From 97f943c1e22f731be3e295e60356b90e342a0494 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Mon, 17 Mar 2025 07:07:20 +0000 Subject: [PATCH 1/2] fix issue Signed-off-by: Yiheng Wang --- modules/omniverse/omniverse_integration.ipynb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/modules/omniverse/omniverse_integration.ipynb b/modules/omniverse/omniverse_integration.ipynb index 8ba6082f5..73b634047 100644 --- a/modules/omniverse/omniverse_integration.ipynb +++ b/modules/omniverse/omniverse_integration.ipynb @@ -57,6 +57,7 @@ "outputs": [], "source": [ "!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel]\"\n", + "!python -c \"import skimage\" || pip install -q scikit-image\n", "!python -c \"import vtk\" || pip install -q vtk\n", "!python -c \"import pxr\" || pip install -q usd-core\n", "!python -c \"import trimesh\" || pip install -q trimesh\n", @@ -466,6 +467,11 @@ " print(f\"Saved whole segmentation {all_organ_filename}\")\n", "\n", "\n", + "# if workflow.run() is uncommented and run, an image and a label files will be generated in the output folder\n", + "# for example, file paths are like this:\n", + "# f\"{bundle_root}/output/sample_20250317_065034_415537_image.nii.gz\n", + "# f\"{bundle_root}/output/sample_20250317_065034_415537_label.nii.gz\n", + "# then you can replace the \"input_nii_path\" below with the generated label file\n", "input_nii_path = f\"{bundle_root}/datasets/IntegrationTest-AbdomenCT.nii.gz\"\n", "output_nii_path = f\"{bundle_root}/datasets/monai/nii\"\n", "output_obj_path = f\"{bundle_root}/datasets/monai/obj\"\n", From 7babda97de51a3dc4f6510ec9971937c802c5b66 Mon Sep 17 00:00:00 2001 From: Yiheng Wang Date: Mon, 17 Mar 2025 07:12:46 +0000 Subject: [PATCH 2/2] update docstring Signed-off-by: Yiheng Wang --- modules/omniverse/omniverse_integration.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/omniverse/omniverse_integration.ipynb b/modules/omniverse/omniverse_integration.ipynb index 73b634047..ea0059611 100644 --- a/modules/omniverse/omniverse_integration.ipynb +++ b/modules/omniverse/omniverse_integration.ipynb @@ -469,8 +469,8 @@ "\n", "# if workflow.run() is uncommented and run, an image and a label files will be generated in the output folder\n", "# for example, file paths are like this:\n", - "# f\"{bundle_root}/output/sample_20250317_065034_415537_image.nii.gz\n", - "# f\"{bundle_root}/output/sample_20250317_065034_415537_label.nii.gz\n", + "# f\"{bundle_root}/output/sample_20250317_065034_415537_image.nii.gz\"\n", + "# f\"{bundle_root}/output/sample_20250317_065034_415537_label.nii.gz\"\n", "# then you can replace the \"input_nii_path\" below with the generated label file\n", "input_nii_path = f\"{bundle_root}/datasets/IntegrationTest-AbdomenCT.nii.gz\"\n", "output_nii_path = f\"{bundle_root}/datasets/monai/nii\"\n",