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% align_detector(1)
NAME
====
align_detector - refine detector geometry
SYNOPSIS
========
align_detector -g _input.geom_ -o _output.geom_ -l _level_ [--out-of-plane] _millepede-files_
DESCRIPTION
===========
**align_detector** refines the detector geometry based on the calibration data
written by **indexamajig**. The refinement takes into account all the
inter-dependencies between crystal orientations, cell parameters and the panel
positions, as if a single large minimisation had been performed with all frames
at once. The algorithm is nevertheless very fast - this is achieved using the
Millepede-II algorithm. For more information, see
https://www.desy.de/~kleinwrt/MP2/doc/html/index.html
To refine the detector geometry, first make sure that the geometry file
includes hierarchy information. For this, see **man crystfel_geometry**,
section **Detector hierarchy**.
Next, run **indexamajig** as usual, but with option **--mille**. This will
produce several files named **mille-data-0.bin**, **mille-data-1.bin**,
**mille-data-2.bin** and so on - as many files as there were indexamajig
subprocesses (set with **indexamajig -j**). Use option **--mille-dir** to
put these files in a useful location. If you are splitting the indexamajig
processing across a cluster, be aware that each sub-task needs to have its
own directory for **--mille-dir**. See scripts/turbo-index-slurm for details.
Finally, run **align_detector**, giving it the input geometry file, the "Mille"
files, a refinement level and a filename for the updated geometry file. The
input geometry file must match the file used for the indexamajig run.
Refinement level **0** allows only the overall detector position to vary.
Higher levels allow groups of panels to move according to the hierarchy. For
example, for a CSPAD detector with hierarchy defined as in the example files,
level **1** would refine the quadrant positions, **2** would refine the 2-by-1
panel "dominoes", and level **3** would refine the individual (roughly square)
ASICs. Higher refinement levels will generally require more and
higher-resolution diffraction data.
You can use **indexamajig** option **--max-mille-level** to reduce the size of
the calibration data files, at the cost of limiting the maximum refinement
level.
The default behaviour is to refine only the position components in the x-y
plane, perpendicular to the beam. In favourable circumstances, you can add
option **--out-of-plane** to refine the panel **translations** out of this
plane. However, be aware that this introduces additional cross-dependencies
and is less stable. Add option **--out-of-plane-tilts** to additionally
refine the panel **tilts** out of the x-y plane, which is even less stable.
The overall detector z-position (camera length) is usually quite strongly
correlated with the crystal cell parameters, making it difficult to refine.
With high-resolution data, it can be possible, however. To refine the overall
camera length, add **--camera-length**. Without this option, the overall
camera length will not be altered, even with **--out-of-plane**. Instead, only
the z-positions of the panels relative to one another will be refined.
**align_detector** relies on the program **pede** from the Millepede-II
package. Usually, this will be installed as part of the CrystFEL installation
procedure. If not, it can easily be installed from the Millepede-II repository
at https://gitlab.desy.de/claus.kleinwort/millepede-ii
OPTIONS
=======
**-g** _input.geom_, **--geometry**=_input.geom_
: Specify the input geometry filename.
**-o** _output.geom_, **--output**=_output.geom_
: Specify the output geometry filename.
: Note that the geometry file will be re-written, meaning that any formatting
: and comments will be lost.
**-l** _level_, **--level**=_level_
: Specify the refinement level. **-l 0** refines the overall detector position
: only. The maximum refinement level is determined by the hierarchy of the
: detector.
**--out-of-plane**
: Additionally refine out-of-plane panel translations, relative to one another
: (see **--camera-length**).
**--out-of-plane-tilts**
: Additionally refine out-of-plane panel tilts.
**--camera-length**
: Additionally refine the overall camera length.
AUTHOR
======
This page was written by Thomas White.
REPORTING BUGS
==============
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
COPYRIGHT AND DISCLAIMER
========================
Copyright © 2023 Deutsches Elektronen-Synchrotron DESY, a research centre of
the Helmholtz Association.
align_detector, and this manual, are part of CrystFEL.
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**(7), **indexamajig**(1), **adjust_detector**(1),
**crystfel_geometry**(5)
|
