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DrPaulSharpDrPaulSharp
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Adds orso script
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‎tests/test_data/make_orso_project.py‎

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import pathlib
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import numpy as np
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import RATapi as RAT
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from RATapi.utils.enums import BackgroundActions
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DATA_PATH = pathlib.Path(__file__).parents[0] / "ORSO_data"
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sld_values = np.loadtxt(DATA_PATH / "test_3_sld.dat")
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def make_orso_project():
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"""Set up a project with all the ORSO validation data included."""
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orso_project = RAT.Project(absorption=True)
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orso_project.parameters.set_fields("Substrate Roughness", min=0.0)
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orso_project.background_parameters.set_fields(0, min=0.0, value=0.0)
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orso_project.resolution_parameters.set_fields(0, min=0.0, value=0.0)
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orso_project.scalefactors.set_fields(0, max=1.0, value=1.0)
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orso_project.bulk_in.extend(
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[
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RAT.models.Parameter(name="Bulk In 0", value=2.07e-6),
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RAT.models.Parameter(name="Bulk In 1", value=0.0),
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RAT.models.Parameter(name="Bulk In 2", value=0.0),
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RAT.models.Parameter(name="Bulk In 3", value=0.0),
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RAT.models.Parameter(name="Bulk In 6", value=2.07e-6),
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RAT.models.Parameter(name="Bulk In 7", value=0.0),
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]
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)
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orso_project.bulk_out.extend(
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[
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RAT.models.Parameter(name="Bulk Out 0", value=6.0e-6),
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RAT.models.Parameter(name="Bulk Out 1", value=2.0704e-6),
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RAT.models.Parameter(name="Bulk Out 2", value=6.36e-6),
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RAT.models.Parameter(name="Bulk Out 3", value=6.36e-6),
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RAT.models.Parameter(name="Bulk Out 6", value=6.36e-6),
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RAT.models.Parameter(name="Bulk Out 7", value=6.36e-6),
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]
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)
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orso_project.data.extend(
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[
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RAT.models.Data(name="Data 0", data=np.loadtxt(DATA_PATH / "test_0.dat")),
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RAT.models.Data(name="Data 1", data=np.loadtxt(DATA_PATH / "test_1.dat")),
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RAT.models.Data(name="Data 2", data=np.loadtxt(DATA_PATH / "test_2.dat")),
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RAT.models.Data(name="Data 3", data=np.loadtxt(DATA_PATH / "test_3.dat")),
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RAT.models.Data(name="Data 6", data=np.loadtxt(DATA_PATH / "test_6.dat")),
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RAT.models.Data(name="Data 7", data=np.loadtxt(DATA_PATH / "test_7.dat")),
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]
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)
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orso_project.contrasts.append(
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name="ORSO Contrast",
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background="Background 1",
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background_action=BackgroundActions.Add,
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scalefactor="Scalefactor 1",
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resolution="Resolution 1",
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resample=False,
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)
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# Now set up parameters and layers for each test
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# Test 0
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orso_project.parameters.append(name="Test 0 Layer 1 Thickness", value=100.0)
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orso_project.parameters.append(name="Test 0 Layer 1 SLD real", value=3.45e-6)
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orso_project.parameters.append(name="Test 0 Layer 1 SLD imaginary", value=1.0e-7)
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orso_project.parameters.append(name="Test 0 Layer 1 Roughness", value=3.0)
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orso_project.layers.append(
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name="Test 0 Layer 1",
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thickness="Test 0 Layer 1 Thickness",
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SLD_real="Test 0 Layer 1 SLD real",
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SLD_imaginary="Test 0 Layer 1 SLD imaginary",
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roughness="Test 0 Layer 1 Roughness",
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)
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orso_project.parameters.append(name="Test 0 Layer 2 Thickness", value=200.0)
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orso_project.parameters.append(name="Test 0 Layer 2 SLD real", value=5.0e-6)
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orso_project.parameters.append(name="Test 0 Layer 2 SLD imaginary", value=1.0e-8)
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orso_project.parameters.append(name="Test 0 Layer 2 Roughness", value=1.0)
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orso_project.layers.append(
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name="Test 0 Layer 2",
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thickness="Test 0 Layer 2 Thickness",
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SLD_real="Test 0 Layer 2 SLD real",
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SLD_imaginary="Test 0 Layer 2 SLD imaginary",
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roughness="Test 0 Layer 2 Roughness",
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)
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# Test 1
