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