Pdfmorph web-page

_templates/menu01.html

@@ -14,6 +14,7 @@
       <li><a href="{{pathto('products/SrMise')}}">SrMise</a></li>
       <li><a href="{{pathto('products/mPDF')}}">mPDF</a></li>
       <li><a href="{{pathto('products/xinterpdf')}}">xINTERPDF</a></li>
+      <li><a href="{{pathto('products/pdfmorph')}}">PDFmorph</a></li>
       <li><a href="{{pathto('products/pythonpackages')}}">Python Packages</a></li>
   </ul>
 </li>

index.rst

@@ -86,3 +86,4 @@ centered at Columbia University and, before that, Michigan State University.
    products/SrMise
    products/mPDF
    products/xinterpdf
+   products/pdfmorph

products/pdfmorph.rst

@@ -0,0 +1,143 @@
+.. include:: ../abbreviations.txt
+
+########
+PDFmorph
+########
+
+Overview
+========
+
+.. note::
+
+	PDFmorph is currently run from the command line, which requires
+	opening and typing into a terminal window or Windows command
+	prompt. It is recommended that you consult online resources and
+	become somewhat familiar before using PDFmorph.
+
+PDFmorph is a Python software package designed to increase the insight
+researchers can obtain from measured atomic pair distribution functions
+(PDFs) in a model-independent way. The program was designed to help a
+researcher answer the question: "Has my material undergone a phase
+transition between these two measurements?"
+
+PDFmorph makes use of several data manipulation techniques to correct
+for benign effects such as thermal expansion (peak shift) and increased
+thermal motion (peak broadening) or a cahnge in scale due to differences
+in incident flux, for example. PDFmorph will do its best to correct
+for these benign effects before computing and plotting a difference
+curve.
+
+One PDF (typically that collected at higher temperature) is identified
+as the "target" PDF and the second is "morphed" by "stretching" (changing
+the r-axis to simulate a uniform lattice expansion), "smearing"
+(broadening peaks through a uniform convolution to simulate increased
+thermal motion), and "scaling" (self-explanatory). PDFmorph will vary
+amplitude of morphing transformations to obtain the best fit between
+morphed and target PDFs, then plot them along with the difference curve
+plotted below.
+
+There are also a few other morphing transformations in the program.
+
+Finally, we note that PDFmorph should work on other spectra that are
+not PDFs, though it has not been extensively tested beyond the PDF.
+
+.. PDFmorph will soon be included in :doc:`xPDFsuite <xPDFsuite>`, a powerful end-to-end software for X-ray PDF analysis. xPDFsuite is designed for flexible, high throughput PDF analyses and contains many features for interrogating, comparing, and modeling data as well as simply doing data reduction.
+
+.. figure:: ../images/pdfmorph_nacl_ex.png
+	:align: center
+
+	Transformation techniques (scale, smear, and stretch, respectively)
+	utilized by PDFmorph applied sequentially on an NaCl sample
+
+
+Installation
+============
+
+By downloading and using this software, you are agreeing to the conditions
+specified in the :doc:`software license <pdfmorph_license>`.
+
+PDFmorph will run on Python 2.7 or higher, but here we give instructions
+for installing the Python 3 version in a conda environment.
+
+.. note::
+	PDFmorph is distributed and best installed using conda. It should
+	run in most Python 3 environments and can be directly installed
+	in an existing environment (using the commands listed below). If
+	you do not currently have conda installed, here are some
+	lightweight instructions for getting started:
+
+		1.) Download and install *Anaconda* or *mini-conda* from
+		`continuum <https://www.continuum.io>`__.
+
+		2.) Create a Python 3 environment with the command ::
+
+			conda create --name=<env_name> python=3
+
+	You can give the environment any name you like.
+	You only need to create the environment once, but every time you
+	want to use PDFmorph you will have to reactivate the environment
+	in which it is installed by opening a terminal and typing ::
+
+		source activate <env_name>
+
+	on Mac/Linux, or ``activate <env_name>`` on Windows.
+
+Once you're in your desired conda environment, you can install PDFmorph
+from either the ``diffpy`` or ``conda-forge`` channels of Anaconda packages
+by running opening a *Terminal* window or *Command Prompt*
+on Windows and using the :program:`conda` command ::
+
+	conda config --add channels conda-forge
+	conda install diffpy.pdfmorph
+
+If you prefer to install from the diffpy channel, simply replace
+``conda-forge`` with ``diffpy`` in the commands above.
+
+By then it should be installed! To make sure that installation has
+completed correctly, run the following command from your PDFmorph-equipped
+conda environment ::
+
+	pdfmorph --version
+
+This command should return the version of PDFmorph you have on your
+machine.
+
+
+PDFmorph Updates
+================
+
+The Anaconda package system makes it easy to prepare and distribute
+software packages and bugfixes. To update the latest version of PDFmorph,
+use ::
+
+	conda update diffpy.pdfmorph
+
+With other Python distributions, the program can be updated to the
+latest version with ::
+
+	easy_install --upgrade diffpy.pdfmorph
+
+To use a development version, visit the project source repository at
+https://github.com/diffpy/diffpy.pdfmorph and consult its README file.
+
+
+Documentation/Help
+==================
+
+0.1.0 - latest
+----------------------
+
+* User manual (available in HTML and PDF)
+* Installation instructions
+* `Sample PDF files <https://github.com/diffpy/diffpy.pdfmorph/tree/master/tests/testdata>`__
+* Tutorial
+* Please, join the :doc:`community forum <../community>` for tips,
+  tricks, and feedback.
+
+
+.. References// # update upon paper resease
+
+.. toctree::
+    :hidden:
+
+    pdfmorph_license

