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blind attempt at compatibility with new DCMTK
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@spalte
spalte committed Feb 1, 2024
1 parent 4143036 commit ec861bc
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Showing 3 changed files with 53 additions and 43 deletions.
8 changes: 4 additions & 4 deletions include/dcmqi/OverlapUtil.h
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Original file line number Diff line number Diff line change
Expand Up @@ -330,8 +330,8 @@ class OverlapUtil
*/
OFCondition checkFramesOverlapBinary(const Uint32& f1,
const Uint32& f2,
const DcmIODTypes::Frame* f1_data,
const DcmIODTypes::Frame* f2_data,
const DcmIODTypes::Frame<Uint8>* f1_data,
const DcmIODTypes::Frame<Uint8>* f2_data,
const Uint16& rows,
const Uint16 cols,
OFBool& overlap);
Expand All @@ -350,8 +350,8 @@ class OverlapUtil
*/
OFCondition checkFramesOverlapUnpacked(const Uint32& f1,
const Uint32& f2,
const DcmIODTypes::Frame* f1_data,
const DcmIODTypes::Frame* f2_data,
const DcmIODTypes::Frame<Uint8>* f1_data,
const DcmIODTypes::Frame<Uint8>* f2_data,
const Uint16& rows,
const Uint16 cols,
OFBool& overlap);
Expand Down
8 changes: 4 additions & 4 deletions libsrc/Dicom2ItkConverter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -151,11 +151,11 @@ itk::SmartPointer<ShortImageType> Dicom2ItkConverter::nextResult()
}
// Handling differs depending on whether the segmentation is binary or fractional
// (we have to unpack binary frames before copying them into the ITK image)
const DcmIODTypes::Frame* rawFrame = m_segDoc->getFrame(*it);
const DcmIODTypes::Frame* unpackedFrame = NULL;
const DcmIODTypes::FrameBase* rawFrame = m_segDoc->getFrame(*it);
const DcmIODTypes::FrameBase* unpackedFrame = NULL;
if (m_segDoc->getSegmentationType() == DcmSegTypes::ST_BINARY)
{
unpackedFrame = DcmSegUtils::unpackBinaryFrame(rawFrame,
unpackedFrame = DcmSegUtils::unpackBinaryFrame(dynamic_cast<DcmIODTypes::Frame<Uint8>*>(rawFrame),
m_imageSize[1], // Rows
m_imageSize[0]); // Cols
}
Expand Down Expand Up @@ -221,7 +221,7 @@ itk::SmartPointer<ShortImageType> Dicom2ItkConverter::nextResult()
{
ShortImageType::PixelType pixel;
unsigned bitCnt = row * m_imageSize[0] + col;
pixel = unpackedFrame->pixData[bitCnt];
unpackedFrame->getUint16AtIndex(pixel, bitCnt);
ShortImageType::IndexType index;
if (labelMapSegmentation ? pixel == *segNum : pixel != 0)
{
Expand Down
80 changes: 45 additions & 35 deletions libsrc/OverlapUtil.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -526,27 +526,23 @@ void OverlapUtil::printNonOverlappingSegments(OFStringStream& ss)

OFCondition OverlapUtil::getSegmentsForLabelMapFrame(const Uint32 frameNumber, std::set<Uint32>& segments)
{
const DcmIODTypes::Frame* f_data = m_seg->getFrame(frameNumber);
const DcmIODTypes::FrameBase* frame = m_seg->getFrame(frameNumber);
Uint16 rows, cols;
rows = cols = 0;
DcmIODImage<IODImagePixelModule<Uint8>>* ip = static_cast<DcmIODImage<IODImagePixelModule<Uint8>>*>(m_seg);
ip->getImagePixel().getRows(rows);
ip->getImagePixel().getColumns(cols);
if (!f_data)
if (frame)
{
DCMSEG_ERROR("getSegmentsForLabelMapFrame(): Cannot access label map frame " << frameNumber);
return EC_IllegalCall;
}

segments.clear();
for (size_t n = 0; n < f_data->length; ++n)
for (size_t n = 0; n < frame->length(); ++n)
{
Uint8 segmentNumber = f_data->pixData[n];
if (segmentNumber > m_seg->getNumberOfSegments())
{
DCMSEG_ERROR("getSegmentsForFrame(): Segment number " << segmentNumber << " is out of range");
return EC_IllegalParameter;
}
Uint16 segmentNumber;
frame->getUint16AtIndex(segmentNumber, n);
segments.insert(segmentNumber);
}
return EC_Normal;
Expand Down Expand Up @@ -587,13 +583,18 @@ OFCondition OverlapUtil::getSegmentForFrame(const Uint32 frameNumber, Uint32& se

