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+indexmajig - bulk indexing and data reduction program
+-----------------------------------------------------
+
+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'.