Put the MorphRGrid at the end of the morphing chain

news/config_order.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* The interpolation of the morphed/objective function onto the target function grid is now done at the end of the morphing chain. Prior, it was done before. This change is desirable as the target function grid may be much smaller/larger than that of the objective, but a morph (e.g. stretch) accounts for that difference. Then, we ensure the morph is done before we regrid for comparison.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/update_tests.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -506,8 +506,6 @@ def single_morph(
 
     # Set up the morphs
     chain = morphs.MorphChain(config)
-    # Add the r-range morph, we will remove it when saving and plotting
-    chain.append(morphs.MorphRGrid())
     refpars = []
 
     # Python-Specific Morphs
@@ -632,6 +630,10 @@ def single_morph(
         refpars.append("qdamp")
         config["qdamp"] = opts.qdamp
 
+    # Add the r-range morph, we will remove it when saving and plotting
+    mrg = morphs.MorphRGrid()
+    chain.append(mrg)
+
     # Now remove non-refinable parameters
     if opts.exclude is not None:
         refpars = list(set(refpars) - set(opts.exclude))
@@ -674,7 +676,8 @@ def single_morph(
     rw = tools.getRw(chain)
     pcc = tools.get_pearson(chain)
     # Replace the MorphRGrid with Morph identity
-    chain[0] = morphs.Morph()
+    # This removes the r-range morph as mentioned above
+    mrg = morphs.Morph()
     chain(x_morph, y_morph, x_target, y_target)
 
     # FOR FUTURE MAINTAINERS

tests/test_morphio.py

@@ -50,6 +50,20 @@ def isfloat(s):
     return False
 
 
+def are_files_same(file1, file2):
+    """Assert that two files have (approximately) the same numerical
+    values."""
+    for f1_row, f2_row in zip(file1, file2):
+        f1_arr = f1_row.split()
+        f2_arr = f2_row.split()
+        assert len(f1_arr) == len(f2_arr)
+        for idx, _ in enumerate(f1_arr):
+            if isfloat(f1_arr[idx]) and isfloat(f2_arr[idx]):
+                assert np.isclose(float(f1_arr[idx]), float(f2_arr[idx]))
+            else:
+                assert f1_arr[idx] == f2_arr[idx]
+
+
 class TestApp:
     @pytest.fixture
     def setup(self):
@@ -106,9 +120,9 @@ def test_morph_outputs(self, setup, tmp_path):
         for file in common:
             with open(tmp_succinct.joinpath(file)) as gf:
                 with open(test_saving_succinct.joinpath(file)) as tf:
-                    generated = filter(ignore_path, gf)
-                    target = filter(ignore_path, tf)
-                    assert all(x == y for x, y in zip(generated, target))
+                    actual = filter(ignore_path, gf)
+                    expected = filter(ignore_path, tf)
+                    are_files_same(actual, expected)
 
         # Save multiple verbose morphs
         tmp_verbose = tmp_path.joinpath("verbose")
@@ -147,9 +161,9 @@ def test_morph_outputs(self, setup, tmp_path):
         for file in common:
             with open(tmp_verbose.joinpath(file)) as gf:
                 with open(test_saving_verbose.joinpath(file)) as tf:
-                    generated = filter(ignore_path, gf)
-                    target = filter(ignore_path, tf)
-                    assert all(x == y for x, y in zip(generated, target))
+                    actual = filter(ignore_path, gf)
+                    expected = filter(ignore_path, tf)
+                    are_files_same(actual, expected)
 
     def test_morphsqueeze_outputs(self, setup, tmp_path):
         # The file squeeze_morph has a squeeze and stretch applied
@@ -182,19 +196,9 @@ def test_morphsqueeze_outputs(self, setup, tmp_path):
         # Check squeeze morph generates the correct output
         with open(sqr) as mf:
             with open(target_file) as tf:
-                morphed = filter(ignore_path, mf)
-                target = filter(ignore_path, tf)
-                for m, t in zip(morphed, target):
-                    m_row = m.split()
-                    t_row = t.split()
-                    assert len(m_row) == len(t_row)
-                    for idx, _ in enumerate(m_row):
-                        if isfloat(m_row[idx]) and isfloat(t_row[idx]):
-                            assert np.isclose(
-                                float(m_row[idx]), float(t_row[idx])
-                            )
-                        else:
-                            assert m_row[idx] == t_row[idx]
+                actual = filter(ignore_path, mf)
+                expected = filter(ignore_path, tf)
+                are_files_same(actual, expected)
 
     def test_morphfuncy_outputs(self, tmp_path):
         def quadratic(x, y, a0, a1, a2):
@@ -215,16 +219,6 @@ def quadratic(x, y, a0, a1, a2):
 
         with open(testdata_dir.joinpath("funcy_target.cgr")) as tf:
             with open(tmp_path.joinpath("funcy_target.cgr")) as gf:
-                generated = filter(ignore_path, gf)
-                target = filter(ignore_path, tf)
-                for m, t in zip(generated, target):
-                    m_row = m.split()
-                    t_row = t.split()
-                    assert len(m_row) == len(t_row)
-                    for idx, _ in enumerate(m_row):
-                        if isfloat(m_row[idx]) and isfloat(t_row[idx]):
-                            assert np.isclose(
-                                float(m_row[idx]), float(t_row[idx])
-                            )
-                        else:
-                            assert m_row[idx] == t_row[idx]
+                actual = filter(ignore_path, gf)
+                expected = filter(ignore_path, tf)
+                are_files_same(actual, expected)

tests/test_morphpy.py

@@ -91,7 +91,14 @@ class Chain:
             assert np.allclose(
                 [rw], [self.morphapp_results[target_file.name]["Rw"]]
             )
-        assert morph_results == self.morphapp_results
+        # Check values in dictionaries are approximately equal
+        for file in morph_results.keys():
+            morph_params = morph_results[file]
+            morphapp_params = self.morphapp_results[file]
+            for key in morph_params.keys():
+                assert morph_params[key] == pytest.approx(
+                    morphapp_params[key], abs=1e-08
+                )
 
     def test_morphpy(self, setup_morph):
         morph_results = {}
@@ -113,7 +120,14 @@ class Chain:
             assert np.allclose(
                 [rw], [self.morphapp_results[target_file.name]["Rw"]]
             )
-        assert morph_results == self.morphapp_results
+            # Check values in dictionaries are approximately equal
+            for file in morph_results.keys():
+                morph_params = morph_results[file]
+                morphapp_params = self.morphapp_results[file]
+                for key in morph_params.keys():
+                    assert morph_params[key] == pytest.approx(
+                        morphapp_params[key], abs=1e-08
+                    )
 
     def test_morphfuncy(self, setup_morph):
         def gaussian(x, mu, sigma):