/*
 *
 *  Copyright (C) 2015-2016, Open Connections GmbH
 *  All rights reserved.  See COPYRIGHT file for details.
 *
 *  This software and supporting documentation are maintained by
 *
 *    OFFIS e.V.
 *    R&D Division Health
 *    Escherweg 2
 *    D-26121 Oldenburg, Germany
 *
 *
 *  Module:  dcmseg
 *
 *  Author:  Michael Onken
 *
 *  Purpose: Class representing a Segmentation object
 *
 */
#include "dcmtk/config/osconfig.h"
#include "dcmtk/dcmdata/dcuid.h"
#include "dcmtk/dcmseg/segdoc.h"
#include "dcmtk/dcmseg/segment.h"
#include "dcmtk/dcmseg/segutils.h"
#include "dcmtk/dcmiod/iodutil.h"
#include "dcmtk/dcmfg/fgseg.h"
#include "dcmtk/dcmfg/fgplanpo.h"
#include "dcmtk/dcmfg/fgplanor.h"
#include "dcmtk/dcmfg/fgfracon.h"
#include "dcmtk/dcmfg/fgfact.h"
#include "dcmtk/dcmfg/fgderimg.h"

// default constructor (protected, instance creation via create() function)
DcmSegmentation::DcmSegmentation()
: DcmSegmentation::IODImage(OFin_place<IODImagePixelModule<Uint8> >),
  m_SegmentationSeries(DcmSegmentation::IODImage::getData(), DcmSegmentation::IODImage::getRules()),
  m_EnhancedGeneralEquipmentModule(DcmSegmentation::IODImage::getData(), DcmSegmentation::IODImage::getRules()),
  m_FG(DcmSegmentation::IODImage::getData(), DcmSegmentation::IODImage::getRules()),
  m_DimensionModule(DcmSegmentation::IODImage::getData(), DcmSegmentation::IODImage::getRules()),
  m_Frames(),
  m_ImageType("DERIVED\\PRIMARY"),
  m_ContentIdentificationMacro(),
  m_SegmentationType(DcmSegTypes::ST_BINARY),
  m_SegmentationFractionalType(DcmSegTypes::SFT_OCCUPANCY),
  m_MaximumFractionalValue(DCM_MaximumFractionalValue),
  m_Segments(),
  m_FGInterface()
{
  DcmSegmentation::initIODRules();
}


void DcmSegmentation::initIODRules()
{
  // ------------ Segmentation Image Module -------------

  // Partly overrides rules from General Image Module
  getRules()->addRule(new IODRule(DCM_ImageType, "2","1", "SegmentationImageModule", DcmIODTypes::IE_IMAGE), OFTrue);
  getRules()->addRule(new IODRule(DCM_SegmentationType, "1","1", "SegmentationImageModule", DcmIODTypes::IE_IMAGE), OFTrue);
  getRules()->addRule(new IODRule(DCM_SegmentationFractionalType, "1","1C", "SegmentationImageModule", DcmIODTypes::IE_IMAGE), OFTrue);
  getRules()->addRule(new IODRule(DCM_MaximumFractionalValue, "1","1C", "SegmentationImageModule", DcmIODTypes::IE_IMAGE), OFTrue);

  // Re-use General Image Module instead of Segmentation Image Module
  getRules()->addRule(new IODRule(DCM_LossyImageCompression, "1","1", "GeneralImageModule", DcmIODTypes::IE_IMAGE), OFTrue);
  getRules()->addRule(new IODRule(DCM_LossyImageCompressionMethod, "1-n", "1C", "GeneralImageModule", DcmIODTypes::IE_IMAGE), OFTrue);
  getRules()->addRule(new IODRule(DCM_LossyImageCompressionRatio, "1-n","1C", "GeneralImageModule", DcmIODTypes::IE_IMAGE), OFTrue);

  // Override rule from General Series Module
  getRules()->addRule(new IODRule(DCM_ReferencedPerformedProcedureStepSequence, "1","1C", "SegmentationSeriesModule", DcmIODTypes::IE_SERIES), OFTrue);
  getRules()->addRule(new IODRule(DCM_SeriesNumber, "1","1", "SegmentationSeriesModule", DcmIODTypes::IE_SERIES), OFTrue);

  // Instance Number is also used within Content Identification Macro, disable it there
  m_ContentIdentificationMacro.getIODRules().deleteRule(DCM_InstanceNumber);
}


DcmSegmentation::~DcmSegmentation()
{
  clearData();
}


// static method for loading segmentation objects
OFCondition DcmSegmentation::loadFile(const OFString& filename,
                                      DcmSegmentation*& segmentation)
{
  DcmFileFormat dcmff;
  DcmDataset *dataset = NULL;
  OFCondition result = loadFile(dcmff, filename, dataset);
  if (result.bad())
    return result;

  return loadDataset(*dataset, segmentation);
}


// static method for loading segmentation objects
OFCondition DcmSegmentation::loadDataset(DcmDataset& dataset,
                                         DcmSegmentation*& segmentation)
{
  OFCondition result = DcmSegmentation::decompress(dataset);
  if (result.bad())
    return result;

  segmentation = new DcmSegmentation();
  if (segmentation == NULL)
  {
    return EC_MemoryExhausted;
  }

  return segmentation->read(dataset);

}


OFCondition DcmSegmentation::createBinarySegmentation(DcmSegmentation*& segmentation,
                                                      const Uint16 rows,
                                                      const Uint16 columns,
                                                      const IODGeneralEquipmentModule::EquipmentInfo& equipmentInfo,
                                                      const ContentIdentificationMacro& contentIdentification)
{

