Single crystal tool: peakfinder
Count the number of Bragg-peaks on an image
Purpose
Bragg peaks are local maxima of the background subtracted signal. Peaks are integrated and variance propagated. The centroids are reported.
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] [–grid-size GRID_SIZE GRID_SIZE] [–zig-zag] [-b BEAMLINE] [-p PONI] [-m MASK] [–dummy DUMMY] [–delta-dummy DELTA_DUMMY] [–radial-range RADIAL_RANGE_MIN RADIAL_RANGE_MAX] [-P POLARIZATION] [-A] [–bins BINS] [–unit UNIT] [–cycle CYCLE] [–cutoff-clip CUTOFF_CLIP] [–error-model ERROR_MODEL] [–cutoff-pick CUTOFF_PICK] [–noise NOISE] [–patch-size PATCH_SIZE] [–connected CONNECTED] [–workgroup WORKGROUP] [–device DEVICE DEVICE] [–device-type DEVICE_TYPE] [IMAGE …]
Options:
- IMAGE
File with input images. All results are concatenated into 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
Scan options:
- –grid-size GRID_SIZE GRID_SIZE
Grid along which the data was acquired
- –zig-zag
The scan was performed with a zig-zag pattern
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
SNR threshold for considering a pixel outlier when performing the sigma-clipping
- –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’
Peak finding options:
- –cutoff-pick CUTOFF_PICK
SNR threshold for considering a pixel high when searching for peaks
- –noise NOISE
Quadratically added noise to the background
- –patch-size PATCH_SIZE
size of the neighborhood for integration
- –connected CONNECTED
Number of high pixels in neighborhood to be considered as a peak
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