Merge pull request #899 from HERA-Team/phase-flip-fix

Update logic for identifying phase flips

hera_cal/smooth_cal.py

@@ -78,11 +78,20 @@ def detect_phase_flips(phases):
         phase_flipped: boolean array the same shape as phases where True means pi radians flipped
             relative to the first unflagged phase.
     """
-    complexes = np.exp(1.0j * phases)
-    first_nonnan = np.ravel(complexes)[np.isfinite(np.ravel(complexes))][0]
-    # check if each number is closer to first_nonnan or -first_nonnan
-    phase_flipped = np.abs(complexes - first_nonnan) > np.abs(complexes + first_nonnan)
-    return phase_flipped
+    original_shape = np.array(phases).shape
+    complexes = np.exp(1.0j * np.ravel(phases))
+    phase_flipped = np.zeros(len(complexes), dtype=bool)
+    currently_flipped = False
+    previous_non_nan = np.nan  # ensures that first non-nan integration is not flipped
+    for i in range(len(complexes)):
+        if not np.isnan(complexes[i]):
+            flip_here = np.abs(complexes[i] - previous_non_nan) > np.abs(complexes[i] + previous_non_nan)
+            phase_flipped[i] = currently_flipped ^ flip_here
+            currently_flipped = phase_flipped[i]
+            previous_non_nan = complexes[i]
+        else:
+            phase_flipped[i] = currently_flipped
+    return phase_flipped.reshape(original_shape)
 
 
 def dpss_filters(freqs, times, freq_scale=10, time_scale=1800, eigenval_cutoff=1e-9):

hera_cal/tests/test_smooth_cal.py

@@ -49,9 +49,9 @@ def test_detect_phase_flips(self):
         np.testing.assert_array_equal(phase_flipped, np.array([False, False, False, True, True, True]))
         # test nan handling
         phase_flipped = smooth_cal.detect_phase_flips(np.array([1, 1, 1, 4, np.nan, 4]))
-        np.testing.assert_array_equal(phase_flipped, np.array([False, False, False, True, False, True]))
+        np.testing.assert_array_equal(phase_flipped, np.array([False, False, False, True, True, True]))
         phase_flipped = smooth_cal.detect_phase_flips(np.array([np.nan, 1, 1, 4, np.nan, 4]))
-        np.testing.assert_array_equal(phase_flipped, np.array([False, False, False, True, False, True]))
+        np.testing.assert_array_equal(phase_flipped, np.array([False, False, False, True, True, True]))
 
     def test_dpss_filters(self):
         times = np.linspace(0, 10 * 10 / 60. / 60. / 24., 40, endpoint=False)