#!/usr/bin/env python
##############################################################################
#
# diffpy.pdfmorph 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.
#
##############################################################################
"""Tools used in morphs and morph chains.
"""
import numpy
import diffpy.utils.parsers as parsers
[docs]
def estimateScale(y_morph_in, y_target_in):
"""Set the scale that best matches the morph to the target."""
dot = numpy.dot
scale = dot(y_morph_in, y_target_in) / dot(y_morph_in, y_morph_in)
return scale
[docs]
def estimateBaselineSlope(r, gr, rmin=None, rmax=None):
"""Estimate the slope of the linear baseline of a PDF.
This fits a slope into the equation slope*r through the bottom of the PDF.
Parameters
----------
r
The r-grid used for the PDF.
gr
The PDF over the r-grid.
rmin
The minimum r-value to consider. If this is None (default) is None, then the minimum of r is used.
rmax
The maximum r-value to consider. If this is None (default) is None, then the maximum of r is used.
Returns
-------
slope: float
The slope of baseline. If the PDF is scaled properly, this is equal to -4*pi*rho0.
"""
from numpy import dot
from scipy.optimize import leastsq
rp = r.copy()
grp = gr.copy()
if rmax is not None:
grp = grp[rp <= rmax]
rp = rp[rp <= rmax]
if rmin is not None:
grp = grp[rp >= rmin]
rp = rp[rp >= rmin]
def chiv(pars):
slope = pars[0]
# This tries to fit the baseline through the center of the PDF.
chiv = grp - slope * rp
# This adds additional penalty if there are negative terms, that
# is, if baseline > PDF.
diff = chiv.copy()
diff[diff > 0] = 0
negpenalty = dot(diff, diff)
chiv *= 1 + 0.5 * negpenalty
return chiv
# Optimize to get the best slope
slope, ier = leastsq(chiv, [0.0])
# Return the slope
return slope
[docs]
def getRw(chain):
"""Get Rw from the outputs of a morph or chain."""
# Make sure we put these on the proper grid
x_morph, y_morph, x_target, y_target = chain.xyallout
diff = y_target - y_morph
rw = numpy.dot(diff, diff)
rw /= numpy.dot(y_target, y_target)
rw = rw**0.5
return rw
[docs]
def get_pearson(chain):
from scipy.stats import pearsonr
x_morph, y_morph, x_target, y_target = chain.xyallout
pcc, pval = pearsonr(y_morph, y_target)
return pcc
[docs]
def readPDF(fname):
"""Reads an .gr file, loads r and G(r) vectors.
Parameters
----------
fname
Name of the file we want to read.
Returns
-------
r,gr
Arrays read from data.
"""
from diffpy.utils.parsers import loadData
rv = loadData(fname, unpack=True)
if len(rv) >= 2:
return rv[:2]
return (None, None)
[docs]
def nn_value(val, name):
"""Convenience function for ensuring certain non-negative inputs."""
if val < 0:
negative_value_warning = f"\n# Negative value for {name} given. Using absolute value instead."
print(negative_value_warning)
return -val
return val
[docs]
def deserialize(serial_file):
"""Call deserialize_data from diffpy.utils.
Parameters
----------
serial_file
Name of file to deserialize.
Returns
-------
dict
Data read from serial file.
"""
return parsers.deserialize_data(serial_file)
[docs]
def case_insensitive_dictionary_search(key: str, dictionary: dict):
"""Search for key in dictionary ignoring case.
Parameters
----------
key: str
dictionary: dict
Returns
-------
value or None
Corresponding value if key is in dictionary. None otherwise.
"""
for ci_key in dictionary.keys():
if key.lower() == ci_key.lower():
key = ci_key
break
return dictionary.get(key)
[docs]
def field_sort(filepaths: list, field, reverse=False, serfile=None, get_field_values=False):
"""Sort a list of files by a field stored in header information.
All files must contain this header information.
Parameters
----------
filepaths
List of paths to files that we want to sort.
field
The field we want to sort by. Not case-sensitive.
reverse
Sort in reverse alphabetical/numerical order.
serfile
Path to a serial file with field information for each file.
get_field_values: bool
Boolean indicating whether to also return a List of field values (default False).
This List of field values is parallel to the sorted list of filepaths with items
in the same position corresponding to each other.
Returns
-------
list
Sorted list of paths. When get_fv is true, also return an associated field list.
"""
# Get the field from each file
files_field_values = []
if serfile is None:
for path in filepaths:
fhd = parsers.loadData(path, headers=True)
files_field_values.append([path, case_insensitive_dictionary_search(field, fhd)])
else:
# deserialize the serial file
des_dict = parsers.deserialize_data(serfile)
# get names of each file to search the serial file
import pathlib
for path in filepaths:
name = pathlib.Path(path).name
fv = case_insensitive_dictionary_search(field, des_dict.get(name))
files_field_values.append([path, fv])
# Sort files by field, reverse if reverse flag true
try:
files_field_values.sort(key=lambda entry: entry[1], reverse=reverse)
# Raised if fields for any file are missing
except (ValueError, TypeError):
raise KeyError("Field missing.")
if get_field_values:
return [pair[0] for pair in files_field_values], [pair[1] for pair in files_field_values]
else:
return [pair[0] for pair in files_field_values]
[docs]
def get_values_from_dictionary_collection(dictionary_collection: iter, target_key):
"""In an (iterable) collection of dictionaries, search for a target key in each dictionary.
Return a list of all found values corresponding to that key.
Parameters
----------
dictionary_collection: iter
The collection of dictionaries to search through.
target_key
The key to search for in each dictionary. For each dictionary in dictionary_collection that has that key,
the corresponding value is appended to a List called values.
Returns
-------
list
The found values.
"""
# Store all values corresponding to the target_key into this list
values = []
# Handle dictionary-type iterable
if type(dictionary_collection) is dict:
# Assume the dictionaries are stored in the values and keys indicate names of the dictionaries
dictionary_collection = dictionary_collection.values()
# All other type iterables are handled the same way as a list
# Perform the (case-insensitive) search
for entry in dictionary_collection:
search_result = case_insensitive_dictionary_search(target_key, entry)
if search_result is not None:
values.append(search_result)
return values