path: root/doc/man/indexamajig.1

.\"
.\" indexamajig man page
.\"
.\" Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
.\"                       a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"

.TH INDEXAMAJIG 1
.SH NAME
indexamajig \- bulk indexing and data reduction program
.SH SYNOPSIS
.PP
.BR indexamajig
\fB-i\fR \fIfilename\fR \fB-o\fR \fIoutput.stream\fR \fB-g\fR \fIdetector.geom\fR \fB--peaks=\fR\fImethod\fR \fB--indexing=\fR\fImethod\fR
[\fBoptions\fR] \fB...\fR
.PP
\fBindexamajig --help\fR

.SH DESCRIPTION

\fBindexamajig\fR takes a list of diffraction snapshots from crystals in random orientations and attempts to find peaks, index and integrate each one.  The input is a list of diffraction image files in HDF5 format and some auxiliary files and parameters.  The output is a long text file ('stream') containing the results from each image in turn.

For minimal basic use, you need to provide the list of diffraction patterns, the method which will be used to index, a file describing the geometry of the detector, and a file which contains the unit cell which will be used for the indexing.  Here is what the minimal use might look like on the command line:

.IP \fBindexamajig\fR
.PD
-i mypatterns.lst -g mygeometry.geom --indexing=mosflm,dirax --peaks=hdf5 -o test.stream -p mycell.pdb

.PP
More typical use includes all the above, but might also include extra parameters to modify the behaviour. For example, you'll probably want to
run more than one indexing job at a time (-j <n>).

See \fBman crystfel_geometry\fR for information about how to create a file describing the detector geometry and beam characteristics.

.SH DIFFRACTION PATTERN LIST

Indexamajig requires an input file with a list of diffraction patterns ("events") to process. In its simplest form, this is just a text files containing a list of HDF5 filenames. The HDF5 files might be in some folder a long way from the current directory, so you might want to specify a full pathname to be added in front of each filename. The geometry file includes a description of the data layout within the HDF5 files. Indexamajig uses this description to determine the number of diffraction patterns stored in each file, and tries to process them all.  You can also specify explicity which event(s) you would like to process by putting a string describing the event after the file name(s) in this list.


.SH PEAK DETECTION

You can control the peak detection on the command line.  Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  There are three possibilities for "method" here.  \fB--peaks=hdf5\fR will take the peak locations from the HDF5 file.  It expects a two dimensional array, by default at /processing/hitfinder/peakinfo, whose size in the first dimension equals the number of peaks and whose size in the second dimension is three.  The first two columns contain the fast scan and slow scan coordinates, the third contains the intensity.  However, the intensity will be ignored since the pattern will always be re-integrated using the unit cell provided by the indexer on the basis of the peaks.  You can tell indexamajig where to find this table inside each HDF5 file using \fB--hdf5-peaks=\fR\fIpath\fR.

\fB--peaks=cxi\fR works similarly to this, but expects four separate HDF5 datasets beneath \fIpath\fR, \fBnPeaks\fR, \fBpeakXPosRaw\fR, \fBpeakYPosRaw\fR and \fBpeakTotalIntensity\fR.  See the specification for the CXI file format at http://www.cxidb.org/ for more details.

CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry (see 'man crystfel_geometry').  The software which generates the HDF5 or CXI files, including Cheetah, may instead consider the peak locations to be pixel indices in the data array.  Therefore, the peak coordinates from \fB--peaks=cxi\fR or \fB--peaks=hdf5\fR will by default have 0.5 added to them.  Use \fB--no-half-pixel-shift\fR if this isn't what you want.

If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000).  You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-squared-gradient\fR.  The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units.  Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below).  They will also be rejected if the peak is closer than twice the inner integration radius from another peak.

If you instead use \fB--peaks=peakfinder8\fR, indexamajig will use the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Note that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored.

If you instead use \fB--peaks=peakfinder9\fR, indexamajig will use the "peakfinder9" peak finding algorithm described in the master thesis "Real-time image analysis and data compression in high throughput X-ray diffraction experiments" by Gevorkov. Other than peakFinder8, peakFinder9 uses local background estimation based on border pixels in a specified radius (\fB--local-bg-radius\fR). For being fast and precise, a hierarchy of conditions is used. First condition is only useful for speed consideration, it demands that a pixel that is the biggest pixel in a peak must be larger than every border pixel by a constant value (\fB--min-peak-over-neighbour\fR). Second condition ensures, that the pixel passing the previous condition is the highest pixel in the peak. It assumes, that peaks rise monotonically towards the biggest pixel. Third condition ensures, that the biggest pixel in the peak is significantly over the noise level (\fB--min-snr-biggest-pix\fR) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (\fB--min-snr-peak-pix\fR) and demands that the whole peak must be significantly over the noise level (\fB--min-snr\fR). Only if all conditions are passed, the peak is accepted.

