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Update tcia prostatex model notebook #1852

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00f3362
Fixed dependency issues with itkwidgets
kirbyju Sep 24, 2024
6e36c64
Revert "Fixed dependency issues with itkwidgets"
kirbyju Oct 3, 2024
f3d172e
Updated tcia_prostatex_prostate_mri_anatomy_model.ipynb
kirbyju Oct 5, 2024
90d0a9f
Merge branch 'main' into update-tcia-prostatex-model-notebook
kirbyju Oct 5, 2024
6fc1435
Update TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
kirbyju Oct 8, 2024
11621f6
Justin Kirby <[email protected]>
kirbyju Oct 9, 2024
17b2c49
Update TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
kirbyju Oct 9, 2024
8592b7f
Update TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
kirbyju Oct 10, 2024
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16 changes: 10 additions & 6 deletions model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
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Expand Up @@ -116,17 +116,21 @@
"!python -c \"import cv2\" || pip install -q opencv-python-headless\n",
"\n",
"# These are the libraries used to read DICOM Seg objects.\n",
"!python -m pip install -q pydicom pydicom-seg\n",
"\n",
"# Install tcia_utils to download the datasets.\n",
"!python -m pip install --upgrade -q --no-deps tcia_utils\n",
"!python -m pip install -q \"pydicom<3\" pydicom-seg\n",
"\n",
"# Install the dependency manually to avoid installing opencv-python.\n",
"!python -m pip install -q plotly bs4 ipywidgets unidecode jsonschema\n",
"!python -m pip install -q plotly bs4 unidecode\n",
"!python -m pip install -q --no-deps rt-utils\n",
"\n",
"# Install tcia_utils to download the datasets.\n",
"!python -m pip install --upgrade -q --no-deps tcia_utils\n",
"\n",
"# This is the installation required for itkWidgets.\n",
"!python -m pip install --upgrade --pre -q \"itkwidgets[all]==1.0a23\" imjoy_elfinder"
"!python -m pip install --upgrade --pre -q \"itkwidgets[all]\" imjoy_elfinder\n",
"\n",
"# TEMPORARY WORKAROUND TO RESOLVE: https://github.com/kirbyju/TCIA_Notebooks/issues/30\n",
"!python -m pip uninstall -y -q zarr ngff_zarr\n",
"!python -m pip install -q zarr ngff_zarr"
]
},
{
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