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Feature #2319

closed

Add Auto Masking (em_hole_finder) to pipeline

Added by Amber Herold over 11 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Amber Herold
Category:
Python scripting
Target version:
Start date:
04/08/2013
Due date:
% Done:

0%

Estimated time:

Description

The code is available here: https://github.com/hbradlow/em_hole_finder

It is a python program with the following pre-reqs:
Cython==0.18
PIL==1.1.7
ipython==0.13.1
numpy==1.7.0
scikit-image==0.8.2
scipy==0.11.0
wsgiref==0.1.2

The basic use case:
  1. User runs Auto Masker from Appion Masking section
    1. Auto Masker will output a mask image
    2. TBD: should it also output a polygon to use for display purposes?
       
  2. User runs the image viewer to display the mask results
    1. The results can be displayed with either:
      1. using redux on the server to overlay a transparent mask on the original image (some redux changes needed)
      2. use alpha channel on the client to to overlay mask (alpha was not working last time this was attempted)
      3. if the auto masker outputs a polygon, just overlay the polygon
    2. Display all masks from all masking runs that do no have a rejected assessment
    3. Allow the user to reject all masks for the image with a "replace mask with manual masking" button, which marks all displayed mask regions as rejected and marks the image for mask redo in the database
       
  3. User runs manual masker to create new masks for the images that were marked for redo
    1. when Man mask starts, it checks the DB for images that need to be redone.
    2. When the masker runs, it should only display the images that need to be redone.

Related issues 2 (0 open2 closed)

Related to Appion - Bug #2437: automasker.py shape mismatch?ClosedGabriel Lander07/24/2013

Actions
Related to Appion - Feature #2326: redux option to overlay a maskClosedAmber Herold04/16/2013

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