bblib 3.1.0

beambusters library to refine the detector center for crystallography data processing.

beambusters library

The beambusters library (bblib) is a library that contains methods to determine the detector center directly from still diffraction patterns collected in serial crystallography experiments.

You can find more information about beambusters on this page.

Installation

To install bblib, run the following command in a terminal:

pip install bblib

Usage

Configuration dictionaries

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 following snippet shows the general structure for both (parameters not used in your case can be omitted):

config = {
    "plots_flag": ...,
	"search_radius": ...,
	"pf8": {
		"max_num_peaks": ...,
		"adc_threshold": ...,
		"minimum_snr": ...,
		"min_pixel_count": ...,
		"max_pixel_count": ...,
		"local_bg_radius": ...,
		"min_res": ...,
		"max_res": ...
		},
	"peak_region":{
		"min": ...,
		"max": ...
		},
	"grid_search_radius": ...,
	"canny":{
		"sigma": ...,
		"low_threshold": ...,
		"high_threshold": ...
		},
	"hough_rank": ...,
	"bragg_peaks_for_center_of_mass_calculation": ...,
	"pixels_for_mask_of_bragg_peaks": ...,
	"polarization": {
		"apply_polarization_correction": ...,
		"axis": ...,
		"value": ...
		}
}

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": ...,
	"pixel_resolution": ...,
	"_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 if you want to save plots:

plots_info =  {
	"filename": ...,
	"folder_name": ...,
	"root_path": ...,
	"value_auto": ...,
	"value_max": ...,
	"value_min": ...,
	"axis_lim_auto": ...,
	"xlim_min": ...,
	"xlim_max": ...,
	"ylim_min": ...,
	"ylim_max": ...,
	"color_map": ...,
	"marker_size": ...
}

Calling the methods

To calculate the refined detector center of raw data frame as a numpy array using the following methods:

from bblib.methods import CenterOfMass
center_of_mass_method = CenterOfMass(config=config, PF8Config=PF8Config, plots_info=plots_info)
center_coordinates_from_center_of_mass = center_of_mass_method(
                        data = ...
                    )

from bblib.methods import CircleDetection
circle_detection_method = CircleDetection(config=config, PF8Config=PF8Config, plots_info=plots_info)
center_coordinates_from_circle_detection = circle_detection_method(
                        data = ...
                    )

The FriedelPairs and MinimizePeakFWHMmethod need an initial guess for the refined detector center coordinates initial_guess = [x_0, y_0]

from bblib.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 = ..., initial_guess = ...
                    )


from bblib.methods import FriedelPairs
friedel_pairs_method = FriedelPairs(
                        config=config, PF8Config=PF8Config, plots_info=plots_info
                    )
center_coordinates_from_friedel_pairs = friedel_pairs_method(
                        data = ..., initial_guess= ...
                    )

Contact

Ana Carolina Rodrigues led the development of bblib from 2021 to 2025 at the Deutsches Elektronen-Synchrotron (DESY) in Hamburg, Germany.

For questions, please contact:

Email: [e-mail]