Python interfacing for PDFmorph

doc/source/api/diffpy.morph.rst

@@ -20,10 +20,10 @@ Subpackages
 Submodules
 ----------
 
-diffpy.morph.pdfplot module
+diffpy.morph.plot module
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.morph.pdfplot
+.. automodule:: diffpy.morph.plot
     :members:
     :undoc-members:
     :show-inheritance:

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

@@ -21,7 +21,7 @@
 import diffpy.morph.morph_helpers as helpers
 import diffpy.morph.morph_io as io
 import diffpy.morph.morphs as morphs
-import diffpy.morph.pdfplot as pdfplot
+import diffpy.morph.plot as plot
 import diffpy.morph.refine as refine
 import diffpy.morph.tools as tools
 from diffpy.morph import __save_morph_as__
@@ -403,22 +403,31 @@ 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"
@@ -603,7 +612,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         maglim = opts.maglim
         mag = opts.mag
         l_width = opts.lwidth
-        pdfplot.comparePDFs(
+        plot.comparePDFs(
             pairlist,
             labels,
             rmin=pmin,
@@ -614,10 +623,14 @@ 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:
+        return morph_results, chain.x_morph_out, chain.y_morph_out
+    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:
@@ -782,13 +795,9 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
         else:
             try:
                 if field_list is not None:
-                    pdfplot.plot_param(
-                        field_list, param_list, param_name, field
-                    )
+                    plot.plot_param(field_list, param_list, param_name, field)
                 else:
-                    pdfplot.plot_param(
-                        target_file_names, param_list, param_name
-                    )
+                    plot.plot_param(target_file_names, param_list, param_name)
             # Can occur for non-refined plotting parameters
             # i.e. --smear is not selected as an option, but smear is the
             # plotting parameter
@@ -798,10 +807,14 @@ def multiple_targets(parser, opts, pargs, stdout_flag=True):
                     "morph and target pair. No plot shown."
                 )
 
-    return morph_results
+    if python_wrap:
+        # FIXME: Return dictionary of morphs
+        return morph_results
+    else:
+        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:
@@ -967,13 +980,9 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
         else:
             try:
                 if field_list is not None:
-                    pdfplot.plot_param(
-                        field_list, param_list, param_name, field
-                    )
+                    plot.plot_param(field_list, param_list, param_name, field)
                 else:
-                    pdfplot.plot_param(
-                        morph_file_names, param_list, param_name
-                    )
+                    plot.plot_param(morph_file_names, param_list, param_name)
             # Can occur for non-refined plotting parameters
             # i.e. --smear is not selected as an option, but smear is the
             # plotting parameter
@@ -983,7 +992,11 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
                     "morph and target pair. No plot shown."
                 )
 
-    return morph_results
+    if python_wrap:
+        # FIXME: Return dictionary of morphs
+        return morph_results
+    else:
+        return morph_results
 
 
 def getPDFFromFile(fn):

src/diffpy/morph/morphpy.py

@@ -0,0 +1,151 @@
+#!/usr/bin/env python
+
+import numpy as np
+
+from diffpy.morph.morphapp import (
+    create_option_parser,
+    multiple_morphs,
+    multiple_targets,
+    single_morph,
+)
+
+
+def morph(morph_file, target_file, **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.
+    kwargs: dict
+        See the diffpy.morph manual for options.
+
+    Returns
+    -------
+    dict:
+        Summary of morphs.
+    """
+
+    parser = create_option_parser()
+
+    inputs = []
+    for key, value in kwargs.items():
+        inputs.append(f"--{key}")
+        inputs.append(f"{value}")
+    (opts, pargs) = parser.parse_args(inputs)
+    pargs = [morph_file, target_file]
+
+    return single_morph(
+        parser, opts, pargs, stdout_flag=False, python_wrap=True
+    )
+
+
+def morphpy(
+    morph_table, target_table, morph_header=None, target_header=None, **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.
+    morph_header: dict
+        Any relevant parameters (e.g. wavelength, composition, temperature)
+        for the morphed function.
+    target_header: dict
+        Any relevant parameters for the target ction.
+    kwargs: dict
+        See the diffpy.morph manual for options.
+
+    Returns
+    -------
+    dict:
+        Summary of morphs.
+    """
+
+    parser = create_option_parser()
+
+    inputs = []
+    for key, value in kwargs.items():
+        inputs.append(f"--{key}")
+        inputs.append(f"{value}")
+    (opts, pargs) = parser.parse_args(inputs)
+
+    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]
+    print(pargs)
+
+    return single_morph(
+        parser, opts, pargs, stdout_flag=False, python_wrap=True
+    )
+
+
+def morph_multiple_targets(file, dir, **kwargs):
+    """Run diffpy.morph with multiple targets at Python level.
+
+    Parameters
+    ----------
+    file1: str
+        Path-like object to the file to be morphed.
+    file2: str
+        Path-like object to the target file.
+    kwargs: dict
+        See the diffpy.morph manual for options.
+
+    Returns
+    -------
+    dict:
+        Summary of morphs.
+    """
+
+    parser = create_option_parser()
+
+    inputs = []
+    for key, value in kwargs.items():
+        inputs.append(f"--{key}")
+        inputs.append(f"{value}")
+    (opts, pargs) = parser.parse_args(inputs)
+    pargs = [file, dir]
+
+    return multiple_targets(parser, opts, pargs)
+
+
+def morph_multiple_morphs(dir, file, **kwargs):
+    """Run diffpy.morph with multiple files morphed at Python level.
+
+    Parameters
+    ----------
+    file1: str
+        Path-like object to the file to be morphed.
+    file2: str
+        Path-like object to the target file.
+    kwargs: dict
+        See the diffpy.morph manual for options.
+
+    Returns
+    -------
+    dict:
+        Summary of morphs.
+    """
+
+    parser = create_option_parser()
+
+    inputs = []
+    for key, value in kwargs.items():
+        inputs.append(f"--{key}")
+        inputs.append(f"{value}")
+    (opts, pargs) = parser.parse_args(inputs)
+    pargs = [dir, file]
+
+    return multiple_morphs(parser, opts, pargs)