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:

bash 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):

```python config = { "plotsflag": ..., "searchradius": ..., "pf8": { "maxnumpeaks": ..., "adcthreshold": ..., "minimumsnr": ..., "minpixelcount": ..., "maxpixelcount": ..., "localbgradius": ..., "minres": ..., "maxres": ... }, "peakregion":{ "min": ..., "max": ... }, "gridsearchradius": ..., "canny":{ "sigma": ..., "lowthreshold": ..., "highthreshold": ... }, "houghrank": ..., "braggpeaksforcenterofmasscalculation": ..., "pixelsformaskofbraggpeaks": ..., "polarization": { "applypolarization_correction": ..., "axis": ..., "value": ... } }

PF8Info = { "maxnumpeaks": "adcthreshold": "minimumsnr": ..., "minpixelcount": ..., "maxpixelcount": ..., "localbgradius": ..., "minres": ..., "maxres": ..., "pf8detectorinfo": ..., "badpixelmapfilename": ..., "badpixelmaphdf5path": ..., "pixelmaps": ..., "pixelresolution": ..., "shiftedpixelmaps":... } ```

The pf8_detector_info parameter is a dictionary containing the detector layout information: python pf8_detector_info = { "asic_nx": ..., "asic_ny": ..., "nasics_x": ..., "nasics_y": ... }

The pixel_maps parameter is a dictionary containing the pixel maps numpy array: python pixel_maps = { "x": ..., "y": ..., "z": ..., "radius": ..., "phi": ... }

The methods FriedelPairs, MinimizePeakFWHM and CircleDetection need a plots_info parameter if you want to save plots: python 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:

```python from bblib.methods import CenterOfMass centerofmassmethod = CenterOfMass(config=config, PF8Config=PF8Config, plotsinfo=plotsinfo) centercoordinatesfromcenterofmass = centerofmass_method( data = ... )

from bblib.methods import CircleDetection circledetectionmethod = CircleDetection(config=config, PF8Config=PF8Config, plotsinfo=plotsinfo) centercoordinatesfromcircledetection = circledetectionmethod( data = ... ) ```

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

```python from bblib.methods import MinimizePeakFWHM minimizepeakfwhmmethod = MinimizePeakFWHM( config=config, PF8Config=PF8Config, plotsinfo=plotsinfo ) centercoordinatesfromminimizepeakfwhm = minimizepeakfwhmmethod( data = ..., initialguess = ... )

from bblib.methods import FriedelPairs friedelpairsmethod = FriedelPairs( config=config, PF8Config=PF8Config, plotsinfo=plotsinfo ) centercoordinatesfromfriedelpairs = friedelpairsmethod( 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: sc.anarodrigues@gmail.com