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Update 2d_classification tutorial for MetaTensor #792

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Merged
wyli merged 2 commits into from
Jul 16, 2022
Merged

Update 2d_classification tutorial for MetaTensor #792

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8a2284c
update mednist
KumoLiu Jul 15, 2022
6bd2e90
Merge branch 'main' into 790-update-2d_classification-tutorial
wyli Jul 16, 2022
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22 changes: 10 additions & 12 deletions 2d_classification/mednist_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,7 @@
"\n",
"from monai.apps import download_and_extract\n",
"from monai.config import print_config\n",
"from monai.data import decollate_batch\n",
"from monai.data import decollate_batch, DataLoader\n",
"from monai.metrics import ROCAUCMetric\n",
"from monai.networks.nets import DenseNet121\n",
"from monai.transforms import (\n",
Expand All @@ -117,7 +117,6 @@
" RandRotate,\n",
" RandZoom,\n",
" ScaleIntensity,\n",
" EnsureType,\n",
")\n",
"from monai.utils import set_determinism\n",
"\n",
Expand Down Expand Up @@ -361,21 +360,20 @@
"source": [
"train_transforms = Compose(\n",
" [\n",
" LoadImage(image_only=True),\n",
" LoadImage(),\n",
" AddChannel(),\n",
" ScaleIntensity(),\n",
" RandRotate(range_x=np.pi / 12, prob=0.5, keep_size=True),\n",
" RandFlip(spatial_axis=0, prob=0.5),\n",
" RandZoom(min_zoom=0.9, max_zoom=1.1, prob=0.5),\n",
" EnsureType(),\n",
" ]\n",
")\n",
"\n",
"val_transforms = Compose(\n",
" [LoadImage(image_only=True), AddChannel(), ScaleIntensity(), EnsureType()])\n",
" [LoadImage(), AddChannel(), ScaleIntensity()])\n",
"\n",
"y_pred_trans = Compose([EnsureType(), Activations(softmax=True)])\n",
"y_trans = Compose([EnsureType(), AsDiscrete(to_onehot=num_class)])"
"y_pred_trans = Compose([Activations(softmax=True)])\n",
"y_trans = Compose([AsDiscrete(to_onehot=num_class)])"
]
},
{
Expand All @@ -398,15 +396,15 @@
"\n",
"\n",
"train_ds = MedNISTDataset(train_x, train_y, train_transforms)\n",
"train_loader = torch.utils.data.DataLoader(\n",
"train_loader = DataLoader(\n",
" train_ds, batch_size=300, shuffle=True, num_workers=10)\n",
"\n",
"val_ds = MedNISTDataset(val_x, val_y, val_transforms)\n",
"val_loader = torch.utils.data.DataLoader(\n",
"val_loader = DataLoader(\n",
" val_ds, batch_size=300, num_workers=10)\n",
"\n",
"test_ds = MedNISTDataset(test_x, test_y, val_transforms)\n",
"test_loader = torch.utils.data.DataLoader(\n",
"test_loader = DataLoader(\n",
" test_ds, batch_size=300, num_workers=10)"
]
},
Expand Down Expand Up @@ -1328,7 +1326,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -1342,7 +1340,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.10"
"version": "3.8.13"
}
},
"nbformat": 4,
Expand Down