Enhance nnUNet bundle notebook with DecathlonDataset integration and …

…logging configuration
Project-MONAI · Feb 26, 2025 · 482bb70 · 482bb70
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commit 482bb70
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Showing 2 changed files with 65 additions and 12 deletions.
diff --git a/bundle/06_nnunet_monai_bundle.ipynb b/bundle/06_nnunet_monai_bundle.ipynb
@@ -65,6 +65,7 @@
    "outputs": [],
    "source": [
     "from monai.config import print_config\n",
+    "from monai.apps import DecathlonDataset\n",
     "import os\n",
     "import tempfile\n",
     "from monai.bundle.config_parser import ConfigParser\n",
@@ -73,6 +74,7 @@
     "from monai.bundle.nnunet import convert_nnunet_to_monai_bundle\n",
     "import json\n",
     "from pathlib import Path\n",
+    "import nnunetv2\n",
     "\n",
     "print_config()"
    ]
@@ -94,7 +96,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "os.environ[\"MONAI_DATA_DIRECTORY\"] = \"/home/maia-user/Documents/GitHub/tutorials/bundle/MONAI/Data\""
+    "os.environ[\"MONAI_DATA_DIRECTORY\"] = \"/home/maia-user/Documents/MONAI/Data\""
    ]
   },
   {
@@ -119,6 +121,15 @@
     "To get the Decathlon Spleen dataset and generate the corresponding data list, you can follow the instructions in the [MSD Datalist Generator Notebook](../auto3dseg/notebooks/msd_datalist_generator.ipynb)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "DecathlonDataset(root_dir, \"Task09_Spleen\", \"training\", download=True)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -230,7 +241,7 @@
     "data_src = {\n",
     "    \"modality\": \"CT\",\n",
     "    \"dataset_name_or_id\": \"09\",\n",
-    "    \"datalist\": os.path.join(root_dir, \"Task09_Spleen/msd_task09_spleen_folds.json\"),\n",
+    "    \"datalist\": str(datalist_file),\n",
     "    \"dataroot\": os.path.join(root_dir, \"Task09_Spleen\"),\n",
     "}\n",
     "\n",
@@ -477,12 +488,12 @@
     "\n",
     "\n",
     "BUNDLE_ROOT=nnUNetBundle\n",
-    "MONAI_DATA_DIRECTORY=/home/maia-user/Documents/GitHub/tutorials/bundle/MONAI/Data\n",
+    "MONAI_DATA_DIRECTORY=/home/maia-user/Documents/MONAI/Data\n",
     "\n",
     "python -m monai.bundle run \\\n",
     "    --config-file $BUNDLE_ROOT/configs/inference.yaml \\\n",
     "    --bundle-root $BUNDLE_ROOT \\\n",
-    "    --data_list_file  $MONAI_DATA_DIRECTORY/Task09_Spleen/msd_task09_spleen_folds.json \\\n",
+    "    --data_list_file  $MONAI_DATA_DIRECTORY/Task09_Spleen/Task09_Spleen_folds.json \\\n",
     "    --output-dir $BUNDLE_ROOT/pred_output \\\n",
     "    --data_dir $MONAI_DATA_DIRECTORY/Task09_Spleen \\\n",
     "    --logging-file$BUNDLE_ROOT/configs/logging.conf"
@@ -755,9 +766,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import nnunetv2\n",
-    "\n",
-    "print(nnunetv2.__file__)"
+    "nnunet_training_file = Path(nnunetv2.training.__file__).parent.joinpath(\"lr_scheduler\", \"polylr.py\")"
    ]
   },
   {
@@ -773,7 +782,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%writefile </path/to/nnunetv2>/training/lr_scheduler/polylr.py\n",
+    "%%writefile $nnunet_training_file\n",
     "\n",
     "from torch.optim.lr_scheduler import _LRScheduler\n",
     "\n",
@@ -816,19 +825,20 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "\n",
+    "export MONAI_DATA_DIRECTORY=/home/maia-user/Documents/MONAI/Data\n",
     "export nnUNet_raw=$MONAI_DATA_DIRECTORY\"/nnUNet/nnUNet_raw_data_base\"\n",
     "export nnUNet_preprocessed=$MONAI_DATA_DIRECTORY\"/nnUNet/nnUNet_preprocessed\"\n",
     "export nnUNet_results=$MONAI_DATA_DIRECTORY\"/nnUNet/nnUNet_trained_models\"\n",
     "\n",
     "export BUNDLE=nnUNetBundle\n",
     "export PYTHONPATH=$BUNDLE\n",
     "\n",
-    "#export nnUNet_def_n_proc=2\n",
-    "#export nnUNet_n_proc_DA=2\n",
+    "export nnUNet_def_n_proc=2\n",
+    "export nnUNet_n_proc_DA=2\n",
     "\n",
     "python -m monai.bundle run \\\n",
     "--bundle-root nnUNetBundle \\\n",
+    "--dataset_name_or_id 009 \\\n",
     "--config-file nnUNetBundle/configs/train.yaml"
    ]
   },

diff --git a/bundle/nnUNet_Bundle.ipynb b/bundle/nnUNet_Bundle.ipynb
@@ -938,6 +938,49 @@
     "which tree && tree nnUNetBundle || true"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "70a37817",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%writefile nnUNetBundle/configs/logging.conf\n",
+    "[loggers]\n",
+    "keys=root\n",
+    "\n",
+    "[handlers]\n",
+    "keys=consoleHandler\n",
+    "\n",
+    "[formatters]\n",
+    "keys=fullFormatter\n",
+    "\n",
+    "[logger_root]\n",
+    "level=INFO\n",
+    "handlers=consoleHandler\n",
+    "\n",
+    "[handler_consoleHandler]\n",
+    "class=StreamHandler\n",
+    "level=INFO\n",
+    "formatter=fullFormatter\n",
+    "args=(sys.stdout,)\n",
+    "\n",
+    "[formatter_fullFormatter]\n",
+    "format=%(asctime)s - %(name)s - %(levelname)s - %(message)s\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4c25feaf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%writefile nnUNetBundle/configs/metadata.json\n",
+    "\n",
+    "##TODO: Add metadata, following the instructions in https://docs.monai.io/en/stable/mb_specification.html"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -1717,7 +1760,7 @@
     "    --bundle_root $BUNDLE_ROOT \\\n",
     "    --config_file $BUNDLE_ROOT/configs/train.yaml\n",
     "\n",
-    "#Option to resume training\n",
+    "# Option to resume training\n",
     "#--config_file \"['$BUNDLE_ROOT/configs/train.yaml','$BUNDLE_ROOT/configs/train_resume.yaml']\"\n",
     "\n",
     "# Log to Local MLFlow\n",