mitkDicomSeriesReader.cpp

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

// uncomment for learning more about the internal sorting mechanisms
//#define MBILOG_ENABLE_DEBUG

#include <legacy/mitkDicomSeriesReader.h>
#include <mitkImage.h>
#include <mitkImageCast.h>
#include <mitkLocaleSwitch.h>

#include <itkGDCMSeriesFileNames.h>

#include <gdcmAttribute.h>
#include <gdcmDirectory.h>
#include <gdcmPixmapReader.h>
#include <gdcmRAWCodec.h>
#include <gdcmScanner.h>
#include <gdcmSorter.h>
#include <gdcmStringFilter.h>
#include <gdcmUIDs.h>

#include "mitkProperties.h"

namespace mitk
{
  std::string DicomSeriesReader::ReaderImplementationLevelToString(const ReaderImplementationLevel &enumValue)
  {
    switch (enumValue)
    {
      case ReaderImplementationLevel_Supported:
        return "Supported";
      case ReaderImplementationLevel_PartlySupported:
        return "PartlySupported";
      case ReaderImplementationLevel_Implemented:
        return "Implemented";
      case ReaderImplementationLevel_Unsupported:
        return "Unsupported";
      default:
        return "<unknown value of enum ReaderImplementationLevel>";
    };
  }

  std::string DicomSeriesReader::PixelSpacingInterpretationToString(const PixelSpacingInterpretation &enumValue)
  {
    switch (enumValue)
    {
      case PixelSpacingInterpretation_SpacingInPatient:
        return "In Patient";
      case PixelSpacingInterpretation_SpacingAtDetector:
        return "At Detector";
      case PixelSpacingInterpretation_SpacingUnknown:
        return "Unknown spacing";
      default:
        return "<unknown value of enum PixelSpacingInterpretation>";
    };
  }

  const DicomSeriesReader::TagToPropertyMapType &DicomSeriesReader::GetDICOMTagsToMITKPropertyMap()
  {
    static bool initialized = false;
    static TagToPropertyMapType dictionary;
    if (!initialized)
    {
      /*
         Selection criteria:
         - no sequences because we cannot represent that
         - nothing animal related (specied, breed registration number), MITK focusses on human medical image processing.
         - only general attributes so far

         When extending this, we should make use of a real dictionary (GDCM/DCMTK and lookup the tag names there)
      */

      // Patient module
      dictionary["0010|0010"] = "dicom.patient.PatientsName";
      dictionary["0010|0020"] = "dicom.patient.PatientID";
      dictionary["0010|0030"] = "dicom.patient.PatientsBirthDate";
      dictionary["0010|0040"] = "dicom.patient.PatientsSex";
      dictionary["0010|0032"] = "dicom.patient.PatientsBirthTime";
      dictionary["0010|1000"] = "dicom.patient.OtherPatientIDs";
      dictionary["0010|1001"] = "dicom.patient.OtherPatientNames";
      dictionary["0010|2160"] = "dicom.patient.EthnicGroup";
      dictionary["0010|4000"] = "dicom.patient.PatientComments";
      dictionary["0012|0062"] = "dicom.patient.PatientIdentityRemoved";
      dictionary["0012|0063"] = "dicom.patient.DeIdentificationMethod";

      // General Study module
      dictionary["0020|000d"] = "dicom.study.StudyInstanceUID";
      dictionary["0008|0020"] = "dicom.study.StudyDate";
      dictionary["0008|0030"] = "dicom.study.StudyTime";
      dictionary["0008|0090"] = "dicom.study.ReferringPhysiciansName";
      dictionary["0020|0010"] = "dicom.study.StudyID";
      dictionary["0008|0050"] = "dicom.study.AccessionNumber";
      dictionary["0008|1030"] = "dicom.study.StudyDescription";
      dictionary["0008|1048"] = "dicom.study.PhysiciansOfRecord";
      dictionary["0008|1060"] = "dicom.study.NameOfPhysicianReadingStudy";

      // General Series module
      dictionary["0008|0060"] = "dicom.series.Modality";
      dictionary["0020|000e"] = "dicom.series.SeriesInstanceUID";
      dictionary["0020|0011"] = "dicom.series.SeriesNumber";
      dictionary["0020|0060"] = "dicom.series.Laterality";
      dictionary["0008|0021"] = "dicom.series.SeriesDate";
      dictionary["0008|0031"] = "dicom.series.SeriesTime";
      dictionary["0008|1050"] = "dicom.series.PerformingPhysiciansName";
      dictionary["0018|1030"] = "dicom.series.ProtocolName";
      dictionary["0008|103e"] = "dicom.series.SeriesDescription";
      dictionary["0008|1070"] = "dicom.series.OperatorsName";
      dictionary["0018|0015"] = "dicom.series.BodyPartExamined";
      dictionary["0018|5100"] = "dicom.series.PatientPosition";
      dictionary["0028|0108"] = "dicom.series.SmallestPixelValueInSeries";
      dictionary["0028|0109"] = "dicom.series.LargestPixelValueInSeries";

      // VOI LUT module
      dictionary["0028|1050"] = "dicom.voilut.WindowCenter";
      dictionary["0028|1051"] = "dicom.voilut.WindowWidth";
      dictionary["0028|1055"] = "dicom.voilut.WindowCenterAndWidthExplanation";

      // Image Pixel module
      dictionary["0028|0004"] = "dicom.pixel.PhotometricInterpretation";
      dictionary["0028|0010"] = "dicom.pixel.Rows";
      dictionary["0028|0011"] = "dicom.pixel.Columns";

      // Image Plane module
      dictionary["0028|0030"] = "dicom.PixelSpacing";
      dictionary["0018|1164"] = "dicom.ImagerPixelSpacing";

      // Misc
      dictionary["0008|0005"] = "dicom.SpecificCharacterSet";

      initialized = true;
    }

    return dictionary;
  }

  DataNode::Pointer DicomSeriesReader::LoadDicomSeries(const StringContainer &filenames,
                                                       bool sort,
                                                       bool check_4d,
                                                       bool correctTilt,
                                                       UpdateCallBackMethod callback,
                                                       Image::Pointer preLoadedImageBlock)
  {
    DataNode::Pointer node = DataNode::New();

    if (DicomSeriesReader::LoadDicomSeries(
          filenames, *node, sort, check_4d, correctTilt, callback, preLoadedImageBlock))
    {
      if (filenames.empty())
      {
        return nullptr;
      }

      return node;
    }
    else
    {
      return nullptr;
    }
  }

  bool DicomSeriesReader::LoadDicomSeries(const StringContainer &filenames,
                                          DataNode &node,
                                          bool sort,
                                          bool check_4d,
                                          bool correctTilt,
                                          UpdateCallBackMethod callback,
                                          itk::SmartPointer<Image> preLoadedImageBlock)
  {
    if (filenames.empty())
    {
      MITK_DEBUG << "Calling LoadDicomSeries with empty filename string container. Probably invalid application logic.";
      node.SetData(nullptr);
      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();

        if (io->GetPixelType() == itk::ImageIOBase::SCALAR || io->GetPixelType() == itk::ImageIOBase::RGB)
        {
          LoadDicom(filenames, node, sort, check_4d, correctTilt, callback, preLoadedImageBlock);
        }

