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Copy file name to clipboardExpand all lines: products/pdfmorph.rst
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========
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.. note::
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The PDFmorph application has a Command Line Interface. If you
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are unfamiliar with the terminal or windows command prompt, it
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is recommended that you consult online resources and become
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somewhat familiar before using PDFmorph.
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PDFmorph is a Python software package designed to increase the insight
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researchers can obtain from measured atomic pair distribution functions
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(PDFs) in a model-independent way. The program was designed to help a
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researcher answer the question: Has my material undergone a phase
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transition between these two measurements?
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PDFmorph makes use of several data manipulation techniques to correct
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for benign effects such as thermal expansion and increased thermal
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motion before computing and plotting a difference curve between two PDFs.
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One PDF is identified as the "target" PDF and the second is "morphed"
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by "stretching", "smearing", and "scaling". PDFmorph will vary amplitude
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of morphing transformations to obtain the best fit between morphed and
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target PDFs, then plot them along with the difference curve plotted
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below.
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PDFmorph is currently run from the command line, which requires
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opening and typing into a terminal window or Windows command
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prompt. It is recommended that you consult online resources and
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become somewhat familiar before using PDFmorph.
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PDFmorph is a Python software package designed to increase the insight
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researchers can obtain from measured atomic pair distribution functions
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(PDFs) in a model-independent way. The program was designed to help a
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researcher answer the question: "Has my material undergone a phase
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transition between these two measurements?"
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PDFmorph makes use of several data manipulation techniques to correct
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for benign effects such as thermal expansion (peak shift) and increased
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thermal motion (peak broadening) or a cahnge in scale due to differences
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in incident flux, for example. PDFmorph will do its best to correct
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for these benign effects before computing and plotting a difference
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curve.
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One PDF (typically that collected at higher temperature) is identified
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as the "target" PDF and the second is "morphed" by "stretching" (changing
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the r-axis to simulate a uniform lattice expansion), "smearing"
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(broadening peaks through a uniform convolution to simulate increased
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thermal motion), and "scaling" (self-explanatory). PDFmorph will vary
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amplitude of morphing transformations to obtain the best fit between
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morphed and target PDFs, then plot them along with the difference curve
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plotted below.
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There are also a few other morphing transformations in the program.
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Finally, we note that PDFmorph should work on other spectra that are
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Finally, we note that PDFmorph should work on other spectra that are
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not PDFs, though it has not been extensively tested beyond the PDF.
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.. 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.
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.. figure:: ../images/pdfmorph_nacl_ex.png
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:align:center
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Transformation techniques (scale, smear, and stretch, respectively)
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Transformation techniques (scale, smear, and stretch, respectively)
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utilized by PDFmorph applied sequentially on an NaCl sample
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Installation
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============
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By downloading and using this software, you are agreeing to the conditions
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By downloading and using this software, you are agreeing to the conditions
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specified in the :doc:`software license <pdfmorph_license>`.
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PDFmorph is distributed using conda. To install software using conda
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you will first have to download and install ``Anaconda`` or ``mini-conda``
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In order to take automatically take care of software dependency
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downloads, we recomment you install PDFmorph using conda. To do that,
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you will first have to download and install *Anaconda* or *mini-conda*
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from `continuum <https://www.continuum.io>`__.
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PDFmorph is available for all operating systems supported by Anaconda,
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PDFmorph is available for all operating systems supported by Anaconda,
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namely for 32 and 64-bit Linux, Mac OS X, and 32 and 64-bit Windows.
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.. note::
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We recommend that you run PDFmorph in a Python 3 conda virtual
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environment. With Anaconda or mini-conda installed on your system,
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environment. With Anaconda or mini-conda installed on your system,
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first create the virtual environment by typing ::
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conda create --name=py3 python=3
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conda create --name=<env_name> python=3
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You can give the environment any name you like but it should
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have some Python version 3 installed. You only need to create
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the environment once, but every time you want to use PDFmorph
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you will have to activate the environment in which it is installed
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by typing ::
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You can give the environment any name you like but it should
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have some Python version 3 installed (though PDFmorph also works
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on Python 2.7). You only need to create the environment once,
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but every time you want to use PDFmorph you will have to
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reactivate the environment in which it is installed by typing ::
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source activate py3
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on Mac/Linux, or ::
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activate py3
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source activate <env_name>
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on Windows.
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on Mac/Linux, or ``activate <env_name>`` on Windows.
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PDFmorph is available from the "conda-forge" channel of Anaconda packages.
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Open a *Terminal* window or *Anaconda Command Prompt* on Windows and
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install PDFmorph using the :program:`conda` command ::
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Once you're in your desired conda environment, you can install PDFmorph
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from either the ``diffpy`` or ``conda-forge`` channels of Anaconda packages
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by running opening a *Terminal* window or *Anaconda Command Prompt*
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on Windows and using the :program:`conda` command ::
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conda config --add channels conda-forge
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conda install diffpy.pdfmorph
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And it should be installed! To make sure that installation has completed
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correctly, run the following command from your relevant conda environment ::
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If you prefer to install from the diffpy channel, simply replace
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``conda-forge`` with ``diffpy`` in the commands above.
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By then it should be installed! To make sure that installation has
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completed correctly, run the following command from your PDFmorph-equipped
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conda environment ::
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pdfmorph --version
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This command should return PDFmorph's current version number.
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This command should return the version of PDFmorph you have on your
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machine.
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PDFmorph Updates
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================
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The Anaconda package system makes it easy to prepare and distribute
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software packages and bugfixes. To update the latest version of PDFmorph,
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The Anaconda package system makes it easy to prepare and distribute
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software packages and bugfixes. To update the latest version of PDFmorph,
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use ::
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conda update diffpy.pdfmorph
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With other Python distributions, the program can be updated to the
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With other Python distributions, the program can be updated to the
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latest version with ::
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easy_install --upgrade diffpy.pdfmorph
@@ -112,15 +123,20 @@ https://github.com/diffpy/diffpy.pdfmorph and consult its README file.
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Documentation/Help
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==================
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0.0.1 - latest
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0.1.0 - latest
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----------------------
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* User manual (available in HTML and PDF)
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* Installation instructions
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* `Sample PDF files <https://github.com/diffpy/diffpy.pdfmorph/tree/master/tests/testdata>`__
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* Tutorial
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* Please, join the :doc:`community forum <../community>` for tips,
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* Please, join the :doc:`community forum <../community>` for tips,
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