diff options
Diffstat (limited to 'doc/man/whirligig.1')
| -rw-r--r-- | doc/man/whirligig.1 | 54 |
1 files changed, 54 insertions, 0 deletions
diff --git a/doc/man/whirligig.1 b/doc/man/whirligig.1 new file mode 100644 index 00000000..e213a007 --- /dev/null +++ b/doc/man/whirligig.1 @@ -0,0 +1,54 @@ +.\" +.\" whirligig man page +.\" +.\" Copyright © 2015 Deutsches Elektronen-Synchrotron DESY, +.\" a research centre of the Helmholtz Association. +.\" +.\" Part of CrystFEL - crystallography with a FEL +.\" + +.TH WHIRLIGIG 1 +.SH NAME +whirligig \- find rotation series +.SH SYNOPSIS +.PP +\fBwhirligig \fR[\fIoptions\fR] \fIinput.stream +.PP +\fBwhirligig --help\fI + +.SH DESCRIPTION +\fBwhirligig\fR takes a stream containing indexing results (e.g. from a previous run of \fBindexamajig\fR) 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 \fBseries-XX.log\fR, where \fBXX\fR is a number starting from zero, which contains the filenames, event IDs and crystal numbers for the frames concerned. +.PP +The program takes into account that the frames may not appear in the stream in chronological order (due, for example, to the use of \fBindexamajig -j\fR), and also that there may be multiple crystals per frame. + +.SH OPTIONS + +.IP \fB--output-dir=\fIfoldername\fR +.PD +Put the output log files in \fIfoldername\fR, instead of the working directory. The folder must exist before running \fBwhirligig\fR. + +.IP \fB--window-size=\fIn\fR +.PD +Set the size of the history buffer to \fIn\fR. 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 \fBindexamajig -j\fR), the larger the history buffer needs to be. \fBwhirligig\fR 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 \fB--window-size=16\fR. + +.SH AUTHOR +This page was written by Thomas White. + +.SH REPORTING BUGS +Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>. + +.SH COPYRIGHT AND DISCLAIMER +Copyright © 2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. +.P +whirligig, and this manual, are part of CrystFEL. +.P +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. +.P +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. +.P +You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. + +.SH SEE ALSO +.BR crystfel (7), +.BR indexamajig (1), +.BR crystfel_geometry (5) |