Add squeeze morph to CLI (#216)

* Add squeeze morph to CLI

* [pre-commit.ci] auto fixes from pre-commit hooks

* Add news and documentation

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: Sparks29032

doc/source/squeeze.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* Squeeze morph now added to CLI.
+
+**Changed:**
+
+* Stretch disabled when squeeze is above polynomial order 0.
+* Horizontal shift morph disabled when squeeze is enabled.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/squeeze_cli.rst

@@ -67,6 +67,17 @@ def single_morph_output(
     )
 
     morphs_out = "# Optimized morphing parameters:\n"
+    # Handle special inputs
+    if "squeeze" in morph_results:
+        sq_dict = morph_results.pop("squeeze")
+        rw_pos = list(morph_results.keys()).index("Rw")
+        morph_results_list = list(morph_results.items())
+        for idx, _ in enumerate(sq_dict):
+            morph_results_list.insert(
+                rw_pos + idx, (f"squeeze a{idx}", sq_dict[f"a{idx}"])
+            )
+        morph_results = dict(morph_results_list)
+    # Normal inputs
     morphs_out += "\n".join(
         f"# {key} = {morph_results[key]:.6f}" for key in morph_results.keys()
     )

src/diffpy/morph/morph_io.py

@@ -148,26 +148,50 @@ def custom_error(self, msg):
         action="append",
         dest="exclude",
         metavar="MANIP",
-        help="""Exclude a manipulation from refinement by name. This can
- appear multiple times.""",
+        help=(
+            "Exclude a manipulation from refinement by name. "
+            "This can appear multiple times."
+        ),
     )
     group.add_option(
         "--scale",
         type="float",
         metavar="SCALE",
-        help="Apply scale factor SCALE.",
+        help=(
+            "Apply scale factor SCALE. "
+            "This multiplies the function ordinate by SCALE."
+        ),
     )
     group.add_option(
         "--stretch",
         type="float",
         metavar="STRETCH",
-        help="Stretch PDF by a fraction STRETCH.",
+        help=(
+            "Stretch function grid by a fraction STRETCH. "
+            "This multiplies the function grid by 1+STRETCH."
+        ),
+    )
+    group.add_option(
+        "--squeeze",
+        metavar="a0,a1,...,an",
+        help=(
+            "Squeeze function grid given a polynomial "
+            "a0+a1*x+a2*x^2+...a_n*x^n."
+            "n is dependent on the number of values in the "
+            "user-inputted comma-separated list. "
+            "When this option is enabled, --hshift is disabled. "
+            "When n>1, --stretch is disabled. "
+            "See online documentation for more information."
+        ),
     )
     group.add_option(
         "--smear",
         type="float",
         metavar="SMEAR",
-        help="Smear peaks with a Gaussian of width SMEAR.",
+        help=(
+            "Smear peaks with a Gaussian of width SMEAR. "
+            "This convolves the function with a Gaussian of width SMEAR."
+        ),
     )
     group.add_option(
         "--slope",
@@ -444,22 +468,37 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
     chain.append(morphs.MorphRGrid())
     refpars = []
 
+    # Squeeze
+    squeeze_poly_deg = -1
+    if opts.squeeze is not None:
+        squeeze_coeffs = opts.squeeze.strip().split(",")
+        squeeze_dict_in = {}
+        for idx, coeff in enumerate(squeeze_coeffs):
+            squeeze_dict_in.update({f"a{idx}": float(coeff)})
+        squeeze_poly_deg = len(squeeze_coeffs) - 1
+        chain.append(morphs.MorphSqueeze())
+        config["squeeze"] = squeeze_dict_in
+        refpars.append("squeeze")
     # Scale
     if opts.scale is not None:
         scale_in = opts.scale
         chain.append(morphs.MorphScale())
         config["scale"] = scale_in
         refpars.append("scale")
     # Stretch
-    if opts.stretch is not None:
+    # Only enable stretch if squeeze is lower than degree 1
+    if opts.stretch is not None and squeeze_poly_deg < 1:
         stretch_in = opts.stretch
         chain.append(morphs.MorphStretch())
         config["stretch"] = stretch_in
         refpars.append("stretch")
     # Shift
-    if opts.hshift is not None or opts.vshift is not None:
+    # Only enable hshift is squeeze is not enabled
+    if (
+        opts.hshift is not None and squeeze_poly_deg < 0
+    ) or opts.vshift is not None:
         chain.append(morphs.MorphShift())
-    if opts.hshift is not None:
+    if opts.hshift is not None and squeeze_poly_deg < 0:
         hshift_in = opts.hshift
         config["hshift"] = hshift_in
         refpars.append("hshift")
@@ -557,13 +596,23 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
     chain[0] = morphs.Morph()
     chain(x_morph, y_morph, x_target, y_target)
 