You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero.


.SH INDEXING METHODS

You can choose between a variety of indexing methods.  You can choose more than one method, in which case each method will be tried in turn until one of them reports that the pattern has been successfully indexed.  Choose from:

.IP \fBdirax\fR
.PD
Invoke DirAx.  To use this option, 'dirax' must be in your shell's search path.  If you see the DirAx version and copyright information when you run \fBdirax\fR on the command line, things are set up correctly.

.IP \fBmosflm\fR
.PD
Invoke Mosflm.  To use this option, 'ipmosflm' must be in your shell's search path.  If you see the MOSFLM version and copyright information when you run \fBipmosflm\fR on the command line, things are set up correctly.

.IP \fBasdf\fR
.PD
This is a implementation of the \fBdirax\fR algorithm, with some very small changes such as using a 1D Fourier transform for finding the lattice repeats.  This algorithm is implemented natively within CrystFEL meaning that no external software is required.

.IP \fBfelix\fR
.PD
Invoke Felix, which will use your cell parameters to find multiple crystals in each pattern.
.sp
The Felix indexer has been developed by Soeren Schmidt <ssch@fysik.dtu.dk>. To use this option, 'Felix' must be in your shell's search path. This can be a link to the latest version of Felix. If you see the Felix version information when you run \fBFelix\fR on the command line, things are set up correctly.

.IP \fBxds\fR
.PD
Invoke XDS, and use its REFIDX procedure to attempt to index the pattern.

.IP \fBtaketwo\fR
.PD
Use the TakeTwo algorithm.  See Ginn et al., Acta Cryst. (2016). D72, 956-965.

.IP \fBxgandalf\fR
.PD
Invoke XGANDALF - eXtended GrAdieNt Descent Algorithm for Lattice Finding. Xgandalf must be installed in order to be able to use it.

.IP \fBpinkIndexer\fR
.PD
Invoke pinkIndexer. pinkIndexer must be installed in order to be able to use it. The geometry file should contain the value photon_energy_bandwidth, which sets the bandwidth as (delta energy)/(mean energy).


.PP
You can add one or more of the following to the above indexing methods, to control what information should be provided to them.  Note that indexamajig performs a series of checks on the indexing results, including checking that the result is consistent with the target unit cell parameters.  To get completely "raw" indexing, you need to disable these checks (see below) \fBand\fR not provide prior information.

.IP \fB-latt\fR
.PD
Provide the Bravais lattice type (e.g. the knowledge that the lattice is tetragonal primitive), as prior information to the indexing engine.

.IP \fB-nolatt\fR
.PD
The opposite of \fB-latt\fR: do not provide Bravais lattice type information to the indexing engine.

.IP \fB-cell\fR
.PD
Provide your unit cell parameters as prior information to the indexing engine.

.IP \fB-nocell\fR
.PD
The opposite of \fB-cell\fR: do not provide unit cell parameters as prior information to the indexing engine.

.PP
Example: \fB--indexing=mosflm-cell-latt\fR means to use Mosflm for indexing, and provide it with unit cell parameters and Bravais lattice type information.

.PP
The default indexing method is 'none', which means no indexing will be done.  This is useful if you just want to check that the peak detection is working properly.

.PP
You do not need to explicitly specify anything more than the indexing method itself (e.g. \fBmosflm\fR or \fBasdf\fR).  The default behaviour for all indexing methods is to make the maximum possible use of prior information such as the lattice type and cell parameters.  If you do not provide this information, for example if you do not give any unit cell file or if the unit cell file does not contain cell parameters (only lattice type information), the indexing methods you give will be modified accordingly.  If you only specify the indexing methods themselves, in most cases \fBindexamajig\fR will do what you want and intuitively expect!  However, the options are available if you need finer control.

If you don't know what to give for this option, leave it out completely.  Indexamajig will then automatically select indexing methods based on the programs available on your computer.

The indexing results from the indexing engine will be put through a number of refinement and checking stages.  See the options \fB--no-check-cell, --no-multi, --no-retry\fR and \fB--no-refine\fR below for more details.

.SH PEAK INTEGRATION
If the pattern could be successfully indexed, peaks will be predicted in the pattern and their intensities measured.  You have a choice of integration methods, and you specify the method using \fB--integration\fR.  Choose from:

.IP \fBrings\fR
.PD
Use three concentric rings to determine the peak, buffer and background estimation regions.  The radius of the smallest circle sets the peak region.  The radius of the middle and outer circles describe an annulus from which the background will be estimated.  You can set the radii of the rings using \fB--int-radius\fR (see below).  The default behaviour with \fBrings\fR is \fBnot\fR to center the peak boxes first.  Use \fBrings-cen\fR if you want to use centering.