  OFCondition result = createCommon(segmentation, rows, columns, equipmentInfo, contentIdentification);
  if (result.bad())
    return result;

  segmentation->m_SegmentationType = DcmSegTypes::ST_BINARY;

  return result;
}


OFCondition DcmSegmentation::createFractionalSegmentation(DcmSegmentation*& segmentation,
                                                          const Uint16 rows,
                                                          const Uint16 columns,
                                                          const DcmSegTypes::E_SegmentationFractionalType fractType,
                                                          const Uint16& maxFractionalValue,
                                                          const IODGeneralEquipmentModule::EquipmentInfo& equipmentInfo,
                                                          const ContentIdentificationMacro& contentIdentification)
{
  OFCondition result = createCommon(segmentation, rows, columns, equipmentInfo, contentIdentification);
  if (result.bad())
    return result;

  segmentation->m_SegmentationType = DcmSegTypes::ST_FRACTIONAL;
  segmentation->m_SegmentationFractionalType = fractType;
  segmentation->m_MaximumFractionalValue.putUint16(maxFractionalValue);

  return result;
}


OFCondition DcmSegmentation::createCommon(DcmSegmentation*& segmentation,
                                          const Uint16 rows,
                                          const Uint16 columns,
                                          const IODGeneralEquipmentModule::EquipmentInfo& equipmentInfo,
                                          const ContentIdentificationMacro& contentIdentification)
{
  if ( (rows == 0) || (columns == 0) )
  {
    DCMSEG_ERROR("Segmentation must have at least 1 row and 1 column");
    return EC_IllegalParameter;
  }

  segmentation = new DcmSegmentation();
  if (segmentation == NULL)
    return EC_MemoryExhausted;

  segmentation->getImagePixel().setRows(rows);
  segmentation->getImagePixel().setColumns(columns);

  OFCondition result = segmentation->setContentIdentification(contentIdentification);
  if (result.good())
  {
    OFString tempstr;
    contentIdentification.getInstanceNumber(tempstr);
    result = segmentation->getGeneralImage().setInstanceNumber(tempstr);
    if (result.bad())
    {
      delete segmentation;
      segmentation = NULL;
      return EC_InvalidValue;
    }

    DcmIODUtil::setContentDateAndTimeNow(segmentation->getGeneralImage());
    result = segmentation->setEquipmentInfo(equipmentInfo, OFTrue /* check */);
  }

  if (result.bad())
  {
    delete segmentation;
    segmentation = NULL;
  }

  return result;
}


FGDerivationImage* DcmSegmentation::createDerivationImageFG(const OFVector< ImageSOPInstanceReferenceMacro >& derivationImages,
                                                            const OFString& derivationDescription)
{
  CodeSequenceMacro derivationCode("113076", "DCM", "Segmentation");
  CodeSequenceMacro purpose("121322", "DCM", "Source Image for Image Processing Operation");
  return FGDerivationImage::createMinimal(derivationImages,
                                          derivationDescription,
                                          derivationCode,
                                          purpose);
}


OFCondition DcmSegmentation::read(DcmItem &dataset)
{

  OFString sopClass;
  if (DcmIODUtil::checkSOPClass(&dataset, UID_SegmentationStorage, sopClass).bad())
  {
    DCMSEG_ERROR("Given file does not seem to be a segmentation storage object since SOP class is: " << sopClass);
    return IOD_EC_WrongSOPClass;
  }

  // Read attributes in base classes
  DcmSegmentation::IODImage::read(dataset);

  // Read Segmentation Series Module
  m_SegmentationSeries.read(dataset);

  // Read Enhanced General Equipment (i.e. make sure all type 1 elements are
  // there, which is not checked in General Equipment Module being part of
  // DcmIODImage.
  m_EnhancedGeneralEquipmentModule.read(dataset);

  // Read functional groups module
  m_FG.read(dataset);

  // Read functional groups itself
  m_FGInterface.read(dataset);

  // Read dimension information
  m_DimensionModule.read(dataset);

  readSegmentationType(dataset);

  readSegments(dataset);

  readFrames(dataset);

  readSegmentationFractionalType(dataset);

  m_ContentIdentificationMacro.read(dataset);

  // Read specific segmentation elements
  DcmIODUtil::getAndCheckElementFromDataset(dataset, m_MaximumFractionalValue, getRules()->getByTag(DCM_MaximumFractionalValue));

  return EC_Normal;
}


OFCondition DcmSegmentation::write(DcmItem &dataset)
{
  if (!check())
  {
    return IOD_EC_InvalidObject;
  }

  OFCondition result;

  // -- Set constant default values written by external modules --
  getGeneralImage().setLossyImageCompression("00");
  getGeneralImage().setImageType(m_ImageType);
  getSOPCommon().setSOPClassUID(UID_SegmentationStorage);

  // -- Extra Study level data --

  // Enhanced Equipment Module
  if (result.good()) result = m_EnhancedGeneralEquipmentModule.write(dataset);

  // -- Extra Series level data --

  // Write segmentation-specific series level attribute (Segmentation Series Module)
  if (result.good()) result = m_SegmentationSeries.write(dataset);

  // -- Extra Image level data --

  // Write Multi-Frame Functional Groups Module
  if (result.good()) result = writeMultiFrameFunctionalGroupsModule(dataset);

  // Write Multi-Frame Dimension Module
  if (result.good()) result = writeMultiFrameDimensionModule(dataset);

  // Write segmentation image module and image pixel module
  if (result.good()) result = writeSegmentationImageModule(dataset);

