Mask Generation Refactoring #1030
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Next Release v0.6.4 (#1012) * 0.6.4 * updated environment.yml * Update README.md * updated windows setup docs * added repo verison in git clone * file fix Deepcell upload loop cleaning (#1023) * loop check for successful deepcell upload * update test zip paths * helper functions pls * zip input, upload, and extract per batch * cleaning * docstring indent * fov -> fovs file name * remove overwrite warning * new dir for each test call * fix bad logic warning testing * remove arg from docstring * add helper function test * batch_num start at 1 * add previously processed warning * set timeouts and scrap retry * correct timeout errors and update tests * timeout 5 mins * add to unprocessed list after loop closes * continue loop after extraction * break instead of continue * skipped processing print fixes * adjust print statements * 3 seconds before second zip call update
alex-l-kong
requested changes
Aug 1, 2023
camisowers
approved these changes
Aug 1, 2023
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alex-l-kong
approved these changes
Aug 1, 2023
ngreenwald
requested changes
Aug 2, 2023
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Cell Clustering Sample Image: Neighborhood Analysis Sample Image: I added a function which converts a numpy array to a discrete colormap. Is there any place in the notebooks for it, or is it better to leave it out of the notebooks? |
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ngreenwald
requested changes
Aug 8, 2023
3 tasks
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…xie (#1051) * Drop cells without any SOM cluster expressions * Add testing for dropping non-expressed cells
* Ensure mantis can read the image sub folder specified * Test on example dataset * Default img_sub_folder to None in create_mantis_dir (standard used elsewhere) * Doc fix and updated example dataset * Update segmentation labels again * Clarify img_sub_folder (mostly for refreshing tests) * Force .github/get_example_dataset.py to use updated revision * Update the file names to look for
* pin to 0.19.3 * requirement less than 0.19.3
…o helper functions (#1058) * Propagate overwrite functionality for pixel clustering * Ensure re-normalization prevented on overwrite for pixel SOM re-assignment * normalize_data should be the opposite of overwrite
* single mantis dir, no recopying * post clustering mask suffix * generic clustering adjustments * mask prefix * remove mask prefix
* added plotting notebook * updated readmed * git merge issues * git merge fixes v2 - docs/landing.md * type * Remove cells that don't have any pixel clusters expressed prior to Pixie (#1051) * Drop cells without any SOM cluster expressions * Add testing for dropping non-expressed cells * Include `img_sub_folder` as parameter in Mantis calls (#1050) * Ensure mantis can read the image sub folder specified * Test on example dataset * Default img_sub_folder to None in create_mantis_dir (standard used elsewhere) * Doc fix and updated example dataset * Update segmentation labels again * Clarify img_sub_folder (mostly for refreshing tests) * Force .github/get_example_dataset.py to use updated revision * Update the file names to look for * fixed clipped plots in the notebooks. * Update HuggingFace version (#1053) * v0.1.10 (#1057) * Added continuous variable segmentation plots * Pin to scikit-image to v0.19.3 (#1060) * pin to 0.19.3 * requirement less than 0.19.3 * Make sure overwrite functionality for pixel clustering propagates into helper functions (#1058) * Propagate overwrite functionality for pixel clustering * Ensure re-normalization prevented on overwrite for pixel SOM re-assignment * normalize_data should be the opposite of overwrite * Single mantis directory (#1061) * single mantis dir, no recopying * post clustering mask suffix * generic clustering adjustments * mask prefix * remove mask prefix * strange merge issue * removed branch filters on CI, so if you branch off of a branch and run GHA, the CI workflow should work * changed ci.yml, filter push on main branch only * python 3.9 doesn't support | for Union type overloading * added fovs parameter for continuous variable plots * updated notebook to include plots * updated cell clustering notebooks to add erosion (default to True), cleaned up some notebook outputs * fixed style imports * re-added test_generate_summary_stats. Was accidently deleted in a refactoring step. * newline at eof fiber_segmentation_test.py * seaborn-paper -> seaborn-v0_8-paper * added cell to view all plotting styles i mask gen nb * pycodestyle --------- Co-authored-by: alex-l-kong <31424707+alex-l-kong@users.noreply.github.com> Co-authored-by: camisowers <38049893+camisowers@users.noreply.github.com>
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What is the purpose of this PR?
Refactors a portion of
plot_pixel_cell_cluster_overlayandplot_neighborhood_cluster_result.How did you implement your changes
Extracts the plotting functionality into a new function
plot_clusterwhich takes a cluster mask, or any image, and colorsthe pixels based on a user provided colormap and normalization object. Cluster labels + colorbar can be removed from the plot as well.
Added tests for
plot_neighborhood_cluster_result.Added a function which takes a numpy array representation of colors (rgb and rgba) and generates a discrete colormap from the colors provided.
Changed the readthedocs python version to 3.11 to support type hints introduced in 3.9.
Remaining issues
N/A