.IP \fBprof2d\fR
.PD
Integrate the peaks using 2D profile fitting with a planar background, close to the method described by Rossmann (1979) J. Appl. Cryst. 12 p225.  The default behaviour with \fBprof2d\fR is to center the peak first - use \fBprof2d-nocen\fR to skip this step.

.PP
You can add one or more of the following to the above integration methods:

.IP \fB-cen\fR
.PD
Center the peak boxes iteratively on the actual peak locations.  The opposite is \fB-nocen\fR, which is the default.

.IP \fB-sat\fR
.PD
Normally, reflections which contain one or more pixels above max_adu (defined in the detector geometry file) will not be integrated and written to the stream.  Using this option skips this check, and allows saturated reflections to be passed to the later merging stages.  This is not usually a good idea, but might be your only choice if there are many saturated reflections.  The opposite is \fB-nosat\fR, which is the default for all integration methods.

.IP \fB-grad\fR
.PD
Fit the background around the reflection using gradients in two dimensions.  This was the default until version 0.6.1.  Without the option (or with its opposite, \fB-nograd\fR, which is the default), the background will be considered to have the same value across the entire integration box.

.SH OPTIMISING THE INTEGRATION RADII
To determine appropriate values for the integration radii, index some patterns with the default values and view the results using \fBcheck-near-bragg\fR (in the scripts folder).  Set the binning in \fBhdfsee\fR to 1, and adjust the ring radius until none of the rings overlap for any of the patterns.  This ring radius is the outer radius to use. Then reduce the radius until the circles match the sizes of the peaks as closely as possible.  This value is the inner radius.  The middle radius should be between the two, ideally between two and three pixels smaller than the outer radius.
.PP
If it's difficult to do this without setting the middle radius to the
same value as the inner radius, then the peaks are too close together to be
accurately integrated.  Perhaps you got greedy with the resolution and put the
detector too close to the interaction region?

.SH BASIC OPTIONS
.PD 0
.IP "\fB-i\fR \fIfilename\fR"
.IP \fB--input=\fR\fIfilename\fR
.PD
Read the list of images to process from \fIfilename\fR.  \fB--input=-\fR means to read from stdin.  There is no default.

.PD 0
.IP "\fB-o\fR \fIfilename\fR"
.IP \fB--output=\fR\fIfilename\fR
.PD
Write the output data stream to \fIfilename\fR.

.PD 0
.IP "\fB-g\fR \fIfilename\fR"
.IP \fB--geometry=\fR\fIfilename\fR
.PD
Read the detector geometry description from \fIfilename\fR.  See \fBman crystfel_geometry\fR for more information.

.PD 0
.IP \fB--basename\fR
.PD
Remove the directory parts of the filenames taken from the input file.  If \fB--prefix\fR or \fB-x\fR is also given, the directory parts of the filename will be removed \fIbefore\fR adding the prefix.

.PD 0
.IP "\fB-x\fR \fIprefix\fR"
.IP \fB--prefix=\fR\fIprefix\fR
.PD
Prefix the filenames from the input file with \fIprefix\fR.  If \fB--basename\fR is also given, the filenames will be prefixed \fIafter\fR removing the directory parts of the filenames.

.PD 0
.IP "\fB-j\fR \fIn\fR"
.PD
Run \fIn\fR analyses in parallel.  Default: 1.

.PD 0
.IP \fB--no-check-prefix\fR
.PD
Don't attempt to correct the prefix (see \fB--prefix\fR) if it doesn't look correct.

.PD 0
.IP \fB--highres=\fIn\fR
.PD
Mark all pixels on the detector higher than \fIn\fR Angstroms as bad.  This might be useful when you have noisy patterns and don't expect any signal above a certain resolution.

.PD 0
.IP \fB--profile
.PD
Display timing data for performance monitoring.

.PD 0
.IP \fB--temp-dir=\fIpath\fR
.PD
Put the temporary folder under \fIpath\fR.

.PD 0
.IP \fB--wait-for-file=\fIn\fR
.PD
Wait at most \fIn\fR seconds for each image file in the input list to be created before trying to process it.  This is useful for some automated processing pipelines.  It obviously only really works for single-frame files.  If a file exists but is not readable when this option is set non-zero, a second attempt will be made after ten seconds.  This is to allow for incompletely written files.  A value of -1 means to wait forever.  The default value is \fB--wait-for-file=0\fR.

.PD 0
.IP \fB--zmq-msgpack\fR
.PD
Receive data as MessagePack objects over ZeroMQ.  The input "file list", given with \fB--input\fR or \fB-i\fR, should contain a socket URL suitable for passing to zmq_connect(), such as "tcp://127.0.0.1:12322".  At the moment, only one URL can be given, but this may change in future.

