#!/usr/bin/env python
##############################################################################
#
# diffpy.morph by DANSE Diffraction group
# Simon J. L. Billinge
# (c) 2010 Trustees of the Columbia University
# in the City of New York. All rights reserved.
#
# File coded by: Chris Farrow
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################
"""Class MorphSmear -- smear the morph."""
import numpy
from diffpy.morph.morphs.morph import LABEL_RA, LABEL_RR, Morph
[docs]
class MorphSmear(Morph):
"""Smear the morph function.
This smears (broadens) the peaks of the morph. Note that this operates
on the RDF. Inputs are not automatically converted to the RDF.
Configuration Variables
-----------------------
smear
The smear factor to apply to y_morph_in.
"""
# Define input output types
summary = "Smear morph by desired amount"
xinlabel = LABEL_RA
yinlabel = LABEL_RR
xoutlabel = LABEL_RA
youtlabel = LABEL_RR
parnames = ["smear"]
[docs]
def morph(self, x_morph, y_morph, x_target, y_target):
"""Resample arrays onto specified grid."""
Morph.morph(self, x_morph, y_morph, x_target, y_target)
if self.smear == 0:
return self.xyallout
# The Gaussian to convolute with. No need to normalize, we'll do that
# later.
r = self.x_morph_in
rr = self.y_morph_in
r0 = r[len(r) // 2]
gaussian = numpy.exp(-0.5 * ((r - r0) / self.smear) ** 2)
# Get the full convolution
c = numpy.convolve(rr, gaussian, mode="full")
# Find the centroid of the RDF, we don't want this to change from the
# convolution.
x1 = numpy.arange(len(rr), dtype=float)
c1idx = numpy.sum(rr * x1) / sum(rr)
# Find the centroid of the convolution
xc = numpy.arange(len(c), dtype=float)
ccidx = numpy.sum(c * xc) / sum(c)
# Interpolate the convolution such that the centroids line up. This
# uses linear interpolation.
shift = ccidx - c1idx
x1 += shift
rrbroad = numpy.interp(x1, xc, c)
# Normalize so that the integrated magnitude of the RDF doesn't change.
rrbroad /= sum(gaussian)
self.y_morph_out = rrbroad
return self.xyallout
# End of class MorphSmear