-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
c08d9cb
commit 564d4e5
Showing
1 changed file
with
100 additions
and
86 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,91 +1,105 @@ | ||
| { | ||
| "command": "train", | ||
| "gpu": 7, | ||
| "target_suffix": "_seg-manual", | ||
| "roi_suffix": null, | ||
| "bids_path": "../duke/sct_testing/large/", | ||
| "random_seed": 1313, | ||
| "contrast_train_validation": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], | ||
| "contrast_balance": {}, | ||
| "contrast_test": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], | ||
| "command": "train", | ||
| "gpu": 1, | ||
| "log_directory": "t2star_sc", | ||
| "debugging": false, | ||
| "loader_parameters": { | ||
| "bids_path": "../duke/sct_testing/large/", | ||
| "target_suffix": ["_seg-manual"], | ||
| "roi_params": { | ||
| "suffix": null, | ||
| "slice_filter_roi": null | ||
| }, | ||
| "contrast_params": { | ||
| "training_validation": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], | ||
| "testing": ["acq-sup_T2star", "acq-c1c3_T2star", "acq-c4c7_T2star", "acq-ax_T2star", "acq-inf_T2star"], | ||
| "balance": {} | ||
| }, | ||
| "slice_filter_params": { | ||
| "filter_empty_mask": false, | ||
| "filter_empty_input": true | ||
| }, | ||
| "slice_axis": "axial", | ||
| "multichannel": false | ||
| }, | ||
| "split_dataset": { | ||
| "fname_split": null, | ||
| "random_seed": 30, | ||
| "center_test": [], | ||
| "retrain_model": null, | ||
| "out_channel": 1, | ||
| "depth": 3, | ||
| "missing_modality": false, | ||
| "method": "per_patient", | ||
| "train_fraction": 0.6, | ||
| "test_fraction": 0.2 | ||
| }, | ||
| "training_parameters": { | ||
| "batch_size": 32, | ||
| "dropout_rate": 0.3, | ||
| "batch_norm_momentum": 0.1, | ||
| "num_epochs": 50, | ||
| "initial_lr": 0.001, | ||
| "lr_scheduler": {"name": "CyclicLR", "base_lr": 0.0001, "max_lr": 0.001}, | ||
| "loss": {"name": "dice"}, | ||
| "log_directory": "log_sct-t2starw", | ||
| "film_layers": [0, 0, 0, 0, 0, 0, 0, 0], | ||
| "attention_unet": false, | ||
| "mixup_bool": false, | ||
| "mixup_alpha": 2, | ||
| "metadata": null, | ||
| "multichannel": false, | ||
| "slice_axis": "axial", | ||
| "split_method": "per_patient", | ||
| "train_fraction": 0.6, | ||
| "test_fraction": 0.2, | ||
| "loss": { | ||
| "name": "DiceLoss" | ||
| }, | ||
| "training_time": { | ||
| "num_epochs": 50, | ||
| "early_stopping_patience": 50, | ||
| "early_stopping_epsilon": 0.001 | ||
| }, | ||
| "scheduler": { | ||
| "initial_lr": 0.001, | ||
| "lr_scheduler": { | ||
| "name": "CyclicLR", | ||
| "base_lr": 0.0001, | ||
| "max_lr": 0.001 | ||
| } | ||
| }, | ||
| "balance_samples": false, | ||
| "slice_filter": {"filter_empty_mask": false, "filter_empty_input": true}, | ||
| "slice_filter_roi": 10, | ||
| "uncertainty": {"epistemic": false, "aleatoric": false, "n_it": 0}, | ||
| "unet_3D": false, | ||
| "binarize_prediction": false, | ||
| "early_stopping_patience": 20, | ||
| "early_stopping_epsilon": 0.1, | ||
| "eval_params": { | ||
| "targetSize": {"unit": "vox", "thr": [20, 100]}, | ||
| "removeSmall": {"unit": "vox", "thr": 3}, | ||
| "overlap": {"unit": "vox", "thr": 3} | ||
| }, | ||
| "transformation_training": { | ||
| "Resample": { | ||
| "wspace": 0.75, | ||
| "hspace": 0.75 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [160, 160] | ||
| }, | ||
| "ElasticTransform": { | ||
| "alpha_range": [28.0, 30.0], | ||
| "sigma_range": [3.5, 4.5], | ||
| "p": 0.1 | ||
| }, | ||
| "RandomAffine": { | ||
| "degrees": 4.6, | ||
| "translate": [0.03, 0.03], | ||
| "scale": [0.98, 1.02] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": {"applied_to": ["im"]} | ||
| }, | ||
| "transformation_validation": { | ||
| "Resample": { | ||
| "wspace": 0.75, | ||
| "hspace": 0.75 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [160, 160] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": {"applied_to": ["im"]} | ||
| }, | ||
| "transformation_testing": { | ||
| "Resample": { | ||
| "wspace": 0.75, | ||
| "hspace": 0.75 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [160, 160] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": {"applied_to": ["im"]} | ||
| }, | ||
| "debugging": false | ||
| "mixup_alpha": null, | ||
| "transfer_learning": { | ||
| "retrain_model": null, | ||
| "retrain_fraction": 1.0 | ||
| } | ||
| }, | ||
| "default_model": { | ||
| "name": "Unet", | ||
| "dropout_rate": 0.3, | ||
| "bn_momentum": 0.1, | ||
| "depth": 3 | ||
| }, | ||
| "testing_parameters": { | ||
| "binarize_prediction": true, | ||
| "uncertainty": { | ||
| "epistemic": false, | ||
| "aleatoric": false, | ||
| "n_it": 1 | ||
| } | ||
| }, | ||
| "evaluation_parameters": { | ||
| "targetSize": {"unit": "vox", "thr": [20, 100]}, | ||
| "removeSmall": {"unit": "vox", "thr": 3}, | ||
| "overlap": {"unit": "vox", "thr": 3} | ||
| }, | ||
| "transformation": { | ||
| "Resample": | ||
| { | ||
| "wspace": 0.75, | ||
| "hspace": 0.75, | ||
| "preprocessing": true | ||
| }, | ||
| "CenterCrop": | ||
| { | ||
| "size": [160, 160], | ||
| "preprocessing": true | ||
| }, | ||
| "ElasticTransform": { | ||
| "alpha_range": [28.0, 30.0], | ||
| "sigma_range": [3.5, 4.5], | ||
| "p": 0.1, | ||
| "applied_to": ["im", "gt"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "RandomAffine": { | ||
| "degrees": 4.6, | ||
| "translate": [0.03, 0.03], | ||
| "scale": [0.98, 1.02], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": {"applied_to": ["im"]} | ||
| } | ||
| } |