STConverter

class pyrost.simulation.STConverter(sim_obj, data, crd_rat=1e-06, basis_vectors=None, translations=None)

Converter class to export simulated data from STSim to a CXI file. Takes an instance of STSim and a generated stack of frames and automatically generates all the attributes necessary for the robust speckle tracking reconstruction (see pyrost.STData).

Parameters

• sim_obj (STSim) – a STSim instance.

• data (ndarray) – Simulated stack of frames from sim_obj. The data may be generated either by STSim.frames() or STSim.ptychograph() method.

• crd_rat (float) – Coordinates ratio between the simulated and saved data.

Notes

Necessary attributes:

• data : Simulated intensity frames.

Automatically generated attributes:

• basis_vectors : Detector basis vectors.

• defocus_x : Defocus distance along the horizontal detector axis.

• defocus_y : Defocus distance along the vertical detector axis.

• distance : Sample-to-detector distance.

• translations : Sample’s translations.

• wavelength : Incoming beam’s wavelength.

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

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

contents()

Return a list of the attributes stored in the container that are initialised.

Return type

List[str]

Returns

List of the attributes stored in the container.

export_data(out_path, apply_transform=True, protocol=CXIProtocol(datatypes={'basis_vectors': 'float', 'data': 'uint', 'defocus_x': 'float', 'defocus_y': 'float', 'distance': 'float', 'mask': 'bool', 'phase': 'float', 'pixel_aberrations': 'float', 'pixel_translations': 'float', 'reference_image': 'float', 'scale_map': 'float', 'translations': 'float', 'wavelength': 'float', 'whitefield': 'float', 'whitefields': 'float', 'x_pixel_size': 'float', 'y_pixel_size': 'float'}, load_paths={'basis_vectors': ['/speckle_tracking/basis_vectors', '/entry_1/instrument_1/detector_1/basis_vectors', '/entry/instrument/detector/basis_vectors'], 'data': ['/entry/data/data', '/entry/instrument/detector/data', '/entry_1/instrument_1/detector_1/data', '/entry_1/data_1/data'], 'defocus_x': ['/speckle_tracking/defocus_x', '/speckle_tracking/defocus_fs', '/speckle_tracking/defocus'], 'defocus_y': ['/speckle_tracking/defocus_y', '/speckle_tracking/defocus_ss'], 'distance': ['/entry/instrument/detector/distance', '/entry_1/instrument_1/detector_1/distance'], 'mask': ['/speckle_tracking/mask', '/mask_maker/mask', '/entry_1/instrument_1/detector_1/mask', '/entry/instrument/detector/mask'], 'phase': ['/speckle_tracking/phase'], 'pixel_aberrations': ['/speckle_tracking/pixel_aberrations'], 'pixel_translations': ['/speckle_tracking/pixel_translations'], 'reference_image': ['/speckle_tracking/reference_image'], 'scale_map': ['/speckle_tracking/scale_map'], 'translations': ['/speckle_tracking/translations', '/entry_1/sample_1/geometry/translations', '/entry/sample/geometry/translations', '/entry_1/sample_1/geometry/translation', '/pos_refine/translation', '/entry_1/sample_3/geometry/translation'], 'wavelength': ['/entry/instrument/source/wavelength', '/entry_1/instrument_1/source_1/wavelength', 'entry/instrument/beam/incident_wavelength'], 'whitefield': ['/speckle_tracking/whitefield', '/process_1/whitefield', '/make_whitefield/whitefield', '/process_2/whitefield', '/process_3/whitefield'], 'whitefields': ['/speckle_tracking/whitefields', '/speckle_tracking/flatfields'], 'x_pixel_size': ['/entry/instrument/detector/x_pixel_size', '/entry_1/instrument_1/detector_1/x_pixel_size'], 'y_pixel_size': ['/entry/instrument/detector/y_pixel_size', '/entry_1/instrument_1/detector_1/y_pixel_size']}, kinds={'basis_vectors': 'sequence', 'data': 'stack', 'defocus_x': 'scalar', 'defocus_y': 'scalar', 'distance': 'scalar', 'mask': 'stack', 'phase': 'frame', 'pixel_aberrations': 'frame', 'pixel_translations': 'sequence', 'reference_image': 'scalar', 'scale_map': 'frame', 'translations': 'sequence', 'wavelength': 'scalar', 'whitefield': 'frame', 'whitefields': 'stack', 'x_pixel_size': 'scalar', 'y_pixel_size': 'scalar'}))

Save simulated data to the path specified in out_path and return pyrost.STData object.

Parameters

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

• apply_transform (bool) – Apply the cropping transform from STSim.get_transform().

• protocol (CXIProtocol) – CXI file protocol.

Return type

STData

Returns

Data container pyrost.STData.

get(attr, value=None)

Retrieve a dataset, return value if the attribute is not found.

