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Updates cpp with resolution and background functions #120

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Merged
StephenNneji merged 1 commit into from
Jan 21, 2025
Merged

Updates cpp with resolution and background functions #120

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15 changes: 15 additions & 0 deletions RATapi/examples/non_polarised/backgroundFunction.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
import numpy as np


def backgroundFunction(xdata, params):
# Split up the params array
Ao = params[0]
k = params[1]
back_const = params[2]

# Make an exponential decay background
background = np.zeros(len(xdata))
for i in range(0, len(xdata)):
background[i] = Ao * np.exp(-k * xdata[i]) + back_const

return background
14 changes: 9 additions & 5 deletions RATapi/inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,6 +223,7 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
data_limits = []
simulation_limits = []
contrast_resolution_params = []
contrast_resolution_types = []

# set data, background and resolution for each contrast
for contrast in project.contrasts:
Expand Down Expand Up @@ -278,11 +279,12 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
all_data.append(np.column_stack((data, np.zeros((data.shape[0], 6 - data.shape[1])))))

# Set resolution parameters, with -1 used to indicate a data resolution
contrast_resolution_param = []
resolution = project.resolutions[contrast.resolution]
if resolution.type == TypeOptions.Data:
contrast_resolution_params.append(-1)
else:
contrast_resolution_params.append(project.resolution_parameters.index(resolution.source, True))
contrast_resolution_types.append(resolution.type)
if resolution.source:
contrast_resolution_param.append(project.resolution_parameters.index(resolution.source, True))
contrast_resolution_params.append(contrast_resolution_param)

problem = ProblemDefinition()

Expand All @@ -306,7 +308,10 @@ def make_problem(project: RATapi.Project, checks: Checks) -> ProblemDefinition:
]
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.contrastResolutionParams = contrast_resolution_params
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]
Expand Down Expand Up @@ -429,7 +434,6 @@ def check_indices(problem: ProblemDefinition) -> None:
"scalefactors": "contrastScalefactors",
"bulkIns": "contrastBulkIns",
"bulkOuts": "contrastBulkOuts",
"resolutionParams": "contrastResolutionParams",
"domainRatios": "contrastDomainRatios",
}

Expand Down
2 changes: 0 additions & 2 deletions RATapi/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,6 @@ class ContrastParams(RATResult):
scalefactors: np.ndarray
bulkIn: np.ndarray
bulkOut: np.ndarray
resolutionParams: np.ndarray
subRoughs: np.ndarray
resample: np.ndarray

Expand Down Expand Up @@ -178,7 +177,6 @@ def make_results(
scalefactors=output_results.contrastParams.scalefactors,
bulkIn=output_results.contrastParams.bulkIn,
bulkOut=output_results.contrastParams.bulkOut,
resolutionParams=output_results.contrastParams.resolutionParams,
subRoughs=output_results.contrastParams.subRoughs,
resample=output_results.contrastParams.resample,
)
Expand Down
35 changes: 15 additions & 20 deletions RATapi/wrappers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,25 +57,24 @@ def getHandle(self) -> Callable[[ArrayLike, ArrayLike, ArrayLike, int, int], tup

"""

def handle(params, bulk_in, bulk_out, contrast, domain=-1):
if domain == -1:
output, sub_rough = getattr(self.engine, self.function_name)(
np.array(params, "float"),
np.array(bulk_in, "float"),
np.array(bulk_out, "float"),
float(contrast + 1),
nargout=2,
def handle(*args):
if len(args) == 2:
output = getattr(self.engine, self.function_name)(
np.array(args[0], "float"), # xdata
np.array(args[1], "float"), # params
nargout=1,
)
return np.array(output, "float").tolist()
else:
output, sub_rough = getattr(self.engine, self.function_name)(
np.array(params, "float"),
np.array(bulk_in, "float"),
np.array(bulk_out, "float"),
float(contrast + 1),
float(domain + 1),
np.array(args[0], "float"), # params
np.array(args[1], "float"), # bulk in
np.array(args[2], "float"), # bulk out
float(args[3] + 1), # contrast
float(-1 if len(args) < 5 else args[4] + 1), # domain
nargout=2,
)
return output, sub_rough
return np.array(output, "float").tolist(), float(sub_rough)

return handle

Expand Down Expand Up @@ -105,11 +104,7 @@ def getHandle(self) -> Callable[[ArrayLike, ArrayLike, ArrayLike, int, int], tup

