Add funcy support to morphpy

Author: Sparks29032

src/diffpy/morph/morph_io.py

@@ -66,20 +66,34 @@ def single_morph_output(
         + "\n"
     )
 
+    mr_copy = morph_results.copy()
     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())
+    # Handle special inputs (numerical)
+    if "squeeze" in mr_copy:
+        sq_dict = mr_copy.pop("squeeze")
+        rw_pos = list(mr_copy.keys()).index("Rw")
+        morph_results_list = list(mr_copy.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)
+        mr_copy = dict(morph_results_list)
+    funcy_function = None
+    if "function" in mr_copy:
+        funcy_function = mr_copy.pop("function")
+        print(funcy_function)
+    if "funcy" in mr_copy:
+        fy_dict = mr_copy.pop("funcy")
+        rw_pos = list(mr_copy.keys()).index("Rw")
+        morph_results_list = list(mr_copy.items())
+        for idx, key in enumerate(fy_dict):
+            morph_results_list.insert(
+                rw_pos + idx, (f"funcy {key}", fy_dict[key])
+            )
+        mr_copy = dict(morph_results_list)
     # Normal inputs
     morphs_out += "\n".join(
-        f"# {key} = {morph_results[key]:.6f}" for key in morph_results.keys()
+        f"# {key} = {mr_copy[key]:.6f}" for key in mr_copy.keys()
     )
 
     # Printing to terminal
@@ -88,7 +102,10 @@ def single_morph_output(
 
     # Saving to file
     if save_file is not None:
-        path_name = str(Path(morph_file).resolve())
+        if not Path(morph_file).exists():
+            path_name = "NO FILE PATH PROVIDED"
+        else:
+            path_name = str(Path(morph_file).resolve())
         header = "# PDF created by diffpy.morph\n"
         header += f"# from {path_name}"
 

src/diffpy/morph/morphapp.py

@@ -452,7 +452,9 @@ def custom_error(self, msg):
     return parser
 
 
-def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
+def single_morph(
+    parser, opts, pargs, stdout_flag=True, python_wrap=False, pymorphs=None
+):
     if len(pargs) < 2:
         parser.error("You must supply FILE1 and FILE2.")
     elif len(pargs) > 2 and not python_wrap:
@@ -507,9 +509,27 @@ def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
     chain.append(morphs.MorphRGrid())
     refpars = []
 
+    # Python-Specific Morphs
+    if pymorphs is not None:
+        # funcy value is a tuple (function,{param_dict})
+        if "funcy" in pymorphs:
+            mfy_function = pymorphs["funcy"][0]
+            mfy_params = pymorphs["funcy"][1]
+            chain.append(morphs.MorphFuncy())
+            config["function"] = mfy_function
+            config["funcy"] = mfy_params
+            refpars.append("funcy")
+
     # Squeeze
     squeeze_poly_deg = -1
     if opts.squeeze is not None:
+        # Handles both list and csv input
+        if (
+            len(opts.squeeze) > 1
+            and opts.squeeze[0] == "["
+            and opts.squeeze[-1] == "]"
+        ):
+            opts.squeeze = opts.squeeze[1:-1]
         squeeze_coeffs = opts.squeeze.strip().split(",")
         squeeze_dict_in = {}
         for idx, coeff in enumerate(squeeze_coeffs):
@@ -531,20 +551,6 @@ def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
         chain.append(morphs.MorphStretch())
         config["stretch"] = stretch_in
         refpars.append("stretch")
-    # Shift
-    # 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 and squeeze_poly_deg < 0:
-        hshift_in = opts.hshift
-        config["hshift"] = hshift_in
-        refpars.append("hshift")
-    if opts.vshift is not None:
-        vshift_in = opts.vshift
-        config["vshift"] = vshift_in
-        refpars.append("vshift")
     # Smear
     if opts.smear_pdf is not None:
         smear_in = opts.smear_pdf
@@ -563,6 +569,20 @@ def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
         chain.append(morphs.MorphSmear())
         refpars.append("smear")
         config["smear"] = smear_in
+    # Shift
+    # 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 and squeeze_poly_deg < 0:
+        hshift_in = opts.hshift
+        config["hshift"] = hshift_in
+        refpars.append("hshift")
+    if opts.vshift is not None:
+        vshift_in = opts.vshift
+        config["vshift"] = vshift_in
+        refpars.append("vshift")
     # Size
     radii = [opts.radius, opts.pradius]
     nrad = 2 - radii.count(None)
@@ -659,6 +679,12 @@ def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
             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}"]})
+    if pymorphs is not None:
+        if "funcy" in pymorphs:
+            for funcy_param in pymorphs["funcy"][1].keys():
+                morph_inputs.update(
+                    {f"funcy {funcy_param}": pymorphs["funcy"][1][funcy_param]}
+                )
 
