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Diffstat (limited to 'doc/man/crystfel_geometry.1')
| -rw-r--r-- | doc/man/crystfel_geometry.1 | 52 |
1 files changed, 49 insertions, 3 deletions
diff --git a/doc/man/crystfel_geometry.1 b/doc/man/crystfel_geometry.1 index 0deb058e..8a3f0903 100644 --- a/doc/man/crystfel_geometry.1 +++ b/doc/man/crystfel_geometry.1 @@ -7,10 +7,8 @@ .\" .TH CRYSTFEL\_GEOMETRY 1 -.SH NAME -CrystFEL detector geometry files -.SH OVERVIEW +.SH 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, @@ -37,7 +35,9 @@ 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) +.br +y points towards the zenith (ceiling). +.br +x completes the right-handed coordinate system. Naively speaking, this means that CrystFEL at the images from the "into the @@ -50,73 +50,119 @@ form: ; Lines which should be ignored start with a semicolon. ; The name before the slash indicates which panel is referred to. You can use +.br ; any name as long as it doesn't start with "bad" (see below). +.br ; The range of pixels in the HDF5 file which correspond to a panel are given: +.br panel0/min_fs = 0 +.br panel0/min_ss = 0 +.br panel0/max_fs = 193 +.br panel0/max_ss = 184 ; The readout direction (x, y or 0). If more than three peaks are found in +.br ; the same readout region, they are all discarded. This helps to avoid +.br ; problems due to streaks appearing along the readout direction. +.br ; If the badrow direction is '-', then the culling described above will not +.br ; be performed for this panel. +.br panel0/badrow_direction = - ; The resolution (in pixels per metre) for this panel +.br panel0/res = 9090.91 ; The characteristic peak separation in pixels. The peak detection will assume +.br ; that genuine peaks are separated by at least this amount. +.br panel0/peak_sep = 6.0 ; You need to specify the peak integration radius, which should be a little +.br ; larger than the actual radii of the peaks in pixels +.br panel0/integr_radius = 2.0 ; The camera length (in metres) for this panel +.br ; You can also specify the HDF path to a scalar floating point value containing +.br ; the camera length in millimetres. +.br panel0/clen = /LCLS/detectorPosition ; For this panel, the fast and slow scan directions correspond to the given +.br ; directions in the lab coordinate system described above, measured in pixels. +.br panel0/fs = +y +.br panel0/ss = -x ; The corner of this panel, defined as the first point in the panel to appear in +.br ; the HDF5 file, is now given a position in the lab coordinate system. +.br ; Note that "first point in the panel" is a conceptual simplification. We refer +.br ; to that corner, and to the very corner of the pixel - NOT, for example, to the +.br ; centre of the first pixel to appear. +.br panel0/corner_x = 429.39 +.br panel0/corner_y = -17.30 ; You can suppress indexing for this panel if required, by setting "no_index" to +.br ; "true" or "1". +.br panel0/no_index = 0 ; You can also specify bad regions. Peaks with centroid locations within such +.br ; a region will not be integrated nor indexed. Bad regions are specified in +.br ; pixel units, but in the lab coordinate system (i.e. "y" points at the ceiling, +.br ; "z" is the beam direction and "x" completes the right-handed system). +.br badregionA/min_x = -20.0 +.br badregionA/max_x = +20.0 +.br badregionA/min_y = -100.0 +.br badregionA/max_y = +100.0 ; If you have a bad pixel mask, you can include it in the HDF5 file as an +.br ; unsigned 16-bit integer array of the same size as the data. You need to +.br ; give its path within each HDF5 file, and two bitmasks. The pixel is +.br ; considered good if all of the bits which are set in "mask_good" are set, AND +.br ; if none of the bits which are set in "mask_bad" are set. +.br mask = /processing/hitfinder/masks +.br mask_good = 0x27 +.br mask_bad = 0x00 ; Any of the per-panel values can be given without a panel prefix, for example: +.br peak_sep = 6.0 +.br ; in which case the value will be used for all *subsequent* panels. |