Added Batching Functionality to Pixel Mask Generation and FOV Saving #643
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srivarra
changed the title
data_utils.generate_pixel_cluster_mask
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srivarra
changed the title
ngreenwald
reviewed
Jul 26, 2022
ngreenwald
requested changes
Jul 26, 2022
ngreenwald
requested changes
Aug 1, 2022
ngreenwald
reviewed
Aug 1, 2022
ngreenwald
requested changes
Aug 10, 2022
ark/utils/notebooks_test_utils.py
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| # cell_mask_save = """ | ||
| # data_utils.save_fov_images( | ||
| # pixel_fovs, | ||
| # os.path.join(base_dir, pixel_output_dir), |
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What's the plan with this stuff?
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To remove it, since we don't check if the user wants to save with the batching system.
ark/utils/notebooks_test_utils.py
Outdated
| # cell_mask_save = """ | ||
| # data_utils.save_fov_images( | ||
| # cell_fovs, | ||
| # os.path.join(base_dir, cell_output_dir), |
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To remove it, since we don't check if the user wants to save with the batching system.
ngreenwald
approved these changes
Aug 10, 2022
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What is the purpose of this PR?
Closes #552
How did you implement your changes
Added two batching functions for the pixel and cell clustering notebooks. In addition added testbook tests.
Remaining issues
None ATM.