Ft itk2label#536
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When converting DICOM binary segmentations to DICOM labelmaps, some pixels are likely not covered from any of the the segments. Since the pixels are initially set to 0, all non-covered pixels will be "background" and must be marked as such. This is done by scanning all pixels after conversion and if a 0 is found, a segment using codes for denoting "background" will be inserted automatically. The alternative would be to set Pixel Padding Value. This could be introduced as an option later, but for now the background segment seems to be better supported by consuming applications.
Also for the newly added background segment, don't write (0062,000D) Recommended Display CIELab Value either. Also some minor changes.
Performance optimizations for segmentation/parametric maps (dcmiod, dcmfg, dcmseg). It also includes a simpler mechanism to add external modules to the DCMTK CMake build (e.g. the JPEG2000 codec from DCMTKcs, see https://github.com/lassoan/DCMTKcs).
Extend itkimage2segimage with a --segmentationType option (default
"binary", preserving prior behavior) that, when set to "labelmap",
emits a DICOM Labelmap Segmentation (Sup 243) directly from an ITK
image. Previously the only way to produce a labelmap was to convert
to a binary Segmentation first and then run bin2labelsegimage;
this removes the intermediate step.
In labelmap mode foreground segments are numbered 1..N (or taken
from labelIDs when --useLabelIDAsSegmentNumber is set); pixel value
0 is reserved for the implicit background. If any frame contains
pixel 0 a Background segment (Property Type DCM 125040) is added
automatically so every pixel value is covered by a Segment Sequence
item, as required by Sup 243. Bit depth is 8-bit when the segment
count fits, else 16-bit. Overlapping foreground segments are
rejected because each labelmap pixel can carry only one segment
number.
The frame-scan + background-segment-creation logic that this new
path needs is identical to what Bin2Label already does for
binary->labelmap conversion. It is consolidated into a shared
ConverterBase::addBackgroundSegmentIfNeeded() helper, and
DcmBinToLabelConverter's member function becomes a thin wrapper
that delegates and adds the PALETTE-mode LUT prepend on top.
Also adds a 2-segment metadata example
(doc/examples/seg-example_liver_spine.json) used by new CTest
entries:
- itkimage2segimage_makeSEG_labelmap: single-segment conversion.
- itkimage2segimage_makeSEG_labelmap_multi: multi-segment
conversion. Regression guard for segment numbering, which is
not exercised by single-segment inputs.
- itkimage2segimage_makeSEG_labelmap_multi_labelID: same with
--useLabelIDAsSegmentNumber.
- itkimage2segimage_makeSEG_labelmap_overlap: liver/heart pair
overlaps on 522 pixels; conversion must fail (WILL_FAIL).
- segimage2itkimage_makeNRRD_from_labelmap_{direct,multi}:
pixel-perfect round-trip back to NRRD against existing baselines.
dciodvfy is intentionally not run on the new labelmap outputs;
all labelmap segmentations emitted by dcmqi today (both Bin2Label
and this new path) fail dciodvfy because Type 2C PatientOrientation
is not populated under GeneralImage. This is a pre-existing
gap and is documented inline in the CMakeLists.
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Add direct ITK to DICOM Labelmap conversion.
Also includes PRs #534 and #535 (the latter being probably optional).
Extend itkimage2segimage with a --segmentationType option (default
"binary", preserving prior behavior) that, when set to "labelmap",
emits a DICOM Labelmap Segmentation (Sup 243) directly from an ITK
image. Previously the only way to produce a labelmap was to convert
to a binary Segmentation first and then run bin2labelsegimage;
this removes the intermediate step.
In labelmap mode foreground segments are numbered 1..N (or taken
from labelIDs when --useLabelIDAsSegmentNumber is set); pixel value
0 is reserved for the implicit background. If any frame contains
pixel 0 a Background segment (Property Type DCM 125040) is added
automatically so every pixel value is covered by a Segment Sequence
item, as required by Sup 243. Bit depth is 8-bit when the segment
count fits, else 16-bit. Overlapping foreground segments are
rejected because each labelmap pixel can carry only one segment
number.
The frame-scan + background-segment-creation logic that this new
path needs is identical to what Bin2Label already does for
binary->labelmap conversion. It is consolidated into a shared
ConverterBase::addBackgroundSegmentIfNeeded() helper, and
DcmBinToLabelConverter's member function becomes a thin wrapper
that delegates and adds the PALETTE-mode LUT prepend on top.
Also adds a 2-segment metadata example
(doc/examples/seg-example_liver_spine.json) used by new CTest
entries:
conversion. Regression guard for segment numbering, which is
not exercised by single-segment inputs.
--useLabelIDAsSegmentNumber.
overlaps on 522 pixels; conversion must fail (WILL_FAIL).
pixel-perfect round-trip back to NRRD against existing baselines.
dciodvfy is intentionally not run on the new labelmap outputs;
all labelmap segmentations emitted by dcmqi today (both Bin2Label
and this new path) fail dciodvfy because Type 2C PatientOrientation
is not populated under GeneralImage. This is a pre-existing
gap and is documented inline in the CMakeLists.