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Merged
merged 3 commits into from
Apr 27, 2022
Merged

Registration tutorial to use MONAI_DATA_DIRECTORY #668

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Registration tutorial to use MONAI_DATA_DIRECTORY
rijobro Apr 22, 2022
1167baf
imports
rijobro Apr 22, 2022
824dd96
Merge branch 'master' into registration_use_MONAI_DATA_DIRECTORY
wyli Apr 27, 2022
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26 changes: 25 additions & 1 deletion 2d_registration/registration_mednist.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -119,12 +119,36 @@
"import torch\n",
"from torch.nn import MSELoss\n",
"import matplotlib.pyplot as plt\n",
"import os\n",
"import tempfile\n",
"\n",
"\n",
"print_config()\n",
"set_determinism(42)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Setup data directory\n",
"\n",
"You can specify a directory with the `MONAI_DATA_DIRECTORY` environment variable. \n",
"This allows you to save results and reuse downloads. \n",
"If not specified a temporary directory will be used."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"directory = os.environ.get(\"MONAI_DATA_DIRECTORY\")\n",
"root_dir = tempfile.mkdtemp() if directory is None else directory\n",
"print(root_dir)"
]
},
{
"cell_type": "markdown",
"metadata": {
Expand Down Expand Up @@ -188,7 +212,7 @@
}
],
"source": [
"train_data = MedNISTDataset(root_dir=\"./\", section=\"training\", download=True, transform=None)\n",
"train_data = MedNISTDataset(root_dir=root_dir, section=\"training\", download=True, transform=None)\n",
"training_datadict = [\n",
" {\"fixed_hand\": item[\"image\"], \"moving_hand\": item[\"image\"]}\n",
" for item in train_data.data if item[\"label\"] == 4 # label 4 is for xray hands\n",
Expand Down