = files.begin(); fIter != files.end(); ++fIter, ++slice ) { filesForSlices.SetTableValue( slice, *fIter ); } image->SetProperty( "files", StringLookupTableProperty::New( filesForSlices ) ); /* TODO DICOM tags for patient, study, series level can easily be copied from io->GetMetaDataDictionary to appropriate mitk::Image::m_PropertyList entries. Keys should follow the format "dicom.patient.gggg.eeee", values the raw strings from ITK initially, no type specific handling. Image level attributes will cause an additional run of the files through gdcm::Scanner probably. Tags of interest would be: (0020,1041) Slice Location (for verification of loading) (0020,0013) Instance Number (for display and visual reference against PACS for users) (0008,0018) SOP Instance UID (for real reference to PACS in applications) */ } } // end namespace mitk #include diff --git a/Core/Code/IO/mitkDicomSeriesReader.h b/Core/Code/IO/mitkDicomSeriesReader.h index cec64c7de8..63117021f0 100644 --- a/Core/Code/IO/mitkDicomSeriesReader.h +++ b/Core/Code/IO/mitkDicomSeriesReader.h @@ -1,437 +1,439 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkDicomSeriesReader_h #define mitkDicomSeriesReader_h #include "mitkDataNode.h" #include "mitkConfig.h" #include #include #include #include #include #include #include #include #include #include namespace mitk { /** \brief Loading DICOM images as MITK images. - \ref DicomSeriesReader_purpose - \ref DicomSeriesReader_limitations - \ref DicomSeriesReader_usage - \ref DicomSeriesReader_sorting - \ref DicomSeriesReader_sorting1 - \ref DicomSeriesReader_sorting2 - \ref DicomSeriesReader_sorting3 - \ref DicomSeriesReader_sorting4 - \ref DicomSeriesReader_tests \section DicomSeriesReader_purpose Purpose DicomSeriesReader serves as a central class for loading DICOM images as mitk::Image. As the term "DICOM image" covers a huge variety of possible modalities and implementations, and since MITK assumes that 3D images are made up of continuous blocks of slices without any gaps or changes in orientation, the loading mechanism must implement a number of decisions and compromises. The main intention of this implementation is not efficiency but correcness of generated slice positions! \section DicomSeriesReader_limitations Assumptions and limitations The class is working only with GDCM 2.0.14 (or possibly newer). This version is the default of an MITK super-build. Support for other versions or ITK's DicomIO was dropped because of the associated complexity of DicomSeriesReader. \b Assumptions - expected to work for SOP Classes CT Image Storage and MR Image Storage (NOT for the "Enhanced" variants containing multi-frame images) - special treatment for a certain type of Philips 3D ultrasound (recogized by tag 3001,0010 set to "Philips3D") - loader will always attempt to read multiple single slices as a single 3D image volume (i.e. mitk::Image) - slices will be grouped by basic properties such as orientation, rows, columns, spacing and grouped into as large blocks as possible \b Options - images that cover the same piece of space (i.e. position, orientation, and dimensions are equal) can be interpreted as time-steps of the same image, i.e. a series will be loaded as 3D+t \b Limitations - the 3D+t assumption only works if all time-steps have an equal number of slices and if all have the Acquisition Time attribute set to meaningful values - Images from tilted CT gantries CAN ONLY be loaded as a series of single-slice images, since mitk::Image or the accompanying mapper are not (yet?) capable of representing such geometries - Secondary Capture images are expected to have the (0018,2010) tag describing the pixel spacing. If only the (0028,0030) tag is set, the spacing will be misinterpreted as (1,1) \section DicomSeriesReader_usage Usage The starting point for an application is a set of DICOM files that should be loaded. For convenience, DicomSeriesReader can also parse a whole directory for DICOM files, but an application should better know exactly what to load. Loading is then done in two steps: 1. Group the files into spatial blocks by calling GetSeries(). This method will sort all passed files into meaningful blocks that could fit into an mitk::Image. Sorting for 3D+t loading is optional but default. The \b return value of this function is a list of identifiers similar to DICOM UIDs, each associated to a sorted list of file names. 2. Load a sorted set of files by calling LoadDicomSeries(). This method expects go receive the sorting output of GetSeries(). The method will then invoke ITK methods to actually load the files into memory and put them into mitk::Images. Again, loading as 3D+t is optional. Example: \code // only a directory is known at this point: /home/who/dicom DicomSeriesReader::UidFileNamesMap allImageBlocks = DicomSeriesReader::GetSeries("/home/who/dicom/"); // file now divided into groups of identical image size, orientation, spacing, etc. // each of these lists should be loadable as an mitk::Image. DicomSeriesReader::StringContainer seriesToLoad = allImageBlocks[...]; // decide what to load // final step: load into DataNode (can result in 3D+t image) DataNode::Pointer node = DicomSeriesReader::LoadDicomSeries( oneBlockSorted ); Image::Pointer image = dynamic_cast( node->GetData() ); \endcode \section DicomSeriesReader_sorting Logic for sorting 2D slices from DICOM images into 3D+t blocks for mitk::Image The general sorting mechanism (implemented in GetSeries) groups and sorts a set of DICOM files, each assumed to contain a single CT/MR slice. In the following we refer to those