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Bug #12483

open

DogPicker can not find any peaks.

Added by Anchi Cheng about 2 years ago. Updated about 2 years ago.

Status:
Assigned
Priority:
High
Assignee:
Sargis Dallakyan
Category:
-
Target version:
Leginon - Appion/Leginon 3.6
Start date:
04/18/2022
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.6
Show in known bugs:
No
Workaround:

Description

broken by Issue #12257

https://emg.nysbc.org/projects/appion/repository/diff/pyami/imagefun.py?utf8=✓&rev=0e22f53c52b9c533783815ce88eaddebe4269db1&rev_to=53e3bcb71d3f2f58daad6b78b7fc666134256bcc

apPeaks.py did not use keyword argument so that the input variables for pyami.imagefun.find_blobs do not match properly.

The new code also does not output moment which apPeaks expect to get.

roundness is a useful parameter to filter. Please fix the bug and add min roundness as an advanced parameter for users on myamiweb such as https://emgweb.nysbc.org/betamyamiweb/processing/runAppionLoop.php?expId=12578&form=DogPickerForm
good default would be a small number like 0.5. 1 is a round object

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 #1

Updated by Anchi Cheng about 2 years ago

Or default to 0, then everything will pass like the old behavior.

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 #2

Updated by Sargis Dallakyan about 2 years ago

  • Status changed from Assigned to In Test

Thank you Anchi. I just committed changes to fix this in the trunk and beta brunch. Please let me know if I miss something.

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 #3

Updated by Anchi Cheng about 2 years ago

Hi, Sargis, thanks.

gui looks good and params do change in apPeaks.py. However, minroundness is not sent to imagefun.find_blobs. Most likely because apPeaks call args do not match the order in imagefun.find_blobs and ended up taking the default minroundness in imagefun.

Please revise.

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 #4

Updated by Anchi Cheng about 2 years ago

  • Status changed from In Test to Assigned
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 #5

Updated by Sargis Dallakyan about 2 years ago

Hi Anchi, thank you. Made a new commit in the trunk with these changes:
- Removed extra argument in apPeaks.findBlobs
- Calling magefun.find_blobs using all keyword arguments.

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