Update 4.2 AI build#16
Merged
emilroz merged 195 commits intoglencoesoftware:compat-4-2-aifrom Apr 26, 2024
Merged
Conversation
Move JSON handling to cp core
* Improve java detection * Optimise * Test putative startup fix * Fix CellProfiler#4457 Co-authored-by: David Stirling <dstirling@broadinstitute.org>
…filer#4445) Co-authored-by: David Stirling <dstirling@broadinstitute.org>
Co-authored-by: David Stirling <dstirling@broadinstitute.org>
Co-authored-by: David Stirling <dstirling@broadinstitute.org>
* Support display of text-based measurements * Add text display test Co-authored-by: David Stirling <dstirling@broadinstitute.org>
* Handle text column writing in ExportToDatabase * Prevent ExportToDatabase crash if an image was skipped Co-authored-by: David Stirling <dstirling@broadinstitute.org>
* Add convex hull mode to FillObjects * documentation added * More docs * Support 3D, add tests * Explicitly set module mode in tests Co-authored-by: David Stirling <dstirling@broadinstitute.org>
Co-authored-by: David Stirling <dstirling@broadinstitute.org>
* Add debug shell * Make Window pane search more reliable * add documentation of debug shell Co-authored-by: David Stirling <dstirling@broadinstitute.org> Co-authored-by: bethac07 <bcimini@broadinstitute.org>
* Added object z measurements to exporttodatabase.py * update exporttodatabase to have 3d tag * trying new values for exporttodatabase process_3D
…ellProfiler#4478) * Fix issue with downsampling when advanced watershed features are on Resize x_data back up to fix mismatch later (line 565) when watershed is generated from distance and downsampling is on (>1). * Updated with David's suggestion to re-generate x_data mask
* Reduce the memory usage of MeasureObjectNeighbors * Switch from np to numpy in measureobjectneighbors memory improvements * Include change mentioned in comment
Co-authored-by: Callum Tromans-Coia <ctromans@wm7c1-0e3.broadinstitute.org>
Add z-dimension resize capabilities The display of the output image needs to be readjusted, at the moment the z planes displayed do not account for differences between the input and output image
Add z-dimension resize capabilities The display of the output image needs to be readjusted, at the moment the both input and output image are displayed with the same dimensions
…r#4452) * Add SaveImages option to save without bit depth conversion * add tests * better test name Co-authored-by: David Stirling <dstirling@broadinstitute.org> Co-authored-by: bethac07 <bcimini@broadinstitute.org>
…ce vectors for MeasureTexture (CellProfiler#4504) * Added in description of correspondence vectors for MeasureTexture * Added in more descriptions of 2D vectors and credits for GeoGebra * added in two images and better description for 3D vectors in measureTexture
Co-authored-by: Callum Tromans-Coia <ctromans@wm7c1-0e3.broadinstitute.org>
Author
|
@emilroz Appveyor is outdated so should be safe to merge this now? |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
14 participants
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.
Brings in changes from Broad CP 4.2.6
Adds support for Cellpose 3. Cellpose 1/2 support dropped (very different API)
Lazy loads cellpose and stardist dependencies