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indexamajig: bulk indexing and data reduction program

Synopsis

indexamajig -i filename -o output.stream -g detector.geom --peaks=method --indexing=method [options] ...
indexamajig --help

Description

indexamajig 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 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:

indexamajig -i mypatterns.lst -g mygeometry.geom --indexing=mosflm,dirax --peaks=hdf5 -o test.stream -p mycell.pdb

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 man crystfel_geometry for information about how to create a file describing the detector geometry and beam characteristics.

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 image filenames. The image 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 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.

Peak detection

You can control the peak detection on the command line. First, you can choose the peak detection method using --peaks=method. --peaks=hdf5 or --peaks=cxi will take the peak locations from the input file. See the documentation for peak_list and peak_list_type in crystfel_geometry for details.

If you use --peaks=zaef, 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 --threshold and --min-squared-gradient. 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 --peaks=peakfinder8, 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 --peaks=peakfinder9, 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 (--local-bg-radius). 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 (--min-peak-over-neighbour). 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 (--min-snr-biggest-pix) by computing the local statistics from the border pixels in a specified radius. Fourth condition sums up all pixels belonging to the peak (--min-snr-peak-pix) and demands that the whole peak must be significantly over the noise level (--min-snr). 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.

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:

dirax

Invoke DirAx. See Duisenberg, J. Applied Crystallography 25 (1992) p92, https://doi.org/10.1107/S0021889891010634.

mosflm

Invoke Mosflm. See Powell, Acta Crystallographica D55 (1999) p1690, https://doi.org/10.1107/S0907444999009506.

asdf

This is a implementation of the dirax 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.

felix

Invoke Felix, which will use your cell parameters to find multiple crystals in each pattern. The Felix indexer has been developed by Soeren Schmidt. 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 Felix on the command line, things are set up correctly.

xds

Invoke XDS, and use its REFIDX procedure to attempt to index the pattern.

taketwo

Use the TakeTwo algorithm. See Ginn et al., Acta Crystallographica D72 (2016), p956, https://doi.org/10.1107/S2059798316010706.

xgandalf

Invoke XGANDALF - eXtended GrAdient Descent Algorithm for Lattice Finding. See Gevorkov et al., Acta Crystallographica A75 (2019) p694, https://doi.org/10.1107/S2053273319010593.

pinkIndexer

Invoke pinkIndexer. See Gevorkov et al., Acta Crystallographica A76 (2020) p121, https://doi.org/10.1107/S2053273319015559.

Most of the indexing methods require some extra software to be installed, either at the time of compiling CrystFEL or afterwards. CrystFEL is distributed with a script (scripts/install-indexers) which can help you to quickly install all the required programs.

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) and not provide prior information.

-latt

Use the lattice type information (e.g. the knowledge that the lattice is tetragonal primitive) as prior information to the indexing engine.

-nolatt

The opposite of -latt: do not provide Bravais lattice type information to the indexing engine.

-cell

Provide your unit cell parameters as prior information to the indexing engine.

-nocell

The opposite of -cell: do not provide unit cell parameters as prior information to the indexing engine.

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

If you don't specify any indexing methods, indexamajig will try to automatically determine which indexing methods are available. You can also specify indexing method none, in which case no indexing will be done. This is useful if you just want to check that the peak detection is working properly.

Usually, you do not need to explicitly specify anything more than the indexing method itself (e.g. mosflm or asdf). 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 indexamajig will do what you want and intuitively expect! However, the options are available if you need finer control.

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

Peak integration

-peaks=method

Find peaks in the images using method. See the second titled Peak Detection (above) for more information.

--peak-radius=inner,middle,outer

Set the inner, middle and outer radii for three-ring integration during the peak search. See the section about Peak Integration, above, for details of how to determine these. The default is to use the same values as for --int-radius.

--min-peaks=n

Do not try to index frames with fewer than n peaks. These frames will still be described in the output stream. To exclude them, use --no-non-hits-in-stream. The default is --min-peaks=0, which means that all frames will be considered hits, even if they have no peaks at all.

--median-filter=n

Apply a median filter with box "radius" n to the image. The median of the values from a (n+1)x(n+1) 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 unfiltered image will be used for the final integration of the peaks. If you also use --noise-filter, the median filter will be applied first.

--filter-noise

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 unfiltered 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 --median-filter, the median filter will be applied first.

--threshold=thres

Set the overall threshold for peak detection using --peaks=zaef or --peaks=peakfinder8 to thres, which has the same units as the detector data. The default is --threshold=800.

--min-squared-gradient=grad

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

--min-snr=snr

Set the minimum I/sigma(I) for peak detection when using --peaks=zaef or --peaks=peakfinder8. The default is --min-snr=5.

--min-snr-biggest-pix=n

(peakFinder9 only) min snr of the biggest pixel in the peak, given as a factor of the standard deviation. Default is 7.0.