        if (node.GetData())
        {
          return true;
        }
      }
    }
    catch ( const itk::MemoryAllocationError &e )
    {
      MITK_ERROR << "Out of memory. Cannot load DICOM series: " << e.what();
    }
    catch ( const 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, itk::SmartPointer<Image> 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) // axial
    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<unsigned char, 4>
      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<ImageType> 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
  }

  std::string DicomSeriesReader::ConstCharStarToString(const char *s) { return s ? std::string(s) : std::string(); }
  bool DicomSeriesReader::DICOMStringToSpacing(const std::string &s, ScalarType &spacingX, ScalarType &spacingY)
  {
    bool successful = false;

    std::istringstream spacingReader(s);
    std::string spacing;
    if (std::getline(spacingReader, spacing, '\\'))
    {
      spacingY = atof(spacing.c_str());

      if (std::getline(spacingReader, spacing, '\\'))
      {
        spacingX = atof(spacing.c_str());

        successful = true;
      }
    }

    return successful;
  }

  Point3D DicomSeriesReader::DICOMStringToPoint3D(const std::string &s, bool &successful)
  {
    Point3D p;
    successful = true;

    std::istringstream originReader(s);
    std::string coordinate;
    unsigned int dim(0);
    while (std::getline(originReader, coordinate, '\\') && dim < 3)
    {
      p[dim++] = atof(coordinate.c_str());
    }

    if (dim && dim != 3)
    {
      successful = false;
      MITK_ERROR << "Reader implementation made wrong assumption on tag (0020,0032). Found " << dim
                 << " instead of 3 values.";
    }
    else if (dim == 0)
    {
      successful = false;
      p.Fill(0.0); // assume default (0,0,0)
    }

    return p;
  }

  void DicomSeriesReader::DICOMStringToOrientationVectors(const std::string &s,
                                                          Vector3D &right,
                                                          Vector3D &up,
                                                          bool &successful)
  {
    successful = true;

    std::istringstream orientationReader(s);
    std::string coordinate;
    unsigned int dim(0);
    while (std::getline(orientationReader, coordinate, '\\') && dim < 6)
    {
      if (dim < 3)
      {
        right[dim++] = atof(coordinate.c_str());
      }
      else
      {
        up[dim++ - 3] = atof(coordinate.c_str());
      }
    }

    if (dim && dim != 6)
    {
      successful = false;
      MITK_ERROR << "Reader implementation made wrong assumption on tag (0020,0037). Found " << dim
                 << " instead of 6 values.";
    }
    else if (dim == 0)
    {
      // fill with defaults
      right.Fill(0.0);
      right[0] = 1.0;

      up.Fill(0.0);
      up[1] = 1.0;

      successful = false;
    }
  }

  DicomSeriesReader::SliceGroupingAnalysisResult DicomSeriesReader::AnalyzeFileForITKImageSeriesReaderSpacingAssumption(
    const StringContainer &files, bool groupImagesWithGantryTilt, 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
    SliceGroupingAnalysisResult result;

    // we const_cast here, because I could not use a map.at(), which would make the code much more readable
    auto &tagValueMappings = const_cast<gdcm::Scanner::MappingType &>(tagValueMappings_);
    const gdcm::Tag tagImagePositionPatient(0x0020, 0x0032); // Image Position (Patient)
    const gdcm::Tag tagImageOrientation(0x0020, 0x0037);     // Image Orientation
    const gdcm::Tag tagGantryTilt(0x0018, 0x1120);           // gantry tilt

    Vector3D fromFirstToSecondOrigin;
    fromFirstToSecondOrigin.Fill(0.0);
    bool fromFirstToSecondOriginInitialized(false);
    Point3D thisOrigin;
    thisOrigin.Fill(0.0f);
    Point3D lastOrigin;
    lastOrigin.Fill(0.0f);
    Point3D lastDifferentOrigin;
    lastDifferentOrigin.Fill(0.0f);

    bool lastOriginInitialized(false);

    MITK_DEBUG << "--------------------------------------------------------------------------------";
    MITK_DEBUG << "Analyzing files for z-spacing assumption of ITK's ImageSeriesReader (group tilted: "
               << groupImagesWithGantryTilt << ")";
    unsigned int fileIndex(0);
    for (auto fileIter = files.begin(); fileIter != files.end(); ++fileIter, ++fileIndex)
    {
      bool fileFitsIntoPattern(false);
      std::string thisOriginString;
      // Read tag value into point3D. PLEASE replace this by appropriate GDCM code if you figure out how to do that
      thisOriginString = ConstCharStarToString(tagValueMappings[fileIter->c_str()][tagImagePositionPatient]);

      if (thisOriginString.empty())
      {
        // don't let such files be in a common group. Everything without position information will be loaded as a single
        // slice:
        // with standard DICOM files this can happen to: CR, DX, SC
        MITK_DEBUG << "    ==> Sort away " << *fileIter
                   << " for later analysis (no position information)"; // we already have one occupying this position

        if (result.GetBlockFilenames().empty()) // nothing WITH position information yet
        {
          // ==> this is a group of its own, stop processing, come back later
          result.AddFileToSortedBlock(*fileIter);

          StringContainer remainingFiles;
          remainingFiles.insert(remainingFiles.end(), fileIter + 1, files.end());
          result.AddFilesToUnsortedBlock(remainingFiles);

          fileFitsIntoPattern = false;
          break; // no files anymore
        }
        else
        {
          // ==> this does not match, consider later
          result.AddFileToUnsortedBlock(*fileIter);
          fileFitsIntoPattern = false;
          continue; // next file
        }
      }

      bool ignoredConversionError(-42); // hard to get here, no graceful way to react
      thisOrigin = DICOMStringToPoint3D(thisOriginString, ignoredConversionError);

      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
        result.AddFileToUnsortedBlock(*fileIter);
        fileFitsIntoPattern = false;
      }
      else
      {
        if (!fromFirstToSecondOriginInitialized &&
            lastOriginInitialized) // calculate vector as soon as possible when we get a new position
        {
          fromFirstToSecondOrigin = thisOrigin - lastDifferentOrigin;
          fromFirstToSecondOriginInitialized = true;

          // Here we calculate if this slice and the previous one are well aligned,
          // i.e. we test if the previous origin is on a line through the current
          // origin, directed into the normal direction of the current slice.

          // If this is NOT the case, then we have a data set with a TILTED GANTRY geometry,
          // which cannot be simply loaded into a single mitk::Image at the moment.
          // For this case, we flag this finding in the result and DicomSeriesReader
          // can correct for that later.

