pdCIFplotter 0.0.9

A program for visualising diffraction data in pdCIF format.

A program for the visualisation of diffraction data in pdCIF format.

Crystallographic Information Framework (CIF; https://www.iucr.org/resources/cif) files are a way of storing crystallographic information in a standard human- and machine-readable format. This particular program is focussed on visualising powder diffraction data stored in CIF format, and, in particular, serial or in situ/operando data.

• Free software: Apache Software License 2.0

Pre-installation

If you are on Windows, you must read this step. If you are on Linux, you can continue.

pdCIFplotter requires PyCifRW >= 4.4.3. If you install PyCifRW from PyPI via pip, then you will also need to compile the included C modules. To do so requires Microsoft Visual C++ 14.0 or greater. If you don’t have this installed, or do not wish to install it, precompiled wheel files are available. You must download the wheel file corresponding to your Python installation.

To obtain information about your Python installation, run the command:

python -VV

An example output is Python 3.9.4 (tags/v3.9.4:1f2e308, Apr 6 2021, 13:40:21) [MSC v.1928 64 bit (AMD64)], showing that this is 64 bit Python 3.9.

Using pip version 19.2 or newer, install your downloaded wheel file as:

pip install c:\path\to\file\name_of_file.whl

This should install PyCifRW, and you can move on to the next step. If you encounter any issues in the installation, please lodge an issue.

Installation

To install the release version of pdCIFplotter from PyPI:

pip install pdCIFplotter

You can also install the in-development version from GitHub with:

pip install https://github.com/rowlesmr/pdCIFplotter/archive/master.zip

Quick usage

To run pdCIFplotter as a standalone program:

python -m pdCIFplotter

or:

pdcifplotter

When you first open pdCIFplotter, you are met with an empty window

Clicking “Load file”, and choosing a CIF file to open will automatically present you with a single plot. You can then alter how that plot is presented, or visualise all diffraction data in the CIF with the Stack and Surface tabs.

Documentation

https://pdCIFplotter.readthedocs.io/en/latest/

Development

This isn’t fully implemented yet.

To run all the tests run:

tox

Note, to combine the coverage data from all the tox environments run:

Windows	set PYTEST_ADDOPTS=--cov-append tox
Other	PYTEST_ADDOPTS=--cov-append tox

Changelog

0.0.9 (2021-12-31)

• Single plot - subtitle now shows the datetime, temperature, pressure, Rwp, and GoF, if available in the CIF file. Rwp and GoF is also calculated and displayed in brackets if possible. Gof calculation uses N, and not N-P, so it is only an approximation.

• Stack plot - Hovertext now shows the datetime, temperature, pressure, Rwp, and GoF, if available in the CIF file.

• Surface plot - Can now plot temperature, pressure, quantitative phase analysis (QPA), Rwp, and GoF (if available in the CIF file) next to the surface plot. QPA phases are linked together by their _pd_phase_name, so it is important that the same string is used to denote the same phases in different patterns.

0.0.8 (2021-12-20)

• Updated some of the zoom behaviour

• Can now use arrow buttons to move between consecutive diffraction patterns in the single plot

0.0.7 (2021-12-18)

• Zoom persists in single plots when changing between diffraction patterns or altering the view in some way.

0.0.6 (2021-12-09)

• Can normalise intensities to counts from provided weights or errors; possible in single, stack, and surface

• hkl ticks labelled by phase name, if present, else, phase id: now including surface plot.

• (ongoing) Refactoring of plot_cif

0.0.5 (2021-11-16)

• Better hkl checkbox checking

• Doesn’t crash if CIF with no diffraction pattern is loaded

• Gracefully handles NANs in data when calculating hkl tick offsets

• Datablock names replaced with block_id values on single plot title and dropdown data box

• hkl ticks labelled by phase name, if present, else, phase id.

• Large refactoring of parse_cif

0.0.4 (2021-11-11)

• Added hkl ticks to stack plot

• Enabled hkl ticks to be plotted above the diffraction patterns

0.0.3 (2021-11-10)

• Separated GUI and plotting code

• Fixed crash on changing to surface tab before opening CIF

0.0.2 (2021-11-07)

• Update install requirements - mplcursors 0.5 is now available, rather than installing from git.

• Can now launch from command line with just > pdcifplotter

0.0.1 (2021-11-06)

• Update install requirements and provided prompting to user on installing packages not available on PyPi.

0.0.0 (2021-11-05)

• First release on PyPI.