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This commit refactors the PyNutil class to make it more modular and easier to read and understand. The load_atlas_data method has been extracted to a separate function, and the coordinate extraction, pixel labeling and counting, and writing of points to Meshview have been extracted to separate methods. These changes make the code more modular and easier to maintain.

This commit refactors the PyNutil class to make it more modular and easier to read and understand. The load_atlas_data method has been extracted to a separate function, and the coordinate extraction, pixel labeling and counting, and writing of points to Meshview have been extracted to separate methods. These changes make the code more modular and easier to maintain.

Create a list of flat file names

"allenID" changed to idx.

Write and run function for correctly formatted label file

Write function to reformat label files so they are compatible with PyNutil

Continued