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Don't output SVG regions if the width or height is not a whole number. #31

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Merged
hsorby merged 3 commits into from
Oct 9, 2025
Merged

Don't output SVG regions if the width or height is not a whole number. #31

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6533c8a
Don't output SVG regions if the width or height is not a whole number.
hsorby Oct 9, 2025
60bfc46
Correct names of rect variables in _define_background_regions.
hsorby Oct 9, 2025
bab9c5e
Update test answer to correct number of root children in test_flatmap…
hsorby Oct 9, 2025
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29 changes: 19 additions & 10 deletions src/cmlibs/exporter/flatmapsvg.py
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Expand Up @@ -1007,16 +1007,25 @@ def _define_background_regions(boundaries, view_box):
cervical_min_y = min_y + brain_height
thoracic_min_y = cervical_min_y + cervical_height
lumbar_min_y = thoracic_min_y + thoracic_height
brain_rect = f'<rect x="{min_x}" y="{min_y}" width="{width}" height="{brain_height}" fill="red"><title>.id(brain_region)</title></rect>'
cervical_rect = f'<rect x="{min_x}" y="{cervical_min_y}" width="{width}" height="{cervical_height}" fill="green"><title>.id(cervical_region)</title></rect>'
thoracic_rect = f'<rect x="{min_x}" y="{thoracic_min_y}" width="{width}" height="{thoracic_height}" fill="grey"><title>.id(thoracic_region)</title></rect>'
lumbar_rect = f'<rect x="{min_x}" y="{lumbar_min_y}" width="{width}" height="{lumbar_height}" fill="blue"><title>.id(lumbar_region)</title></rect>'
features = {
"brain_region": {"name": "Brain"},
"cervical_region": {"name": "Cervical C1-C7"},
"thoracic_region": {"name": "Thoracic T1-T12"},
"lumbar_region": {"name": "Lumbar L1-"}
}

brain_rect = ''
cervical_rect = ''
thoracic_rect = ''
lumbar_rect = ''
features = {}
if width > 0:
if brain_height > 0:
features["brain_region"] = {"name": "Brain"}
brain_rect = f'<rect x="{min_x}" y="{min_y}" width="{width}" height="{brain_height}" fill="red"><title>.id(brain_region)</title></rect>'
if cervical_height > 0:
features["cervical_region"] = {"name": "Cervical C1-C7"}
cervical_rect = f'<rect x="{min_x}" y="{cervical_min_y}" width="{width}" height="{cervical_height}" fill="green"><title>.id(cervical_region)</title></rect>'
if thoracic_height > 0:
features["thoracic_region"] = {"name": "Thoracic T1-T12"}
thoracic_rect = f'<rect x="{min_x}" y="{thoracic_min_y}" width="{width}" height="{thoracic_height}" fill="grey"><title>.id(thoracic_region)</title></rect>'
if lumbar_height > 0:
features["lumbar_region"] = {"name": "Lumbar L1-"}
lumbar_rect = f'<rect x="{min_x}" y="{lumbar_min_y}" width="{width}" height="{lumbar_height}" fill="blue"><title>.id(lumbar_region)</title></rect>'

