diff --git a/API/makeEmptyResultStruct.m b/API/makeEmptyResultStruct.m index 527fef828..01fa0f869 100644 --- a/API/makeEmptyResultStruct.m +++ b/API/makeEmptyResultStruct.m @@ -134,8 +134,8 @@ end coder.varsize('resampledLayers{:}',[10000 4],[1 1]); - fitParams = zeros(nParams,1); - coder.varsize('fitParams',[maxArraySize 1],[1 0]); + fitParams = zeros(1,nParams); + coder.varsize('fitParams',[1 maxArraySize],[0 1]); fitNames = cell(nParams,1); for i = 1:nParams diff --git a/compile/fullCompile/makeCompileArgsFull.m b/compile/fullCompile/makeCompileArgsFull.m index 0ec4f9f54..efa317165 100644 --- a/compile/fullCompile/makeCompileArgsFull.m +++ b/compile/fullCompile/makeCompileArgsFull.m @@ -56,8 +56,8 @@ ARGS_1_1.numberOfDomainContrasts = coder.typeof(0); ARG = coder.typeof(0,[1 maxArraySize],[1 1]); ARGS_1_1.domainContrastLayers = coder.typeof({ARG}, [1 maxArraySize],[0 1]); -ARGS_1_1.fitParams = coder.typeof(0,[maxArraySize 1],[1 0]); -ARGS_1_1.otherParams = coder.typeof(0,[maxArraySize 1],[1 0]); +ARGS_1_1.fitParams = coder.typeof(0,[1 maxArraySize],[0 1]); +ARGS_1_1.otherParams = coder.typeof(0,[1 maxArraySize],[0 1]); ARGS_1_1.fitLimits = coder.typeof(0,[maxArraySize 2],[1 0]); ARGS_1_1.otherLimits = coder.typeof(0,[maxArraySize 2],[1 0]); ARGS_1_1_names = struct; diff --git a/compile/reflectivityCalculation/makeCompileArgs.m b/compile/reflectivityCalculation/makeCompileArgs.m index 60518f3e1..5b2a93e48 100644 --- a/compile/reflectivityCalculation/makeCompileArgs.m +++ b/compile/reflectivityCalculation/makeCompileArgs.m @@ -56,8 +56,8 @@ ARGS_1_1.numberOfDomainContrasts = coder.typeof(0); ARG = coder.typeof(0,[1 maxArraySize],[1 1]); ARGS_1_1.domainContrastLayers = coder.typeof({ARG}, [1 maxArraySize],[0 1]); -ARGS_1_1.fitParams = coder.typeof(0,[maxArraySize 1],[1 0]); -ARGS_1_1.otherParams = coder.typeof(0,[maxArraySize 1],[1 0]); +ARGS_1_1.fitParams = coder.typeof(0,[1 maxArraySize],[0 1]); +ARGS_1_1.otherParams = coder.typeof(0,[1 maxArraySize],[0 1]); ARGS_1_1.fitLimits = coder.typeof(0,[maxArraySize 2],[1 0]); ARGS_1_1.otherLimits = coder.typeof(0,[maxArraySize 2],[1 0]); ARGS_1_1_names = struct; diff --git a/minimisers/DE/runDE.m b/minimisers/DE/runDE.m index 85ea0a673..936a663bd 100644 --- a/minimisers/DE/runDE.m +++ b/minimisers/DE/runDE.m @@ -93,7 +93,7 @@ function [S_MSE,result] = intrafun(p,problemStruct,controls) - problemStruct.fitParams = p'; + problemStruct.fitParams = p; problemStruct = unpackParams(problemStruct); result = reflectivityCalculation(problemStruct,controls); fval = result.calculationResults.sumChi; diff --git a/minimisers/NS/parseBayesResults.m b/minimisers/NS/parseBayesResults.m index 00272c433..4ebf35700 100644 --- a/minimisers/NS/parseBayesResults.m +++ b/minimisers/NS/parseBayesResults.m @@ -79,7 +79,7 @@ end %Also calculate the best fit -problemStruct.fitParams = values(:,1); +problemStruct.fitParams = values(:,1)'; problemStruct = unpackParams(problemStruct); result = reflectivityCalculation(problemStruct,controls); bestFit = result.reflectivity; diff --git a/minimisers/generalUtils/bayesStats/packPriors.m b/minimisers/generalUtils/bayesStats/packPriors.m index 3565c511c..81f213380 100644 --- a/minimisers/generalUtils/bayesStats/packPriors.m +++ b/minimisers/generalUtils/bayesStats/packPriors.m @@ -19,8 +19,8 @@ % length(problemStruct.bulkOuts) + ... % length(problemStruct.resolutionParams); -% fitParams = problemStruct.fitParams;%zeros(numberOfFitted,1); -% otherParams = zeros((numberOfTotal-numberOfFitted),1); +% fitParams = problemStruct.fitParams;%zeros(1,numberOfFitted); +% otherParams = zeros(1,(numberOfTotal-numberOfFitted)); % fitLimits = zeros(numberOfFitted,2); % otherLimits = zeros((numberOfTotal-numberOfFitted),2); % %limits = problemStruct.limits; diff --git a/minimisers/generalUtils/packParams.m b/minimisers/generalUtils/packParams.m index 009e314d4..990bc6f65 100644 --- a/minimisers/generalUtils/packParams.m +++ b/minimisers/generalUtils/packParams.m @@ -15,8 +15,8 @@ numberOfTotal = numberOfTotal + length(problemStruct.(fields{i})); end - fitParams = zeros(numberOfFitted, 1); - otherParams = zeros((numberOfTotal-numberOfFitted), 1); + fitParams = zeros(1, numberOfFitted); + otherParams = zeros(1, (numberOfTotal-numberOfFitted)); fitLimits = zeros(numberOfFitted,2); otherLimits = zeros((numberOfTotal-numberOfFitted),2); diff --git a/minimisers/generalUtils/packParamsPriors.m b/minimisers/generalUtils/packParamsPriors.m index 62c33d61e..5f3aff4de 100644 --- a/minimisers/generalUtils/packParamsPriors.m +++ b/minimisers/generalUtils/packParamsPriors.m @@ -14,9 +14,9 @@ numberOfFitted = numberOfFitted + sum(problemStruct.checks.(fields{i})); numberOfTotal = numberOfTotal + length(problemStruct.(fields{i})); end - - fitParams = zeros(numberOfFitted, 1); - otherParams = zeros((numberOfTotal-numberOfFitted), 1); + + fitParams = zeros(1, numberOfFitted); + otherParams = zeros(1, (numberOfTotal-numberOfFitted)); fitLimits = zeros(numberOfFitted,2); otherLimits = zeros((numberOfTotal-numberOfFitted),2); diff --git a/minimisers/simplex/runSimplex.m b/minimisers/simplex/runSimplex.m index a8e741012..8ffbde1c5 100644 --- a/minimisers/simplex/runSimplex.m +++ b/minimisers/simplex/runSimplex.m @@ -113,7 +113,7 @@ % final reshape %x = reshape(x,xsize); -problemStruct.fitParams = x; +problemStruct.fitParams = x'; problemStruct = unpackParams(problemStruct); result = reflectivityCalculation(problemStruct,controls); diff --git a/minimisers/simplex/simplexIntrafun.m b/minimisers/simplex/simplexIntrafun.m index 750ee54ec..6db56ed0c 100644 --- a/minimisers/simplex/simplexIntrafun.m +++ b/minimisers/simplex/simplexIntrafun.m @@ -4,7 +4,7 @@ xtrans = simplexXTransform(x,params); %Unpck the params.. -problemStruct.fitParams = xtrans; +problemStruct.fitParams = xtrans'; problemStruct = unpackParams(problemStruct); result = reflectivityCalculation(problemStruct,controls); diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat index 0ab71ee98..a0e33b1fb 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat and b/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat differ diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat index b199092dd..1724b8096 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat and b/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat differ diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat index 58ce643df..42cd54260 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat and 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