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Removes qzshift from user-facing code #28

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Apr 26, 2024
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Removes qzshift from user-facing code #28

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11 changes: 7 additions & 4 deletions RAT/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@ def make_input(project: RAT.Project, controls: Union[RAT.controls.Calculate, RAT
parameter_field = {'parameters': 'param',
'bulk_in': 'bulkIn',
'bulk_out': 'bulkOut',
'qz_shifts': 'qzshift',
'scalefactors': 'scalefactor',
'domain_ratios': 'domainRatio',
'background_parameters': 'backgroundParam',
Expand All @@ -48,7 +47,6 @@ def make_input(project: RAT.Project, controls: Union[RAT.controls.Calculate, RAT
checks_field = {'parameters': 'fitParam',
'bulk_in': 'fitBulkIn',
'bulk_out': 'fitBulkOut',
'qz_shifts': 'fitQzshift',
'scalefactors': 'fitScalefactor',
'domain_ratios': 'fitDomainRatio',
'background_parameters': 'fitBackgroundParam',
Expand All @@ -71,6 +69,11 @@ def make_input(project: RAT.Project, controls: Union[RAT.controls.Calculate, RAT
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.fitQzshift = []
limits.qzshift = []
priors.qzshift = []

priors.priorNames = [param.name for class_list in RAT.project.parameter_class_lists
for param in getattr(project, class_list)]
priors.priorValues = [[prior_id[param.prior_type], param.mu, param.sigma]
Expand Down Expand Up @@ -115,7 +118,7 @@ def make_problem(project: RAT.Project) -> ProblemDefinition:
problem.params = [param.value for param in project.parameters]
problem.bulkIn = [param.value for param in project.bulk_in]
problem.bulkOut = [param.value for param in project.bulk_out]
problem.qzshifts = [param.value for param in project.qz_shifts]
problem.qzshifts = []
problem.scalefactors = [param.value for param in project.scalefactors]
problem.domainRatio = [param.value for param in project.domain_ratios]
problem.backgroundParams = [param.value for param in project.background_parameters]
Expand Down Expand Up @@ -216,7 +219,7 @@ def make_cells(project: RAT.Project) -> Cells:
cells.f7 = [param.name for param in project.parameters]
cells.f8 = [param.name for param in project.background_parameters]
cells.f9 = [param.name for param in project.scalefactors]
cells.f10 = [param.name for param in project.qz_shifts]
cells.f10 = [] # Placeholder for qzshifts
cells.f11 = [param.name for param in project.bulk_in]
cells.f12 = [param.name for param in project.bulk_out]
cells.f13 = [param.name for param in project.resolution_parameters]
Expand Down
8 changes: 2 additions & 6 deletions RAT/project.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@
model_in_classlist = {'parameters': 'Parameter',
'bulk_in': 'Parameter',
'bulk_out': 'Parameter',
'qz_shifts': 'Parameter',
'scalefactors': 'Parameter',
'domain_ratios': 'Parameter',
'background_parameters': 'Parameter',
Expand Down Expand Up @@ -73,7 +72,7 @@
}

# Note that the order of these parameters is hard-coded into RAT
parameter_class_lists = ['parameters', 'background_parameters', 'scalefactors', 'qz_shifts', 'bulk_in', 'bulk_out',
parameter_class_lists = ['parameters', 'background_parameters', 'scalefactors', 'bulk_in', 'bulk_out',
'resolution_parameters', 'domain_ratios']
class_lists = [*parameter_class_lists, 'backgrounds', 'resolutions', 'custom_files', 'data', 'layers',
'domain_contrasts', 'contrasts']
Expand All @@ -100,9 +99,6 @@ class Project(BaseModel, validate_assignment=True, extra='forbid', arbitrary_typ
fit=False, prior_type=Priors.Uniform, mu=0.0,
sigma=np.inf))

qz_shifts: ClassList = ClassList(RAT.models.Parameter(name='Qz shift 1', min=-1e-4, value=0.0, max=1e-4, fit=False,
prior_type=Priors.Uniform, mu=0.0, sigma=np.inf))

scalefactors: ClassList = ClassList(RAT.models.Parameter(name='Scalefactor 1', min=0.02, value=0.23, max=0.25,
fit=False, prior_type=Priors.Uniform, mu=0.0,
sigma=np.inf))
Expand Down Expand Up @@ -137,7 +133,7 @@ class Project(BaseModel, validate_assignment=True, extra='forbid', arbitrary_typ
_contrast_model_field: str
_protected_parameters: dict

