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

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

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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
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4 changes: 2 additions & 2 deletions bundle/05_spleen_segmentation_lightning.ipynb
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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",
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2 changes: 1 addition & 1 deletion competitions/MICCAI/surgtoolloc/preprocess_detect_scene_and_split_fold.ipynb
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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()}\")"
]
},
{
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100 changes: 3 additions & 97 deletions computer_assisted_intervention/endoscopic_inbody_classification.ipynb
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6 changes: 3 additions & 3 deletions deep_atlas/deep_atlas_tutorial.ipynb
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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()"
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