angelolab / ark-analysis / 4272
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Add QC metrics and corresponding visualizations (#476)

* Initial commit of qc metrics

* Address some uncaught testing scenarios

* Add option to Gaussian blur the images before extracting QC metrics

* Minor documentation fix

* Address issues that came up during testing Erin's data

* Change Gaussian blurring scheme (TODO: need to make sure values are actually assigned)

* Change return type of qc computation to dict, and add notebook

* PYCODESTYLE

* Add notebook testing for qc metric computation

* Remove full notebook test for now (it's been hardcoded with Erin's data for testing)

* Add base visualization code

* Add new testing notebook tags to QC comp notebook

* Speed up the QC computation pipeline a ton

* Add opencv to docs

* Remove numba import

* Update process to be faster for computing QC metrics

* Fix = to ==

* Fix the notebook tests

* Add sub_dir argument to create_tiff_files

* Separate batching as a separate function

* Remove comments and add new notebook

* Update process

* Switch back to OpenCV Gaussian blur

* Use scipy.ndimage for Gaussian filtering in line with Erin's request

* Remove unnecessary inputs and change paths to actual input data in our directory

* Docstring fix

* Generalize fov sorting to "weirder" names

* Change default sub_folder to "TIFs"

* Remove cv2 from conf.py

* Fix folder test for QC comp, and add test to run entire qc notebook

* Fix axes labels in graph

* Generalize QC comp notebook test to arbitrary number of fovs and chans

* Clarify that qc_metric_df is melted in visualize_qc_metrics

* Fix metric names in qc_comp_test

2151 of 2273 relevant lines covered (94.63%)

0.95 hits per line

Jobs
ID Job ID Ran Files Coverage
1 4272.1 (MPLBACKEND=Agg) 0
94.63
 Travis Job 4272.1
Source Files on build 4272
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