feat: detect extrapolation for morphstretch (#258)

* feat: detect extrapolation for `morphstretch`

* fix: set `stretch_morph` to None when it is excluded

* chore: add extension to temporary morph file

Author: ycexiao

news/stretch-extrapolation.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Add warning for extrapolation in morphstretch and tests for extrapolations.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -585,9 +585,11 @@ def single_morph(
         refpars.append("scale")
     # Stretch
     # Only enable stretch if squeeze is lower than degree 1
+    stretch_morph = None
     if opts.stretch is not None and squeeze_poly_deg < 1:
+        stretch_morph = morphs.MorphStretch()
+        chain.append(stretch_morph)
         stretch_in = opts.stretch
-        chain.append(morphs.MorphStretch())
         config["stretch"] = stretch_in
         refpars.append("stretch")
     # Smear
@@ -665,6 +667,8 @@ def single_morph(
     # Now remove non-refinable parameters
     if opts.exclude is not None:
         refpars = list(set(refpars) - set(opts.exclude))
+        if "stretch" in opts.exclude:
+            stretch_morph = None
 
     # Refine or execute the morph
     refiner = refine.Refiner(
@@ -703,6 +707,7 @@ def single_morph(
     # THROW ANY WARNINGS HERE
     io.handle_warnings(squeeze_morph)
     io.handle_warnings(shift_morph)
+    io.handle_warnings(stretch_morph)
 
     # Get Rw for the morph range
     rw = tools.getRw(chain)

src/diffpy/morph/morphs/morphstretch.py

@@ -48,6 +48,7 @@ def morph(self, x_morph, y_morph, x_target, y_target):
 
         r = self.x_morph_in / (1.0 + self.stretch)
         self.y_morph_out = numpy.interp(r, self.x_morph_in, self.y_morph_in)
+        self.set_extrapolation_info(self.x_morph_in, r)
         return self.xyallout
 
 

tests/helper.py

@@ -0,0 +1,16 @@
+def create_morph_data_file(
+    data_dir_path, x_morph, y_morph, x_target, y_target
+):
+    morph_file = data_dir_path / "morph_data.txt"
+    morph_data_text = [
+        str(x_morph[i]) + " " + str(y_morph[i]) for i in range(len(x_morph))
+    ]
+    morph_data_text = "\n".join(morph_data_text)
+    morph_file.write_text(morph_data_text)
+    target_file = data_dir_path / "target_data.txt"
+    target_data_text = [
+        str(x_target[i]) + " " + str(y_target[i]) for i in range(len(x_target))
+    ]
+    target_data_text = "\n".join(target_data_text)
+    target_file.write_text(target_data_text)
+    return morph_file, target_file

tests/test_morphshift.py

@@ -6,7 +6,10 @@
 import numpy
 import pytest
 
+import diffpy.morph.morphpy as morphpy
+from diffpy.morph.morphapp import create_option_parser, single_morph
 from diffpy.morph.morphs.morphshift import MorphShift
+from tests.helper import create_morph_data_file
 
 # useful variables
 thisfile = locals().get("__file__", "file.py")
@@ -44,3 +47,61 @@ def test_morph(self, setup):
         assert numpy.allclose(self.x_target, x_target)
         assert numpy.allclose(self.y_target, y_target)
         return
+
+
+@pytest.mark.parametrize(
+    "hshift, wmsg_gen",
+    [
+        # extrapolate below
+        (
+            0.01,
+            lambda x: (
+                "Warning: points with grid value below "
+                f"{x[0]} are extrapolated."
+            ),
+        ),
+        # extrapolate above
+        (
+            -0.01,
+            lambda x: (
+                "Warning: points with grid value above "
+                f"{x[1]} are extrapolated."
+            ),
+        ),
+    ],
+)
+def test_morphshift_extrapolate(user_filesystem, capsys, hshift, wmsg_gen):
+    x_morph = numpy.linspace(0, 10, 101)
+    y_morph = numpy.sin(x_morph)
+    x_target = x_morph.copy()
+    y_target = y_morph.copy()
+    with pytest.warns() as w:
+        morphpy.morph_arrays(
+            numpy.array([x_morph, y_morph]).T,
+            numpy.array([x_target, y_target]).T,
+            hshift=hshift,
+            apply=True,
+        )
+        assert len(w) == 1
+        assert w[0].category is UserWarning
+        actual_wmsg = str(w[0].message)
+    expected_wmsg = wmsg_gen([min(x_morph), max(x_morph)])
+    assert actual_wmsg == expected_wmsg
+
+    # CLI test
+    morph_file, target_file = create_morph_data_file(
+        user_filesystem / "cwd_dir", x_morph, y_morph, x_target, y_target
+    )
+
+    parser = create_option_parser()
+    (opts, pargs) = parser.parse_args(
+        [
+            f"--hshift={hshift}",
+            f"{morph_file.as_posix()}",
+            f"{target_file.as_posix()}",
+            "--apply",
+            "-n",
+        ]
+    )
+    with pytest.warns(UserWarning, match=expected_wmsg):
+        single_morph(parser, opts, pargs, stdout_flag=False)

