new test for testing refactor

meteor/testing.py

@@ -9,6 +9,7 @@
 import numpy as np
 
 from .rsmap import Map
+from .settings import MAP_SAMPLING
 
 
 @dataclass
@@ -27,11 +28,9 @@ def assert_phases_allclose(array1: np.ndarray, array2: np.ndarray, atol: float =
         raise AssertionError(msg)
 
 
-# TODO: test
-def rms_between_coefficients(map1: Map, map2: Map) -> float:
-    map_sampling = 3
-    map1_array = np.array(map1.to_ccp4_map(map_sampling=map_sampling).grid)
-    map2_array = np.array(map2.to_ccp4_map(map_sampling=map_sampling).grid)
+def diffmap_realspace_rms(map1: Map, map2: Map) -> float:
+    map1_array = np.array(map1.to_ccp4_map(map_sampling=MAP_SAMPLING).grid)
+    map2_array = np.array(map2.to_ccp4_map(map_sampling=MAP_SAMPLING).grid)
 
     # standardize
     map1_array /= map1_array.std()

test/unit/test_iterative.py

@@ -8,7 +8,7 @@
     iterative_tv_phase_retrieval,
 )
 from meteor.rsmap import Map
-from meteor.testing import rms_between_coefficients
+from meteor.testing import diffmap_realspace_rms
 from meteor.validate import map_negentropy
 
 
@@ -45,9 +45,14 @@ def test_tv_denoise_complex_difference_sf() -> None:
 
 def test_iterative_tv_different_indices(noise_free_map: Map, very_noisy_map: Map) -> None:
     # regression test to make sure we can accept maps with different indices
-    hkl = [(1, 2),] * 3,
-    labels = pd.MultiIndex.from_arrays(hkl, names=("H", "K", "L"))
-
+    labels = pd.MultiIndex.from_arrays(
+        [
+            (1, 2),
+        ]
+        * 3,
+        names=("H", "K", "L"),
+    )
+
     n = len(very_noisy_map)
     very_noisy_map.drop(labels, inplace=True)
     assert len(very_noisy_map) == n - 2
@@ -79,8 +84,8 @@ def test_iterative_tv(noise_free_map: Map, very_noisy_map: Map) -> None:
     assert isinstance(metadata, pd.DataFrame)
 
     # test correctness by comparing denoised dataset to noise-free
-    noisy_error = rms_between_coefficients(very_noisy_map, noise_free_map)
-    denoised_error = rms_between_coefficients(denoised_map, noise_free_map)
+    noisy_error = diffmap_realspace_rms(very_noisy_map, noise_free_map)
+    denoised_error = diffmap_realspace_rms(denoised_map, noise_free_map)
 
     # insist on 1% or better improvement
     assert 1.01 * denoised_error < noisy_error

test/unit/test_testing.py

@@ -3,6 +3,7 @@
 import pytest
 
 from meteor import testing as mt
+from meteor.rsmap import Map
 
 
 def test_map_columns_smoke() -> None:
@@ -21,6 +22,19 @@ def test_phases_allclose() -> None:
         mt.assert_phases_allclose(close1, far)
 
 
+def test_diffmap_realspace_rms(noise_free_map: Map) -> None:
+    assert mt.diffmap_realspace_rms(noise_free_map, noise_free_map) == 0.0
+
+    map2 = noise_free_map.copy()
+    map2 += 1
+    map3 = noise_free_map.copy()
+    map3 += 2
+
+    dist12 = mt.diffmap_realspace_rms(noise_free_map, map2)
+    dist13 = mt.diffmap_realspace_rms(noise_free_map, map3)
+    assert dist13 > dist12
+
+
 def test_single_carbon_structure_smoke() -> None:
     carbon_position = (4.0, 5.0, 6.0)
     space_group = gemmi.find_spacegroup_by_name("P212121")

test/unit/test_tv.py

@@ -10,7 +10,7 @@
 
 from meteor import tv
 from meteor.rsmap import Map
-from meteor.testing import rms_between_coefficients
+from meteor.testing import diffmap_realspace_rms
 from meteor.validate import map_negentropy
 
 DEFAULT_WEIGHTS_TO_SCAN = np.logspace(-2, 0, 25)
@@ -88,7 +88,7 @@ def test_tv_denoise_map(
     noisy_map: Map,
 ) -> None:
     def rms_to_noise_free(test_map: Map) -> float:
-        return rms_between_coefficients(test_map, noise_free_map)
+        return diffmap_realspace_rms(test_map, noise_free_map)
 
     # Normally, the `tv_denoise_difference_map` function only returns the best result -- since we
     # know the ground truth, work around this to test all possible results.