Pin to scikit-image to v0.19.3 #1060
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alex-l-kong
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Sep 12, 2023
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I looked at the frangi implementation in skimage.filters.ridges and it looks like one of the key differences is in the handling of the gamma parameter. In 0.19.3, it's automatically set to 15, whereas in >=0.20.0, it's dynamically computed based on the eigenvalues by default. Maybe as a step 0 try manually setting the gamma param to 15 and see how that turns out?
Sorry I added this comment to the issue, but not the PR description: I was able to get something comparable to the previous implementation by tweaking a few parameters (gamma for one, and also the fiber widths). It's much better than the current version but still not as good as using scikit-learn v0.19.3. I can further look into adjusting the code with v0.21 at the end of the month, but in the interim we should pin it. |
srivarra
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Sep 12, 2023
alex-l-kong
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Sep 12, 2023
ngreenwald
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Sep 12, 2023
Less than or equal should be fine. |
ngreenwald
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Sep 12, 2023
srivarra
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Sep 13, 2023
* pin to 0.19.3 * requirement less than 0.19.3
srivarra
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Sep 13, 2023
* pin to 0.19.3 * requirement less than 0.19.3
ngreenwald
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Sep 17, 2023
* 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>
ngreenwald
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Sep 18, 2023
* plot_cluster 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 * updated readthedocs python version * updated plot_utils docstring * docstrings v2 * use GS [1,1] if cbar_visible is False, otherwise use GS [1, 2] for plot + colorbar * added cbar_visible T/F for tests * pycodestyle * added numpy list to cmap / norm function * 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 * Update HuggingFace version (#1053) * v0.1.10 (#1057) * 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 * Mass plotting notebook (#1052) * 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> * default ero * added erode=True for generate_cluster_mask --------- 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?
Closes #1055. Improves fiber segmentation results by pinning scikit-image to an older version.
How did you implement your changes
Update pyproject.toml.
Remaining issues
Short term solution. Should be looked into for a more permanent fix in the future.