pynx-cdi-regrid#
Instructions to run the pynx-cdi-regrid command-line script to prepare a 3D cdi CXI file from multiple projections.
Rebuild the 3D reciprocal space by projecting a set of 2d speckle SAXS pattern taken at various rotation angles into a 3D regular volume
usage: pynx-cdi-regrid [-h] [-V] [-v] [--debug] [-o OUTPUT] [-s SHAPE] [--scale SCALE] [-m MASK] [--dry-run] [--profile] [--maxi MAXI] [-d DISTANCE] [-b BEAM BEAM] [-p PIXELSIZE] [--rot ROT] [--scan SCAN] [--scan-len SCAN_LEN] [--oversampling-img OVERSAMPLING_IMG] [--oversampling-rot OVERSAMPLING_ROT]
[--device DEVICE DEVICE]
[IMAGE ...]
Positional Arguments#
- IMAGE
file with input images in Bliss format HDF5
Named Arguments#
- -V, --version
output version and exit
- -v, --verbose
show information for each conversions
Default: False
- --debug
show debug information
Default: False
main arguments#
- -o, --output
output filename in CXI format
Default: “reciprocal_volume.cxi”
- -s, --shape
Size of the reciprocal volume, by default 512³
Default: 1024
- --scale
Scale (down) the voxel coordinates. For example a factor 2 is similar to a 2x2x2 binning of the volume
Default: 1.0
- -m, --mask
Path for the mask file containing both invalid pixels and beam-stop shadow
optional behaviour arguments#
- --dry-run
do everything except modifying the file system
Default: False
- --profile
Turn on the profiler and print OpenCL profiling at output
Default: False
- --maxi
Limit the processing to a given number of frames
Experimental setup options#
- -d, --distance
Detector distance in meter
- -b, --beam
Direct beam in pixels x, y, by default, the center of the image
- -p, --pixelsize
pixel size, by default 172µm
Default: 0.000172
Scan setup#
- --rot
Name of the rotation motor
Default: “ths”
- --scan
Name of the rotation motor
Default: “dscan sz”
- --scan-len
Pick scan which match that length (unless take all scans
Default: “1”
Oversampling options to reduces the moiré pattern#
- --oversampling-img
How many sub-pixel there are in one pixel (squared)
Default: 7
- --oversampling-rot
How many times a frame is projected
Default: 7
OpenCL options#
- --device
Platform and device ids
Assumption: There is enough memory to hold all frames in memory
return codes: 0 means a success. 1 means the conversion contains a failure, 2 means there was an error in the arguments