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Feature #15146
openSmart Leginon - add Jenks grouping and option to randomize Ptolemy scores, other features
Start date:
08/03/2023
Due date:
% Done:
0%
Estimated time:
Deliverable:
Description
- Added a new option to group square targets, Jenks Sorting, which is analogous to a 1-dimensional K-means grouping.
- This requires the Jenks module as well as cython. The yum version of cython for CentOS 7 works. All other required packages come with Leginon
- Also added GUI option to randomize Ptolemy scores for the square selection, since the current scores may not correlate well with quality. Current version chooses the square with the highest score in a group.
- Added a new option to sort on signal (=area*mean brightness) which is sometimes useful for grouping.
- Score used for grouping (mean,score,area,signal) is now a dropdown menu rather than freeform typing.
- Added an option for "simple" blob merging for finding the squares in the atlas (when squares overlap). The current method occasionally chooses the grid bar instead of the square. With the "simple" option, it chooses the area with the most signal instead of the average position. Works well for us.
- When selections are limited to 2 (eg for hl or exposure targets), it chooses the brightest and the dimmest from the set of targets found. This is useful if you add a matrix of hl targets and want to screen only the thinnest and thickest part of the square.
- new branch smart_leginon_jenks made for these changes
Updated by William Rice 9 months ago
- Subject changed from Smart Leginon - add Jenks sorting and option to randomize Ptolemy scores, other features to Smart Leginon - add Jenks grouping and option to randomize Ptolemy scores, other features
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