1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
|
.\"
.\" whirligig man page
.\"
.\" Copyright © 2015-2021 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 © 2015-2021 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)
|