OFCondition OverlapUtil::buildOverlapMatrix()
{
// TODO This corresponds to the list of segments in a binary or fractional
// segmentation IOD, we still need to get the actual list if this is a labelmap
const Uint32 numSegments = m_seg->getNumberOfSegments();
if (!m_seg)
{
DCMSEG_ERROR("getFramesForSegment(): No segmentation object set");
return EC_IllegalCall;
}

std::set<Uint32> segmentNumbers;
for (Uint32 i = 1; i <= numSegments; ++i)
OFVector<DcmSegment*> segments;
m_seg->getSegments(segments);
for (int i = 0; i < segments.size(); i++)
{
segmentNumbers.insert(i);
segmentNumbers.insert(segments[i]->getSegmentNumber());
}

// Make 2 dimensional matrix of Sint8 type for (segment numbers) X (segment numbers).
Expand Down Expand Up @@ -718,8 +719,8 @@ OFCondition OverlapUtil::checkFramesOverlapLabelMap(const SegNumAndFrameNum& sf1
const Uint32& f1 = sf1.m_frameNumber;
const Uint32& f2 = sf2.m_frameNumber;
OFCondition result;
const DcmIODTypes::Frame* f1_data = m_seg->getFrame(sf1.m_frameNumber);
const DcmIODTypes::Frame* f2_data = m_seg->getFrame(sf2.m_frameNumber);
const DcmIODTypes::FrameBase* f1_data = m_seg->getFrame(sf1.m_frameNumber);
const DcmIODTypes::FrameBase* f2_data = m_seg->getFrame(sf2.m_frameNumber);
Uint16 rows, cols;
rows = cols = 0;
DcmIODImage<IODImagePixelModule<Uint8>>* ip = static_cast<DcmIODImage<IODImagePixelModule<Uint8>>*>(m_seg);
Expand All @@ -734,16 +735,19 @@ OFCondition OverlapUtil::checkFramesOverlapLabelMap(const SegNumAndFrameNum& sf1
DCMSEG_ERROR("checkFramesOverlapLabelMap(): Cannot access label map frames " << f1 << " and " << f2 << " for comparison");
return EC_IllegalCall;
}
if (f1_data->length != f2_data->length)
if (f1_data->length() != f2_data->length())
{
DCMSEG_ERROR("checkFramesOverlapLabelMap(): Frames " << f1 << " and " << f2
<< " have different length, cannot compare");
return EC_IllegalCall;
}

for (size_t n = 0; n < f1_data->length; ++n)
for (size_t n = 0; n < f1_data->length(); ++n)
{
if (f1_data->pixData[n] == sf1.m_segmentNumber && f2_data->pixData[n] == sf2.m_segmentNumber)
Uint16 f1Pixel, f2Pixel;
f1_data->getUint16AtIndex(f1Pixel, n);
f2_data->getUint16AtIndex(f2Pixel, n);
if (f1Pixel == sf1.m_segmentNumber && f2Pixel == sf2.m_segmentNumber)
{
DCMSEG_DEBUG("checkFramesOverlapLabelMap(): Frame " << f1 << ", segment " << sf1.m_segmentNumber << ", and frame "
<< f2 << ", segment " << sf2.m_segmentNumber << ", do overlap at index " << n);
Expand All @@ -764,8 +768,8 @@ OFCondition OverlapUtil::checkFramesOverlap(const Uint32& f1, const Uint32& f2,
}
overlap = OFFalse;
OFCondition result;
const DcmIODTypes::Frame* f1_data = m_seg->getFrame(f1);
const DcmIODTypes::Frame* f2_data = m_seg->getFrame(f2);
const DcmIODTypes::FrameBase* f1_data = m_seg->getFrame(f1);
const DcmIODTypes::FrameBase* f2_data = m_seg->getFrame(f2);
Uint16 rows, cols;
rows = cols = 0;
DcmIODImage<IODImagePixelModule<Uint8>>* ip = static_cast<DcmIODImage<IODImagePixelModule<Uint8>>*>(m_seg);
Expand All @@ -774,12 +778,14 @@ OFCondition OverlapUtil::checkFramesOverlap(const Uint32& f1, const Uint32& f2,
if (rows * cols % 8 != 0)
{
// We must compare pixel by pixel of the unpacked frames (for now)
result = checkFramesOverlapUnpacked(f1, f2, f1_data, f2_data, rows, cols, overlap);
result = checkFramesOverlapUnpacked(f1, f2, dynamic_cast<DcmIODTypes::Frame<Uint8>*>(f1_data),
dynamic_cast<DcmIODTypes::Frame<Uint8>*>(f2_data), rows, cols, overlap);
}
else
{
// We can compare byte by byte using bitwise AND (if both have a 1 at the same position, they overlap)
result = checkFramesOverlapBinary(f1, f2, f1_data, f2_data, rows, cols, overlap);
result = checkFramesOverlapBinary(f1, f2, dynamic_cast<DcmIODTypes::Frame<Uint8>*>(f1_data),
dynamic_cast<DcmIODTypes::Frame<Uint8>*>(f2_data), rows, cols, overlap);
}
if (result.good() && !overlap)
{
Expand All @@ -790,8 +796,8 @@ OFCondition OverlapUtil::checkFramesOverlap(const Uint32& f1, const Uint32& f2,

