NAME

sparsify-Bragg - Sparsify 2D single crystall 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.

DESCRIPTION

usage: spasify-Bragg [-h] [-V] [-v] [--debug] [-o OUTPUT] [--save-source]

[-b BEAMLINE] [-p PONI] [-m MASK] [--dummy DUMMY]: [--delta-dummy DELTA_DUMMY] [--radial-range RADIAL_RANGE RADIAL_RANGE] [--bins BINS] [--cycle CYCLE] [--cutoff-clip CUTOFF_CLIP] [--cutoff-pick CUTOFF_PICK] [--error-model ERROR_MODEL] [--noise NOISE] [--device DEVICE DEVICE] [--device-type DEVICE_TYPE] [IMAGE ...]

Sparsify 2D single crystall 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.

positional arguments:

IMAGE: File with input images. All frames will be concatenated in a single HDF5 file.

optional arguments:

-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

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

Sigma-clipping options:

--bins BINS: Number of radial bins to consider
--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)
--noise NOISE: Noise level: n-sigma cannot be smaller than this value

Opencl setup options:

--device DEVICE DEVICE: definition of thee platform and device identifyer: 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: status

February 2021

sparsify-Bragg 0.20.0