Refactor to Remove set_alpha Method and Consolidate Visibility Management Under set_roi_visibility_flags

[ashmeigh]

Current Behaviour

The current implementation includes both set_alpha and set_roi_visibility_flags for managing the visibility and transparency of ROIs. This issue proposes removing the set_alpha method and consolidating visibility management under set_roi_visibility_flags

The set_alpha method overlaps with set_roi_visibility_flags - ROIs invisible (setting alpha to 0 vs toggling visibility). It adds complexity, and there are two ways to achieve the same result.

Potential Concerns:

Loss of Transparency Control: If semi-transparent ROIs are useful in certain scenarios (setting alpha to 0.5 for partial visibility), removing set_alpha would eliminate this feature.

Pen and Color Management: set_alpha also updates the pen and hoverPen with the new alpha value. By removing it, colour updates will need to be managed elsewhere.

Proposed Solution

Remove set_alpha: Eliminate the set_alpha method, which currently manages ROI transparency by adjusting the alpha value of the pen.

Rely on set_roi_visibility_flags: Use set_roi_visibility_flags to manage visibility entirely, both for toggling visibility and updating handles.