     # Output morph parameters
     morph_results = dict(config.items())

src/diffpy/morph/morphpy.py

@@ -19,6 +19,7 @@ def get_args(parser, params, kwargs):
     return opts, pargs
 
 
+# Take in file names as input.
 def morph(
     morph_file,
     target_file,
@@ -29,11 +30,12 @@ def morph(
     **kwargs,
 ):
     """Run diffpy.morph at Python level.
+
     Parameters
     ----------
-    morph_file: str
+    morph_file: str or numpy.array
         Path-like object to the file to be morphed.
-    target_file: str
+    target_file: str or numpy.array
         Path-like object to the target file.
     scale: float, optional
         Initial guess for the scaling parameter.
@@ -57,22 +59,39 @@ def morph(
         morph_table[:,1] is the ordinate.
     """
 
+    # Check for Python-specific morphs
+    python_morphs = ["funcy"]
+    pymorphs = {}
+    for pmorph in python_morphs:
+        if pmorph in kwargs:
+            pmorph_value = kwargs.pop(pmorph)
+            pymorphs.update({pmorph: pmorph_value})
+
+    # Wrap the CLI
     parser = create_option_parser()
     params = {
         "scale": scale,
         "stretch": stretch,
         "smear": smear,
         "noplot": True if not plot else None,
     }
-    opts, pargs = get_args(parser, params, kwargs)
+    opts, _ = get_args(parser, params, kwargs)
 
     pargs = [morph_file, target_file]
 
+    if not len(pymorphs) > 0:
+        pymorphs = None
     return single_morph(
-        parser, opts, pargs, stdout_flag=False, python_wrap=True
+        parser,
+        opts,
+        pargs,
+        stdout_flag=False,
+        python_wrap=True,
+        pymorphs=pymorphs,
     )
 
 
+# Take in array-like objects as input.
 def morphpy(
     morph_table,
     target_table,
@@ -83,6 +102,7 @@ def morphpy(
     **kwargs,
 ):
     """Run diffpy.morph at Python level.
+
     Parameters
     ----------
     morph_table: numpy.array
@@ -110,15 +130,23 @@ def morphpy(
         Function after morph where morph_table[:,0] is the abscissa and
         morph_table[:,1] is the ordinate.
     """
-
+    # Check for Python-specific morphs
+    python_morphs = ["funcy"]
+    pymorphs = {}
+    for pmorph in python_morphs:
+        if pmorph in kwargs:
+            pmorph_value = kwargs.pop(pmorph)
+            pymorphs.update({pmorph: pmorph_value})
+
+    # Wrap the CLI
     parser = create_option_parser()
     params = {
         "scale": scale,
         "stretch": stretch,
         "smear": smear,
         "noplot": True if not plot else None,
     }
-    opts, pargs = get_args(parser, params, kwargs)
+    opts, _ = get_args(parser, params, kwargs)
 
     morph_table = np.array(morph_table)
     target_table = np.array(target_table)
@@ -130,6 +158,13 @@ def morphpy(
 
     pargs = ["Morph", "Target", x_morph, y_morph, x_target, y_target]
 
