Skip to content

Updates submodule with bug fixes #111

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
DrPaulSharp merged 2 commits into from
Jan 7, 2025
Merged

Updates submodule with bug fixes #111

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
56c3741
Updates submodule with bug fixes
DrPaulSharp Jan 6, 2025
d905f5a
Refactors C++ functions
DrPaulSharp Jan 7, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion cpp/RAT
Open in desktop
Submodule RAT updated 59 files
+5 −288 DREAMWrapper.cpp
+130 −703 RATMain.cpp
+51 −97 RATMain_internal_types.h
+3 −4 RATMain_rtwutil.cpp
+1 −1 RATMain_rtwutil.h
+42 −42 RATMain_types.h
+3 −4 allocateLayersForContrast.cpp
+2 −2 allocateLayersForContrast.h
+3 −5 allocateParamsToLayers.cpp
+2 −2 allocateParamsToLayers.h
+85 −350 customLayers.cpp
+0 −14 customLayers.h
+84 −428 customLayers1.cpp
+0 −15 customLayers1.h
+54 −345 customXY.cpp
+0 −12 customXY.h
+56 −395 customXY1.cpp
+0 −13 customXY1.h
+5 −5 deopt.cpp
+2 −2 deopt.h
+1 −1 extractProblemParams.cpp
+2 −2 extractProblemParams.h
+2 −2 fMinSearch.cpp
+2 −2 fMinSearch.h
+1 −1 initializeDREAM.cpp
+2 −2 initializeDREAM.h
+182 −183 makeEmptyBayesResultsStruct.cpp
+29 −27 nsIntraFun.cpp
+25 −23 packParams.cpp
+11 −275 processBayes.cpp
+4 −6 processBayes.h
+96 −96 ratDREAM.cpp
+2 −2 ratDREAM.h
+4 −5 refPercentileConfidenceIntervals.cpp
+2 −2 refPercentileConfidenceIntervals.h
+15 −15 reflectivityCalculation.cpp
+5 −6 reflectivityCalculation.h
+26 −292 runDE.cpp
+5 −7 runDE.h
+23 −33 runDREAM.cpp
+6 −16 runDREAM.h
+19 −22 runNestedSampler.cpp
+11 −13 runNestedSampler.h
+17 −10 runSimplex.cpp
+2 −2 runSimplex.h
+1 −1 setupDREAM.cpp
+2 −2 setupDREAM.h
+9 −3 simplexIntrafun.cpp
+2 −2 simplexIntrafun.h
+161 −429 standardLayers.cpp
+0 −14 standardLayers.h
+89 −470 standardLayers1.cpp
+0 −15 standardLayers1.h
+2 −2 structConstructorHelper.cpp
+4 −4 structConstructorHelper.h
+1 −2 triggerEvent.cpp
+2 −2 triggerEvent.h
+0 −233 unpackParams.cpp
+0 −2 unpackParams.h
80 changes: 30 additions & 50 deletions cpp/rat.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -545,27 +545,7 @@ void stringFromRatBoundedArray(const char_T array_data[], const int32_T array_si
memcpy(&result[0], array_data, array_size[1]);
}

coder::array<real_T, 1U> pyArrayToRatRowArray1d(py::array_t<real_T> value)
{
coder::array<real_T, 1U> result;

py::buffer_info buffer_info = value.request();

if (buffer_info.size == 0)
return result;

if (buffer_info.ndim != 1)
throw std::runtime_error("Expects a 1D numeric array");

result.set_size(buffer_info.shape[0]);
for (int32_T idx0{0}; idx0 < buffer_info.shape[0]; idx0++) {
result[idx0] = value.at(idx0);
}

return result;
}

coder::array<real_T, 2U> pyArrayToRatColArray1d(py::array_t<real_T> value)
coder::array<real_T, 2U> pyArrayToRatRowArray1d(py::array_t<real_T> value)
{
coder::array<real_T, 2U> result;

