Bug #1055: Add helicalstep parameter in runManualPicker.php - Appion - Electron Microscopy Group

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Bug #1055

closed

Add helicalstep parameter in runManualPicker.php

Added by Lauren Fisher over 13 years ago. Updated over 8 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Arne Moeller

Category:

Web interface

Target version:

Appion/Leginon 3.1.0

Start date:

11/23/2010

Due date:

% Done:

Estimated time:

Affected Version:

Appion/Leginon 2.1.0

Show in known bugs:

Workaround:

Description

Manual picker was recently fixed so that helical filaments can be selected, but the command requires a helical step input which is currently not included in the web form. As it is now this parameter has to be manually added into the command, otherwise manual picker will give an "unknown helical step size" warning and will not select filaments. The php code needs to be updated to be compatible with the python.

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Updated by Lauren Fisher over 13 years ago

Status changed from New to In Code Review
Assignee changed from Lauren Fisher to Anchi Cheng

Added helical step parameter on the php form and command line output in r15102. Added help info in r15103.

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Updated by Anchi Cheng over 13 years ago

Status changed from In Code Review to Assigned
Assignee changed from Anchi Cheng to Lauren Fisher

Could you move the php input to be after particle diameter? Since most particle pickers have particle diameter as the first input, it made me to input in the wrong place when I, and majority of the users, don't need helical parameters.

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Updated by Lauren Fisher over 13 years ago

Status changed from Assigned to In Code Review
Assignee changed from Lauren Fisher to Anchi Cheng

No problem, r15227 moved the helical parameters below the particle parameters. Hopefully this helps eliminate some of the confusion for users who are familiar with the previous layout.

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Updated by Anchi Cheng over 13 years ago

Status changed from In Code Review to Closed

code reviewed and tested

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Updated by Gabriel Lander almost 13 years ago

Status changed from Closed to In Code Review

"$_POST" check for helical stepsize in wrong place, moved it up 1 line.
r15622

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Updated by Anchi Cheng almost 13 years ago

Status changed from In Code Review to In Test
Assignee changed from Anchi Cheng to Arne Moeller

code is good

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Updated by Arne Moeller almost 13 years ago

found 2 things:

the wrapper is not in front of the command - in just show command

2nd
encountered these bugs:
... Pixel size: 1.64
... reading filtered image from mrc file
... writing peak JPEG: /ami/data00/appion/10aug27a/extract/manrun39/jpgs/10aug27a_00023gr_00006sq_v01_00004hl_v01_00003en.prtl.jpg
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 646, in ?
imgLoop.run()
File "/ami/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 70, in run
results = self.loopProcessImage(imgdata)
File "/ami/sw/packages/myamitrunk/appion/appionlib/particleLoop2.py", line 104, in loopProcessImage
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
File "/ami/sw/packages/myamitrunk/appion/appionlib/filterLoop.py", line 87, in loopProcessImage
peaktree = self.processImage(imgdata, self.filtarray)
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 417, in processImage
peaktree = self.runManualPicker(imgdata)
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 619, in runManualPicker
anyangles = reduce(operator.or_, haveangles)
TypeError: reduce() of empty sequence with no initial value

... writing peak JPEG: /ami/data00/appion/10aug27a/extract/manrun39/jpgs/10aug27a_00023gr_00006sq_v01_00002hl_v01_00015en.prtl.jpg
Traceback (most recent call last):
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 646, in ?
imgLoop.run()
File "/ami/sw/packages/myamitrunk/appion/appionlib/appionLoop2.py", line 70, in run
results = self.loopProcessImage(imgdata)
File "/ami/sw/packages/myamitrunk/appion/appionlib/particleLoop2.py", line 104, in loopProcessImage
self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)
File "/ami/sw/packages/myamitrunk/appion/appionlib/filterLoop.py", line 87, in loopProcessImage
peaktree = self.processImage(imgdata, self.filtarray)
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 417, in processImage
peaktree = self.runManualPicker(imgdata)
File "/ami/sw/packages/myamitrunk/appion/bin/manualpicker.py", line 619, in runManualPicker
anyangles = reduce(operator.or_, haveangles)
TypeError: reduce() of empty sequence with no initial value
[moeller@amibox02 ~]$

which caused manpicker to crash

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