Various improvements and bug fixes in VP, TP and HA

[mca-sh]

New functionalities

Video processing

• Generating pixel intensity trajectory by click is now available for average image in Video processing (VP).

  Trace processing

• Options gauss. and single count are now available in Trace manager (TM) - Auto sorting (AS) tab for 2D histogram-based molecule sorting. Option gauss. activates Gaussian filtering of the TDP, whereas option single count activates single histogram count per molecule.
• Option hold scale is now available in Trace processing (TP). It allows to set particular limits minI and maxI to the intensity axis of the trajectory and hold them for all molecules.
• Project merging is now available for projects having different laser wavelengths and emitter labels. In these cases, the user is asked to decide for one set of emitter labels and/or laser wavelengths to apply to the merged project.

Bug fixes / corrections

Trace processing

• The requirement of state sequences for molecule sorting in TM was incorrectly checked for trajectory-based projects (NaN values filling the gap between trajectory lengths), which blocked the user at this stage while giving the annoying advice of discretizing all traces prior using this functionality. This is now done correctly.
• A bug occurred when switching to Histogram analysis (HA) or Transition analysis (TA) after changing the molecule selection or tags, which required an additional UPDATE ALL action. HA and TA results are now reset after such change in panel TP - Sample management or in TM, which solved the bug.
• Default histogram limits for total intensity data in TM-AS were ill-defined, which showed an empty histogram. They are now correctly initialized using extremum of the data.
• Project selection was ill-defined when merging projects, which yield incorrect data in merged project when the project index in the selection did not correspond to the index in the project list. The selection is now correctly defined using index in the project list.
• Molecule tags newly created or modified by the user were not stored in memory and thus were not available in new projects. Therefore, the user had to defined them again and again. Tag names and colors are now automatically saved as default settings in the default_param.ini file after pressing button TO MASH in TM - Overview.
• Processing parameters that truncate trajectory lengths were saved as defaults settings for new projects. This had for effect to cut new trajectories to arbitrary places in a sneaky way. These parameters are now automatically resets when creating a new project.
• TP panel Sample management was an expendable/collapsible panel, which made the molecule list disappear when the panel was collapsed. To have the molecule list always in view, Sample management was made a regular non-collapsible panel and the space organization of collapsible panels was reviewed accordingly.

Histogram analysis

• The value of BOBA checkbox was not correctly updated. This is now done correctly.

Remaining tasks

• [x] test routine for TP
• [x] update online documentation

Thanks to @Befazl and @nsivan16 for signalling issues and requesting features!