--min-snr-peak-pix=n

(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.

--min-sig=n

(peakFinder9 only) minimum standard deviation of the background. Prevents finding of peaks in erroneous or highly shadowed unmasked regions. Default is 11.0.

--min-peak-over-neighbour=n

(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.

--min-pix-count=n

Accepts peaks only if they include more than n pixels, when using --peaks=peakfinder8. The default is --min-pix-count=2.

--max-pix-count=n

Accepts peaks only if they include less than n pixels, when using --peaks=peakfinder8. The default is --max-pix-count=200.

--local-bg-radius=n

Radius (in pixels) used for the estimation of the local background when using --peaks=peakfinder8 or --peaks=peakfinder9. The default is --local-bg-radius=3.

--min-res=n

Only accept peaks if they lay at more than n pixels from the center of the detector when using --peaks=peakfinder8. The default is --min-res=0.

--max-res=n

Only accept peaks if they lay at less than n pixels from the center of the detector when using --peaks=peakfinder8. The default is --max-res=1200.

--no-use-saturated

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 --use-saturated, which is the default.

--no-revalidate

When using --peaks=hdf5, --peaks=cxi or --peaks=msgpack, the peaks will be put through some of the same checks as if you were using --peaks=zaef. These checks reject peaks which are too close to panel edges, are saturated (unless you use --use-saturated), have other nearby peaks (closer than twice the inner integration radius, see --int-radius), or have any part in a bad region. Using this option skips this validation step, and uses the peaks directly.

--no-half-pixel-shift

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 image data files, including Cheetah, may instead consider the peak locations to be pixel indices in the data array. Therefore, the peak coordinates from --peaks=cxi or --peaks=hdf5 will by default have 0.5 added to them. This option disables this half-pixel offset.

--check-hdf5-snr

With this option and --peaks=hdf5 (or cxi or msgpack), the peaks will additionally be checked to see that they satisfy the minimum SNR specified with --min-snr.

--peakfinder8-fast

(peakfinder8 only) Increase speed by pre-calculating some coordinate tables.

Indexing options

--indexing=method

Index the patterns using method. See the section titled Indexing Methods (above) for more information. The default is to automatically detect which indexing methods to use.

-p unitcell.cell
-p unitcell.pdb
--pdb=unitcell.pdb

Specify the name of the file containing the unit cell information, in PDB or CrystFEL format.

--tolerance=tol

Set the tolerances for unit cell comparison. tol takes the form a,b,c,ang. a, b and c are the tolerances, in percent, for the respective reciprocal space axis lengths, and ang 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.

The default is --tolerance=5,5,5,1.5.

--no-check-cell

Do not check the cell parameters against the reference unit cell (given with -p). If you've used older versions of CrystFEL, this replaces putting "-raw" in the indexing method.

--no-check-peaks

Do not check that most of the peaks can be accounted for by the indexing solution. The thresholds for a successful result are influenced by option --multi.

--multi

Enable multi-lattice indexing. This refers to 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.

This option also adjusts the thresholds for identifying successful indexing results (see --no-check-peaks).

--wavelength-estimate=m
--camera-length-estimate=m

Some indexing algorithms need to know the camera length or the wavelength of the incident radiation in advance, e.g. to prepare an internal look-up table. However, if these values are taken from image headers, then they are not available at start-up. In this case, you will be prompted to add one of these options to give approximate values (in metres). A warning will be generated if the actual value differs from this value by more than 10%.

--max-indexer-threads=n

Some indexing algorithms (e.g. pinkIndexer) can use multiple threads for faster calculations. This is in addition to the frame-based parallelism already available in indexamajig (see -j). This option sets the maximum number of threads that each indexing engine is allowed to use. Default: 1.

--no-retry

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.

--no-refine

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.

--taketwo-member-threshold=n
--taketwo-len-tolerance=n
--taketwo-angle-tolerance=n
--taketwo-trace-tolerance=n

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 matrix trace tolerance (in degrees) for considering rotation matrices as equal.

The defaults are: --taketwo-member-threshold=20, --taketwo-len-tolerance=0.001, --taketwo-angle-tolerance=0.6 and --taketwo-trace-tolerance=3.

--felix-domega=n
--felix-fraction-max-visits=n
--felix-max-internal-angle=n
--felix-max-uniqueness=n
--felix-min-completeness=n
--felix-min-visits=n
--felix-num-voxels=n
--felix-sigma=n
--felix-tthrange-max=n
--felix-tthrange-min=n

These set low-level parameters for the Felix indexing algorithm.

--xgandalf-sampling-pitch=n
--xgandalf-grad-desc-iterations=n
--xgandalf-tolerance=n
--xgandalf-no-deviation-from-provided-cell
--xgandalf-max-lattice-vector-length=n
--xgandalf-min-lattice-vector-length=n
--xgandalf-max-peaks=n
--xgandalf-fast-execution

These set low-level parameters for the XGANDALF indexing algorithm.

