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Review and update base I/O code
A good starting point for the new code development would be the I/O code for loading data from images and .dat files to numpy ndarrays.
This issue depends on #6 as the new models for the resultant data will need to be worked on at the same time.
Some work on this was finished in #12, however, there is still work to be done to streamline the loading process for loading a full directory of images as well as to update the YAML parsing code.