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Feature #1876

closed

add Xmipp CTF estimation to Appion

Added by Neil Voss over 12 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
-
Category:
Image Processing
Target version:
Appion/Leginon 3.0.0
Start date:
06/21/2012
Due date:
% Done:

0%

Estimated time:

Related issues 4 (0 open — 4 closed)

Related to Appion - Feature #1206: CTF display and control needs work. Let's discussClosed02/27/2011

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Related to Appion - Feature #1847: Implement next generation CTF display toolsClosedNeil Voss06/11/2012

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Related to Appion - Feature #1881: create a new selection menu for CTF programsClosedAnchi Cheng06/25/2012

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Related to Appion - Feature #1882: Implement an interactive CTF for experimenting with new algorithmClosedNeil Voss06/25/2012

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 #1

Updated by Neil Voss over 12 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Neil Voss to Dmitry Lyumkis
  • Target version changed from Appion/Leginon 2.2.0 to Appion/Leginon 2.3.0
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 #2

Updated by Dmitry Lyumkis over 12 years ago

  • Assignee changed from Dmitry Lyumkis to Neil Voss

I think I remember someone trying this out at the last hackathon without great results. Neil, have you had any luck with it?

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 #3

Updated by Neil Voss over 12 years ago

  • Status changed from In Code Review to In Test
  • Assignee changed from Neil Voss to Dmitry Lyumkis

Hi Dmitry, I think the Xmipp CTF works great if you give it something close to the right answer, otherwise it fails miserably. So, if you run CTFfind or ACE2, and then run Xmipp CTF typically you can get a better answer. But do not even bother running it if you are just giving it the Leginon nominal defocus values.

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 #4

Updated by Dmitry Lyumkis over 12 years ago

so what are you exactly looking for to test in this bug? Just that it runs?

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 #5

Updated by Neil Voss over 12 years ago

Yeah, I guess. I learned the Assigned->Code Review->Test process from Amber. Since I filed the bug, I need someone else to test it. Preferably at AMI.

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 #6

Updated by Dmitry Lyumkis over 12 years ago

  • Assignee changed from Dmitry Lyumkis to Neil Voss

this isn't working for me. I'm getting the following error (directory /ami/data00/appion/zz09apr14b/ctf/xmippctfrun2):

Starting image 1 ( skip:174, remain:1 ) id:1498256, file: 09apr14b_a_014gr_01sq_02hl_03en
... Pixel size: 1.5465
... Looking up session, zz09apr14b

['/home/dlyumkis/myami/appion', '/home/dlyumkis/myami/appion/appionlib']
Traceback (most recent call last):
File "/home/dlyumkis/myami/appion/bin/xmippCtf.py", line 298, in ?
imgLoop.run()
File "/home/dlyumkis/myami/appion/appionlib/appionLoop2.py", line 70, in run
results = self.loopProcessImage(imgdata)
File "/home/dlyumkis/myami/appion/appionlib/appionLoop2.py", line 117, in loopProcessImage
return self.processImage(imgdata)
File "/home/dlyumkis/myami/appion/bin/xmippCtf.py", line 122, in processImage
nominal = (ctfvalue['defocus1']+ctfvalue['defocus2'])/2.0
TypeError: unsubscriptable object

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 #7

Updated by Amber Herold over 12 years ago

  • Target version changed from Appion/Leginon 2.3.0 to Appion/Leginon 3.0.0
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 #8

Updated by Neil Voss over 10 years ago

  • Status changed from In Test to Closed
  • Assignee deleted (Neil Voss)

kind of works...

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