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Removes unused properties from the API #137

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Merged
DrPaulSharp merged 2 commits into from
Feb 28, 2025
Merged

Removes unused properties from the API #137

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fc72c0a
Removes unused properties from the API
DrPaulSharp Feb 27, 2025
805bdf3
Updates "define.h"
DrPaulSharp Feb 28, 2025
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22 changes: 0 additions & 22 deletions RATapi/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,9 +142,6 @@ def make_input(project: RATapi.Project, controls: RATapi.Controls) -> tuple[Prob
[[element.min, element.max] for element in getattr(project, class_list)],
)

# Use dummy value for qzshifts
limits.qzshifts = []

if project.model == LayerModels.CustomXY:
controls.calcSldDuringFit = True

Expand Down Expand Up @@ -298,15 +295,13 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
problem.dataPresent = make_data_present(project)
problem.dataLimits = data_limits
problem.simulationLimits = simulation_limits
problem.oilChiDataPresent = [0] * len(project.contrasts)
problem.numberOfContrasts = len(project.contrasts)
problem.geometry = project.geometry
problem.useImaginary = project.absorption
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.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 @@ -317,7 +312,6 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
problem.contrastResolutionTypes = contrast_resolution_types

problem.backgroundParams = [param.value for param in project.background_parameters]
problem.qzshifts = [0.0]
problem.scalefactors = [param.value for param in project.scalefactors]
problem.bulkIns = [param.value for param in project.bulk_in]
problem.bulkOuts = [param.value for param in project.bulk_out]
Expand Down Expand Up @@ -358,18 +352,6 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
for param in getattr(project, class_list)
if param.fit
]
problem.otherParams = [
param.value
for class_list in RATapi.project.parameter_class_lists
for param in getattr(project, class_list)
if not param.fit
]
problem.otherLimits = [
[param.min, param.max]
for class_list in RATapi.project.parameter_class_lists
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)
]
Expand All @@ -392,10 +374,6 @@ def make_problem(project: RATapi.Project) -> ProblemDefinition:
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
Expand Down
2 changes: 1 addition & 1 deletion cpp/RAT
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Submodule RAT updated 59 files
+ − RATMain.a
+84 −122 RATMain.cpp
+0 −1 RATMain_data.cpp
+0 −1 RATMain_data.h
+0 −1 RATMain_initialize.cpp
+0 −6 RATMain_internal_types.h
+0 −8 RATMain_types.h
+6 −15 all.cpp
+2 −3 all.h
+6 −24 allOrAny.cpp
+2 −2 allOrAny.h
+1 −1 anyNonFinite.cpp
+6 −7 backSort.cpp
+5 −6 backSort.h
+87 −126 calcEllipsoid.cpp
+1 −1 calcEllipsoid.h
+83 −87 customLayers.cpp
+127 −126 customLayers1.cpp
+68 −69 customXY.cpp
+141 −142 customXY1.cpp
+0 −6 drawMultiNest.cpp
+22 −26 extractProblemParams.cpp
+13 −14 extractProblemParams.h
+36 −75 getFitNames.cpp
+20 −25 getFitNames.h
+2 −4 ifWhileCond.cpp
+2 −2 kmeans.cpp
+42 −42 makeEmptyBayesResultsStruct.cpp
+1 −6 nestedSampler.cpp
+1 −83 norm.cpp
+1 −3 norm.h
+18 −78 optimalEllipsoids.cpp
+152 −277 packParams.cpp
+0 −1 packParams.h
+0 −8 print_processing.cpp
+0 −2 print_processing.h
+75 −75 ratDREAM.cpp
+0 −242 rcond.cpp
+0 −31 rcond.h
+9 −39 reflectivityCalculation.cpp
+3 −4 runDE.cpp
+0 −1 runDE.h
+3 −3 runDREAM.cpp
+3 −4 runNestedSampler.cpp
+0 −1 runNestedSampler.h
+4 −5 runSimplex.cpp
+1 −2 runSimplex.h
+3 −14 shiftData.cpp
+3 −3 shiftData.h
+155 −200 splitEllipsoid.cpp
+81 −81 standardLayers.cpp
+128 −127 standardLayers1.cpp
+48 −205 unpackParams.cpp
+2 −43 vAllOrAny.cpp
+2 −3 vAllOrAny.h
+0 −36 xgetrf.cpp
+0 −1 xgetrf.h
+0 −102 xtrsv.cpp
+0 −44 xtrsv.h
24 changes: 0 additions & 24 deletions cpp/includes/defines.h
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Original file line number Diff line number Diff line change
Expand Up @@ -397,8 +397,6 @@ backgroundParams : np.ndarray[np.float]
Limits for backgroundParams in the problem definition.
scalefactors : np.ndarray[np.float]
Limits for scalefactors in the problem definition.
qzshifts : np.ndarray[np.float]
Limits for qzshifts in the problem definition.
