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Merge pull request #11 from ivadomed/um/baseline_ivadomed_training
`ivadomed` configs for training lesion segmentation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| { | ||
| "command": "train", | ||
| "gpu_ids": [0], | ||
| "path_output": "seg_lesion_output", | ||
| "model_name": "seg_lesion_model", | ||
| "debugging": true, | ||
| "object_detection_params": { | ||
| "object_detection_path": null, | ||
| "safety_factor": [1.0, 1.0, 1.0] | ||
| }, | ||
| "loader_parameters": { | ||
| "path_data": ["basel-mp2rage-preprocessed/data_processed_lesionseg"], | ||
| "subject_selection": { | ||
| "n": [], | ||
| "metadata": [], | ||
| "value": [] | ||
| }, | ||
| "target_suffix": [["_lesion-manual", "_lesion-manual2"]], | ||
| "extensions": [], | ||
| "roi_params": { | ||
| "suffix": null, | ||
| "slice_filter_roi": null | ||
| }, | ||
| "contrast_params": { | ||
| "training_validation": ["UNIT1"], | ||
| "testing": ["UNIT1"], | ||
| "balance": {} | ||
| }, | ||
| "slice_filter_params": { | ||
| "filter_empty_mask": false, | ||
| "filter_empty_input": false | ||
| }, | ||
| "slice_axis": "sagittal", | ||
| "multichannel": false, | ||
| "soft_gt": false | ||
| }, | ||
| "split_dataset": { | ||
| "fname_split": null, | ||
| "random_seed": 42, | ||
| "center_test": [], | ||
| "method": "per_patient", | ||
| "balance": null, | ||
| "train_fraction": 0.75, | ||
| "test_fraction": 0.2 | ||
| }, | ||
| "training_parameters": { | ||
| "batch_size": 4, | ||
| "loss": { | ||
| "name": "DiceLoss" | ||
| }, | ||
| "training_time": { | ||
| "num_epochs": 500, | ||
| "early_stopping_patience": 200, | ||
| "early_stopping_epsilon": 0.001 | ||
| }, | ||
| "scheduler": { | ||
| "initial_lr": 1e-3, | ||
| "lr_scheduler": { | ||
| "name": "CosineAnnealingLR", | ||
| "base_lr": 1e-5, | ||
| "max_lr": 1e-3 | ||
| } | ||
| }, | ||
| "balance_samples": { | ||
| "applied": false, | ||
| "type": "gt" | ||
| }, | ||
| "mixup_alpha": null, | ||
| "transfer_learning": { | ||
| "retrain_model": null, | ||
| "retrain_fraction": 1.0, | ||
| "reset": true | ||
| } | ||
| }, | ||
| "default_model": { | ||
| "name": "Unet", | ||
| "dropout_rate": 0.3, | ||
| "bn_momentum": 0.1, | ||
| "depth": 4, | ||
| "is_2d": false, | ||
| "final_activation": "sigmoid" | ||
| }, | ||
| "uncertainty": { | ||
| "epistemic": false, | ||
| "aleatoric": false, | ||
| "n_it": 0 | ||
| }, | ||
| "postprocessing": {"binarize_prediction": {"thr": 0.5}}, | ||
| "evaluation_parameters": {}, | ||
| "transformation": { | ||
| "Resample": { | ||
| "wspace": 1.0, | ||
| "hspace": 1.0, | ||
| "dspace": 1.0 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [128, 64, 32] | ||
| }, | ||
| "RandomReverse": { | ||
| "applied_to": ["im", "gt"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "RandomAffine": { | ||
| "degrees": 10, | ||
| "scale": [0.3, 0.3, 0.3], | ||
| "translate": [0.1, 0.1, 0.1], | ||
| "applied_to": ["im", "gt"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "ElasticTransform": { | ||
| "alpha_range": [25.0, 35.0], | ||
| "sigma_range": [3.5, 5.5], | ||
| "p": 0.5, | ||
| "applied_to": ["im", "gt"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "RandomGamma": { | ||
| "log_gamma_range": [-1.5, 1.5], | ||
| "p": 0.5, | ||
| "applied_to": ["im"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "RandomBiasField": { | ||
| "coefficients": 0.5, | ||
| "order": 3, | ||
| "p": 0.3, | ||
| "applied_to": ["im"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "RandomBlur": { | ||
| "sigma_range": [0.0, 1.0], | ||
| "p": 0.3, | ||
| "applied_to": ["im"], | ||
| "dataset_type": ["training"] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": { | ||
| "applied_to": ["im"] | ||
| } | ||
| }, | ||
| "Modified3DUNet": { | ||
| "applied": true, | ||
| "length_3D": [128, 64, 32], | ||
| "stride_3D": [128, 64, 32], | ||
| "attention": false, | ||
