Fix saving of flow fields and cell probability in GUI #1103
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1103 +/- ##
==========================================
- Coverage 52.69% 52.68% -0.02%
==========================================
Files 18 18
Lines 4302 4328 +26
==========================================
+ Hits 2267 2280 +13
- Misses 2035 2048 +13 ☔ View full report in Codecov by Sentry. |
|
Just realised there’s no notification when saving starts or finishes. Now: ...
...
2025-02-10 02:37:12,482 [INFO] ~~~ FINDING MASKS ~~~
2025-02-10 02:37:15,230 [INFO] >>>> TOTAL TIME 2.75 sec
2025-02-10 02:37:15,239 [INFO] 111 cells found with model in 2.968 sec
GUI_INFO: 111 masks found
GUI_INFO: creating cellcolors and drawing masks <---- segmentation finishes here
GUI_INFO: saving flows and cellprob to tiff <---- after CTRL + F
GUI_INFO: saved flows and cellprob |
|
thanks so much! made a few small changes and merged it |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Hi @carsen-stringer, I noticed that _save_flows() was obsolete while trying to save flows in the GUI. I updated the function and tested it on a 3D TIFF and a 2D PNG. I hope this covers all cases.