OSF Version 6

ivadomed · Jun 30, 2020 · 2a63a4d · 2a63a4d
1 parent 3a8027c
commit 2a63a4d
Showing 1 changed file with 102 additions and 84 deletions.
diff --git a/mice_uqueensland_sc.json b/mice_uqueensland_sc.json
@@ -1,87 +1,105 @@
 {
     "command": "train",
-    "gpu": 5,
-    "target_suffix": "_scseg",
-    "roi_suffix": null,
-    "bids_path": "../duke/projects/ivado-medical-imaging/data_mice_abdullah-UQ/",
-    "random_seed": 1313,
-    "contrast_train_validation": ["t1"],
-    "contrast_balance": {},
-    "contrast_test": ["t1"],
-    "center_test": [],
-    "batch_size": 8,
-    "dropout_rate": 0.3,
-    "batch_norm_momentum": 0.3,
-    "num_epochs": 200,
-    "initial_lr": 0.001,
-    "lr_scheduler": {"name": "CosineAnnealingWarmRestarts", "T_0": 20, "T_mult": 2},
-    "loss": {"name": "dice"},
-    "log_directory": "log_mice",
-    "film_layers": [0, 0, 0, 0, 0, 0, 0, 0],
-    "mixup_bool": false,
-    "mixup_alpha": 2,
-    "metadata": "contrast",
-    "missing_modality": false,
-    "multichannel": false,
-    "out_channel": 1,
-    "depth": 2,
-    "train_fraction": 0.6,
-    "test_fraction": 0.2,
-    "early_stopping_patience": 50,
-    "early_stopping_epsilon": 0.05,
-    "slice_axis": "axial",
-    "balance_samples": false,
-    "retrain_model": null,
-    "split_method": "per_patient",
-    "slice_filter": {"filter_empty_mask": true, "filter_empty_input": true},
-    "slice_filter_roi": 10,
-    "attention_unet": false,
-    "uncertainty": {"epistemic": true, "aleatoric": false, "n_it": 10},
-    "unet_3D": false,
-    "binarize_prediction": true,
-    "eval_params": {},
-    "transformation_training": {
-                "Resample": {
-                        "wspace": 0.04,
-                        "hspace": 0.04
-                        },
-                "CenterCrop": {
-                        "size": [96, 96]
-                },
-                "ElasticTransform": {
-                        "alpha_range": [28.0, 30.0],
-                        "sigma_range":  [3.5, 4.5],
-                        "p": 0.3
-                        },
-                "RandomAffine": {
-                        "degrees": 20,
-                        "translate": [0.03, 0.03],
-                        "scale": [0.98, 1.02]
-                        },
-                "NumpyToTensor": {},
-                "NormalizeInstance": {"applied_to": ["im"]}
-                },
-        "transformation_validation": {
-                "Resample": {
-                        "wspace": 0.04,
-                        "hspace": 0.04
-                        },
-                "CenterCrop": {
-                        "size": [96, 96]
-                },
-                "NumpyToTensor": {},
-                "NormalizeInstance": {"applied_to": ["im"]}
-                },
-        "transformation_testing": {
-                "Resample": {
-                        "wspace": 0.04,
-                        "hspace": 0.04
-                        },
-                "CenterCrop": {
-                        "size": [96, 96]
-                },
-                "NumpyToTensor": {},
-                "NormalizeInstance": {"applied_to": ["im"]}
-                },
-        "debugging": true
+    "gpu": 1,
+    "log_directory": "mice_sc",
+    "debugging": false,
+    "loader_parameters": {
+        "bids_path": "../duke/projects/ivado-medical-imaging/data_mice_abdullah-UQ/",
+        "target_suffix": ["_scseg"],
+        "roi_params": {
+            "suffix": null,
+            "slice_filter_roi": null
+        },
+        "contrast_params": {
+            "training_validation": ["t1"],
+            "testing": ["t1"],
+            "balance": {}
+        },
+        "slice_filter_params": {
+            "filter_empty_mask": true,
+            "filter_empty_input": true
+        },
+        "slice_axis": "axial",
+        "multichannel": false
+    },
+    "split_dataset": {
+        "fname_split": null,
+        "random_seed": 30,
+        "center_test": [],
+        "method": "per_patient",
+        "train_fraction": 0.6,
+        "test_fraction": 0.2
+    },
+    "training_parameters": {
+        "batch_size": 8,
+        "loss": {
+            "name": "DiceLoss"
+        },
+        "training_time": {
+            "num_epochs": 200,
+            "early_stopping_patience": 50,
+            "early_stopping_epsilon": 0.05
+        },
+        "scheduler": {
+            "initial_lr": 0.001,
+            "lr_scheduler": {
+                "name": "CosineAnnealingWarmRestarts",
+                "T_0": 20,
+                "T_mult": 2
+            }
+        },
+        "balance_samples": false,
+        "mixup_alpha": null,
+        "transfer_learning": {
+            "retrain_model": null,
+            "retrain_fraction": 1.0
+        }
+    },
+    "default_model": {
+        "name": "Unet",
+        "dropout_rate": 0.3,
+        "bn_momentum": 0.3,
+        "depth": 2
+    },
+    "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": 0.04,
+            "hspace": 0.04,
+            "preprocessing": true
+        },
+        "CenterCrop":
+        {
+            "size": [96, 96],
+            "preprocessing": true
+        },
+        "ElasticTransform": {
+            "alpha_range": [28.0, 30.0],
+            "sigma_range":  [3.5, 4.5],
+            "p": 0.3,
+            "applied_to": ["im", "gt"],
+            "dataset_type": ["training"]
+        },
+        "RandomAffine": {
+            "degrees": 20,
+            "translate": [0.03, 0.03],
+            "scale": [0.98, 1.02],
+            "dataset_type": ["training"]
+        },
+        "NumpyToTensor": {},
+        "NormalizeInstance": {"applied_to": ["im"]}
+    }
 }