fixed issue where PyNutil would fail on sections that have 0 pixels, or where min object size was set too high

Slice reports and whole series reports now correct

There is an error in the combined_report (it sums the area_fraction).

per_section_meshview
per_section_reports
sections_combined_meshview
sections_combined_report

Working session with Harry.
Read in flat files from a folder. Scale flat files to size of seg. Calculate region areas per slice. Create slice reports with region areas and object areas. Create report for all slices by summing slice reports. In progress.

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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.