Upload an EMAN2 bdb layer to OMERO

[wmoore]

This would have to be a local running script (not scripting service) that parsed a directory of a bdb and uploaded all the images to a new OMERO dataset, putting all the attributes of each image in an original metadata file.

This code may be based on the e2proc2d.py script described here ​http://blake.bcm.edu/emanwiki/Eman2DataStorage

Command usage:

wjm:EMAN-export will$ e2proc3d.py bdb:/Users/will/Documents/EM-data/EMAN2-tutorial/eman_demo/raw_data/particles#1160_ptcls particles.mrc
the images are 2D - I will now make a 3D image out of the 2D images
331 images, processing 0-330......
wjm:EMAN-export will$ e2proc2d.py bdb:/Users/will/Documents/EM-data/EMAN2-tutorial/eman_demo/raw_data/particles#1160_ptcls particles2d.spi
331 images, processing 0-330
331 images
wjm:EMAN-export will$ 

Both these command above output all the image planes in the 1160_ptcls bdb into a single image.

NB. If you use e2proc2d.py command and specify output as particles.mrc, then you only get a single plane, since mrc is considered a 3d format (need e2proc3d.py). But spi is considered a stack of 2d planes, so it is OK to use the e2proc2d.py to put multiple planes in this format!

[wmoore]

r6162 Script mostly working but rendering not working. E.g. min: -3.42475 max: 3.57214
Image looks black in Insight, but rendering doesn't work.

[wmoore]

r6163 Import metadata.
r6168 Cleaning up a bit.