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author | Thomas White <taw@physics.org> | 2011-06-16 17:53:28 +0200 |
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committer | Thomas White <taw@physics.org> | 2012-02-22 15:27:28 +0100 |
commit | 34b21127ea75e6a714a6c04a09f226180b2eb541 (patch) | |
tree | db5d75b4365cbbda4728f0d512d24abcdd3ece88 /doc/geometry.txt | |
parent | aa4d05d94275baa8c87acc6343a23d16f1877b24 (diff) |
Move documentation to manpages
Diffstat (limited to 'doc/geometry.txt')
-rw-r--r-- | doc/geometry.txt | 112 |
1 files changed, 0 insertions, 112 deletions
diff --git a/doc/geometry.txt b/doc/geometry.txt deleted file mode 100644 index c215d27c..00000000 --- a/doc/geometry.txt +++ /dev/null @@ -1,112 +0,0 @@ -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). |