Expand Down Expand Up @@ -750,7 +730,7 @@ coder::array<RAT::cell_wrap_4, 2U> pyListToRatCellWrap4(py::list values)
for (py::handle array: values)
{
py::array_t<real_T> casted_array = py::cast<py::array>(array);
result[idx].f1 = customCaller("$id[" + std::to_string(idx) +"]", pyArrayToRatColArray1d, casted_array);
result[idx].f1 = customCaller("$id[" + std::to_string(idx) +"]", pyArrayToRatRowArray1d, casted_array);
idx++;
}

Expand Down Expand Up @@ -827,14 +807,14 @@ RAT::struct1_T createStruct1(const NameStore& names)
RAT::struct2_T createStruct2(const Checks& checks)
{
RAT::struct2_T checks_struct;
checks_struct.params = customCaller("Checks.params", pyArrayToRatColArray1d, checks.params);
checks_struct.backgroundParams = customCaller("Checks.backgroundParams", pyArrayToRatColArray1d, checks.backgroundParams);
checks_struct.scalefactors = customCaller("Checks.scalefactors", pyArrayToRatColArray1d, checks.scalefactors);
checks_struct.qzshifts = customCaller("Checks.qzshifts", pyArrayToRatColArray1d, checks.qzshifts);
checks_struct.bulkIns = customCaller("Checks.bulkIns", pyArrayToRatColArray1d, checks.bulkIns);
checks_struct.bulkOuts = customCaller("Checks.bulkOuts", pyArrayToRatColArray1d, checks.bulkOuts);
checks_struct.resolutionParams = customCaller("Checks.resolutionParams", pyArrayToRatColArray1d, checks.resolutionParams);
checks_struct.domainRatios = customCaller("Checks.domainRatios", pyArrayToRatColArray1d, checks.domainRatios);
checks_struct.params = customCaller("Checks.params", pyArrayToRatRowArray1d, checks.params);
checks_struct.backgroundParams = customCaller("Checks.backgroundParams", pyArrayToRatRowArray1d, checks.backgroundParams);
checks_struct.scalefactors = customCaller("Checks.scalefactors", pyArrayToRatRowArray1d, checks.scalefactors);
checks_struct.qzshifts = customCaller("Checks.qzshifts", pyArrayToRatRowArray1d, checks.qzshifts);
checks_struct.bulkIns = customCaller("Checks.bulkIns", pyArrayToRatRowArray1d, checks.bulkIns);
checks_struct.bulkOuts = customCaller("Checks.bulkOuts", pyArrayToRatRowArray1d, checks.bulkOuts);
checks_struct.resolutionParams = customCaller("Checks.resolutionParams", pyArrayToRatRowArray1d, checks.resolutionParams);
checks_struct.domainRatios = customCaller("Checks.domainRatios", pyArrayToRatRowArray1d, checks.domainRatios);

return checks_struct;
}
Expand All @@ -844,39 +824,39 @@ RAT::struct0_T createStruct0(const ProblemDefinition& problem)
RAT::struct0_T problem_struct;