tests/test_morphsqueeze.py

@@ -5,6 +5,7 @@
 import diffpy.morph.morphpy as morphpy
 from diffpy.morph.morphapp import create_option_parser, single_morph
 from diffpy.morph.morphs.morphsqueeze import MorphSqueeze
+from tests.helper import create_morph_data_file
 
 squeeze_coeffs_dic = [
     # The order of coefficients is {a0, a1, a2, ..., an}
@@ -128,9 +129,7 @@ def test_morphsqueeze(x_morph, x_target, squeeze_coeffs):
         ),
     ],
 )
-def test_morphsqueeze_extrapolate(
-    user_filesystem, capsys, squeeze_coeffs, wmsg_gen
-):
+def test_morphsqueeze_extrapolate(user_filesystem, squeeze_coeffs, wmsg_gen):
     x_morph = np.linspace(0, 10, 101)
     y_morph = np.sin(x_morph)
     x_target = x_morph.copy()
@@ -171,21 +170,3 @@ def test_morphsqueeze_extrapolate(
     )
     with pytest.warns(UserWarning, match=expected_wmsg):
         single_morph(parser, opts, pargs, stdout_flag=False)
-
-
-def create_morph_data_file(
-    data_dir_path, x_morph, y_morph, x_target, y_target
-):
-    morph_file = data_dir_path / "morph_data"
-    morph_data_text = [
-        str(x_morph[i]) + " " + str(y_morph[i]) for i in range(len(x_morph))
-    ]
-    morph_data_text = "\n".join(morph_data_text)
-    morph_file.write_text(morph_data_text)
-    target_file = data_dir_path / "target_data"
-    target_data_text = [
-        str(x_target[i]) + " " + str(y_target[i]) for i in range(len(x_target))
-    ]
-    target_data_text = "\n".join(target_data_text)
-    target_file.write_text(target_data_text)
-    return morph_file, target_file

tests/test_morphstretch.py

@@ -6,7 +6,10 @@
 import numpy
 import pytest
 
+import diffpy.morph.morphpy as morphpy
+from diffpy.morph.morphapp import create_option_parser, single_morph
 from diffpy.morph.morphs.morphstretch import MorphStretch
+from tests.helper import create_morph_data_file
 
 # useful variables
 thisfile = locals().get("__file__", "file.py")
@@ -70,3 +73,61 @@ def heaviside(x, lb, ub):
     y[x < lb] = 0.0
     y[x > ub] = 0.0
     return y
+
+
+@pytest.mark.parametrize(
+    "stretch, wmsg_gen",
+    [
+        # extrapolate below
+        (
+            0.01,
+            lambda x: (
+                "Warning: points with grid value below "
+                f"{x[0]} are extrapolated."
+            ),
+        ),
+        # extrapolate above
+        (
+            -0.01,
+            lambda x: (
+                "Warning: points with grid value above "
+                f"{x[1]} are extrapolated."
+            ),
+        ),
+    ],
+)
+def test_morphshift_extrapolate(user_filesystem, stretch, wmsg_gen):
+    x_morph = numpy.linspace(1, 10, 101)
+    y_morph = numpy.sin(x_morph)
+    x_target = x_morph.copy()
+    y_target = y_morph.copy()
+    with pytest.warns() as w:
+        morphpy.morph_arrays(
+            numpy.array([x_morph, y_morph]).T,
+            numpy.array([x_target, y_target]).T,
+            stretch=stretch,
+            apply=True,
+        )
+        assert len(w) == 1
+        assert w[0].category is UserWarning
+        actual_wmsg = str(w[0].message)
+    expected_wmsg = wmsg_gen([min(x_morph), max(x_morph)])
+    assert actual_wmsg == expected_wmsg
+
+    # CLI test
+    morph_file, target_file = create_morph_data_file(
+        user_filesystem / "cwd_dir", x_morph, y_morph, x_target, y_target
+    )
+
+    parser = create_option_parser()
+    (opts, pargs) = parser.parse_args(
+        [
+            f"--stretch={stretch}",
+            f"{morph_file.as_posix()}",
+            f"{target_file.as_posix()}",
+            "--apply",
+            "-n",
+        ]
+    )
+    with pytest.warns(UserWarning, match=expected_wmsg):
+        single_morph(parser, opts, pargs, stdout_flag=False)