+    # FOR FUTURE MAINTAINERS
+    # Any new morph should have their input morph parameters updated here
     # Input morph parameters
     morph_inputs = {
         "scale": scale_in,
         "stretch": stretch_in,
         "smear": smear_in,
     }
     morph_inputs.update({"hshift": hshift_in, "vshift": vshift_in})
+    # More complex input morph parameters are only displayed conditionally
+    if opts.squeeze is not None:
+        squeeze_coeffs = opts.squeeze.strip().split(",")
+        squeeze_dict = {}
+        for idx, coeff in enumerate(squeeze_coeffs):
+            squeeze_dict.update({f"a{idx}": float(coeff)})
+        for idx, _ in enumerate(squeeze_dict):
+            morph_inputs.update({f"squeeze a{idx}": squeeze_dict[f"a{idx}"]})
 
     # Output morph parameters
     morph_results = dict(config.items())

src/diffpy/morph/morphapp.py

@@ -2,6 +2,7 @@
 
 from pathlib import Path
 
+import numpy as np
 import pytest
 
 from diffpy.morph.morphapp import (
@@ -27,6 +28,27 @@
 tssf = testdata_dir.joinpath("testsequence_serialfile.json")
 
 
+# Ignore PATH data when comparing files
+def ignore_path(line):
+    # Lines containing FILE PATH data begin with '# from '
+    if "# from " in line:
+        return False
+    # Lines containing DIRECTORY PATH data begin with '# with '
+    if "# with " in line:
+        return False
+    return True
+
+
+def isfloat(s):
+    """True if s is convertible to float."""
+    try:
+        float(s)
+        return True
+    except ValueError:
+        pass
+    return False
+
+
 class TestApp:
     @pytest.fixture
     def setup(self):
@@ -46,16 +68,6 @@ def setup(self):
         return
 
     def test_morph_outputs(self, setup, tmp_path):
-        # Ignore PATH data when comparing files
-        def ignore_path(line):
-            # Lines containing FILE PATH data begin with '# from '
-            if "# from " in line:
-                return False
-            # Lines containing DIRECTORY PATH data begin with '# with '
-            if "# with " in line:
-                return False
-            return True
-
         morph_file = self.testfiles[0]
         target_file = self.testfiles[-1]
 
@@ -137,3 +149,46 @@ def ignore_path(line):
                     generated = filter(ignore_path, gf)
                     target = filter(ignore_path, tf)
                     assert all(x == y for x, y in zip(generated, target))
+
+    def test_morph_squeeze_outputs(self, setup, tmp_path):
+        # The file squeeze_morph has a squeeze and stretch applied
+        morph_file = testdata_dir / "squeeze_morph.cgr"
+        target_file = testdata_dir / "squeeze_target.cgr"
+        sqr = tmp_path / "squeeze_morph_result.cgr"
+        sqr_name = sqr.resolve().as_posix()
+        # Note that stretch and hshift should not be considered
+        (opts, _) = self.parser.parse_args(
+            [
+                "--scale",
+                "2",
+                "--squeeze",
+                "0,-0.001,-0.0001,0.0001",
+                "--stretch",
+                "1",
+                "--hshift",
+                "1",
+                "-s",
+                sqr_name,
+                "-n",
+                "--verbose",
+            ]
+        )
+        pargs = [morph_file, target_file]
+        single_morph(self.parser, opts, pargs, stdout_flag=False)
+
+        # 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]

tests/test_morphio.py

@@ -0,0 +1,105 @@
+# PDF created by diffpy.morph
+# from PATH
+
+# Labels: [r] [gr]
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