Add Linear PNG Output: Closes #22

run_trim.py:
    make_trimmed_pngs:
        - Created a new wrapper function to create subimage pngs.
    run_trim:
        - Replaced subimage code with calls to make_trimmed_pngs.
        - Added linear full and trimmed outputs for wide images.
        - Added a median_switch and turned off median steps.
    replace_by_weight:
        Changed the subimage indices to go from -1, +1 to -1, +2 because of how numpy does slices. The corrected version creates a 3x3 subarray instead of a 2x2.