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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, but 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**).
+
+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.
+
+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 tilts and shifts out of this
+plane.  However, be aware that this introduces additional cross-dependencies
+and is less stable.
+
+**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_
+: Specify the input geometry filename.
+
+**-o** _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_
+: 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 positions and tilts of the detector.
+
+
+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)