          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
          DICOMStringToOrientationVectors(
            tagValueMappings[fileIter->c_str()][tagImageOrientation], right, up, ignoredConversionError);

          GantryTiltInformation tiltInfo(lastDifferentOrigin, thisOrigin, right, up, 1);

          if (tiltInfo.IsSheared()) // mitk::eps is too small; 1/1000 of a mm should be enough to detect tilt
          {
            /* optimistic approach, accepting gantry tilt: save file for later, check all further files */

            // at this point we have TWO slices analyzed! if they are the only two files, we still split, because there
            // is
            // no third to verify our tilting assumption.
            // later with a third being available, we must check if the initial tilting vector is still valid. if yes,
            // continue.
            // if NO, we need to split the already sorted part (result.first) and the currently analyzed file
            // (*fileIter)

            // tell apart gantry tilt from overall skewedness
            // sort out irregularly sheared slices, that IS NOT tilting

            if (groupImagesWithGantryTilt && tiltInfo.IsRegularGantryTilt())
            {
              // check if this is at least roughly the same angle as recorded in DICOM tags
              if (tagValueMappings[fileIter->c_str()].find(tagGantryTilt) != tagValueMappings[fileIter->c_str()].end())
              {
                // read value, compare to calculated angle
                std::string tiltStr = ConstCharStarToString(tagValueMappings[fileIter->c_str()][tagGantryTilt]);
                double angle = atof(tiltStr.c_str());

                MITK_DEBUG << "Comparing recorded tilt angle " << angle << " against calculated value "
                           << tiltInfo.GetTiltAngleInDegrees();
                // TODO we probably want the signs correct, too (that depends: this is just a rough check, nothing
                // serious)
                // TODO TODO TODO when angle -27 and tiltangle 63, this will never trigger the if-clause... useless
                // check
                // in this case! old bug..?!
                if (fabs(angle) - tiltInfo.GetTiltAngleInDegrees() > 0.25)
                {
                  result.AddFileToUnsortedBlock(*fileIter); // sort away for further analysis
                  fileFitsIntoPattern = false;
                }
                else // tilt angle from header is less than 0.25 degrees different from what we calculated, assume this
                     // is
                     // fine
                {
                  result.FlagGantryTilt();
                  result.AddFileToSortedBlock(*fileIter); // this file is good for current block
                  fileFitsIntoPattern = true;
                }
              }
              else // we cannot check the calculated tilt angle against the one from the dicom header (so we assume we
                   // are
                   // right)
              {
                result.FlagGantryTilt();
                result.AddFileToSortedBlock(*fileIter); // this file is good for current block
                fileFitsIntoPattern = true;
              }
            }
            else // caller does not want tilt compensation OR shearing is more complicated than tilt
            {
              result.AddFileToUnsortedBlock(*fileIter); // sort away for further analysis
              fileFitsIntoPattern = false;
            }
          }
          else // not sheared
          {
            result.AddFileToSortedBlock(*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_DEBUG << "  File does not fit into the inter-slice distance pattern (diff = " << norm << ", allowed "
                       << toleratedError << ").";
            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

            /* Optimistic approach: check if any of the remaining slices fits in */
            result.AddFileToUnsortedBlock(*fileIter); // sort away for further analysis
            fileFitsIntoPattern = false;
          }
          else
          {
            result.AddFileToSortedBlock(*fileIter); // this file is good for current block
            fileFitsIntoPattern = true;
          }
        }
        else // this should be the very first slice
        {
          result.AddFileToSortedBlock(*fileIter); // this file is good for current block
          fileFitsIntoPattern = true;
        }
      }

      // record current origin for reference in later iterations
      if (!lastOriginInitialized || (fileFitsIntoPattern && (thisOrigin != lastOrigin)))
      {
        lastDifferentOrigin = thisOrigin;
      }

      lastOrigin = thisOrigin;
      lastOriginInitialized = true;
    }

    if (result.ContainsGantryTilt())
    {
      // check here how many files were grouped.
      // IF it was only two files AND we assume tiltedness (e.g. save "distance")
      // THEN we would want to also split the two previous files (simple) because
      // we don't have any reason to assume they belong together

      if (result.GetBlockFilenames().size() == 2)
      {
        result.UndoPrematureGrouping();
      }
    }

    return result;
  }

  DicomSeriesReader::FileNamesGrouping DicomSeriesReader::GetSeries(const StringContainer &files,
                                                                    bool groupImagesWithGantryTilt,
                                                                    const StringContainer &restrictions)
  {
    return GetSeries(files, true, groupImagesWithGantryTilt, restrictions);
  }

  DicomSeriesReader::FileNamesGrouping DicomSeriesReader::GetSeries(const StringContainer &files,
                                                                    bool sortTo3DPlust,
                                                                    bool groupImagesWithGantryTilt,
                                                                    const StringContainer & /*restrictions*/)
  {
    // 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 tagSOPClassUID(0x0008, 0x0016); // SOP class UID
    scanner.AddTag(tagSOPClassUID);

    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 tagImagerPixelSpacing(0x0018, 0x1164); // imager pixel spacing
    scanner.AddTag(tagImagerPixelSpacing);

    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);

    const gdcm::Tag tagGantryTilt(0x0018, 0x1120); // gantry tilt
    scanner.AddTag(tagGantryTilt);

    const gdcm::Tag tagModality(0x0008, 0x0060); // modality
    scanner.AddTag(tagModality);

    const gdcm::Tag tagNumberOfFrames(0x0028, 0x0008); // number of frames
    scanner.AddTag(tagNumberOfFrames);

    // 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 (when anybody asks for it)

    FileNamesGrouping result;

    // let GDCM scan files
    if (!scanner.Scan(files))
    {
      MITK_ERROR << "gdcm::Scanner failed when scanning " << files.size() << " input files.";
      return result;
    }

    // assign files IDs that will separate them for loading into image blocks
    for (auto fileIter = scanner.Begin(); fileIter != scanner.End(); ++fileIter)
    {
      if (std::string(fileIter->first).empty())
        continue; // TODO understand why Scanner has empty string entries
      if (std::string(fileIter->first) == std::string("DICOMDIR"))
        continue;

      /* sort out multi-frame
      if ( scanner.GetValue( fileIter->first , tagNumberOfFrames ) )
      {
        MITK_INFO << "Ignoring " << fileIter->first << " because we cannot handle multi-frame images.";
        continue;
      }
      */

      // 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<gdcm::Scanner::TagToValue &>(fileIter->second));
      result[moreUniqueSeriesId].AddFile(fileIter->first);
    }

    // PART II: sort slices spatially (or at least consistently if this is NOT possible, see method)

    for (FileNamesGrouping::const_iterator groupIter = result.begin(); groupIter != result.end(); ++groupIter)
    {
      try
      {
        result[groupIter->first] =
          ImageBlockDescriptor(SortSeriesSlices(groupIter->second.GetFilenames())); // sort each slice group spatially
      }
      catch (...)
      {
        MITK_ERROR << "Caught something.";
      }
    }

    // PART III: 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
    //              * this includes images which DO NOT PROVIDE spatial information, i.e. all images w/o
    //              ImagePositionPatient will be loaded separately

    FileNamesGrouping groupsOf3DPlusTBlocks; // final result of this function
    for (FileNamesGrouping::const_iterator groupIter = result.begin(); groupIter != result.end(); ++groupIter)
    {
      FileNamesGrouping groupsOf3DBlocks; // intermediate result for only this group(!)
      StringContainer filesStillToAnalyze = groupIter->second.GetFilenames();
      std::string groupUID = groupIter->first;
      unsigned int subgroup(0);
      MITK_DEBUG << "Analyze group " << groupUID << " of " << groupIter->second.GetFilenames().size() << " files";

      while (!filesStillToAnalyze.empty()) // repeat until all files are grouped somehow
      {
        SliceGroupingAnalysisResult analysisResult = AnalyzeFileForITKImageSeriesReaderSpacingAssumption(
          filesStillToAnalyze, groupImagesWithGantryTilt, scanner.GetMappings());

        // enhance the UID for additional groups
        std::stringstream newGroupUID;
        newGroupUID << groupUID << '.' << subgroup;

