get the transforms from the config file

fishjaw/model/data.py

@@ -12,7 +12,7 @@
 from tqdm import tqdm
 
 from ..images import io, transform
-from ..util import files
+from ..util import files, util
 
 
 def get_patch_size(config: dict) -> tuple[int, int, int]:
@@ -234,22 +234,24 @@ def test_loader(
     )
 
 
-def _load_transform(transform: dict) -> tio.transforms.Transform:
+def _load_transform(transform_name: str, args: dict) -> tio.transforms.Transform:
     """
     Load a transform from the configuration, which should be provided as a dict of {"name": {"arg1": value1, ...}}
 
     """
-    if not isinstance(transform, dict):
-        raise ValueError(f"Transform {transform} is not a dict")
+    return util.load_class(transform_name)(**args)
 
 
-def _transforms(config: dict) -> tio.transforms.Transform:
+def _transforms(transform_dict: dict) -> tio.transforms.Transform:
     """
     Define the transforms to apply to the training data
 
     """
     return tio.Compose(
-        [_load_transform(transform_fcn) for transform_fcn in config["transforms"]]
+        [
+            _load_transform(transform_name, args)
+            for transform_name, args in transform_dict.items()
+        ]
     )
 
 
@@ -308,7 +310,7 @@ def read_dicoms_from_disk(
     print(f"Test: {test_idx=}")
 
     train_subjects = tio.SubjectsDataset(
-        [subjects[i] for i in train_idx], transform=_transforms()
+        [subjects[i] for i in train_idx], transform=_transforms(config["transforms"])
     )
     val_subjects = tio.SubjectsDataset([subjects[i] for i in val_idx])
     test_subject = subjects[test_idx]

fishjaw/util/util.py

@@ -69,10 +69,10 @@ def config() -> dict:
 
 def load_class(name: str) -> type:
     """
-    Load a class from a string.
+    Load a class from a module given a string.
 
     :param name: the name of the class to load. Should be in the format module.class,
-                 where module can also contain "."s
+                 where module can also contain "."s (e.g. module.submodule.class)
     :returns: the class object
 
     """

userconf.yml

@@ -40,20 +40,20 @@ lr_lambda: 0.9999 # Exponential decay factor (multiplicative with each epoch)
 
 # Options should be passed
 transforms:
-  tio.RandomFlip:
-    - axes: [0, 1, 2]
-    - flip_probability: 0.5
-  tio.RandomAffine:
-    - p: 0.25
-    - degrees: 10
-    - scales: 0.2
+  torchio.RandomFlip:
+    axes: [0, 1, 2]
+    flip_probability: 0.5
+  torchio.RandomAffine:
+    p: 0.25
+    degrees: 10
+    scales: 0.2
 # Other options might be
-# tio.RandomBlur(p=0.3),
-# tio.RandomBiasField(0.4, p=0.5),
-# tio.RandomNoise(0.1, 0.01, p=0.25),
-# tio.RandomGamma((-0.3, 0.3), p=0.25),
-# tio.ZNormalization(),
-# tio.RescaleIntensity(percentiles=(0.5, 99.5)),
+# torchio.RandomBlur(p=0.3),
+# torchio.RandomBiasField(0.4, p=0.5),
+# torchio.RandomNoise(0.1, 0.01, p=0.25),
+# torchio.RandomGamma((-0.3, 0.3), p=0.25),
+# torchio.ZNormalization(),
+# torchio.RescaleIntensity(percentiles=(0.5, 99.5)),
 
 model_params:
   model_name: "monai.networks.nets.AttentionUnet"