@field_validator('parameters', 'bulk_in', 'bulk_out', 'qz_shifts', 'scalefactors', 'background_parameters',
@field_validator('parameters', 'bulk_in', 'bulk_out', 'scalefactors', 'background_parameters',
'backgrounds', 'resolution_parameters', 'resolutions', 'custom_files', 'data', 'layers',
'domain_contrasts', 'contrasts')
@classmethod
Expand Down
60 changes: 29 additions & 31 deletions tests/test_inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,14 +70,14 @@ def standard_layers_problem():
problem.params = [3.0, 0.0, 0.0, 0.0]
problem.bulkIn = [0.0]
problem.bulkOut = [6.35e-06]
problem.qzshifts = [0.0]
problem.qzshifts = []
problem.scalefactors = [0.23]
problem.domainRatio = []
problem.backgroundParams = [1e-06]
problem.resolutionParams = [0.03]
problem.contrastBulkIns = [1]
problem.contrastBulkOuts = [1]
problem.contrastQzshifts = [1]
problem.contrastQzshifts = []
problem.contrastScalefactors = [1]
problem.contrastBackgrounds = [1]
problem.contrastBackgroundActions = [1]
Expand All @@ -91,10 +91,10 @@ def standard_layers_problem():
problem.numberOfLayers = 1
problem.numberOfDomainContrasts = 0
problem.fitParams = [3.0]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 0.0, 6.35e-06, 0.03]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 6.35e-06, 0.03]
problem.fitLimits = [[1.0, 5.0]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [-0.0001, 0.0001],
[0.0, 0.0], [6.2e-06, 6.35e-06], [0.01, 0.05]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [0.0, 0.0],
[6.2e-06, 6.35e-06], [0.01, 0.05]]

return problem

Expand All @@ -110,14 +110,14 @@ def domains_problem():
problem.params = [3.0, 0.0, 0.0, 0.0]
problem.bulkIn = [0.0]
problem.bulkOut = [6.35e-06]
problem.qzshifts = [0.0]
problem.qzshifts = []
problem.scalefactors = [0.23]
problem.domainRatio = [0.5]
problem.backgroundParams = [1e-06]
problem.resolutionParams = [0.03]
problem.contrastBulkIns = [1]
problem.contrastBulkOuts = [1]
problem.contrastQzshifts = [1]
problem.contrastQzshifts = []
problem.contrastScalefactors = [1]
problem.contrastBackgrounds = [1]
problem.contrastBackgroundActions = [1]
Expand All @@ -131,10 +131,10 @@ def domains_problem():
problem.numberOfLayers = 1
problem.numberOfDomainContrasts = 2
problem.fitParams = [3.0]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 0.0, 6.35e-06, 0.03, 0.5]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 6.35e-06, 0.03, 0.5]
problem.fitLimits = [[1.0, 5.0]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [-0.0001, 0.0001],
[0.0, 0.0], [6.2e-06, 6.35e-06], [0.01, 0.05], [0.4, 0.6]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [0.0, 0.0],
[6.2e-06, 6.35e-06], [0.01, 0.05], [0.4, 0.6]]

return problem

Expand All @@ -150,14 +150,14 @@ def custom_xy_problem():
problem.params = [3.0, 0.0, 0.0, 0.0]
problem.bulkIn = [0.0]
problem.bulkOut = [6.35e-06]
problem.qzshifts = [0.0]
problem.qzshifts = []
problem.scalefactors = [0.23]
problem.domainRatio = []
problem.backgroundParams = [1e-06]
problem.resolutionParams = [0.03]
problem.contrastBulkIns = [1]
problem.contrastBulkOuts = [1]
problem.contrastQzshifts = [1]
problem.contrastQzshifts = []
problem.contrastScalefactors = [1]
problem.contrastBackgrounds = [1]
problem.contrastBackgroundActions = [1]
Expand All @@ -171,10 +171,10 @@ def custom_xy_problem():
problem.numberOfLayers = 0
problem.numberOfDomainContrasts = 0
problem.fitParams = [3.0]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 0.0, 6.35e-06, 0.03]
problem.otherParams = [0.0, 0.0, 0.0, 1e-06, 0.23, 0.0, 6.35e-06, 0.03]
problem.fitLimits = [[1.0, 5.0]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [-0.0001, 0.0001],
[0.0, 0.0], [6.2e-06, 6.35e-06], [0.01, 0.05]]
problem.otherLimits = [[0.0, 0.0], [0.0, 0.0], [0.0, 0.0], [1e-07, 1e-05], [0.02, 0.25], [0.0, 0.0],
[6.2e-06, 6.35e-06], [0.01, 0.05]]