        ImageBlockDescriptor thisBlock(analysisResult.GetBlockFilenames());

        std::string firstFileInBlock = thisBlock.GetFilenames().front();

        thisBlock.SetImageBlockUID(newGroupUID.str());
        thisBlock.SetSeriesInstanceUID(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagSeriesInstanceUID)));
        thisBlock.SetHasGantryTiltCorrected(analysisResult.ContainsGantryTilt());
        thisBlock.SetSOPClassUID(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagSOPClassUID)));
        thisBlock.SetNumberOfFrames(
          ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagNumberOfFrames)));
        thisBlock.SetModality(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagModality)));
        thisBlock.SetPixelSpacingInformation(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagPixelSpacing)),
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(firstFileInBlock.c_str(), tagImagerPixelSpacing)));
        thisBlock.SetHasMultipleTimePoints(false);

        groupsOf3DBlocks[newGroupUID.str()] = thisBlock;

        // MITK_DEBUG << "Result: sorted 3D group " << newGroupUID.str() << " with " << groupsOf3DBlocks[
        // newGroupUID.str() ].GetFilenames().size() << " files";
        MITK_DEBUG << "Result: sorted 3D group with " << groupsOf3DBlocks[newGroupUID.str()].GetFilenames().size()
                   << " files";
        StringContainer debugOutputFiles = analysisResult.GetBlockFilenames();
        for (StringContainer::const_iterator siter = debugOutputFiles.begin(); siter != debugOutputFiles.end(); ++siter)
          MITK_DEBUG << "  IN  " << *siter;

        ++subgroup;

        filesStillToAnalyze = analysisResult.GetUnsortedFilenames(); // remember what needs further analysis
        for (StringContainer::const_iterator siter = filesStillToAnalyze.begin(); siter != filesStillToAnalyze.end();
             ++siter)
          MITK_DEBUG << " OUT  " << *siter;
      }

      // end of grouping, now post-process groups

      // PART IV: attempt to group blocks to 3D+t blocks if requested
      //           inspect entries of groupsOf3DBlocks
      //            - 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
        groupsOf3DPlusTBlocks.insert(groupsOf3DBlocks.begin(), groupsOf3DBlocks.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 (FileNamesGrouping::const_iterator block3DIter = groupsOf3DBlocks.begin();
             block3DIter != groupsOf3DBlocks.end();
             ++block3DIter)
        {
          unsigned int numberOfFilesInThisBlock = block3DIter->second.GetFilenames().size();
          std::string thisBlockKey = block3DIter->first;

          if (numberOfFilesInPreviousBlock == 0)
          {
            numberOfFilesInPreviousBlock = numberOfFilesInThisBlock;
            groupsOf3DPlusTBlocks[thisBlockKey] = block3DIter->second;
            MITK_DEBUG << "  3D+t group " << thisBlockKey;
            previousBlockKey = thisBlockKey;
          }
          else
          {
            bool identicalOrigins;
            try
            {
              // 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

              const char *origin_value = scanner.GetValue(groupsOf3DBlocks[thisBlockKey].GetFilenames().front().c_str(),
                                                          tagImagePositionPatient),
                         *previous_origin_value = scanner.GetValue(
                           groupsOf3DBlocks[previousBlockKey].GetFilenames().front().c_str(), tagImagePositionPatient),
                         *destination_value = scanner.GetValue(
                           groupsOf3DBlocks[thisBlockKey].GetFilenames().back().c_str(), tagImagePositionPatient),
                         *previous_destination_value = scanner.GetValue(
                           groupsOf3DBlocks[previousBlockKey].GetFilenames().back().c_str(), tagImagePositionPatient);

              if (!origin_value || !previous_origin_value || !destination_value || !previous_destination_value)
              {
                identicalOrigins = false;
              }
              else
              {
                std::string thisOriginString = ConstCharStarToString(origin_value);
                std::string previousOriginString = ConstCharStarToString(previous_origin_value);

                // also compare last origin, because this might differ if z-spacing is different
                std::string thisDestinationString = ConstCharStarToString(destination_value);
                std::string previousDestinationString = ConstCharStarToString(previous_destination_value);

                identicalOrigins =
                  ((thisOriginString == previousOriginString) && (thisDestinationString == previousDestinationString));
              }
            }
            catch (...)
            {
              identicalOrigins = false;
            }

            if (identicalOrigins && (numberOfFilesInPreviousBlock == numberOfFilesInThisBlock))
            {
              // group with previous block
              groupsOf3DPlusTBlocks[previousBlockKey].AddFiles(block3DIter->second.GetFilenames());
              groupsOf3DPlusTBlocks[previousBlockKey].SetHasMultipleTimePoints(true);
              MITK_DEBUG << "  --> group enhanced with another timestep";
            }
            else
            {
              // start a new block
              groupsOf3DPlusTBlocks[thisBlockKey] = block3DIter->second;
              int numberOfTimeSteps =
                groupsOf3DPlusTBlocks[previousBlockKey].GetFilenames().size() / numberOfFilesInPreviousBlock;
              MITK_DEBUG << "  ==> group closed with " << numberOfTimeSteps << " time steps";
              previousBlockKey = thisBlockKey;
              MITK_DEBUG << "  3D+t group " << thisBlockKey << " started";
            }
          }

          numberOfFilesInPreviousBlock = numberOfFilesInThisBlock;
        }
      }
    }

    MITK_DEBUG << "================================================================================";
    MITK_DEBUG << "Summary: ";
    for (FileNamesGrouping::const_iterator groupIter = groupsOf3DPlusTBlocks.begin();
         groupIter != groupsOf3DPlusTBlocks.end();
         ++groupIter)
    {
      ImageBlockDescriptor block = groupIter->second;
      MITK_DEBUG << "  " << block.GetFilenames().size() << " '" << block.GetModality() << "' images ("
                 << block.GetSOPClassUIDAsString() << ") in volume " << block.GetImageBlockUID();
      MITK_DEBUG << "    (gantry tilt : " << (block.HasGantryTiltCorrected() ? "Yes" : "No") << "; "
                                                                                                "pixel spacing : "
                 << PixelSpacingInterpretationToString(block.GetPixelSpacingType()) << "; "
                                                                                       "3D+t: "
                 << (block.HasMultipleTimePoints() ? "Yes" : "No") << "; "
                                                                      "reader support: "
                 << ReaderImplementationLevelToString(block.GetReaderImplementationLevel()) << ")";
      StringContainer debugOutputFiles = block.GetFilenames();
      for (StringContainer::const_iterator siter = debugOutputFiles.begin(); siter != debugOutputFiles.end(); ++siter)
        MITK_DEBUG << "  F " << *siter;
    }
    MITK_DEBUG << "================================================================================";

    return groupsOf3DPlusTBlocks;
  }

  DicomSeriesReader::FileNamesGrouping DicomSeriesReader::GetSeries(const std::string &dir,
                                                                    bool groupImagesWithGantryTilt,
                                                                    const StringContainer &restrictions)
  {
    gdcm::Directory directoryLister;
    directoryLister.Load(dir.c_str(), false); // non-recursive
    return GetSeries(directoryLister.GetFilenames(), groupImagesWithGantryTilt, 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 ( const std::exception & )
    {
      // we are happy with even nothing, this will just group images of a series
      // 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 tagImagerPixelSpacing(0x0018, 0x1164); // imager 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
    const gdcm::Tag tagNumberOfFrames(0x0028, 0x0008);     // number of frames

    const char *tagSeriesInstanceUid = tagValueMap[tagSeriesInstanceUID];
    if (!tagSeriesInstanceUid)
    {
      mitkThrow() << "CreateMoreUniqueSeriesIdentifier() could not access series instance UID. Something is seriously "
                     "wrong with this image, so stopping here.";
    }
    std::string constructedID = tagSeriesInstanceUid;

