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Refactor utils code into iter_tiled_full_frame_data
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@CPBridge
CPBridge committed Aug 18, 2023
1 parent 74d5e83 commit cde407d
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Showing 2 changed files with 220 additions and 171 deletions.
158 changes: 87 additions & 71 deletions src/highdicom/seg/sop.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1677,11 +1677,7 @@ def __init__(
self.copy_patient_and_study_information(src_img)

# Build lookup tables for efficient decoding
if (
dimension_organization_type is not None and
dimension_organization_type.value != "TILED_FULL"
):
self._build_luts()
self._build_luts()

def add_segments(
self,
Expand Down Expand Up @@ -2610,6 +2606,11 @@ def _build_luts(self) -> None:
referenced_uids = self._get_ref_instance_uids()
all_referenced_sops = {uids[2] for uids in referenced_uids}

is_tiled_full = (
hasattr(self, 'DimensionOrganizationType')
and self.DimensionOrganizationType == 'TILED_FULL'
)

segment_numbers = []
referenced_instances: Optional[List[str]] = []
referenced_frames: Optional[List[int]] = []
Expand All @@ -2636,80 +2637,95 @@ def _build_luts(self) -> None:
locations_list_type = List[Optional[SpatialLocationsPreservedValues]]
locations_preserved: locations_list_type = []
self._single_source_frame_per_seg_frame = True
for frame_item in self.PerFrameFunctionalGroupsSequence:
# Get segment number for this frame
seg_id_seg = frame_item.SegmentIdentificationSequence[0]
seg_num = seg_id_seg.ReferencedSegmentNumber
segment_numbers.append(int(seg_num))

# Get dimension indices for this frame
indices = frame_item.FrameContentSequence[0].DimensionIndexValues
if not isinstance(indices, (MultiValue, list)):
# In case there is a single dimension index
indices = [indices]
if len(indices) != len(self._dim_ind_pointers) + 1:
# (+1 because referenced segment number is ignored)

if is_tiled_full:
tiled_full_dim_indices = {
tag_for_keyword('RowPositionInTotalImagePixelMatrix'),
tag_for_keyword('ColumnPositionInTotalImagePixelMatrix'),
}
if set(dim_indices.keys()) != tiled_full_dim_indices:
raise RuntimeError(
'Unexpected mismatch between dimension index values in '
'per-frames functional groups sequence and items in the '
'dimension index sequence.'
'Expected segmentation images with '
'"DimensionOrganizationType" of "TILED_FULL" are expected '
'to have the following dimension index pointers: '
'SegmentNumber, RowPositionInTotalImagePixelMatrix, '
'ColumnPositionInTotalImagePixelMatrix.'
)
for ptr in self._dim_ind_pointers:
dim_indices[ptr].append(indices[dim_ind_positions[ptr]])

frame_source_instances = []
frame_source_frames = []
for der_im in frame_item.DerivationImageSequence:
for src_im in der_im.SourceImageSequence:
frame_source_instances.append(
src_im.ReferencedSOPInstanceUID
else:
for frame_item in self.PerFrameFunctionalGroupsSequence:
# Get segment number for this frame
seg_id_seg = frame_item.SegmentIdentificationSequence[0]
seg_num = seg_id_seg.ReferencedSegmentNumber
segment_numbers.append(int(seg_num))

# Get dimension indices for this frame
indices = frame_item.FrameContentSequence[0].DimensionIndexValues
if not isinstance(indices, (MultiValue, list)):
# In case there is a single dimension index
indices = [indices]
if len(indices) != len(self._dim_ind_pointers) + 1:
# (+1 because referenced segment number is ignored)
raise RuntimeError(
'Unexpected mismatch between dimension index values in '
'per-frames functional groups sequence and items in the '
'dimension index sequence.'
)
if hasattr(src_im, 'SpatialLocationsPreserved'):
locations_preserved.append(
SpatialLocationsPreservedValues(
src_im.SpatialLocationsPreserved
)
for ptr in self._dim_ind_pointers:
dim_indices[ptr].append(indices[dim_ind_positions[ptr]])

frame_source_instances = []
frame_source_frames = []
for der_im in frame_item.DerivationImageSequence:
for src_im in der_im.SourceImageSequence:
frame_source_instances.append(
src_im.ReferencedSOPInstanceUID
)
else:
locations_preserved.append(
None
)

if hasattr(src_im, 'ReferencedFrameNumber'):
if isinstance(
src_im.ReferencedFrameNumber,
MultiValue
):
frame_source_frames.extend(
[
int(f)
for f in src_im.ReferencedFrameNumber
]
if hasattr(src_im, 'SpatialLocationsPreserved'):
locations_preserved.append(
SpatialLocationsPreservedValues(
src_im.SpatialLocationsPreserved
)
)
else:
frame_source_frames.append(
int(src_im.ReferencedFrameNumber)
locations_preserved.append(
None
)
else:
frame_source_frames.append(_NO_FRAME_REF_VALUE)

if (
len(set(frame_source_instances)) != 1 or
len(set(frame_source_frames)) != 1
):
self._single_source_frame_per_seg_frame = False
else:
ref_instance_uid = frame_source_instances[0]
if ref_instance_uid not in all_referenced_sops:
raise AttributeError(
f'SOP instance {ref_instance_uid} referenced in the '
'source image sequence is not included in the '
'Referenced Series Sequence or Studies Containing '
'Other Referenced Instances Sequence. This is an '
'error with the integrity of the Segmentation object.'
)
referenced_instances.append(ref_instance_uid)
referenced_frames.append(frame_source_frames[0])
if hasattr(src_im, 'ReferencedFrameNumber'):
if isinstance(
src_im.ReferencedFrameNumber,
MultiValue
):
frame_source_frames.extend(
[
int(f)
for f in src_im.ReferencedFrameNumber
]
)
else:
frame_source_frames.append(
int(src_im.ReferencedFrameNumber)
)
else:
frame_source_frames.append(_NO_FRAME_REF_VALUE)

if (
len(set(frame_source_instances)) != 1 or
len(set(frame_source_frames)) != 1
):
self._single_source_frame_per_seg_frame = False
else:
ref_instance_uid = frame_source_instances[0]
if ref_instance_uid not in all_referenced_sops:
raise AttributeError(
f'SOP instance {ref_instance_uid} referenced in the '
'source image sequence is not included in the '
'Referenced Series Sequence or Studies Containing '
'Other Referenced Instances Sequence. This is an '
'error with the integrity of the Segmentation object.'
)
referenced_instances.append(ref_instance_uid)
referenced_frames.append(frame_source_frames[0])

# Summarise
if any(
Expand Down
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