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Bug #4720
closedMakestack not working
Start date:
01/25/2017
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:
Description
Making stack crashes, either boxfiles only or to make actual stack. This is after latest update, working yesterday
Session 17jan23d, name stack5.appionsub.job
Beginning Main Loop ... Pixel size: 0.854905 ... Found 334 particles 1 Traceback (most recent call last): File "/opt/myamisnap/bin/makestack2.py", line 1325, in makeStack.run() File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 88, in run results = self.loopProcessImage(imgdata) File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 146, in loopProcessImage return self.processImage(imgdata) File "/opt/myamisnap/lib/appionlib/apParticleExtractor.py", line 531, in processImage total_processed_particles = self.processParticles(imgdata,partdatas,shiftdata) File "/opt/myamisnap/bin/makestack2.py", line 126, in processParticles self.boxedpartdatas, self.imgstackfile, self.partmeantree = self.boxParticlesFromImage(imgdata, partdatas, shiftdata) File "/opt/myamisnap/bin/makestack2.py", line 269, in boxParticlesFromImage partdatas, shiftdata, boxfile, rotate=self.params['rotate'], checkInside=self.params['checkInside']) TypeError: processParticleData() got an unexpected keyword argument 'checkInside'
Updated by Carl Negro almost 8 years ago
- Assignee set to Gabriel Lander
When I add the checkInside parameter to appionlib/apBoxer.py, I can run makestack2 correctly. However there is still no behavior inside apBoxer.py. Gabe, do you have any uncommitted changes?
Updated by Gabriel Lander almost 8 years ago
sorry, I totally forgot to commit this, should work now. 9b7ca555
Updated by Anchi Cheng almost 8 years ago
- Status changed from New to Assigned
- Priority changed from Urgent to High
- Target version set to Appion/Leginon 3.3
- Affected Version changed from Appion/Leginon 3.2 to Appion/Leginon 3.3
Hi, Gabe,
Your code in apBoxer.py will still go through checkBoxInImage as is. You should put checkInside is False at the front. Saves a fraction of second, I suppose.
Updated by Gabriel Lander almost 8 years ago
- Assignee changed from Gabriel Lander to Anchi Cheng
good point, I swapped its position.
Updated by Neil Voss over 7 years ago
- Related to Bug #4842: makestack with only boxfiles checked, produces no boxfiles added
Updated by William Rice over 7 years ago
- Status changed from Assigned to Closed
Working now. Found that box files are now in a subdirectory
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