    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagNumberOfRows);
    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagNumberOfColumns);
    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagPixelSpacing);
    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagImagerPixelSpacing);
    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagSliceThickness);
    constructedID += CreateSeriesIdentifierPart(tagValueMap, tagNumberOfFrames);

    // be a bit tolerant for orienatation, let only the first few digits matter
    // (http://bugs.mitk.org/show_bug.cgi?id=12263)
    // NOT constructedID += CreateSeriesIdentifierPart( tagValueMap, tagImageOrientation );
    if (tagValueMap.find(tagImageOrientation) != tagValueMap.end())
    {
      bool conversionError(false);
      Vector3D right;
      right.Fill(0.0);
      Vector3D up;
      right.Fill(0.0);
      DICOMStringToOrientationVectors(tagValueMap[tagImageOrientation], right, up, conversionError);
      // string  newstring sprintf(simplifiedOrientationString, "%.3f\\%.3f\\%.3f\\%.3f\\%.3f\\%.3f", right[0],
      // right[1],
      // right[2], up[0], up[1], up[2]);
      std::ostringstream ss;
      ss.setf(std::ios::fixed, std::ios::floatfield);
      ss.precision(5);
      ss << right[0] << "\\" << right[1] << "\\" << right[2] << "\\" << up[0] << "\\" << up[1] << "\\" << up[2];
      std::string simplifiedOrientationString(ss.str());

      constructedID += IDifyTagValue(simplifiedOrientationString);
    }

    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 < IDifiedValue.size(); i++)
    {
      while (i < IDifiedValue.size() &&
             !(IDifiedValue[i] == '.' || (IDifiedValue[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,
                                                                  bool groupImagesWithGantryTilt,
                                                                  const StringContainer &restrictions)
  {
    FileNamesGrouping allSeries = GetSeries(dir, groupImagesWithGantryTilt, restrictions);
    StringContainer resultingFileList;

    for (FileNamesGrouping::const_iterator idIter = allSeries.begin(); idIter != allSeries.end(); ++idIter)
    {
      if (idIter->first.find(series_uid) == 0) // this ID starts with given series_uid
      {
        return idIter->second.GetFilenames();
      }
    }

    return resultingFileList;
  }

  DicomSeriesReader::StringContainer DicomSeriesReader::SortSeriesSlices(const StringContainer &unsortedFilenames)
  {
    /* we CAN expect a group of equal
       - series instance uid
       - image orientation
       - pixel spacing
       - imager pixel spacing
       - slice thickness
       - number of rows/columns

       (each piece of information except the rows/columns might be missing)

       sorting with GdcmSortFunction tries its best by sorting by spatial position
       and more hints (acquisition number, acquisition time, trigger time) but will
       always produce a sorting by falling back to SOP Instance UID.
    */
    gdcm::Sorter sorter;

    sorter.SetSortFunction(DicomSeriesReader::GdcmSortFunction);
    try
    {
      if (sorter.Sort(unsortedFilenames))
      {
        return sorter.GetFilenames();
      }
      else
      {
        MITK_WARN << "Sorting error. Leaving series unsorted.";
        return unsortedFilenames;
      }
    }
    catch ( const std::logic_error & )
    {
      MITK_WARN << "Sorting error. Leaving series unsorted.";
      return unsortedFilenames;
    }
  }

  bool DicomSeriesReader::GdcmSortFunction(const gdcm::DataSet &ds1, const gdcm::DataSet &ds2)
  {
    // This method MUST accept missing location and position information (and all else, too)
    // because we cannot rely on anything
    // (restriction on the sentence before: we have to provide consistent sorting, so we
    // rely on the minimum information all DICOM files need to provide: SOP Instance UID)

    /* we CAN expect a group of equal
       - series instance uid
       - image orientation
       - pixel spacing
       - imager pixel spacing
       - slice thickness
       - number of rows/columns
    */
    static const gdcm::Tag tagImagePositionPatient(0x0020, 0x0032); // Image Position (Patient)
    static const gdcm::Tag tagImageOrientation(0x0020, 0x0037);     // Image Orientation

    // see if we have Image Position and Orientation
    if (ds1.FindDataElement(tagImagePositionPatient) && ds1.FindDataElement(tagImageOrientation) &&
        ds2.FindDataElement(tagImagePositionPatient) && ds2.FindDataElement(tagImageOrientation))
    {
      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);

      /*
         we tolerate very small differences in image orientation, since we got to know about
         acquisitions where these values change across a single series (7th decimal digit)
         (http://bugs.mitk.org/show_bug.cgi?id=12263)

         still, we want to check if our assumption of 'almost equal' orientations is valid
       */
      for (unsigned int dim = 0; dim < 6; ++dim)
      {
        if (fabs(image_orientation2[dim] - image_orientation1[dim]) > 0.0001)
        {
          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;

      // this computes the distance from world origin (0,0,0) ALONG THE NORMAL of the image planes
      for (unsigned char i = 0u; i < 3u; ++i)
      {
        dist1 += normal[i] * image_pos1[i];
        dist2 += normal[i] * image_pos2[i];
      }

      // if we can sort by just comparing the distance, we do exactly that
      if (fabs(dist1 - dist2) >= mitk::eps)
      {
        // default: compare position
        return dist1 < dist2;
      }
      else // we need to check more properties to distinguish slices
      {
        // try to sort by Acquisition Number
        static const gdcm::Tag tagAcquisitionNumber(0x0020, 0x0012);
        if (ds1.FindDataElement(tagAcquisitionNumber) && ds2.FindDataElement(tagAcquisitionNumber))
        {
          gdcm::Attribute<0x0020, 0x0012> acquisition_number1; // Acquisition number
          gdcm::Attribute<0x0020, 0x0012> acquisition_number2;

          acquisition_number1.Set(ds1);
          acquisition_number2.Set(ds2);

          if (acquisition_number1 != acquisition_number2)
          {
            return acquisition_number1 < acquisition_number2;
          }
          else // neither position nor acquisition number are good for sorting, so check more
          {
            // try to sort by Acquisition Time
            static const gdcm::Tag tagAcquisitionTime(0x0008, 0x0032);
            if (ds1.FindDataElement(tagAcquisitionTime) && ds2.FindDataElement(tagAcquisitionTime))
            {
              gdcm::Attribute<0x0008, 0x0032> acquisition_time1; // Acquisition time
              gdcm::Attribute<0x0008, 0x0032> acquisition_time2;

              acquisition_time1.Set(ds1);
              acquisition_time2.Set(ds2);

              if (acquisition_time1 != acquisition_time2)
              {
                return acquisition_time1 < acquisition_time2;
              }
              else // we gave up on image position, acquisition number and acquisition time now
              {
                // let's try trigger time
                static const gdcm::Tag tagTriggerTime(0x0018, 0x1060);
                if (ds1.FindDataElement(tagTriggerTime) && ds2.FindDataElement(tagTriggerTime))
                {
                  gdcm::Attribute<0x0018, 0x1060> trigger_time1; // Trigger time
                  gdcm::Attribute<0x0018, 0x1060> trigger_time2;

                  trigger_time1.Set(ds1);
                  trigger_time2.Set(ds2);

                  if (trigger_time1 != trigger_time2)
                  {
                    return trigger_time1 < trigger_time2;
                  }
                  // ELSE!
                  // for this and many previous ifs we fall through if nothing lets us sort
                } // .
              }   // .
            }     // .
          }
        }
      }
    } // .