file groups as "blocks", since this is what they are meant to become when loaded into an mitk::Image. \subsection DicomSeriesReader_sorting1 Step 1: Avoiding pure non-sense A first pass separates slices that cannot possibly be loaded together because of restrictions of mitk::Image. After this steps, each block contains only slices that match in all of the following DICOM tags: - (0020,0037) Image Orientation - (0028,0030) Pixel Spacing - (0018,0050) Slice Thickness - (0028,0010) Number Of Rows - (0028,0011) Number Of Columns - (0020,000e) Series Instance UID : could be argued about, might be dropped in the future (optionally) \subsection DicomSeriesReader_sorting2 Step 2: Sort slices spatially Before slices are further analyzed, they are sorted spatially. As implemented by GdcmSortFunction(), slices are sorted by 1. distance from origin (calculated using (0020,0032) Image Position Patient and (0020,0037) Image Orientation) 2. when distance is equal, (0008,0032) Acquisition Time is used as a backup criterion (necessary for meaningful 3D+t sorting) \subsection DicomSeriesReader_sorting3 Step 3: Ensure equal z spacing Since inter-slice distance is not recorded in DICOM tags, we must ensure that blocks are made up of slices that have equal distances between neighboring slices. This is especially necessary because itk::ImageSeriesReader is later used for the actual loading, and this class expects (and does nocht verify) equal inter-slice distance. To achieve such grouping, the inter-slice distance is calculated from the first two different slice positions of a block. Following slices are added to a block as long as they can be added by adding the calculated inter-slice distance to the - last slice of the block. If an unexpected gap is detected, the block is split up. + last slice of the block. Slices that do not fit into the expected distance pattern, are set aside for further analysis. + This grouping is done until each file has been assigned to a group. - Slices that share a position in space are also separated during this step. So the result of this step is a set - of blocks that contain only slices with equal z spacing and uniqe slices at each position. + Slices that share a position in space are also sorted into separate blocks during this step. + So the result of this step is a set of blocks that contain only slices with equal z spacing + and uniqe slices at each position. \subsection DicomSeriesReader_sorting4 Step 4 (optional): group 3D blocks as 3D+t when possible This last step depends on an option of GetSeries(). When requested, image blocks from the previous step are merged again whenever two blocks occupy the same portion of space (i.e. same origin, number of slices and z-spacing). \section DicomSeriesReader_tests Tests regarding DICOM loading A number of tests have been implemented to check our assumptions regarding DICOM loading. Please see \ref DICOMTesting */ class MITK_CORE_EXPORT DicomSeriesReader { public: /** \brief Lists of filenames. */ typedef std::vector StringContainer; /** \brief For grouped lists of filenames, assigned an ID each. */ typedef std::map UidFileNamesMap; /** \brief Interface for the progress callback. */ typedef void (*UpdateCallBackMethod)(float); /** \brief Provide combination of preprocessor defines that was active during compilation. Since this class is a combination of several possible implementations, separated only by ifdef's, calling instances might want to know which flags were active at compile time. */ static std::string GetConfigurationString(); /** \brief Checks if a specific file contains DICOM data. */ static bool IsDicom(const std::string &filename); /** \brief see other GetSeries(). Find all series (and sub-series -- see details) in a particular directory. */ static UidFileNamesMap GetSeries(const std::string &dir, const StringContainer &restrictions = StringContainer()); /** \brief see other GetSeries(). \warning Untested, could or could not work. This differs only by having an additional restriction to a single known DICOM series. Internally, it uses the other GetSeries() method. */ static StringContainer GetSeries(const std::string &dir, const std::string &series_uid, const StringContainer &restrictions = StringContainer()); /** \brief PREFERRED version of this method - scan and sort DICOM files. Parse a list of files for images of DICOM series. For each series, an enumeration of the files contained in it is created. \return The resulting maps UID-like keys (based on Series Instance UID and slice properties) to sorted lists of file names. SeriesInstanceUID will be enhanced to be unique for each set of file names that is later loadable as a single mitk::Image. This implies that Image orientation, slice thickness, pixel spacing, rows, and columns must be the same for each file (i.e. the image slice contained in the file). If this separation logic requires that a SeriesInstanceUID must be made more specialized, it will follow the same logic as itk::GDCMSeriesFileNames to enhance the UID with more digits and dots. Optionally, more tags can be used to separate files into different logical series by setting the restrictions parameter. \warning Adding restrictions is not yet implemented! */ static UidFileNamesMap GetSeries(const StringContainer& files, bool sortTo3DPlust, const StringContainer &restrictions = StringContainer()); /** \brief See other GetSeries(). Use GetSeries(const StringContainer& files, bool sortTo3DPlust, const StringContainer &restrictions) instead. */ static UidFileNamesMap GetSeries(const StringContainer& files, const