Skip to content

Commit a857999

Browse files
pre-commit-ci[bot]pre-commit-ci[bot]
committed
[pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
1 parent 2183084 commit a857999

File tree

2 files changed

+166
-154
lines changed

2 files changed

+166
-154
lines changed

‎modules/omniverse/omniverse_integration.ipynb‎

Lines changed: 139 additions & 128 deletions
Original file line numberDiff line numberDiff line change
@@ -191,10 +191,10 @@
191191
"bundle_root = os.path.join(\"/workspace/Code/tutorials/modules/omniverse\", \"vista3d\")\n",
192192
"input_dict = {\"image\": \"/workspace/Code/tutorials/modules/totalSegmentator_mergedLabel_samples/imagesTr/s0001.nii.gz\"}\n",
193193
"workflow = create_workflow(\n",
194-
" config_file=os.path.join(bundle_root,\"configs/inference.json\"),\n",
194+
" config_file=os.path.join(bundle_root, \"configs/inference.json\"),\n",
195195
" workflow_type=\"inference\",\n",
196196
" bundle_root=bundle_root,\n",
197-
" input_dict=input_dict\n",
197+
" input_dict=input_dict,\n",
198198
")\n",
199199
"workflow.run()"
200200
]
@@ -277,135 +277,130 @@
277277
"source": [
278278
"# 17 groupings that cover 101 segments/regions out of 140\n",
279279
"labels = {\n",
280-
" \"Liver\": 1,\n",
281-
" \"Spleen\": 3,\n",
282-
" \"Pancreas\": 4,\n",
283-
" \"Heart\": 115,\n",
284-
" \"Body\": 200,\n",
285-
" \"Gallbladder\": 10,\n",
286-
" \"Stomach\": 12,\n",
287-
" \"Small_bowel\": 19,\n",
288-
" \"Colon\": 62,\n",
289-
" \"Kidney\": {\"right_kidney\": 5,\n",
290-
" \"left_kidney\": 14\n",
291-
" },\n",
292-
" \"Veins\": {\"aorta\": 6,\n",
293-
" \"inferior_vena_cava\": 7,\n",
294-
" \"portal_vein_and_splenic_vein\": 17,\n",
295-
" \"left_iliac_artery\": 58,\n",
296-
" \"right_iliac_artery\": 59,\n",
297-
" \"left_iliac_vena\": 60,\n",
298-
" \"right_iliac_vena\": 61,\n",
299-
" \"pulmonary_vein\": 119,\n",
300-
" \"left_subclavian_artery\": 123,\n",
301-
" \"right_subclavian_artery\": 124,\n",
302-
" \"superior_vena_cava\": 125,\n",
303-
" \"brachiocephalic_trunk\": 109,\n",
304-
" \"left_brachiocephalic_vein\": 110,\n",
305-
" \"right_brachiocephalic_vein\": 111,\n",
306-
" \"left_common_carotid_artery\": 112,\n",
307-
" \"right_common_carotid_artery\": 113,\n",
308-
" },\n",
309-
" \"Lungs\": {\"left_lung_upper_lobe\": 28,\n",
310-
" \"left_lung_lower_lobe\": 29,\n",
311-
" \"right_lung_upper_lobe\": 30,\n",
312-
" \"right_lung_middle_lobe\": 31,\n",
313-
" \"right_lung_lower_lobe\": 32\n",
314-
" },\n",
315-
" \"Spine\": {\n",
316-
" # \"vertebrae_L6\": 131,\n",
317-
" \"vertebrae_L5\": 33,\n",
318-
" \"vertebrae_L4\": 34,\n",
319-
" \"vertebrae_L3\": 35,\n",
320-
" \"vertebrae_L2\": 36,\n",
321-
" \"vertebrae_L1\": 37,\n",
322-
" \"vertebrae_T12\": 38,\n",
323-
" \"vertebrae_T11\": 39,\n",
324-
" \"vertebrae_T10\": 40,\n",
325-
" \"vertebrae_T9\": 41,\n",
326-
" \"vertebrae_T8\": 42,\n",
327-
" \"vertebrae_T7\": 43,\n",
328-
" \"vertebrae_T6\": 44,\n",
329-
" \"vertebrae_T5\": 45,\n",
330-
" \"vertebrae_T4\": 46,\n",
331-
" \"vertebrae_T3\": 47,\n",
332-
" \"vertebrae_T2\": 48,\n",
333-
