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update modules/inverse_transforms_and_test_time_augmentations.ipynb #799

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Merged
wyli merged 3 commits into from
Jul 18, 2022
Merged

update modules/inverse_transforms_and_test_time_augmentations.ipynb #799

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054788f
update based on new API
wyli Jul 17, 2022
e102c8a
fixes pep8
wyli Jul 17, 2022
275550d
Merge branch 'main' into update-inverse-demo
wyli Jul 18, 2022
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8 changes: 3 additions & 5 deletions modules/inverse_transforms_and_test_time_augmentations.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,6 @@
" Dataset,\n",
" pad_list_data_collate,\n",
" TestTimeAugmentation,\n",
" decollate_batch,\n",
")\n",
"from monai.inferers import sliding_window_inference\n",
"from monai.losses import DiceLoss\n",
Expand Down Expand Up @@ -228,8 +227,7 @@
" def __call__(self, data):\n",
" d = dict(data)\n",
" im = d[self.label_key]\n",
" _im = im.detach().cpu().numpy()\n",
" q = np.sum((_im > 0).reshape(-1, _im.shape[-1]), axis=0)\n",
" q = np.sum((im.array > 0).reshape(-1, im.array.shape[-1]), axis=0)\n",
" _slice = np.where(q == np.max(q))[0][0]\n",
" for key in self.keys:\n",
" d[key] = d[key][..., _slice]\n",
Expand All @@ -247,7 +245,7 @@
" fname = os.path.basename(\n",
" data[key + \"_meta_dict\"][\"filename_or_obj\"])\n",
" path = os.path.join(self.path, key, fname)\n",
" nib.save(nib.Nifti1Image(data[key].detach().cpu().numpy(), np.eye(4)), path)\n",
" nib.save(nib.Nifti1Image(data[key].array, np.eye(4)), path)\n",
" d[key] = path\n",
" return d\n",
"\n",
Expand Down Expand Up @@ -443,7 +441,7 @@
"def infer_seg(images, model, roi_size=(96, 96), sw_batch_size=4):\n",
" val_outputs = sliding_window_inference(\n",
" images, roi_size, sw_batch_size, model)\n",
" return torch.stack([post_trans(i) for i in decollate_batch(val_outputs)])\n",
" return pad_list_data_collate([post_trans(i) for i in val_outputs])\n",
"\n",
"\n",
"# Create network, loss fn., etc.\n",
Expand Down