StringContainer &restrictions = StringContainer()); /** Loads a DICOM series composed by the file names enumerated in the file names container. If a callback method is supplied, it will be called after every progress update with a progress value in [0,1]. \param filenames The filenames to load. \param sort Whether files should be sorted spatially (true) or not (false - maybe useful if presorted) \param load4D Whether to load the files as 3D+t (if possible) */ static DataNode::Pointer LoadDicomSeries(const StringContainer &filenames, bool sort = true, bool load4D = true, UpdateCallBackMethod callback = 0); /** \brief See LoadDicomSeries! Just a slightly different interface. */ static bool LoadDicomSeries(const StringContainer &filenames, DataNode &node, bool sort = true, bool load4D = true, UpdateCallBackMethod callback = 0); protected: /** \brief for internal sorting. */ typedef std::pair TwoStringContainers; /** \brief Ensure an equal z-spacing for a group of files. Internally used by GetSeries. Returns two lists: the first one contins slices of equal inter-slice spacing. The second list contains remaining files, which need to be run through AnalyzeFileForITKImageSeriesReaderSpacingAssumption again. Relevant code that is matched here is in itkImageSeriesReader.txx (ImageSeriesReader::GenerateOutputInformation(void)), lines 176 to 245 (as of ITK 3.20) */ static TwoStringContainers AnalyzeFileForITKImageSeriesReaderSpacingAssumption(const StringContainer& files, const gdcm::Scanner::MappingType& tagValueMappings); /** \brief Sort a set of file names in an order that is meaningful for loading them into an mitk::Image. \warning This method assumes that input files are similar in basic properties such as slice thicknes, image orientation, pixel spacing, rows, columns. It should always be ok to put the result of a call to GetSeries(..) into this method. Sorting order is determined by 1. image position along its normal (distance from world origin) 2. acquisition time If P denotes a position and T denotes a time step, this method will order slices from three timesteps like this: \verbatim P1T1 P1T2 P1T3 P2T1 P2T2 P2T3 P3T1 P3T2 P3T3 \endverbatim */ static StringContainer SortSeriesSlices(const StringContainer &unsortedFilenames); public: /** \brief Checks if a specific file is a Philips3D ultrasound DICOM file. */ static bool IsPhilips3DDicom(const std::string &filename); protected: /** \brief Read a Philips3D ultrasound DICOM file and put into an mitk::Image. */ static bool ReadPhilips3DDicom(const std::string &filename, mitk::Image::Pointer output_image); /** \brief Construct a UID that takes into account sorting criteria from GetSeries(). */ static std::string CreateMoreUniqueSeriesIdentifier( gdcm::Scanner::TagToValue& tagValueMap ); /** \brief Helper for CreateMoreUniqueSeriesIdentifier */ static std::string CreateSeriesIdentifierPart( gdcm::Scanner::TagToValue& tagValueMap, const gdcm::Tag& tag ); /** \brief Helper for CreateMoreUniqueSeriesIdentifier */ static std::string IDifyTagValue(const std::string& value); typedef itk::GDCMImageIO DcmIoType; /** \brief Progress callback for DicomSeriesReader. */ class CallbackCommand : public itk::Command { public: CallbackCommand(UpdateCallBackMethod callback) : m_Callback(callback) { } void Execute(const itk::Object *caller, const itk::EventObject&) { (*this->m_Callback)(static_cast(caller)->GetProgress()); } void Execute(itk::Object *caller, const itk::EventObject&) { (*this->m_Callback)(static_cast(caller)->GetProgress()); } protected: UpdateCallBackMethod m_Callback; }; /** \brief Performs actual loading of a series and creates an image having the specified pixel type. */ template static void LoadDicom(const StringContainer &filenames, DataNode &node, bool sort, bool check_4d, UpdateCallBackMethod callback); /** \brief Feed files into itk::ImageSeriesReader and retrieve a 3D MITK image. \param command can be used for progress reporting */ template static Image::Pointer LoadDICOMByITK( const StringContainer&, CallbackCommand* command = NULL); /** \brief Sort files into time step blocks of a 3D+t image. Called by LoadDicom. Expects to be fed a single list of filenames that have been sorted by GetSeries previously (one map entry). This method will check how many timestep can be filled with given files. Assumption is that the number of time steps is determined by how often the first position in space repeats. I.e. if the first three files in the input parameter all describe the same location in space, we'll construct three lists of files. and sort the remaining files into them. \todo We can probably remove this method if we somehow transfer 3D+t information from GetSeries to LoadDicomSeries. */ static std::list SortIntoBlocksFor3DplusT( const StringContainer& presortedFilenames, bool sort, bool& canLoadAs4D ); /** \brief Defines spatial sorting for sorting by GDCM 2. Sorts by image position along image normal (distance from world origin). In cases of conflict, acquisition time is used as a secondary sort criterium. */ static bool GdcmSortFunction(const gdcm::DataSet &ds1, const gdcm::DataSet &ds2); /** \brief Copy information about files and DICOM tags from ITK's MetaDataDictionary and from the list of input files to the PropertyList of mitk::Image. \todo Tag copy must follow; image level will cause some additional files parsing, probably. */ static void CopyMetaDataToImageProperties( const StringContainer& files, DcmIoType* io, Image* image ); }; } #endif /* MITKDICOMSERIESREADER_H_ */ diff --git a/Core/Code/IO/mitkDicomSeriesReader.txx