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Feature #2

closed

Get FREALIGN integrated into appion

Added by Neil Voss almost 15 years ago. Updated about 13 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
Start date:
01/08/2010
Due date:
02/08/2010
% Done:

100%

Estimated time:
Spent time:

Description

There are numerous steps to get this working the major ones are:

  • rebuild a EMAN reconstructed stack into a FREALIGN not CTF-corrected stack with black particles
  • install FREALIGN on garibaldi and get it working
  • upload the FREALIGN results into the database

It would be nice to have this working before Cathy Lawson visits (Feb 8).


Related issues 2 (0 open2 closed)

Blocked by Appion - Feature #191: Rebuild a EMAN reconstructed stack into a FREALIGN not CTF-corrected stack with black particlesClosed03/07/2010

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Blocked by Appion - Feature #219: Create Frealign web interfaceClosedNeil Voss03/17/2010

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Actions #1

Updated by Neil Voss almost 15 years ago

  • % Done changed from 0 to 20

In relation to 'rebuild a EMAN reconstructed stack into a FREALIGN not CTF-corrected stack with black particles',

Changed makestack2.py to take a stack id instead of a particle selection id, r4049.

Still need to update appionweb to use this feature.

Actions #2

Updated by Amber Herold almost 15 years ago

  • Priority changed from High to Normal
Actions #3

Updated by Neil Voss over 14 years ago

  • Priority changed from Normal to High
Actions #4

Updated by Neil Voss over 14 years ago

  • Tracker changed from Bug to Feature
Actions #5

Updated by Neil Voss over 14 years ago

  • % Done changed from 20 to 40
Actions #6

Updated by Neil Voss over 14 years ago

  • % Done changed from 40 to 100
Actions #7

Updated by Neil Voss over 14 years ago

  • Target version set to Appion/Leginon 2.0.0
Actions #8

Updated by Neil Voss over 14 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Neil Voss to Amber Herold
  • Priority changed from High to Normal

FREALIGN is finally implemented! Instead of posting revisions for code reivew, I suggest that the entire programs get reviewed it will be easier.

source:trunk/appion/bin/prepFrealign.py
source:trunk/appion/bin/uploadFrealign.py
source:trunk/myamiweb/processing/prepareFrealign.php
source:trunk/myamiweb/processing/runFrealign.php
source:trunk/myamiweb/processing/uploadFrealign.php

Actions #9

Updated by Amber Herold over 14 years ago

  • Target version changed from Appion/Leginon 2.0.0 to Appion/Leginon 2.0.1

Will review and test this after 2.0 release

Actions #10

Updated by Amber Herold about 14 years ago

  • Status changed from In Code Review to In Test
Actions #11

Updated by Amber Herold about 13 years ago

  • Status changed from In Test to Closed

The frealign recon code has been refactored. See #1324.

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