Copying data from online repository dataset related to distortion estimation of CBED patterns

In order to execute the cells in the Jupyter notebooks in the directory at the path <emicroml_root>/examples/modelling/cbed/distortion/estimation/notebooks — where <emicroml_root> is the root of the emicroml repository — a subset of the output that results from performing a set of “actions” are required. Descriptions of these actions can be found through this page. One can obtain this subset of output by executing said actions, however this requires significant computational resources, including significant walltime. Alternatively, one can copy this subset of output from the Federated Research Data Repository (FRDR) dataset found here. Below we describe how one should copy the data from this FRDR dataset.

First, download a copy of the FRDR dataset to the machine on which you intend to launch the Jupyter notebooks; Secondly, for every file in every subdirectory of the directory at the path <frdr_dataset_root>/emicroml — where <frdr_dataset_root> is the root of the local copy of the FRDR dataset — copy said file to <emicroml_root>/<relative_path_to_file_in_frdr_dataset> — where <relative_path_to_file_in_frdr_dataset> is the path to said file relative to <frdr_dataset_root>/emicroml — and create any new directories as required. For example, the file at the path <frdr_dataset_root>/emicroml/examples/modelling/cbed/simulations/MoS2/data/atomic_coords.xyz should be copied to <emicroml_root>/examples/modelling/cbed/simulations/MoS2/data/atomic_coords.xyz.