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Project#

pydantic model RATapi.Project#

Defines the input data for a reflectivity calculation in RAT.

This class combines the data defined in each of the pydantic models included in “models.py” into the full set of inputs required for a reflectivity calculation.

Fields:

  • absorption (bool)

  • background_parameters (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • backgrounds (RATapi.classlist.ClassList[RATapi.models.Background])

  • bulk_in (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • bulk_out (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • calculation (RATapi.utils.enums.Calculations)

  • contrasts (RATapi.classlist.ClassList[RATapi.models.Contrast] | RATapi.classlist.ClassList[RATapi.models.ContrastWithRatio])

  • custom_files (RATapi.classlist.ClassList[RATapi.models.CustomFile])

  • data (RATapi.classlist.ClassList[RATapi.models.Data])

  • domain_contrasts (RATapi.classlist.ClassList[RATapi.models.DomainContrast])

  • domain_ratios (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • geometry (RATapi.utils.enums.Geometries)

  • layers (RATapi.classlist.ClassList[RATapi.models.Layer] | RATapi.classlist.ClassList[RATapi.models.AbsorptionLayer])

  • model (RATapi.utils.enums.LayerModels)

  • name (str)

  • parameters (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • resolution_parameters (RATapi.classlist.ClassList[RATapi.models.Parameter])

  • resolutions (RATapi.classlist.ClassList[RATapi.models.Resolution])

  • scalefactors (RATapi.classlist.ClassList[RATapi.models.Parameter])

field absorption: bool = False#

Whether imaginary SLD (absorption) should be accounted for.

field background_parameters: ClassList[Parameter] = [Parameter(name='Background Param 1', min=1e-07, value=1e-06, max=1e-05, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for models of backgrounds.

field backgrounds: ClassList[Background] = [Background(name='Background 1', type='constant', source='Background Param 1', value_1='', value_2='', value_3='', value_4='', value_5='')]#

The list of models for background noise in the project.

field bulk_in: ClassList[Parameter] = [Parameter(name='SLD Air', min=0.0, value=0.0, max=0.0, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for SLD of the entry interfaces of a model.

field bulk_out: ClassList[Parameter] = [Parameter(name='SLD D2O', min=6.2e-06, value=6.35e-06, max=6.35e-06, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for SLD of the exit interfaces of a model.

field calculation: Calculations = Calculations.Normal#

What calculation type should be used. Can be ‘normal’ or ‘domains’.

field contrasts: Annotated[ClassList[Contrast], Tag(tag=no_ratio)] | Annotated[ClassList[ContrastWithRatio], Tag(tag=ratio)] = []#

All groups of components used to define each model in the project.

field custom_files: ClassList[CustomFile] = []#

Handles for custom files used by the project.

field data: ClassList[Data] = []#

Experimental data for a model.

field domain_contrasts: ClassList[DomainContrast] = []#

The groups of layers required by each domain in a domains model.

field domain_ratios: ClassList[Parameter] = [Parameter(name='Domain Ratio 1', min=0.4, value=0.5, max=0.6, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for weighting between domains of a domains model.

field geometry: Geometries = Geometries.AirSubstrate#

What geometry should be used. Can be ‘air/substrate’ or ‘substrate/liquid’

field layers: Annotated[ClassList[Layer], Tag(tag=no_abs)] | Annotated[ClassList[AbsorptionLayer], Tag(tag=abs)] = []#

The layers of a standard layer model.

field model: LayerModels = LayerModels.StandardLayers#

What layer model should be used. Can be ‘standard layers’, ‘custom layers’, or ‘custom xy’.

field name: str = ''#

The name of the project.

field parameters: ClassList[Parameter] = []#

The list of parameters used in the layers of a model.

field resolution_parameters: ClassList[Parameter] = [Parameter(name='Resolution Param 1', min=0.01, value=0.03, max=0.05, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for models of resolutions.

field resolutions: ClassList[Resolution] = [Resolution(name='Resolution 1', type='constant', source='Resolution Param 1', value_1='', value_2='', value_3='', value_4='', value_5='')]#

The list of models for instrument resolution in the project.

field scalefactors: ClassList[Parameter] = [Parameter(name='Scalefactor 1', min=0.02, value=0.23, max=0.25, fit=False, prior_type='uniform', mu=0.0, sigma=inf, show_priors=False)]#

The list of parameters for scale factors to handle systematic error in model data.

check_allowed_source(attribute)#

Check that the source of a background or resolution is defined in the relevant field for its type.

  • A constant background or resolution source should be defined in background_parameters or resolution_parameters respectively;

  • A data background source should be defined in data

  • A function background source should be defined in custom_files

Parameters:

attribute (str) – The attribute of Project being validated.

Raises:

ValueError – Raised if any field in field_list has a value not specified in allowed_constants or allowed_data as appropriate.

Return type:

None

check_allowed_values(attribute, field_list, allowed_values)#

Check the values of the given fields in the given model are in the supplied list of allowed values.

Parameters:

  • attribute (str) – The attribute of Project being validated.

  • field_list (list [str]) – The fields of the attribute to be checked for valid values.

  • allowed_values (list [str]) – The list of allowed values for the fields given in field_list.

Raises:

ValueError – Raised if any field in field_list has a value not specified in allowed_values.

Return type:

None

check_contrast_model_allowed_values(contrast_attribute, allowed_values, allowed_field)#

The contents of the “model” field of “contrasts” and “domain_contrasts” must be defined elsewhere in the project.

Parameters:

  • contrast_attribute (str) – The specific contrast attribute of Project being validated (either “contrasts” or “domain_contrasts”).

  • allowed_values (list [str]) – The list of allowed values for the model of the contrast_attribute.

  • allowed_field (str) – The name of the field in the project in which the allowed_values are defined.

Raises:

ValueError – Raised if any model in contrast_attribute has a value not specified in allowed_values.

Return type:

None

get_all_names()#

Record the names of all models defined in the project.

get_all_protected_parameters()#

Record the protected parameters defined in the project.

get_contrast_model_field()#

Get the field used to define the contents of the “model” field in contrasts.

Returns:

model_field – The name of the field used to define the contrasts’ model field.

Return type:

str

hide_priors()#

Hide priors for all parameters in the model.

classmethod load(path)#

Load a project from file.

Parameters:

path (str or Path) – The path to the project file.

Return type:

Project

model_post_init(context, /)#

We need to both initialize private attributes and call the user-defined model_post_init method.

Parameters:

  • self (BaseModel)

  • context (Any)

Return type:

None

save(path, filename='project')#

Save a project to a JSON file.

Parameters:

  • path (str or Path) – The path in which the project will be written.

  • filename (str) – The name of the generated project file.

set_prior_visibility(priors_visible)#

Set whether priors are visible or invisible for all parameters.

Parameters:

priors_visible (bool) – Whether priors should be shown.

show_priors()#

Show priors for all parameters in the model.

write_script(obj_name='problem', script='project_script.py')#

Write a python script that can be run to reproduce this project object.

Parameters:

  • obj_name (str, optional) – The name given to the project object under construction (default is “problem”).

  • script (str, optional) – The filepath of the generated script (default is “project_script.py”).

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