    // LAST RESORT: all valuable information for sorting is missing.
    // Sort by some meaningless but unique identifiers to satisfy the sort function
    static const gdcm::Tag tagSOPInstanceUID(0x0008, 0x0018);
    if (ds1.FindDataElement(tagSOPInstanceUID) && ds2.FindDataElement(tagSOPInstanceUID))
    {
      MITK_DEBUG
        << "Dicom images are missing attributes for a meaningful sorting, falling back to SOP instance UID comparison.";
      gdcm::Attribute<0x0008, 0x0018> SOPInstanceUID1; // SOP instance UID is mandatory and unique
      gdcm::Attribute<0x0008, 0x0018> SOPInstanceUID2;

      SOPInstanceUID1.Set(ds1);
      SOPInstanceUID2.Set(ds2);

      return SOPInstanceUID1 < SOPInstanceUID2;
    }
    else
    {
      // no DICOM file should really come down here, this should only be reached with unskillful and unlucky
      // manipulation
      // of files
      std::string error_message("Malformed DICOM images, which do not even contain a SOP Instance UID.");
      MITK_ERROR << error_message;
      throw std::logic_error(error_message);
    }
  }

  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(StringContainer filenames,
                                                        const gdcm::Scanner::MappingType &tagValueMappings_,
                                                        DcmIoType *io,
                                                        const ImageBlockDescriptor &blockInfo,
                                                        Image *image)
  {
    std::list<StringContainer> imageBlock;
    imageBlock.push_back(filenames);
    CopyMetaDataToImageProperties(imageBlock, tagValueMappings_, io, blockInfo, image);
  }

  void DicomSeriesReader::CopyMetaDataToImageProperties(std::list<StringContainer> imageBlock,
                                                        const gdcm::Scanner::MappingType &tagValueMappings_,
                                                        DcmIoType *io,
                                                        const ImageBlockDescriptor &blockInfo,
                                                        Image *image)
  {
    if (!io || !image)
      return;

    StringLookupTable filesForSlices;
    StringLookupTable sliceLocationForSlices;
    StringLookupTable instanceNumberForSlices;
    StringLookupTable SOPInstanceNumberForSlices;

    auto &tagValueMappings = const_cast<gdcm::Scanner::MappingType &>(tagValueMappings_);

    // DICOM tags which should be added to the image properties
    const gdcm::Tag tagSliceLocation(0x0020, 0x1041); // slice location

    const gdcm::Tag tagInstanceNumber(0x0020, 0x0013); // (image) instance number

    const gdcm::Tag tagSOPInstanceNumber(0x0008, 0x0018); // SOP instance number
    unsigned int timeStep(0);

    std::string propertyKeySliceLocation = "dicom.image.0020.1041";
    std::string propertyKeyInstanceNumber = "dicom.image.0020.0013";
    std::string propertyKeySOPInstanceNumber = "dicom.image.0008.0018";

    // tags for each image
    for (auto i = imageBlock.begin(); i != imageBlock.end(); i++, timeStep++)
    {
      const StringContainer &files = (*i);
      unsigned int slice(0);
      for (auto fIter = files.begin(); fIter != files.end(); ++fIter, ++slice)
      {
        filesForSlices.SetTableValue(slice, *fIter);
        gdcm::Scanner::TagToValue tagValueMapForFile = tagValueMappings[fIter->c_str()];
        if (tagValueMapForFile.find(tagSliceLocation) != tagValueMapForFile.end())
          sliceLocationForSlices.SetTableValue(slice, tagValueMapForFile[tagSliceLocation]);
        if (tagValueMapForFile.find(tagInstanceNumber) != tagValueMapForFile.end())
          instanceNumberForSlices.SetTableValue(slice, tagValueMapForFile[tagInstanceNumber]);
        if (tagValueMapForFile.find(tagSOPInstanceNumber) != tagValueMapForFile.end())
          SOPInstanceNumberForSlices.SetTableValue(slice, tagValueMapForFile[tagSOPInstanceNumber]);
      }

      image->SetProperty("files", StringLookupTableProperty::New(filesForSlices));

      // If more than one time step add postfix ".t" + timestep
      if (timeStep != 0)
      {
        std::ostringstream postfix;
        postfix << ".t" << timeStep;

        propertyKeySliceLocation.append(postfix.str());
        propertyKeyInstanceNumber.append(postfix.str());
        propertyKeySOPInstanceNumber.append(postfix.str());
      }
      image->SetProperty(propertyKeySliceLocation.c_str(), StringLookupTableProperty::New(sliceLocationForSlices));
      image->SetProperty(propertyKeyInstanceNumber.c_str(), StringLookupTableProperty::New(instanceNumberForSlices));
      image->SetProperty(propertyKeySOPInstanceNumber.c_str(),
                         StringLookupTableProperty::New(SOPInstanceNumberForSlices));
    }

    // Copy tags for series, study, patient level (leave interpretation to application).
    // These properties will be copied to the DataNode by DicomSeriesReader.

    // tags for the series (we just use the one that ITK copied to its dictionary (proably that of the last slice)
    const itk::MetaDataDictionary &dict = io->GetMetaDataDictionary();
    const TagToPropertyMapType &propertyLookup = DicomSeriesReader::GetDICOMTagsToMITKPropertyMap();

    auto dictIter = dict.Begin();
    while (dictIter != dict.End())
    {
      // MITK_DEBUG << "Key " << dictIter->first;
      std::string value;
      if (itk::ExposeMetaData<std::string>(dict, dictIter->first, value))
      {
        // MITK_DEBUG << "Value " << value;

        auto valuePosition = propertyLookup.find(dictIter->first);
        if (valuePosition != propertyLookup.end())
        {
          std::string propertyKey = valuePosition->second;
          // MITK_DEBUG << "--> " << propertyKey;

          image->SetProperty(propertyKey.c_str(), StringProperty::New(value));
        }
      }
      else
      {
        MITK_WARN << "Tag " << dictIter->first << " not read as string as expected. Ignoring...";
      }
      ++dictIter;
    }

    // copy imageblockdescriptor as properties
    image->SetProperty("dicomseriesreader.SOPClass", StringProperty::New(blockInfo.GetSOPClassUIDAsString()));
    image->SetProperty(
      "dicomseriesreader.ReaderImplementationLevelString",
      StringProperty::New(ReaderImplementationLevelToString(blockInfo.GetReaderImplementationLevel())));
    image->SetProperty("dicomseriesreader.ReaderImplementationLevel",
                       GenericProperty<ReaderImplementationLevel>::New(blockInfo.GetReaderImplementationLevel()));
    image->SetProperty("dicomseriesreader.PixelSpacingInterpretationString",
                       StringProperty::New(PixelSpacingInterpretationToString(blockInfo.GetPixelSpacingType())));
    image->SetProperty("dicomseriesreader.PixelSpacingInterpretation",
                       GenericProperty<PixelSpacingInterpretation>::New(blockInfo.GetPixelSpacingType()));
    image->SetProperty("dicomseriesreader.MultiFrameImage", BoolProperty::New(blockInfo.IsMultiFrameImage()));
    image->SetProperty("dicomseriesreader.GantyTiltCorrected", BoolProperty::New(blockInfo.HasGantryTiltCorrected()));
    image->SetProperty("dicomseriesreader.3D+t", BoolProperty::New(blockInfo.HasMultipleTimePoints()));
  }

  void DicomSeriesReader::FixSpacingInformation(mitk::Image *image, const ImageBlockDescriptor &imageBlockDescriptor)
  {
    // spacing provided by ITK/GDCM
    Vector3D imageSpacing = image->GetGeometry()->GetSpacing();
    ScalarType imageSpacingX = imageSpacing[0];
    ScalarType imageSpacingY = imageSpacing[1];

