ADR: Analysis

[henrikjacobsenfys]

General

The Analysis class is where fitting takes place. It was discussed in easyscience/dynamics#5

This ADR records the current implementation

Current implementation

There are three Analysis classes: AnalysisBase, Analysis1d and Analysis. The base class handles all shared logic, of course.
Analysis1d has a Q_index property, and will work with data (intensity with variances as function of energy) for that single Q_index. The Analysis class contains a list of Analysis1d objects; one for each Q_index in the underlying experimental data.

AnalysisBase

AnalysisBase inherits from ModelBase.

It takes the following input:
display_name and unique_name
experiment: An EasyDynamics Experiment object, which contains a scipp DataArray with coordinates energy and Q. The Q from the Experiment will be used as the true Q (e.g. the one that the Analysis getters will refer to)
sample_model: An EasyDynamics SampleModel object, which contains a ComponentCollection for each Q_index instrument_model: An EasyDynamics InstrumentModelobject, which contains an optionalResolutionModelandBackgroundModel(similar to theSampleModel), and a list of energy_offset Parameters, one for each Q. convolution_settings`: settings for the convolution class to improve accuracy.

It contains setters and getters for all these models.

Analysis1d

It also takes the following two inputs:
a Q_index, which selects a particular Q of the data and all the attached models.
extra_parameters: A Parameter or a list of Parameter, which the user can define as they please. I do not know exactly how users will use this, but they may, for example, decide that the widths of the Lorentzians in their model should be dependent Parameters with some custom dependency on another Parameter. Most users will not touch it, but it's there to allow flexibility for advanced users.

Other methods:
get_all_variables(): gets all the variables of the relevant models at self._Q_index, all shared Parameters like the temperature of the SampleModel and any Parameters from DiffusionModels. And of course the extra Parameters that users can pass to it
calculate : Calculate the scattering at self._Q_index. Includes checks and may regenerate the Convolution object if needed
_calculate: do the actual calculation with minimal checks for speed for the
fit: uses the EasyScience Fitter to fit the data at the given Q_index
calculate_individual_component: calculates individual components including resolution abd background contributions for
plot_data_and_model
_create_convolver method, which creates a EasyDynamics Convolution object for a given Q_index, which handles the convolution of the sample ComponentCollection with the instrument resolution ComponentCollection

Analysis

Contains a list of Analysis1d objects and the following primary methods:
fit: fits the data with various settings, calling various sub-functions, such as
_fit_single_Q: calls the relevant Analysis1d.
_fit_all_Q_independently: calls all the relevant Analysis1d objects one after the other
_fit_all_Q_simultaneously: This is the fun one! It passes all the Analysis1d objects and the correct fit functions to do what the name implies, allowing fits of full diffusion models
plot_data_and_model: uses a Scipp Dataset and plopp to make slicers and other types of plots easily
plot_fit_parameter: plot e.g. the width of one (or more) of the Lorentzians.
parameters_to_dataset: extract the value and vaariance of all parameters and create a scipp Dataset to hold them

Extensions:

For the fitting I also want utility such as:

• fit a single Q_index, then copy the values of the fit to the other ones to have better start guesses
• Fit all Q independently, but use the previous fit as the start guess for the next one
• easy access to fix Parameters across Q, and to make Parameters dependent on each other.
• See Extend Analysis #98
• fit settings