.IP \fB--no-image-data\fR
.PD
Do not load the actual image data (or bad pixel masks), only the metadata.  This allows you to check if patterns can be indexed, without high data bandwidth requirements.  Obviously, any feature requiring the image data, especially peak search procedures and integration, cannot be used in this case.  At the moment, this option only works when \fB--zmq-msgpack\fR is also used.  You will probably want to use \fB--peaks=msgpack\fR.


.SH PEAK SEARCH OPTIONS
.PD 0
.IP \fB--peaks=\fR\fImethod\fR
.PD
Find peaks in the images using \fImethod\fR.  See the second titled \fBPEAK DETECTION\fB (above) for more information.

.PD 0
.IP \fB--peak-radius=\fR\fIinner,middle,outer\fR
.PD
Set the inner, middle and outer radii for three-ring integration during the peak search.  See the section about \fBPEAK INTEGRATION\fR, above, for details of how to determine
these.  The default is to use the same values as for \fB--int-radius\fR.

.PD 0
.IP \fB--min-peaks=\fIn\fR
.PD
Do not try to index frames with fewer than \fIn\fR peaks.  These frames will still be described in the output stream.  To exclude them, use \fB--no-non-hits-in-stream\fR.

.PD 0
.IP \fB--hdf5-peaks=\fR\fIpath\fR
.PD
When using \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR, read the peak positions from location \fIpath\fR.  The path can include placeholders, e.g. \fB--hdf5-peaks=/%/peaks\fR.  See \fBPEAK DETECTION\fR above.

.PD 0
.IP \fB--median-filter=\fR\fIn\fR
.PD
Apply a median filter with box "radius" \fIn\fR to the image.  The median of the values from a \fI(n+1)\fRx\fI(n+1)\fR square centered on the pixel will be subtracted from each pixel.  This might help with peak detection if the background is high and/or noisy.  The \fIunfiltered\fR image will be used for the final integration of the peaks.  If you also use \fB--noise-filter\fR, the median filter will be applied first.

.PD 0
.IP \fB--filter-noise\fR
.PD
Apply a noise filter to the image with checks 3x3 squares of pixels and sets all of them to zero if any of the nine pixels have a negative value.  This filter may help with peak detection under certain circumstances.  The \fIunfiltered\fR image will be used for the final integration of the peaks, because the filter is destroys a lot of information from the pattern.  If you also use \fB--median-filter\fR, the median filter will be applied first.

.PD 0
.IP \fB--threshold=\fR\fIthres\fR
.PD
Set the overall threshold for peak detection using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR to \fIthres\fR, which has the same units as the detector data.  The default is \fB--threshold=800\fR.

.PD 0
.IP \fB--min-squared-gradient=\fR\fIgrad\fR
.PD
Set the square of the gradient threshold for peak detection using \fB--peaks=zaef\fR to \fIgrad\fR, which has units of "squared detector units per pixel".  The default is \fB--min-squared-gradient=100000\fR.  \fB--min-sq-gradient\fR and \fB--min-gradient\fR are synonyms for this option, however the latter should not be used to avoid confusion.

.PD 0
.IP \fB--min-snr=\fR\fIsnr\fR
.PD
Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR, \fB--peaks=peakfinder8\fR or \fB--peaks=peakfinder9\fR.  The default is \fB--min-snr=5\fR.

.PD 0
.IP \fB--min-snr-biggest-pix=<n>\fR
.PD
(peakFinder9 only) min snr of the biggest pixel in the peak, given as a factor of the standard deviation. Default is 7.0.

.PD 0
.IP \fB--min-snr-peak-pix=<n>\fR
.PD
(peakFinder9 only) min snr of a peak pixel, given as a factor of the standard deviation. Should be smaller or equal to sig_fac_biggest_pix. Default is 6.0.

.PD 0
.IP \fB--min-sig=<n>\fR
.PD
(peakFinder9 only) minimum standard deviation of the background. Prevents finding of peaks in erroneous or highly shadowed unmasked regions. Default is 11.0.

.PD 0
.IP \fB--min-peak-over-neighbour=<n>\fR
.PD
(peakFinder9 only) just for speed. Biggest pixel must be n higher than the pixels in window_radius distance to be a candidate for the biggest pixel in a peak. Should be chosen as a small positive number, a few times smaller than the weakest expected peak. The default is -INFINITY, which turns off the speedup and searches with maximum precision.

.PD 0
.IP \fB--min-pix-count=\fR\fIcnt\fR
.PD
Accepts peaks only if they include more than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR.  The default is \fB--min-pix-count=2\fR.

.PD 0
.IP \fB--max-pix-count=\fR\fIcnt\fR
.PD
Accepts peaks only if they include less than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR.  The default is \fB--max-pix-count=200\fR.

