Update extraction pipeline to per-region as opposed to aggregate

[alex-l-kong]

What is the purpose of this PR?

An entire MALDI dataset across a whole TMA is extremely expensive to extract and analyze. To improve efficiency, we update the pipeline to run on a per-region basis.

How did you implement your changes

We use the poslog to identify which coordinate belongs to which region. This is similar to the workflow for the core cropping step. By specifying a region_num param during the extraction process, we can exclude coordinates outside the region of interest.

Remaining issues

Potential improvements

1. Include a param in the extraction step to automatically generate all regions in a single pass, as opposed to looping the whole .imzML for each region.
2. Include options for smaller subsets of pixels. This will be useful for tissue samples.

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