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Description
Describe the bug
Current setup environment:
!python -c "import monai" || pip install -q "monai-weekly[nibabel]"
!python -c "import vtk" || pip install -q vtk
!python -c "import pxr" || pip install -q usd-core
!python -c "import trimesh" || pip install -q trimesh
!python -c "import ipyvtklink" || pip install -q ipyvtklink
!apt update
!apt install -y libgl1-mesa-glx
!apt install libxrender1
is not enough, when uncomment workflow.run(), will see missing skimage error like:
bundle_root = os.path.join(root_dir, "maisi_ct_generative")
override = {
"output_size_xy": 256,
"output_size_z": 256,
"spacing_xy": 1.5,
"spacing_z": 1.5,
"autoencoder_def#num_splits": 16,
"mask_generation_autoencoder_def#num_splits": 16,
}
workflow = create_workflow(
config_file=os.path.join(bundle_root, "configs/inference.json"),
workflow_type="inference",
bundle_root=bundle_root,
**override,
)
# uncomment this line to run the inference workflow
# then you will get the generated CT images and paired masks which can be used for the following steps.
# In this tutorial, we just use the tested data (IntegrationTest-AbdomenCT.nii.gz) from bundle for demonstration.
workflow.run()
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