623 fixes downloading issue (#629)

* update dataset

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update dataset

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update downloads

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove dep

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Author: wyli

3d_registration/paired_lung_ct.ipynb

@@ -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"
    ]
@@ -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))"
@@ -1267,7 +1267,7 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -1281,7 +1281,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,

deepgrow/ignite/inference_3d.ipynb

@@ -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]\""
    ]
   },
   {
@@ -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",
@@ -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)"
    ]
   },
   {

modules/interpretability/class_lung_lesion.ipynb

@@ -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)"
    ]
   },
   {
@@ -748,7 +748,7 @@
    "provenance": []
   },
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -762,7 +762,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.12"
   }
  },
  "nbformat": 4,