Update TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb

Updated with the guidance provided in #1852.
Project-MONAI · Oct 8, 2024 · 6fc1435 · 6fc1435
1 parent 90d0a9f
commit 6fc1435
Showing 1 changed file with 23 additions and 18 deletions.
diff --git a/model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb b/model_zoo/TCIA_PROSTATEx_Prostate_MRI_Anatomy_Model.ipynb
@@ -108,29 +108,28 @@
     "#   such as voxel image, image orientation, and image directions,\n",
     "#   which are critical to image processing and display.\n",
     "\n",
+    "import sys\n",
+    "\n",
     "# Upgrade pip, just in case.\n",
-    "!python -m pip install --upgrade -q pip\n",
+    "!{sys.executable} -m pip install --upgrade -q pip\n",
     "\n",
     "# installations required for monai\n",
-    "!python -c \"import monai\" || pip install -q \"monai[nibabel,itk,tqdm,pandas,skimage]\"\n",
-    "!python -c \"import cv2\" || pip install -q opencv-python-headless\n",
+    "!{sys.executable} -m pip install -q \"monai[nibabel,itk,tqdm,pandas,skimage]\"\n",
+    "!{sys.executable} -m 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<3\" pydicom-seg\n",
+    "!{sys.executable} -m pip install -q \"pydicom==2.4.4\" pydicom-seg\n",
     "\n",
     "# Install the dependency manually to avoid installing opencv-python.\n",
-    "!python -m pip install -q plotly bs4 unidecode\n",
-    "!python -m pip install -q --no-deps rt-utils\n",
+    "!{sys.executable} -m pip install -q plotly bs4 unidecode\n",
+    "!{sys.executable} -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",
+    "!{sys.executable} -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]\" 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"
+    "!{sys.executable} -m pip install --upgrade -q \"itkwidgets[all]==1.0a53\" imjoy_elfinder\n",
+    "\n"
    ]
   },
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@@ -586,7 +587,9 @@
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@@ -753,9 +758,9 @@
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+   "display_name": "monai",
    "language": "python",
-   "name": "python3"
+   "name": "monai"
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@@ -771,5 +776,5 @@
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