" \"vertebrae_T1\": 49,\n",
334-
" \"vertebrae_C7\": 50,\n",
335-
" \"vertebrae_C6\": 51,\n",
336-
" \"vertebrae_C5\": 52,\n",
337-
" \"vertebrae_C4\": 53,\n",
338-
" \"vertebrae_C3\": 54,\n",
339-
" \"vertebrae_C2\": 55,\n",
340-
" \"vertebrae_C1\": 56,\n",
341-
" \"sacrum\": 97,\n",
342-
" \"vertebrae_S1\": 127,\n",
343-
" },\n",
344-
" \"Ribs\": {\n",
345-
" \"left_rib_1\": 63,\n",
346-
" \"left_rib_2\": 64,\n",
347-
" \"left_rib_3\": 65,\n",
348-
" \"left_rib_4\": 66,\n",
349-
" \"left_rib_5\": 67,\n",
350-
" \"left_rib_6\": 68,\n",
351-
" \"left_rib_7\": 69,\n",
352-
" \"left_rib_8\": 70,\n",
353-
" \"left_rib_9\": 71,\n",
354-
" \"left_rib_10\": 72,\n",
355-
" \"left_rib_11\": 73,\n",
356-
" \"left_rib_12\": 74,\n",
357-
" \"right_rib_1\": 75,\n",
358-
" \"right_rib_2\": 76,\n",
359-
" \"right_rib_3\": 77,\n",
360-
" \"right_rib_4\": 78,\n",
361-
" \"right_rib_5\": 79,\n",
362-
" \"right_rib_6\": 80,\n",
363-
" \"right_rib_7\": 81,\n",
364-
" \"right_rib_8\": 82,\n",
365-
" \"right_rib_9\": 83,\n",
366-
" \"right_rib_10\": 84,\n",
367-
" \"right_rib_11\": 85,\n",
368-
" \"right_rib_12\": 86,\n",
369-
" \"costal_cartilages\": 114,\n",
370-
" \"sternum\": 122,\n",
371-
" },\n",
372-
" \"Shoulders\": {\n",
373-
" \"left_scapula\": 89,\n",
374-
" \"right_scapula\": 90,\n",
375-
" \"left_clavicula\": 91,\n",
376-
" \"right_clavicula\": 92\n",
377-
" },\n",
378-
" \"Hips\": {\n",
379-
" \"left_hip\": 95,\n",
380-
" \"right_hip\": 96\n",
381-
" },\n",
382-
" \"Back_muscles\": {\n",
383-
" \"left_gluteus_maximus\": 98,\n",
384-
" \"right_gluteus_maximus\": 99,\n",
385-
" \"left_gluteus_medius\": 100,\n",
386-
" \"right_gluteus_medius\": 101,\n",
387-
" \"left_gluteus_minimus\": 102,\n",
388-
" \"right_gluteus_minimus\": 103,\n",
389-
" \"left_autochthon\": 104,\n",
390-
" \"right_autochthon\": 105,\n",
391-
" \"left_iliopsoas\": 106,\n",
392-
" \"right_iliopsoas\": 107\n",
393-
" }\n",
280+
" \"Liver\": 1,\n",
281+
" \"Spleen\": 3,\n",
282+
" \"Pancreas\": 4,\n",
283+
" \"Heart\": 115,\n",
284+
" \"Body\": 200,\n",
285+
" \"Gallbladder\": 10,\n",
286+
" \"Stomach\": 12,\n",
287+
" \"Small_bowel\": 19,\n",
288+
" \"Colon\": 62,\n",
289+
" \"Kidney\": {\"right_kidney\": 5, \"left_kidney\": 14},\n",
290+
" \"Veins\": {\n",
291+
" \"aorta\": 6,\n",
292+
" \"inferior_vena_cava\": 7,\n",
293+
" \"portal_vein_and_splenic_vein\": 17,\n",
294+
" \"left_iliac_artery\": 58,\n",
295+
" \"right_iliac_artery\": 59,\n",
296+
" \"left_iliac_vena\": 60,\n",
297+
" \"right_iliac_vena\": 61,\n",
298+
" \"pulmonary_vein\": 119,\n",
299+
" \"left_subclavian_artery\": 123,\n",
300+
" \"right_subclavian_artery\": 124,\n",
301+
" \"superior_vena_cava\": 125,\n",
302+
" \"brachiocephalic_trunk\": 109,\n",
303+
" \"left_brachiocephalic_vein\": 110,\n",
304+
" \"right_brachiocephalic_vein\": 111,\n",
305+
" \"left_common_carotid_artery\": 112,\n",
306+
" \"right_common_carotid_artery\": 113,\n",
307+
" },\n",
308+
" \"Lungs\": {\n",
309+
" \"left_lung_upper_lobe\": 28,\n",
310+
" \"left_lung_lower_lobe\": 29,\n",
311+
" \"right_lung_upper_lobe\": 30,\n",
312+
