CorMapAnalysis

Library to visualise the CorMap (Correlation Map) test results for SAXS data. If you use this library for your work, please cite [1].

Contents

• Introduction
• Installation
• Usage
• Known Issues
• References

Introduction

The library provided in this repository provides methods to analyse and visualise results from the CorMap test [2] which is performed by the DATCMP program within the ATSAS software suite [3]. Mostly it allows users to assess the similarity of frames and hence has the potential to determine systematically which frames can be merged for SAXS data processing.

Note: This program also uses DATCROP for cropping portions of the 1D scattering curves.

Installation

Currently the only way to use this package is get the code from the CorMapAnalysis.py file. If you use Github then you can clone the repository to obtain it by running

git clone https://github.com/GarmanGroup/CorMapAnalysis.git

in the command prompt/terminal. Otherwise you can fork this repository or just copy and paste the Python code into a new .py file.

Usage

After installing the CorMapAnalysis module, the ScatterAnalysis class can be imported in the usual fashion. Below is a small script that shows how straightforward it is to create the ScatterAnalysis object and generate a heatmap from the data

from CorMapAnalysis import ScatterAnalysis
scat_obj = ScatterAnalysis.from_1d_curves("path/to/mydata_00*")
scat_obj.plot_heatmap()

Which generates the following

To get information on each method, use the inbuilt help method in Python. For example to get the documentation for the heatmap method type

help(scat_obj.plot_heatmap)

All methods have been thoroughly documented using the Numpy style docstring format. For a tutorial that you can follow with sample data check out the tutorial.

Known Issues

There are no known issues. However, if you find any issues or feature requests please submit an issue or email the Garman group [email protected]

References

[1] Brooks-Bartlett, J.C., Batters, R.A., Bury, C.S., Lowe, E.D., Ginn, H.M., Round, A. & Garman, E.F.
Development of tools to automate quantitative analysis of radiation damage in SAXS experiments
J. Synchrotron Rad. (2017). 24, 63-72
doi:10.1107/S1600577516015083.

[2] Franke, Daniel, Cy M. Jeffries, and Dmitri I. Svergun.
"Correlation Map, a goodness-of-fit test for one-dimensional X-ray scattering spectra"
Nature methods (2015). 12.5, 419-422
doi:10.1038/nmeth.3358

[3] Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gorba, C., Mertens, H.D.T., Konarev, P.V. and Svergun, D.I. (2012)
"New developments in the ATSAS program package for small-angle scattering data analysis"
J. Appl. Cryst. 45, 342-350 doi:10.1107/S0021889812007662