Python Interfacing for PDFmorph (Clean Branch)

news/morphpy.rst

@@ -0,0 +1,24 @@
+**Added:**
+
+* Python interfacing to call PDFmorph
+* Returns dictionary of morph metrics (dict) and the r, gr pair for plotting or further manipulation
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morphapp.py

@@ -18,6 +18,8 @@
 import sys
 from pathlib import Path
 
+import numpy
+
 import diffpy.morph.morph_helpers as helpers
 import diffpy.morph.morph_io as io
 import diffpy.morph.morphs as morphs
@@ -403,22 +405,31 @@ def custom_error(self, msg):
     return parser
 
 
-def single_morph(parser, opts, pargs, stdout_flag=True):
+def single_morph(parser, opts, pargs, stdout_flag=True, python_wrap=False):
     if len(pargs) < 2:
         parser.error("You must supply FILE1 and FILE2.")
-    elif len(pargs) > 2:
+    elif len(pargs) > 2 and not python_wrap:
         parser.error(
             "Too many arguments. Make sure you only supply FILE1 and FILE2."
         )
+    elif not (len(pargs) == 2 or len(pargs) == 6) and python_wrap:
+        parser.error("Python wrapper error.")
 
     # Get the PDFs
-    x_morph, y_morph = getPDFFromFile(pargs[0])
-    x_target, y_target = getPDFFromFile(pargs[1])
+    # If we get from python, we may wrap, which has input size 4
+    if len(pargs) == 6 and python_wrap:
+        x_morph = pargs[2]
+        y_morph = pargs[3]
+        x_target = pargs[4]
+        y_target = pargs[5]
+    else:
+        x_morph, y_morph = getPDFFromFile(pargs[0])
+        x_target, y_target = getPDFFromFile(pargs[1])
 
     if y_morph is None:
-        parser.error(f"No data table found in file: {pargs[0]}.")
+        parser.error(f"No data table found in: {pargs[0]}.")
     if y_target is None:
-        parser.error(f"No data table found in file: {pargs[1]}.")
+        parser.error(f"No data table found in: {pargs[1]}.")
 
     # Get configuration values
     scale_in = "None"
@@ -614,10 +625,16 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
             l_width=l_width,
         )
 
-    return morph_results
+    # Return different things depending on whether it is python interfaced
+    if python_wrap:
+        morph_info = morph_results
+        morph_table = numpy.array([chain.x_morph_out, chain.y_morph_out]).T
+        return morph_info, morph_table
+    else:
+        return morph_results
 
 
-def multiple_targets(parser, opts, pargs, stdout_flag=True):
+def multiple_targets(parser, opts, pargs, stdout_flag=True, python_wrap=False):
     # Custom error messages since usage is distinct when --multiple tag is
     # applied
     if len(pargs) < 2:
@@ -800,7 +817,7 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
     return morph_results
 
 
-def multiple_morphs(parser, opts, pargs, stdout_flag=True):
+def multiple_morphs(parser, opts, pargs, stdout_flag=True, python_wrap=False):
     # Custom error messages since usage is distinct when --multiple tag is
     # applied
     if len(pargs) < 2:

src/diffpy/morph/morphpy.py

@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+
+import numpy as np
+
+from diffpy.morph.morphapp import create_option_parser, single_morph
+
+
+def get_args(parser, params, kwargs):
+    inputs = []
+    for key, value in params.items():
+        if value is not None:
+            inputs.append(f"--{key}")
+            inputs.append(f"{value}")
+    for key, value in kwargs.items():
+        key = key.replace("_", "-")
+        inputs.append(f"--{key}")
+        inputs.append(f"{value}")
+    (opts, pargs) = parser.parse_args(inputs)
+    return opts, pargs
+
+
+def morph(
+    morph_file,
+    target_file,
+    scale=None,
+    stretch=None,
+    smear=None,
+    plot=False,
+    **kwargs,
+):
+    """Run diffpy.morph at Python level.
+    Parameters
+    ----------
+    morph_file: str
+        Path-like object to the file to be morphed.
+    target_file: str
+        Path-like object to the target file.
+    scale: float, optional
+        Initial guess for the scaling parameter.
+        Refinement is done only for parameter that are not None.
+    stretch: float, optional
+        Initial guess for the stretching parameter.
+    smear: float, optional
+        Initial guess for the smearing parameter.
+    plot: bool
+        Show a plot of the morphed and target functions as well as the
+        difference curve (default: False).
+    kwargs: dict
+        See the diffpy.morph website for full list of options.
+    Returns
+    -------
+    morph_info: dict
+        Summary of morph parameters (e.g. scale, stretch, smear, rmin, rmax)
+        and results (e.g. Pearson, Rw).
+    morph_table: list
+        Function after morph where morph_table[:,0] is the abscissa and
+        morph_table[:,1] is the ordinate.
+    """
+
+    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)
+
+    pargs = [morph_file, target_file]
+
+    return single_morph(
+        parser, opts, pargs, stdout_flag=False, python_wrap=True
+    )
+
+
+def morphpy(
+    morph_table,
+    target_table,
+    scale=None,
+    stretch=None,
+    smear=None,
+    plot=False,
+    **kwargs,
+):
+    """Run diffpy.morph at Python level.
+    Parameters
+    ----------
+    morph_table: numpy.array
+        Two-column array of (r, gr) for morphed function.
+    target_table: numpy.array
+        Two-column array of (r, gr) for target function.
+    scale: float, optional
+        Initial guess for the scaling parameter.
+        Refinement is done only for parameter that are not None.
+    stretch: float, optional
+        Initial guess for the stretching parameter.
+    smear: float, optional
+        Initial guess for the smearing parameter.
+    plot: bool
+        Show a plot of the morphed and target functions as well as the
+        difference curve (default: False).
+    kwargs: dict
+        See the diffpy.morph website for full list of options.
+    Returns
+    -------
+    morph_info: dict
+        Summary of morph parameters (e.g. scale, stretch, smear, rmin, rmax)
+        and results (e.g. Pearson, Rw).
+    morph_table: list
+        Function after morph where morph_table[:,0] is the abscissa and
+        morph_table[:,1] is the ordinate.
+    """
+
+    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)
+
+    morph_table = np.array(morph_table)
+    target_table = np.array(target_table)
+
+    x_morph = morph_table[:, 0]
+    y_morph = morph_table[:, 1]
+    x_target = target_table[:, 0]
+    y_target = target_table[:, 1]
+
+    pargs = ["Morph", "Target", x_morph, y_morph, x_target, y_target]
+
+    return single_morph(
+        parser, opts, pargs, stdout_flag=False, python_wrap=True
+    )

