indexmajig - bulk indexing and data reduction program
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The indexamajig program takes as input a list of diffraction image files,
currently in HDF5 format.  For each image, it attempts to find peaks and then
index the pattern.  If successful, it will measure the intensities of the peaks
at Bragg locations and produce a list in the form "h k l I", with some extra
information about the locations of the peaks.

For minimal basic use, you need to provide the list of diffraction patterns,
the method which will be used to index (currently there is only one available
method), a file describing the geometry of the detector, and a PDB file which
contains the unit cell which will be used for the indexing.

Syntax: src/indexamajig [options]

Process and index FEL diffraction images.

  -h, --help              Display this help message.

  -i, --input=<filename>  Specify file containing list of images to process.
                           '-' means stdin, which is the default.

      --indexing=<method> Use 'method' for indexing.  Choose from:
                           none     : no indexing
                           dirax    : invoke DirAx
  -g. --geometry=<file>   Get detector geometry from file.


With just the above options, this program does not do much of practical use.
You should also enable some of the following:

      --near-bragg        Output a list of reflection intensities to stdout.
                           When pixels with fractional indices within 0.1 of
                           integer values (the Bragg condition) are found,
                           the integral of pixels within a ten pixel radius
                           of the nearest-to-Bragg pixel will be reported as
                           the intensity.  The centroid of the pixels will
                           be given as the coordinates, as well as the h,k,l
                           (integer) indices of the reflection.  If a peak
                           was located by the initial peak search close to
                           the "near Bragg" location, its coordinates will
                           be taken as the centre instead.
      --simulate          Simulate the diffraction pattern using the indexed
                           unit cell.  The simulated pattern will be saved
                           as "simulated.h5".  You can TRY to combine this
                           with "-j <n>" with n greater than 1, but it's
                           not a good idea.
      --filter-cm         Perform common-mode noise subtraction on images
                           before proceeding.  Intensities will be extracted
                           from the image as it is after this processing.
      --filter-noise      Apply an aggressive noise filter which sets all
                           pixels in each 3x3 region to zero if any of them
                           have negative values.  Intensity measurement will
                           be performed on the image as it was before this.
      --write-drx         Write 'xfel.drx' for visualisation of reciprocal
                           space.  Implied by any indexing method other than
                           'none'.  Beware: the units in this file are
                           reciprocal Angstroms.
      --dump-peaks        Write the results of the peak search to stdout.
                           The intensities in this list are from the
                           centroid/integration procedure.
      --no-match          Don't attempt to match the indexed cell to the
                           model, just proceed with the one generated by the
                           auto-indexing procedure.
      --unpolarized       Don't correct for the polarisation of the X-rays.
      --check-sanity      Check that indexed locations approximately correspond
                           with detected peaks.


Options for greater performance or verbosity:

      --verbose           Be verbose about indexing.
      --gpu               Use the GPU to speed up the simulation.
  -j <n>                  Run <n> analyses in parallel.  Default 1.


Control of model and data input:

     --intensities=<file> Specify file containing reflection intensities
                           to use when simulating.
 -p, --pdb=<file>         PDB file from which to get the unit cell to match.
 -x, --prefix=<p>         Prefix filenames from input file with 'p'.