EMEN2 - EMAN2 Integration
In addition to batch upload/download support, emen2client.py offers some basic EMAN2 synchronization capabilities. These are still being developed, but are already useful.
[irees@mbp ~/data]$ emen2client.py sync --help Usage: emen2client.py [options] <project record ID> This program will upload CTF parameters, boxes, and particle sets into an EMEN2 database. Because filenames are not always globally unique, you must specify a base project that will be searched for files. If run with "--check", it will only test to see if it can make the correct file mappings between the local EMAN2 project and the remote database. Nothing will be written. This is a good way to test to see if the correct mappings can be made before you attempt to commit any changes. Options: -h, --help show this help message and exit -U USERNAME, --username=USERNAME Username -P PASSWORD, --password=PASSWORD Password (Note: specifying passwords in shell commands is not secure) -H HOST, --host=HOST Host endpoint URI -C CTXID, --ctxid=CTXID Valid Context ID --check Do not upload anything; just check file mappings --ctf Upload CTF Parameters --boxes Upload Boxes --eman1 Look in EMAN1-style files instead of EMAN2 project database --ptcls Upload Particle Sets
Upload CTF parameters
The "--ctf" option will search for CTF parameters in several places.
If EMAN1 files are being searched (--eman1), ctfparm.txt in the local directory will be checked. Otherwise, two locations are checked for EMAN2 CTF parameters. First, any phase flipped particles that have been written out will be checked, as these are considered more authoritative than the e2ctf.py settings. If particles have been corrected but not written out, the script will then use the values from the e2ctf.py settings.
Upload box coordinates
The "--boxes" option will search for particle coordinates to upload to the database. They will be attached to the CCD or Scan record as a "box" child. The coordinates are attached as a .box file, in EMAN1 format.
EMAN1 boxes are loaded from .box files in the local directory. EMAN2 box locations are read from the "ptcl_source_coords" tag in the particle headers.
Upload particle stacks
This feature is still being implemented
THis feautre is still being implemented