stringToRatBoundedArray(problem.TF, problem_struct.TF.data, problem_struct.TF.size);
problem_struct.resample = customCaller("Problem.resample", pyArrayToRatColArray1d, problem.resample);
problem_struct.resample = customCaller("Problem.resample", pyArrayToRatRowArray1d, problem.resample);
problem_struct.data = customCaller("Problem.data", pyListToRatCellWrap1, problem.data);
problem_struct.dataPresent = customCaller("Problem.dataPresent", pyArrayToRatColArray1d, problem.dataPresent);
problem_struct.dataPresent = customCaller("Problem.dataPresent", pyArrayToRatRowArray1d, problem.dataPresent);
problem_struct.dataLimits = customCaller("Problem.dataLimits", pyListToRatCellWrap2, problem.dataLimits);
problem_struct.simulationLimits = customCaller("Problem.simulationLimits", pyListToRatCellWrap2, problem.simulationLimits);
problem_struct.oilChiDataPresent = customCaller("Problem.oilChiDataPresent", pyArrayToRatColArray1d, problem.oilChiDataPresent);
problem_struct.oilChiDataPresent = customCaller("Problem.oilChiDataPresent", pyArrayToRatRowArray1d, problem.oilChiDataPresent);
problem_struct.numberOfContrasts = problem.numberOfContrasts;
stringToRatBoundedArray(problem.geometry, problem_struct.geometry.data, problem_struct.geometry.size);
problem_struct.useImaginary = problem.useImaginary;
problem_struct.repeatLayers = customCaller("Problem.repeatLayers", pyListToRatCellWrap2, problem.repeatLayers);
problem_struct.contrastBackgroundParams = customCaller("Problem.contrastBackgroundParams", pyListToRatCellWrap3, problem.contrastBackgroundParams);
problem_struct.contrastBackgroundTypes = customCaller("Problem.contrastBackgroundTypes", pyListToRatCellWrap0, problem.contrastBackgroundTypes);
problem_struct.contrastBackgroundActions = customCaller("Problem.contrastBackgroundActions", pyListToRatCellWrap0, problem.contrastBackgroundActions);
problem_struct.contrastQzshifts = customCaller("Problem.contrastQzshifts", pyArrayToRatColArray1d, problem.contrastQzshifts);
problem_struct.contrastScalefactors = customCaller("Problem.contrastScalefactors", pyArrayToRatColArray1d, problem.contrastScalefactors);
problem_struct.contrastBulkIns = customCaller("Problem.contrastBulkIns", pyArrayToRatColArray1d, problem.contrastBulkIns);
problem_struct.contrastBulkOuts = customCaller("Problem.contrastBulkOuts", pyArrayToRatColArray1d, problem.contrastBulkOuts);
problem_struct.contrastResolutionParams = customCaller("Problem.contrastResolutionParams", pyArrayToRatColArray1d, problem.contrastResolutionParams);
problem_struct.backgroundParams = customCaller("Problem.backgroundParams", pyArrayToRatColArray1d, problem.backgroundParams);
problem_struct.qzshifts = customCaller("Problem.qzshifts", pyArrayToRatColArray1d, problem.qzshifts);
problem_struct.scalefactors = customCaller("Problem.scalefactors", pyArrayToRatColArray1d, problem.scalefactors);
problem_struct.bulkIns = customCaller("Problem.bulkIns", pyArrayToRatColArray1d, problem.bulkIns);
problem_struct.bulkOuts = customCaller("Problem.bulkOuts", pyArrayToRatColArray1d, problem.bulkOuts);
problem_struct.resolutionParams = customCaller("Problem.resolutionParams", pyArrayToRatColArray1d, problem.resolutionParams);
problem_struct.params = customCaller("Problem.params", pyArrayToRatColArray1d, problem.params);
problem_struct.contrastQzshifts = customCaller("Problem.contrastQzshifts", pyArrayToRatRowArray1d, problem.contrastQzshifts);
problem_struct.contrastScalefactors = customCaller("Problem.contrastScalefactors", pyArrayToRatRowArray1d, problem.contrastScalefactors);
problem_struct.contrastBulkIns = customCaller("Problem.contrastBulkIns", pyArrayToRatRowArray1d, problem.contrastBulkIns);
