Refactor: Replace hardcoded if elif chains for project colormaps with a centralized configuration

[k0rosh]

Description

Currently, the get_inference_from_file and saveMap functions contain extensive, hardcoded if-elif chains to determine color mappings based on the FLAGS.project variable (e.g., 00_Adjacency, 01_METbrain, etc.).

While functional, this approach violates the Open-Closed Principle (OCP). Every time a new project or class is added, the core logic of these functions must be manually modified, which increases the risk of introducing bugs and clutters the processing logic.

Benefits

Maintainability: Adding a new project requires zero changes to the core function logic; developers only need to update the mapping dictionary.

Readability: Drastically reduces the line count and cyclomatic complexity of get_inference_from_file and saveMap.

Modularity: Paves the way for loading configurations dynamically via external JSON files in future releases.

I would be happy to work on this refactoring and submit a Pull Request if the maintainers agree with this architectural improvement.

Proposed Solution

Extract the project-specific colormap configurations into a centralized Python dictionary (or an external config.json file).

Example Implementation Idea:

# Centralized configuration mapping
PROJECT_COLORMAPS = {
    '00_Adjacency': {
        1: [c('white'), c('red')],
        2: [c('white'), c('orange')],
        # ...
    },
    '01_METbrain': {
        1: [c('white'), c('black')],
        # ...
    }
}

# Simplified logic inside functions
def get_inference_from_file(lineProb_st):
    # ...
    if FLAGS.project in PROJECT_COLORMAPS:
        cmap_colors = PROJECT_COLORMAPS[FLAGS.project].get(oClass, default_colors)
        cmap = make_colormap(cmap_colors)
    # ...