Task #1846 (assigned)
Opened 14 years ago
Last modified 14 years ago
Upload an EMAN2 bdb layer to OMERO — at Version 2
Reported by: | wmoore | Owned by: | wmoore |
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Priority: | n.a. | Milestone: | OMERO-Beta4.2 |
Component: | n.a. | Version: | n.a. |
Keywords: | n.a. | Cc: | |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | 2.0d |
Sprint: | 2010-02-19 (3) |
Description (last modified by 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!
Change History (2)
comment:1 Changed 14 years ago by wmoore
- Status changed from new to assigned
comment:2 Changed 14 years ago by wmoore
- Description modified (diff)