b/Core/Code/IO/mitkDicomSeriesReader.txx index c7d55d2242..bb85786ef1 100644 --- a/Core/Code/IO/mitkDicomSeriesReader.txx +++ b/Core/Code/IO/mitkDicomSeriesReader.txx @@ -1,270 +1,270 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKDICOMSERIESREADER_TXX_ #define MITKDICOMSERIESREADER_TXX_ #include #include namespace mitk { template void DicomSeriesReader::LoadDicom(const StringContainer &filenames, DataNode &node, bool sort, bool load4D, UpdateCallBackMethod callback) { const char* previousCLocale = setlocale(LC_NUMERIC, NULL); setlocale(LC_NUMERIC, "C"); std::locale previousCppLocale( std::cin.getloc() ); std::locale l( "C" ); std::cin.imbue(l); try { mitk::Image::Pointer image = mitk::Image::New(); CallbackCommand *command = callback ? new CallbackCommand(callback) : 0; /* special case for Philips 3D+t ultrasound images */ if ( DicomSeriesReader::IsPhilips3DDicom(filenames.front().c_str()) ) { ReadPhilips3DDicom(filenames.front().c_str(), image); } else { /* default case: assume "normal" image blocks, possibly 3D+t */ bool canLoadAs4D(true); std::list imageBlocks = SortIntoBlocksFor3DplusT( filenames, sort, canLoadAs4D ); unsigned int volume_count = imageBlocks.size(); - if (!canLoadAs4D || !load4D) + if (volume_count == 1 || !canLoadAs4D || !load4D) { image = LoadDICOMByITK( imageBlocks.front() , command ); // load first 3D block } else { // It is 3D+t! Read it and store into mitk image typedef itk::Image ImageType; typedef itk::ImageSeriesReader ReaderType; DcmIoType::Pointer io = DcmIoType::New(); typename ReaderType::Pointer reader = ReaderType::New(); reader->SetImageIO(io); reader->ReverseOrderOff(); if (command) { reader->AddObserver(itk::ProgressEvent(), command); } unsigned int act_volume = 1u; reader->SetFileNames(imageBlocks.front()); reader->Update(); image->InitializeByItk(reader->GetOutput(), 1, volume_count); image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), 0u); DicomSeriesReader::CopyMetaDataToImageProperties( imageBlocks.front(), io, image ); MITK_DEBUG << "Volume dimension: [" << image->GetDimension(0) << ", " << image->GetDimension(1) << ", " << image->GetDimension(2) << ", " << image->GetDimension(3) << "]"; #if (GDCM_MAJOR_VERSION == 2) && (GDCM_MINOR_VERSION < 1) && (GDCM_BUILD_VERSION < 15) // workaround for a GDCM 2 bug until version 2.0.15: // GDCM read spacing vector wrongly. Instead of "row spacing, column spacing", it misinterprets the DICOM tag as "column spacing, row spacing". // this is undone here, until we use a GDCM that has this issue fixed. // From the commit comments, GDCM 2.0.15 fixed the spacing interpretation with bug 2901181 // http://sourceforge.net/tracker/index.php?func=detail&aid=2901181&group_id=137895&atid=739587 Vector3D correctedImageSpacing = image->GetGeometry()->GetSpacing(); std::swap( correctedImageSpacing[0], correctedImageSpacing[1] ); image->GetGeometry()->SetSpacing( correctedImageSpacing ); #endif MITK_DEBUG << "Volume spacing: [" << image->GetGeometry()->GetSpacing()[0] << ", " << image->GetGeometry()->GetSpacing()[1] << ", " << image->GetGeometry()->GetSpacing()[2] << "]"; for (std::list::iterator df_it = ++imageBlocks.begin(); df_it != imageBlocks.end(); ++df_it) { reader->SetFileNames(*df_it); reader->Update(); image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), act_volume++); } } } node.SetData( image ); setlocale(LC_NUMERIC, previousCLocale); std::cin.imbue(previousCppLocale); } catch (std::exception& e) { // reset locale then throw up setlocale(LC_NUMERIC, previousCLocale); std::cin.imbue(previousCppLocale); throw e; } } template Image::Pointer DicomSeriesReader::LoadDICOMByITK( const StringContainer& filenames, CallbackCommand* command ) { /******** Normal Case, 3D (also for GDCM < 2 usable) ***************/ mitk::Image::Pointer image = mitk::Image::New(); typedef itk::Image ImageType; typedef itk::ImageSeriesReader ReaderType; DcmIoType::Pointer io = DcmIoType::New(); typename ReaderType::Pointer reader = ReaderType::New(); reader->SetImageIO(io); reader->ReverseOrderOff(); if (command) { reader->AddObserver(itk::ProgressEvent(), command); } reader->SetFileNames(filenames); reader->Update(); image->InitializeByItk(reader->GetOutput()); image->SetImportVolume(reader->GetOutput()->GetBufferPointer()); MITK_DEBUG << "Volume dimension: [" << image->GetDimension(0) << ", " << image->GetDimension(1) << ", " << image->GetDimension(2) << "]"; #if (GDCM_MAJOR_VERSION == 2) && (GDCM_MINOR_VERSION < 1) && (GDCM_BUILD_VERSION < 15) // workaround for a GDCM 2 bug until version 2.0.15: // GDCM read spacing vector wrongly. Instead of "row spacing, column spacing", it misinterprets the DICOM tag as "column spacing, row spacing". // this is undone here, until we use a GDCM that has this issue fixed. // From the commit comments, GDCM 2.0.15 fixed the spacing interpretation with bug 2901181 // http://sourceforge.net/tracker/index.php?func=detail&aid=2901181&group_id=137895&atid=739587 Vector3D correctedImageSpacing = image->GetGeometry()->GetSpacing(); std::swap( correctedImageSpacing[0], correctedImageSpacing[1] ); image->GetGeometry()->SetSpacing( correctedImageSpacing ); #endif MITK_DEBUG << "Volume spacing: [" << image->GetGeometry()->GetSpacing()[0] << ", " << image->GetGeometry()->GetSpacing()[1] << ", " << image->GetGeometry()->GetSpacing()[2] << "]"; return image; } std::list DicomSeriesReader::SortIntoBlocksFor3DplusT( const StringContainer& presortedFilenames, bool sort, bool& canLoadAs4D ) { std::list imageBlocks; // ignore sort request, because most likely re-sorting is now needed due