.PD 0
.IP \fB--local-bg-radius=\fR\fIr\fR
.PD
Radius (in pixels) used for the estimation of the local background when using \fB--peaks=peakfinder8 or --peaks=peakfinder9\fR.  The default is \fB--local-bg-radius=3\fR.

.PD 0
.IP \fB--min-res=\fR\fIpx\fR
.PD
Only accept peaks if they lay at more than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR.  The default is \fB--min-res=0\fR.

.PD 0
.IP \fB--max-res=\fR\fIpx\fR
.PD
Only accept peaks if they lay at less than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR.  The default is \fB--max-res=1200\fR.

.PD 0
.IP \fB--no-use-saturated\fR
.PD
Normally, peaks which contain one or more pixels above max_adu (defined in the detector geometry file) will be used for indexing (but not used in the final integration - see the section on peak integration above).  Using this option causes saturated peaks to be ignored completely.  The opposite is \fB--use-saturated\fR, which is the default.

.PD 0
.IP \fB--no-revalidate\fR
.PD
When using \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR, the peaks will be put through some of the same checks as if you were using \fB--peaks=zaef\fR.  These checks reject peaks which are too close to panel edges, are saturated (unless you use \fB--use-saturated\fR), have other nearby peaks (closer than twice the inner integration radius, see \fB--int-radius\fR), or have any part in a bad region.  Using this option skips this validation step, and uses the peaks directly.

.PD 0
.IP \fB--no-half-pixel-shift\fR
.PD
CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry (see 'man crystfel_geometry').  The software which generates the HDF5 or CXI files, including Cheetah, may instead consider the peak locations to be pixel indices in the data array.  Therefore, the peak coordinates from \fB--peaks=cxi\fR or \fB--peaks=hdf5\fR will by default have 0.5 added to them.  This option \fBdisables\fR this half-pixel offset.

.PD 0
.IP \fB--check-hdf5-snr\fR
.PD
With this option with \fB--peaks=hdf5\fR, the peaks will additionally be checked to see that they satisfy the minimum SNR specified with \fB--min-snr\fR.

.SH INDEXING OPTIONS
.PD 0
.IP \fB--indexing=\fR\fImethod\fR
.PD
Index the patterns using \fImethod\fR.  See the section titled \fBINDEXING METHODS\fR (above) for more information.  The default is to automatically detect which indexing methods to use.

.PD 0
.IP "\fB-p\fR \fIunitcell.cell\fR"
.IP "\fB-p\fR \fIunitcell.pdb\fR"
.IP \fB--pdb=\fR\fIunitcell.pdb\fR
.PD
Specify the name of the file containing unit cell information, in PDB or CrystFEL format.

.PD 0
.IP \fB--tolerance=\fR\fItol\fR
.PD
Set the tolerances for unit cell comparison.  \fItol\fR takes the form \fIa\fR,\fIb\fR,\fIc\fR,\fIang\fR.  \fIa\fR, \fIb\fR and \fIc\fR are the tolerances, in percent, for the respective \fIreciprocal\fR space axes, and \fIang\fR is the tolerance in degrees for the reciprocal space angles.  If the unit cell is centered, the tolerances are applied to the corresponding primitive unit cell.
.PD
The default is \fB--tolerance=5,5,5,1.5\fR.

.PD 0
.IP \fB--no-check-cell
.PD
Do not check the cell parameters against the reference unit cell (given with \fB-p\fR).  If you've used older versions of CrystFEL, this replaces putting "-raw" in the indexing method.

.PD 0
.IP \fB--multi
.PD
Enable the "subtract and retry" method, where after a successful indexing attempt the spots accounted for by the indexing solution are removed before trying to index again in the hope of finding a second lattice.  This doesn't have anything to do with the multi-lattice indexing algorithms such as Felix.

.PD 0
.IP \fB--no-retry
.PD
Disable retry indexing.  After an unsuccessful indexing attempt, indexamajig would normally remove the 10% weakest peaks and try again.  This option disables that, which makes things much faster but decreases the indexing success rate.

.PD 0
.IP \fB--no-refine
.PD
Skip the prediction refinement step.  Usually this will decrease the quality of the results and allow false solutions to get through, but occasionally it might be necessary.

.PD 0
.IP \fB--check-peaks
.PD
Check that most of the peaks can be accounted for by the indexing solution.  This usually increases the quality of the indexing solutions, but prevents "subtract and retry" multi-lattice indexing from working well.