  // -- Write common multi frame image IOD attributes --

  // Patient Module
  // General Study Module
  // General Series Module
  // Frame of Reference Module
  // General Equipment Module
  // General Image Module
  // Multi-frame Functional Groups Module (except functional groups itself)
  // SOP Common Module
  // Common Instance Reference Module
  if (result.good()) result = DcmSegmentation::IODImage::write(dataset);

  return result;
}


FGInterface& DcmSegmentation::getFunctionalGroups()
{
  return m_FGInterface;
}


size_t DcmSegmentation::getNumberOfFrames()
{
  return m_FGInterface.getNumberOfFrames();
}



size_t DcmSegmentation::getNumberOfSegments()
{
  return m_Segments.size();
}


IODGeneralEquipmentModule& DcmSegmentation::getEquipment()
{
  return DcmSegmentation::IODImage::getEquipment();
}


IODSegmentationSeriesModule & DcmSegmentation::getSegmentationSeriesModule()
{
  return m_SegmentationSeries;
}


OFCondition DcmSegmentation::addSegment(DcmSegment* seg,
                                        Uint16& segmentNumber)
{
  segmentNumber = 0;
  if (seg == NULL)
    return EC_IllegalParameter;

  if (m_Segments.size() == DCM_SEG_MAX_SEGMENTS)
  {
    return SG_EC_MaxSegmentsReached;
  }

  segmentNumber = m_Segments.size() + 1;
  m_Segments.push_back(seg);
  return EC_Normal;
}


OFCondition DcmSegmentation::addFrame(Uint8* pixData)
{
  OFCondition result;

  Uint16 rows, cols;
  if (getImagePixel().getRows(rows).good() && getImagePixel().getColumns(cols).good())
  {
    DcmIODTypes::Frame* frame = NULL;
    if (m_SegmentationType == DcmSegTypes::ST_BINARY)
    {
      frame = DcmSegUtils::packBinaryFrame(pixData, rows, cols);
      if (!frame)
      {
        result = IOD_EC_CannotInsertFrame;
      }
    }
    else // fractional
    {
      frame = new DcmIODTypes::Frame();
      if (frame)
      {
        frame->length = rows*cols;
        frame->pixData = pixData;
      }
      else
        result = EC_MemoryExhausted;
    }
    if (result.good())
    {
      m_Frames.push_back(frame);
    }
  }
  else
  {
    DCMSEG_ERROR("Cannot add frame since rows and/or columns are unknown");
    result = IOD_EC_CannotInsertFrame;
  }

  return result;
}


SOPInstanceReferenceMacro& DcmSegmentation::getReferencedPPS()
{
  return getSeries().getReferencedPPS();
}


const DcmIODTypes::Frame* DcmSegmentation::getFrame(const size_t& frameNo)
{
  if (frameNo > m_Frames.size() - 1)
  {
    return NULL;
  }

  return m_Frames[frameNo];
}


void DcmSegmentation::getFramesForSegment(const size_t& segmentNumber,
                                          OFVector<size_t>& frameNumbers)
{
  size_t numFrames = getNumberOfFrames();
  for (size_t count = 0; count < numFrames; count++)
  {
    FGSegmentation* fg = OFstatic_cast(FGSegmentation*, m_FGInterface.get(count, DcmFGTypes::EFG_SEGMENTATION));
    if (fg == NULL)
    {
      DCMSEG_ERROR("Cannot get segmentation functional group for frame " << count);
      return;
    }
    Uint16 refSeg;
    if (fg->getReferencedSegmentNumber(refSeg).good())
    {
      if (refSeg == segmentNumber)
      {
        frameNumbers.push_back(count);
      }
    }
  }
}


OFCondition DcmSegmentation::addForAllFrames(const FGBase& group)
{
  return m_FGInterface.addShared(group);
}


OFCondition DcmSegmentation::addFrame(Uint8* pixData,
                                      const Uint16 segmentNumber,
                                      const OFVector<FGBase*>& perFrameInformation)
{
  Uint32 frameNo = m_Frames.size(); // will be the index of the frame (counted from 0)
  OFCondition result;

  // Check input parameters
  if ( pixData == NULL )
  {
    DCMSEG_ERROR("No pixel data provided or zero length");
    result = EC_IllegalParameter;
  }
  if (segmentNumber > m_Segments.size() )
  {
    DCMSEG_ERROR("Cannot add frame: Segment with given number " << segmentNumber << " does not exist");
    result = SG_EC_NoSuchSegment;
  }
  if (result.bad())
    return result;

  OFVector<FGBase*>::const_iterator it = perFrameInformation.begin();
  while (it != perFrameInformation.end())
  {
    result = (*it)->check();
    if (result.bad())
    {
      DCMSEG_ERROR("Could not add new frame since functional group of type: " << (*it)->getType() << " is invalid: " << result.text());
      break;
    }
    result = m_FGInterface.addPerFrame(frameNo, *(*it));
    if (result.bad())
    {
      DCMSEG_ERROR("Could not add new frame since functional group of type " << (*it)->getType() << ": " << result.text());
      break;
    }
    it++;
  }

  // Now also add Segmentation Functional Group
  if (result.good())
  {
    FGSegmentation seg;
    result = seg.setReferencedSegmentNumber(segmentNumber);
    if (result.good())
    {
      result = m_FGInterface.addPerFrame(frameNo, seg);
    }
    else
    {
      DCMSEG_ERROR("Could not add new frame, invalid segment number " << segmentNumber << ": " << result.text());
    }
  }

  // Insert pixel data
  if (result.good())
  {
    result = addFrame(pixData);
  }

  // Cleanup any per-frame groups that might have been inserted and return
  if (result.bad())
  {
    for (OFVector<FGBase*>::const_iterator it2 = perFrameInformation.begin(); it2 != perFrameInformation.end(); it2++ )
    {
      m_FGInterface.deletePerFrame(frameNo, (*it2)->getType());
    }
  }

  return result;
}


ContentIdentificationMacro& DcmSegmentation::getContentIdentification()
{
  return m_ContentIdentificationMacro;
}