return problem

Expand All @@ -192,7 +192,7 @@ def standard_layers_cells():
cells.f7 = ['Substrate Roughness', 'Test Thickness', 'Test SLD', 'Test Roughness']
cells.f8 = ['Background Param 1']
cells.f9 = ['Scalefactor 1']
cells.f10 = ['Qz shift 1']
cells.f10 = []
cells.f11 = ['SLD Air']
cells.f12 = ['SLD D2O']
cells.f13 = ['Resolution Param 1']
Expand Down Expand Up @@ -220,7 +220,7 @@ def domains_cells():
cells.f7 = ['Substrate Roughness', 'Test Thickness', 'Test SLD', 'Test Roughness']
cells.f8 = ['Background Param 1']
cells.f9 = ['Scalefactor 1']
cells.f10 = ['Qz shift 1']
cells.f10 = []
cells.f11 = ['SLD Air']
cells.f12 = ['SLD D2O']
cells.f13 = ['Resolution Param 1']
Expand Down Expand Up @@ -248,7 +248,7 @@ def custom_xy_cells():
cells.f7 = ['Substrate Roughness', 'Test Thickness', 'Test SLD', 'Test Roughness']
cells.f8 = ['Background Param 1']
cells.f9 = ['Scalefactor 1']
cells.f10 = ['Qz shift 1']
cells.f10 = []
cells.f11 = ['SLD Air']
cells.f12 = ['SLD D2O']
cells.f13 = ['Resolution Param 1']
Expand All @@ -269,7 +269,7 @@ def non_polarised_limits():
limits = Limits()
limits.param = [[1.0, 5.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
limits.backgroundParam = [[1e-7, 1e-5]]
limits.qzshift = [[-1e-4, 1e-4]]
limits.qzshift = []
limits.scalefactor = [[0.02, 0.25]]
limits.bulkIn = [[0.0, 0.0]]
limits.bulkOut = [[6.2e-6, 6.35e-6]]
Expand All @@ -285,7 +285,7 @@ def domains_limits():
limits = Limits()
limits.param = [[1.0, 5.0], [0.0, 0.0], [0.0, 0.0], [0.0, 0.0]]
limits.backgroundParam = [[1e-7, 1e-5]]
limits.qzshift = [[-1e-4, 1e-4]]
limits.qzshift = []
limits.scalefactor = [[0.02, 0.25]]
limits.bulkIn = [[0.0, 0.0]]
limits.bulkOut = [[6.2e-6, 6.35e-6]]
Expand All @@ -304,16 +304,16 @@ def non_polarised_priors():
['Test SLD', RAT.utils.enums.Priors.Uniform, 0.0, np.inf],
['Test Roughness', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.backgroundParam = [['Background Param 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.qzshift = [['Qz shift 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.qzshift = []
priors.scalefactor = [['Scalefactor 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.bulkIn = [['SLD Air', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.bulkOut = [['SLD D2O', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.resolutionParam = [['Resolution Param 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.domainRatio = []
priors.priorNames = ['Substrate Roughness', 'Test Thickness', 'Test SLD', 'Test Roughness', 'Background Param 1',
'Scalefactor 1', 'Qz shift 1', 'SLD Air', 'SLD D2O', 'Resolution Param 1']
'Scalefactor 1', 'SLD Air', 'SLD D2O', 'Resolution Param 1']
priors.priorValues = [[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf],
[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf]]
[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf]]

return priors

Expand All @@ -327,17 +327,16 @@ def domains_priors():
['Test SLD', RAT.utils.enums.Priors.Uniform, 0.0, np.inf],
['Test Roughness', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.backgroundParam = [['Background Param 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.qzshift = [['Qz shift 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.qzshift = []
priors.scalefactor = [['Scalefactor 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.bulkIn = [['SLD Air', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.bulkOut = [['SLD D2O', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.resolutionParam = [['Resolution Param 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.domainRatio = [['Domain Ratio 1', RAT.utils.enums.Priors.Uniform, 0.0, np.inf]]
priors.priorNames = ['Substrate Roughness', 'Test Thickness', 'Test SLD', 'Test Roughness', 'Background Param 1',
'Scalefactor 1', 'Qz shift 1', 'SLD Air', 'SLD D2O', 'Resolution Param 1', 'Domain Ratio 1']
'Scalefactor 1', 'SLD Air', 'SLD D2O', 'Resolution Param 1', 'Domain Ratio 1']
priors.priorValues = [[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf],
[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf],
[1, 0.0, np.inf]]
[1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf], [1, 0.0, np.inf]]

