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Updates C++ and some unit tests #97

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Merged
StephenNneji merged 4 commits into from
Dec 6, 2024
Merged

Updates C++ and some unit tests #97

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4ced2ca
Updates C++ and some unit tests
StephenNneji Dec 6, 2024
8bd15e2
Updates jupyter notebooks and clears outputs
StephenNneji Dec 6, 2024
40d926d
linting
StephenNneji Dec 6, 2024
8f7985b
Addresses review comments
StephenNneji Dec 6, 2024
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linting
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@StephenNneji
StephenNneji committed Dec 6, 2024
commit 40d926d8a9895a70d90f2c7a9050cec2b939b408
32 changes: 15 additions & 17 deletions RATapi/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,13 @@
import os
import pathlib
from typing import Callable, Union

import numpy as np

import RATapi
import RATapi.controls
import RATapi.wrappers
from RATapi.rat_core import NameStore, Checks, Control, Limits, Priors, ProblemDefinition
from RATapi.rat_core import Checks, Control, Limits, NameStore, Priors, ProblemDefinition
from RATapi.utils.enums import Calculations, Languages, LayerModels, TypeOptions


Expand Down Expand Up @@ -49,7 +51,7 @@ class FileHandles:
def __init__(self, files=None):
self.index = 0
self.files = [] if files is None else [file.dict() for file in files]

def __iter__(self):
self.index = 0
return self
Expand Down Expand Up @@ -89,9 +91,7 @@ def __next__(self):
raise StopIteration


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, Priors, Control]:
"""Constructs the inputs required for the compiled RAT code using the data defined in the input project and
controls.

Expand Down Expand Up @@ -192,8 +192,6 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:

"""
hydrate_id = {"bulk in": 1, "bulk out": 2}
action_id = {"add": 1, "subtract": 2}


# Set contrast parameters according to model type
if project.model == LayerModels.StandardLayers:
Expand All @@ -208,7 +206,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
]
else:
contrast_models = [[]] * len(project.contrasts)

# Set contrast parameters according to model type
if project.model == LayerModels.StandardLayers:
contrast_custom_files = [float("NaN")] * len(project.contrasts)
Expand All @@ -230,7 +228,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
layer_params.append(hydrate_id[layer.hydrate_with])

layer_details.append(layer_params)

for contrast in project.contrasts:
background = project.backgrounds[contrast.background]
contrast_background_types.append(background.type)
Expand All @@ -251,10 +249,10 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
contrast_resolution_params.append(-1)
else:
contrast_resolution_params.append(project.resolution_parameters.index(resolution.value_1, True))

data_index = project.data.index(contrast.data)
data = project.data[data_index].data
all_data.append(np.column_stack((data, np.zeros((data.shape[0], 6-data.shape[1])))))
all_data.append(np.column_stack((data, np.zeros((data.shape[0], 6 - data.shape[1])))))
data_range = project.data[data_index].data_range
simulation_range = project.data[data_index].simulation_range

Expand All @@ -267,7 +265,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
simulation_limits.append(simulation_range)
else:
simulation_limits.append([0.0, 0.0])

problem = ProblemDefinition()

problem.TF = project.calculation
Expand All @@ -283,7 +281,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
problem.repeatLayers = [[0, 1]] * len(project.contrasts) # This is marked as "to do" in RAT
problem.contrastBackgroundParams = contrast_background_params
problem.contrastBackgroundTypes = contrast_background_types
problem.contrastBackgroundActions = [contrast.background_action for contrast in project.contrasts]
problem.contrastBackgroundActions = [contrast.background_action for contrast in project.contrasts]
problem.contrastQzshifts = [1] * len(project.contrasts) # This is marked as "to do" in RAT
problem.contrastScalefactors = [
project.scalefactors.index(contrast.scalefactor, True) for contrast in project.contrasts
Expand All @@ -304,15 +302,15 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
problem.customFiles = FileHandles(project.custom_files)
problem.modelType = project.model
problem.contrastCustomFiles = contrast_custom_files

problem.contrastDomainRatios = [
project.domain_ratios.index(contrast.domain_ratio, True) if hasattr(contrast, "domain_ratio") else 0
for contrast in project.contrasts
]

problem.domainRatios = [param.value for param in project.domain_ratios]
problem.numberOfDomainContrasts = len(project.domain_contrasts)

domain_contrast_models = [
[project.layers.index(layer, True) for layer in domain_contrast.model]
for domain_contrast in project.domain_contrasts
Expand Down Expand Up @@ -345,7 +343,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
for param in getattr(project, class_list)
if not param.fit
]

# Names
problem.names = NameStore()
problem.names.params = [param.name for param in project.parameters]
Expand All @@ -357,7 +355,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
problem.names.resolutionParams = [param.name for param in project.resolution_parameters]
problem.names.domainRatios = [param.name for param in project.domain_ratios]
problem.names.contrasts = [contrast.name for contrast in project.contrasts]

# Checks
problem.checks = checks
check_indices(problem)
Expand Down
5 changes: 1 addition & 4 deletions tests/test_inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,6 @@

import pathlib
import pickle
from itertools import chain
from unittest import mock

import numpy as np
import pytest
Expand All @@ -13,14 +11,14 @@
from RATapi.inputs import check_indices, make_controls, make_input, make_problem
from RATapi.rat_core import Checks, Control, Limits, Priors, ProblemDefinition
from RATapi.utils.enums import (
BackgroundActions,
BoundHandling,
Calculations,
Display,
Geometries,
LayerModels,
Parallel,
Procedures,
BackgroundActions,
)
from tests.utils import dummy_function

Expand Down Expand Up @@ -785,4 +783,3 @@ def check_controls_equal(actual_controls, expected_controls) -> None:

for field in controls_fields:
assert getattr(actual_controls, field) == getattr(expected_controls, field)