IODMultiframeDimensionModule& DcmSegmentation::getDimensions()
{
  return m_DimensionModule;
}


OFCondition DcmSegmentation::setLossyImageCompressionFlag(const OFString& ratios,
                                                          const OFString& methods,
                                                          const OFBool checkValues)
{
  OFCondition result = getGeneralImage().setLossyImageCompression("01");
  if (result.good() || !checkValues)
    result = getGeneralImage().setLossyImageCompressionMethod(methods);
  if (result.good() || !checkValues)
    result = getGeneralImage().setLossyImageCompressionRatio(ratios);

  if (checkValues)
    return result;
  else
    return EC_Normal;
}


OFCondition DcmSegmentation::saveFile(const OFString& filename,
                                      const E_TransferSyntax writeXfer)
{
  if ( (writeXfer != EXS_LittleEndianExplicit) &&
       (writeXfer != EXS_BigEndianExplicit) &&
       (writeXfer != EXS_LittleEndianImplicit))
  {
    DcmXfer ts(writeXfer);
    DCMSEG_ERROR("Cannot write transfer syntax: " << ts.getXferName() << " (can only write uncompressed)");
    return EC_CannotChangeRepresentation;
  }
  DcmFileFormat dcmff;
  OFCondition result = write( *(dcmff.getDataset()) );
  if (result.good())
  {
    result = dcmff.saveFile(filename.c_str(), EXS_LittleEndianExplicit);
  }
  if (result.bad())
  {
    DCMSEG_ERROR("Cannot save segmentation document to file " << filename << ": " << result.text());
  }

  return result;
}


/* -- Setter for DICOM attributes -- */

OFCondition DcmSegmentation::setEquipmentInfo(const IODGeneralEquipmentModule::EquipmentInfo& equipmentInfo,
                                              const OFBool checkValue)
{

  if (checkValue)
  {
    if ( equipmentInfo.m_Manufacturer.empty()
      || equipmentInfo.m_ManufacturerModelName.empty()
      || equipmentInfo.m_DeviceSerialNumber.empty()
      || equipmentInfo.m_SoftwareVersions.empty() )
    {
      return EC_InvalidValue;
    }
  }

  OFCondition result = getEquipment().setManufacturer(equipmentInfo.m_Manufacturer, checkValue);
  if ( result.good() )
    result = getEquipment().setManufacturerModelName(equipmentInfo.m_ManufacturerModelName, checkValue);
  if (result.good())
    result = getEquipment().setDeviceSerialNumber(equipmentInfo.m_DeviceSerialNumber, checkValue);
  if (result.good())
    result = getEquipment().setSoftwareVersions(equipmentInfo.m_SoftwareVersions, checkValue);

  return result;
}


OFCondition DcmSegmentation::setContentIdentification(const ContentIdentificationMacro& contentIdentification,
                                                      const OFBool checkValue)
{
  // Instance Number and Content Label must be filled out, rest can be empty
  OFCondition result;
  if (checkValue)
  {
    result = OFconst_cast(ContentIdentificationMacro*,&contentIdentification)->check();
  }
  if (result.bad())
    return result;

  m_ContentIdentificationMacro = contentIdentification;

  return result;
}



/* -- Getter for DICOM attributes -- */

DcmSegment* DcmSegmentation::getSegment(const unsigned int segmentNumber)
{
  // check for invalid index
  if ( (segmentNumber == 0) || (segmentNumber > m_Segments.size()) )
  {
    return NULL;
  }

  // logical segment numbering starts with 1, so subtract 1 for vector index
  return m_Segments[segmentNumber-1];
}


OFBool DcmSegmentation::getSegmentNumber(const DcmSegment* segment,
                                         unsigned int& segmentNumber)
{
  segmentNumber = 0;
  size_t max = m_Segments.size();
  for (size_t count = 0; count < max; count++)
  {
    if (m_Segments.at(count) == segment)
    {
      // logical segment numbering starts with 1 but vector index with 0
      segmentNumber = count + 1;
      return OFTrue;
    }
  }
  // not found
  return OFFalse;
}


OFCondition DcmSegmentation::getModality(OFString& value,
                                         const long signed int pos) const
{
  (void)pos;
  // Fixed for Segmentations to value "SEG"
  value = "SEG";
  return EC_Normal;
}


/* protected functions */

OFCondition DcmSegmentation::writeSegments(DcmItem& item)
{
  OFCondition result;
  DcmIODUtil::writeSubSequence<OFVector<DcmSegment*> >(result, DCM_SegmentSequence, m_Segments, item, "1-n", "1", "SegmentationImageModule");
  return result;
}


OFCondition DcmSegmentation::readSegments(DcmItem& item)
{
  return DcmIODUtil::readSubSequence<OFVector<DcmSegment*> >(item, DCM_SegmentSequence, m_Segments, "1-n", "1", "SegmentationImageModule");
}


OFCondition DcmSegmentation::readFrames(DcmItem& dataset)
{
  OFCondition result;
  Uint16 allocated, stored, high, spp, pixelRep, rows, cols, numberOfFrames;
  allocated = stored = high = spp = rows = cols = numberOfFrames = 0;
  pixelRep = 2; // invalid value for this attribute
  OFString colorModel;

  /* check the typical image pixel attributes and get correct(ed) values */
  result = getAndCheckImagePixelAttributes(dataset, allocated, stored, high, spp, pixelRep, rows, cols, numberOfFrames, colorModel);
  if (result.bad())
    return result;

  /* Check length of pixel data element */
  DcmElement* pixelData = NULL;
  if (dataset.findAndGetElement(DCM_PixelData, pixelData).bad())
    return IOD_EC_InvalidPixelData;
  if (!checkPixDataLength(pixelData, rows, cols, numberOfFrames))
    return IOD_EC_InvalidPixelData;