.PD 0
.IP \fB--taketwo-member-threshold=\fIn\fR
.IP \fB--taketwo-len-tolerance=\fIn\fR
.IP \fB--taketwo-angle-tolerance=\fIn\fR
.IP \fB--taketwo-trace-tolerance=\fIn\fR
.PD
These set low-level parameters for the TakeTwo indexing algorithm.  Respectively, the minimum number of vectors in the network before the pattern is considered indexed, the length and angle tolerances (in reciprocal Angstroms and degrees, respectively) and the rotation matrix angle tolerance (in degrees) for considering rotation matrices as equal.
.IP
The defaults are: \fB--taketwo-member-threshold=20\fR, \fB--taketwo-len-tolernace=0.001\fR, \fB--taketwo-angle-tolerance=0.6\fR and \fB--taketwo-trace-tolerance=3\fR.

.PD 0
.IP \fB--felix-domega=\fIn\fR
.IP \fB--felix-fraction-max-visits=\fIn\fR
.IP \fB--felix-max-internal-angle=\fIn\fR
.IP \fB--felix-max-uniqueness=\fIn\fR
.IP \fB--felix-min-completeness=\fIn\fR
.IP \fB--felix-min-visits=\fIn\fR
.IP \fB--felix-num-voxels=\fIn\fR
.IP \fB--felix-sigma=\fIn\fR
.IP \fB--felix-tthrange-max=\fIn\fR
.IP \fB--felix-tthrange-min=\fIn\fR
.PD 0
These set low-level parameters for the Felix indexing algorithm.

.PD 0
.IP \fB--xgandalf-sampling-pitch=\fIn\fR
.IP \fB--xgandalf-grad-desc-iterations=\fIn\fR
.IP \fB--xgandalf-tolerance=\fIn\fR
.IP \fB--xgandalf-no-deviation-from-provided-cell\fR
.IP \fB--xgandalf-max-lattice-vector-length=\fIn\fR
.IP \fB--xgandalf-min-lattice-vector-length=\fIn\fR
.IP \fB--xgandalf-max-peaks=\fIn\fR
.IP \fB--xgandalf-fast-execution\fR
.PD
These set low-level parameters for the XGANDALF indexing algorithm.
.IP
\fB--xgandalf-sampling-pitch\fR selects how dense the reciprocal space is sampled. [0-4]: extremelyLoose to extremelyDense. [5-7]: standardWithSeondaryMillerIndices to extremelyDenseWithSeondaryMillerIndices. Default is 6 (denseWithSeondaryMillerIndices).
.IP
\fB--xgandalf-grad-desc-iterations\fR  selects how many gradient descent iterations are performed. [0-5]: veryFew to extremelyMany. Default is 4 (manyMany).
.IP
\fB--xgandalf-tolerance\fR relative tolerance of the lattice vectors. Default is 0.02.
.IP
\fB--xgandalf-no-deviation-from-provided-cell\fR if a prior unit cell was provided, and this flag is set, the found unit cell will have exactly the same size as the provided one.
.IP
\fB--xgandalf-min-lattice-vector-length\fR and \fB--xgandalf-min-lattice-vector-length\fR minimum and maximum possible lattice vector lengths (unit is A). Used for fitting without prior lattice as starting point for gradient descent, so the final minimum lattice vector length can be smaller/highier as min/max. Note: This is valid for the uncentered cell, i.e. the P-cell! Default is 30A and 250A respectively.
.IP
\fB--xgandalf-max-peaks\fR maximum number of peaks used for indexing. For refinement all peaks are used. Peaks are selected by increasing radius. Limits the maximum execution time for patterns with a huge amount of peaks - either real ones or false positives. Default is 250.
.IP
\fB--xgandalf-fast-execution\fR Shortcut to set --xgandalf-sampling-pitch=2 --xgandalf-grad-desc-iterations=3

.PD 0
.IP \fB--pinkIndexer-considered-peaks-count=\fIn\fR
.IP \fB--pinkIndexer-angle-resolution=\fIn\fR
.IP \fB--pinkIndexer-refinement-type=\fIn\fR
.IP \fB--pinkIndexer-tolerance=\fIn\fR
.IP \fB--pinkIndexer-reflection-radius=\fIn\fR
.IP \fB--pinkIndexer-max-resolution-for-indexing=\fIn\fR
.IP \fB--pinkIndexer-multi=\fIn\fR
.IP \fB--pinkIndexer-thread-count=\fIn\fR
.IP \fB--pinkIndexer-no-check-indexed=\fIn\fR
.IP \fB--pinkIndexer-override-bandwidth=\fIn\fR
.IP \fB--pinkIndexer-override-photon-energy=\fIn\fR
.IP \fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR

.PD
These set low-level parameters for the PinkIndexer indexing algorithm.
.IP
\fB--pinkIndexer-considered-peaks-count\fR selects how many peaks are considered for indexing. [0-4] (veryFew to manyMany). Default is 4 (manyMany).
.IP
\fB--pinkIndexer-angle-resolution\fR selects how dense the orientation angles of the sample lattice are sampled. [0-4] (extremelyLoose to extremelyDense). Default is 2 (normal).
.IP
\fB--pinkIndexer-refinement-type\fR selects the refinement type. 0 = none, 1 = fixedLatticeParameters, 2 = variableLatticeParameters, 3 = firstFixedThenVariableLatticeParameters, 4 = firstFixedThenVariableLatticeParametersMultiSeed, 5 = firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed.
.IP
\fB--pinkIndexer-tolerance\fR selects the tolerance of the pinkIndexer (relative tolerance of the lattice vectors). Default is 0.06. For bad geometrys or cell parameters use a high tolerance. For a well known geometry and cell use a small tolerance. Only important for refinement and indexed/not indexed identificaton. Too small tolerance will lead to refining to only a fraction of the peaks and possibly discarding of correctly indexed images. Too high tolerance will lead to bad fitting in presence of multiples or noise and can mark wrongly-indexed patterns as indexed.
.IP
\fB--pinkIndexer-reflection-radius\fR sets radius of the reflections in reciprocal space in 1/A. Default is 2%% of a* (which works quiet well for X-rays). Should be chosen much bigger for electrons (~0.002).
.IP
\fB--pinkIndexer-max-resolution-for-indexing\fR sets the maximum resolition in 1/A used for indexing. Peaks at high resolution don't add much information, but they add a lot of computation time. Default is infinity. Does not influence the refinement.
.IP
\fB--pinkIndexer-multi\fR Use pinkIndexers own multi indexing. Should be combined with the --no-multi flag.
.IP
\fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFEL's parallelization does. For HPCs typically a mixture of both parallelizations leads to best results.
.IP
\fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFEL's prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented.
.IP
\fB--pinkIndexer-override-bandwidth=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-photon-energy=\fIn\fR. Note: this option sets the borders for the spectrum, whereas the option in the geometry file sets the standard deviation for a Gaussian that fits the spectrum. Internally, the standard deviation is multiplied by 5 to compute the hard borders of the spectrum. I.e., photon_energy_bandwith = 0.005 in the geometry file equals --pinkIndexer-override-bandwidth=0.025. For monochromatic experiments usually --pinkIndexer-override-bandwidth=0.02 is sufficiently large. If in doubt, use --pinkIndexer-override-visible-energy-range.
.IP
\fB--pinkIndexer-override-photon-energy=\fIn\fR Overrides the mean energy in eV to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR
.IP
\fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR Overrides photon energy and bandwidth according to a range of energies that have high enough intensity to produce visible Bragg spots on the detector. min and max range borders are separated by a minus sign (no whitespace).

.SH INTEGRATION OPTIONS
.PD 0
.IP \fB--integration=\fR\fImethod\fR
.PD
Integrate the reflections using \fImethod\fR.  See the section titled \fBPEAK INTEGRATION\fR (above) for more information.  The default is \fB--integration=rings-nocen\fR.

.PD 0
.IP \fB--fix-profile-radius=\fIn\fR
.IP \fB--fix-divergence=\fIn\fR
.PD
Fix the beam and crystal paramters to the given values.  The profile radius is given in m^-1 and the divergence in radians (full angle).  The default is to set the divergence to zero, and then to automatically determine the profile radius.
.IP
You do not have to use all three of these options together.  For example, if the automatic profile radius determination is not working well for your data set, you could fix that alone and continue using the default values for the other parameters (which might be automatically determined in future versions of CrystFEL, but are not currently).

.PD 0
.IP \fB--int-radius=\fR\fIinner,middle,outer\fR
.PD
Set the inner, middle and outer radii for three-ring integration.  See the
section about \fBPEAK INTEGRATION\fR, above, for details of how to determine
these.  The defaults are probably not appropriate for your situation.
.PD
The default is \fB--int-radius=4,5,7\fR.

.PD 0
.IP \fB--int-diag=\fIcondition\fR
.PD
Show detailed information about reflection integration when \fIcondition\fR is met.  The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR.  \fBrandom\fR means to show information about a random 1% of the peaks.  \fBnegative\fR means to show peaks with intensities which are negative by more than 3 sigma.  \fBimplausible\fR means to show peaks with intensities which are negative by more than 5 sigma.  \fBstrong\fR means to show peaks with intensities which are positive by more than 3 sigma  The default is \fB--int-diag=none\fR.

.PD 0
.IP \fB--push-res=\fIn\fR
.PD
Integrate \fIn\fR nm^-1 higher than the apparent resolution limit of each individual crystal.  \fIn\fR can be negative to integrate \fIlower\fR than the apparent resolution limit.  The default is \fB--push-res=infinity\fR, which means that no cutoff is applied.  Note that you can also apply this cutoff at the merging stage using \fBprocess_hkl/partialator --push-res\fR, which is usually better: reflections which are thrown away at the integration stage cannot be brought back later.  However, applying a resolution cutoff during integration will make the stream file significantly smaller and faster to merge.