return f'{brain_rect}{cervical_rect}{thoracic_rect}{lumbar_rect}', features

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297 changes: 297 additions & 0 deletions tests/resources/properties.json
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@@ -0,0 +1,297 @@
{
"features": {
"brain_region": {
"name": "Brain"
},
"marker_10001": {
"colour": "orange",
"label": "Label 'right level of superior border of jugular foramen on the vagus nerve' for term 'UBERON:9947841' was not found during lookup.",
"models": "UBERON:9947841"
},
"marker_10002": {
"colour": "orange",
"label": "Label 'right level of inferior border of jugular foramen on the vagus nerve' for term 'UBERON:9936083' was not found during lookup.",
"models": "UBERON:9936083"
},
"marker_10003": {
"colour": "orange",
"label": "Label 'right level of angle of the mandible on the vagus nerve' for term 'UBERON:9986030' was not found during lookup.",
"models": "UBERON:9986030"
},
"marker_10004": {
"colour": "orange",
"label": "Label 'right level of carotid bifurcation on the vagus nerve' for term 'UBERON:9936336' was not found during lookup.",
"models": "UBERON:9936336"
},
"marker_10005": {
"colour": "orange",
"label": "Label 'right level of laryngeal prominence on the vagus nerve' for term 'UBERON:9931228' was not found during lookup.",
"models": "UBERON:9931228"
},
"marker_10006": {
"colour": "orange",
"label": "Label 'right level of superior border of the clavicle on the vagus nerve' for term 'UBERON:9968398' was not found during lookup.",
"models": "UBERON:9968398"
},
"marker_10007": {
"colour": "orange",
"label": "Label 'right level of jugular notch on the vagus nerve' for term 'UBERON:9967307' was not found during lookup.",
"models": "UBERON:9967307"
},
"marker_10008": {
"colour": "orange",
"label": "Label 'right level of sternal angle on the vagus nerve' for term 'UBERON:9987408' was not found during lookup.",
"models": "UBERON:9987408"
},
"nerve_feature_01": {
"label": "Label 'Right hypoglossal nerve' for term 'ILX:987654' was not found during lookup."
},
"nerve_feature_02": {
"label": "Label 'Right spinal accessory nerve' for term 'ILX:345678' was not found during lookup."
},
"nerve_feature_03": {
"label": "Label 'cardiovascular/cardiopulmonary branch of right cervical vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_04": {
"label": "Label 'cardiovascular/cardiopulmonary branch of right thoracic vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_08": {
"label": "Label 'right A branch of cervical vagus nerve to sympathetic chain, cardiovascular, and pulmonary structures' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_09": {
"label": "Label 'right A branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_10": {
"label": "Label 'right A cardiovascular branch of cervical vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_11": {
"label": "Label 'right A cardiovascular branch of cranial nerve bundle' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_12": {
"label": "Label 'right A lateral pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_13": {
"label": "Label 'right A medial pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_14": {
"label": "Label 'right A thoracic cardiopulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_15": {
"label": "Label 'right B branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_16": {
"label": "Label 'right B cardiovascular branch of cranial nerve bundle' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_17": {
"label": "Label 'right B lateral pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_18": {
"label": "Label 'right B medial pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_19": {
"label": "Label 'right B thoracic cardiopulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_20": {
"label": "Label 'right C branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_21": {
"label": "Label 'right C lateral pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_22": {
"label": "Label 'right C medial pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_23": {
"label": "Label 'right C thoracic cardiopulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_24": {
"label": "Label 'right D branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_25": {
"label": "Label 'right D lateral pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_26": {
"label": "Label 'right D medial pulmonary branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_27": {
"label": "Label 'right E branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_28": {
"label": "Label 'right F branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_29": {
"label": "Label 'right G branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_30": {
"label": "Label 'right H branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_31": {
"label": "Label 'right I branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_32": {
"label": "Label 'right J branch of thoracic vagus nerve to esophageal plexus' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_33": {
"label": "Label 'right branch between cranial nerve bundle and superior cervical ganglion' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_35": {
"label": "Label 'right branch of cervical vagus nerve to sympathetic chain, cardiovascular, and pulmonary structures' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_36": {
"label": "Label 'right cardiovascular branch of cervical vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_38": {
"label": "Label 'right cervical vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_39": {
"label": "Label 'right cranial nerve bundle to cervical spinal nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_42": {
"label": "Label 'right pharyngeal branch of cranial nerve bundle' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_43": {
"label": "Label 'right recurrent laryngeal nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_44": {
"label": "Label 'right superior laryngeal nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_46": {
"label": "Label 'right thoracic vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_47": {
"label": "Label 'right unknown branch of vagus nerve' for term '<missing-annotation>' was not found during lookup."
},
"nerve_feature_48": {
"label": "Label 'right vagus nerve' for term '<missing-annotation>' was not found during lookup."
}
},
"networks": [
{
"centrelines": [
{
"id": "nerve_feature_38"
},
{
"id": "nerve_feature_48"
},
{
"id": "nerve_feature_46"
},
{
"id": "nerve_feature_01",
"models": "ILX:987654"
},
{
"id": "nerve_feature_02",
"models": "ILX:345678"
},
{
"id": "nerve_feature_03"
},
{
"id": "nerve_feature_04"
},
{
"id": "nerve_feature_08"
},
{
"id": "nerve_feature_35"
},
{
"id": "nerve_feature_09"
},
{
"id": "nerve_feature_10"
},
{
"id": "nerve_feature_36"
},
{
"id": "nerve_feature_11"
},
{
"id": "nerve_feature_12"
},
{
"id": "nerve_feature_13"
},
{
"id": "nerve_feature_14"
},
{
"id": "nerve_feature_15"
},
{
"id": "nerve_feature_16"
},
{
"id": "nerve_feature_17"
},
{
"id": "nerve_feature_18"
},
{
"id": "nerve_feature_19"
},
{
"id": "nerve_feature_20"
},
{
"id": "nerve_feature_21"
},
{
"id": "nerve_feature_22"
},
{
"id": "nerve_feature_23"
},
{
"id": "nerve_feature_24"
},
{
"id": "nerve_feature_25"
},
{
"id": "nerve_feature_26"
},
{
"id": "nerve_feature_27"
},
{
"id": "nerve_feature_28"
},
{
"id": "nerve_feature_29"
},
{
"id": "nerve_feature_30"
},
{
"id": "nerve_feature_31"
},
{
"id": "nerve_feature_32"
},
{
"id": "nerve_feature_33"
},
{
"id": "nerve_feature_39"
},
{
"id": "nerve_feature_42"
},
{
"id": "nerve_feature_43"
},
{
"id": "nerve_feature_44"
},
{
"id": "nerve_feature_47"
}
],
"id": "vagus",
"type": "nerve"
}
]
}
270 changes: 270 additions & 0 deletions tests/resources/vagus.svg
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2 changes: 1 addition & 1 deletion tests/test_flatmapsvg.py
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Expand Up @@ -91,7 +91,7 @@ def test_flatmap_svg_user_mesh(self):
tree = ET.parse(flatmap_svg_file)
root = tree.getroot()

self.assertEqual(92, len(root))
self.assertEqual(89, len(root))

with open(properties_file) as f:
content = json.load(f)
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