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orso_project.parameters.append(name="Test 1 Layer 1 Thickness", value=30.0)
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orso_project.parameters.append(name="Test 1 Layer 1 SLD real", value=-1.9493e-6)
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orso_project.parameters.append(name="Test 1 Layer 1 SLD imaginary", value=0.0)
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orso_project.parameters.append(name="Test 1 Layer 1 Roughness", value=0.0)
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orso_project.layers.append(
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name="Test 1 Layer 1",
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thickness="Test 1 Layer 1 Thickness",
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SLD_real="Test 1 Layer 1 SLD real",
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SLD_imaginary="Test 1 Layer 1 SLD imaginary",
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roughness="Test 1 Layer 1 Roughness",
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)
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orso_project.parameters.append(name="Test 1 Layer 2 Thickness", value=70.0)
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orso_project.parameters.append(name="Test 1 Layer 2 SLD real", value=9.4245e-6)
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orso_project.parameters.append(name="Test 1 Layer 2 SLD imaginary", value=0.0)
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orso_project.parameters.append(name="Test 1 Layer 2 Roughness", value=0.0)
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orso_project.layers.append(
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name="Test 1 Layer 2",
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thickness="Test 1 Layer 2 Thickness",
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SLD_real="Test 1 Layer 2 SLD real",
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SLD_imaginary="Test 1 Layer 2 SLD imaginary",
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roughness="Test 1 Layer 2 Roughness",
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)
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# Test 2
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orso_project.parameters.append(name="Test 2 Layer 1 Thickness", value=0.0)
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orso_project.parameters.append(name="Test 2 Layer 1 SLD real", value=0.0)
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orso_project.parameters.append(name="Test 2 Layer 1 SLD imaginary", value=0.0)
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orso_project.parameters.append(name="Test 2 Layer 1 Roughness", value=0.0)
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orso_project.layers.append(
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name="Test 2 Layer 1",
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thickness="Test 2 Layer 1 Thickness",
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SLD_real="Test 2 Layer 1 SLD real",
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SLD_imaginary="Test 2 Layer 1 SLD imaginary",
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roughness="Test 2 Layer 1 Roughness",
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)
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# Test 3
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orso_project.parameters.append(name="Test 3 Thickness", value=0.025)
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orso_project.parameters.append(name="Test 3 SLD imaginary", value=0.0)
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orso_project.parameters.append(name="Test 3 Roughness", value=0.0)
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for i, sld in enumerate(sld_values):
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orso_project.parameters.append(name=f"Test 3 Layer {i} SLD real", value=sld)
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orso_project.layers.append(
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name=f"Test 3 Layer {i}",
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thickness="Test 3 Thickness",
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SLD_real=f"Test 3 Layer {i} SLD real",
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SLD_imaginary="Test 3 SLD imaginary",
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roughness="Test 3 Roughness",
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)
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# Test 6
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orso_project.parameters.append(name="Test 6 Layer 1 Thickness", value=1200.0)
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orso_project.parameters.append(name="Test 6 Layer 1 SLD real", value=4.66e-6)
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orso_project.parameters.append(name="Test 6 Layer 1 SLD imaginary", value=1.6e-8)
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orso_project.parameters.append(name="Test 6 Layer 1 Roughness", value=10.0)
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orso_project.layers.append(
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name="Test 6 Layer 1",
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thickness="Test 6 Layer 1 Thickness",
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SLD_real="Test 6 Layer 1 SLD real",
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SLD_imaginary="Test 6 Layer 1 SLD imaginary",
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roughness="Test 6 Layer 1 Roughness",
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)
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# Test 7
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orso_project.parameters.append(name="Test 7 Layer 1 Thickness", value=1200.0)
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orso_project.parameters.append(name="Test 7 Layer 1 SLD real", value=4.66e-6)
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orso_project.parameters.append(name="Test 7 Layer 1 SLD imaginary", value=1.6e-8)
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orso_project.parameters.append(name="Test 7 Layer 1 Roughness", value=10.0)
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orso_project.layers.append(
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name="Test 7 Layer 1",
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thickness="Test 7 Layer 1 Thickness",
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SLD_real="Test 7 Layer 1 SLD real",
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SLD_imaginary="Test 7 Layer 1 SLD imaginary",
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roughness="Test 7 Layer 1 Roughness",
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)
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return orso_project
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if __name__ == "__main__":
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orso_project = make_orso_project()
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orso_project.save(pathlib.Path(__file__).parents[0] / "orso_validation.json")

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