--xgandalf-sampling-pitch selects how dense the reciprocal space is sampled. [0-4]: extremelyLoose to extremelyDense. [5-7]: standardWithSeondaryMillerIndices to extremelyDenseWithSeondaryMillerIndices. Default is 6 (denseWithSeondaryMillerIndices).

--xgandalf-grad-desc-iterations selects how many gradient descent iterations are performed. [0-5]: veryFew to extremelyMany. Default is 4 (manyMany).

--xgandalf-tolerance relative tolerance of the lattice vectors. Default is 0.02.

--xgandalf-no-deviation-from-provided-cell 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.

--xgandalf-min-lattice-vector-length and --xgandalf-min-lattice-vector-length 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.

-xgandalf-max-peaks 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.

--xgandalf-fast-execution shortcut to set --xgandalf-sampling-pitch=2 --xgandalf-grad-desc-iterations=3

--pinkIndexer-considered-peaks-count=n
--pinkIndexer-angle-resolution=n
--pinkIndexer-refinement-type=n
--pinkIndexer-tolerance=n
--pinkIndexer-reflection-radius=n
--pinkIndexer-max-resolution-for-indexing=n
--pinkIndexer-max-refinement-disbalance=n

These set low-level parameters for the PinkIndexer indexing algorithm.

--pinkIndexer-considered-peaks-count selects how many peaks are considered for indexing. [0-4] (veryFew to manyMany). Default is 4 (manyMany).

--pinkIndexer-angle-resolution selects how dense the orientation angles of the sample lattice are sampled. [0-4] (extremelyLoose to extremelyDense). Default is 2 (normal).

--pinkIndexer-refinement-type selects the refinement type. 0 = none, 1 = fixedLatticeParameters, 2 = variableLatticeParameters, 3 = firstFixedThenVariableLatticeParameters, 4 = firstFixedThenVariableLatticeParametersMultiSeed, 5 = firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed.

--pinkIndexer-tolerance 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.

--pinkIndexer-reflection-radius 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).

--pinkIndexer-max-resolution-for-indexing 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.

--pinkIndexer-multi Use pinkIndexers own multi indexing. Should be combined with the --no-multi flag.

--pinkIndexer-max-refinement-disbalance=n Indexing solutions are dismissed if the refinement refined very well to one side of the detector and very badly to the other side. Allowed values range from 0 (no disbalance) to 2 (extreme disbalance), default 0.4. Disbalance after refinement usually appears for bad geometries or bad prior unit cell parameters.

Integration options

-integration=method

Integrate the reflections using method. See the section titled Peak Integration (above) for more information. The default is --integration=rings-nocen.

--fix-profile-radius=n
--fix-divergence=n

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.

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).

--int-radius=inner,middle,outer

Set the inner, middle and outer radii for three-ring integration. See the section about Peak Integration, above, for details of how to determine these. The defaults are probably not appropriate for your situation.

The default is --int-radius=4,5,7.

--int-diag=condition

Show detailed information about reflection integration when condition is met. The condition can be all, none, a set of Miller indices separated by commas, random, implausible or negative. random means to show information about a random 1% of the peaks. negative means to show peaks with intensities which are negative by more than 3 sigma. implausible means to show peaks with intensities which are negative by more than 5 sigma. strong means to show peaks with intensities which are positive by more than 3 sigma. The default is --int-diag=none.

Output options

--no-non-hits-in-stream

Completely exclude 'non-hit' frames in the stream. Which this option is give, frames with fewer than the number of peaks given to --min-peaks will not have chunks written to the stream at all. Note that the default value for --min-peaks is zero, which means all frames will be written to the stream, even if they have no peaks at all.

--copy-hheader=header

Copy the information from header in the image file into the output stream. For HDF5 files, header is interpreted as a path within the file. 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.

The old option --copy-hdf5-field is a synonym for this option.

--no-peaks-in-stream

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.

--no-refls-in-stream

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.

--serial-offset

Start the serial numbers in the stream at n 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 whirligig.

--harvest-file=fn

Write a list of parameters to fn, in JSON format. This is intended to be used for harvesting data into a database system. This option has no effect if --serial-offset is set to a number larger than 1, to avoid the file being overwritten multiple times in a batch system.

Historical optoins

--no-sat-corr

This option is here for historical purposes only, to disable a correction which is done if certain extra information is included in the image data file.

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:

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

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

The event list contains the following line:

filename.h5  event1//

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

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

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

The event list contains the following line:

filename.h5  //3

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 man crystfel_geometry.

You can use list_events 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.

Author

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

Reporting bugs

Report bugs to taw@physics.org

Copyright and Disclaimer

Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.

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

If CrystFEL is installed on your computer, you can read this manual page offline using the command man indexamajig.