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Meeting notes microscope-cockpit development meeting 2023-09-12

Attendees

Attending:

  • David Miguel Susano Pinto
  • Ian Dobbie
  • Julio Mateos-Langerak

Notes

  • OMERO-metrics - side discussion.

Meeting started with a discussion of the latest QUAREP work, particularly Julio's work towards OMERO-metrics, a OMERO based platform to inject image data and process and then track metrics of the imaging system, resolution, field flatness etc...

Julio utilized LinkML to get the OMERO data model into his code.

  • Cockpit timers

The fixes to the timers within cockpit were then discussed, Hopefully this is now a solved problem. It took many years (!) to track down the issue, but now there are two timer types. Events based timers, and wx.timer type timers but they should all be kept track of and terminated by the relevant module on window delete.

  • Cockpit joystick code.

David asked about the cockpit joystick code and its issue with Mac. This seems to have been fixed in wxPython and the code now correctly senses if there is a joystick present on the Mac, returning if there isn't.

Ian has a slight update that the xbox controller he tried worked but was way too sensitive. He will introduce a config parameter and a useful default so the system is usable out of the box.

  • Scipy API issue

Ian had problems running cockpit as he had upgraded python and running into scipy API issues. Turns out scipy has made some of the calls private accessed via another route. David has since updated the code to call the correct functions

  • Logging in cockpit

We had extensive discussions about logging in cockpit. David and Julio were unhappy wit the current prints going to stdout which is then trapped by the logging window and sent to an arbitrary log.

David is keen on removing the print approach and moving it to a proper Python logging objects. This might also help solve the issue with messages before or after the logging panels start.

Julio is keen to try and add experiment specific log files. Ian has always been keen on this as a human readable log file can be invaluable. However there is also an argument to ensure that most of this data is captured into the image file metadata as well.