angelolab / ark-analysis / 5416

94%

push

travis-ci-com

Run expensive per-FOV pixel clustering processes in parallel (#596)

* Initial attempt at multiprocessing

* Add new looped multiprocess scheme for create_pixel_matrix

* Add timing tests

* Prevent multiprocessing from crashing on Jupyter

* Draft parallelizing pixel SOM cluster assignment

* Add multiprocessing for consensus clustering and remapping

* More updates from master

* Typo in pixel_norm_val argument passed to create_pixel_matrix partial

* Ensure channel_norm and pixel_norm don't make it into verification files for cluster_pixels

* Rough draft finished

* Add batch_size arguments to functions

* Add another batch_size argument for remapping function

* Fix test cases and documentation in som_utils for parallel processing

* Add test for preprocess_fov

* Add test for update_pixel_meta_labels

* Add print statements to update user on how many FOVs have been processed per iteration

* Doc fix in preprocess_fov

* Deploy to Docker

* Rebuild Docker with updated FlowSOM

* Docker passed: don't build on parallel_som anymore

* Remove extraneous print statement in pixel_consensus_cluster.R

* Only return pixel_mat from preprocess_fov as that's all create_pixel_matrix needs to compute quant_dat

* Nuke pixel_consensus_path in test_calculate_p2c_weighted_channel_avg

49 of 49 new or added lines in 1 file covered. (100.0%)

2595 of 2728 relevant lines covered (95.12%)

0.95 hits per line