Leginon

It may be a problem of matching what the database says the file is and what the file system need the file path to be. As we have said before, no one used Windows PC as the main Leginon computer for a long time. It may just not work any more. You really want to run Leginon on Windows?

You will need to do some test to find out if the path is translated right. Also first check where the files are really saved to.
reference files will be saved in a special session with name like 13feb14_ref_a

Run this python script. Get help on running python script if you need to:

#!/usr/bin/env python
import os
from leginon import leginondata

cam = leginondata.InstrumentData(name='GatanK2Counting').query(results=1)[0]
camem = leginondata.CameraEMData(ccdcamera=cam)

refpath = None
norm = leginondata.NormImageData(camera=camem).query(results=1)
if norm:
  # If norm image is indeed saved as a database entry, then database would know where it is saved
  refpath = norm[0]['session']['image path']
  print 'norm image path', refpath
  print 'file can be found', os.path.isfile(os.path.join(refpath,norm[0]['filename']+'.mrc'))
else:
  print 'norm image never saved in the database.  Looking for bright...'
  bright = leginondata.BrightImageData(camera=camem).query(results=1)
  if bright:
    refpath = bright[0]['session']['image path']
    print 'bright image path', refpath
    print 'file can be found', os.path.isfile(os.path.join(refpath,bright[0]['filename']+'.mrc'))
  else:
    print 'No reference ever saved'

We ran the script on our Windows installation and it did not find the reference mrcs.
The issue is that the path is not constructed correctly on Windows due to the "Drive Mapping".

Examining the leginon code I modified the script tno a universally working version by include the mapping functions:

#!/usr/bin/env python
import os
import sys
from leginon import leginondata
import leginon.leginonconfig

cam = leginondata.InstrumentData(name='GatanK2Counting').query(results=1)[0]
camem = leginondata.CameraEMData(ccdcamera=cam)

print 'platform is ',sys.platform

refpath = None
norm = leginondata.NormImageData(camera=camem).query(results=1)
if norm:
  # If norm image is indeed saved as a database entry, then database would know where it is saved
  refpath = norm[0]['session']['image path']
  print 'norm image path', refpath
  print 'norm image win path',leginon.leginonconfig.mapPath(refpath)

  print 'file can be found', os.path.isfile(os.path.join(leginon.leginonconfig.mapPath(refpath),norm[0]['filename']+'.mrc').replace('\\','/'))
else:
  print 'norm image never saved in the database.  Looking for bright...'
  bright = leginondata.BrightImageData(camera=camem).query(results=1)
  if bright:
    refpath = bright[0]['session']['image path']
    print 'bright image path', refpath
    print 'file can be found', os.path.isfile(os.path.join(leginon.leginonconfig.mapPath(refpath),bright[0]['filename']+'.mrc').replace('\\','/'))
  else:
    print 'No reference ever saved'

This revised version does find the reference files.
I think that the leginon.leginonconfig.mapPath(path) was omitted at a few places in the leginon code and this was not noticed as it does nothing when running on Unix.

I found an old implementation that might help:

If you add the drive mapping in sinedon.cfg on the Windows PC like this, it will map the path of the files when it needs to read a file through file reference.

[Windows Drives]
z: /your linux equivalent path

This will not change the path print from my test script but should allow the image to be read by Leginon on Windows. Give it a try.