Rename _feature_0 to _whole_cell and _feature_1 to _nuclear
#786
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
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
…eate_deepcell_output
alex-l-kong
commented
Nov 10, 2022
alex-l-kong
commented
Nov 10, 2022
ngreenwald
requested changes
Nov 10, 2022
Yes, and I've verified that all the spatial notebooks are purged of old references. |
|
@ngreenwald can you merge this PR for me? It seems like |
srivarra
pushed a commit
that referenced
this pull request
Nov 21, 2022
…786) * Initial commit of replacing _feature_0 with _whole_cell and _feature_1 with _nuclear * Make sure dataset tests include _whole_cell and _nuclear * Update distance matrix column to be dist_whole_cell * Patch up marker quantification loading * Ensure channels for stitch_images test are being passed in correctly * Rename segmentation label saving to _whole_cell and _nuclear * Define both the whole cell and nuclear suffix renaming choices for create_deepcell_output * Change revision to match current PR on HuggingFace with new suffix names * Patch up calc_dist_matrix suffix * PYCODESTYLE in data_utils.py * Patch up deepcell_utils * Use new HuggingFace commit hash without hidden old files * Change legacy example_dataset extensions to _whole_cell.tiff * Make sure neighborhood mask uses _whole_cell.tiff * Update comment to _whole_cell.tiff too * Aesthetics * Patch _feature_0 to _whole_cell to pass neighborhood mask generation test * Change suffix in the README * Refer to main branch for HuggingFace
ngreenwald
pushed a commit
that referenced
this pull request
Jan 20, 2023
* added OME-TIFF support * requirements update * requirement went missing? * Added tmi to requirements * set pillow requirement * update numpy * add xmltodict to docs * added tmi to docs/conf.py * added utility notebook * switched lambda/map for list comprehension * switched lambda/map for list comprehension in test function * Rename `_feature_0` to `_whole_cell` and `_feature_1` to `_nuclear` (#786) * Initial commit of replacing _feature_0 with _whole_cell and _feature_1 with _nuclear * Make sure dataset tests include _whole_cell and _nuclear * Update distance matrix column to be dist_whole_cell * Patch up marker quantification loading * Ensure channels for stitch_images test are being passed in correctly * Rename segmentation label saving to _whole_cell and _nuclear * Define both the whole cell and nuclear suffix renaming choices for create_deepcell_output * Change revision to match current PR on HuggingFace with new suffix names * Patch up calc_dist_matrix suffix * PYCODESTYLE in data_utils.py * Patch up deepcell_utils * Use new HuggingFace commit hash without hidden old files * Change legacy example_dataset extensions to _whole_cell.tiff * Make sure neighborhood mask uses _whole_cell.tiff * Update comment to _whole_cell.tiff too * Aesthetics * Patch _feature_0 to _whole_cell to pass neighborhood mask generation test * Change suffix in the README * Refer to main branch for HuggingFace * updated ome-tiff notebook renamed utility notebook * undid strange merge * undid strange merge * added support for OME-TIFFs with images of multiple resolutions * added support for OME-TIFFs with images of multiple resolutions * renamed conversion notebook * removed unused imports * fixed channel extraction if a channel has no name * added example ome_tiff to the Example Dataset * added example dataset blurb * updated example dataset * updated ex dataset commit id * pycodestyle * dataset updated * dataset revision set to main Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com>
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.
What is the purpose of this PR?
Closes #745. The current suffixes for the segmented images are unclear, they need to be renamed.
How did you implement your changes
See title.