to changes in GetSeries(bug #8022) StringContainer sorted_filenames = DicomSeriesReader::SortSeriesSlices(presortedFilenames); gdcm::Tag ippTag(0x0020,0x0032); //Image position (Patient) gdcm::Scanner scanner; scanner.AddTag(ippTag); scanner.Scan(sorted_filenames); // make available image position for each file std::string firstPosition; unsigned int numberOfBlocks(0); // number of 3D image blocks // loop files to determine number of image blocks for (StringContainer::const_iterator fileIter = sorted_filenames.begin(); fileIter != sorted_filenames.end(); ++fileIter) { std::string position = scanner.GetValue( fileIter->c_str(), ippTag); - MITK_DEBUG << "File " << *fileIter << " at " << position; + MITK_DEBUG << " " << *fileIter << " at " << position; if (firstPosition.empty()) { firstPosition = position; } if ( position == firstPosition ) { ++numberOfBlocks; } else { break; // enough information to know the number of image blocks } } - MITK_DEBUG << "Assuming " << numberOfBlocks << " image blocks"; + MITK_DEBUG << " ==> Assuming " << numberOfBlocks << " time steps"; if (numberOfBlocks == 0) return imageBlocks; // only possible if called with no files // loop files to sort them into image blocks unsigned int numberOfExpectedSlices(0); for (unsigned int block = 0; block < numberOfBlocks; ++block) { StringContainer filesOfCurrentBlock; for ( StringContainer::const_iterator fileIter = sorted_filenames.begin() + block; fileIter != sorted_filenames.end(); //fileIter += numberOfBlocks) // TODO shouldn't this work? give invalid iterators on first attempts ) { filesOfCurrentBlock.push_back( *fileIter ); for (unsigned int b = 0; b < numberOfBlocks; ++b) { if (fileIter != sorted_filenames.end()) ++fileIter; } } imageBlocks.push_back(filesOfCurrentBlock); if (block == 0) { numberOfExpectedSlices = filesOfCurrentBlock.size(); } else { if (filesOfCurrentBlock.size() != numberOfExpectedSlices) { MITK_WARN << "DicomSeriesReader expected " << numberOfBlocks << " image blocks of " << numberOfExpectedSlices << " images each. Block " << block << " got " << filesOfCurrentBlock.size() << " instead. Cannot load this as 3D+t"; // TODO implement recovery (load as many slices 3D+t as much as possible) canLoadAs4D = false; } } } return imageBlocks; } } #endif diff --git a/Core/Code/Testing/DICOMTesting/DICOMTesting.dox b/Core/Code/Testing/DICOMTesting/DICOMTesting.dox index a751217c9c..2847dbf68c 100644 --- a/Core/Code/Testing/DICOMTesting/DICOMTesting.dox +++ b/Core/Code/Testing/DICOMTesting/DICOMTesting.dox @@ -1,144 +1,145 @@ /** \page DICOMTesting MITK DICOM testing \section DICOMTesting_introduction Introduction Reading DICOM data into mitk::Images is a complicated business since DICOM and MITK have very different ideas of images. DicomSeriesReader brings DICOM and MITK as close together as possible by offering methods to load DICOM CT and MR images into mitk::Images, optionally grouping slices to 3D+t images. Since there are so many possible sources for mistakes with any change to this loading process, testing the many assumptions implemented in DicomSeriesReader is worthwhile. This document describes what kind of tests are implemented and what how. \section DICOMTesting_problem Problem description The task of loading DICOM files into mitk::Images is a challenge because of major differences in the way that DICOM and MITK represent images: - DICOM images - are mostly stored as one slice per file - do not describe how they can be arraged into image stacks with orthogonal axis - sometimes they cannot be arranged in image stacks as described above (e.g. tilted gantry) - mitk::Image (at least its mature areas) - represents image stacks with orthogonal axis (nothing like a tilted gantry) - have a concept of a fourth dimension (time steps) Because image processing applications based on MITK still need a way to load DICOM images into mitk::Image objects, MITK needs to put a lot of effort into building image stacks as best as it can. And this needs to be well tested. For more background information, see David Clunie's most valuable posts on comp.protocols.dicom, e.g.: - http://groups.google.com/group/comp.protocols.dicom/browse_thread/thread/6db91972e161f0d4/6e0304ac264a6eb5 - http://groups.google.com/group/comp.protocols.dicom/browse_thread/thread/e9bd1497bea3e66b/187a7dc8810613d2 - http://groups.google.com/group/comp.protocols.dicom/browse_thread/thread/5d80bb0b7fafcb81/cf96119e3b024ed8 - http://groups.google.com/group/comp.protocols.dicom/browse_thread/thread/4568635e083a3fba/e2a8ceec23032601 \section DICOMTesting_testidea Test principle The general idea for DICOM loaing tests is to run a set of known DICOM files through DicomSeriesReader's methods GetSeries() and LoadDicomSeries() to generate mitk::Images. These images are then compared to expected image properties, such as the number of individual mitk::Images, positions, orientations, spacings, etc. Stored expectations look like this (should be self-explanatory): \verbatim -- Image 1 Pixeltype: s BitsPerPixel: 16 Dimension: 4 Dimensions: 64 64 6 1 Geometry: Matrix: 5.25 0 0 0 5.2468 0.139598 0 -0.183222 3.99757 Offset: -159.672 -309.974 -69.0122 Center: 0 0 0 Translation: -159.672 -309.974 -69.0122 Scale: 1 1 1 Origin: -159.672 -309.974 -69.0122 Spacing: 5.25 5.25 4 TimeBounds: 0 1 -- Image 2 Pixeltype: s BitsPerPixel: 16 Dimension: 4 Dimensions: 64 64 41 1 Geometry: Matrix: 5.25 0 0 0 5.25 0 0 0 4 Offset: -160.672 -311.672 -285 Center: 0 0 0 Translation: -160.672 -311.672 -285 Scale: 1 1 1 Origin: -160.672 -311.672 -285 Spacing: 5.25 5.25 4 TimeBounds: 0 