Renames parameters to match matlab updates

Author: DrPaulSharp

RAT.egg-info/SOURCES.txt

@@ -5,6 +5,7 @@ RAT/__init__.py
 RAT/classlist.py
 RAT/controls.py
 RAT/events.py
+RAT/inputs.py
 RAT/misc.py
 RAT/models.py
 RAT/project.py
@@ -16,6 +17,7 @@ RAT.egg-info/requires.txt
 RAT.egg-info/top_level.txt
 RAT/utils/__init__.py
 RAT/utils/custom_errors.py
+RAT/utils/dataclasses.py
 RAT/utils/enums.py
 cpp/rat.cpp
 cpp/RAT/CoderTimeAPI.cpp
@@ -241,234 +243,12 @@ cpp/RAT/xzlascl.cpp
 cpp/RAT/xztgevc.cpp
 cpp/RAT/xzungqr.cpp
 cpp/RAT/events/eventManager.cpp
-cpp/RAT/CoderTimeAPI.cpp
-cpp/RAT/DREAMWrapper.cpp
-cpp/RAT/RATMain.cpp
-cpp/RAT/RATMain_data.cpp
-cpp/RAT/RATMain_initialize.cpp
-cpp/RAT/RATMain_rtwutil.cpp
-cpp/RAT/RATMain_terminate.cpp
-cpp/RAT/SLDFunction.cpp
-cpp/RAT/abelesParallelPoints.cpp
-cpp/RAT/abelesSingle.cpp
-cpp/RAT/abs.cpp
-cpp/RAT/acos.cpp
-cpp/RAT/adaptPCR.cpp
-cpp/RAT/adaptive.cpp
-cpp/RAT/all.cpp
-cpp/RAT/allOrAny.cpp
-cpp/RAT/allocateLayersForContrast.cpp
-cpp/RAT/allocateParamsToLayers.cpp
-cpp/RAT/anyNonFinite.cpp
-cpp/RAT/applyBackgroundCorrection.cpp
-cpp/RAT/applyHydrationImag.cpp
-cpp/RAT/applyHydrationReal.cpp
-cpp/RAT/asinh.cpp
-cpp/RAT/asymconvstep.cpp
-cpp/RAT/backSort.cpp
-cpp/RAT/blockedSummation.cpp
-cpp/RAT/boundaryHandling.cpp
-cpp/RAT/bsearch.cpp
-cpp/RAT/bsxfun.cpp
-cpp/RAT/calcDensity.cpp
-cpp/RAT/calcEllipsoid.cpp
-cpp/RAT/calcProposal.cpp
-cpp/RAT/callCppFunction.cpp
-cpp/RAT/callReflectivity.cpp
-cpp/RAT/chiSquared.cpp
-cpp/RAT/coder_posix_time.c
-cpp/RAT/coder_setenv.c
-cpp/RAT/colon.cpp
-cpp/RAT/combineVectorElements.cpp
-cpp/RAT/complexTimes.cpp
-cpp/RAT/coreLayersCalculation.cpp
-cpp/RAT/cov.cpp
-cpp/RAT/customLayers.cpp
-cpp/RAT/customLayers1.cpp
-cpp/RAT/customXY.cpp
-cpp/RAT/customXY1.cpp
-cpp/RAT/dataResolutionPolly.cpp
-cpp/RAT/deopt.cpp
-cpp/RAT/det.cpp
-cpp/RAT/diag.cpp
-cpp/RAT/drawCR.cpp
-cpp/RAT/drawEllipsoidPoints.cpp
-cpp/RAT/drawMCMC.cpp
-cpp/RAT/drawMultiNest.cpp
-cpp/RAT/eig.cpp
-cpp/RAT/eigHermitianStandard.cpp
-cpp/RAT/eml_erfcore.cpp
-cpp/RAT/eml_rand_mt19937ar.cpp