  /* Get pixel data values */
  Uint8* pixels = NULL;
  result = pixelData->getUint8Array(pixels);
  if (result.bad())
  {
    DCMSEG_ERROR("Cannot read pixel data");
    return result;
  }

  /* Read all frames into dedicated data structure */
  size_t pixelsPerFrame = rows * cols;
  if (m_SegmentationType == DcmSegTypes::ST_BINARY)
  {
      extractFrames(pixels, numberOfFrames, pixelsPerFrame, m_Frames);
  }
  else if (m_SegmentationType == DcmSegTypes::ST_FRACTIONAL)
  {
    for (size_t count = 0; count < numberOfFrames; count++)
    {
      DcmIODTypes::Frame *frame = new DcmIODTypes::Frame();
      frame->length = pixelsPerFrame;
      frame->pixData= new Uint8[pixelsPerFrame];
      memcpy(frame->pixData, pixels + count* pixelsPerFrame, pixelsPerFrame);
      m_Frames.push_back(frame);
    }
  }

  return result;
}



OFCondition DcmSegmentation::getAndCheckImagePixelAttributes(DcmItem& dataset,
                                                             Uint16& allocated,
                                                             Uint16& stored,
                                                             Uint16& high,
                                                             Uint16& spp,
                                                             Uint16& pixelRep,
                                                             Uint16& rows,
                                                             Uint16& cols,
                                                             Uint16& numberOfFrames,
                                                             OFString& colorModel)
{
  OFBool fail = OFFalse;
  dataset.findAndGetUint16(DCM_BitsAllocated, allocated);
  dataset.findAndGetUint16(DCM_BitsStored, stored);
  dataset.findAndGetUint16(DCM_HighBit, high);
  dataset.findAndGetUint16(DCM_PixelRepresentation, pixelRep);
  dataset.findAndGetUint16(DCM_SamplesPerPixel, spp);
  dataset.findAndGetOFStringArray(DCM_PhotometricInterpretation, colorModel);

  /* Rows and Columns */
  OFCondition result = getImagePixel().getRows(rows);
  if (result.good())
    result = getImagePixel().getColumns(cols);
  if (result.bad())
  {
    DCMSEG_ERROR("Cannot find Rows or Columns in dataset");
    fail = OFTrue;
  }

  /* Number of Frames */
  Sint32 numFrames = 0;
  result = m_FG.getNumberOfFrames(numFrames);
  if (result.bad())
  {
    DCMSEG_ERROR("Number of Frames not set");
    fail = OFTrue;
  }
  else
  {
    if ( numFrames < 0 )
    {
      DCMSEG_ERROR("Number of Frames must be greater than 0");
      fail = OFTrue;
    }
    else
    {
      numberOfFrames = OFstatic_cast(Uint16, numFrames);
    }
  }

  Uint16 depth = 0;
  if (m_SegmentationType == DcmSegTypes::ST_BINARY)
    depth = 1;
  else
    depth = 8;

  if (allocated != depth)
  {
    DCMSEG_WARN("Bits Allocated is not set correctly (" << allocated << ", ignored), assuming value " << depth << " as required for " << DcmSegTypes::segtype2OFString(m_SegmentationType) << " segmentation objects");
    allocated = depth;
  }
  if (stored != depth)
  {
    DCMSEG_WARN("Bits Stored is not set correctly (" << stored << ", ignored), assuming value " << depth << " as required for " << DcmSegTypes::segtype2OFString(m_SegmentationType) << " segmentation objects");
    stored = depth;
  }
  if (high != depth-1)
  {
    DCMSEG_WARN("High Bit is not set correctly (" << high << ", ignored), assuming value " << depth-1 << " as required for " << DcmSegTypes::segtype2OFString(m_SegmentationType) << " segmentation objects");
    high = depth -1;
  }
  if (spp != 1)
  {
    DCMSEG_WARN("Samples per Pixel is not set correctly (" << spp << ", ignored), assuming value 1 as required for segmentation objects");
    spp = 1;
  }
  if (pixelRep != 0)
  {
    DCMSEG_WARN("Pixel Representation is not set correctly (" << pixelRep << ", ignored), assuming value 0 as required for segmentation objects");
    pixelRep = 0;
  }
  if (colorModel != "MONOCHROME2")
  {
    DCMSEG_WARN("Photometric Interpretation is not set correctly (ignored), assuming value MONOCHROME2 as required for segmentation objects");
    colorModel = "MONOCHROME2";
  }
  if (rows == 0)
  {
    DCMSEG_ERROR("Rows is not set correctly (0)");
    fail = OFTrue;
  }
  if (cols == 0)
  {
    DCMSEG_ERROR("Columns is not set correctly (0)");
    fail = OFTrue;
  }

  if (fail)
    return EC_InvalidValue;

  return EC_Normal;
}


OFCondition DcmSegmentation::writeDataset(DcmItem& dataset)
{
  return write(dataset);
}


OFCondition DcmSegmentation::writeMultiFrameFunctionalGroupsModule(DcmItem& dataset)
{
  m_FG.setNumberOfFrames(m_Frames.size());
  OFCondition result = m_FG.write(dataset);
  if (result.good())
    m_FGInterface.write(dataset);
  return result;
}


OFCondition DcmSegmentation::writeMultiFrameDimensionModule(DcmItem& dataset)
{
  OFCondition result = m_DimensionModule.checkDimensions(&dataset);
  if (result.good())
  {
    result = m_DimensionModule.write(dataset);
  }
  return result;
}