bulkIns : np.ndarray[np.float]
Limits for bulkIns in the problem definition.
bulkOuts : np.ndarray[np.float]
Expand All @@ -413,7 +411,6 @@ struct Limits {
py::array_t<real_T> params;
py::array_t<real_T> backgroundParams;
py::array_t<real_T> scalefactors;
py::array_t<real_T> qzshifts;
py::array_t<real_T> bulkIns;
py::array_t<real_T> bulkOuts;
py::array_t<real_T> resolutionParams;
Expand All @@ -431,8 +428,6 @@ backgroundParams : list
Names of backgroundParams in the problem definition.
scalefactors : list
Names of scalefactors in the problem definition.
qzshifts : list
Names of qzshifts in the problem definition.
bulkIns : list
Names of bulkIns in the problem definition.
bulkName: list
Expand All @@ -447,7 +442,6 @@ struct NameStore {
py::list params;
py::list backgroundParams;
py::list scalefactors;
py::list qzshifts;
py::list bulkIns;
py::list bulkOuts;
py::list resolutionParams;
Expand All @@ -469,8 +463,6 @@ backgroundParams : np.ndarray[np.float]
Non-zero values indicates which backgroundParams is fitted.
scalefactors : np.ndarray[np.float]
Non-zero values indicates which scalefactors is fitted.
qzshifts : np.ndarray[np.float]
Non-zero values indicates which qzshifts is fitted.
bulkIns : np.ndarray[np.float]
Non-zero values indicates which bulkIns is fitted.
bulkOuts : np.ndarray[np.float]
Expand All @@ -484,7 +476,6 @@ domainRatios : np.ndarray[np.float]
struct Checks {
py::array_t<real_T> params;
py::array_t<real_T> backgroundParams;
py::array_t<real_T> qzshifts;
py::array_t<real_T> scalefactors;
py::array_t<real_T> bulkIns;
py::array_t<real_T> bulkOuts;
Expand All @@ -508,8 +499,6 @@ dataLimits : list
Data limits for each contrast.
simulationLimits : list;
Simulation for each contrast.
oilChiDataPresent : np.ndarray[np.float]
If ``dataPresent[i]`` is non-zero, then contrast ``i`` has oilChi data. This is currently not being used.
numberOfContrasts : int
Number of contrasts.
geometry : str
Expand All @@ -525,8 +514,6 @@ contrastBackgroundTypes : list
Background type for each contrast.
contrastBackgroundActions : list
Background action for each contrast.
contrastQzshifts : np.ndarray[np.float]
Indices of Qzshifts used for each contrast. This is currently not being used.
contrastScalefactors : np.ndarray[np.float]
Indices of scalefactors used for each contrast.
contrastBulkIns : np.ndarray[np.float]
Expand All @@ -539,8 +526,6 @@ contrastResolutionTypes : list
Resolution type for each contrast.
backgroundParams : np.ndarray[np.float]
Background parameter values.
qzshifts : np.ndarray[np.float]
Qzshift values. This currently not being used.
scalefactors : np.ndarray[np.float]
Scalefactors values.
bulkIns : np.ndarray[np.float]
Expand Down Expand Up @@ -573,12 +558,8 @@ domainContrastLayers : list
Indices of layers added to the model of each domain contrast.
fitParams : np.ndarray[np.float]
Values of fitted parameters.
otherParams : np.ndarray[np.float]
Values of non-fitted parameters.
fitLimits : np.ndarray[np.float]
Limits of fitted parameters.
otherLimits : np.ndarray[np.float]
Limits of non fitted parameters.
priorNames : list
Parameter names for for all parameters in the problem definition.
priorValues : np.ndarray[np.float]
Expand All @@ -596,22 +577,19 @@ struct ProblemDefinition {
py::array_t<real_T> dataPresent;
py::list dataLimits;
py::list simulationLimits;
py::array_t<real_T> oilChiDataPresent;
real_T numberOfContrasts;
std::string geometry {};
boolean_T useImaginary {};
py::list repeatLayers;
py::list contrastBackgroundParams;
py::list contrastBackgroundTypes;
py::list contrastBackgroundActions;
py::array_t<real_T> contrastQzshifts;
py::array_t<real_T> contrastScalefactors;
py::array_t<real_T> contrastBulkIns;
py::array_t<real_T> contrastBulkOuts;
py::list contrastResolutionParams;
py::list contrastResolutionTypes;
py::array_t<real_T> backgroundParams;
py::array_t<real_T> qzshifts;
py::array_t<real_T> scalefactors;
py::array_t<real_T> bulkIns;
py::array_t<real_T> bulkOuts;
Expand All @@ -628,9 +606,7 @@ struct ProblemDefinition {
real_T numberOfDomainContrasts {};
py::list domainContrastLayers;
py::array_t<real_T> fitParams;
py::array_t<real_T> otherParams;
py::array_t<real_T> fitLimits;
py::array_t<real_T> otherLimits;
py::list priorNames;
py::array_t<real_T> priorValues;
NameStore names;
Expand Down
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