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Vikash/updated monai 1 6 release #2078

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2da7e97
runner.sh review fixes and load_medical_images URL update
vikashg Sep 20, 2026
df98606
Pass hash_type="md5" explicitly to download_and_extract
vikashg Sep 20, 2026
1bf0bf9
Use SQLite MLflow tracking URIs instead of the filesystem backend
vikashg Sep 20, 2026
14724e3
auto3dseg: use algo_to_json instead of the disabled algo_to_pickle
vikashg Sep 20, 2026
8ee04e1
Fix zarr v3 API usage, a dead logo URL and a stale batchgenerators pin
vikashg Sep 20, 2026
f4b7da4
fix: restore MONAI 1.6.0rc1 compatibility for two MLflow notebooks
vikashg Sep 22, 2026
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2 changes: 1 addition & 1 deletion 2d_classification/mednist_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@
"compressed_file = os.path.join(root_dir, \"MedNIST.tar.gz\")\n",
"data_dir = os.path.join(root_dir, \"MedNIST\")\n",
"if not os.path.exists(data_dir):\n",
" download_and_extract(resource, compressed_file, root_dir, md5)"
" download_and_extract(resource, compressed_file, root_dir, md5, hash_type=\"md5\")"
]
},
{
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2 changes: 1 addition & 1 deletion 3d_classification/densenet_training_array.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@
" dataset_dir = os.path.join(root_dir, \"ixi\")\n",
" tarfile_name = f\"{dataset_dir}.tar\"\n",
"\n",
" download_and_extract(resource, tarfile_name, dataset_dir, md5)"
" download_and_extract(resource, tarfile_name, dataset_dir, md5, hash_type=\"md5\")"
]
},
{
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2 changes: 1 addition & 1 deletion 3d_regression/densenet_training_array.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -211,7 +211,7 @@
" dataset_dir = os.path.join(root_dir, \"ixi\")\n",
" tarfile_name = f\"{dataset_dir}.tar\"\n",
"\n",
" download_and_extract(resource, tarfile_name, dataset_dir, md5)"
" download_and_extract(resource, tarfile_name, dataset_dir, md5, hash_type=\"md5\")"
]
},
{
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2 changes: 1 addition & 1 deletion 3d_segmentation/spleen_segmentation_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@
"compressed_file = os.path.join(root_dir, \"Task09_Spleen.tar\")\n",
"data_dir = os.path.join(root_dir, \"Task09_Spleen\")\n",
"if not os.path.exists(data_dir):\n",
" download_and_extract(resource, compressed_file, root_dir, md5)"
" download_and_extract(resource, compressed_file, root_dir, md5, hash_type=\"md5\")"
]
},
{
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2 changes: 1 addition & 1 deletion 3d_segmentation/spleen_segmentation_3d_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -206,7 +206,7 @@
"compressed_file = os.path.join(root_dir, \"Task09_Spleen.tar\")\n",
"data_dir = os.path.join(root_dir, \"Task09_Spleen\")\n",
"if not os.path.exists(data_dir):\n",
" download_and_extract(resource, compressed_file, root_dir, md5)"
" download_and_extract(resource, compressed_file, root_dir, md5, hash_type=\"md5\")"
]
},
{
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2 changes: 1 addition & 1 deletion 3d_segmentation/spleen_segmentation_3d_visualization_basic.ipynb
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Expand Up @@ -230,7 +230,7 @@
"compressed_file = os.path.join(root_dir, \"Task09_Spleen.tar\")\n",
"data_dir = os.path.join(root_dir, \"Task09_Spleen\")\n",
"if not os.path.exists(data_dir):\n",
" download_and_extract(resource, compressed_file, root_dir, md5)"
" download_and_extract(resource, compressed_file, root_dir, md5, hash_type=\"md5\")"
]
},
{
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10 changes: 5 additions & 5 deletions 3d_segmentation/unet_segmentation_3d_ignite.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,6 @@
"import glob\n",
"import logging\n",
"import os\n",
"from pathlib import Path\n",
"import shutil\n",
"import sys\n",
"import tempfile\n",
Expand Down Expand Up @@ -332,8 +331,9 @@
"train_tensorboard_stats_handler.attach(trainer)\n",
"\n",
"# MLFlowHandler plots loss at every iteration on MLFlow web UI\n",
"mlflow_dir = os.path.join(log_dir, \"mlruns\")\n",
"train_mlflow_handler = MLFlowHandler(tracking_uri=Path(mlflow_dir).as_uri(), output_transform=lambda x: x)\n",
"# MLflow no longer supports the filesystem tracking backend, so track into a local SQLite database\n",
"mlflow_uri = \"sqlite:///\" + os.path.join(log_dir, \"mlruns.db\")\n",
"train_mlflow_handler = MLFlowHandler(tracking_uri=mlflow_uri, output_transform=lambda x: x)\n",
"train_mlflow_handler.attach(trainer)"
]
},
Expand Down Expand Up @@ -419,7 +419,7 @@
"\n",
"# add handler to record metrics to MLFlow at every validation epoch\n",
"val_mlflow_handler = MLFlowHandler(\n",
" tracking_uri=Path(mlflow_dir).as_uri(),\n",
" tracking_uri=mlflow_uri,\n",
" # no need to plot loss value, so disable per iteration output\n",
" output_transform=lambda x: None,\n",
" # fetch global epoch number from trainer\n",
Expand Down Expand Up @@ -516,7 +516,7 @@
"source": [
"## Visualizing training status in MLFlow\n",
"\n",
"As `mlflow` is not IPython component, please switch to the `log_dir` and execute command `mlflow ui` to launch MLFlow UI.\n",
"As `mlflow` is not IPython component, please switch to the `log_dir` and execute command `mlflow ui --backend-store-uri sqlite:///mlruns.db` to launch MLFlow UI.\n",
"\n",
"Expected training curve on MLFlow UI:\n",
"\n",
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