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-CrystFEL detector geometry files
---------------------------------
-
-The detector geometry is taken from a text file rather than hardcoded into the
-program.  Programs which care about the geometry (particularly indexamajig,
-pattern_sim and powder_plot) take an argument "--geometry=<file>"
-(or "-g <file>"), where <file> contains the geometry.
-
-A flexible (and pedantic) representation of the detector has been developed to
-avoid all possible sources of ambiguity.  CrystFEL's representation of a
-detector is broken down into one or more "panels", each of which has its own
-camera length, geometry, resolution and so on.  Each panel fits into the overall
-image taken from the HDF5 file, defined by minimum and maximum coordinates in
-the "fast scan" and "slow scan" directions.  "Fast scan" refers to the direction
-whose coordinate changes most quickly as the bytes in the HDF5 file are moved
-through.  The coordinates are specified inclusively, meaning that a minimum of 0
-and a maximum of 9 results in a width of ten pixels.  Counting begins from zero.
-All pixels in the image must be assigned to a panel - gaps are not permitted.
-
-In the current version, panels are assumed to be perpendicular to the incident
-beam and to have their edges parallel.  Within these limitations, any geometry
-can be constructed.
-
-The job of the geometry file is to establish a relationship between the array
-of pixel values in the HDF5 file, defined in terms only of the "fast scan" and
-"slow scan" directions, and the laboratory coordinate system defined as follows:
-
-+z is the beam direction, and points along the beam (i.e. away from the source)
-+y points towards the zenith (ceiling).
-+x completes the right-handed coordinate system.
-
-Naively speaking, this means that CrystFEL at the images from the "into the
-beam" perspective, but please avoid thinking of things in this way.  It's much
-better to consider the precise way in which the coordinates are mapped.
-
-The syntax for a simple geometry might include several entires of the following
-form:
-
-; Lines which should be ignored start with a semicolon.
-
-; The name before the slash indicates which panel is referred to.  You can use
-; any name as long as it doesn't start with "bad" (see below).
-; The range of pixels in the HDF5 file which correspond to a panel are given:
-panel0/min_fs = 0
-panel0/min_ss = 0
-panel0/max_fs = 193
-panel0/max_ss = 184
-
-; The readout direction (x, y or 0).  If more than three peaks are found in
-; the same readout region, they are all discarded.  This helps to avoid
-; problems due to streaks appearing along the readout direction.
-; If the badrow direction is '-', then the culling described above will not
-; be performed for this panel.
-panel0/badrow_direction = -
-
-; The resolution (in pixels per metre) for this panel
-panel0/res = 9090.91
-
-; The characteristic peak separation in pixels.  The peak detection will assume
-; that genuine peaks are separated by at least this amount.
-panel0/peak_sep = 6.0
-
-; You need to specify the peak integration radius, which should be a little
-; larger than the actual radii of the peaks in pixels
-panel0/integr_radius = 2.0
-
-; The camera length (in metres) for this panel
-; You can also specify the HDF path to a scalar floating point value containing
-; the camera length in millimetres.
-panel0/clen = /LCLS/detectorPosition
-
-; For this panel, the fast and slow scan directions correspond to the given
-; directions in the lab coordinate system described above, measured in pixels.
-panel0/fs = +y
-panel0/ss = -x
-
-; The corner of this panel, defined as the first point in the panel to appear in
-; the HDF5 file, is now given a position in the lab coordinate system.
-; Note that "first point in the panel" is a conceptual simplification.  We refer
-; to that corner, and to the very corner of the pixel - NOT, for example, to the
-; centre of the first pixel to appear.
-panel0/corner_x = 429.39
-panel0/corner_y = -17.30
-
-; You can suppress indexing for this panel if required, by setting "no_index" to
-; "true" or "1".
-panel0/no_index = 0
-
-; You can also specify bad regions.  Peaks with centroid locations within such
-; a region will not be integrated nor indexed.  Bad regions are specified in
-; pixel units, but in the lab coordinate system (i.e. "y" points at the ceiling,
-; "z" is the beam direction and "x" completes the right-handed system).
-badregionA/min_x = -20.0
-badregionA/max_x = +20.0
-badregionA/min_y = -100.0
-badregionA/max_y = +100.0
-
-; If you have a bad pixel mask, you can include it in the HDF5 file as an
-; unsigned 16-bit integer array of the same size as the data.  You need to
-; give its path within each HDF5 file, and two bitmasks.  The pixel is
-; considered good if all of the bits which are set in "mask_good" are set, AND
-; if none of the bits which are set in "mask_bad" are set.
-mask = /processing/hitfinder/masks
-mask_good = 0x27
-mask_bad = 0x00
-
-; Any of the per-panel values can be given without a panel prefix, for example:
-peak_sep = 6.0
-; in which case the value will be used for all *subsequent* panels.
-
-
-See the "examples" folder for some examples (look at the ones ending in .geom).