"""

def handle(params, bulk_in, bulk_out, contrast, domain=-1):
if domain == -1:
output, sub_rough = self.engine.invoke(params, bulk_in, bulk_out, contrast)
else:
output, sub_rough = self.engine.invoke(params, bulk_in, bulk_out, contrast, domain)
return output, sub_rough
def handle(*args):
return self.engine.invoke(*args)

return handle
2 changes: 1 addition & 1 deletion cpp/RAT
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Submodule RAT updated 94 files
+61 −45 RATMain.cpp
+40 −38 RATMain_internal_types.h
+27 −6 RATMain_rtwutil.cpp
+8 −6 RATMain_rtwutil.h
+38 −32 RATMain_types.h
+2 −2 adaptive.cpp
+3 −3 adaptive.h
+1 −1 allocateLayersForContrast.cpp
+2 −2 allocateLayersForContrast.h
+1 −1 allocateParamsToLayers.cpp
+3 −3 allocateParamsToLayers.h
+2 −2 applyBackgroundCorrection.cpp
+5 −18 backSort.cpp
+5 −7 backSort.h
+3 −3 boundaryHandling.cpp
+171 −79 callCppFunction.cpp
+14 −9 callCppFunction.h
+43 −105 callReflectivity.cpp
+8 −7 callReflectivity.h
+4 −2 classHandle.hpp
+125 −25 constructBackground.cpp
+10 −8 constructBackground.h
+124 −0 constructResolution.cpp
+33 −0 constructResolution.h
+8 −6 coreLayersCalculation.cpp
+4 −3 coreLayersCalculation.h
+291 −210 customLayers.cpp
+31 −28 customLayers.h
+289 −211 customLayers1.cpp
+31 −31 customLayers1.h
+207 −152 customXY.cpp
+17 −15 customXY.h
+266 −205 customXY1.cpp
+19 −17 customXY1.h
+0 −71 dataResolutionPolly.cpp
+0 −30 dataResolutionPolly.h
+4 −4 deopt.cpp
+1 −1 drawMCMC.cpp
+13 −17 extractProblemParams.cpp
+14 −13 extractProblemParams.h
+1 −1 fMinSearch.cpp
+10 −10 getFitNames.cpp
+11 −11 getFitNames.h
+5 −5 getFittedPriors.cpp
+3 −3 getFittedPriors.h
+9 −9 groupLayersMod.cpp
+1 −1 groupLayersMod.h
+9 −9 groupLayersModImaginary.cpp
+1 −1 groupLayersModImaginary.h
+1 −1 isRATStopped.cpp
+3 −3 makeCell.cpp
+4 −4 makeCell.h
+26 −26 makeEmptyBayesResultsStruct.cpp
+5 −5 makeEmptyBayesResultsStruct.h
+1 −1 nestedSampler.cpp
+8 −0 nsIntraFun.cpp
+1 −1 packParams.cpp
+2 −2 packParams.h
+19 −34 processCustomFunction.cpp
+4 −4 processCustomFunction.h
+6 −20 processCustomFunction1.cpp
+4 −4 processCustomFunction1.h
+29 −56 processCustomFunction2.cpp
+4 −4 processCustomFunction2.h
+7 −33 processCustomFunction3.cpp
+4 −4 processCustomFunction3.h
+3 −3 ratDREAM.cpp
+8 −8 refPercentileConfidenceIntervals.cpp
+5 −5 refPercentileConfidenceIntervals.h
+72 −100 reflectivityCalculation.cpp
+2 −2 resampleLayers.cpp
+1 −1 resampleLayersReIm.cpp
+14 −25 resolutionPolly.cpp
+3 −2 resolutionPolly.h
+2 −2 runDE.cpp
+1 −1 runDREAM.cpp
+4 −4 runNestedSampler.cpp
+2 −2 runNestedSampler.h
+5 −5 runSimplex.cpp
+2 −2 splitEllipsoid.cpp
+287 −202 standardLayers.cpp
+30 −28 standardLayers.h
+300 −217 standardLayers1.cpp
+30 −30 standardLayers1.h
+122 −93 strcmp.cpp
+8 −7 strcmp.h
+2 −2 strjoin.cpp
+3 −3 strjoin.h
+1 −1 strlength.cpp
+2 −2 strlength.h
+3 −3 structConstructorHelper.cpp
+6 −6 structConstructorHelper.h
+9 −9 triggerEvent.cpp
+2 −2 triggerEvent.h
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