Use frame label to index for labelmaps without frame of reference

src/highdicom/seg/content.py

@@ -340,11 +340,7 @@ def __init__(
             segment_number_index.DimensionDescriptionLabel = 'Segment Number'
             self.append(segment_number_index)
 
-        if self._coordinate_system is None:
-            # TODO what on earth to do here?
-            pass
-
-        elif self._coordinate_system == CoordinateSystemNames.SLIDE:
+        if self._coordinate_system == CoordinateSystemNames.SLIDE:
 
             x_axis_index = Dataset()
             x_axis_index.DimensionIndexPointer = tag_for_keyword(
@@ -428,6 +424,19 @@ def __init__(
 
             self.append(image_position_index)
 
+        elif self._coordinate_system is None:
+            if not include_segment_number:
+                # Use frame label here just for the sake of using something
+                frame_label_index = Dataset()
+                frame_label_index.DimensionIndexPointer = tag_for_keyword(
+                    'FrameLabel'
+                )
+                frame_label_index.FunctionalGroupPointer = tag_for_keyword(
+                    'FrameContentSequence'
+                )
+                frame_label_index.DimensionOrganizationUID = dim_uid
+                frame_label_index.DimensionDescriptionLabel = 'Frame Label'
+                self.append(frame_label_index)
         else:
             raise ValueError(
                 f'Unknown coordinate system "{self._coordinate_system}"'

src/highdicom/seg/sop.py

@@ -1546,6 +1546,7 @@ def __init__(
                     plane_position_values=plane_position_values,
                     has_ref_frame_uid=has_ref_frame_uid,
                     coordinate_system=self._coordinate_system,
+                    segmentation_type=segmentation_type,
                 )
                 pffg_item = self._get_pffg_item(
                     segment_number=segment_number,
@@ -2123,6 +2124,7 @@ def _get_dimension_index_values(
         plane_position_values: np.ndarray,
         has_ref_frame_uid: bool,
         coordinate_system: Optional[CoordinateSystemNames],
+        segmentation_type: SegmentationTypeValues,
     ) -> List[int]:
         """Get dimension index values for a frame.
 
@@ -2147,7 +2149,13 @@ def _get_dimension_index_values(
 
         """
         if not has_ref_frame_uid:
-            index_values = []
+            if segmentation_type == SegmentationTypeValues.LABELMAP:
+                # Here we have to return the "Frame Label" dimension value
+                # (which is used just to have one index since Referenced
+                # Segment cannot be used)
+                index_values = [1]
+            else:
+                index_values = []
         else:
             # Look up the position of the plane relative to the indexed
             # dimension.
@@ -2243,6 +2251,13 @@ def _get_pffg_item(
         else:
             all_index_values = [int(segment_number)] + index_values
         frame_content_item.DimensionIndexValues = all_index_values
+
+        # If this is an labelmap segmentation of an image that has no frame
+        # of reference, we need to create a dummy frame label to be pointed to
+        # as a dimension index because there is nothing else appropriate to
+        # use
+        if segment_number is None and coordinate_system is None:
+            frame_content_item.FrameLabel = "Segmentation Frame"
         pffg_item.FrameContentSequence = [frame_content_item]
         if has_ref_frame_uid:
             if coordinate_system == CoordinateSystemNames.SLIDE:

tests/test_seg.py

@@ -1413,6 +1413,35 @@ def test_construction_7(self):
         assert SegmentsOverlapValues[instance.SegmentsOverlap] == \
             SegmentsOverlapValues.NO
 
+    def test_construction_8(self):
+        # A chest X-ray with no frame of reference, LABELMAP
+        instance = Segmentation(
+            [self._cr_image],
+            self._cr_pixel_array,
+            SegmentationTypeValues.LABELMAP,
+            self._segment_descriptions,
+            self._series_instance_uid,
+            self._series_number,
+            self._sop_instance_uid,
+            self._instance_number,
+            self._manufacturer,
+            self._manufacturer_model_name,
+            self._software_versions,
+            self._device_serial_number,
+            content_label=self._content_label
+        )
+        assert (
+            instance.DimensionIndexSequence[0].DimensionIndexPointer ==
+            tag_for_keyword('FrameLabel')
+        )
+        dim_ind_vals = (
+            instance
+            .PerFrameFunctionalGroupsSequence[0]
+            .FrameContentSequence[0]
+            .DimensionIndexValues
+        )
+        assert dim_ind_vals == 1
+
     def test_pixel_types_fractional(
         self,
         fractional_transfer_syntax_uid,