solve axes issue

clinicadl/transforms/config/base.py

@@ -131,15 +131,3 @@ def validator_masking_method(cls, v):
             except ValueError:
                 pass
         return v
-
-
-class _AnatomicalAxesConfig(ClinicaDLConfig):
-    """Config class for 'axes' option when it supports anatomical values."""
-
-    axes: Union[
-        NumericalAxis,
-        Tuple[NumericalAxis, ...],
-        AnatomicalAxis,
-        Tuple[AnatomicalAxis, ...],
-        DefaultFromLibrary,
-    ] = DefaultFromLibrary.YES

clinicadl/transforms/config/enum.py

@@ -138,7 +138,7 @@ class AnatomicalAxis(str, Enum):
     """
 
     LEFT_RIGHT = "LR"
-    ANTERIOR_POSTERIOR = "AP"
+    POSTERIOR_ANTERIOR = "PA"
     INFERIOR_SUPERIOR = "IS"
 
 

clinicadl/transforms/config/intensity_augmentations.py

@@ -10,8 +10,8 @@
 
 from clinicadl.utils.factories import DefaultFromLibrary
 
-from .base import TransformConfig, _AnatomicalAxesConfig
-from .enum import ImplementedTransform, InterpolationMode
+from .base import TransformConfig
+from .enum import ImplementedTransform, InterpolationMode, NumericalAxis
 
 __all__ = [
     "RandomMotionConfig",
@@ -54,12 +54,15 @@ def validate_tuples(cls, v, field):
         return v
 
 
-class RandomGhostingConfig(TransformConfig, _AnatomicalAxesConfig):
+class RandomGhostingConfig(TransformConfig):
     """Config class for RandomGhosting augmentation."""
 
     num_ghosts: Union[
         NonNegativeInt, Tuple[NonNegativeInt, NonNegativeInt], DefaultFromLibrary
     ] = DefaultFromLibrary.YES
+    axes: Union[
+        NumericalAxis, Tuple[NumericalAxis, ...], DefaultFromLibrary
+    ] = DefaultFromLibrary.YES
     intensity: Union[
         NonNegativeFloat, Tuple[NonNegativeFloat, NonNegativeFloat], DefaultFromLibrary
     ] = DefaultFromLibrary.YES

clinicadl/transforms/config/spatial_augmentations.py

@@ -10,8 +10,9 @@
 
 from clinicadl.utils.factories import DefaultFromLibrary
 
-from .base import TransformConfig, _AnatomicalAxesConfig
+from .base import TransformConfig
 from .enum import (
+    AnatomicalAxis,
     CenterMode,
     ImplementedTransform,
     InterpolationMode,
@@ -28,9 +29,16 @@
 ]
 
 
-class RandomFlipConfig(TransformConfig, _AnatomicalAxesConfig):
+class RandomFlipConfig(TransformConfig):
     """Config class for RandomFlip augmentation."""
 
+    axes: Union[
+        NumericalAxis,
+        Tuple[NumericalAxis, ...],
+        AnatomicalAxis,
+        Tuple[AnatomicalAxis, ...],
+        DefaultFromLibrary,
+    ] = DefaultFromLibrary.YES
     flip_probability: Union[float, DefaultFromLibrary] = DefaultFromLibrary.YES
 
     @computed_field

tests/unittests/transforms/config/test_intensity_augmentations.py

@@ -14,7 +14,8 @@
     ({"num_ghosts": (-1, 1)}, "RandomGhosting"),
     ({"intensity": -0.1}, "RandomGhosting"),
     ({"intensity": (-0.1, 0.1)}, "RandomGhosting"),
-    ({"axes": "abc"}, "RandomGhosting"),
+    ({"axes": "R"}, "RandomGhosting"),
+    ({"axes": 3}, "RandomGhosting"),
     ({"restore": 1.1}, "RandomGhosting"),
     ({"num_spikes": 1.1}, "RandomSpike"),
     ({"num_spikes": -1}, "RandomSpike"),
@@ -35,8 +36,11 @@
 GOOD_INPUTS = [
     ({"degrees": 0.5, "translation": 0.5, "num_transforms": 1}, "RandomMotion"),
     ({"degrees": (-0.5, 0.5), "translation": (-0.5, 0.5)}, "RandomMotion"),
-    ({"num_ghosts": 0, "intensity": 0.1, "restore": 0.5}, "RandomGhosting"),
-    ({"num_ghosts": (1, 5), "intensity": (0.1, 0.2), "restore": 0}, "RandomGhosting"),
+    ({"num_ghosts": 0, "axes": 0, "intensity": 0.1, "restore": 0.5}, "RandomGhosting"),
+    (
+        {"num_ghosts": (1, 5), "axes": (0, 2), "intensity": (0.1, 0.2), "restore": 0},
+        "RandomGhosting",
+    ),
     ({"num_spikes": (0, 1), "intensity": 1.0}, "RandomSpike"),
     ({"num_spikes": 1, "intensity": (-1.0, 1.0)}, "RandomSpike"),
     ({"coefficients": 0, "order": 0}, "RandomBiasField"),
@@ -88,10 +92,3 @@ def test_interpolation():
         for transform in ["RandomMotion"]:
             c = create_transform_config(transform)(image_interpolation=mode)
             assert c.image_interpolation == mode
-
-
-def test_axes():
-    axes = [0, 1, 2, (0, 1), "AP", "LR", "IS", ("AP", "LR", "IS")]
-    for ax in axes:
-        c = create_transform_config("RandomGhosting")(axes=ax)
-        assert c.axes == ax

tests/unittests/transforms/config/test_spatial_augmentations.py

@@ -133,7 +133,7 @@ def test_interpolation():
 
 
 def test_axes():
-    axes = [0, 1, 2, (0, 1), "AP", "LR", "IS", ("AP", "LR", "IS")]
+    axes = [0, 1, 2, (0, 1), "LR", "PA", "IS", ("LR", "PA", "IS")]
     for ax in axes:
         c = create_transform_config("RandomFlip")(axes=ax)
         assert c.axes == ax