Merge pull request #438 from EIT-ALIVE/437_fix_pixelbreath_bug

Fix bug in pixel breath for NaN pixels

Author: JulietteFrancovich

eitprocessing/features/pixel_breath.py

@@ -20,7 +20,7 @@
 
 
 def _return_sentinel_breath_detection() -> BreathDetection:
-    # Returns a sential of a BreathDetection, which only exists to signal that the default value for breath_detection
+    # Returns a sentinel of a BreathDetection, which only exists to signal that the default value for breath_detection
     # was used.
     return _SENTINEL_BREATH_DETECTION
 
@@ -190,9 +190,13 @@ def find_pixel_breaths(  # noqa: C901, PLR0912, PLR0915
                 raise ValueError(msg)
 
         for row, col in itertools.product(range(n_rows), range(n_cols)):
+            if all_nan_mask[row, col]:
+                # pixel has no amplitude
+                continue
             mean_tiv = mean_tiv_pixel[row, col]
 
-            if np.std(pixel_impedance[:, row, col]) == 0:
+            pi = np.copy(pixel_impedance[:, row, col])  # TODO: check whether copying is necessary
+            if np.std(pi) == 0:
                 # pixel has no amplitude
                 continue
 
@@ -204,7 +208,7 @@ def find_pixel_breaths(  # noqa: C901, PLR0912, PLR0915
 
                 cd = np.copy(continuous_data.values)
                 cd = signal.detrend(cd, type="linear")
-                pi = np.copy(pixel_impedance[:, row, col])
+
                 if not np.all(np.isnan(pi)):
                     pi = signal.detrend(pi, type="linear")
 

tests/test_pixel_breath.py

@@ -169,16 +169,23 @@ def none_sequence():
 
 def mock_compute_pixel_parameter(mean: int):
     def _mock(*_args, **_kwargs) -> SparseData:
+        n_breaths = 3
+        n_rows, n_cols = 2, 2
+        values = [np.full((n_rows, n_cols), mean, dtype=float) for _ in range(n_breaths)]
+
+        # Time must have the same length as values
+        time = np.linspace(0, 10, n_breaths)
+
         return SparseData(
             label="mock_sparse_data",
             name="Tidal impedance variation",
             unit=None,
             category="impedance difference",
-            time=np.linspace(0, 100, 100),
+            time=time,
             description="Mock tidal impedance variation",
             parameters={},
             derived_from=[],
-            values=np.full(100, np.sign(mean)),
+            values=values,
         )
 
     return _mock
@@ -351,6 +358,7 @@ def test_with_data(draeger1: Sequence, timpel1: Sequence, pytestconfig: pytest.C
         ssequence = sequence
         pi = PixelBreath()
         eit_data = ssequence.eit_data["raw"]
+        eit_data.pixel_impedance[:, 0, 0] = np.nan  # set one pixel to NaN to test handling of NaNs
         cd = ssequence.continuous_data["global_impedance_(raw)"]
         pixel_breaths = pi.find_pixel_breaths(eit_data, cd)
         test_result = np.stack(pixel_breaths.values)