return priors

Expand Down Expand Up @@ -376,7 +375,7 @@ def standard_layers_controls():
controls.boundHandling = BoundHandling.Fold
controls.checks.fitParam = [1, 0, 0, 0]
controls.checks.fitBackgroundParam = [0]
controls.checks.fitQzshift = [0]
controls.checks.fitQzshift = []
controls.checks.fitScalefactor = [0]
controls.checks.fitBulkIn = [0]
controls.checks.fitBulkOut = [0]
Expand Down Expand Up @@ -419,7 +418,7 @@ def custom_xy_controls():
controls.boundHandling = BoundHandling.Fold
controls.checks.fitParam = [1, 0, 0, 0]
controls.checks.fitBackgroundParam = [0]
controls.checks.fitQzshift = [0]
controls.checks.fitQzshift = []
controls.checks.fitScalefactor = [0]
controls.checks.fitBulkIn = [0]
controls.checks.fitBulkOut = [0]
Expand All @@ -435,7 +434,7 @@ def test_checks():
checks = Checks()
checks.fitParam = [1, 0, 0, 0]
checks.fitBackgroundParam = [0]
checks.fitQzshift = [0]
checks.fitQzshift = []
checks.fitScalefactor = [0]
checks.fitBulkIn = [0]
checks.fitBulkOut = [0]
Expand Down Expand Up @@ -535,7 +534,6 @@ def check_problem_equal(actual_problem, expected_problem) -> None:
for scalar_field in scalar_fields:
assert getattr(actual_problem, scalar_field) == getattr(expected_problem, scalar_field)
for array_field in array_fields:
print(array_field)
assert (getattr(actual_problem, array_field) == getattr(expected_problem, array_field)).all()

# Need to account for "NaN" entries in contrastCustomFiles field
Expand Down
9 changes: 0 additions & 9 deletions tests/test_project.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,12 +60,6 @@ def default_project_repr():
'+-------+---------+---------+----------+----------+-------+------------+-----+-------+\n'
'| 0 | SLD D2O | 6.2e-06 | 6.35e-06 | 6.35e-06 | False | uniform | 0.0 | inf |\n'
'+-------+---------+---------+----------+----------+-------+------------+-----+-------+\n\n'
'Qz Shifts: -----------------------------------------------------------------------------------------\n\n'
'+-------+------------+---------+-------+--------+-------+------------+-----+-------+\n'
'| index | name | min | value | max | fit | prior type | mu | sigma |\n'
'+-------+------------+---------+-------+--------+-------+------------+-----+-------+\n'
'| 0 | Qz shift 1 | -0.0001 | 0.0 | 0.0001 | False | uniform | 0.0 | inf |\n'
'+-------+------------+---------+-------+--------+-------+------------+-----+-------+\n\n'
'Scalefactors: --------------------------------------------------------------------------------------\n\n'
'+-------+---------------+------+-------+------+-------+------------+-----+-------+\n'
'| index | name | min | value | max | fit | prior type | mu | sigma |\n'
Expand Down Expand Up @@ -116,7 +110,6 @@ def test_project_script():
" Parameter(name='Test Roughness', min=0.0, value=0.0, max=0.0, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
" background_parameters=RAT.ClassList([Parameter(name='Background Param 1', min=1e-07, value=1e-06, max=1e-05, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
" scalefactors=RAT.ClassList([Parameter(name='Scalefactor 1', min=0.02, value=0.23, max=0.25, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
" qz_shifts=RAT.ClassList([Parameter(name='Qz shift 1', min=-0.0001, value=0.0, max=0.0001, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
" bulk_in=RAT.ClassList([Parameter(name='SLD Air', min=0.0, value=0.0, max=0.0, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
" bulk_out=RAT.ClassList([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)]),\n"
" resolution_parameters=RAT.ClassList([Parameter(name='Resolution Param 1', min=0.01, value=0.03, max=0.05, fit=False, prior_type='uniform', mu=0.0, sigma=inf)]),\n"
Expand Down Expand Up @@ -603,7 +596,6 @@ def test_get_all_names(test_project) -> None:
'Test Roughness'],
'bulk_in': ['SLD Air'],
'bulk_out': ['SLD D2O'],
'qz_shifts': ['Qz shift 1'],
'scalefactors': ['Scalefactor 1'],
'domain_ratios': [],
'background_parameters': ['Background Param 1'],
Expand All @@ -623,7 +615,6 @@ def test_get_all_protected_parameters(test_project) -> None:
assert test_project.get_all_protected_parameters() == {'parameters': ['Substrate Roughness'],
'bulk_in': [],
'bulk_out': [],
'qz_shifts': [],
'scalefactors': [],
'domain_ratios': [],
'background_parameters': [],
Expand Down
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