Removes priors struct, adding relevant fields to the project (RascalSoftware#135)

* Removes priors struct, adding relevant fields to the project

* Addresses review comments

Author: DrPaulSharp

RATapi/examples/normal_reflectivity/background_function.py

@@ -1,7 +1,7 @@
 import numpy as np
 
 
-def backgroundFunction(xdata, params):
+def background_function(xdata, params):
     # Split up the params array
     Ao = params[0]
     k = params[1]

RATapi/inputs.py

@@ -10,9 +10,19 @@
 import RATapi
 import RATapi.controls
 import RATapi.wrappers
-from RATapi.rat_core import Checks, Control, Limits, NameStore, Priors, ProblemDefinition
+from RATapi.rat_core import Checks, Control, Limits, NameStore, ProblemDefinition
 from RATapi.utils.enums import Calculations, Languages, LayerModels, TypeOptions
 
+parameter_field = {
+    "parameters": "params",
+    "bulk_in": "bulkIns",
+    "bulk_out": "bulkOuts",
+    "scalefactors": "scalefactors",
+    "domain_ratios": "domainRatios",
+    "background_parameters": "backgroundParams",
+    "resolution_parameters": "resolutionParams",
+}
+
 
 def get_python_handle(file_name: str, function_name: str, path: Union[str, pathlib.Path] = "") -> Callable:
     """Get the function handle from a function defined in a python module located anywhere within the filesystem.
@@ -94,7 +104,7 @@ def __len__(self):
         return len(self.files)
 
 
-def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[ProblemDefinition, Limits, Priors, Control]:
+def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[ProblemDefinition, Limits, Control]:
     """Constructs the inputs required for the compiled RAT code using the data defined in the input project and
     controls.
 
@@ -111,65 +121,32 @@ def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[Prob
         The problem input used in the compiled RAT code.
     limits : RAT.rat_core.Limits
         A list of min/max values for each parameter defined in the project.
-    priors : RAT.rat_core.Priors
-        The priors defined for each parameter in the project.
     cpp_controls : RAT.rat_core.Control
         The controls object used in the compiled RAT code.
 
     """
-    parameter_field = {
-        "parameters": "params",
-        "bulk_in": "bulkIns",
-        "bulk_out": "bulkOuts",
-        "scalefactors": "scalefactors",
-        "domain_ratios": "domainRatios",
-        "background_parameters": "backgroundParams",
-        "resolution_parameters": "resolutionParams",
-    }
-
-    prior_id = {"uniform": 1, "gaussian": 2, "jeffreys": 3}
-
-    checks = Checks()
     limits = Limits()
-    priors = Priors()
 
     for class_list in RATapi.project.parameter_class_lists:
-        setattr(checks, parameter_field[class_list], [int(element.fit) for element in getattr(project, class_list)])
         setattr(
             limits,
             parameter_field[class_list],
             [[element.min, element.max] for element in getattr(project, class_list)],
         )
-        setattr(
-            priors,
-            parameter_field[class_list],
-            [[element.name, element.prior_type, element.mu, element.sigma] for element in getattr(project, class_list)],
-        )
 
-    # Use dummy values for qzshifts
-    checks.qzshifts = []
+    # Use dummy value for qzshifts
     limits.qzshifts = []
-    priors.qzshifts = []
-
-    priors.priorNames = [
-        param.name for class_list in RATapi.project.parameter_class_lists for param in getattr(project, class_list)
-    ]
-    priors.priorValues = [
-        [prior_id[param.prior_type], param.mu, param.sigma]
-        for class_list in RATapi.project.parameter_class_lists
-        for param in getattr(project, class_list)
-    ]
 
     if project.model == LayerModels.CustomXY:
         controls.calcSldDuringFit = True
 
-    problem = make_problem(project, checks)
+    problem = make_problem(project)
     cpp_controls = make_controls(controls)
 
-    return problem, limits, priors, cpp_controls
+    return problem, limits, cpp_controls
 
 
-def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
+def make_problem(project: RATapi.Project) -> ProblemDefinition:
     """Constructs the problem input required for the compiled RAT code.
 
     Parameters
@@ -184,6 +161,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
 
     """
     hydrate_id = {"bulk in": 1, "bulk out": 2}
+    prior_id = {"uniform": 1, "gaussian": 2, "jeffreys": 3}
 
     # Set contrast parameters according to model type
     if project.model == LayerModels.StandardLayers:
@@ -384,21 +362,32 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
         for param in getattr(project, class_list)
         if not param.fit
     ]
+    problem.priorNames = [
+        param.name for class_list in RATapi.project.parameter_class_lists for param in getattr(project, class_list)
+    ]
+    problem.priorValues = [
+        [prior_id[param.prior_type], param.mu, param.sigma]
+        for class_list in RATapi.project.parameter_class_lists
+        for param in getattr(project, class_list)
+    ]
 
     # Names
     problem.names = NameStore()
-    problem.names.params = [param.name for param in project.parameters]
-    problem.names.backgroundParams = [param.name for param in project.background_parameters]
-    problem.names.scalefactors = [param.name for param in project.scalefactors]
-    problem.names.qzshifts = []  # Placeholder for qzshifts
-    problem.names.bulkIns = [param.name for param in project.bulk_in]
-    problem.names.bulkOuts = [param.name for param in project.bulk_out]
-    problem.names.resolutionParams = [param.name for param in project.resolution_parameters]
-    problem.names.domainRatios = [param.name for param in project.domain_ratios]
+    for class_list in RATapi.project.parameter_class_lists:
+        setattr(problem.names, parameter_field[class_list], [param.name for param in getattr(project, class_list)])
     problem.names.contrasts = [contrast.name for contrast in project.contrasts]
 
     # Checks
-    problem.checks = checks
+    problem.checks = Checks()
+    for class_list in RATapi.project.parameter_class_lists:
+        setattr(
+            problem.checks, parameter_field[class_list], [int(element.fit) for element in getattr(project, class_list)]
+        )
+
+    # Use dummy values for qz shifts
+    problem.names.qzshifts = []
+    problem.checks.qzshifts = []
+
     check_indices(problem)
 
     return problem

RATapi/run.py

@@ -104,7 +104,7 @@ def run(project, controls):
 
     horizontal_line = "\u2500" * 107 + "\n"
     display_on = controls.display != Display.Off
-    problem_definition, limits, priors, cpp_controls = make_input(project, controls)
+    problem_definition, limits, cpp_controls = make_input(project, controls)
 
     if display_on:
         print("Starting RAT " + horizontal_line)
@@ -115,7 +115,6 @@ def run(project, controls):
             problem_definition,
             limits,
             cpp_controls,
-            priors,
         )
     end = time.time()