Merge branch 'main' into strictly-increasing-squeeze

ycexiao · web-flow · commit 0bc478a8abdd · 2025-09-11T15:53:05.000-04:00
diff --git a/docs/source/tutorials.rst b/docs/source/tutorials.rst
@@ -67,7 +67,7 @@ selected directory and plot resulting :math:`R_w` values from each morph.
 
 4. Between 192K and 198K, the Rw has a sharp increase, indicating that
    we may have a phase change. To confirm, let us now apply morphs
-   onto `` SrFe2As2_150K.gr`` with all other files in
+   onto ``SrFe2As2_150K.gr`` with all other files in
    ``morphsequence`` as targets ::
 
        diffpy.morph --scale=1 --stretch=0 SrFe2As2_150K.gr . --multiple-targets --sort-by=temperature
@@ -191,10 +191,10 @@ Currently, the supported nanoparticle shapes include: spheres and spheroids.
 
 * Within the ``additionalData`` directory, ``cd`` into the
   ``morphShape`` subdirectory. Inside, you will find a sample Ni bulk
-  material PDF ``Ni_bulk.gr``. This PDF is from `"Atomic Pair
-  Distribution Function Analysis:
-  A primer" <https://global.oup.com/academic/product/
-   atomic-pair-distribution-function-analysis-9780198885801>`_.
+  material PDF ``Ni_bulk.gr``. This PDF is from
+  `"Atomic Pair Distribution Function Analysis: A primer"
+  <https://global.oup.com/academic/product/
+  atomic-pair-distribution-function-analysis-9780198885801>`_.
   There are also multiple ``.cgr`` files with calculated Ni nanoparticle PDFs.
 
 * Let us apply various shape effect morphs on the bulk material to
diff --git a/news/enough-regression-points.rst b/news/enough-regression-points.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* Raise ``ValueError`` if the number of shared grid points between morphed and target functions is less than the number of parameters.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/news/extrapolate-warning.rst b/news/extrapolate-warning.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Add warning for extrapolation in morphsqueeze.py.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/news/no-subprocess.rst b/news/no-subprocess.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* Removed subprocess calls in test functions.
diff --git a/news/reduce-warns.rst b/news/reduce-warns.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Only give user extrapolation warning after refinement.
+
+**Security:**
+
+* <news item>
diff --git a/news/rst-markup.rst b/news/rst-markup.rst
@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Fix rst markup in the documentation.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/requirements/conda.txt b/requirements/conda.txt
@@ -1,5 +1,5 @@
 numpy
 scipy
-diffpy.utils
+diffpy.utils>=3.6.1
 matplotlib-base
 bg-mpl-stylesheets
diff --git a/src/diffpy/morph/morph_io.py b/src/diffpy/morph/morph_io.py
@@ -18,6 +18,7 @@
 
 import inspect
 import sys
+import warnings
 from pathlib import Path
 
 import numpy
@@ -26,6 +27,13 @@
 from diffpy.morph import __save_morph_as__
 
 
+def custom_formatwarning(msg, *args, **kwargs):
+    return f"{msg}\n"
+
+
+warnings.formatwarning = custom_formatwarning
+
+
 def single_morph_output(
     morph_inputs,
     morph_results,
@@ -398,3 +406,34 @@ def tabulate_results(multiple_morph_results):
             }
         )
     return tabulated_results
+
+
+def handle_warnings(squeeze_morph):
+    if squeeze_morph is not None:
+        eil = squeeze_morph.extrap_index_low
+        eih = squeeze_morph.extrap_index_high
+
+        if eil is not None or eih is not None:
+            if eih is None:
+                wmsg = (
+                    "Warning: points with grid value below "
+                    f"{squeeze_morph.squeeze_cutoff_low} "
+                    f"will be extrapolated."
+                )
+            elif eil is None:
+                wmsg = (
+                    "Warning: points with grid value above "
+                    f"{squeeze_morph.squeeze_cutoff_high} "
+                    f"will be extrapolated."
+                )
+            else:
+                wmsg = (
+                    "Warning: points with grid value below "
+                    f"{squeeze_morph.squeeze_cutoff_low} and above "
+                    f"{squeeze_morph.squeeze_cutoff_high} "
+                    f"will be extrapolated."
+                )
+            warnings.warn(
+                wmsg,
+                UserWarning,
+            )
diff --git a/src/diffpy/morph/morphapp.py b/src/diffpy/morph/morphapp.py
@@ -546,6 +546,7 @@ def single_morph(
     # Squeeze
     squeeze_poly_deg = -1
     squeeze_dict_in = {}
+    squeeze_morph = None
     if opts.squeeze is not None:
         # Handles both list and csv input
         if (
@@ -570,7 +571,8 @@ def single_morph(
                 except ValueError:
                     parser.error(f"{coeff} could not be converted to float.")
         squeeze_poly_deg = len(squeeze_dict_in.keys())
-        chain.append(morphs.MorphSqueeze())
+        squeeze_morph = morphs.MorphSqueeze()
+        chain.append(squeeze_morph)
         config["squeeze"] = squeeze_dict_in
         # config["extrap_index_low"] = None
         # config["extrap_index_high"] = None
@@ -696,6 +698,9 @@ def single_morph(
     else:
         chain(x_morph, y_morph, x_target, y_target)
 
