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Simplify overlay_segmentations using MergeLabelMap + LabelMapContourOverlay #513

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Merged
blowekamp merged 2 commits into from
Sep 23, 2026
Merged

Simplify overlay_segmentations using MergeLabelMap + LabelMapContourOverlay #513

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888bfe1
Simplify overlay_segmentations using MergeLabelMap + LabelMapContourO…
blowekamp Sep 21, 2026
e9e3478
Adding missing words to additional_dictionary
zivy Sep 23, 2026
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44 changes: 19 additions & 25 deletions Python/05_Results_Visualization.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -1085,33 +1085,27 @@
" for c in colors:\n",
" if c == [0, 0, 0]:\n",
" raise ValueError(\"Colors include black [0,0,0], not allowed\")\n",
" empty_image = image * 0\n",
" overlay_boundaries = [\n",
" sitk.LabelMapContourOverlay(\n",
" sitk.Cast(seg, sitk.sitkLabelUInt8),\n",
" empty_image,\n",
" opacity=1,\n",
" contourThickness=thickness,\n",
" dilationRadius=dilation_radius,\n",
" colormap=color,\n",
" )\n",
" for seg, color in zip(binary_segmentations, colors)\n",
"\n",
" # Merge into a single label map (MergeLabelMapFilter's default KEEP method\n",
" # keeps each input's region distinct even though they all use label 1),\n",
" # so LabelMapContourOverlay handles overlapping contours itself in a\n",
" # single pass instead of manually compositing per-segmentation results.\n",
" merged_labels = sitk.MergeLabelMap(\n",
" [sitk.Cast(seg, sitk.sitkLabelUInt8) for seg in binary_segmentations],\n",
" sitk.MergeLabelMapFilter.Keep,\n",
" )\n",
" flat_colormap = [\n",
" channel for color in colors[: len(binary_segmentations)] for channel in color\n",
" ]\n",
"\n",
" current_image = sitk.Compose([image] * 3)\n",
" for o_image in overlay_boundaries:\n",
" current_mask = (\n",
" sitk.NaryAdd(\n",
" [\n",
" sitk.VectorIndexSelectionCast(o_image, 0),\n",
" sitk.VectorIndexSelectionCast(o_image, 1),\n",
" sitk.VectorIndexSelectionCast(o_image, 2),\n",
" ]\n",
" )\n",
" == 0\n",
" )\n",
" current_image = mask_image_multiply(current_mask, current_image) + o_image\n",
" return current_image\n",
" return sitk.LabelMapContourOverlay(\n",
" merged_labels,\n",
" image,\n",
" opacity=1,\n",
" contourThickness=thickness,\n",
" dilationRadius=dilation_radius,\n",
" colormap=flat_colormap,\n",
" )\n",
"\n",
"\n",
"binary_segmentations = [\n",
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2 changes: 2 additions & 0 deletions tests/additional_dictionary.txt
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@@ -1,3 +1,5 @@
LabelMapContourOverlay
MergeLabelMapFilter's
ipympl
ACM
ANTSNeighborhoodCorrelation
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