Adding an AnalysisParams class to hold all default analysis params #14
Description
New Feature
I have added an AnalysisParam(). This is a class that encapsulates all user defined analysis parameters like spine parameters to construct a spine roi, like extend, radius, etc.
An analysisParams object can be passed into the Loader(). By default Loader() creates a default AnalysisParams() object.
An analysisParams object is stored in AnnotationsBase during runtime
self._analysisParams = loader.analysisParams()It is saved in annotations/base.py save():
group.attrs['analysisParams'] = self._analysisParams.getJson()It is loaded in MMapLoaderLazy():
_analysisParams_json = group.attrs['analysisParams'] # json str
analysisParams = AnalysisParams(loadJson=_analysisParams_json)Usage
An AnalysisParam() object can be created and tweaked in our scripts to make a map. Once a map is created, the AnalysisParams() object is saved and loaded from the zarr file.
Rational
We do not want to hard-code any analysis params. We need it in a class that allows the values to be set during runtime.
For example, a user can set roiExtend to a new value and then re-run all the analysis.
TODO
We need to expand the keys in AnalysisParams() to include all our hard coded analysis parameters!!!