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diff --git a/doc/indexamajig b/doc/indexamajig new file mode 100644 index 00000000..7d6e0d16 --- /dev/null +++ b/doc/indexamajig @@ -0,0 +1,83 @@ +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'. |