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471 Update CSV datasets tutorial #472

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Merged
merged 2 commits into from
Dec 7, 2021
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471 Update CSV datasets tutorial #472

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093e786
[DLMED] update csv tutorial
Nic-Ma Dec 7, 2021
4c62ce8
[DLMED] update tcia
Nic-Ma Dec 7, 2021
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18 changes: 9 additions & 9 deletions modules/csv_datasets.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -263,7 +263,7 @@
}
],
"source": [
"dataset = CSVDataset(filename=filepath1)\n",
"dataset = CSVDataset(src=filepath1)\n",
"# construct pandas table to show the data, `CSVDataset` inherits from PyTorch Dataset\n",
"print(pd.DataFrame(dataset.data))"
]
Expand Down Expand Up @@ -308,7 +308,7 @@
}
],
"source": [
"dataset = CSVDataset([filepath1, filepath2, filepath3], on=\"subject_id\")\n",
"dataset = CSVDataset(src=[filepath1, filepath2, filepath3], on=\"subject_id\")\n",
"# construct pandas table to show the joined data of 3 tables\n",
"print(pd.DataFrame(dataset.data))"
]
Expand Down Expand Up @@ -339,7 +339,7 @@
],
"source": [
"dataset = CSVDataset(\n",
" filename=[filepath1, filepath2, filepath3],\n",
" src=[filepath1, filepath2, filepath3],\n",
" row_indices=[[0, 2], 3], # load row: 0, 1, 3\n",
" col_names=[\"subject_id\", \"label\", \"ehr_1\", \"ehr_7\", \"meta_1\"],\n",
")\n",
Expand Down Expand Up @@ -396,7 +396,7 @@
],
"source": [
"dataset = CSVDataset(\n",
" filename=[filepath1, filepath2, filepath3],\n",
" src=[filepath1, filepath2, filepath3],\n",
" col_names=[\"subject_id\", \"image\", *[f\"ehr_{i}\" for i in range(11)], \"meta_0\", \"meta_1\", \"meta_2\"],\n",
" col_groups={\"ehr\": [f\"ehr_{i}\" for i in range(11)], \"meta\": [\"meta_0\", \"meta_1\", \"meta_2\"]},\n",
")\n",
Expand Down Expand Up @@ -433,7 +433,7 @@
],
"source": [
"dataset = CSVDataset(\n",
" filename=[filepath1, filepath2, filepath3],\n",
" src=[filepath1, filepath2, filepath3],\n",
" col_names=[\"subject_id\", \"label\", \"ehr_0\", \"ehr_1\", \"ehr_9\", \"meta_1\"],\n",
" col_types={\"label\": {\"default\": \"No label\"}, \"ehr_1\": {\"type\": int, \"default\": 0}},\n",
" how=\"outer\", # will load the NaN values in this merge mode\n",
Expand Down Expand Up @@ -481,7 +481,7 @@
],
"source": [
"dataset = CSVDataset(\n",
" filename=[filepath1, filepath2, filepath3],\n",
" src=[filepath1, filepath2, filepath3],\n",
" col_groups={\"ehr\": [f\"ehr_{i}\" for i in range(5)]},\n",
" transform=Compose([LoadImaged(keys=\"image\"), ToNumpyd(keys=\"ehr\")]),\n",
")\n",
Expand Down Expand Up @@ -527,7 +527,7 @@
}
],
"source": [
"dataset = CSVIterableDataset(filename=[filepath1, filepath2, filepath3], shuffle=False)\n",
"dataset = CSVIterableDataset(src=[filepath1, filepath2, filepath3], shuffle=False)\n",
"# set num workers = 0 for mac / win\n",
"num_workers = 2 if sys.platform == \"linux\" else 0\n",
"dataloader = DataLoader(dataset=dataset, num_workers=num_workers, batch_size=2)\n",
Expand All @@ -546,7 +546,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 13,
"metadata": {},
"outputs": [
{
Expand All @@ -563,7 +563,7 @@
"dataset = CSVIterableDataset(\n",
" chunksize=2,\n",
" buffer_size=4,\n",
" filename=[filepath1, filepath2, filepath3],\n",
" src=[filepath1, filepath2, filepath3],\n",
" col_names=[\"subject_id\", \"label\", \"ehr_1\", \"ehr_7\", \"meta_1\"],\n",
" transform=ToNumpyd(keys=\"ehr_1\"),\n",
" shuffle=True,\n",
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2 changes: 1 addition & 1 deletion modules/tcia_csv_processing.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@
" download_url(url=u, filepath=f)\n",
"\n",
" super().__init__(\n",
" filename=filename,\n",
" src=filename,\n",
" row_indices=row_indices,\n",
" col_names=col_names,\n",
" col_types=col_types,\n",
Expand Down