Merge pull request #142 from bioimage-io/update_scale_range

Update scale range

Author: constantinpape

bioimageio/core/prediction_pipeline/_processing.py

@@ -166,6 +166,7 @@ class ScaleRange(Processing):
     axes: Optional[Sequence[str]] = None
     min_percentile: float = 0.0
     max_percentile: float = 100.0
+    eps: float = 1e-6
     reference_tensor: Optional[str] = None
 
     def get_required_dataset_statistics(self) -> Dict[str, Set[Measure]]:
@@ -209,7 +210,7 @@ def apply(self, tensor: xr.DataArray) -> xr.DataArray:
         v_lower = get_stat(ref_name, Percentile(self.min_percentile, axes=axes))
         v_upper = get_stat(ref_name, Percentile(self.max_percentile, axes=axes))
 
-        return ensure_dtype((tensor - v_lower) / v_upper, dtype="float32")
+        return ensure_dtype((tensor - v_lower) / (v_upper - v_lower + self.eps), dtype="float32")
 
     def __post_init__(self):
         super().__post_init__()

tests/prediction_pipeline/test_preprocessing.py

@@ -131,11 +131,14 @@ def test_scale_range():
         )
     )
 
-    exp_data = (np_data - np_data.min()) / np_data.max()
+    eps = 1.0e-6
+    mi, ma = np_data.min(), np_data.max()
+    exp_data = (np_data - mi) / (ma - mi + eps)
     expected = xr.DataArray(exp_data, dims=("x", "y"))
 
     result = preprocessing(data)
-    xr.testing.assert_allclose(expected, result)
+    # NOTE xarray.testing.assert_allclose compares irrelavant properties here and fails although the result is correct
+    np.testing.assert_allclose(expected, result)
 
 
 def test_scale_range_axes():
@@ -156,13 +159,15 @@ def test_scale_range_axes():
         )
     )
 
+    eps = 1.0e-6
     p_low = np.percentile(np_data, min_percentile, axis=(1, 2), keepdims=True)
     p_up = np.percentile(np_data, max_percentile, axis=(1, 2), keepdims=True)
-    exp_data = (np_data - p_low) / p_up
+    exp_data = (np_data - p_low) / (p_up - p_low + eps)
     expected = xr.DataArray(exp_data, dims=("c", "x", "y"))
 
     result = preprocessing(data)
-    xr.testing.assert_allclose(expected, result)
+    # NOTE xarray.testing.assert_allclose compares irrelavant properties here and fails although the result is correct
+    np.testing.assert_allclose(expected, result)
 
 
 def test_sigmoid():