1 \endverbatim \section DICOMTesting_implementation Implementation \section DICOMTesting_implementation_utils Test helpers (applications and classes) Application DumpDICOMMitkImage Takes a list of DICOM images, loads them using TestDICOMLoading, then dumps information about the resulting mitk::Images to standard output. This application is helpful when defining reference data for tests. Application VerifyDICOMMitkImageDump Takes a list of DICOM images and loads them using TestDICOMLoading. Takes a dump file as generated by DumpDICOMMitkImage, parses it and compares it to actually generated mitk::Images. This application is used to implement the majority of test cases. They all load images, then verify the expected result structure. Class TestDICOMLoading \section PageDICOMLoadingTests_testcaseimplementation Test case implementation Individual test cases are stored in the MITK-Data repository and constructed by Core/Code/Testing/DICOMTesting/Testing/CMakeLists.txt The CMake file parses given directories for subdirectories containing specific test cases. Each directory contains two files: - File "input": lists DICOM files that should be loaded for this test case - File "expected.dump": contains the image properties in the above mentioned dump format Each test case is translated into a CTest test which evaluates the return value of a call to VerifyDICOMMitkImageDump. \section PageDICOMLoadingTests_testcases Implemented test cases From test set TinyCTAbdomen (see description.txt in this directory for details on test images): - singleslice : just a single slice (should work and contain meaningful spacing) - two_slices : two slices, spacing should be calculated correctly - all : load a "normal" series as a single 3D block - 3D_and_T : load a small set of slices with multiple time-steps - diff_orientation : load a set of files containing two differently oriented image blocks - diff_orientation_gaps : load a set of files containing two differently oriented image blocks, each missing slices, so blocks must be split - diff_spacing : load a set of files containint two set of slices with different spacings - gap : load slices that cannot form a single 3D block, because single slices are missing - gaps : slices missing in differnt locations, so multiple splits needed - unsorted_gaps : as before, just file names are unsorted - single_negative_spacing : from reported bug related to single MR images with misleading spacing information - tilted_gantry : slice origins do not align along first slice normal (happens with tilted gantries) + - interleaved : two volumes of slices with origins along the same line. The volumes' slices interleave in their border region. This test is meant to correctly sort apart the two blocks instead of generating many two-slices groups in the interleaved region. \section DICOMTesting_othertests Specific other tests This list is meant to provide an up-to-date list of all implemented DICOM loading tests. If you ever find this outdated, please update it or make the persons who invalidated the list update it. mitkDICOMTestingSanityTest_* These tests implement basic testing of the implemented helper classes. The tests use DicomSeriesReader to load a number of DICOM image. They verify: - DicomSeriesReader recognizes all input files as DICOM images - DicomSeriesReader generates a number of mitk::Images from the DICOM images - the number of mitk::Images matches a number given on the command line or CTest's add_test() - helper methods in class TestDICOMLoading make minimal sense (comparison of an image dump to itself must be valid) */ diff --git a/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.cpp b/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.cpp index 3319055d7f..4077d49a02 100644 --- a/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.cpp +++ b/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.cpp @@ -1,331 +1,417 @@ //#define MBILOG_ENABLE_DEBUG #include "mitkTestDICOMLoading.h" #include mitk::TestDICOMLoading::TestDICOMLoading() :m_PreviousCLocale(NULL) { } void mitk::TestDICOMLoading::SetDefaultLocale() { // remember old locale only once if (m_PreviousCLocale == NULL) { m_PreviousCLocale = setlocale(LC_NUMERIC, NULL); // set to "C" setlocale(LC_NUMERIC, "C"); m_PreviousCppLocale = std::cin.getloc(); std::locale l( "C" ); std::cin.imbue(l); std::cout.imbue(l); } } void mitk::TestDICOMLoading::ResetUserLocale() { if (m_PreviousCLocale) { setlocale(LC_NUMERIC, m_PreviousCLocale); std::cin.imbue(m_PreviousCppLocale); std::cout.imbue(m_PreviousCppLocale); m_PreviousCLocale = NULL; } } mitk::TestDICOMLoading::ImageList mitk::TestDICOMLoading::LoadFiles( const StringContainer& files ) { for (StringContainer::const_iterator iter = files.begin(); iter != files.end(); ++iter) { MITK_DEBUG << "File " << *iter; } ImageList result; DicomSeriesReader::UidFileNamesMap seriesInFiles = DicomSeriesReader::GetSeries( files ); // TODO sort series UIDs, implementation of map iterator might differ on different platforms (or verify this is a standard topic??) for (DicomSeriesReader::UidFileNamesMap::const_iterator seriesIter = seriesInFiles.begin(); seriesIter != seriesInFiles.end(); ++seriesIter) { StringContainer files = seriesIter->second; DataNode::Pointer node = DicomSeriesReader::LoadDicomSeries( files ); if (node.IsNotNull()) { Image::Pointer image = dynamic_cast( node->GetData() ); result.push_back( image ); } else { } } return result; } std::string mitk::TestDICOMLoading::TypeIDToString(const std::type_info& ti) { if (ti == typeid(unsigned char)) return "UCHAR"; else