.PD 0
.IP \fB--overpredict\fR
.PD
Over-predict reflections.  This is needed to provide a buffer zone when using post-refinement, but makes it difficult to judge the accuracy of the predictions because there are so many reflections.  It will also reduce the quality of the merged data if you merge without partiality estimation.

.SH OUTPUT OPTIONS

.PD 0
.IP \fB--no-non-hits-in-stream\fR
.PD
Completely exclude 'non-hit' frames in the stream.  When this option is given, frames with fewer than the number of peaks given to \fB--min-peaks\fR will not have chunks written to the stream at all.

.PD 0
.IP \fB--copy-hdf5-field=\fR\fIpath\fR
.PD
Copy the information from \fR\fIpath\fR in the HDF5 file into the output stream.  The information must be a single scalar value.  This option is sometimes useful to allow data to be separated after indexing according to some condition such the presence of an optical pump pulse.  You can give this option as many times as you need to copy multiple bits of information.

.PD 0
.IP \fB--no-peaks-in-stream\fR
.PD
Do not record peak search results in the stream.  You won't be able to check that the peak detection was any good, but the stream will be around 30% smaller.

.PD 0
.IP \fB--no-refls-in-stream\fR
.PD
Do not record integrated reflections in the stream.  The resulting output won't be usable for merging, but will be a lot smaller.  This option might be useful if you're only interested in things like unit cell parameters and orientations.

.PD 0
.IP \fB--serial-offset=\fIn\fR
.PD
Start the serial numbers in the stream at \fIn\fR instead of 1.  Use this if you are splitting an indexing job up into several smaller ones, so that the streams can be concatenated into a single one with consistent numbering.  This is important if you use \fBwhirligig\fR.

.SH HISTORICAL OPTIONS

.PD 0
.IP \fB--no-sat-corr\fR
.PD
This option is here for historical purposes only, to disable a correction which is done if certain extra information is included in the HDF5 file.

.SH IDENTIFYING SINGLE PATTERNS IN THE INPUT FILE

By default indexamajig processes all diffraction patterns ("events") in each of the data files listed in the input list. It is however, possible, to only process single events in a multi-event file, by adding in the list an event description string after the data filename. The event description always includes a first section with alphanumeric strings separated by forward slashes ("/") and a second section with integer numbers also separated by forward slashes. The two sections are in turn separated by a double forward slash ('//'). Any of the two sections can be empty, but the double forward slash separator must always be present.  Indexamajig matches the strings and the numbers in the event description with the event placeholders ('%') present respectively in the 'data' and 'dim' properties defined in the geometry file, and tries to retrieve the full HDF path to the event data and the the its location in a multi-dimensional data space. Consider the following examples:

\fBExample 1:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:

.br
data = /data/%/rawdata
.br
dim0 = ss
.br
dim1 = fs

The event list contains the following line:
.br

filename.h5  event1//
.br

This identifies an event in the 2-dimensional data block located at /data/event1/rawdata in the HDF5 file called filename.h5.

\fBExample 2:\fR The 'data' and 'dim' properties have been defined like this in the geometry file:

.br
data = /data/rawdata
.br
dim0 = %
.br
dim1 = ss
.br
dim2 = fs

The event list contains the following line:
.br

filename.h5  //3
.br

This identifies an event in the 3-dimensional data block located at /data/rawdata in the HDF5 file called filename.h5, specifically the 2-dimensional data slice defined by the value 3 of the first axis of the data space.

Indexamajig tries to match the alphanumerical strings to the placeholders in the 'dim' property defined in the geometry file. The first string is matched to the first placeholder, the second to
the second placeholder, and so on. A similar strategy is followed to match integer numbers to the placeholders in the 'dim' property defined in the geometry file.
For a full explanation of how the internal layout of the data file can be  described in the geometry file, please see \fBman crystfel_geometry\fR.

You can use \fBlist_events\fR to prepare a list of each event in one or more input files.  Note that you only need to do this if you need to perform some sorting or filtering on this list.  If you want to process every event in a file, simply specify the filename in the input file.

.SH AUTHOR
This page was written by Thomas White, Yaroslav Gevorkov and Valerio Mariani.

.SH REPORTING BUGS
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.

.SH COPYRIGHT AND DISCLAIMER
Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
indexamajig, 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 crystfel_geometry (5),
.BR cell_explorer (1),
.BR process_hkl (1),
.BR partialator (1),
.BR list_events (1),
.BR whirligig (1)