OFCondition OverlapUtil::checkFramesOverlapBinary(const Uint32& f1,
const Uint32& f2,
const DcmIODTypes::Frame* f1_data,
const DcmIODTypes::Frame* f2_data,
const DcmIODTypes::Frame<Uint8>* f1_data,
const DcmIODTypes::Frame<Uint8>* f2_data,
const Uint16& rows,
const Uint16 cols,
OFBool& overlap)
Expand All @@ -802,16 +808,18 @@ OFCondition OverlapUtil::checkFramesOverlapBinary(const Uint32& f1,
DCMSEG_ERROR("checkFramesOverlap(): Cannot access binary frames " << f1 << " and " << f2 << " for comparison");
return EC_IllegalCall;
}
if (f1_data->length != f2_data->length)
if (f1_data->length() != f2_data->length())
{
DCMSEG_ERROR("checkFramesOverlap(): Frames " << f1 << " and " << f2
<< " have different length, cannot compare");
return EC_IllegalCall;
}
// Compare byte (8 pixels at once) using bitwise AND (if both have a 1 at the same position, they overlap)
for (size_t n = 0; n < f1_data->length; ++n)
Uint8 *pixelData1 = f1_data->getPixelDataTyped();
Uint8 *pixelData2 = f2_data->getPixelDataTyped();
for (size_t n = 0; n < f1_data->length(); ++n)
{
if (f1_data->pixData[n] & f2_data->pixData[n])
if (pixelData1[n] & pixelData2[n])
{
DCMSEG_DEBUG("checkFramesOverlap(): Frames " << f1 << " and " << f2 << " do overlap, pixel value "
<< OFstatic_cast(Uint16, f1_data->pixData[n]) << " at index "
Expand All @@ -825,32 +833,34 @@ OFCondition OverlapUtil::checkFramesOverlapBinary(const Uint32& f1,

OFCondition OverlapUtil::checkFramesOverlapUnpacked(const Uint32& f1,
const Uint32& f2,
const DcmIODTypes::Frame* f1_data,
const DcmIODTypes::Frame* f2_data,
const DcmIODTypes::Frame<Uint8>* f1_data,
const DcmIODTypes::Frame<Uint8>* f2_data,
const Uint16& rows,
const Uint16 cols,
OFBool& overlap)
{
DCMSEG_DEBUG("checkFramesOverlap(): Comparing frames " << f1 << " and " << f2
<< " for overlap (slow unpacked mode)");
OFunique_ptr<DcmIODTypes::Frame> f1_unpacked(DcmSegUtils::unpackBinaryFrame(f1_data, rows, cols));
OFunique_ptr<DcmIODTypes::Frame> f2_unpacked(DcmSegUtils::unpackBinaryFrame(f2_data, rows, cols));
OFunique_ptr<DcmIODTypes::Frame<Uint8>> f1_unpacked(DcmSegUtils::unpackBinaryFrame(f1_data, rows, cols));
OFunique_ptr<DcmIODTypes::Frame<Uint8>> f2_unpacked(DcmSegUtils::unpackBinaryFrame(f2_data, rows, cols));
if (!f1_unpacked || !f2_unpacked)
{
DCMSEG_ERROR("checkFramesOverlap(): Cannot unpack frames " << f1 << " and " << f2 << " for comparison");
return EC_IllegalCall;
}
if (f1_unpacked->length != f2_unpacked->length)
if (f1_unpacked->length() != f2_unpacked->length())
{
DCMSEG_ERROR("checkFramesOverlap(): Frames " << f1 << " and " << f2
<< " have different length, cannot compare");
return EC_IllegalCall;
}
// Compare pixels of both frames and check whether at least one has the same value
DCMSEG_DEBUG("checkFramesOverlap(): Comparing frames " << f1 << " and " << f2 << " for overlap");
for (size_t n = 0; n < f1_unpacked->length; ++n)
Uint8 *pixelDataUnpacked1 = f1_unpacked->getPixelDataTyped();
Uint8 *pixelDataUnpacked2 = f2_unpacked->getPixelDataTyped();
for (size_t n = 0; n < f1_unpacked->length(); ++n)
{
if (f1_unpacked->pixData[n] != 0 && (f1_unpacked->pixData[n] == f2_unpacked->pixData[n]))
if (pixelDataUnpacked1[n] != 0 && (pixelDataUnpacked1[n] == pixelDataUnpacked2[n]))
{
DCMSEG_DEBUG("checkFramesOverlap(): Frames " << f1 << " and " << f2 << " do overlap, pixel value "
<< OFstatic_cast(Uint16, f1_unpacked->pixData[n])
Expand Down

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