if (ti == typeid(char)) return "CHAR"; else if (ti == typeid(unsigned short)) return "USHORT"; else if (ti == typeid(short)) return "SHORT"; else if (ti == typeid(unsigned int)) return "UINT"; else if (ti == typeid(int)) return "INT"; else if (ti == typeid(long unsigned int)) return "ULONG"; else if (ti == typeid(long int)) return "LONG"; else if (ti == typeid(float)) return "FLOAT"; else if (ti == typeid(double)) return "DOUBLE"; else return "UNKNOWN"; } // add a line to stringstream result (see DumpImageInformation #define DumpLine(field, data) DumpILine(0, field, data) // add an indented(!) line to stringstream result (see DumpImageInformation #define DumpILine(indent, field, data) \ { \ std::string DumpLine_INDENT; DumpLine_INDENT.resize(indent, ' ' ); \ result << DumpLine_INDENT << field << ": " << data << "\n"; \ } std::string mitk::TestDICOMLoading::DumpImageInformation( const Image* image ) { std::stringstream result; if (image == NULL) return result.str(); SetDefaultLocale(); // basic image data DumpLine( "Pixeltype", TypeIDToString( *(image->GetPixelType().GetTypeId()) )); DumpLine( "BitsPerPixel", image->GetPixelType().GetBpe() ); DumpLine( "Dimension", image->GetDimension() ); result << "Dimensions: "; for (unsigned int dim = 0; dim < image->GetDimension(); ++dim) result << image->GetDimension(dim) << " "; result << "\n"; // geometry data result << "Geometry: \n"; Geometry3D* geometry = image->GetGeometry(); if (geometry) { AffineTransform3D* transform = geometry->GetIndexToWorldTransform(); if (transform) { result << " " << "Matrix: "; const AffineTransform3D::MatrixType& matrix = transform->GetMatrix(); for (unsigned int i = 0; i < 3; ++i) for (unsigned int j = 0; j < 3; ++j) result << matrix[i][j] << " "; result << "\n"; result << " " << "Offset: "; const AffineTransform3D::OutputVectorType& offset = transform->GetOffset(); for (unsigned int i = 0; i < 3; ++i) result << offset[i] << " "; result << "\n"; result << " " << "Center: "; const AffineTransform3D::InputPointType& center = transform->GetCenter(); for (unsigned int i = 0; i < 3; ++i) result << center[i] << " "; result << "\n"; result << " " << "Translation: "; const AffineTransform3D::OutputVectorType& translation = transform->GetTranslation(); for (unsigned int i = 0; i < 3; ++i) result << translation[i] << " "; result << "\n"; result << " " << "Scale: "; const double* scale = transform->GetScale(); for (unsigned int i = 0; i < 3; ++i) result << scale[i] << " "; result << "\n"; result << " " << "Origin: "; const Point3D& origin = geometry->GetOrigin(); for (unsigned int i = 0; i < 3; ++i) result << origin[i] << " "; result << "\n"; result << " " << "Spacing: "; const Vector3D& spacing = geometry->GetSpacing(); for (unsigned int i = 0; i < 3; ++i) result << spacing[i] << " "; result << "\n"; result << " " << "TimeBounds: "; const TimeBounds timeBounds = geometry->GetTimeBounds(); for (unsigned int i = 0; i < 2; ++i) result << timeBounds[i] << " "; result << "\n"; } } ResetUserLocale(); return result.str(); } +std::string +mitk::TestDICOMLoading::trim(const std::string& pString, + const std::string& pWhitespace) +{ + const size_t beginStr = pString.find_first_not_of(pWhitespace); + if (beginStr == std::string::npos) + { + // no content + return ""; + } + + const size_t endStr = pString.find_last_not_of(pWhitespace); + const size_t range = endStr - beginStr + 1; + + return pString.substr(beginStr, range); +} + +std::string +mitk::TestDICOMLoading::reduce(const std::string& pString, + const std::string& pFill, + const std::string& pWhitespace) +{ + // trim first + std::string result(trim(pString, pWhitespace)); + + // replace sub ranges + size_t beginSpace = result.find_first_of(pWhitespace); + while (beginSpace != std::string::npos) + { + const size_t endSpace = + result.find_first_not_of(pWhitespace, beginSpace); + const size_t range = endSpace - beginSpace; + + result.replace(beginSpace, range, pFill); + + const size_t newStart = beginSpace + pFill.length(); + beginSpace = result.find_first_of(pWhitespace, newStart); + } + + return result; +} + + bool mitk::TestDICOMLoading::CompareSpacedValueFields( const std::string& reference, const std::string& test, double eps ) { - // TODO this should better do a real comparison and tolerate float differences up to 'eps' + bool result(true); + + // tokenize string, compare each token, if possible by float comparison + std::stringstream referenceStream(reduce(reference)); + std::stringstream testStream(reduce(test)); - return reference == test; + std::string refToken; + std::string testToken; + while ( std::getline( referenceStream, refToken, ' ' ) && + std::getline ( testStream, testToken, ' ' ) ) + { + float refNumber; + float testNumber; + if ( this->StringToNumber(refToken, refNumber) ) + { + MITK_DEBUG << "Reference Token '" << refToken << "'" << " value " << refNumber + << ", test Token '" << refToken << "'" << " value " << refNumber; + if ( this->StringToNumber(testToken, testNumber) ) + { + result &= ( fabs(refNumber - testNumber) < mitk::eps ); + } + else + { + MITK_ERROR << refNumber << " cannot be compared to '" << testToken << "'"; + } + } + else + { + MITK_DEBUG << "Token '" << refToken << "'" << " handled as string"; + result &= refToken == testToken; + } + } + + if ( std::getline( referenceStream, refToken, ' ' ) ) + { + MITK_ERROR << "Reference string still had values when test string was already parsed: ref '" << reference << "', test '" << test << "'"; + result = false; + } + else if ( std::getline( testStream, testToken, ' ' ) ) + { + MITK_ERROR << "Test string still had values when reference string was already parsed: ref '" << reference << "', test '" << test << "'"; + result = false; + } + + return result; } bool mitk::TestDICOMLoading::CompareImageInformationDumps( const std::string& referenceDump, const std::string& testDump ) { KeyValueMap reference = ParseDump(referenceDump); KeyValueMap test = ParseDump(testDump); bool testResult(true); // verify all expected values for (KeyValueMap::const_iterator refIter = reference.begin(); refIter != reference.end(); ++refIter) { const std::string& refKey = refIter->first; const std::string& refValue = refIter->second; if ( test.find(refKey) != test.end() ) { const std::string& testValue = test[refKey]; - MITK_DEBUG << refKey << ": " << refValue << " == " << testValue << "?"; - - testResult &= CompareSpacedValueFields( refValue, testValue ); + bool thisTestResult = CompareSpacedValueFields( refValue, testValue ); + testResult &= thisTestResult; + + MITK_DEBUG << refKey << ": '" << refValue << "' == '" << testValue << "' ? " << (thisTestResult?"YES":"NO"); } else { MITK_ERROR << "Reference dump contains a key'" << refKey << "' (value '" << refValue << "')." ; MITK_ERROR << "This key is expected to be generated for tests (but was not). Most probably you need to update your test data."; return false; } } // now check test dump does not contain any additional keys for (KeyValueMap::const_iterator testIter = test.begin(); testIter != test.end(); ++testIter) { const std::string& key = testIter->first; const std::string& value = testIter->second; if ( reference.find(key) == reference.end() ) { MITK_ERROR << "Test dump contains an unexpected key'" << key << "' (value '" << value << "')." ; MITK_ERROR << "This key is not expected. Most probably you need to update your test data."; return false; } } return testResult; } mitk::TestDICOMLoading::KeyValueMap mitk::TestDICOMLoading::ParseDump( const std::string& dump ) { KeyValueMap parsedResult; std::string shredder(dump); std::stack surroundingKeys; std::stack expectedIndents; expectedIndents.push(0); while (true) { std::string::size_type newLinePos = shredder.find( '\n' ); if (newLinePos == std::string::npos || newLinePos == 0) break; std::string line = shredder.substr( 0, newLinePos ); shredder = shredder.erase( 0, newLinePos+1 ); std::string::size_type keyPosition = line.find_first_not_of( ' ' ); std::string::size_type colonPosition = line.find( ':' ); std::string key = line.substr(keyPosition, colonPosition - keyPosition); std::string::size_type firstSpacePosition = key.find_first_of(" "); if (firstSpacePosition != std::string::npos) { key.erase(firstSpacePosition); } if ( keyPosition > expectedIndents.top() ) { // more indent than before expectedIndents.push(keyPosition); } else if (keyPosition == expectedIndents.top() ) { if (!surroundingKeys.empty()) { surroundingKeys.pop(); // last of same length } } else { // less indent than before do expectedIndents.pop(); while (expectedIndents.top() != keyPosition); // unwind until current indent is found } if (!surroundingKeys.empty()) { key = surroundingKeys.top() + "." + key; // construct current key name } surroundingKeys.push(key); // this is the new embracing key std::string value = line.substr(colonPosition+1); MITK_DEBUG << " Key: '" << key << "' value '" << value << "'" ; parsedResult[key] = value; // store parsing result } return parsedResult; } diff --git a/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.h b/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.h index b261dc7a8f..ad546f5812 100644 --- a/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.h +++ b/Core/Code/Testing/DICOMTesting/mitkTestDICOMLoading.h @@ -1,64 +1,90 @@ #ifndef mitkTestDICOMLoading_h #define mitkTestDICOMLoading_h #include "mitkDicomSeriesReader.h" #include "mitkDICOMTestingExports.h" namespace mitk { class mitkDICOMTesting_EXPORT TestDICOMLoading { public: typedef DicomSeriesReader::StringContainer StringContainer; typedef std::list NodeList; typedef std::list ImageList; TestDICOMLoading(); ImageList LoadFiles( const StringContainer& files ); /** \brief Dump relevant image information for later comparison. \sa CompareImageInformationDumps */ std::string DumpImageInformation( const Image* image ); /** \brief Compare two image information dumps. \return true, if dumps are sufficiently equal (see parameters) \sa DumpImageInformation */ bool CompareImageInformationDumps( const std::string& reference, const std::string& test ); private: typedef std::map KeyValueMap; void SetDefaultLocale(); void ResetUserLocale(); std::string TypeIDToString( const std::type_info& ); KeyValueMap ParseDump( const std::string& dump ); bool CompareSpacedValueFields( const std::string& reference, const std::string& test, double eps = mitk::eps ); + /** + Compress whitespace in string + \param pString input string + \param pFill replacement whitespace (only whitespace in string after reduction) + \param pWhitespace characters handled as whitespace + */ + std::string reduce(const std::string& pString, + const std::string& pFill = " ", + const std::string& pWhitespace = " \t"); + + /** + Remove leading and trailing whitespace + \param pString input string + \param pWhitespace characters handled as whitespace + */ + std::string trim(const std::string& pString, + const std::string& pWhitespace = " \t"); + + template + bool StringToNumber(const std::string& s, T& value) + { + std::stringstream stream(s); + stream >> value; + return !stream.fail(); + } + const char* m_PreviousCLocale; std::locale m_PreviousCppLocale; }; } #endif