Feature #648
openAdd EMAN refine2d.py to the alignment pipeline
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Description
Add EMAN refine2d.py to the alignment pipeline.
Updated by Amber Herold over 14 years ago
- Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon Future Version
Updated by Amber Herold about 14 years ago
Neil, what is the status on this one?
Updated by Neil Voss about 14 years ago
We implemented running the program during the appion workshop, but I found out that EMAN re-sorts all the particles in the stack, so we need to implement a method to figure out the new position of the particles in the stack to properly link them in the database. Other than that everything else works fine. So, it can create class averages it is just that the information is not properly uploaded into the database.
I have some ideas on how to do this, but never got around to doing it. The information may be in the log file otherwise the particles in the stack can be number in the .hed file and read back after the program has run.
Updated by Amber Herold almost 14 years ago
Reza ran into a problem b/c of not having the values in the DB. He tried running rctVolume.py and gets the following error:
Traceback (most recent call last): File "/home/amber/amiworkspace/myami/appion/bin/rctVolume.py", line 671, in ? rctVolume.start() File "/home/amber/amiworkspace/myami/appion/bin/rctVolume.py", line 606, in start eulerfile = self.makeEulerDoc(tiltParticlesData) File "/home/amber/amiworkspace/myami/appion/bin/rctVolume.py", line 355, in makeEulerDoc totrot = -1.0*(notrot + inplane) TypeError: unsupported operand type(s) for +: 'float' and 'NoneType'
I think we should add a warning in the gui for eman refine 2d or finish this up soon.
Updated by Neil Voss almost 14 years ago
It is not even close to ready and should not be included in any release. ETA this summer.