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update 3d seg demo #326

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Merged
wyli merged 1 commit into from
Aug 31, 2021
Merged

update 3d seg demo #326

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12 changes: 3 additions & 9 deletions 3d_segmentation/spleen_segmentation_3d_lightning.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel]\"\n",
"!python -c \"import matplotlib\" || pip install -q matplotlib\n",
"!pip install -q pytorch-lightning==0.9.0\n",
"!pip install -q pytorch-lightning==1.4.0\n",
"%matplotlib inline"
]
},
Expand Down Expand Up @@ -145,8 +145,6 @@
"from monai.apps import download_and_extract\n",
"import torch\n",
"import pytorch_lightning\n",
"from pytorch_lightning.callbacks.model_checkpoint \\\n",
" import ModelCheckpoint\n",
"import matplotlib.pyplot as plt\n",
"import tempfile\n",
"import shutil\n",
Expand Down Expand Up @@ -424,17 +422,13 @@
"tb_logger = pytorch_lightning.loggers.TensorBoardLogger(\n",
" save_dir=log_dir\n",
")\n",
"checkpoint_callback = ModelCheckpoint(\n",
" filepath=os.path.join(\n",
" log_dir, \"{epoch}-{val_loss:.2f}-{val_dice:.2f}\")\n",
")\n",
"\n",
"# initialise Lightning's trainer.\n",
"trainer = pytorch_lightning.Trainer(\n",
" gpus=[0],\n",
" max_epochs=600,\n",
" logger=tb_logger,\n",
" checkpoint_callback=checkpoint_callback,\n",
" checkpoint_callback=True,\n",
" num_sanity_val_steps=1,\n",
")\n",
"\n",
Expand Down Expand Up @@ -710,7 +704,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
"version": "3.7.10"
}
},
"nbformat": 4,
Expand Down