    // spacing as desired by MITK (preference for "in patient", else "on detector", or "1.0/1.0")
    ScalarType desiredSpacingX = imageSpacingX;
    ScalarType desiredSpacingY = imageSpacingY;
    imageBlockDescriptor.GetDesiredMITKImagePixelSpacing(desiredSpacingX, desiredSpacingY);

    MITK_DEBUG << "Loaded spacing: " << imageSpacingX << "/" << imageSpacingY;
    MITK_DEBUG << "Corrected spacing: " << desiredSpacingX << "/" << desiredSpacingY;

    imageSpacing[0] = desiredSpacingX;
    imageSpacing[1] = desiredSpacingY;
    image->GetGeometry()->SetSpacing(imageSpacing);
  }

  void DicomSeriesReader::LoadDicom(const StringContainer &filenames,
                                    DataNode &node,
                                    bool sort,
                                    bool load4D,
                                    bool correctTilt,
                                    UpdateCallBackMethod callback,
                                    Image::Pointer preLoadedImageBlock)
  {
    mitk::LocaleSwitch localeSwitch("C");
    std::locale previousCppLocale(std::cin.getloc());
    std::locale l("C");
    std::cin.imbue(l);

    ImageBlockDescriptor imageBlockDescriptor;

    const gdcm::Tag tagImagePositionPatient(0x0020, 0x0032); // Image Position (Patient)
    const gdcm::Tag tagImageOrientation(0x0020, 0x0037);     // Image Orientation
    const gdcm::Tag tagSeriesInstanceUID(0x0020, 0x000e);    // Series Instance UID
    const gdcm::Tag tagSOPClassUID(0x0008, 0x0016);          // SOP class UID
    const gdcm::Tag tagModality(0x0008, 0x0060);             // modality
    const gdcm::Tag tagPixelSpacing(0x0028, 0x0030);         // pixel spacing
    const gdcm::Tag tagImagerPixelSpacing(0x0018, 0x1164);   // imager pixel spacing
    const gdcm::Tag tagNumberOfFrames(0x0028, 0x0008);       // number of frames

    try
    {
      Image::Pointer image = preLoadedImageBlock.IsNull() ? Image::New() : preLoadedImageBlock;
      CallbackCommand *command = callback ? new CallbackCommand(callback) : nullptr;
      bool initialize_node = false;

      /* special case for Philips 3D+t ultrasound images */
      if (DicomSeriesReader::IsPhilips3DDicom(filenames.front().c_str()))
      {
        // TODO what about imageBlockDescriptor?
        // TODO what about preLoadedImageBlock?
        ReadPhilips3DDicom(filenames.front().c_str(), image);
        initialize_node = true;
      }
      else
      {
        /* default case: assume "normal" image blocks, possibly 3D+t */
        bool canLoadAs4D(true);
        gdcm::Scanner scanner;
        ScanForSliceInformation(filenames, scanner);

        // need non-const access for map
        auto &tagValueMappings = const_cast<gdcm::Scanner::MappingType &>(scanner.GetMappings());

        std::list<StringContainer> imageBlocks =
          SortIntoBlocksFor3DplusT(filenames, tagValueMappings, sort, canLoadAs4D);
        unsigned int volume_count = imageBlocks.size();

        imageBlockDescriptor.SetSeriesInstanceUID(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagSeriesInstanceUID)));
        imageBlockDescriptor.SetSOPClassUID(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagSOPClassUID)));
        imageBlockDescriptor.SetModality(
          DicomSeriesReader::ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagModality)));
        imageBlockDescriptor.SetNumberOfFrames(
          ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagNumberOfFrames)));
        imageBlockDescriptor.SetPixelSpacingInformation(
          ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagPixelSpacing)),
          ConstCharStarToString(scanner.GetValue(filenames.front().c_str(), tagImagerPixelSpacing)));

        GantryTiltInformation tiltInfo;

        // check possibility of a single slice with many timesteps. In this case, don't check for tilt, no second slice
        // possible
        if (!imageBlocks.empty() && imageBlocks.front().size() > 1 && correctTilt)
        {
          // check tiltedness here, potentially fixup ITK's loading result by shifting slice contents
          // check first and last position slice from tags, make some calculations to detect tilt

          std::string firstFilename(imageBlocks.front().front());
          // calculate from first and last slice to minimize rounding errors
          std::string secondFilename(imageBlocks.front().back());

          std::string imagePosition1(
            ConstCharStarToString(tagValueMappings[firstFilename.c_str()][tagImagePositionPatient]));
          std::string imageOrientation(
            ConstCharStarToString(tagValueMappings[firstFilename.c_str()][tagImageOrientation]));
          std::string imagePosition2(
            ConstCharStarToString(tagValueMappings[secondFilename.c_str()][tagImagePositionPatient]));

          bool ignoredConversionError(-42); // hard to get here, no graceful way to react
          Point3D origin1(DICOMStringToPoint3D(imagePosition1, ignoredConversionError));
          Point3D origin2(DICOMStringToPoint3D(imagePosition2, ignoredConversionError));

          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
          DICOMStringToOrientationVectors(imageOrientation, right, up, ignoredConversionError);

          tiltInfo = GantryTiltInformation(origin1, origin2, right, up, filenames.size() - 1);
          correctTilt = tiltInfo.IsSheared() && tiltInfo.IsRegularGantryTilt();
        }
        else
        {
          correctTilt = false; // we CANNOT do that
        }

        imageBlockDescriptor.SetHasGantryTiltCorrected(correctTilt);

        if (volume_count == 1 || !canLoadAs4D || !load4D)
        {
          DcmIoType::Pointer io;
          image = MultiplexLoadDICOMByITK(
            imageBlocks.front(), correctTilt, tiltInfo, io, command, preLoadedImageBlock); // load first 3D block

          imageBlockDescriptor.AddFiles(imageBlocks.front()); // only the first part is loaded
          imageBlockDescriptor.SetHasMultipleTimePoints(false);

          FixSpacingInformation(image, imageBlockDescriptor);
          CopyMetaDataToImageProperties(imageBlocks.front(), scanner.GetMappings(), io, imageBlockDescriptor, image);

          initialize_node = true;
        }
        else if (volume_count > 1)
        {
          imageBlockDescriptor.AddFiles(filenames); // all is loaded
          imageBlockDescriptor.SetHasMultipleTimePoints(true);

