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Bug #1286
closedDiscontinue use of Eman boxer within Appion
Status:
Closed
Priority:
Normal
Assignee:
Category:
Python scripting
Target version:
Start date:
05/05/2011
Due date:
% Done:
0%
Estimated time:
Affected Version:
Pre-2.0
Show in known bugs:
No
Workaround:
Description
Stop using EMAN boxer and instead write our own python code for particle selection and rotation in Appion.
From Neil, Issue #1056:
I think it is time to drop EMAN boxer and just do it in python. It would be so much cleaner...
For each image:
image = mrc.read(...)
rotated = scipy.ndimage.rotate(image, angle=##, reshape=False, order=1)
partlist = []
For each particle:
part = rotate[x1':x2',y1':y2'] #note: rotated coordinate system, x2' = x1' + boxsize
partlist.append(part)
apImagicFile.writeImagic(partlist, image1stack)
apImagicFile.mergeStacks(image1stack, image2stack, ...)
and then (1) skip the whole proc2d/batchboxer non-sense, (2) do it in one pass, and (3) it would be much faster.
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