" \"right_lung_middle_lobe\": 31,\n",
313+
" \"right_lung_lower_lobe\": 32,\n",
314+
" },\n",
315+
" \"Spine\": {\n",
316+
" # \"vertebrae_L6\": 131,\n",
317+
" \"vertebrae_L5\": 33,\n",
318+
" \"vertebrae_L4\": 34,\n",
319+
" \"vertebrae_L3\": 35,\n",
320+
" \"vertebrae_L2\": 36,\n",
321+
" \"vertebrae_L1\": 37,\n",
322+
" \"vertebrae_T12\": 38,\n",
323+
" \"vertebrae_T11\": 39,\n",
324+
" \"vertebrae_T10\": 40,\n",
325+
" \"vertebrae_T9\": 41,\n",
326+
" \"vertebrae_T8\": 42,\n",
327+
" \"vertebrae_T7\": 43,\n",
328+
" \"vertebrae_T6\": 44,\n",
329+
" \"vertebrae_T5\": 45,\n",
330+
" \"vertebrae_T4\": 46,\n",
331+
" \"vertebrae_T3\": 47,\n",
332+
" \"vertebrae_T2\": 48,\n",
333+
" \"vertebrae_T1\": 49,\n",
334+
" \"vertebrae_C7\": 50,\n",
335+
" \"vertebrae_C6\": 51,\n",
336+
" \"vertebrae_C5\": 52,\n",
337+
" \"vertebrae_C4\": 53,\n",
338+
" \"vertebrae_C3\": 54,\n",
339+
" \"vertebrae_C2\": 55,\n",
340+
" \"vertebrae_C1\": 56,\n",
341+
" \"sacrum\": 97,\n",
342+
" \"vertebrae_S1\": 127,\n",
343+
" },\n",
344+
" \"Ribs\": {\n",
345+
" \"left_rib_1\": 63,\n",
346+
" \"left_rib_2\": 64,\n",
347+
" \"left_rib_3\": 65,\n",
348+
" \"left_rib_4\": 66,\n",
349+
" \"left_rib_5\": 67,\n",
350+
" \"left_rib_6\": 68,\n",
351+
" \"left_rib_7\": 69,\n",
352+
" \"left_rib_8\": 70,\n",
353+
" \"left_rib_9\": 71,\n",
354+
" \"left_rib_10\": 72,\n",
355+
" \"left_rib_11\": 73,\n",
356+
" \"left_rib_12\": 74,\n",
357+
" \"right_rib_1\": 75,\n",
358+
" \"right_rib_2\": 76,\n",
359+
" \"right_rib_3\": 77,\n",
360+
" \"right_rib_4\": 78,\n",
361+
" \"right_rib_5\": 79,\n",
362+
" \"right_rib_6\": 80,\n",
363+
" \"right_rib_7\": 81,\n",
364+
" \"right_rib_8\": 82,\n",
365+
" \"right_rib_9\": 83,\n",
366+
" \"right_rib_10\": 84,\n",
367+
" \"right_rib_11\": 85,\n",
368+
" \"right_rib_12\": 86,\n",
369+
" \"costal_cartilages\": 114,\n",
370+
" \"sternum\": 122,\n",
371+
" },\n",
372+
" \"Shoulders\": {\"left_scapula\": 89, \"right_scapula\": 90, \"left_clavicula\": 91, \"right_clavicula\": 92},\n",
373+
" \"Hips\": {\"left_hip\": 95, \"right_hip\": 96},\n",
374+
" \"Back_muscles\": {\n",
375+
" \"left_gluteus_maximus\": 98,\n",
376+
" \"right_gluteus_maximus\": 99,\n",
377+
" \"left_gluteus_medius\": 100,\n",
378+
" \"right_gluteus_medius\": 101,\n",
379+
" \"left_gluteus_minimus\": 102,\n",
380+
" \"right_gluteus_minimus\": 103,\n",
381+
" \"left_autochthon\": 104,\n",
382+
" \"right_autochthon\": 105,\n",
383+
" \"left_iliopsoas\": 106,\n",
384+
" \"right_iliopsoas\": 107,\n",
385+
" },\n",
394386
"}\n",
395387
"\n",
388+
"\n",
396389
"def nii_to_obj(input_nii_path, output_nii_path, output_obj_path):\n",
397390
" if not os.path.exists(output_nii_path):\n",
398391
" os.makedirs(output_nii_path)\n",
399-
" pre_trans = Compose([\n",
400-
" LoadImaged(keys=\"label\", ensure_channel_first=True),\n",
401-
" BorderPadd(keys=\"label\", spatial_border=2),\n",
402-
" SqueezeDimd(keys=\"label\", dim=0),\n",
403-
" ])\n",
392+
" pre_trans = Compose(\n",
393+
" [\n",
394+
" LoadImaged(keys=\"label\", ensure_channel_first=True),\n",
395+
