Many modules fail to import without a display server about clearmap2

[ChristophKirst]

This is a good point, we are working on a headless version for cluster computation that catches these types of errors.
Meanwhile you could simply move those imports from the top of the module into the routines that use them...

hope that helps.

Christoph

[slitvinov]

Meanwhile you could simply move those imports from the top of the module into the routines that use them...

I think it would work. I am trying to keep local changes at minimum.

I found that this line causes problems:
https://github.com/ChristophKirst/ClearMap2/blob/master/ClearMap/Visualization/Qt/DataViewer.py#L32

Can it be conditional?

if 'DISPLAY' in os.environ and not pg.QAPP: 
  pg.mkQApp()

[ZachPenn]

I ran into the same issue. Since notebooks are utilized, perhaps using interactive jupyter notebook visualizations in lieu of gui would be an option.

[ZachPenn]

My labmate came up with a potentially great solution that works in ClearMap2's current form when running from a remote, headless, Ubuntu setup. This provides a way to load the ClearMap.Environment in full without commenting out GUI dependencies. Additionally, it should allow the GUI to be displayed locally, though I haven't tested this extensively. Because it handles X11 window managers, I'm not sure this will work when running a windows setup locally. However, I was able to use it while running OSX locally.

In order to link a local window to a headless server to avoid ClearMap2 GUI dependency issues, we took the following route:

• Install xpra (https://www.xpra.org/) on both remote/server and local computers
• On the server, initiate an empty display port from the terminal: xpra start :X, where x is any integer. This step should persist, and will therefore only need to be redone if the server is stopped, or if xpra stop is called.
• Add the following lines to the beginning of ClearMap, prior to importing the ClearMap.Environment:

import os
os.environ['DISPLAY'] = ':X'

Note that at this point all ClearMap modules can be loaded, but visualization steps will not work. The next step should allow the GUI to be generated locally

• From your local terminal, attach the empty display port. When the GUI is subsequently called, it should display locally:
  xpra attach ssh://me@myserver/X