Expose additional schema parameters for segmentation and binarization

wbwakeman commented 4 years ago

In order to make it easier to override individual parameters for development purposes, would like to expose additional schema parameters for the segmentation and binarization steps.

Tasks:

[x] Create Jira Issue for LIMS work: http://jira.corp.alleninstitute.org/projects/PBS
[x] Reorganize input json generated by LIMS for the segmentation/binarization
[x] Rewrite schema in repo to nest the two transform schemas
[x] Convert_rois argument suite2p stat path needs to have validation changed (because file won't exist yet)

Validation criteria:

[x] Can run pipeline offline and specify all the parameters
[x] LIMS strategy will produce a valid input json file

LIMS cutoff dates: 10/8 for 10/15 release

njmei commented 4 years ago

LIMS Jira ticket can be found at: http://jira.corp.alleninstitute.org/browse/PBS-2463

njmei commented 4 years ago

For validation see: https://github.com/AllenInstitute/ophys_etl_pipelines/pull/70#issuecomment-701626331

AllenInstitute / ophys_etl_pipelines

Expose additional schema parameters for segmentation and binarization #68