Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[WIP] communication protocol with BigDataViewer proofreading client #87

Merged
merged 45 commits into from Sep 21, 2016
Merged

[WIP] communication protocol with BigDataViewer proofreading client #87

merged 45 commits into from Sep 21, 2016

Conversation

jni
Copy link
Collaborator

@jni jni commented Jul 8, 2016

This additionally includes a prototype version of the compact watershed, which, combined with regularly-spaced seeds, gives some very nice fragments for leaky membrane maps.

jni and others added 30 commits July 2, 2016 00:21
@jni
Clean up gala.morpho imports
dd42b56
@jni
Add compact watershed transform
dd7c73e
@jni
Add new multiple separation message type
db6f19a 
This enables separating a fragment from all its neighbors, and makes
the separation interface more compact.

Additionally, the beginnings of using an ID service have been put in
place.
@jni
Bug fixes on new multi-split protocol
385e72e 
- when encountering boundary_id, continue, don't return
- when the number of separate neighbors is zero, don't send any message
@jni
Allow null ID service; better config overrides
41985a1
@jni
Remap output IDs to unique ones from server
38ac9fe
@jni
Add (passing) test with Solver using ID service
86d1f29
@jni
Use daemon threads for solver it server tests
68c14e0
@jni
Resolve when idle, and periodically
749b3ec
@jni
Fix parameters in compact_watershed
9a0e612
@jni
Add multiscale grid seeding and related functions
00bb8b7
@jni
Don't die if you don't recognize a message
921b191
@jni
Revert "Use daemon threads for solver it server tests"
f8c17cb 
This reverts commit 68c14e0.
@jni
Normalize labels before plotting data points in decision boundary
f90c563
@jni
Ravel arrays to prevent shape warnings
934f811
@jni
Add print statements to server to diagnose ZMQ
4b1b416
@jni
Sleep between bouts of proofreading to allow solver to catch up
5c92b7b
@jni
Send segmentations non-blocking in case proofreader is gone
4c71401
@jni
Learn separations at a fragment level only
c311ee8
@jni
Don't replay merge history, use classifier
a1a282f
@jni
Starting ID can be consumed by 0 or boundary_body
26ae97c
@jni
Check whether original graph has edge between separated fragments
85f92cd
@jni
Add more diagnostic communication prints
d840ad9
@jni
Bug fix: expecting wrong key for merges
18d8bcd
@jni
Don't re-solve if you only have one kind of label
00ad1cc
@jni
Add new function to plot seed points on image
9565cdf
@jni
Add tqdm as progressbar dependency
f121e14
@jni
Bug fix: proofreader also needs merge keyword update
2d1013b
@jni
Add pipelined compact watershed function
b12c871
@jni
Remove silly call
d502470
@coveralls
Copy link

Coverage Status

Coverage decreased (-0.03%) to 49.308% when pulling 40d9aa3 on jni:id-service into effb31a on janelia-flyem:master.

@coveralls
Copy link

Coverage Status

Coverage increased (+0.1%) to 49.475% when pulling cb70694 on jni:id-service into effb31a on janelia-flyem:master.

@jni jni merged commit 21c0a54 into janelia-flyem:master Sep 21, 2016
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
2 participants
@jni @coveralls