RascalSoftware · DrPaulSharp · Jan 2, 2025 · Dec 11, 2024
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat
diff --git a/tests/normalTFReflectivityCalculation/customLayersInputs.mat b/tests/normalTFReflectivityCalculation/customLayersInputs.mat
diff --git a/tests/normalTFReflectivityCalculation/customLayersOutputs.mat b/tests/normalTFReflectivityCalculation/customLayersOutputs.mat
diff --git a/tests/normalTFReflectivityCalculation/customLayersTFParams.mat b/tests/normalTFReflectivityCalculation/customLayersTFParams.mat
diff --git a/tests/normalTFReflectivityCalculation/customXYInputs.mat b/tests/normalTFReflectivityCalculation/customXYInputs.mat
diff --git a/tests/normalTFReflectivityCalculation/customXYOutputs.mat b/tests/normalTFReflectivityCalculation/customXYOutputs.mat
diff --git a/tests/normalTFReflectivityCalculation/customXYTFParams.mat b/tests/normalTFReflectivityCalculation/customXYTFParams.mat
diff --git a/tests/normalTFReflectivityCalculation/standardLayersInputs.mat b/tests/normalTFReflectivityCalculation/standardLayersInputs.mat
diff --git a/tests/normalTFReflectivityCalculation/standardLayersOutputs.mat b/tests/normalTFReflectivityCalculation/standardLayersOutputs.mat
diff --git a/tests/normalTFReflectivityCalculation/standardLayersTFParams.mat b/tests/normalTFReflectivityCalculation/standardLayersTFParams.mat
diff --git a/tests/testProjectConversion/DSPCBilayerProjectClass.mat b/tests/testProjectConversion/DSPCBilayerProjectClass.mat
diff --git a/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat b/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat