ADR: SampleModel, ResolutionModel, BackgroundModel

[henrikjacobsenfys]

General

This describes the implementation of SampleModel, ResolutionModel and BackgroundModel, which all follow the same pattern. They all inherit from ModelBase.
The implementation has been discussed in easyscience/dynamics#4, where it was decided to create `ComponentCollection' #108

SampleModel describes the scattering from a sample at multiple Q. At each Q, the model generates a ComponentCollection (#108 ) with appropriate ModelComponents.

#ModelBase
Provides common functionality for all the models described above.
Input:

• display_name: the name of the model to be displayed e.g. in the GUI
• unique_name: unique name to be able to refer to the component
• unit: unit of all underlying components
• components: template components that will be copied to each Q. WIll be made clearer (Make the distinction between templates and components in sample models clearer #101 )
• Q: the Q values where the model is evaluated. In most cases, this will be automatically filled out by the Analysis class, which takes the Q from the experiment.

It has the following methods:

• evaluate: calculate the model contribution at each Q, returns a np.ndarray of calculated intensity
• append_component/remove_component: adds/removes components to the template. These will be copied to each Q
• various setters and getters for unit, components, Q
• fix/free all variables: fixes/frees all variables of the model
• get_all_variables: gets all variables at all Q, or all variables at a particular Q index
• get_component_collection: gets the ComponentCollection at a particular Q index
• _generate_component_collections: generates ComponentCollection at each Q based on the templates

BackgroundModel

Currently is identical to the ModelBase. It may in the future be expanded with various options specific to background.

ResolutionModel

Currently is identical to the ModelBase, except it does not allow DeltaFunction and Polynomial components, as these cannot form a meaningful model of a resolution.

Some care must be taken in not overwriting the ResolutionModel (#101 )

SampleModel

Is extended with the following:

• temperature: if set, applies detailed balancing (`ADR`: DetailedBalance #107 ) to the components when evaluating
• diffusion_models: a list of DiffusionModel (`ADR`: DiffusionModel #106 ). When generating components, the ComponentCollections generated by the DiffusionModels will be appended to the components generated by the component templates

InstrumentModel

Describes everything that has to do with the instrument. It contains:

• Q: just like the other Model's described here.
• ResolutionModel: a model of the instrument resolution
• BackgroundModel: a model of the background
• energy_offset: a Parameter for each Q that by default is free to be fitted. Offsets the intensity of the entire ComponentCollection to account for small instrument misalignment
• fix/free resolution parameters: helpers to make it easy to not accidentally fit the resolution when it should be fixed