+    # THROW ANY WARNINGS HERE
+    io.handle_warnings(squeeze_morph)
+
     # Get Rw for the morph range
     rw = tools.getRw(chain)
     pcc = tools.get_pearson(chain)
diff --git a/src/diffpy/morph/morphs/morphsqueeze.py b/src/diffpy/morph/morphs/morphsqueeze.py
@@ -66,6 +66,11 @@ class MorphSqueeze(Morph):
     # extrap_index_high: first index after interpolation region
     extrap_index_low = None
     extrap_index_high = None
+    squeeze_cutoff_low = None
+    squeeze_cutoff_high = None
+
+    def __init__(self, config=None):
+        super().__init__(config)
 
     def morph(self, x_morph, y_morph, x_target, y_target):
         """Apply a polynomial to squeeze the morph function.
@@ -85,11 +90,15 @@ def morph(self, x_morph, y_morph, x_target, y_target):
                 "Please change the input x_morph or the squeeze "
                 "coefficients."
             )
+
+        self.squeeze_cutoff_low = min(x_squeezed)
+        self.squeeze_cutoff_high = max(x_squeezed)
         self.y_morph_out = CubicSpline(x_squeezed, self.y_morph_in)(
             self.x_morph_in
         )
-        low_extrap = np.where(self.x_morph_in < x_squeezed[0])[0]
-        high_extrap = np.where(self.x_morph_in > x_squeezed[-1])[0]
+        low_extrap = np.where(self.x_morph_in < self.squeeze_cutoff_low)[0]
+        high_extrap = np.where(self.x_morph_in > self.squeeze_cutoff_high)[0]
         self.extrap_index_low = low_extrap[-1] if low_extrap.size else None
         self.extrap_index_high = high_extrap[0] if high_extrap.size else None
+
         return self.xyallout
diff --git a/src/diffpy/morph/refine.py b/src/diffpy/morph/refine.py
@@ -83,7 +83,15 @@ def _residual(self, pvals):
             self.x_morph, self.y_morph, self.x_target, self.y_target
         )
         rvec = _y_target - _y_morph
-
+        if len(rvec) < len(pvals):
+            raise ValueError(
+                f"\nNumber of parameters (currently {len(pvals)}) cannot "
+                "exceed the number of shared grid points "
+                f"(currently {len(rvec)}). "
+                "Please reduce the number of morphing parameters or "
+                "provide new morphing and target functions with more "
+                "shared grid points."
+            )
         # If first time computing residual
         if self.res_length is None:
             self.res_length = len(rvec)
@@ -145,6 +153,9 @@ def refine(self, *args, **kw):
         ------
         ValueError
             Exception raised if a minimum cannot be found.
+        ValueError
+            If the number of shared grid points between morphed function and
+            target function is smaller than the number of parameters.
         """
 
         self.pars = args or self.chain.config.keys()
diff --git a/tests/test_morphsqueeze.py b/tests/test_morphsqueeze.py
@@ -2,6 +2,8 @@
 import pytest
 from numpy.polynomial import Polynomial
 
+import diffpy.morph.morphpy as morphpy
+from diffpy.morph.morphapp import create_option_parser, single_morph
 from diffpy.morph.morphs.morphsqueeze import MorphSqueeze
 
 squeeze_coeffs_dic = [
@@ -85,3 +87,96 @@ def test_morphsqueeze(x_morph, x_target, squeeze_coeffs):
     assert np.allclose(x_morph_actual, x_morph_expected)
     assert np.allclose(x_target_actual, x_target)
     assert np.allclose(y_target_actual, y_target)
+
+
+@pytest.mark.parametrize(
+    "squeeze_coeffs, wmsg_gen",
+    [
+        # extrapolate below
+        (
+            {"a0": 0.01},
+            lambda x: (
+                "Warning: points with grid value below "
+                f"{x[0]} will be extrapolated."
+            ),
+        ),
+        # extrapolate above
+        (
+            {"a0": -0.01},
+            lambda x: (
+                "Warning: points with grid value above "
+                f"{x[1]} will be extrapolated."
+            ),
+        ),
+        # extrapolate below and above
+        (
+            {"a0": 0.01, "a1": -0.002},
+            lambda x: (
+                "Warning: points with grid value below "
+                f"{x[0]} and above {x[1]} will be "
+                "extrapolated."
+            ),
+        ),
+    ],
+)
+def test_morphsqueeze_extrapolate(
+    user_filesystem, capsys, squeeze_coeffs, wmsg_gen
+):
+    x_morph = np.linspace(0, 10, 101)
+    y_morph = np.sin(x_morph)
+    x_target = x_morph.copy()
+    y_target = y_morph.copy()
+    morph = MorphSqueeze()
+    morph.squeeze = squeeze_coeffs
+    coeffs = [squeeze_coeffs[f"a{i}"] for i in range(len(squeeze_coeffs))]
+    squeeze_polynomial = Polynomial(coeffs)
+    x_squeezed = x_morph + squeeze_polynomial(x_morph)
+    with pytest.warns() as w:
+        morphpy.morph_arrays(
+            np.array([x_morph, y_morph]).T,
+            np.array([x_target, y_target]).T,
+            squeeze=coeffs,
+            apply=True,
+        )
+        assert len(w) == 1
+        assert w[0].category is UserWarning
+        actual_wmsg = str(w[0].message)
+    expected_wmsg = wmsg_gen([min(x_squeezed), max(x_squeezed)])
+    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(
+        [
+            "--squeeze",
+            ",".join(map(str, coeffs)),
+            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)
+
+
+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
diff --git a/tests/test_refine.py b/tests/test_refine.py
