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.
Description
suspect similar problem with other functions that used apImagicFile.writeImagic
- 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.
- Target version changed from Appion/Leginon 2.0.1 to Appion/Leginon 2.0.2
- Target version changed from Appion/Leginon 2.0.2 to Appion/Leginon 2.1.0
- Affected Version set to Myami 2.0.1
- Affected Version changed from Myami 2.0.1 to Appion/Leginon 2.0.1
- Show in known bugs set to Yes
- Affected Version changed from Appion/Leginon 2.0.1 to Pre-2.0
- Target version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
- 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.
- 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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