Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[pre-commit.ci] pre-commit suggestions #1685

Merged
merged 2 commits into from
Apr 2, 2024
Merged

[pre-commit.ci] pre-commit suggestions #1685

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9d4bf31
[pre-commit.ci] pre-commit suggestions
pre-commit-ci[bot] Apr 1, 2024
cc1147d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 1, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .pre-commit-config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ repos:
- id: detect-private-key

- repo: https://github.com/psf/black
rev: "23.12.1"
rev: "24.3.0"
hooks:
- id: black
- id: black-jupyter
Expand Down
62 changes: 34 additions & 28 deletions deep_atlas/deep_atlas_tutorial.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -543,14 +543,16 @@
" monai.transforms.LoadImageD(keys=[\"img\", \"seg\"], image_only=True),\n",
" monai.transforms.TransposeD(keys=[\"img\", \"seg\"], indices=(2, 1, 0)),\n",
" monai.transforms.EnsureChannelFirstD(keys=[\"img\", \"seg\"]),\n",
" monai.transforms.ResizeD(\n",
" keys=[\"img\", \"seg\"],\n",
" spatial_size=(resize, resize, resize),\n",
" mode=[\"trilinear\", \"nearest\"],\n",
" align_corners=[False, None],\n",
" )\n",
" if resize is not None\n",
" else monai.transforms.Identity(),\n",
" (\n",
" monai.transforms.ResizeD(\n",
" keys=[\"img\", \"seg\"],\n",
" spatial_size=(resize, resize, resize),\n",
" mode=[\"trilinear\", \"nearest\"],\n",
" align_corners=[False, None],\n",
" )\n",
" if resize is not None\n",
" else monai.transforms.Identity()\n",
" ),\n",
" ]\n",
")\n",
"\n",
Expand Down Expand Up @@ -776,15 +778,17 @@
" monai.transforms.EnsureChannelFirstD(keys=[\"img1\", \"seg1\", \"img2\", \"seg2\"], allow_missing_keys=True),\n",
" monai.transforms.ConcatItemsD(keys=[\"img1\", \"img2\"], name=\"img12\", dim=0),\n",
" monai.transforms.DeleteItemsD(keys=[\"img1\", \"img2\"]),\n",
" monai.transforms.ResizeD(\n",
" keys=[\"img12\", \"seg1\", \"seg2\"],\n",
" spatial_size=(resize, resize, resize),\n",
" mode=[\"trilinear\", \"nearest\", \"nearest\"],\n",
" allow_missing_keys=True,\n",
" align_corners=[False, None, None],\n",
" )\n",
" if resize is not None\n",
" else monai.transforms.Identity(),\n",
" (\n",
" monai.transforms.ResizeD(\n",
" keys=[\"img12\", \"seg1\", \"seg2\"],\n",
" spatial_size=(resize, resize, resize),\n",
" mode=[\"trilinear\", \"nearest\", \"nearest\"],\n",
" allow_missing_keys=True,\n",
" align_corners=[False, None, None],\n",
" )\n",
" if resize is not None\n",
" else monai.transforms.Identity()\n",
" ),\n",
" ]\n",
")"
]
Expand Down Expand Up @@ -1608,21 +1612,23 @@
"# The following are dictionaries that map segmentation availability labels 00,10,01,11 to MONAI dataloaders\n",
"\n",
"dataloader_pairs_train_subdivided = {\n",
" seg_availability: monai.data.DataLoader(dataset, batch_size=2, num_workers=4, shuffle=True)\n",
" if len(dataset) > 0\n",
" else [] # empty dataloaders are not a thing-- put an empty list if needed\n",
" seg_availability: (\n",
" monai.data.DataLoader(dataset, batch_size=2, num_workers=4, shuffle=True) if len(dataset) > 0 else []\n",
" ) # empty dataloaders are not a thing-- put an empty list if needed\n",
" for seg_availability, dataset in dataset_pairs_train_subdivided.items()\n",
"}\n",
"\n",
"dataloader_pairs_valid_subdivided = {\n",
" seg_availability: monai.data.DataLoader(\n",
" dataset,\n",
" batch_size=4,\n",
" num_workers=4,\n",
" shuffle=True, # Shuffle validation data because we will only take a sample for validation each time\n",
" )\n",
" if len(dataset) > 0\n",
" else [] # empty dataloaders are not a thing-- put an empty list if needed\n",
" seg_availability: (\n",
" monai.data.DataLoader(\n",
" dataset,\n",
" batch_size=4,\n",
" num_workers=4,\n",
" shuffle=True, # Shuffle validation data because we will only take a sample for validation each time\n",
" )\n",
" if len(dataset) > 0\n",
" else []\n",
" ) # empty dataloaders are not a thing-- put an empty list if needed\n",
" for seg_availability, dataset in dataset_pairs_valid_subdivided.items()\n",
"}"
]
Expand Down
4 changes: 1 addition & 3 deletions deepgrow/ignite/inference.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -486,9 +486,7 @@
" image = (\n",
" image\n",
" if tname == \"Fetch2DSliced\"\n",
" else image[:, :, slice_idx]\n",
" if tname in (\"LoadImaged\")\n",
" else image[slice_idx, :, :]\n",
" else image[:, :, slice_idx] if tname in (\"LoadImaged\") else image[slice_idx, :, :]\n",
" )\n",
" label = None\n",
"\n",
Expand Down
4 changes: 1 addition & 3 deletions deepgrow/ignite/inference_3d.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -215,9 +215,7 @@
" image = (\n",
" image[:, :, slice_idx]\n",
" if tname in (\"LoadImaged\")\n",
" else image[slice_idx]\n",
" if tname in (\"Transposed\", \"Spacingd\", \"AddGuidanceFromPointsd\")\n",
" else image[0][slice_idx]\n",
" else image[slice_idx] if tname in (\"Transposed\", \"Spacingd\", \"AddGuidanceFromPointsd\") else image[0][slice_idx]\n",
" )\n",
" label = None\n",
"\n",
Expand Down
Loading