-cpp/RAT/eml_rand_mt19937ar_stateful.cpp
-cpp/RAT/eml_setop.cpp
-cpp/RAT/eps.cpp
-cpp/RAT/erf.cpp
-cpp/RAT/evaluateModel.cpp
-cpp/RAT/exp.cpp
-cpp/RAT/eye.cpp
-cpp/RAT/fMinSearch.cpp
-cpp/RAT/find.cpp
-cpp/RAT/flip.cpp
-cpp/RAT/gamma.cpp
-cpp/RAT/gelman.cpp
-cpp/RAT/getFittedPriors.cpp
-cpp/RAT/getTime.cpp
-cpp/RAT/getenv.cpp
-cpp/RAT/groupLayersMod.cpp
-cpp/RAT/groupLayersModImaginary.cpp
-cpp/RAT/histc.cpp
-cpp/RAT/ifWhileCond.cpp
-cpp/RAT/inEllipsoids.cpp
-cpp/RAT/initializeDREAM.cpp
-cpp/RAT/interp1.cpp
-cpp/RAT/ishermitian.cpp
-cpp/RAT/isrow.cpp
-cpp/RAT/ixamax.cpp
-cpp/RAT/kmeans.cpp
-cpp/RAT/leftWin.cpp
-cpp/RAT/length.cpp
-cpp/RAT/linspace.cpp
-cpp/RAT/log.cpp
-cpp/RAT/log1p.cpp
-cpp/RAT/log2.cpp
-cpp/RAT/logPlus.cpp
-cpp/RAT/lower.cpp
-cpp/RAT/lusolve.cpp
-cpp/RAT/makeCell.cpp
-cpp/RAT/makeD.cpp
-cpp/RAT/makeEmptyBayesResultsStruct.cpp
-cpp/RAT/makeEmptyResultStruct.cpp
-cpp/RAT/makeSLDProfileXY.cpp
-cpp/RAT/makeSLDProfiles.cpp
-cpp/RAT/matrix_to_integer_power.cpp
-cpp/RAT/mchol.cpp
-cpp/RAT/mean.cpp
-cpp/RAT/mergesort.cpp
-cpp/RAT/metropolisRule.cpp
-cpp/RAT/minOrMax.cpp
-cpp/RAT/mod.cpp
-cpp/RAT/mrdivide_helper.cpp
-cpp/RAT/mtimes.cpp
-cpp/RAT/multrnd.cpp
-cpp/RAT/nest2pos.cpp
-cpp/RAT/nestedSampler.cpp
-cpp/RAT/nonSingletonDim.cpp
-cpp/RAT/norm.cpp
-cpp/RAT/nsIntraFun.cpp
-cpp/RAT/nullAssignment.cpp
-cpp/RAT/optimalEllipsoids.cpp
-cpp/RAT/packParams.cpp
-cpp/RAT/percentileConfidenceIntervals.cpp
-cpp/RAT/pow2.cpp
-cpp/RAT/power.cpp
-cpp/RAT/prctile.cpp
-cpp/RAT/print_processing.cpp
-cpp/RAT/processBayes.cpp
-cpp/RAT/processCustomFunction.cpp
-cpp/RAT/processCustomFunction1.cpp
-cpp/RAT/processCustomFunction2.cpp
-cpp/RAT/processCustomFunction3.cpp
-cpp/RAT/qrsolve.cpp
-cpp/RAT/rand.cpp
-cpp/RAT/randn.cpp
-cpp/RAT/randperm.cpp
-cpp/RAT/randsample.cpp
-cpp/RAT/ratDREAM.cpp
-cpp/RAT/rcond.cpp
-cpp/RAT/refPercentileConfidenceIntervals.cpp
-cpp/RAT/reflectivityCalculation.cpp
-cpp/RAT/reflectivityCalculation1.cpp
-cpp/RAT/reflectivityCalculation2.cpp
-cpp/RAT/relop.cpp
-cpp/RAT/rem.cpp
-cpp/RAT/removeOutlier.cpp