OFCondition DcmSegmentation::writeFractionalFrames(DcmItem& dataset)
{
  OFCondition result;
  Uint16 rows,cols;
  rows = cols = 0;
  getImagePixel().getRows(rows);
  getImagePixel().getColumns(cols);
  size_t numBytes = getTotalBytesRequired(rows, cols, m_Frames.size());
  Uint8* pixdata = new Uint8[numBytes];
  OFVector<DcmIODTypes::Frame*>::iterator it = m_Frames.begin();
  // Just copy bytes for each frame as is
  for (size_t count = 0; it != m_Frames.end(); count++)
  {
    memcpy(pixdata + count*(*it)->length, (*it)->pixData, (*it)->length);
    it++;
  }
  dataset.putAndInsertUint8Array(DCM_PixelData, pixdata, numBytes, OFTrue);
  delete[] pixdata;
  return result;
}


OFCondition DcmSegmentation::writeBinaryFrames(DcmItem& dataset)
{
  OFCondition result;
  Uint16 rows,cols;
  rows = cols = 0;
  getImagePixel().getRows(rows);
  getImagePixel().getColumns(cols);
  size_t numBytes = getTotalBytesRequired(rows, cols, m_Frames.size());
  // Holds the pixels for all frames. Each bit represents a pixel which is either
  // 1 (part of segment) or 0 (not part of segment. All frames are directly
  // concatenated, i.e. there are no unused bits between the frames.
  Uint8* pixdata = new Uint8[numBytes];
  memset(pixdata, 0, numBytes);

  // Fill Pixel Data Element
  concatFrames(m_Frames, pixdata, rows*cols);
  result = dataset.putAndInsertUint8Array(DCM_PixelData, pixdata, numBytes, OFTrue);
  delete [] pixdata;
  return result;
}


OFCondition DcmSegmentation::writeSegmentationImageModule(DcmItem& dataset)
{
  dataset.putAndInsertOFStringArray(DCM_ImageType, "DERIVED\\PRIMARY");

  OFCondition result = m_ContentIdentificationMacro.write(dataset);

  /* Write hardcoded values */
  if (result.good())
  {
    getImagePixel().setSamplesPerPixel(1);
    getImagePixel().setPhotometricInterpretation("MONOCHROME2");
    getImagePixel().setPixelRepresentation(0);

    /* Write Bits Allocated/Stored, High Bit, Segmentation Fractional Type,
     * Segmentation Type, Maximum Fractional Value
     */
    switch (m_SegmentationType)
    {
      case DcmSegTypes::ST_BINARY:
      {
        getImagePixel().setBitsAllocated(1);
        getImagePixel().setBitsStored(1);
        getImagePixel().setHighBit(0);
        dataset.putAndInsertOFStringArray(DCM_SegmentationType, "BINARY");
        break;
      }
      case DcmSegTypes::ST_FRACTIONAL:
      {
        getImagePixel().setBitsAllocated(8);
        getImagePixel().setBitsStored(8);
        getImagePixel().setHighBit(7);
        dataset.putAndInsertOFStringArray(DCM_SegmentationType, "FRACTIONAL");
        if (m_SegmentationFractionalType == DcmSegTypes::SFT_OCCUPANCY)
        {
          dataset.putAndInsertOFStringArray(DCM_SegmentationFractionalType, "OCCUPANCY");
        }
        else
        {
          dataset.putAndInsertOFStringArray(DCM_SegmentationFractionalType, "PROBABILITY");
        }
        // Maximum Fractional Value: Attribute is type 1C but "required if .. FRACTIONAL", i.e. write type 1
        DcmIODUtil::copyElementToDataset(result, dataset, m_MaximumFractionalValue, "1", "1", "SegmentationImageModule");
        break;
      }
      case DcmSegTypes::ST_UNKNOWN:
      {  DCMSEG_ERROR("Internal error, segmentation type not set");
        result = EC_InternalError;
        break;
      }
    }
  }

  /* Write segments */
  OFVector<DcmItem*> segmentItems;
  if (result.good())
  {
    OFVector<DcmSegment*>::iterator it = m_Segments.begin();
    dataset.findAndDeleteElement(DCM_SegmentSequence);
    for ( Uint16 itemCount = 0; (it != m_Segments.end()) && result.good(); itemCount++)
    {
      DcmItem* segmentItem = NULL;
      dataset.findOrCreateSequenceItem(DCM_SegmentSequence, segmentItem, itemCount);
      if (segmentItem)
      {
        result = (*it)->write(*segmentItem);
        /* Insert segment number for the segment, starting from 1 and increasing monotonically. */
        if (result.good())
        {
          segmentItem->putAndInsertUint16(DCM_SegmentNumber, itemCount+1);
        }
      }
      else
      {
        DCMIOD_ERROR("Cannot create/get item in Segment Sequence (internal error)");
        result = EC_InternalError;
      }
      it++;
    }
  }

  /* Write frame pixel data */
  if (result.good())
  {
    if (m_SegmentationType == DcmSegTypes::ST_BINARY) result = writeBinaryFrames(dataset);
    else if (m_SegmentationType == DcmSegTypes::ST_BINARY) result = writeFractionalFrames(dataset);
    else result = SG_EC_UnknownSegmentationType;
  }

  return result;
}

// -- private helpers --

void DcmSegmentation::clearData()
{
  DcmSegmentation::IODImage::clearData();
  m_FG.clearData();
  m_FGInterface.clear();
  DcmIODUtil::freeContainer(m_Frames);
  DcmIODUtil::freeContainer(m_Segments);
  m_MaximumFractionalValue.clear();
  m_SegmentationFractionalType = DcmSegTypes::SFT_UNKNOWN;
  m_SegmentationType = DcmSegTypes::ST_UNKNOWN;
}