| "n_filters": 8 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| { | ||
| "command": "test", | ||
| "gpu_ids": [0], | ||
| "path_output": "seg_lesion_output", | ||
| "model_name": "seg_lesion_model", | ||
| "debugging": true, | ||
| "object_detection_params": { | ||
| "object_detection_path": null, | ||
| "safety_factor": [1.0, 1.0, 1.0] | ||
| }, | ||
| "loader_parameters": { | ||
| "path_data": ["basel-mp2rage-preprocessed/data_processed_lesionseg"], | ||
| "subject_selection": { | ||
| "n": [], | ||
| "metadata": [], | ||
| "value": [] | ||
| }, | ||
| "target_suffix": ["_lesion-manual"], | ||
| "extensions": [], | ||
| "roi_params": { | ||
| "suffix": null, | ||
| "slice_filter_roi": null | ||
| }, | ||
| "contrast_params": { | ||
| "training_validation": ["UNIT1"], | ||
| "testing": ["UNIT1"], | ||
| "balance": {} | ||
| }, | ||
| "slice_filter_params": { | ||
| "filter_empty_mask": true, | ||
| "filter_empty_input": true | ||
| }, | ||
| "slice_axis": "sagittal", | ||
| "multichannel": false, | ||
| "soft_gt": false | ||
| }, | ||
| "split_dataset": { | ||
| "fname_split": null, | ||
| "random_seed": 42, | ||
| "center_test": [], | ||
| "method": "per_patient", | ||
| "balance": null, | ||
| "train_fraction": 0.75, | ||
| "test_fraction": 0.2 | ||
| }, | ||
| "uncertainty": { | ||
| "epistemic": false, | ||
| "aleatoric": false, | ||
| "n_it": 0 | ||
| }, | ||
| "postprocessing": {"binarize_prediction": {"thr": 0.5}}, | ||
| "evaluation_parameters": {}, | ||
| "transformation": { | ||
| "Resample": { | ||
| "wspace": 1.0, | ||
| "hspace": 1.0, | ||
| "dspace": 1.0 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [128, 64, 32] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": { | ||
| "applied_to": ["im"] | ||
| } | ||
| }, | ||
| "Modified3DUNet": { | ||
| "applied": true, | ||
| "length_3D": [128, 64, 32], | ||
| "stride_3D": [128, 64, 32], | ||
| "attention": false, | ||
| "n_filters": 8 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,74 @@ | ||
| { | ||
| "command": "test", | ||
| "gpu_ids": [0], | ||
| "path_output": "seg_lesion_output", | ||
| "model_name": "seg_lesion_model", | ||
| "debugging": true, | ||
| "object_detection_params": { | ||
| "object_detection_path": null, | ||
| "safety_factor": [1.0, 1.0, 1.0] | ||
| }, | ||
| "loader_parameters": { | ||
| "path_data": ["basel-mp2rage-preprocessed/data_processed_lesionseg"], | ||
| "subject_selection": { | ||
| "n": [], | ||
| "metadata": [], | ||
| "value": [] | ||
| }, | ||
| "target_suffix": ["_lesion-manual2"], | ||
| "extensions": [], | ||
| "roi_params": { | ||
| "suffix": null, | ||
| "slice_filter_roi": null | ||
| }, | ||
| "contrast_params": { | ||
| "training_validation": ["UNIT1"], | ||
| "testing": ["UNIT1"], | ||
| "balance": {} | ||
| }, | ||
| "slice_filter_params": { | ||
| "filter_empty_mask": true, | ||
| "filter_empty_input": true | ||
| }, | ||
| "slice_axis": "sagittal", | ||
| "multichannel": false, | ||
| "soft_gt": false | ||
| }, | ||
| "split_dataset": { | ||
| "fname_split": null, | ||
| "random_seed": 42, | ||
| "center_test": [], | ||
| "method": "per_patient", | ||
| "balance": null, | ||
| "train_fraction": 0.75, | ||
| "test_fraction": 0.2 | ||
| }, | ||
| "uncertainty": { | ||
| "epistemic": false, | ||
| "aleatoric": false, | ||
| "n_it": 0 | ||
| }, | ||
| "postprocessing": {"binarize_prediction": {"thr": 0.5}}, | ||
| "evaluation_parameters": {}, | ||
| "transformation": { | ||
| "Resample": { | ||
| "wspace": 1.0, | ||
| "hspace": 1.0, | ||
| "dspace": 1.0 | ||
| }, | ||
| "CenterCrop": { | ||
| "size": [128, 64, 32] | ||
| }, | ||
| "NumpyToTensor": {}, | ||
| "NormalizeInstance": { | ||
| "applied_to": ["im"] | ||
| } | ||
| }, | ||
| "Modified3DUNet": { | ||
| "applied": true, | ||
| "length_3D": [128, 64, 32], | ||
| "stride_3D": [128, 64, 32], | ||
| "attention": false, | ||
| "n_filters": 8 | ||
| } | ||
| } |