Merge branch 'Project-MONAI:main' into main

Project-MONAI · Jul 14, 2024 · 4a994fd · 4a994fd
2 parents 6f0eb03 + b92f9db
commit 4a994fd
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diff --git a/.github/contributing_templates/notebook/example_feature.ipynb b/.github/contributing_templates/notebook/example_feature.ipynb
@@ -126,6 +126,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
@@ -23,7 +23,7 @@ repos:
       - id: detect-private-key
 
   - repo: https://github.com/psf/black
-    rev: "24.3.0"
+    rev: "24.4.2"
     hooks:
       - id: black
       - id: black-jupyter

diff --git a/2d_classification/mednist_tutorial.ipynb b/2d_classification/mednist_tutorial.ipynb
@@ -158,6 +158,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/2d_classification/monai_101.ipynb b/2d_classification/monai_101.ipynb
@@ -152,6 +152,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/2d_classification/monai_201.ipynb b/2d_classification/monai_201.ipynb
@@ -116,6 +116,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/2d_registration/registration_mednist.ipynb b/2d_registration/registration_mednist.ipynb
@@ -168,6 +168,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/3d_classification/densenet_training_array.ipynb b/3d_classification/densenet_training_array.ipynb
@@ -132,6 +132,8 @@
    "source": [
     "# Set data directory\n",
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/3d_registration/learn2reg_nlst_paired_lung_ct.ipynb b/3d_registration/learn2reg_nlst_paired_lung_ct.ipynb
@@ -194,6 +194,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]

diff --git a/3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb b/3d_registration/learn2reg_oasis_unpaired_brain_mr.ipynb
@@ -131,7 +131,7 @@
     "from torch.utils.tensorboard import SummaryWriter\n",
     "\n",
     "# MONAI imports\n",
-    "from monai.apps import download_and_extract\n",
+    "from monai.apps import extractall\n",
     "from monai.data import Dataset, DataLoader\n",
     "from monai.losses import BendingEnergyLoss, DiceLoss\n",
     "from monai.metrics import DiceMetric\n",
@@ -186,6 +186,8 @@
    ],
    "source": [
     "directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
+    "if directory is not None:\n",
+    "    os.makedirs(directory, exist_ok=True)\n",
     "root_dir = tempfile.mkdtemp() if directory is None else directory\n",
     "print(root_dir)"
    ]
@@ -207,12 +209,13 @@
    "outputs": [],
    "source": [
     "resource = \"https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.v1.0.tar\"\n",
+    "!wget https://surfer.nmr.mgh.harvard.edu/ftp/data/neurite/data/neurite-oasis.v1.0.tar --no-check-certificate\n",
     "\n",
-    "compressed_file = os.path.join(root_dir, \"neurite-oasis.v1.0.tar\")\n",
+    "compressed_file = \"./neurite-oasis.v1.0.tar\"\n",
     "data_dir = os.path.join(root_dir, \"OASIS\")\n",
     "if not os.path.exists(data_dir):\n",
     "    os.mkdir(data_dir)\n",
-    "    download_and_extract(resource, compressed_file, data_dir)"
+    "    extractall(compressed_file, data_dir)"
    ]
   },
   {

diff --git a/3d_registration/paired_lung_ct.ipynb b/3d_registration/paired_lung_ct.ipynb
diff --git a/3d_regression/README.md b/3d_regression/README.md
@@ -0,0 +1,7 @@
+3D Regression
+=============
+
+How to run the 3D regression tutorial.
+--------------------------------------
+
+Running this notebook is straightforward.  It works well in Colab.