Refactor transforms

.gitignore

@@ -6,3 +6,5 @@ ivadomed/loader/__pycache__/
 ivadomed/FiLM/__pycache__/
 dev/.bin/
 dev/__pycache__/
+testing/__pycache__/
+

dev/class_balance.py

@@ -42,8 +42,8 @@ def run_main(args):
 
     transform_lst = torch_transforms.Compose([
         imed_transforms.Resample(wspace=0.75, hspace=0.75),
-        imed_transforms.CenterCrop2D((128, 128)),
-        imed_transforms.ToTensor(),
+        imed_transforms.CenterCrop([128, 128]),
+        imed_transforms.NumpyToTensor(),
         imed_transforms.NormalizeInstance(),
     ])
 

dev/metadata_config.py

@@ -13,8 +13,8 @@
 
 def run_main(context):
     no_transform = torch_transforms.Compose([
-        imed_transforms.CenterCrop2D((128, 128)),
-        imed_transforms.ToTensor(),
+        imed_transforms.CenterCrop([128, 128]),
+        imed_transforms.NumpyToTensor(),
         imed_transforms.NormalizeInstance(),
     ])
 

dev/plot_cluster_metadata.py

@@ -51,8 +51,8 @@ def plot_decision_boundaries(data, model, x_range, metadata_name, fname_out):
 
 def run_main(context):
     no_transform = torch_transforms.Compose([
-        imed_transforms.CenterCrop2D((128, 128)),
-        imed_transforms.ToTensor(),
+        imed_transforms.CenterCrop([128, 128]),
+        imed_transforms.NumpyToTensor(),
         imed_transforms.NormalizeInstance(),
     ])
 

ivadomed/config/config.json

@@ -47,10 +47,7 @@
             "wspace": 0.75,
             "hspace": 0.75
 			},
-		"DilateGT": {
-			"dilation_factor": 0
-			},
-		"CenterCrop2D": {
+		"CenterCrop": {
 			"size": [128, 128]
 			},
 		"ElasticTransform": {
@@ -63,30 +60,30 @@
 			"translate": [0.03, 0.03],
 			"scale": [0.98, 1.02]
 			},
-		"ToTensor": {},
-		"NormalizeInstance": {}
+		"NumpyToTensor": {},
+		"NormalizeInstance": {"applied_to": ["im"]}
 		},
 	"transformation_validation": {
 		"Resample": {
 			"wspace": 0.75,
 			"hspace": 0.75
 			},
-		"CenterCrop2D": {
+		"CenterCrop": {
 			"size": [128, 128]
 			},
-		"ToTensor": {},
-		"NormalizeInstance": {}
+		"NumpyToTensor": {},
+		"NormalizeInstance": {"applied_to": ["im"]}
 		},
         "transformation_testing": {
                 "Resample": {
                         "wspace": 0.75,
                         "hspace": 0.75
                         },
-                "CenterCrop2D": {
+                "CenterCrop": {
                         "size": [128, 128]
                         },
-                "ToTensor": {},
-                "NormalizeInstance": {}
+                "NumpyToTensor": {},
+                "NormalizeInstance": {"applied_to": ["im"]}
                 },
 
     "debugging": true

ivadomed/config/config_gm.json

@@ -45,10 +45,7 @@
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "DilateGT": {
-            "dilation_factor": 0
-        },
-        "CenterCrop2D": {
+        "CenterCrop": {
             "size": [128, 128]
         },
         "ElasticTransform": {
@@ -61,30 +58,30 @@
             "translate": [0.03, 0.03],
             "scale": [0.98, 1.02]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {}
+        "NumpyToTensor": {},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_validation": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "CenterCrop2D": {
+        "CenterCrop": {
             "size": [128, 128]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {}
+        "NumpyToTensor": {},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_testing": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "CenterCrop2D": {
+        "CenterCrop": {
             "size": [128, 128]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {}
+        "NumpyToTensor": {},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "debugging": false
 }

ivadomed/config/config_sctTesting.json

@@ -50,49 +50,45 @@
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "DilateGT": {
-            "dilation_factor": 0
-        },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
         "ElasticTransform": {
             "alpha_range": [28.0, 30.0],
             "sigma_range":  [3.5, 4.5],
-            "p": 0.1
+            "p": 0.1,
+            "applied_to": ["im", "gt"]
         },
         "RandomAffine": {
             "degrees": 4.6,
             "translate": [0.03, 0.03],
-            "scale": [0.98, 1.02]
+            "scale": [0.98, 1.02],
+            "applied_to": ["im", "gt"]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_validation": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_testing": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "debugging": false
 }

