Skip to content

fix: update runner.sh and endoscopic notebook for MONAI 1.6 tutorial runner compatibility #2065

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

Open
garciadias wants to merge 9 commits into
base: main
Choose a base branch
from
Open

fix: update runner.sh and endoscopic notebook for MONAI 1.6 tutorial runner compatibility #2065

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
d6e252e
fix: update runner.sh and endoscopic notebook for MONAI 1.6 compatibi…
garciadias Jun 11, 2026
7877af8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2026
a862ed1
fix: apply PEP8 autofix to 3 notebooks (E225/E231 whitespace violations)
garciadias Jun 11, 2026
252b9d6
Fix bundle/05_spleen_segmentation_lightning: upgrade pytorch-lightnin…
garciadias Jun 11, 2026
f3f49ff
fix: revert return_state_dict change; update R5/R8 diagnostics
garciadias Jun 11, 2026
a581217
style: add trailing newline to endoscopic_inbody_classification.ipynb
garciadias Jun 11, 2026
c62cc06
fix: skip 05_spleen_segmentation_lightning in CPU CI
garciadias Jun 11, 2026
3d198d8
fix: skip deep_atlas_tutorial in CPU CI
garciadias Jun 11, 2026
d38d101
fix: remove non-existent hovernet_infer_compare from doesnt_contain_m…
garciadias Jun 11, 2026
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
4 changes: 2 additions & 2 deletions bundle/05_spleen_segmentation_lightning.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@
"outputs": [],
"source": [
"!python -c \"import monai\" || pip install -q \"monai-weekly[ignite,pyyaml]\"\n",
"!pip install -q pytorch-lightning~=2.0.0"
"!pip install -q pytorch-lightning>=2.1"
]
},
{
Expand Down Expand Up @@ -855,7 +855,7 @@
"execution_count": 11,
"id": "c5ba337d-a5b0-47de-9ae2-1554a2cb4f86",
"metadata": {},
"outputs": [
"outputs": [
{
"name": "stdout",
"output_type": "stream",
Expand Down
2 changes: 1 addition & 1 deletion competitions/MICCAI/surgtoolloc/preprocess_detect_scene_and_split_fold.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -398,7 +398,7 @@
],
"source": [
"for lb in labels:\n",
" print(f\"{lb:30} {df_scene[df_scene[lb]>0].scene.nunique()}\")"
" print(f\"{lb:30} {df_scene[df_scene[lb] > 0].scene.nunique()}\")"
]
},
{
Expand Down
100 changes: 3 additions & 97 deletions computer_assisted_intervention/endoscopic_inbody_classification.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

6 changes: 3 additions & 3 deletions deep_atlas/deep_atlas_tutorial.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1255,7 +1255,7 @@
"val_interval = 5\n",
"\n",
"for epoch_number in range(max_epochs):\n",
" print(f\"Epoch {epoch_number+1}/{max_epochs}:\")\n",
" print(f\"Epoch {epoch_number + 1}/{max_epochs}:\")\n",
"\n",
" seg_net.train()\n",
" losses = []\n",
Expand Down Expand Up @@ -1797,7 +1797,7 @@
"best_reg_validation_loss = float(\"inf\")\n",
"\n",
"for epoch_number in range(max_epochs):\n",
" print(f\"Epoch {epoch_number+1}/{max_epochs}:\")\n",
" print(f\"Epoch {epoch_number + 1}/{max_epochs}:\")\n",
"\n",
" # ------------------------------------------------\n",
" # reg_net training, with seg_net frozen\n",
Expand Down Expand Up @@ -2320,7 +2320,7 @@
"preview_image(det, normalize_by=\"slice\", threshold=0)\n",
"loss = lncc_loss(example_warped_image, img12[:, [0], :, :, :]).item()\n",
"print(f\"Similarity loss: {loss}\")\n",
"print(f\"number of folds: {(det<=0).sum()}\")\n",
"print(f\"number of folds: {(det <= 0).sum()}\")\n",
"\n",
"del reg_net_example_output, img12, example_warped_image\n",
"torch.cuda.empty_cache()"
Expand Down
Loading