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623 fixes downloading issue #629

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Merged
merged 4 commits into from
Mar 24, 2022
Merged

623 fixes downloading issue #629

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1f1feb1
update dataset
wyli Mar 24, 2022
76b7708
update dataset
wyli Mar 24, 2022
7b46205
update downloads
wyli Mar 24, 2022
c663eae
remove dep
wyli Mar 24, 2022
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8 changes: 4 additions & 4 deletions 3d_registration/paired_lung_ct.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
},
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[gdown, nibabel, tqdm]\"\n",
"!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\"\n",
"!python -c \"import matplotlib\" || pip install -q matplotlib\n",
"%matplotlib inline"
]
Expand Down Expand Up @@ -892,7 +892,7 @@
}
],
"source": [
"resource = \"https://drive.google.com/uc?id=1SUS8qknkxyF_lRLmjNqMz_DvH3Nygj68\"\n",
"resource = \"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/pair_lung_ct.pth\"\n",
"dst = f\"{root_dir}/pretrained_weight.pth\"\n",
"download_url(resource, dst)\n",
"model.load_state_dict(torch.load(dst))"
Expand Down Expand Up @@ -1267,7 +1267,7 @@
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -1281,7 +1281,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
"version": "3.8.12"
}
},
"nbformat": 4,
Expand Down
12 changes: 6 additions & 6 deletions deepgrow/ignite/inference_3d.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
"metadata": {},
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[gdown, nibabel, tqdm]\""
"!python -c \"import monai\" || pip install -q \"monai-weekly[nibabel, tqdm]\""
]
},
{
Expand All @@ -15,13 +15,13 @@
"metadata": {},
"outputs": [],
"source": [
"import gdown\n",
"import os\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"import torch\n",
"from torch import jit\n",
"\n",
"import monai\n",
"from monai.apps.deepgrow.transforms import (\n",
" AddGuidanceFromPointsd,\n",
" AddGuidanceSignald,\n",
Expand Down Expand Up @@ -105,16 +105,16 @@
"source": [
"# Download data and model\n",
"\n",
"resource = \"https://drive.google.com/uc?id=1cIlDXWx4pEFpldoIXMEe-5JeaOxzB05Z\"\n",
"resource = \"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/_image.nii.gz\"\n",
"dst = \"_image.nii.gz\"\n",
"\n",
"if not os.path.exists(dst):\n",
" gdown.download(resource, dst, quiet=False)\n",
" monai.apps.download_url(resource, dst)\n",
"\n",
"resource = \"https://drive.google.com/uc?id=1BcU4Z-wdkw7xjydDNd28iVBUVDJYKqCO\"\n",
"resource = \"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/deepgrow_3d.ts\"\n",
"dst = \"deepgrow_3d.ts\"\n",
"if not os.path.exists(dst):\n",
" gdown.download(resource, dst, quiet=False)"
" monai.apps.download_url(resource, dst)"
]
},
{
Expand Down
8 changes: 4 additions & 4 deletions modules/interpretability/class_lung_lesion.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -122,8 +122,8 @@
")\n",
"\n",
"data_path = os.path.join(root_dir, \"patch\")\n",
"!cd {root_dir} && [ -f \"lung_lesion_patches.tar.gz\" ] || gdown --id 1Jte6L7B_5q9XMgOCAq1Ldn29F1aaIxjW \\\n",
" && mkdir -p {data_path} && tar -xvf \"lung_lesion_patches.tar.gz\" -C {data_path} > /dev/null"
"url = \"https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/lung_lesion_patches.tar.gz\"\n",
"monai.apps.download_and_extract(url, output_dir=data_path)"
]
},
{
Expand Down Expand Up @@ -748,7 +748,7 @@
"provenance": []
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -762,7 +762,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.8.12"
}
},
"nbformat": 4,
Expand Down