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ENH: Track physicsnemo_mgn_heart weights via Git LFS #95

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Merged
aylward merged 1 commit into from
Jul 23, 2026
Merged

ENH: Track physicsnemo_mgn_heart weights via Git LFS #95

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4 changes: 4 additions & 0 deletions .gitattributes
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
*.hdf filter=lfs diff=lfs merge=lfs -text
*.mha filter=lfs diff=lfs merge=lfs -text
docs/assets/*.gif filter=lfs diff=lfs merge=lfs -text
tutorials/network_weights/physicsnemo_mgn_heart/*.pt filter=lfs diff=lfs merge=lfs -text
tutorials/network_weights/physicsnemo_mgn_heart/*.vtu filter=lfs diff=lfs merge=lfs -text
tutorials/network_weights/physicsnemo_mgn_heart/*.vtp filter=lfs diff=lfs merge=lfs -text
tutorials/network_weights/physicsnemo_mgn_heart/pca_model.json filter=lfs diff=lfs merge=lfs -text
5 changes: 5 additions & 0 deletions .gitignore
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Expand Up @@ -31,6 +31,11 @@ docs/_static/.buildinfo
# Network weights
network_weights

# Track the MGN heart model weights (other network_weights stay ignored)
!tutorials/network_weights/
tutorials/network_weights/*
!tutorials/network_weights/physicsnemo_mgn_heart/

# Data files
*.gz
*.mat
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3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/mgn_stage_model.pt
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86 changes: 86 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/mgn_stage_model_metadata.json
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{
"architecture": "physicsnemo.models.meshgraphnet.MeshGraphNet",
"input_features": [
"mean_shape_x",
"mean_shape_y",
"mean_shape_z",
"pca_c1",
"pca_c2",
"pca_c3",
"pca_c4",
"pca_c5",
"pca_c6",
"pca_c7",
"pca_c8",
"pca_c9",
"pca_c10",
"pca_c11",
"pca_c12",
"pca_c13",
"pca_c14",
"pca_c15",
"stage"
],
"output_features": [
"dx",
"dy",
"dz"
],
"in_features": 19,
"n_mesh_points": 167240,
"epochs": 1500,
"learning_rate": 0.001,
"batch_size_samples": 4,
"coordinate_mean": [
-7.199598789215088,
-3.9089744091033936,
9.961953163146973
],
"coordinate_scale": [
30.08570671081543,
27.07874298095703,
29.782752990722656
],
"pca_mean": [
0.7269748449325562,
-0.07803090661764145,
-1.3384027481079102,
0.021359410136938095,
-0.3058125376701355,
-0.12345822155475616,
-0.14261603355407715,
-0.9997884035110474,
0.4026827812194824,
-0.5299767255783081,
-0.43278786540031433,
0.7046552300453186,
0.13237492740154266,
0.4630051255226135,
0.6216614842414856
],
"pca_scale": [
0.7048464417457581,
0.557181715965271,
0.5016987323760986,
0.4974881112575531,
0.7341663241386414,
0.6494237184524536,
0.7575852274894714,
0.6247227787971497,
0.6713169813156128,
0.8278525471687317,
0.9181209802627563,
0.9691786170005798,
0.6127719879150391,
1.4163326025009155,
1.1147863864898682
],
"displacement_scale": 21.72310447692871,
"displacement_convention": "Option B: relative to subject reference surface",
"resumed_from": "C:\\src\\Projects\\PhysioTwin4D\\physiotwin4d\\tutorials\\output\\tutorial_09_byod_mgn_2\\mgn_stage_model_epoch_00200.pt",

@coderabbitai coderabbitai Bot Jul 21, 2026

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📐 Maintainability & Code Quality | 🟡 Minor | ⚡ Quick win

Remove the machine-specific absolute checkpoint path.

Store a repository-relative path, checkpoint basename, or stable run ID instead of committing C:\src\Projects\...; the current value is not portable.

Proposed fix 
-  "resumed_from": "C:\\src\\Projects\\PhysioTwin4D\\physiotwin4d\\tutorials\\output\\tutorial_09_byod_mgn_2\\mgn_stage_model_epoch_00200.pt",
+  "resumed_from": "mgn_stage_model_epoch_00200.pt",
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
"resumed_from": "C:\\src\\Projects\\PhysioTwin4D\\physiotwin4d\\tutorials\\output\\tutorial_09_byod_mgn_2\\mgn_stage_model_epoch_00200.pt",
"resumed_from": "mgn_stage_model_epoch_00200.pt",
🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In
`@tutorials/network_weights/physicsnemo_mgn_heart/mgn_stage_model_metadata.json`
at line 80, Replace the machine-specific absolute value in the resumed_from
metadata field with a portable repository-relative checkpoint path, checkpoint
basename, or stable run ID, while preserving the metadata’s reference to the
resumed checkpoint.

"processor_size": 3,
"hidden_dim": 128,
"num_layers": 2,
"num_processor_checkpoint_segments": 0,
"input_dim_edges": 4
}
3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/pca_mean.vtu
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3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/pca_mean_surface.vtp
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3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/pca_model.json
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3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/shared_edge_features.pt
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3 changes: 3 additions & 0 deletions tutorials/network_weights/physicsnemo_mgn_heart/shared_edge_index.pt
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