2.5.7. prismatique.load.cbed_wavefunctions

cbed_wavefunctions(filename, multi_dim_slice=None, use_two_axes_to_map_probe_position_if_possible=False, skip_validation_and_conversion=False)

From a given STEM simulation output file that stores CBED wavefunction patterns, load a specified subcollection of said CBED wavefunction patterns into a hyperspy signal.

See the documentation for the class prismatique.cbed.Params for a discussion on CBED wavefunction patterns, which we denote as \(\left|\psi_{t}\left(\delta_{f};\mathbf{u}_{1}, \ldots,\mathbf{u}_{N}; \boldsymbol{\delta}_{\beta}\right)\right\rangle\) throughout the documentation. See also the documentation for the class prismatique.thermal.Params for additional information and context on said patterns.

Parameters:

filenamestr

The relative or absolute path to the file containing the CBED wavefunction patterns. Any non-temporary file generated by the function prismatique.stem.sim.run(), with originally a basename of the form "stem_sim_wavefunction_output_of_subset_"+str(i)+".h5" is valid, where i is a nonnegative integer. See the documentation for the class prismatique.stem.output.Params for a discussion on the layout and structuring of prismatique STEM simulation output files.

multi_dim_slicetuple (int | slice | list (int)) | None, optional

The “multidimensional slice object”, which specifies the subcollection of CBED wavefunction patterns to load from file. We define a multi-dimensional slice object as a tuple of items which contains at most one item being a list of integers, and the remaining items being slice and/or int objects.

If multi_dim_slice is a tuple of length 4, then then multi_dim_slice[0] specifies a set of output layer indices, where each output layer index corresponds to a different output layer; multi_dim_slice[1] specifies a set of atomic configuration indices, where each atomic configuration index corresponds to a frozen phonon configuration; multi_dim_slice[2] specifies a set of defocus indices, where each defocus index corresponds to a different beam defocus; and multi_dim_slice[3] specifies a set of probe indices, where each probe index corresponds to a different probe position. In this case, the current Python function will load the CBED wavefunction patterns of the frozen phonon configurations specified by multi_dim_slice[1], generated by electrons exiting from the output layers specified by multi_dim_slice[0], the electrons of which coming from probes operating at the defocii specified by multi_dim_slice[2] and centered at the positions specified by multi_dim_slice[3]. Note that prismatique.load.output_layer_depths(filename)[multi_dim_slice[0]] yields the depths of the specified output layers; prismatique.load.defocii(filename)[multi_dim_slice[2]] yields the specified defocii; and prismatique.load.probe_positions(filename, force_2_col_shape=True)[multi_dim_slice[3]] yields the specified probe positions.

Otherwise, if multi_dim_slice is set to None, then all the CBED wavefunction patterns stored in the file are loaded.

use_two_axes_to_map_probe_position_if_possiblebool, optional

If use_two_axes_to_map_probe_position_if_possible is set to True, prismatique.load.scan_pattern_type(filename) == "rectangular grid", and multi_dim_slice satisfies either multi_dim_slice[-1]==slice(None) or multi_dim_slice is None, then two hyperspy axes are used rather than one to map the probe position. In this case, the two axes have the same dimensions as the rectangular grid on which the probe positions lie. Otherwise, one hyperspy axis is used to map the probe positions.

skip_validation_and_conversionbool, optional

If skip_validation_and_conversion is set to False, then validations and conversions are performed on the above parameters.

Otherwise, if skip_validation_and_conversion is set to True, no validations and conversions are performed on the above parameters. This option is desired primarily when the user wants to avoid potentially expensive validation and/or conversion operations.

Returns:

cbed_wavefunction_signalhyperspy._signals.complex_signal2d.ComplexSignal2D

The subcollection of CBED wavefunction patterns, stored in an instance of the hyperspy._signals.complex_signal2d.ComplexSignal2D class. See the documentation and/or reference guide for the hyperspy package for details on how to use instances of the hyperspy._signals.complex_signal2d.ComplexSignal2D class.

navigational_to_original_indices_mapdict

A dictionary that maps the navigational indices of the hyperspy signal cbed_wavefunction_signal to the original indices specified by multi_dim_slice. For example, if the original atomic configuration indices map to a set of corresponding navigational indices, then navigational_to_original_indices_map["atomic_config_indices"][i] yields the atomic configuration index specified in the expression single_dim_slice=multi_dim_slice[1] if multi_dim_slice is not None else slice(None) that corresponds to the i th atomic configuration index in the nagivation index space of cbed_wavefunction_signal, where i is a nonnegative integer smaller than the total number of atomic configuration indices specified in single_dim_slice.