comments from @alisiafadini

rs-station · Aug 22, 2024 · 08ef8be · 08ef8be
1 parent 7dd2fb2
commit 08ef8be
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Showing 4 changed files with 22 additions and 17 deletions.
diff --git a/meteor/utils.py b/meteor/utils.py
@@ -11,7 +11,7 @@
 @dataclass
 class MapLabels:
     amplitude: str
-    phases: str
+    phase: str
 
 
 def resolution_limits(dataset: rs.DataSet) -> tuple[float, float]:

diff --git a/test/conftest.py b/test/conftest.py
@@ -10,7 +10,7 @@
 def diffmap_labels() -> MapLabels:
     return MapLabels(
         amplitude="DF",
-        phases="PHIC",
+        phase="PHIC",
     )
 
 
@@ -30,7 +30,7 @@ def random_difference_map(diffmap_labels: MapLabels) -> rs.DataSet:
             "K": k,
             "L": l,
             diffmap_labels.amplitude: np.random.randn(number_of_reflections),
-            diffmap_labels.phases: np.random.uniform(-180, 180, size=number_of_reflections),
+            diffmap_labels.phase: np.random.uniform(-180, 180, size=number_of_reflections),
         },
         spacegroup=space_group,
         cell=cell,

diff --git a/test/unit/test_tv.py b/test/unit/test_tv.py
@@ -80,13 +80,13 @@ def rms_between_coefficients(ds1: rs.DataSet, ds2: rs.DataSet, diffmap_labels: M
     map1 = compute_map_from_coefficients(
         map_coefficients=ds1,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
         map_sampling=3,
     )
     map2 = compute_map_from_coefficients(
         map_coefficients=ds2,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
         map_sampling=3,
     )
 
@@ -116,7 +116,7 @@ def noisy_map() -> rs.DataSet:
     [
         None,
         [
-            1.0,
+            0.01,
         ],
     ],
 )
@@ -160,21 +160,21 @@ def test_tv_denoise_difference_map(
     # testmap = compute_map_from_coefficients(
     #     map_coefficients=noise_free_map,
     #     amplitude_label=diffmap_labels.amplitude,
-    #     phase_label=diffmap_labels.phases,
+    #     phase_label=diffmap_labels.phase,
     #     map_sampling=1,
     # )
     # testmap.write_ccp4_map("original.ccp4")
     # testmap = compute_map_from_coefficients(
     #     map_coefficients=noisy_map,
     #     amplitude_label=diffmap_labels.amplitude,
-    #     phase_label=diffmap_labels.phases,
+    #     phase_label=diffmap_labels.phase,
     #     map_sampling=1,
     # )
     # testmap.write_ccp4_map("noisy.ccp4")
     # testmap = compute_map_from_coefficients(
     #     map_coefficients=denoised_map,
     #     amplitude_label=diffmap_labels.amplitude,
-    #     phase_label=diffmap_labels.phases,
+    #     phase_label=diffmap_labels.phase,
     #     map_sampling=1,
     # )
     # testmap.write_ccp4_map("denoised.ccp4")
diff --git a/test/unit/test_utils.py b/test/unit/test_utils.py
@@ -50,25 +50,30 @@ def test_cut_resolution(
 def test_canonicalize_amplitudes(
     inplace: bool, random_difference_map: rs.DataSet, diffmap_labels: utils.MapLabels
 ) -> None:
+    # ensure at least one amplitude is negative, one phase is outside [-180,180)
+    index_single_hkl = 0
+    random_difference_map.loc[index_single_hkl, diffmap_labels.amplitude] = -1.0
+    random_difference_map.loc[index_single_hkl, diffmap_labels.phase] = -470.0
+
     if inplace:
         canonicalized = random_difference_map
         utils.canonicalize_amplitudes(
             canonicalized,
             amplitude_label=diffmap_labels.amplitude,
-            phase_label=diffmap_labels.phases,
+            phase_label=diffmap_labels.phase,
             inplace=inplace,
         )
     else:
         canonicalized = utils.canonicalize_amplitudes(
             random_difference_map,
             amplitude_label=diffmap_labels.amplitude,
-            phase_label=diffmap_labels.phases,
+            phase_label=diffmap_labels.phase,
             inplace=inplace,
         )
 
     assert (canonicalized[diffmap_labels.amplitude] >= 0.0).all(), "not all amplitudes positive"
-    assert (canonicalized[diffmap_labels.phases] >= -180.0).all(), "not all phases > -180"
-    assert (canonicalized[diffmap_labels.phases] <= 180.0).all(), "not all phases < +180"
+    assert (canonicalized[diffmap_labels.phase] >= -180.0).all(), "not all phases > -180"
+    assert (canonicalized[diffmap_labels.phase] <= 180.0).all(), "not all phases < +180"
 
     np.testing.assert_almost_equal(
         np.array(np.abs(random_difference_map[diffmap_labels.amplitude])),
@@ -82,7 +87,7 @@ def test_compute_map_from_coefficients(
     map = utils.compute_map_from_coefficients(
         map_coefficients=random_difference_map,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
         map_sampling=1,
     )
     assert isinstance(map, gemmi.Ccp4Map)
@@ -95,7 +100,7 @@ def test_map_to_coefficients_round_trip(
     map = utils.compute_map_from_coefficients(
         map_coefficients=random_difference_map,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
         map_sampling=map_sampling,
     )
 
@@ -105,13 +110,13 @@ def test_map_to_coefficients_round_trip(
         ccp4_map=map,
         high_resolution_limit=dmin,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
     )
 
     utils.canonicalize_amplitudes(
         output_coefficients,
         amplitude_label=diffmap_labels.amplitude,
-        phase_label=diffmap_labels.phases,
+        phase_label=diffmap_labels.phase,
         inplace=True,
     )
     pd.testing.assert_frame_equal(left=random_difference_map, right=output_coefficients, atol=0.5)