mstimberg
commented
5 years ago I did a few changes to the code and refactored the tracking a bit. More of the logic is now included in the paramecium_tracking.py file (the idea being that this could be useful independent of the GUI). The where_is_paramecium function also moved into a ParameciumTracker class (that stores previous positions) and has been renamed to locate.
This locate function now returns an info dictionary together with the coordinates/size of the best fitted ellipse. This dictionary contains stuff like all the detected contours and the fitted ellipses. I added two options to the paramecium configuration (under "debugging") that switch on drawing these contours and/or ellipses. It's probably too much, but it should give an idea how to use this information. If everything is switched on it plots:
- contours that were too short or did not have at least 5 points (yellow)
- contours that were good enough to be fitted by an ellipse (red)
- contour that was used for the best-fitting ellipse (green)
- fitted ellipses that were not considered (too long/short, etc.) (light blue)
- fitted ellipses that were considered for the final choice (purple)
I also added a slowdown option to the RecordedVideoCamera class so that it shows frames from a video repeatedly (this is not implemented in any kind of clever way, e.g. the processing still happens for each frame, even if it did not change).
I made all these changes in the refactor_tracking branch because I did not test it very thoroughly yet and I did not want to break the master branch. Feel free to merge it into master if it works for you.
romainbrette
It's still not very good. I have a good video here: http://82.253.119.171/owncloud/index.php/s/Uvq6N0otsUevWCV and I use 0.62 pixel/um for the setup_script.
One thing that might be useful is to be able to display processed images (eg contours) (to replace the video), I guess that should be simple enough? Marcel could you perhaps add a couple of lines just to show me how to do this? (I guess in where_is_paramecium and the caller script ?)