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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 (indexamajig, pattern_sim and
powder_plot) take an argument "--geometry=<file>" (or "-g <file>"), where <file>
contains the geometry. CrystFEL's representation of a detector is broken down
into one or more "panels", each of which has its own location for the centre of
the panel (i.e. the location of the central beam), its own camera length,
resolution and so on. Each panel fits into the overall image taken from the
HDF5 file, defined by minimum and maximum coordinates in x and y. The
coordinates are specified inclusively, meaning that a minimum of 0 and a maximum
of 9 results in ten items. Counting begins from zero. All pixels in the image
must be assigned to a panel.
See "A note on data orientation" below for important information about how
CrystFEL defines the axes. All coordinates (including the centre coordinates
for each panel) are measured according to these axes: there is no coordinate
system local to a panel.
The syntax for a simple geometry might be as follows:
; The number of panels
n_panels = 1
; "0/" specifies the first (and only) panel. If we had more panels, there would
; be a copy of the following lines but prefixes with "1/", "2/" and so on.
; The region of the image which belongs to this panel:
0/min_x = 0
0/max_x = 1023
0/min_y = 512
0/max_y = 1023
; The coordinates of the central beam which should be
; used for pixels in this panel:
0/cx = 491.9
0/cy = 440.7
; The camera length (in metres) for this panel
0/clen = 67.8e-3
; The resolution (in pixels per metre) for this panel
0/res = 13333.3 ; 75 micron pixel size
; 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 '0', then the culling described above will not
; be performed for this panel.
0/badrow_direction = y
; If "no_index" is "true", then peaks in this panel will not be used for
; indexing nor integrated and recorded in the stream.
0/no_index = false
; The lower bound on true peak separation is about 50 pixels
0/peak_sep = 50
See the "examples" folder for some examples.
A note on data orientation
--------------------------
In the image data extracted from the HDF5 file, CrystFEL defines "x" as the most
quickly varying coordinate in the data, and "y" as the second most quickly
varying coordinate in the data. It doesn't know what to do with any extra
dimensions in the HDF5 dataset beyond the second.
The origin, which is considered the lower left corner of the image, is defined
by CrystFEL as the first element in the image data. Positive x points in a
direction to the right, and positive y points upwards. CrystFEL considers the
positive z direction to be the direction of the incident beam completing the
right-handed set of axes.
The detector surface is currently always assumed to be perpendicular to the
incident beam.
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