certain containers weren't registering very well. Their average projections looked difficult to align, while their max projections looked to have more detail in them for potential success. This was shown to rescue a few struggling containers.
The quick-fix for using this switch is to add:
--substitute_max_for_avg True
to the LIMS executable args.
Details
nway_matching has a new arg substitute_max_for_avg (default=False) which will substitute maxInt_a13a.png in for avgInt_a1X.png
these are both segmentation outputs.
Note: this is not robust to future changes of what the strategy supplies to this module. So, exceptions are raised if the substitution is attempted and the input image does not have the name avgInt_a1X.png and if the corresponding maxInt_a13a.png does not exist.
verbose INFO logging is in place to indicate when this has been used:
INFO:NwayMatching:substituting max for avg projections.
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_846871218/ophys_experiment_847267630/processed/ophys_cell_segmentation_run_1080713533/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_846871218/ophys_experiment_847267630/processed/ophys_cell_segmentation_run_1080713533/avgInt_a1X.png as registration input
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_847758278/ophys_experiment_848039125/processed/ophys_cell_segmentation_run_1080714550/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_847758278/ophys_experiment_848039125/processed/ophys_cell_segmentation_run_1080714550/avgInt_a1X.png as registration input
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_848401585/ophys_experiment_848760990/processed/ophys_cell_segmentation_run_1080714490/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_848401585/ophys_experiment_848760990/processed/ophys_cell_segmentation_run_1080714490/avgInt_a1X.png as registration input
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_848983781/ophys_experiment_849233404/processed/ophys_cell_segmentation_run_1080709335/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_848983781/ophys_experiment_849233404/processed/ophys_cell_segmentation_run_1080709335/avgInt_a1X.png as registration input
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_850894918/ophys_experiment_851085109/processed/ophys_cell_segmentation_run_1080714071/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_850894918/ophys_experiment_851085109/processed/ophys_cell_segmentation_run_1080714071/avgInt_a1X.png as registration input
INFO:NwayMatching:substituted /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_851740017/ophys_experiment_851958809/processed/ophys_cell_segmentation_run_1080713386/maxInt_a13a.png for /allen/programs/braintv/production/neuralcoding/prod0/specimen_810573072/ophys_session_851740017/ophys_experiment_851958809/processed/ophys_cell_segmentation_run_1080713386/avgInt_a1X.png as registration input
Purpose
certain containers weren't registering very well. Their average projections looked difficult to align, while their max projections looked to have more detail in them for potential success. This was shown to rescue a few struggling containers.
The quick-fix for using this switch is to add:
to the LIMS executable args.
Details
substitute_max_for_avg(default=False) which will substitutemaxInt_a13a.pngin foravgInt_a1X.pngavgInt_a1X.pngand if the correspondingmaxInt_a13a.pngdoes not exist.