tests/test_morphpy.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+from pathlib import Path
+
+import numpy
+import pytest
+
+from diffpy.morph.morphapp import create_option_parser, single_morph
+from diffpy.morph.morphpy import morph, morphpy
+from diffpy.morph.tools import getRw
+
+thisfile = locals().get("__file__", "file.py")
+tests_dir = Path(thisfile).parent.resolve()
+testdata_dir = tests_dir.joinpath("testdata")
+testsequence_dir = testdata_dir.joinpath("testsequence")
+
+nickel_PDF = testdata_dir.joinpath("nickel_ss0.01.cgr")
+serial_JSON = testdata_dir.joinpath("testsequence_serialfile.json")
+
+testsaving_dir = testsequence_dir.joinpath("testsaving")
+test_saving_succinct = testsaving_dir.joinpath("succinct")
+test_saving_verbose = testsaving_dir.joinpath("verbose")
+tssf = testdata_dir.joinpath("testsequence_serialfile.json")
+
+
+class TestMorphpy:
+    @pytest.fixture
+    def setup_morph(self):
+        self.parser = create_option_parser()
+        filenames = [
+            "g_174K.gr",
+            "f_180K.gr",
+            "e_186K.gr",
+            "d_192K.gr",
+            "c_198K.gr",
+            "b_204K.gr",
+            "a_210K.gr",
+        ]
+        self.testfiles = []
+        self.morphapp_results = {}
+
+        # Parse arguments sorting by field
+        (opts, pargs) = self.parser.parse_args(
+            [
+                "--scale",
+                "1",
+                "--stretch",
+                "0",
+                "-n",
+                "--sort-by",
+                "temperature",
+            ]
+        )
+        for filename in filenames:
+            self.testfiles.append(testsequence_dir.joinpath(filename))
+
+            # Run multiple single morphs
+            morph_file = self.testfiles[0]
+            for target_file in self.testfiles[1:]:
+                pargs = [morph_file, target_file]
+                # store in same format of dictionary as multiple_targets
+                self.morphapp_results.update(
+                    {
+                        target_file.name: single_morph(
+                            self.parser, opts, pargs, stdout_flag=False
+                        )
+                    }
+                )
+        return
+
+    def test_morph(self, setup_morph):
+        morph_results = {}
+        morph_file = self.testfiles[0]
+        for target_file in self.testfiles[1:]:
+            mr, grm = morph(
+                morph_file,
+                target_file,
+                scale=1,
+                stretch=0,
+                sort_by="temperature",
+            )
+            _, grt = morph(target_file, target_file)
+            morph_results.update({target_file.name: mr})
+
+            class Chain:
+                xyallout = grm[:, 0], grm[:, 1], grt[:, 0], grt[:, 1]
+
+            chain = Chain()
+            rw = getRw(chain)
+            del chain
+            assert numpy.allclose(
+                [rw], [self.morphapp_results[target_file.name]["Rw"]]
+            )
+        assert morph_results == self.morphapp_results
+
+    def test_morphpy(self, setup_morph):
+        morph_results = {}
+        morph_file = self.testfiles[0]
+        for target_file in self.testfiles[1:]:
+            _, grm0 = morph(morph_file, morph_file)
+            _, grt = morph(target_file, target_file)
+            mr, grm = morphpy(
+                grm0, grt, scale=1, stretch=0, sort_by="temperature"
+            )
+            morph_results.update({target_file.name: mr})
+
+            class Chain:
+                xyallout = grm[:, 0], grm[:, 1], grt[:, 0], grt[:, 1]
+
+            chain = Chain()
+            rw = getRw(chain)
+            del chain
+            assert numpy.allclose(
+                [rw], [self.morphapp_results[target_file.name]["Rw"]]
+            )
+        assert morph_results == self.morphapp_results
+
+
+if __name__ == "__main__":
+    TestMorphpy()