FindROI.plotBox tends to display boxes with the localization at the NW corner

[MJWester]

On work with Emmy, the box plots produced usually have the localization on the northwest corner of the drawn box, as if a shift of 1/2 pixel needs to be applied to the box outlines to center the localization. Not sure if this is purely a display problem or a box choosing problem, but the boxes look odd.

[kalidke]

Root Cause Analysis

This is a coordinate system mismatch between MATLAB array indices and imshow display coordinates.

The Issue:

• FindROI stores box corners as MATLAB array indices (integers starting at 1)
• plotBox.m lines 28-31 plot these indices directly
• But imshow uses a display coordinate system where pixel centers are at integer coordinates
• This creates a 0.5 pixel shift in the visual display

Example:

• Box corner at array index (10, 10)
• In imshow display, pixel (10,10) center is at display coordinate (10, 10)
• But the pixel extends from (9.5, 9.5) to (10.5, 10.5)
• Plotting a box edge at coordinate 10 puts it through the pixel center, not at the edge

Fix: Subtract 0.5 from XCorners and YCorners in plotBox.m lines 28-31 to align with the imshow coordinate system.

Impact: Low - this is purely a cosmetic display issue in a debugging function (comment line 6: "This routine is only really needed for debugging"). Does not affect actual data processing, fitting, or results.

Status: Known cosmetic issue in visualization. Could be fixed but low priority since it doesn't affect scientific results.