Skip to content

Commit 195ee48

Browse files
committed
chore: fix long description in readme and license info
1 parent 195b302 commit 195ee48

2 files changed

Lines changed: 60 additions & 7 deletions

File tree

README.rst

Lines changed: 41 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -36,18 +36,54 @@
3636
.. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
3737
:target: https://github.com/diffpy/diffpy.srmise/issues
3838

39-
Peak extraction and peak fitting tool for atomic pair distribution functions.
40-
41-
* LONGER DESCRIPTION HERE
39+
Implementation of the ParSCAPE algorithm for peak extraction from atomic pair distribution functions (PDFs)
40+
41+
SrMise is an implementation of the `ParSCAPE algorithm
42+
<https://dx.doi.org/10.1107/S2053273315005276>`_ for peak extraction from
43+
atomic pair distribution functions (PDFs). It is designed to function even
44+
when *a priori* knowledge of the physical sample is limited, utilizing the
45+
Akaike Information Criterion (AIC) to estimate whether peaks are
46+
statistically justified relative to alternate models. Three basic use cases
47+
are anticipated for SrMise. The first is peak fitting a user-supplied
48+
collections of peaks. The second is peak extraction from a PDF with no (or
49+
only partial) user-supplied peaks. The third is an AIC-driven multimodeling
50+
analysis where the output of multiple SrMise trials are ranked.
51+
52+
The framework for peak extraction defines peak-like clusters within the data,
53+
extracts a single peak within each cluster, and iteratively combines nearby
54+
clusters while performing a recursive search on the residual to identify
55+
occluded peaks. Eventually this results in a single global cluster
56+
containing many peaks fit over all the data. Over- and underfitting are
57+
discouraged by use of the AIC when adding or, during a pruning step, removing
58+
peaks. Termination effects, which can lead to physically spurious peaks in
59+
the PDF, are incorporated in the mathematical peak model and the pruning step
60+
attempts to remove peaks which are fit better as termination ripples due to
61+
another peak.
62+
63+
Where possible, SrMise provides physically reasonable default values
64+
for extraction parameters. However, the PDF baseline should be estimated by
65+
the user before extraction, or by performing provisional peak extraction with
66+
varying baseline parameters. The package defines a linear (crystalline)
67+
baseline, arbitrary polynomial baseline, a spherical nanoparticle baseline,
68+
and an arbitrary baseline interpolated from a list of user-supplied values.
69+
In addition, PDFs with accurate experimentally-determined uncertainties are
70+
necessary to provide the most reliable results, but historically such PDFs
71+
are rare. In the absence of accurate uncertainties an *ad hoc* uncertainty
72+
must be specified.
4273

4374
For more information about the diffpy.srmise library, please consult our `online documentation <https://diffpy.github.io/diffpy.srmise>`_.
4475

4576
Citation
4677
--------
4778

48-
If you use diffpy.srmise in a scientific publication, we would like you to cite this package as
79+
If you use this program for a scientific research that leads
80+
to publication, we ask that you acknowledge use of the program
81+
by citing the following paper in your publication:
4982

50-
diffpy.srmise Package, https://github.com/diffpy/diffpy.srmise
83+
L. Granlund, S. J. L. Billinge and P. M. Duxbury,
84+
`Algorithm for systematic peak extraction from atomic pair distribution functions
85+
<http://dx.doi.org/10.1107/S2053273315005276>`__,
86+
*Acta Crystallogr. A* **4**, 392-409 (2015).
5187

5288
Installation
5389
------------

docs/source/license.rst

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,8 +9,25 @@ OPEN SOURCE LICENSE AGREEMENT
99
=============================
1010
BSD 3-Clause License
1111

12-
Copyright (c) 2026, The Trustees of Columbia University in the City of New York.
13-
All Rights Reserved.
12+
Copyright 2014-2015, Board of Trustees of Michigan State University
13+
14+
Copyright 2016-2026, The Trustees of Columbia University in the City of New York.
15+
16+
All rights reserved.
17+
18+
If you use this program to do productive scientific research that
19+
leads to publication, we ask that you acknowledge use of the
20+
program by citing the following paper in your publication:
21+
22+
L. Granlund, S.J.L. Billinge, P.M. Duxbury, Algorithm for
23+
systematic peak extraction from atomic pair distribution
24+
functions, Acta Crystallographica A 71(4), 392-409 (2015).
25+
doi:10.1107/S2053273315005276
26+
27+
For more information please visit the diffpy web-page at
28+
http://www.diffpy.org
29+
or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
30+
Billinge at sb2896@columbia.edu.
1431

1532
Redistribution and use in source and binary forms, with or without
1633
modification, are permitted provided that the following conditions are met:

0 commit comments

Comments
 (0)