-cpp/RAT/repmat.cpp
-cpp/RAT/resampleLayers.cpp
-cpp/RAT/resampleLayersReIm.cpp
-cpp/RAT/rescale.cpp
-cpp/RAT/rescaleKernel.cpp
-cpp/RAT/rescaleParameters.cpp
-cpp/RAT/reshapeSizeChecks.cpp
-cpp/RAT/resolutionPolly.cpp
-cpp/RAT/rng.cpp
-cpp/RAT/rtGetInf.cpp
-cpp/RAT/rtGetNaN.cpp
-cpp/RAT/rt_nonfinite.cpp
-cpp/RAT/runDE.cpp
-cpp/RAT/runDREAM.cpp
-cpp/RAT/runNestedSampler.cpp
-cpp/RAT/runSimplex.cpp
-cpp/RAT/scaleParameters.cpp
-cpp/RAT/scaledGaussPrior.cpp
-cpp/RAT/schur.cpp
-cpp/RAT/setupDREAM.cpp
-cpp/RAT/shiftData.cpp
-cpp/RAT/simplexIntrafun.cpp
-cpp/RAT/simplexXTransform.cpp
-cpp/RAT/sort.cpp
-cpp/RAT/sortAscendLE.cpp
-cpp/RAT/sortIdx.cpp
-cpp/RAT/sortLE.cpp
-cpp/RAT/sortrows.cpp
-cpp/RAT/splitEllipsoid.cpp
-cpp/RAT/sprintf.cpp
-cpp/RAT/sqrt.cpp
-cpp/RAT/sqrt1.cpp
-cpp/RAT/standardLayers.cpp
-cpp/RAT/standardLayers1.cpp
-cpp/RAT/std.cpp
-cpp/RAT/str2double.cpp
-cpp/RAT/str2double1.cpp
-cpp/RAT/strcmp.cpp
-cpp/RAT/structConstructorHelper.cpp
-cpp/RAT/sum.cpp
-cpp/RAT/tic.cpp
-cpp/RAT/timeKeeper.cpp
-cpp/RAT/toc.cpp
-cpp/RAT/triggerEvent.cpp
-cpp/RAT/triu.cpp
-cpp/RAT/unpackParams.cpp
-cpp/RAT/useConstantDim.cpp
-cpp/RAT/vAllOrAny.cpp
-cpp/RAT/var.cpp
-cpp/RAT/varstd.cpp
-cpp/RAT/xdhseqr.cpp
-cpp/RAT/xdlanv2.cpp
-cpp/RAT/xgehrd.cpp
-cpp/RAT/xgemm.cpp
-cpp/RAT/xgemv.cpp
-cpp/RAT/xgeqp3.cpp
-cpp/RAT/xgerc.cpp
-cpp/RAT/xgeru.cpp
-cpp/RAT/xgetrf.cpp
-cpp/RAT/xnrm2.cpp
-cpp/RAT/xrot.cpp
-cpp/RAT/xswap.cpp
-cpp/RAT/xtrsm.cpp
-cpp/RAT/xtrsv.cpp
-cpp/RAT/xungorghr.cpp
-cpp/RAT/xunormqr.cpp
-cpp/RAT/xzgeev.cpp
-cpp/RAT/xzgeqp3.cpp
-cpp/RAT/xzggbak.cpp
-cpp/RAT/xzggbal.cpp
-cpp/RAT/xzggev.cpp
-cpp/RAT/xzgghrd.cpp
-cpp/RAT/xzhgeqz.cpp
-cpp/RAT/xzlangeM.cpp
-cpp/RAT/xzlanhs.cpp
-cpp/RAT/xzlarf.cpp
-cpp/RAT/xzlarfg.cpp
-cpp/RAT/xzlartg.cpp
-cpp/RAT/xzlascl.cpp
-cpp/RAT/xztgevc.cpp
-cpp/RAT/xzungqr.cpp
-cpp/RAT/events/eventManager.cpp
 tests/__init__.py
 tests/test_classlist.py
 tests/test_controls.py
 tests/test_custom_errors.py
 tests/test_events.py
+tests/test_inputs.py
 tests/test_models.py
 tests/test_project.py
 tests/test_wrappers.py