ivadomed/config/config_sctTesting_lesionAx.json

@@ -51,52 +51,49 @@
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "DilateGT": {
-            "dilation_factor": 0
-        },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
         "ElasticTransform": {
             "alpha_range": [28.0, 30.0],
             "sigma_range":  [3.5, 4.5],
-            "p": 0.1
+            "p": 0.1,
+            "applied_to": ["im", "gt"]
         },
         "RandomAffine": {
             "degrees": 4.6,
             "translate": [0.03, 0.03],
-            "scale": [0.98, 1.02]
+            "scale": [0.98, 1.02],
+            "applied_to": ["im", "gt"]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_validation": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_testing": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "ROICrop2D": {
+        "ROICrop": {
             "size": [48, 48]
         },
         "RandomRotation": {
-            "degrees": 30
+            "degrees": 30,
+            "applied_to": ["im", "gt"],
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "debugging": false
 }

ivadomed/config/config_small.json

@@ -2,24 +2,25 @@
     "command": "train",
     "gpu": 4,
     "target_suffix": ["_seg-manual"],
-    "roi_suffix": null,
+    "roi_suffix": "_seg-manual",
     "bids_path": "../duke/projects/ivado-medical-imaging/spineGeneric_201907041011/result/",
     "random_seed": 1313,
-    "contrast_train_validation": ["T1w", "T2w", "T2star", "acq-MToff_MTS", "acq-MTon_MTS", "acq-T1w_MTS"],
+    "contrast_train_validation": ["T2star"],
     "contrast_balance": {},
-    "contrast_test": ["T1w", "T2w", "T2star", "acq-MToff_MTS", "acq-MTon_MTS", "acq-T1w_MTS"],
-    "center_test": ["stanford", "amu", "queensland", "cardiff", "barcelona", "strasbourg", "perform", "milan", "geneva", "mni"],
+    "contrast_test": ["T2star"],
+    "center_test": ["amu"],
     "batch_size": 18,
     "dropout_rate": 0.3,
     "batch_norm_momentum": 0.1,
     "num_epochs": 100,
     "initial_lr": 0.001,
-    "lr_scheduler": {"name": "CosineAnnealingWarmRestarts", "T_0": 10},
+    "lr_scheduler": {"name": "CyclicLR", "base_lr": 0.0001, "max_lr": 0.001},
     "loss": {"name": "dice"},
     "log_directory": "log_sc_small",
     "film_layers": [0, 0, 0, 0, 0, 0, 0, 0],
-    "mixup_bool": true,
+    "mixup_bool": false,
     "mixup_alpha": 2,
+    "balance_samples": false,
     "metadata": "without",
     "multichannel": false,
     "out_channel": 1,
@@ -38,59 +39,54 @@
     "retrain_fraction": 1.0,
     "slice_filter": {
         "filter_empty_mask": true,
-        "filter_empty_input": true,
-        "nb_nonzero_thr": 10
+        "filter_empty_input": true
     },
+    "slice_filter_roi": 10,
     "split_method": "per_center",
     "eval_params": {},
+    "uncertainty": {"epistemic": false, "aleatoric": false, "n_it": 0},
     "transformation_training": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "DilateGT": {
-            "dilation_factor": 0
-        },
-        "CenterCrop2D": {
+        "ROICrop": {
             "size": [128, 128]
         },
         "ElasticTransform": {
-            "alpha_range": [28.0, 30.0],
-            "sigma_range":  [3.5, 4.5],
-            "p": 0.1
+            "alpha_range": [200, 300],
+            "sigma_range":  [8, 12],
+            "p": 0.3,
+            "applied_to": ["im", "gt"]
         },
-        "RandomAffine": {
-            "degrees": 4.6,
-            "translate": [0.03, 0.03],
-            "scale": [0.98, 1.02]
+        "RandomRotation": {
+            "degrees": 10,
+            "applied_to": ["im", "gt"]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_validation": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "CenterCrop2D": {
+        "ROICrop": {
             "size": [128, 128]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "transformation_testing": {
         "Resample": {
             "wspace": 0.75,
             "hspace": 0.75
         },
-        "CenterCrop2D": {
+        "ROICrop": {
             "size": [128, 128]
         },
-        "ToTensor": {},
-        "NormalizeInstance": {},
-        "StackTensors": {}
+        "NumpyToTensor": {"applied_to": ["im", "gt"]},
+        "NormalizeInstance": {"applied_to": ["im"]}
     },
     "debugging": false
 }