OFBool DcmSegmentation::checkPixDataLength(DcmElement* pixelData,
                                           const Uint16 rows,
                                           const Uint16 cols,
                                           const Uint16& numberOfFrames)
{
  // Get actual length of pixel data in bytes
  size_t length = pixelData->getLengthField();

  // Find out how many bytes are needed
  size_t bytesRequired = getTotalBytesRequired(rows, cols, numberOfFrames);
  // Length found in Pixel Data element is always even
  if (bytesRequired % 2 == 1) bytesRequired++;
  /* Compare expected and actual length */
  if (length < bytesRequired)
  {
    DCMSEG_ERROR("Not enough bytes found in Pixel Data element. Found " << length << " bytes but " << bytesRequired << " bytes expected");
    return OFFalse;
  }
  else if (length > bytesRequired)
  {
    DCMSEG_WARN("Too many bytes found in Pixel Data element. Found " << length << " bytes but " << bytesRequired << " bytes expected");
    return OFTrue;
  }
  else
  {
    DCMSEG_TRACE("Found " << length << " bytes in Pixel Data element as expected");
  }
  return OFTrue;
}


size_t DcmSegmentation::getBitsPerFrame(const Uint16& rows,
                                        const Uint16& cols)
{
  size_t bitsRequired = 0;
  bitsRequired = rows * cols;
  /* For fractional segmentations we need 1 byte instead of 1 bit for a single pixel */
  if (m_SegmentationType == DcmSegTypes::ST_FRACTIONAL)
  {
    bitsRequired *= 8;
  }
  return bitsRequired;
}


size_t DcmSegmentation::getTotalBytesRequired(const Uint16& rows,
                                              const Uint16& cols,
                                              const Uint16& numberOfFrames)
{
  size_t bytesRequired = rows * cols * numberOfFrames;
  /* for binary, we only need one bit per pixel */
  size_t remainder = 0;
  if (m_SegmentationType == DcmSegTypes::ST_BINARY)
  {
    // check whether the 1-bit pixels exactly fit into bytes
    remainder = (rows * cols) % 8;
    // number of bytes that work on an exact fit
    bytesRequired = bytesRequired / 8;
    // add one byte if we have a remainder
    if (remainder > 0)
    {
      bytesRequired++;
    }

  }
  return bytesRequired;
}


OFCondition DcmSegmentation::loadFile(DcmFileFormat& dcmff,
                                      const OFString& filename,
                                      DcmDataset*& dset)
{
  dset = NULL;
  OFCondition result = dcmff.loadFile(filename.c_str());
  if (result.bad())
  {
    DCMSEG_ERROR("Could not load file " << filename << ": " << result.text());
    return result;
  }
  dset = dcmff.getDataset();
  if (dset == NULL)
  {
    DCMSEG_ERROR("Could not load file " << filename << ": No dataset");
    return IOD_EC_InvalidObject;
  }
  return result;
}


OFCondition DcmSegmentation::readSegmentationFractionalType(DcmItem& item)
{
  DcmCodeString element(DCM_SegmentationFractionalType);
  OFCondition result = DcmIODUtil::getAndCheckElementFromDataset(item, element, getRules()->getByTag(DCM_SegmentationFractionalType));
  OFString str;
  if (result.good())
  {
    element.getOFStringArray(str);
    m_SegmentationFractionalType = DcmSegTypes::OFString2FractionalType(str);
  }

  if (m_SegmentationFractionalType  == DcmSegTypes::SFT_UNKNOWN)
  {
    DCMSEG_ERROR("Invalid value for attribute Segmentation Fractional Type: " << str);
    return EC_InvalidValue;
  }
  else
    return EC_Normal;
}


OFCondition DcmSegmentation::readSegmentationType(DcmItem& item)
{
  DcmCodeString element(DCM_SegmentationType);
  OFCondition result = DcmIODUtil::getAndCheckElementFromDataset(item, element, getRules()->getByTag(DCM_SegmentationType));
  OFString str;
  if (result.good())
  {
    element.getOFStringArray(str);
    m_SegmentationType = DcmSegTypes::OFString2Segtype(str);
  }

  if (m_SegmentationType == DcmSegTypes::ST_UNKNOWN)
  {
    DCMSEG_ERROR("Invalid value for attribute Segmentation Type: " << str);
    result = EC_InvalidValue;
  }

  return result;
}


// protected override of public base class function
IODImagePixelModule<Uint8>& DcmSegmentation::getImagePixel()
{
  return *OFget<IODImagePixelModule<Uint8> >( &DcmSegmentation::IODImage::getImagePixel() );
}


OFBool DcmSegmentation::check()
{
  if (m_Frames.size() == 0)
  {
    DCMSEG_ERROR("No frame data available");
    return OFFalse;
  }
  if (m_Segments.size() == 0)
  {
    DCMSEG_ERROR("No segments defined");
    return OFFalse;
  }
  if (m_Segments.size() > m_Frames.size())
  {
    DCMSEG_ERROR("There are more segments than frames defined");
    return OFFalse;
  }

  if (!m_FGInterface.check())
  {
    return OFFalse;
  }

  // Check whether we have a Frame Content Macro for each frame
  for (size_t count = 0; count < m_Frames.size(); count++)
  {
    OFBool isPerFrame;
    FGBase* group = m_FGInterface.get(count, DcmFGTypes::EFG_FRAMECONTENT, isPerFrame);
    if (group == NULL)
    {
      DCMSEG_ERROR("Frame Content Functional Group not present for frame " << count);
      return OFFalse;
    }
    else if (!isPerFrame)
    {
      DCMSEG_ERROR("Frame Content Functional Group must be per-frame but is shared");
      return OFFalse;
    }
  }

