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Update decollate tutorial to use EnsureTyped #258

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Merged
Nic-Ma merged 1 commit into from
Jul 9, 2021
Merged

Update decollate tutorial to use EnsureTyped #258

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16 changes: 8 additions & 8 deletions modules/decollate_batch.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -76,11 +76,11 @@
"name": "stdout",
"output_type": "stream",
"text": [
"MONAI version: 0.4.0+540.g8803885\n",
"MONAI version: 0.4.0+544.g5e7345d\n",
"Numpy version: 1.21.0\n",
"Pytorch version: 1.9.0+cu102\n",
"MONAI flags: HAS_EXT = False, USE_COMPILED = False\n",
"MONAI rev id: 88038854f6cd256989695c2368e3ee9fca213e8d\n",
"MONAI rev id: 5e7345d384ae08011b0e250b93f615d6d5190258\n",
"\n",
"Optional dependencies:\n",
"Pytorch Ignite version: 0.4.5\n",
Expand Down Expand Up @@ -134,6 +134,7 @@
"from monai.transforms import (\n",
" Activationsd,\n",
" EnsureChannelFirstd,\n",
" EnsureTyped,\n",
" AsDiscreted,\n",
" Compose,\n",
" Invertd,\n",
Expand All @@ -142,7 +143,6 @@
" Resized,\n",
" SaveImaged,\n",
" ScaleIntensityd,\n",
" ToTensord,\n",
")\n",
"from monai.utils import set_determinism\n",
"\n",
Expand Down Expand Up @@ -248,7 +248,7 @@
" Orientationd(keys=\"img\", axcodes=\"RAS\"),\n",
" Resized(keys=\"img\", spatial_size=(96, 96, 96), mode=\"trilinear\", align_corners=True),\n",
" ScaleIntensityd(keys=\"img\"),\n",
" ToTensord(keys=[\"img\", \"seg\"]),\n",
" EnsureTyped(keys=[\"img\", \"seg\"]),\n",
" ]\n",
")\n",
"dataset = Dataset(data=files, transform=preprocessing)\n",
Expand All @@ -262,20 +262,20 @@
"## Setup postprocessing transforms, metrics\n",
"Here we try to invert the preprocessing predictions for `pred` and save into Nifti files.\n",
"\n",
"As all the post processing transforms expect `Tensor` input, apply `ToTensord` first to ensure the data type after `decollate_batch`."
"As all the post processing transforms expect `Tensor` input, apply `EnsureTyped` first to ensure the data type after `decollate_batch`."
]
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 6,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"postprocessing = Compose(\n",
" [\n",
" ToTensord(keys=[\"pred\", \"seg\"]), # ensure Tensor type after `decollate`\n",
" EnsureTyped(keys=[\"pred\", \"seg\"]), # ensure Tensor type after `decollate`\n",
" Activationsd(keys=\"pred\", sigmoid=True),\n",
" Invertd(\n",
" keys=\"pred\", # invert the `pred` data field, also support multiple fields\n",
Expand Down Expand Up @@ -353,7 +353,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 8,
"metadata": {
"pycharm": {
"is_executing": true
Expand Down