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WIP: Add reporter using circular buffer

Gerhard Burger requested to merge lacdr-tox/morpheus:feat_movavg_reporter into develop

Hi Jorn, Walter,

Currently with the reporter you can only get the instantaneous speed from the motility reporter, but I needed something that was a little smoother (my cells are a bit jumpy, so the movement direction can complete reverse from one frame to the next). So I wrote a moving avarage/sum reporter using boost::circular_buffer and I thought maybe you would be interested as well.

(In hindsight I probably could have used the same approach as in the persistent motion plugin, as Margriet pointed out after I wrote the code 😓, but maybe this plugin could be the starting point for a more complex reporter plugin that let's you do all kind of transformations on aggregated values...)

Pros:

  • Works in logger/plots (see attached movie)
  • Less code duplication in plugins

Cons:

  • Requires boost (header only) (could roll your own circular buffer, but this works with all kinds of nice STL stuff)
  • Getting the buffered value into other plugins is a little more work (need more symbol refs -> more complex xml)

Questions:

  • I stored the values in a map<CPM::CELL_ID, std::unique_ptr<boost::circular_buffer<VDOUBLE>>>, but I guess I should use cellType->addProperty? Would that work?
  • Currently I need to specify a time step, but I see in other plugins that you use stuff like registerCellPositionDependency, does that take care of setting the time-step as well? In principle I would like the plugin to work for arbitrary SymbolRefs/Expressions, are there similar tricks I could use (register symbol dependencies)?
  • Does the reworked symbol stuff you emailed me/us about change anything for this plugin? Is there a better way to do it?

Hope to hear from you!

Attachment: I took the RunAndTumble example, and added a buffered move_dir variable:
movie buffered_reporter_model.xml

Edited by Gerhard Burger

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