  return OFTrue;
}


OFCondition DcmSegmentation::decompress(DcmDataset& dset)
{
  DcmXfer xfer = dset.getOriginalXfer();
  OFCondition result;
  // If the original transfer syntax could have been lossy, print warning
  if (dset.hasRepresentation(EXS_LittleEndianExplicit, NULL))
  {
    if ( xfer.isEncapsulated() && (xfer.getXfer() != EXS_RLELossless) && (xfer.getXfer() != EXS_DeflatedLittleEndianExplicit) )
    {
      DCMSEG_WARN("Dataset has been compressed using a (possibly) lossy compression scheme (ignored)");
    }
  }
  // If the original transfer is encapsulated and we do not already have an uncompressed version, decompress or reject the file
  else if (xfer.isEncapsulated())
  {
    // RLE compression is fine (truly lossless). Deflated is handled internally by DCMTK.
    if (xfer.getXfer() == EXS_RLELossless)
    {
      DCMSEG_DEBUG("DICOM file is RLE-compressed, converting to uncompressed transfer syntax first");
      result = DcmIODUtil::decompress(dset);
    }
    else // We do not accept any transfer syntax that could be lossy compressed
    {
      DCMSEG_ERROR("Transfer syntax " << DcmXfer(xfer).getXferName() << " uses lossy compression, not supported for Segmentation objects!");
      result = IOD_EC_CannotDecompress;
    }
  }
  return result;
}


void DcmSegmentation::extractFrames(Uint8* pixData,
                                   const size_t numFrames,
                                   const size_t bitsPerFrame,
                                   OFVector< DcmIODTypes::Frame* >& results)
{
  // Will hold the bit position (0-7) that the current frame starts from. The
  // first frame will always start at bit 0.
  Uint8  bitShift = 0;
  // Compute length in bytes we need to consider for each frame.
  size_t frameLengthBytes = bitsPerFrame / 8;
  // If the number of bits is not dividable by 8, we need part of an extra
  // byte in the end. Since we like to set the unused bits to 0 in such a last
  // byte to 0, remember the number.
  size_t overlapBits = (8 - (bitsPerFrame % 8)) % 8;
  // Add an extra byte if we we fill a partial byte in the end
  if (overlapBits != 0) frameLengthBytes++;
  // Points to current reading position within pixeldata
  Uint8* readPos = pixData;
  // Loop over each frame and copy it to Frame structures
  for (size_t f = 0; f < numFrames; f++)
  {
    // Create frame with correct length and copy 1:1 from pixel data
    DcmIODTypes::Frame* frame = new DcmIODTypes::Frame();
    frame->length = frameLengthBytes;
    frame->pixData = new Uint8[frameLengthBytes];
    memcpy(frame->pixData, readPos, frame->length);
    // If we have been copying too much, i.e the first bits of the frame
    // actually belong to the former frame, shift the whole frame this amount
    // of bits to the left in order to shift the superfluous bits out
    if (bitShift > 0)
    {
      DcmSegUtils::shiftLeft(frame->pixData, frame->length, 8-bitShift);
    }
    // Adapt last byte by masking out unused bits (i.e. those belonging to next frame).
    // A reader should ignore those unused bits anyway.
    frame->pixData[frame->length-1] = (frame->pixData[frame->length-1] >> (overlapBits)) << (overlapBits);
    // Store frame
    results.push_back(frame);
    // Compute the bitshift created by this frame
    bitShift = ( 8- ((f+1) * bitsPerFrame) % 8 ) % 8;
    // If the last byte read has not been used completely, i.e. it contains
    // also bytes of the next frame, rewind read position to the last byte
    // that was partially read. Otherwise skip to the next full byte.
    if (bitShift > 0)
    {
      readPos = readPos + frame->length - 1;
    }
    else
    {
      readPos = readPos + frame->length;
    }
  }
}


void DcmSegmentation::concatFrames(OFVector< DcmIODTypes::Frame* > frames,
                                   Uint8* pixData,
                                   const size_t bitsPerFrame)
{
  // Writing position within the pixData memory
  Uint8 *writePos = pixData;
  OFVector<DcmIODTypes::Frame*>::iterator frame = frames.begin();
  Uint8 freeBits = 0;
  Uint8 firstByte = 0;
  // Iterate over frames and copy each to pixData memory
  for (size_t f = 0; frame != frames.end(); f++)
  {
    DCMSEG_DEBUG("Packing segmentation frame #" << f+1 << "/" << frames.size());
    // Backup first byte of the destination since it may contain bits of the
    // last frame; mask out those bits not belonging to last frame.
    firstByte = (writePos[0] >> freeBits) << freeBits;
    memcpy(writePos, (*frame)->pixData, (*frame)->length);
    // If the last frame left over some unused bits, shift the current frame
    // that number of bits to the right and restore the original bits of the
    // last frame
    if (freeBits > 0)
    {
      DcmSegUtils::shiftRight(writePos, (*frame)->length, 8-freeBits);
      writePos[0] |= firstByte;
    }
    // Compute free bits left over from this frame in the last byte written
    freeBits = (8 - (( (f+1) * bitsPerFrame ) % 8)) % 8;
    // If we have free bits, the last byte written to will be the first byte
    // we write to for the next frame. Otherwise start with a fresh destination
    // byte.
    if (freeBits > 0)
    {
      writePos = writePos + (*frame)->length - 1;
    }
    else
    {
      writePos = writePos + (*frame)->length;
    }
    // Next frame
    frame++;
  }
  // Through shifting we can have non-zero bits within the unused bits of the
  // last byte. Fill them with zeros (though not required by the standard).
  if (freeBits > 0)
  {
    *writePos = (*writePos >> freeBits) << freeBits;
  }
}