products/pdfmorph_license.rst

@@ -0,0 +1,6 @@
+.. This page only contains the LICENSE text for PDFmorph
+
+.. title:: PDFmorph License
+
+.. literalinclude:: pdfmorph_license.txt
+   :language: text

products/pdfmorph_license.txt

@@ -0,0 +1,36 @@
+This program is part of the DiffPy open-source project at Columbia
+University and is available subject to the conditions and terms laid
+out below.
+
+Copyright © 2009-2019, Trustees of Columbia University in the City of
+New York, all rights reserved.
+
+For more information please visit the diffpy web-page at
+http://diffpy.org or email Prof. Simon Billinge at [email protected].
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+  * Redistributions of source code must retain the above copyright
+    notice, this list of conditions and the following disclaimer.
+
+  * Redistributions in binary form must reproduce the above copyright
+    notice, this list of conditions and the following disclaimer in the
+    documentation and/or other materials provided with the distribution.
+
+  * The name of COLUMBIA UNIVERSITY nor the names of its contributors
+    may be used to endorse or promote products derived from this
+    software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

products/pythonpackages.rst

@@ -4,8 +4,8 @@ Python Packages
 This is a complete list of all Python packages developed by the DiffPy
 team. For more information about a specific package, follow the link to
 the corresponding github page. With the exception of PDFfit2, SrMise,
-and mPDF, all of the packages listed below are bundled in the |DiffPyCMI|
-release.
+mPDF, and PDFmorph, all of the packages listed below are bundled in the
+|DiffPyCMI| release.
 
 ======================      ============================================
 Module                      Description
@@ -37,11 +37,16 @@ Module                      Description
 
 `diffpy.mpdf`_              Tools for calculating and refining magnetic
                             PDFs.
+
+`diffpy.pdfmorph`_          Tools for comparing and manipulating two
+                            PDFs.
+
 ======================      ============================================
 
 .. URL definitions below -----------------------------------------------
 
 .. _diffpy.srmise: https://github.com/diffpy/diffpy.srmise
 .. _diffpy.pdffit2: https://github.com/diffpy/diffpy.pdffit2
+.. _diffpy.pdfmorph: https://github.com/diffpy/diffpy.pdfmorph
 
 .. include:: ../abbreviations.txt