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Ran 09 Nov 2022 01:08AM UTC

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Committed 09 Nov 2022 12:56AM UTC coverage: 92.996% (-0.006%) from 93.002%

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push

travis-ci-com

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web-flow

Commit Message

Refactor distance matrix saving (#803)

* Extract distance matrix calculation out to a separate folder

* Refactor spatial analysis to run with individually-saved dist mats

* Add workflow for neighborhood analysis (except label map generation)

* Remove old calc_dist_matrix

* Condense neighborhood analysis using new dist matrix saving method

* Ensure label maps now load individually in neighborhood mask generation

* Make sure label_dir passed into neighborhood matrix mask generation in notebook

* Adjust neighborhood mask saving tests

* PYCODESTYLE fixes

* Documentation fix

* Change label_dir to seg_output

* Clarify save_path in calc_dist_matrix

* Don't hard code _feature_0, use prefix argument for calc_dist_matrix

* Make sure conditional else for non context-based channel analysis added

* Add tqdm status bar to distance matrix creation

* Add protection for specifying excluded_channels=None in channel spatial enrichment

* Change fovs to fov_files in calc_dist_matrix

* Update spatial analysis progress bars to be more informative

* Support and provide documentation for setting channels to None in spatial analysis notebook

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master: 94%

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