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Bug #632

closed

particle flipped upside down after running through Beam Tilt corrected subStack.py

Added by Anchi Cheng over 14 years ago. Updated over 14 years ago.

Status:
Closed
Priority:
High
Assignee:
Anchi Cheng
Category:
-
Target version:
Appion/Leginon 2.1.0
Start date:
06/04/2010
Due date:
% Done:

100%

Estimated time:
Affected Version:
Pre-2.0
Show in known bugs:
Yes
Workaround:

Description

suspect similar problem with other functions that used apImagicFile.writeImagic

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 #1

Updated by Anchi Cheng over 14 years ago

  • Status changed from New to Assigned
  • Assignee changed from Anchi Cheng to Neil Voss
  • Priority changed from Normal to High
  • % Done changed from 0 to 50

Particle array read from Imagic stack file need to fliplr to give the same orientation as Leginon's mrc image coordinate. By testing, I found that it needs flipup before writeImagic() This addition is applied to apBeamTilt.py in r14287 in trunk. apXmipp.getSingleFilesIntoStack uses the same writeImaigic() function. It should be tested for correctness.

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 #2

Updated by Amber Herold over 14 years ago

  • Target version changed from Appion/Leginon 2.0.1 to Appion/Leginon 2.0.2
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 #3

Updated by Amber Herold over 14 years ago

  • Target version changed from Appion/Leginon 2.0.2 to Appion/Leginon 2.1.0
  • Affected Version set to Myami 2.0.1
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 #4

Updated by Amber Herold over 14 years ago

  • Affected Version changed from Myami 2.0.1 to Appion/Leginon 2.0.1
  • Show in known bugs set to Yes
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 #5

Updated by Neil Voss over 14 years ago

  • Affected Version changed from Appion/Leginon 2.0.1 to Pre-2.0
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 #6

Updated by Amber Herold over 14 years ago

  • Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
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 #7

Updated by Neil Voss over 14 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Neil Voss to Anchi Cheng
  • Target version changed from Appion/Leginon 2.2.0 to Appion/Leginon 2.1.0

I've fixed this feature, we need to mirror the particles both on read and write of IMAGIC data r14483. Run the function appion/test/testStacks.py to make sure it works on your system.

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 #8

Updated by Anchi Cheng over 14 years ago

  • Status changed from In Code Review to Closed
  • % Done changed from 50 to 100

found it changed so that I modified apBeamTilt.py back in r144668. This change has a side effect of web stackviewer showing image in the opposite orientation from images in stack summary since the former is based on EMAN v2 orientation where (0,0) is at bottom_left while leginon in general is based on (0,0) at top_left.

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