beambuster library for detector center refinement in serial crystallography data processing.
Project description
beambusters library
Beam swepeing serial crystallography data processing library. Methods implementation for detector center determination based on Friedel pairs inversion symmetry.
Python version
Python 3.10.5 (main, Jun 21 2022, 11:18:08) [GCC 4.8.5 20150623 (Red Hat 4.8.5-44)] on linux
Usage
To utilize the methods CenterOfMass
, FriedelPairs
, MinimizePeakFWHM
and CircleDetection
it is required to have two configuration dictionaries, one for PeakFinder8 and another one for this library itself. The follow snippet shows the expected structure for both:
config = {
"pf8_max_num_peaks": ...,
"pf8_adc_threshold": ...,
"pf8_minimum_snr": ...,
"pf8_min_pixel_count": ...,
"pf8_max_pixel_count": ...,
"pf8_local_bg_radius": ...,
"pf8_min_res": ...,
"pf8_max_res": ...,
"min_peak_region": ...,
"max_peak_region": ...,
"canny_sigma": ...,
"canny_low_thr": ...,
"canny_high_thr": ...,
"outlier_distance": ...,
"search_radius": ...,
"method": ...,
"bragg_peaks_positions_for_center_of_mass_calculation": ...,
"pixels_for_mask_of_bragg_peaks": ...,
"skipped_methods": ...,
"skipped_polarization": ...,
"offset_x": ...,
"offset_y": ...,
"force_center_mode": ...,
"force_center": ...,
}
PF8Info = {
"max_num_peaks":
"adc_threshold":
"minimum_snr": ...,
"min_pixel_count": ...,
"max_pixel_count": ...,
"local_bg_radius": ...,
"min_res": ...,
"max_res": ...,
"pf8_detector_info": ...,
"bad_pixel_map_filename": ...,
"bad_pixel_map_hdf5_path": ...,
"pixel_maps": ...,
"_shifted_pixel_maps":...
}
The pf8_detector_info
parameter is a dictionary containing the detector layout information:
pf8_detector_info = {
"asic_nx": ...,
"asic_ny": ...,
"nasics_x": ...,
"nasics_y": ...
}
The pixel_maps
parameter is a dictionary containing the pixel maps numpy array:
pixel_maps = {
"x": ...,
"y": ...,
"z": ...,
"radius": ...,
"phi": ...
}
The methods FriedelPairs
, MinimizePeakFWHM
and CircleDetection
need a plots_info
parameter:
plots_info = {
"file_label": ...,
"run_label": ...,
"frame_index": ...,
"args": ...
}
To calculate the refined detector center of a frame in numpy array using the methods:
from methods import CenterOfMass
center_of_mass_method = CenterOfMass(config=config, PF8Config=PF8Config)
center_coordinates_from_center_of_mass = center_of_mass_method(
data=frame
)
from methods import CircleDetection
circle_detection_method = CircleDetection(config=config, PF8Config=PF8Config, plots_info=plots_info)
center_coordinates_from_circle_detection = circle_detection_method(
data=frame
)
from methods import MinimizePeakFWHM
minimize_peak_fwhm_method = MinimizePeakFWHM(
config=config, PF8Config=PF8Config, plots_info=plots_info
)
center_coordinates_from_minimize_peak_fwhm = minimize_peak_fwhm_method(
data=frame
)
The FriedelPairs
method need an initial guess for the refined detector center coordinates initial_guess = [x_0, y_0]
from methods import FriedelPairs
friedel_pairs_method = FriedelPairs(
config=config, PF8Config=PF8Config, plots_info=plots_info
)
center_coordinates_from_friedel_pairs = friedel_pairs_method(
data=frame, initial_guess= ...
)
Author:
Ana Carolina Rodrigues (2021 - )
email: ana.rodrigues@desy.de
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