Merge pull request #34 from 8bitsam/cookie-src

Cookiecutting - src directory

Author: sbillinge

src/diffpy/__init__.py

@@ -0,0 +1,23 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""Blank namespace package for module diffpy."""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file

src/diffpy/pdffit2/__init__.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2024 The Trustees of Columbia University in the City of New York.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################
+
+"""PDFfit2 - real space structure refinement program."""
+
+# package version
+from diffpy.pdffit2.version import __version__
+
+# silence the pyflakes syntax checker
+assert __version__ or True
+
+# End of file

src/diffpy/pdffit2/ipy_ext.py

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+#!/usr/bin/env python
+
+"""This module defines functions within IPython session to simulate
+the old pdffit2 interactive session.
+
+Usage: %load_ext diffpy.pdffit2.ipy_ext
+"""
+
+
+def load_ipython_extension(ipython):
+    from diffpy.pdffit2 import PdfFit
+
+    pf = PdfFit()
+    pdf = EasyPDFPlotting(pf)
+    print("        Type  help(pdffit)  or  help(topic)  for information.\n")
+    ns = dict(pdffit=PdfFit, pdf=pdf)
+    pf._exportAll(ns)
+    ipython.user_ns.update(ns)
+    return
+
+
+class EasyPDFPlotting(object):
+    """Convenience functions for accessing and plotting PDFfit2 data."""
+
+    def __init__(self, pdffit_instance):
+        self._pdffit = pdffit_instance
+        return
+
+    @property
+    def r(self):
+        "R-grid for PDF simulation."
+        return self._asarray(self._pdffit.getR(), dtype=float)
+
+    @property
+    def Gobs(self):
+        "Observed PDF data."
+        return self._asarray(self._pdffit.getpdf_obs(), dtype=float)
+
+    @property
+    def Gcalc(self):
+        "Calculated PDF data."
+        return self._asarray(self._pdffit.getpdf_fit())
+
+    @property
+    def Gdiff(self):
+        "Difference between the observed and simulated PDF."
+        return self.Gobs - self.Gcalc
+
+    def showfit(self, offset=None):
+        """Plot observed and simulated PDFs and the difference curve.
+
+        offset   -- offset for the difference curve.
+
+        No return value.
+        """
+        from math import floor
+
+        from matplotlib.pyplot import gca
+
+        cr = self.r
+        cGobs = self.Gobs
+        cGcalc = self.Gcalc
+        cGdiff = self.Gdiff
+        if offset is None:
+            offset = floor(min([min(cGobs), min(cGcalc)]) - max(cGdiff))
+        ax = gca()
+        ax.plot(cr, cGobs, "r.", cr, cGcalc, "b-", cr, cGdiff + offset, "g-")
+        xl = ax.xaxis.get_label().get_text()
+        yl = ax.yaxis.get_label().get_text()
+        if xl == "":
+            ax.set_xlabel("r (A)")
+        if yl == "":
+            ax.set_ylabel("G (A**-2)")
+        return
+
+    def showRw(self):
+        "Plot cumulative Rw."
+        from matplotlib.pyplot import gca
+
+        cRw = self._asarray(self._pdffit.getcrw())
+        ax = gca()
+        ax.plot(self.r, cRw)
+        ax.set_title("Cumulative Rw = %.4f" % cRw[-1])
+        ax.set_xlabel("r")
+        ax.set_ylabel("Rw")
+        return
+
+    @staticmethod
+    def _asarray(x, dtype=None):
+        import numpy
+
+        return numpy.asarray(x, dtype=dtype)
+
+
+# End of class EasyPDFPlotting

src/diffpy/pdffit2/output.py

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+#!/usr/bin/env python
+##############################################################################
+#
+# pdffit2           by DANSE Diffraction group
+#                   Simon J. L. Billinge
+#                   (c) 2007 trustees of the Michigan State University.
+#                   All rights reserved.
+#
+# File coded by:    Pavol Juhas
+#
+# See AUTHORS.txt for a list of people who contributed.
+# See LICENSE.txt for license information.
+#
+##############################################################################
+
+"""Take care of sending engine output to given file-like object.
+The output file is stored in local module variable stdout.
+"""
+
+
+# create module variable stdout
+
+from sys import stdout as stdout
+
+# silence pyflakes checker
+assert stdout
+
+
+def redirect_stdout(dst):
+    """Redirect PDFfit2 standard output to a file-like object dst.
+    The dst value is stored in module variable stdout.
+    """
+    from diffpy.pdffit2.pdffit2 import redirect_stdout
+
+    redirect_stdout(dst)
+    global stdout
+    stdout = dst
+    return
+
+
+#  End of file