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whirligig: find rotation series

Synopsis

whirligig [options] input.stream
whirligig --help

Description

whirligig takes a stream containing indexing results (e.g. from a previous run of indexamajig) and searches for runs of crystals in adjacent frames which have similar orientations and unit cell parameters. For each series found, a log file will be output with a filename in the form series-XX.log, where XX is a number starting from zero, which contains the filenames, event IDs and crystal numbers for the frames concerned.

The program takes into account that the frames may not appear in the stream in chronological order (due, for example, to the use of indexamajig -j), and also that there may be multiple crystals per frame.

Options

--output-dir=foldername

Put the output log files in foldername, instead of the working directory. The folder must exist before running whirligig.

--window-size=n

Set the size of the history buffer to n. The further apart adjacent frames can be in the input stream, for example the higher a number of parallel processes were used during indexing (see indexamajig -j), the larger the history buffer needs to be. whirligig will print a warning if it seems the window is too small. Increasing the window size increases the amount of computation and memory required. The default is --window-size=16.

Author

This page was written by Thomas White.

Reporting bugs

Report bugs to taw@physics.org

Copyright and Disclaimer

Copyright © 2015-2020 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.

CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CrystFEL. If not, see http://www.gnu.org/licenses/.

See also

crystfel

indexamajig

crystfel_geometry

If CrystFEL is installed on your computer, you can read this manual page offline using the command man whirligig.