Updating Timepix3 Calibration Pipeline for compatibility with new Karabo Implementation + some general improvements

final changes related by differentiating between module index and module numbers. This should all be replaced with CALCAT metadata

1.Plot agipd single module geometry for correct and darks
2.Fix sorting dark runs
3.Fix reading a single module which doesnt start at 0

- With this commit dark processing should work with no summary chapters
- Remove RedBu cmap as a bonus change

- replace np.percentile(, [0,100]) with min(), max()
- put back histogram plots with get_range for no need of change.
- improve gain plot and add clamp function