          DcmIoType::Pointer io;
          image = MultiplexLoadDICOMByITK4D(
            imageBlocks, imageBlockDescriptor, correctTilt, tiltInfo, io, command, preLoadedImageBlock);

          initialize_node = true;
        }
      }

      if (initialize_node)
      {
        // forward some image properties to node
        node.GetPropertyList()->ConcatenatePropertyList(image->GetPropertyList(), true);

        std::string patientName = "NoName";
        if (node.GetProperty("dicom.patient.PatientsName"))
          patientName = node.GetProperty("dicom.patient.PatientsName")->GetValueAsString();

        node.SetData(image);
        node.SetName(patientName);
        std::cin.imbue(previousCppLocale);
      }

      MITK_DEBUG << "--------------------------------------------------------------------------------";
      MITK_DEBUG << "DICOM files loaded (from series UID " << imageBlockDescriptor.GetSeriesInstanceUID() << "):";
      MITK_DEBUG << "  " << imageBlockDescriptor.GetFilenames().size() << " '" << imageBlockDescriptor.GetModality()
                 << "' files (" << imageBlockDescriptor.GetSOPClassUIDAsString() << ") loaded into 1 mitk::Image";
      MITK_DEBUG << "  multi-frame: " << (imageBlockDescriptor.IsMultiFrameImage() ? "Yes" : "No");
      MITK_DEBUG << "  reader support: "
                 << ReaderImplementationLevelToString(imageBlockDescriptor.GetReaderImplementationLevel());
      MITK_DEBUG << "  pixel spacing type: "
                 << PixelSpacingInterpretationToString(imageBlockDescriptor.GetPixelSpacingType()) << " "
                 << image->GetGeometry()->GetSpacing()[0] << "/" << image->GetGeometry()->GetSpacing()[0];
      MITK_DEBUG << "  gantry tilt corrected: " << (imageBlockDescriptor.HasGantryTiltCorrected() ? "Yes" : "No");
      MITK_DEBUG << "  3D+t: " << (imageBlockDescriptor.HasMultipleTimePoints() ? "Yes" : "No");
      MITK_DEBUG << "--------------------------------------------------------------------------------";
    }
    catch ( const std::exception &e )
    {
      // reset locale then throw up
      std::cin.imbue(previousCppLocale);

      MITK_DEBUG << "Caught exception in DicomSeriesReader::LoadDicom";

      throw e;
    }
  }

  void DicomSeriesReader::ScanForSliceInformation(const StringContainer &filenames, gdcm::Scanner &scanner)
  {
    const gdcm::Tag tagImagePositionPatient(0x0020, 0x0032); // Image position (Patient)
    scanner.AddTag(tagImagePositionPatient);

    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 tagSliceLocation(0x0020, 0x1041); // slice location
    scanner.AddTag(tagSliceLocation);

    const gdcm::Tag tagInstanceNumber(0x0020, 0x0013); // (image) instance number
    scanner.AddTag(tagInstanceNumber);

    const gdcm::Tag tagSOPInstanceNumber(0x0008, 0x0018); // SOP instance number
    scanner.AddTag(tagSOPInstanceNumber);

    const gdcm::Tag tagPixelSpacing(0x0028, 0x0030); // Pixel Spacing
    scanner.AddTag(tagPixelSpacing);

    const gdcm::Tag tagImagerPixelSpacing(0x0018, 0x1164); // Imager Pixel Spacing
    scanner.AddTag(tagImagerPixelSpacing);

    const gdcm::Tag tagModality(0x0008, 0x0060); // Modality
    scanner.AddTag(tagModality);

    const gdcm::Tag tagSOPClassUID(0x0008, 0x0016); // SOP Class UID
    scanner.AddTag(tagSOPClassUID);

    const gdcm::Tag tagNumberOfFrames(0x0028, 0x0008); // number of frames
    scanner.AddTag(tagNumberOfFrames);

    scanner.Scan(filenames); // make available image information for each file
  }

  std::list<DicomSeriesReader::StringContainer> DicomSeriesReader::SortIntoBlocksFor3DplusT(
    const StringContainer &presortedFilenames,
    const gdcm::Scanner::MappingType &tagValueMappings,
    bool /*sort*/,
    bool &canLoadAs4D)
  {
    std::list<StringContainer> 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);

    std::string firstPosition;
    unsigned int numberOfBlocks(0); // number of 3D image blocks

    static const gdcm::Tag tagImagePositionPatient(0x0020, 0x0032); // Image position (Patient)
    const gdcm::Tag tagModality(0x0008, 0x0060);

    // loop files to determine number of image blocks
    for (StringContainer::const_iterator fileIter = sorted_filenames.begin(); fileIter != sorted_filenames.end();
         ++fileIter)
    {
      gdcm::Scanner::TagToValue tagToValueMap = tagValueMappings.find(fileIter->c_str())->second;

      if (tagToValueMap.find(tagImagePositionPatient) == tagToValueMap.end())
      {
        const std::string &modality = tagToValueMap.find(tagModality)->second;
        if (modality.compare("RTIMAGE ") == 0 || modality.compare("RTIMAGE") == 0)
        {
          MITK_WARN << "Modality " << modality << " is not fully supported yet.";
          numberOfBlocks = 1;
          break;
        }
        else
        {
          // we expect to get images w/ missing position information ONLY as separated blocks.
          assert(presortedFilenames.size() == 1);
          numberOfBlocks = 1;
          break;
        }
      }

      std::string position = tagToValueMap.find(tagImagePositionPatient)->second;
      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 << " 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;
  }

  Image::Pointer DicomSeriesReader::MultiplexLoadDICOMByITK(const StringContainer &filenames,
                                                            bool correctTilt,
                                                            const GantryTiltInformation &tiltInfo,
                                                            DcmIoType::Pointer &io,
                                                            CallbackCommand *command,
                                                            Image::Pointer preLoadedImageBlock)
  {
    io = DcmIoType::New();
    io->SetFileName(filenames.front().c_str());
    io->ReadImageInformation();

    if (io->GetPixelType() == itk::ImageIOBase::SCALAR)
    {
      return MultiplexLoadDICOMByITKScalar(filenames, correctTilt, tiltInfo, io, command, preLoadedImageBlock);
    }
    else if (io->GetPixelType() == itk::ImageIOBase::RGB)
    {
      return MultiplexLoadDICOMByITKRGBPixel(filenames, correctTilt, tiltInfo, io, command, preLoadedImageBlock);
    }
    else
    {
      return nullptr;
    }
  }

  Image::Pointer DicomSeriesReader::MultiplexLoadDICOMByITK4D(std::list<StringContainer> &imageBlocks,
                                                              ImageBlockDescriptor imageBlockDescriptor,
                                                              bool correctTilt,
                                                              const GantryTiltInformation &tiltInfo,
                                                              DcmIoType::Pointer &io,
                                                              CallbackCommand *command,
                                                              Image::Pointer preLoadedImageBlock)
  {
    io = DcmIoType::New();
    io->SetFileName(imageBlocks.front().front().c_str());
    io->ReadImageInformation();

    if (io->GetPixelType() == itk::ImageIOBase::SCALAR)
    {
      return MultiplexLoadDICOMByITK4DScalar(
        imageBlocks, imageBlockDescriptor, correctTilt, tiltInfo, io, command, preLoadedImageBlock);
    }
    else if (io->GetPixelType() == itk::ImageIOBase::RGB)
    {
      return MultiplexLoadDICOMByITK4DRGBPixel(
        imageBlocks, imageBlockDescriptor, correctTilt, tiltInfo, io, command, preLoadedImageBlock);
    }
    else
    {
      return nullptr;
    }
  }
} // end namespace mitk