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Feature #1363

closed

prepFrealign.py needs

Added by Anchi Cheng over 13 years ago. Updated over 12 years ago.

Status:
Closed
Priority:
High
Assignee:
Amber Herold
Category:
-
Target version:
Appion/Leginon 2.2.0
Start date:
07/20/2011
Due date:
% Done:

0%

Estimated time:

Description

need to pass into prepFrealign.py from web form the following:

--reconiterid : an integer that is the DEF_id of a previous EMAN refinement iteration for initializing particle orientation. This is an optional parameter. When not included, the orientation will be initialized with zeros.

--noctf : a flag,
makes frealign to do its own ctf estimation. This also means that Angular increment and Initial LP filter that are currently defined in prepareFrealign.php will need to go in selectPreparedRecon.php form.
Without this flag, the ctf estimation from appion will be used.

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 #1

Updated by Amber Herold almost 13 years ago

  • Status changed from Assigned to Won't Fix or Won't Do

These were just some notes for refine refactor...nothing to see here.

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 #2

Updated by Anchi Cheng almost 13 years ago

  • Status changed from Won't Fix or Won't Do to Assigned
  • Priority changed from Normal to High
  • Target version set to Appion/Leginon 2.2.0

This is still not done. The two options are still in selectPreparedRecon.php. They are flags that need to be set and functions performed in the preparation because the database interaction.

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 #3

Updated by Amber Herold almost 13 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Amber Herold to Anchi Cheng

Anchi,
The new flags have been moved from the run refinement step for frealign to the prep step. I tried running through a complete frealign refinement, but am getting the following error, with and without the new flags:

self.convertToRefineStack() 
File "/opt/myamisnap/bin/prepRefineFrealign.py", line 110, in convertToRefineStack 
self.ImagicStackToFrealignMrcStack() 
File "/opt/myamisnap/bin/prepRefineFrealign.py", line 94, in ImagicStackToFrealignMrcStack 
apIMAGIC.convertImagicStackToMrcStack(stackroot,stackbaseroot+'.mrc') 
File "/opt/myamisnap/lib/appionlib/apIMAGIC.py", line 410, in convertImagicStackToMrcStack 
imagic2mrc.imagic_to_mrc(infile,outfile) 
File "/opt/myamisnap/lib/pyami/imagic2mrc.py", line 20, in imagic_to_mrc 
mrc_header['mode'] = pyami.mrc.numpy2mrc[mrc_header['dtype']] 
KeyError: dtype('float32')

Checking in the code for these changes anyway, will work on frealign debug seperatly.

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 #4

Updated by Anchi Cheng almost 13 years ago

  • Assignee changed from Anchi Cheng to Amber Herold

/opt/myamisnap/lib/pyami need an update. trunk r16262 has fixed that bug. I will do a merge to redux branch tomorrow on that fix.

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 #5

Updated by Amber Herold almost 13 years ago

I'm surprised that a revision from last week has not make it into the installation yet.

Shouldn't the beta code be updated nightly? I'll check with Sargis what the update script is expected to do.

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 #6

Updated by Sargis Dallakyan almost 13 years ago

I have found /root/bin/buildMyamiSnapshot.py used in /var/spool/cron/root on guppy. This script was failing on svn update because of the lock file and suggested to do svn cleanup. I did

cd /root/src/myamisnap
svn cleanup

Now the script is working fine. I'll check on this tomorrow and close this issue if everything works as expected.

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 #7

Updated by Anchi Cheng almost 13 years ago

I tested the feature in my sandbox with show command and it is good there.

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 #8

Updated by Amber Herold over 12 years ago

  • Status changed from In Code Review to Closed
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