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Updates indices #71

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Merged
DrPaulSharp merged 3 commits into from
Sep 2, 2024
Merged

Updates indices #71

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3075555
Applies use of strings for Classlist __getitem__
DrPaulSharp Aug 1, 2024
4877002
Bug fix for qzshift index in inputs.py
DrPaulSharp Aug 22, 2024
2ceec4e
Bug fix
DrPaulSharp Sep 2, 2024
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10 changes: 4 additions & 6 deletions RATapi/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,7 +128,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
contrast_background_params = []

for contrast in project.contrasts:
background = project.backgrounds[project.backgrounds.index(contrast.background)]
background = project.backgrounds[contrast.background]
if background.type == TypeOptions.Data:
contrast_background_params.append(-1)
else:
Expand All @@ -138,7 +138,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
contrast_resolution_params = []

for contrast in project.contrasts:
resolution = project.resolutions[project.resolutions.index(contrast.resolution)]
resolution = project.resolutions[contrast.resolution]
if resolution.type == TypeOptions.Data:
contrast_resolution_params.append(-1)
else:
Expand All @@ -160,7 +160,7 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
problem.resolutionParams = [param.value for param in project.resolution_parameters]
problem.contrastBulkIns = [project.bulk_in.index(contrast.bulk_in, True) for contrast in project.contrasts]
problem.contrastBulkOuts = [project.bulk_out.index(contrast.bulk_out, True) for contrast in project.contrasts]
problem.contrastQzshifts = [0] * len(project.contrasts) # This is marked as "to do" in RAT
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 Down Expand Up @@ -239,9 +239,7 @@ def make_data_present(project: RATapi.Project) -> list[int]:
The "dataPresent" field of the problem input used in the compiled RAT code.

"""
return [
1 if project.data[project.data.index(contrast.data)].data.size != 0 else 0 for contrast in project.contrasts
]
return [1 if project.data[contrast.data].data.size != 0 else 0 for contrast in project.contrasts]


def check_indices(problem: ProblemDefinition) -> None:
Expand Down
2 changes: 1 addition & 1 deletion RATapi/project.py
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Expand Up @@ -285,7 +285,7 @@ def model_post_init(self, __context: Any) -> None:
)
elif "Substrate Roughness" not in [name.title() for name in self.get_all_protected_parameters()["parameters"]]:
# If substrate roughness is included as a standard parameter replace it with a protected parameter
substrate_roughness_values = self.parameters[self.parameters.index("Substrate Roughness")].model_dump()
substrate_roughness_values = self.parameters["Substrate Roughness"].model_dump()
self.parameters.remove("Substrate Roughness")
self.parameters.insert(0, RATapi.models.ProtectedParameter(**substrate_roughness_values))

Expand Down