+    if not len(pymorphs) > 0:
+        pymorphs = None
     return single_morph(
-        parser, opts, pargs, stdout_flag=False, python_wrap=True
+        parser,
+        opts,
+        pargs,
+        stdout_flag=False,
+        python_wrap=True,
+        pymorphs=pymorphs,
     )

src/diffpy/morph/morphs/morphfuncy.py

@@ -11,7 +11,7 @@ class MorphFuncy(Morph):
     yinlabel = LABEL_GR
     xoutlabel = LABEL_RA
     youtlabel = LABEL_GR
-    parnames = ["funcy"]
+    parnames = ["function", "funcy"]
 
     def morph(self, x_morph, y_morph, x_target, y_target):
         """General morph function that applies a user-supplied function
@@ -63,7 +63,6 @@ def morph(self, x_morph, y_morph, x_target, y_target):
         >>> parameters_out = morph.funcy
         """
         Morph.morph(self, x_morph, y_morph, x_target, y_target)
-
         self.y_morph_out = self.function(
             self.x_morph_in, self.y_morph_in, **self.funcy
         )

tests/test_morphio.py

@@ -11,6 +11,8 @@
     single_morph,
 )
 
+# from diffpy.morph.morphpy import morphpy
+
 # Support Python 2
 try:
     from future_builtins import filter, zip
@@ -150,7 +152,7 @@ def test_morph_outputs(self, setup, tmp_path):
                     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):
+    def test_morphsqueeze_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"
@@ -192,3 +194,7 @@ def test_morph_squeeze_outputs(self, setup, tmp_path):
                             )
                         else:
                             assert m_row[idx] == t_row[idx]
+
+    def test_morphfuncy_outputs(self, tmp_path):
+        def quadratic(x, y, a0, a1, a2):
+            return a0 + a1 * x + a2 * y**2

tests/test_morphpy.py

@@ -2,7 +2,7 @@
 
 from pathlib import Path
 
-import numpy
+import numpy as np
 import pytest
 
 from diffpy.morph.morphapp import create_option_parser, single_morph
@@ -88,7 +88,7 @@ class Chain:
             chain = Chain()
             rw = getRw(chain)
             del chain
-            assert numpy.allclose(
+            assert np.allclose(
                 [rw], [self.morphapp_results[target_file.name]["Rw"]]
             )
         assert morph_results == self.morphapp_results
@@ -110,11 +110,61 @@ class Chain:
             chain = Chain()
             rw = getRw(chain)
             del chain
-            assert numpy.allclose(
+            assert np.allclose(
                 [rw], [self.morphapp_results[target_file.name]["Rw"]]
             )
         assert morph_results == self.morphapp_results
 
+    def test_morphfuncy(self, setup_morph):
+        def gaussian(x, mu, sigma):
+            return np.exp(-((x - mu) ** 2) / (2 * sigma**2)) / (
+                sigma * np.sqrt(2 * np.pi)
+            )
+
+        def gaussian_like_function(x, y, mu):
+            return gaussian((x + y) / 2, mu, 3)
+
+        morph_r = np.linspace(0, 100, 1001)
+        morph_gr = np.linspace(0, 100, 1001)
+
+        target_r = np.linspace(0, 100, 1001)
+        target_gr = 0.5 * gaussian(target_r, 50, 5) + 0.05
+
+        morph_info, _ = morphpy(
+            np.array([morph_r, morph_gr]).T,
+            np.array([target_r, target_gr]).T,
+            scale=1,
+            vshift=0.01,
+            smear=3.75,
+            funcy=(gaussian_like_function, {"mu": 47.5}),
+            tolerance=1e-12,
+        )
+
+        assert pytest.approx(morph_info["scale"]) == 0.5
+        assert pytest.approx(morph_info["vshift"]) == 0.05
+        assert pytest.approx(abs(morph_info["smear"])) == 4.0
+        assert pytest.approx(morph_info["funcy"]["mu"]) == 50.0
+
+    def test_morphpy_outputs(self, tmp_path):
+        r = np.linspace(0, 1, 11)
+        gr = np.linspace(0, 1, 11)
+
+        def linear(x, y, s):
+            return s * (x + y)
+
+        morph_info, _ = morphpy(
+            np.array([r, gr]).T,
+            np.array([r, gr]).T,
+            squeeze=[1, 2, 3, 4, 5],
+            funcy=(linear, {"s": 2.5}),
+            apply=True,
+        )
+
+        print(morph_info)
+        for i in range(5):
+            assert pytest.approx(morph_info["squeeze"][f"a{i}"]) == i + 1
+        assert pytest.approx(morph_info["funcy"]["s"]) == 2.5
+
 
 if __name__ == "__main__":
     TestMorphpy()