" BorderPadd(keys=\"label\", spatial_border=2),\n",
396+
" SqueezeDimd(keys=\"label\", dim=0),\n",
397+
" ]\n",
398+
" )\n",
404399
" orig_seg = pre_trans({\"label\": input_nii_path})[\"label\"]\n",
405400
" all_organ = np.zeros_like(orig_seg, dtype=np.uint8)\n",
406-
" \n",
401+
"\n",
407402
" save_trans = SaveImage(output_ext=\"nii.gz\", output_dtype=np.uint8)\n",
408-
"# save_trans.set_options(write_kwargs = {\"compression\":True})\n",
403+
" # save_trans.set_options(write_kwargs = {\"compression\":True})\n",
409404
" for j, (organ_name, label_val) in enumerate(labels.items(), start=1):\n",
410405
" single_organ = np.zeros_like(orig_seg, dtype=np.uint8)\n",
411406
" print(f\"Assigning index {j} to label {organ_name}\")\n",
@@ -418,14 +413,28 @@
418413
" single_organ[orig_seg == label_val] = j\n",
419414
" organ_filename = os.path.join(output_nii_path, organ_name)\n",
420415
" save_trans(single_organ[None], meta_data=orig_seg.meta, filename=organ_filename)\n",
421-
" convert_to_mesh(f\"{organ_filename}.nii.gz\", output_obj_path, f\"{organ_name}.obj\", label_value=j, smoothing_factor=0.5, reduction_ratio=0.0)\n",
422-
"\n",
416+
" convert_to_mesh(\n",
417+
" f\"{organ_filename}.nii.gz\",\n",
418+
" output_obj_path,\n",
419+
" f\"{organ_name}.obj\",\n",
420+
" label_value=j,\n",
421+
" smoothing_factor=0.5,\n",
422+
" reduction_ratio=0.0,\n",
423+
" )\n",
423424
"\n",
424425
" all_organ_filename = os.path.join(output_nii_path, \"all_organs\")\n",
425426
" save_trans(all_organ[None], meta_data=orig_seg.meta, filename=all_organ_filename)\n",
426-
" convert_to_mesh(f\"{all_organ_filename}.nii.gz\", output_obj_path, \"all_organs.gltf\", label_value=list(range(1, 18)), smoothing_factor=0.6, reduction_ratio=0.0)\n",
427+
" convert_to_mesh(\n",
428+
" f\"{all_organ_filename}.nii.gz\",\n",
429+
" output_obj_path,\n",
430+
" \"all_organs.gltf\",\n",
431+
" label_value=list(range(1, 18)),\n",
432+
" smoothing_factor=0.6,\n",
433+
" reduction_ratio=0.0,\n",
434+
" )\n",
427435
" print(f\"Saved whole segmentation {all_organ_filename}\")\n",
428436
"\n",
437+
"\n",
429438
"input_nii_path = \"/workspace/Data/maisi_ct_generative/datasets/IntegrationTest-AbdomenCT.nii.gz\"\n",
430439
"output_nii_path = \"/workspace/Data/maisi_ct_generative/datasets/monai/nii\"\n",
431440
"output_obj_path = \"/workspace/Data/maisi_ct_generative/datasets/monai/obj\"\n",
@@ -470,7 +479,9 @@
470479
"source": [
471480
"# Step 1: Read the mesh\n",
472481
"reader = vtk.vtkOBJReader()\n",
473-
"reader.SetFileName(\"/workspace/Data/maisi_ct_generative/datasets/monai/obj/Heart.obj\") # Provide the path to your STL file\n",
482+
"reader.SetFileName(\n",
483+
" \"/workspace/Data/maisi_ct_generative/datasets/monai/obj/Heart.obj\"\n",
484+
") # Provide the path to your STL file\n",
474485
"reader.Update()\n",
475486
"\n",
476487
"# Step 2: Create a mapper\n",
@@ -497,7 +508,7 @@
497508
"\n",
498509
"# Step 6: Use ipyvtklink for notebook rendering\n",
499510
"widget = ViewInteractiveWidget(render_window)\n",
500-
"widget\n"
511+
"widget"
501512
]
502513
},
503514
{

0 commit comments

Comments
 (0)