Parameters

• attr (str) – Data attribute.

• value (Optional[Any]) – Data which is returned if the attribute is not found.

Return type

Any

Returns

Attribute’s data stored in the container, value if attr is not found.

get_transform()

Return a pyrost.Crop transform corresponding to the ROI of the beam on the detector.

Returns

pyrost.Crop transform corresponding to the ROI of the beam.

items()

Return (key, value) pairs of the datasets stored in the container.

Return type

ItemsView

Returns

(key, value) pairs of the datasets stored in the container.

keys()

Return a list of the attributes available in the container.

Return type

List[str]

Returns

List of the attributes available in the container.

replace(**kwargs)

Return a new container object with a set of attributes replaced.

Parameters

kwargs (Any) – A set of attributes and the values to to replace.

Return type

~D

Returns

A new container object with updated attributes.

save(out_path, apply_transform=True, protocol=CXIProtocol(datatypes={'basis_vectors': 'float', 'data': 'uint', 'defocus_x': 'float', 'defocus_y': 'float', 'distance': 'float', 'mask': 'bool', 'phase': 'float', 'pixel_aberrations': 'float', 'pixel_translations': 'float', 'reference_image': 'float', 'scale_map': 'float', 'translations': 'float', 'wavelength': 'float', 'whitefield': 'float', 'whitefields': 'float', 'x_pixel_size': 'float', 'y_pixel_size': 'float'}, load_paths={'basis_vectors': ['/speckle_tracking/basis_vectors', '/entry_1/instrument_1/detector_1/basis_vectors', '/entry/instrument/detector/basis_vectors'], 'data': ['/entry/data/data', '/entry/instrument/detector/data', '/entry_1/instrument_1/detector_1/data', '/entry_1/data_1/data'], 'defocus_x': ['/speckle_tracking/defocus_x', '/speckle_tracking/defocus_fs', '/speckle_tracking/defocus'], 'defocus_y': ['/speckle_tracking/defocus_y', '/speckle_tracking/defocus_ss'], 'distance': ['/entry/instrument/detector/distance', '/entry_1/instrument_1/detector_1/distance'], 'mask': ['/speckle_tracking/mask', '/mask_maker/mask', '/entry_1/instrument_1/detector_1/mask', '/entry/instrument/detector/mask'], 'phase': ['/speckle_tracking/phase'], 'pixel_aberrations': ['/speckle_tracking/pixel_aberrations'], 'pixel_translations': ['/speckle_tracking/pixel_translations'], 'reference_image': ['/speckle_tracking/reference_image'], 'scale_map': ['/speckle_tracking/scale_map'], 'translations': ['/speckle_tracking/translations', '/entry_1/sample_1/geometry/translations', '/entry/sample/geometry/translations', '/entry_1/sample_1/geometry/translation', '/pos_refine/translation', '/entry_1/sample_3/geometry/translation'], 'wavelength': ['/entry/instrument/source/wavelength', '/entry_1/instrument_1/source_1/wavelength', 'entry/instrument/beam/incident_wavelength'], 'whitefield': ['/speckle_tracking/whitefield', '/process_1/whitefield', '/make_whitefield/whitefield', '/process_2/whitefield', '/process_3/whitefield'], 'whitefields': ['/speckle_tracking/whitefields', '/speckle_tracking/flatfields'], 'x_pixel_size': ['/entry/instrument/detector/x_pixel_size', '/entry_1/instrument_1/detector_1/x_pixel_size'], 'y_pixel_size': ['/entry/instrument/detector/y_pixel_size', '/entry_1/instrument_1/detector_1/y_pixel_size']}, kinds={'basis_vectors': 'sequence', 'data': 'stack', 'defocus_x': 'scalar', 'defocus_y': 'scalar', 'distance': 'scalar', 'mask': 'stack', 'phase': 'frame', 'pixel_aberrations': 'frame', 'pixel_translations': 'sequence', 'reference_image': 'scalar', 'scale_map': 'frame', 'translations': 'sequence', 'wavelength': 'scalar', 'whitefield': 'frame', 'whitefields': 'stack', 'x_pixel_size': 'scalar', 'y_pixel_size': 'scalar'}), mode='overwrite', idxs=None)

Save simulated data to the path specified in out_path.

Parameters

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

• apply_transform (bool) – Apply the cropping transform from STSim.get_transform().

• protocol (CXIProtocol) – CXI file protocol.

• mode (str) –

  Writing mode:

  • append : Append the data array to already existing dataset.

  • insert : Insert the data under the given indices idxs.

  • overwrite : Overwrite the existing dataset.

• idxs (Optional[Iterable[int]]) – A set of frame indices where the data is saved if mode is insert.

Returns

None

values()

Return the attributes’ data stored in the container.

Return type

ValuesView

Returns

List of data stored in the container.