Refactor parameter checks

[carnisj]

Before this modification, parameters check and configuration were all over the place in bcdi_strain.py and bcdi_preprocessing_bcdi.py. Now everything is managed by a single class.

Partially related to #146

• implement the class bcdi.utils.parameters.ConfigChecker and the child classes bcdi.utils.parameters.PostprocessingChecker and bcdi.utils.parameters.PreprocessingChecker to perform the script-dependent configuration of parameters.
• the parameter scan in bcdi_strain.py was renamed scans to match preprocessing terminology
• the parameter sdd was renamed detector_distance to match PyNX terminology
• it is now possible to perform a strain analysis of several scans y providing the scan numbers as a list, and if relevant data_dir, save_dir, specfile_name, template_imagefile and reconstruction_file as lists of strings
• parameters from the config are accessed directly from the config dictionary: this will help when later refactoring the runners (splitting the scripts into meaningful small functions)

Type of change

• Breaking change (will cause existing functionality to not work as expected)

How has this been tested?

Example dataset with a series of 2 scans (post & preprocessing)

Checklist:

• I have made corresponding changes to the documentation
• I have added corresponding unit tests
• I have run doit and all tasks have passed

[carnisj]

I am still working on adding unit tests.

The interesting parts are the classes ConfigChecker, PostprocessingChecker and PreprocessingChecker and the way they are instantiated in preprocessing_runner.py (line 188) and postprocessing_runner.py (line 44).

The rest is just (a lot of) cleaning up.

[DSimonne]

From what I saw the changes are consistent, looks nice !

[clatlan]

Thanks, it seems great.
By the way, I have just noticed that 'None' is not understood by yaml as python does. I have to write 'null' instead.

[carnisj]

Thanks, it seems great. By the way, I have just noticed that 'None' is not understood by yaml as python does. I have to write 'null' instead.

None will be loaded as the string 'None', then you have to convert it to Python None when validating the parameters (this is done in parameters.valid_params)

[clatlan]

Yes. Then it means the run() functions of preprocess_runner and postprocess_runner implicitly need parameters that have already been loaded by bcdi. I parse my own dictionaries to these runners. Anyway, problem solved with 'null' (directly converted to None when read by yaml python loader).