STConverter

class pyrost.simulation.STConverter(protocol, coord_ratio=1e-06)

Converter class to export simulated data from STSim to a CXI file. STConverter also exports experimental parameters and the used protocol to INI files.

Parameters

  • protocol (Protocol) – CXI protocol, which contains all the attribute’s paths and data types.

  • coord_ratio (float, optional) – Coordinates ratio between the simulated and saved data.

Variables

  • templates_dir (str) – Path to ini templates (for exporting protocol and STParams).

  • write_attrs (dict) – Dictionary with all the attributes which are saved in CXI file.

  • protocol (Protocol) – CXI protocol, which contains all the attribute’s paths and data types.

  • coord_ratio (float, optional) – Coordinates ratio between the simulated and saved data.

Notes

List of the attributes saved in CXI file:

  • basis_vectors : Detector basis vectors.

  • data : Measured intensity frames.

  • defocus_fs : Defocus distance along the fast detector axis.

  • defocus_ss : Defocus distance along the slow detector axis.

  • distance : Sample-to-detector distance.

  • energy : Incoming beam photon energy [eV].

  • good_frames : An array of good frames’ indices.

  • mask : Bad pixels mask.

  • roi : Region of interest in the detector’s plane.

  • translations : Sample’s translations.

  • wavelength : Incoming beam’s wavelength.

  • whitefield : Measured frames’ whitefield.

  • x_pixel_size : Pixel’s size along the fast detector axis.

  • y_pixel_size : Pixel’s size along the slow detector axis.

export_data(data, st_params)

Export simulated data data (fetched from STSim.frames() or STSim.ptychograph()) and st_params to a data container.

Parameters
Returns

Data container with all the data from data and st_params.

Return type

STData

See also

STConverter

export_dict(data, st_params)

Export simulated data data (fetched from STSim.frames() or STSim.ptychograph()) and st_params to dict object.

Parameters
Returns

data_dict – Dictionary with all the data from data and st_params.

Return type

dict

See also

STConverter

save(data, st_params, dir_path)

Export simulated data data (fetched from STSim.frames() or STSim.ptychograph()) and st_params to dir_path folder.

Parameters

  • data (numpy.ndarray) – Simulated data.

  • st_params (STParams) – Experimental parameters.

  • dir_path (str) – Path to the folder, where all the files are saved.

See also

STConverter.save_sim

Full list of the files saved in dir_path.

save_sim(data, st_sim, dir_path)

Export simulated data data (fetched from STSim.frames() or STSim.ptychograph()) and a STSim object st_sim to dir_path folder.

Parameters

  • data (numpy.ndarray) – Simulated data.

  • st_sim (STSim) – Speckle Tracking simulation object.

  • dir_path (str) – Path to the folder, where all the files are saved.

Notes

List of the files saved in dir_path:

  • ‘data.cxi’ : CXI file with all the data attributes.

  • ‘protocol.ini’ : CXI protocol.

  • ‘parameters.ini’ : experimental parameters.

  • {‘calc_error.ini’, ‘calculate_phase.ini’, ‘generate_pixel_map.ini’, ‘make_reference.ini’, ‘speckle_gui.ini’, ‘update_pixel_map.ini’, ‘update_translations.ini’, ‘zernike.ini’} : INI files to work with Andrew’s speckle_tracking GUI.