problem_struct.contrastBulkOuts = customCaller("Problem.contrastBulkOuts", pyArrayToRatRowArray1d, problem.contrastBulkOuts);
problem_struct.contrastResolutionParams = customCaller("Problem.contrastResolutionParams", pyArrayToRatRowArray1d, problem.contrastResolutionParams);
problem_struct.backgroundParams = customCaller("Problem.backgroundParams", pyArrayToRatRowArray1d, problem.backgroundParams);
problem_struct.qzshifts = customCaller("Problem.qzshifts", pyArrayToRatRowArray1d, problem.qzshifts);
problem_struct.scalefactors = customCaller("Problem.scalefactors", pyArrayToRatRowArray1d, problem.scalefactors);
problem_struct.bulkIns = customCaller("Problem.bulkIns", pyArrayToRatRowArray1d, problem.bulkIns);
problem_struct.bulkOuts = customCaller("Problem.bulkOuts", pyArrayToRatRowArray1d, problem.bulkOuts);
problem_struct.resolutionParams = customCaller("Problem.resolutionParams", pyArrayToRatRowArray1d, problem.resolutionParams);
problem_struct.params = customCaller("Problem.params", pyArrayToRatRowArray1d, problem.params);
problem_struct.numberOfLayers = problem.numberOfLayers;
problem_struct.contrastLayers = customCaller("Problem.contrastLayers", pyListToRatCellWrap4, problem.contrastLayers);
problem_struct.layersDetails = customCaller("Problem.layersDetails", pyListToRatCellWrap5, problem.layersDetails);
problem_struct.customFiles = customCaller("Problem.customFiles", py_function_array_to_rat_cell_wrap_0, problem.customFiles);
stringToRatBoundedArray(problem.modelType, problem_struct.modelType.data, problem_struct.modelType.size);
problem_struct.contrastCustomFiles = customCaller("Problem.contrastCustomFiles", pyArrayToRatColArray1d, problem.contrastCustomFiles);
problem_struct.contrastDomainRatios = customCaller("Problem.contrastDomainRatios", pyArrayToRatColArray1d, problem.contrastDomainRatios);
problem_struct.domainRatios = customCaller("Problem.domainRatios", pyArrayToRatColArray1d, problem.domainRatios);
problem_struct.contrastCustomFiles = customCaller("Problem.contrastCustomFiles", pyArrayToRatRowArray1d, problem.contrastCustomFiles);
problem_struct.contrastDomainRatios = customCaller("Problem.contrastDomainRatios", pyArrayToRatRowArray1d, problem.contrastDomainRatios);
problem_struct.domainRatios = customCaller("Problem.domainRatios", pyArrayToRatRowArray1d, problem.domainRatios);
problem_struct.numberOfDomainContrasts = problem.numberOfDomainContrasts;
problem_struct.domainContrastLayers = customCaller("Problem.domainContrastLayers", pyListToRatCellWrap4, problem.domainContrastLayers);
problem_struct.fitParams = customCaller("Problem.fitParams", pyArrayToRatRowArray1d, problem.fitParams);
Expand Down Expand Up @@ -1221,8 +1201,8 @@ ProblemDefinition problemDefinitionFromStruct0T(const RAT::struct0_T problem)
problem_def.domainRatios = pyArrayFromRatArray1d<coder::array<real_T, 2U>>(problem.domainRatios);
problem_def.numberOfDomainContrasts = problem.numberOfDomainContrasts;
problem_def.domainContrastLayers = pyList1DFromRatCellWrap2D<coder::array<RAT::cell_wrap_4, 2U>>(problem.domainContrastLayers);
problem_def.fitParams = pyArrayFromRatArray1d<coder::array<real_T, 1U>>(problem.fitParams, false);
problem_def.otherParams = pyArrayFromRatArray1d<coder::array<real_T, 1U>>(problem.otherParams, false);
problem_def.fitParams = pyArrayFromRatArray1d<coder::array<real_T, 2U>>(problem.fitParams);
problem_def.otherParams = pyArrayFromRatArray1d<coder::array<real_T, 2U>>(problem.otherParams);
problem_def.fitLimits = pyArrayFromRatArray2d(problem.fitLimits);
problem_def.otherLimits = pyArrayFromRatArray2d(problem.otherLimits);

Expand Down
Loading