Single crystal tool: sparsify-Bragg
Compress single crystal datasets by removing the background noise
Purpose
Sparsify 2D single crystal diffraction images by separating Bragg peaks from background signal.
Positive outlier pixels (i.e. Bragg peaks) are all recorded as they are without destruction. Peaks are not integrated.
Background is calculated by an iterative sigma-clipping in the polar space. The number of iteration, the clipping value and the number of radial bins could be adjusted.
This program requires OpenCL. The device needs be properly selected.
Usage:
spasify-Bragg [-h] [-V] [-v] [–debug] [–profile] [-o OUTPUT] [–save-source] [-b BEAMLINE] [-p PONI] [-m MASK] [–dummy DUMMY] [–delta-dummy DELTA_DUMMY] [–radial-range RADIAL_RANGE RADIAL_RANGE] [-P POLARIZATION] [-A] [–bins BINS] [–unit UNIT] [–cycle CYCLE] [–cutoff-clip CUTOFF_CLIP] [–cutoff-pick CUTOFF_PICK] [–error-model ERROR_MODEL] [–noise NOISE] [–workgroup WORKGROUP] [–device DEVICE DEVICE] [–device-type DEVICE_TYPE] [IMAGE …]
Options:
- IMAGE
File with input images. All frames will be concatenated in a single HDF5 file.
- -h, –help
show this help message and exit
- -V, –version
output version and exit
- -v, –verbose
show information for each frame
- –debug
show debug information
- –profile
show profiling information
Main arguments:
- -o OUTPUT, –output OUTPUT
Output filename
- –save-source
save the path for all source files
Experimental setup options:
- -b BEAMLINE, –beamline BEAMLINE
Name of the instument (for the HDF5 NXinstrument)
- -p PONI, –poni PONI
geometry description file
- -m MASK, –mask MASK
mask to be used for invalid pixels
- –dummy DUMMY
value of dynamically masked pixels
- –delta-dummy DELTA_DUMMY
precision for dummy value
- –radial-range RADIAL_RANGE RADIAL_RANGE
radial range as a 2-tuple of number of pixels, by default all available range
- -P POLARIZATION, –polarization POLARIZATION
Polarization factor of the incident beam [-1:1], by default disabled, 0.99 is a good guess
- -A, –solidangle
Correct for solid-angle correction (important if the detector is not mounted normally to the incident beam, off by default
Sigma-clipping options:
- –bins BINS
Number of radial bins to consider
- –unit UNIT
radial unit to perform the calculation
- –cycle CYCLE
precision for dummy value
- –cutoff-clip CUTOFF_CLIP
Threshold to be used when performing the sigmaclipping
- –cutoff-pick CUTOFF_PICK
Threshold to be used when picking the pixels to be saved
- –error-model ERROR_MODEL
Statistical model for the signal error, may be `poisson`(default) or `azimuthal` (slower) or even a simple formula like ‘5*I+8’
- –noise NOISE
Noise level: quadratically added to the background uncertainty
Opencl setup options:
- –workgroup WORKGROUP
Enforce the workgroup size for OpenCL kernel. Impacts only on the execution speed, not on the result.
- –device DEVICE DEVICE
definition of the platform and device identifier: 2 integers. Use `clinfo` to get a description of your system
- –device-type DEVICE_TYPE
device type like `cpu` or `gpu` or `acc`. Can help to select the proper device.
Current status of the program: Production