Bug #1533
closedBug #1323: Recon Refactoring
uploaded EMAN eulers are incorrect
0%
Description
According to appion/bin/uploadEMANRefine.py particle_data...txt file is in EMAN's euler definition taken from proj.n.txt in combination to its class.m.txt.
However, appion/appionlib/uploadRecon.py insertRefineParticleData function goes through
alt, az, phi = apXmipp.convertXmippEulersToEman(particledata[i]['phi'], particledata[i]['theta'], particledata[i]['omega'])
So what should be changed? Making EMAN not to go through XmippToEman convertion or change how particle_data.txt writes them?
Updated by Dmitry Lyumkis over 12 years ago
- Status changed from Assigned to In Code Review
- Assignee changed from Dmitry Lyumkis to Anchi Cheng
Anchi, that is a bug on my part when I wrote the EMAN uploader. The reason why the particle_data...txt is in 3DEM format is because we wanted to standardize the parameters. However, our database is made to work with EMAN Eulers, and there are a number of functions that rely on EMAN Euler format. We didn't want to go in and change everything. This means that for EMAN, we actually have to convert to 3DEM in uploadEMANRefine.py, then back to EMAN when uploading, inside reconUploader.py.
I have checked in a revision to uploadEMANRefine.py, which now converts EMAN Eulers to Xmipp (same Eulers as 3DEM) during the writing of particle_data...txt. I used the convertEmanEulersToXmipp() function, which is based on the paper. See if it works now (I didn't test the upload script, as I don't have an example EMAN upload to try out)
Updated by Anchi Cheng over 12 years ago
- Assignee changed from Anchi Cheng to Dmitry Lyumkis
You should have at least check that you can import the module in python command. r16289 fix syntax errors.
Updated by Dmitry Lyumkis about 12 years ago
- Status changed from In Code Review to In Test
- Assignee changed from Dmitry Lyumkis to Amber Herold
Updated by Amber Herold about 10 years ago
- Status changed from In Test to Closed
- Affected Version changed from Appion/Leginon 2.2.0 (trunk) to Appion/Leginon 2.2.0