Indexing and integration

In principle, one could attempt to index and integrate every single image recorded during a "diffract-and-destroy" experiment. Typically only a small fraction of the recorded images exhibit an indexable lattice, and in practice a hit-finder is needed to triage the stream of images, and preserve computational resources.

Indexing and integration are tightly coupled; it is impossible to integrate an image without first obtaining an indexing solution. The result of successfully indexing an image is essentially a model of crystal–beam interaction. The model not only describes how the crystal is oriented with respect to the direction of the X-ray pulse, but also its degree of imperfection (i.e. mosaicity), and qualities of the illuminating pulse (e.g. bandwidth). The integration algorithm uses this model to predict where Bragg spots appear on the image, and integrates the intensities around those predications. The integration algorithm thus exploits the regularity of the underlying crystal lattice to recover signal where it was too weak to be detected.

pyana section

For historical reasons, hit-finding and indexing/integration are both implemented in the same analysis module, called mod_hitfind. To chain the two functions together, pyana must be configured to pass each event through two different instances of the same module. The two instances are differentiated by their name following the colon. In the example below, the first instance is called hitfind, and the second is index.

[pyana]
modules = my_ana_pkg.mod_hitfind:hitfind \
          my_ana_pkg.mod_hitfind:index

Any instance of an analysis module can signal pyana to skip further processing of the event. In the case above, the hitfind instance of mod_hitfind would signal pyana to skip the event if it determines that the image associated with the event is not a hit. In that case, the second instance, index, will never see the event. Otherwise, the event is fed to the second instance, which will attempt indexing and integration on the associated image.

The pyana-section of the processing configuration used for this part of the tutorial has one more feature.

[pyana]
modules = my_ana_pkg.mod_hitfind:hitfind \
          my_ana_pkg.mod_dump:hit        \
          my_ana_pkg.mod_hitfind:index   \
          my_ana_pkg.mod_dump:indexed

Each instance of mod_hitfind is followed by an instance of mod_dump. mod_dump is a simple module that just outputs the image associated with the event to the file system. In the above configuration, images are written to disk if they are determined to be hits, and then written again—possibly using a different name—if indexing and integration succeeds.

Hit-finding

Hit-finding may be viewed as a pattern-recognition problem, separate from whatever methods are used for actual processing of a diffraction image. The hit-finder in cctbx.xfel, however, is based on the same algorithms as are used for data analysis. In particular, the hit-finder implemented in mod_hitfind uses the Spotfinder (Zhang et al., 2006) algorithm to detect strong, low-resolution peaks.

The configuration for the hitfind instance of mod_hitfind is shown below.

[my_ana_pkg.mod_hitfind:hitfind]
address         = CxiDs1-0|Cspad-0
calib_dir       = /reg/d/ffb/cxi/temp/cctbx/cctbx_xfel/sources/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0:Cspad.0
dark_path       = /reg/d/ffb/cxi/temp/cctbx/tutorials/darks/Ds1-r0002-avg.pickle
dark_stddev     = /reg/d/ffb/cxi/temp/cctbx/tutorials/darks/Ds1-r0002-stddev.pickle
detz_offset     = 581
dispatch        = nop
distl_flags     = permissive
distl_min_peaks = 16
threshold       = 450
xtal_target     = /reg/d/ffb/cxi/temp/cctbx/cctbx_xfel/sources/labelit_regression/xfel/hitfind-7.1.phil

address

Full data source address of the DAQ device, see Data Source Address in the Pyana User Manual. This identifies the detector from which images are to be extracted.

calib_dir

This value defines the initial placement of the detector elements. cctbx.xfel implements its metrology corrections with respect to these initial definitions. As a result, the value of this option should not be changed.

dark_path

Path to an average image from a dark run (i.e. pedestal) to use for dark-subtraction.

dark_stddev

Path to a standard-deviation image from a dark run.

detz_offset

The distance from the interaction region, where the X-ray pulse and the sample jet intersect, to the back of the detector stage, in mm.

dispatch

What action mod_hitfind is to take. The value should be nop for hit-finding.

distl_flags

General behavior of the hit-finder, either permissive or restrictive.

distl_min_peaks

How many strong, low-resolution peaks are required to classify the image as a hit.

threshold

How high a peak must be above the background to be classified as strong, in analog-to-digital units (ADU).

xtal_target

phil-file containing further configuration options for the hit-finder.

Image output

The configuration section for image output is given below.

[my_ana_pkg.mod_dump:hit]
address      = CxiDs1-0|Cspad-0
calib_dir    = /reg/d/ffb/cxi/temp/cctbx/cctbx_xfel/sources/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0:Cspad.0
out_dirname  = /reg/d/ffb/cxi/temp/cctbx/tutorials/scratch/<username>/lysozyme
out_basename = shot-

The address and calib_dir options were explained in Hit-finding above.

out_dirname

Directory portion of output image pathname.

out_basename

Filename prefix of output image pathname.

The actual pathname of the image as it is written to the file system is determined by joining out_dirname and out_basename using the directory separator (/ on Unix), and appending a textual representation of the timestamp when the image was recorded.

Indexing and integration

address              = CxiDs1-0|Cspad-0
calib_dir            = /reg/d/ffb/cxi/temp/cctbx/cctbx_xfel/sources/cctbx_project/xfel/metrology/CSPad/run4/CxiDs1.0:Cspad.0
dark_path       = /reg/d/ffb/cxi/temp/cctbx/tutorials/darks/Ds1-r0002-avg.pickle
dark_stddev     = /reg/d/ffb/cxi/temp/cctbx/tutorials/darks/Ds1-r0002-stddev.pickle
detz_offset          = 581
dispatch             = index
integration_dirname  = /reg/d/ffb/cxi/temp/cctbx/tutorials/scratch/<username>/lysozyme
integration_basename = int-
xtal_target          = /reg/d/ffb/cxi/temp/cctbx/cctbx_xfel/sources/labelit_regression/xfel/LXXX-lysozyme.phil

The options not already explained in Hit-finding are:

dispatch

What action mod_hitfind is to take. The value should be index for indexing.

integration_dirname

Directory portion of output integration file pathname.

integration_basename

Filename prefix of output integration file pathname.

xtal_target

phil-file containing further configuration options for the indexing and integration algorithms.

The integration file is not an image file, but a list of Miller indices, their integrated intensities, and estimated uncertainties. The actual pathname of the integration file as it is written to the file system is determined by joining out_dirname and out_basename using the directory separator (/ on Unix), and appending a textual representation of the timestamp when the corresponding image was recorded.

Processing the tutorial data

The complete configuration is stored at XXX. To submit a processing job to the cluster

$ ./lsf.sh -c LXXX-lysozyme.cfg -o /reg/d/ffb/cxi/temp/cctbx/tutorials/scratch/<username>/lysozyme -p 6 -q psfehq  -r 69 -x cxiXXXXX

But note that lsf.sh must be patched first. How to monitor progress, check on number of hits, number of integrated images. How to inspect sample images. etc