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