A few problems I'm running into.
In one instance (Ubuntu 11) I’m getting an error in importing wx. The error is “AttributeError: ‘module’ object has no attribute ‘Log’” on CellProfiler.py line 289 “wx.Log.EnableLogging(False)” The funny thing is that if I pop into a python shell I can ‘import wx’ without error. If I comment out wx.Log.— then it will fail trying to load icons for the gui I think. I’ve confirmed my PYTHONPATH is set for the version of python I’ve been using since I started compiling the deps and also that this is the pythonpath that has wx. This is (almost) I 100% clone of a working instance of CP from another box.
On another instance (RHEL6) I’m getting an error in ‘external_dependencies’, no idea what this error corresponds to … ">Traceback (most recent call last):
File “CellProfiler.py”, line 216, in
ImportError: No module named external_dependencies<
Is there anything I could do to decrease deps for a purely headless instance of CP? (wx, gtk, etc)
Are there guides that anyone knows of to integrate headless CP into Omero? We are playing around with Omero and would like to send jobs to CP. I’m familiar with writing scripts to send jobs to the command line but was wondering if there was something more elegant designed. Ultimately I’d like to choose a few images, run a pipeline on them, collect the resulting marked up output images back into omero as well as somehow making note of where the measurement files ended up. I can use the dropbox functionality and just make the output folder of the pipeline as a dropbox folder with set metadata but it doesn’t seem like the ‘best’ option.