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Improvements on 3D dimension organization
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@CPBridge
CPBridge committed Jan 4, 2025
1 parent aa8f07e commit 14e4669
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Showing 2 changed files with 74 additions and 50 deletions.
112 changes: 68 additions & 44 deletions src/highdicom/seg/sop.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1320,6 +1320,17 @@ def __init__(
else:
included_plane_indices = list(range(len(plane_positions)))

# Dimension Organization Type
dimension_organization_type = self._check_tiled_dimension_organization(
dimension_organization_type=dimension_organization_type,
is_tiled=is_tiled,
omit_empty_frames=omit_empty_frames,
plane_positions=plane_positions,
tile_pixel_array=tile_pixel_array,
rows=self.Rows,
columns=self.Columns,
)

if (
has_ref_frame_uid and
dimension_organization_type !=
Expand All @@ -1341,56 +1352,61 @@ def __init__(
else:
unique_dimension_values = [None]

# Dimension Organization Type
dimension_organization_type = self._check_tiled_dimension_organization(
dimension_organization_type=dimension_organization_type,
is_tiled=is_tiled,
omit_empty_frames=omit_empty_frames,
plane_positions=plane_positions,
tile_pixel_array=tile_pixel_array,
rows=self.Rows,
columns=self.Columns,
)

if self._coordinate_system == CoordinateSystemNames.PATIENT:
if from_volume:
# Skip checks as this is 3D by construction
# TODO what about omitted frames
dimension_organization_type = (
DimensionOrganizationTypeValues.THREE_DIMENSIONAL
)
else:
# TODO calculate spacing before omitting frames?
spacing, _ = get_volume_positions(
image_positions=np.array(
plane_position_values[plane_sort_index, 0, :]
),
image_orientation=np.array(
plane_orientation[0].ImageOrientationPatient
),
inferred_dim_org_type = None

# To be considered "3D", a segmentation should have frames that are
# differentiated only by location. This rules out any non-labelmap
# segmentations with more than a single segment.
# Further, only segmentation with multiple spatial positions in the
# final segmentation should be considered to have 3D dimension
# organization type
if (
len(included_plane_indices) > 1 and
(
segmentation_type == SegmentationTypeValues.LABELMAP
or len(described_segment_numbers) == 1
)

if spacing is not None and spacing > 0.0:
# The image is a regular volume, so we should record this
dimension_organization_type = (
):
if from_volume:
# Skip checks as this is 3D by construction
# TODO what about omitted frames
inferred_dim_org_type = (
DimensionOrganizationTypeValues.THREE_DIMENSIONAL
)
# Also add the slice spacing to the pixel measures
(
self.SharedFunctionalGroupsSequence[0]
.PixelMeasuresSequence[0]
.SpacingBetweenSlices
) = spacing
else:
if (
dimension_organization_type ==
DimensionOrganizationTypeValues.THREE_DIMENSIONAL
):
raise ValueError(
'Dimension organization "3D" has been specified, '
'but the source image is not a regularly-spaced 3D '
'volume.'
# TODO calculate spacing before omitting frames?
spacing, _ = get_volume_positions(
image_positions=np.array(
plane_position_values[plane_sort_index, 0, :]
),
image_orientation=np.array(
plane_orientation[0].ImageOrientationPatient
),
)

if spacing is not None and spacing > 0.0:
# The image is a regular volume, so we should record this
inferred_dim_org_type = (
DimensionOrganizationTypeValues.THREE_DIMENSIONAL
)
# Also add the slice spacing to the pixel measures
(
self.SharedFunctionalGroupsSequence[0]
.PixelMeasuresSequence[0]
.SpacingBetweenSlices
) = spacing

if (
dimension_organization_type ==
DimensionOrganizationTypeValues.THREE_DIMENSIONAL
) and inferred_dim_org_type is None:
raise ValueError(
'Dimension organization "3D" has been specified, '
'but the source image is not a regularly-spaced 3D '
'volume.'
)
dimension_organization_type = inferred_dim_org_type

if dimension_organization_type is not None:
self.DimensionOrganizationType = dimension_organization_type.value
Expand Down Expand Up @@ -2017,6 +2033,14 @@ def _check_tiled_dimension_organization(
DimensionOrganizationType to use for the output Segmentation.
""" # noqa: E501
if (
dimension_organization_type ==
DimensionOrganizationTypeValues.THREE_DIMENSIONAL_TEMPORAL
):
raise ValueError(
"Value of 'THREE_DIMENSIONAL_TEMPORAL' for "
"parameter 'dimension_organization_type' is not supported."
)
if is_tiled and dimension_organization_type is None:
dimension_organization_type = \
DimensionOrganizationTypeValues.TILED_SPARSE
Expand Down
12 changes: 6 additions & 6 deletions tests/test_seg.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1840,7 +1840,7 @@ def test_construction_volume(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down Expand Up @@ -1882,7 +1882,7 @@ def test_construction_volume_channels(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down Expand Up @@ -1980,7 +1980,7 @@ def test_construction_volume_fractional(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down Expand Up @@ -2023,7 +2023,7 @@ def test_construction_volume_fractional_channels(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down Expand Up @@ -2066,7 +2066,7 @@ def test_construction_volume_labelmap(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down Expand Up @@ -2109,7 +2109,7 @@ def test_construction_volume_labelmap_channels(self):
assert len(shared_item.PixelMeasuresSequence) == 1
pm_item = shared_item.PixelMeasuresSequence[0]
assert pm_item.PixelSpacing == self._ct_volume_pixel_spacing
assert not hasattr(pm_item, 'SliceThickness')
assert pm_item.SliceThickness == self._ct_volume_slice_spacing
assert len(shared_item.PlaneOrientationSequence) == 1
po_item = shared_item.PlaneOrientationSequence[0]
assert po_item.ImageOrientationPatient == \
Expand Down

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