Programmatic
Running a Workflow
The --workflow command-line flag, the LatticeData(workflow=) Python parameter, and the Workflow tab of the plugin can be used to specify the path to a workflow .yml file .
If you're using the Python interface, you need to use LatticeData.process_workflow() rather than .process().
Outputs
lls_core supports workflows that have exactly one "leaf" task. This is defined as a task that is not used by any other tasks. In other works, it's the final task of the workflow.
If you want multiple return values, this task can return a tuple of values. Each of these values must be:
- An array, in which case it is treated as an image slice
- A
dict, in which case it is treated as a single row of a data frame whose columns are the keys of thedict - A
list, in which case it is treated as a single row of a data frame whose columns are unnamed
Then, each slice is combined at the end. Image slices are stacked together into their original dimensionality, and data frame rows are stacked into a data frame with one row per channel, timepoint and ROI.