py4xs is a collection of python modules for processing x-ray scattering data. It helps the experimenter to translate the experimental data from raw detector images to a form that can be further analyzed using generic numerical tools, by taking into account the configuration of the x-ray scattering instrumentation.

The development of py4xs started at the X9 beamline at NSLS and continued at the LiX beamline after the transition to NSLS-II, where it is being actively used for processing data in solution scattering and microbeam mapping experiments.

py4xs provides the following generic functionalities:

• Reciprocal coordinates translation Once the scattering geometry is defined, the reciprocal coordinates for each detector pixel is calculated. Functions are provided to translate the data into maps of various coordinates.

• Plotting Scattering data are plotted using matplotlib with awareness of the experimental configuration

• Solution scattering Support for azimuthal average, merging of data from multiple detectors, and buffer scattering subtraction.

• HDF5 packaging All information relevant to the scattering experiment, including scattering geometry, raw data, and processed data, can be packaged into a single hdf5 file. For now it is assumed that the hdf layout is based on export from the nsls2 databroker.

py4xs project layout

README.md        
py4xs/
    exp_para.py  # experimental parameters
    detector_config.py
                 # detector configuration
    data2d.py    # functions related to 2d data
    slnxs.py     # functions related to 1d data
    mask.py      # mask used for azimuthal average
    plot.py      # functions for plotting 2D data
    hdf.py       # python interface to the hdf5 data file 
    utils.py     # utility functions
doc/             
                 # documentation pages

In principle py4xs can be used to process scattering data collected on any instruments, as long as the detector configurations are defined. Functionalities specific to data collected at the LiX beamline are implemented under lixtools, to provide the class definition and processing GUI for the supported types of experiments:

lixtools project layout

README.md        
lixtool/
    hdf/
        sol.py         # python classes for static solution scattering data
        hplc.py        # python class for in-line SEC data
        an.py          # base class for processed data stored separately from raw data 
        scan.py        # python class for scanning imaging data
    notebooks/
        generic.py     # GUI for generic solution scatterintg/powder diffraction data
        sol_static.py  # GUI for static solution scattering
        sol_hplc.py    # GUI for in-line SEC
        scanning.py    # GUI for scanning mapping and tomography
    mapping/
        common.py      # functions for structural mapping
        plants.py      # functions specific to scattering data from plant samples
    tomo/
        common.py      # functions for tomography
        FLcorrections.py
                       # functions for XRF absorption correction, from Mingyuan Ge
    inst/
        check_deck_config2.py
                       # script for sample prep using Opentrons OT2, runs on the RasPi 
        ot2_gen_prot.py
                       # script for reading the QR codes and generate transfer protocol
                       # run from data directory
        webcam.py      # read QR codes from a webcam