RAT/controls.py

@@ -11,17 +11,17 @@ class Calculate(BaseModel, validate_assignment=True, extra='forbid'):
     procedure: Literal[Procedures.Calculate] = Procedures.Calculate
     parallel: Parallel = Parallel.Single
     calcSldDuringFit: bool = False
-    resamPars: list[float] = Field([0.9, 50], min_length=2, max_length=2)
+    resampleParams: list[float] = Field([0.9, 50], min_length=2, max_length=2)
     display: Display = Display.Iter
 
-    @field_validator("resamPars")
+    @field_validator("resampleParams")
     @classmethod
-    def check_resamPars(cls, resamPars):
-        if not 0 < resamPars[0] < 1:
-            raise ValueError('resamPars[0] must be between 0 and 1')
-        if resamPars[1] < 0:
-            raise ValueError('resamPars[1] must be greater than or equal to 0')
-        return resamPars
+    def check_resample_params(cls, resampleParams):
+        if not 0 < resampleParams[0] < 1:
+            raise ValueError('resampleParams[0] must be between 0 and 1')
+        if resampleParams[1] < 0:
+            raise ValueError('resampleParams[1] must be greater than or equal to 0')
+        return resampleParams
 
     def __repr__(self) -> str:
         table = prettytable.PrettyTable()
@@ -33,10 +33,10 @@ def __repr__(self) -> str:
 class Simplex(Calculate):
     """Defines the additional fields for the simplex procedure."""
     procedure: Literal[Procedures.Simplex] = Procedures.Simplex
-    tolX: float = Field(1.0e-6, gt=0.0)
-    tolFun: float = Field(1.0e-6, gt=0.0)
-    maxFunEvals: int = Field(10000, gt=0)
-    maxIter: int = Field(1000, gt=0)
+    xTolerance: float = Field(1.0e-6, gt=0.0)
+    funcTolerance: float = Field(1.0e-6, gt=0.0)
+    maxFuncEvals: int = Field(10000, gt=0)
+    maxIterations: int = Field(1000, gt=0)
     updateFreq: int = -1
     updatePlotFreq: int = 1
 
@@ -55,8 +55,8 @@ class DE(Calculate):
 class NS(Calculate):
     """Defines the additional fields for the Nested Sampler procedure."""
     procedure: Literal[Procedures.NS] = Procedures.NS
-    Nlive: int = Field(150, ge=1)
-    Nmcmc: float = Field(0.0, ge=0.0)
+    nLive: int = Field(150, ge=1)
+    nMCMC: float = Field(0.0, ge=0.0)
     propScale: float = Field(0.1, gt=0.0, lt=1.0)
     nsTolerance: float = Field(0.1, ge=0.0)
 

RAT/events.py

@@ -18,6 +18,7 @@ def notify(event_type: EventTypes, data: Union[str, PlotEventData, ProgressEvent
     for callback in callbacks:
         callback(data)
 
+
 def get_event_callback(event_type: EventTypes) -> List[Callable[[Union[str, PlotEventData, ProgressEventData]], None]]:
     """Returns all callbacks registered for the given event type.
 

RAT/inputs.py

@@ -127,7 +127,7 @@ def make_problem(project: RAT.Project) -> RAT.utils.dataclasses.Problem:
         contrastDomainRatios=[project.domain_ratios.index(contrast.domain_ratio, 1)
                               if hasattr(contrast, 'domain_ratio') else 0 for contrast in project.contrasts],
         contrastBackgrounds=[project.backgrounds.index(contrast.background, 1) for contrast in project.contrasts],
-        contrastBackgroundsType=[1] * len(project.contrasts),
+        contrastBackgroundsActions=[1] * len(project.contrasts),
         contrastResolutions=[project.resolutions.index(contrast.resolution, 1) for contrast in project.contrasts],
         contrastCustomFiles=contrast_custom_files,
         resample=[contrast.resample for contrast in project.contrasts],

RAT/misc.py

@@ -39,15 +39,16 @@ def getHandle(self)\
         """
         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)                      
+                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)
             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), nargout=2)
+                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),
+                                                                             nargout=2)
             return output, sub_rough                         
         return handle 
 
@@ -58,7 +59,7 @@ class DylibWrapper:
     Parameters
     ----------
     filename : str
-        The path of the dyanamic library
+        The path of the dynamic library
     function_name : str
         The name of the function to call
     """

RAT/models.py

@@ -11,6 +11,7 @@
 except ImportError:
     from strenum import StrEnum
 
+
 def int_sequence():
     """Iterate through integers for use as model counters."""
     num = 1
@@ -130,7 +131,7 @@ def model_post_init(self, __context: Any) -> None:
     @model_validator(mode='after')
     def check_ranges(self) -> 'Data':
         """The limits of the "data_range" field must lie within the range of the supplied data, whilst the limits
-        of the "simulation_range" field must lie outside of the range of the supplied data.
+        of the "simulation_range" field must lie outside the range of the supplied data.
         """
         if len(self.data[:, 0]) > 0:
             data_min = np.min(self.data[:, 0])