Removes "bestFitMean" from "BayesResults" (#234)

RascalSoftware · Jun 10, 2024 · f0cc59c · f0cc59c
1 parent 7e96acd
commit f0cc59c
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Showing 25 changed files with 11 additions and 57 deletions.
diff --git a/minimisers/DREAM/runDREAM.m b/minimisers/DREAM/runDREAM.m
@@ -63,7 +63,7 @@
 
 % This will change...
 % Initial sampling and parameter range
-paramInfo.prior = coderEnums.priorTypes.Uniform;
+parInfo.prior = coderEnums.priorTypes.Uniform;
 ParInfo.min = problemStruct.fitLimits(:,1)';
 ParInfo.max = problemStruct.fitLimits(:,2)';
 ParInfo.boundhandling = controls.boundHandling;
@@ -99,7 +99,6 @@
 [outProblemStruct,result,dreamResults] = processBayes(output,problemStruct,problemCells,problemLimits,controls);
 
 % Populate the output struct
-bayesResults.bestFitMean = dreamResults.bestFitMean;
 bayesResults.predictionIntervals = dreamResults.predictionIntervals;
 bayesResults.confidenceIntervals = dreamResults.confidenceIntervals;
 bayesResults.dreamParams = dreamOutput.DREAMPar;

diff --git a/minimisers/NS/runNestedSampler.m b/minimisers/NS/runNestedSampler.m
@@ -53,7 +53,6 @@
 [problemStruct,result,nestResults] = processBayes(bayesOutputs,problemStruct,problemCells,problemLimits,controls);
 
 bayesResults.predictionIntervals = nestResults.predictionIntervals;
-bayesResults.bestFitMean = nestResults.bestFitMean;
 bayesResults.confidenceIntervals = nestResults.confidenceIntervals;
 bayesResults.chain = chain;
 bayesResults.nestedSamplerOutput.LogZ = logZ;

diff --git a/minimisers/generalUtils/bayesStats/processBayes.m b/minimisers/generalUtils/bayesStats/processBayes.m
@@ -10,10 +10,6 @@
 
 % Calculate 'mean' best fit curves
 result = reflectivityCalculation(problemStruct,problemCells,problemLimits,controls);
-bestFitMean.reflectivity = result.reflectivity;
-bestFitMean.sld = result.sldProfiles;
-bestFitMean.chi = result.calculationResults.sumChi;
-bestFitMean.data = result.shiftedData;
 
 % 2. Reflectivity and SLD shading
 predInts = refPercentileConfidenceIntervals(bayesOutputs,problemStruct,problemCells,problemLimits,controls);
@@ -22,7 +18,7 @@
 
 
 % bayesResults.chain = bayesOutputs.chain;
-bayesResults = struct('bestFitMean',bestFitMean,'predictionIntervals',predInts,...
+bayesResults = struct('predictionIntervals',predInts,...
                       'confidenceIntervals',confidenceIntervals);
 
 end
diff --git a/minimisers/generalUtils/makeEmptyBayesResultsStruct.m b/minimisers/generalUtils/makeEmptyBayesResultsStruct.m
@@ -9,7 +9,6 @@
     % 
     %   struct with fields:
     % 
-    %         bestFitMean: [1×1 struct]
     % predictionIntervals: [1×1 struct]
     % confidenceIntervals: [1×1 struct]
     %           allChains: [1×1 struct]
@@ -20,45 +19,7 @@
 
     % -----------------------------------------------------------
     % Make the individual structs....
-    % (1) bayesResults.bestFitMean
-
-    reflectivity = cell(nContrasts, 1);
-    reflectivityCell = [1 1 1];
-    coder.varsize('reflectivityCell',[1e7 4],[1 1]);
-    for i = 1:nContrasts
-        reflectivity{i} = reflectivityCell;
-    end
-
-    if isDomains
-        sld = cell(nContrasts,2);
-        sldCell = [1 1; 1 1];
-        coder.varsize('sldCell',[1e7 3],[1 1]); 
-        for i = 1:nContrasts
-            sld{i,1} = sldCell;
-            sld{i,2} = sldCell;
-        end
-    else
-        sld = cell(nContrasts, 1);
-        sldCell = [1 1];
-        coder.varsize('sldCell',[1e7 3],[1 1]);
-        for i = 1:nContrasts
-            sld{i} = sldCell;
-        end
-    end
-
-    chi = 0;
-
-    data = cell(nContrasts, 1);
-    dataCell = [1 1 1];
-    coder.varsize('dataCell',[1e7 5],[1 1]);
-    for i = 1:nContrasts
-        data{i} = dataCell;
-    end
-
-    bestFitMean = struct('reflectivity',{reflectivity},'sld',{sld},'chi',chi,'data',{data});
-
-    % --------------------------------------------------------------------
-    % (2) bayesResults.predictionIntervals
+    % (1) bayesResults.predictionIntervals
 
     reflectivityIntervals = cell(nContrasts,1);
     reflectivityIntervalsCell = [1 1 1];
@@ -116,7 +77,7 @@
         'sldXData',{sldXData},'sampleChi',sampleChi);
 
     % ------------------------------------------------------------------
-    % (3) bayesResults.confidenceIntervals
+    % (2) bayesResults.confidenceIntervals
 
     percentile95 = zeros(2,1);
     coder.varsize('percentile95',[2 1e3],[0 1]);
@@ -131,7 +92,7 @@
         'percentile65',percentile65,'mean',mean);
 
     % -------------------------------------------------------------------
-    % (4) bayesResults.dreamParams
+    % (3) bayesResults.dreamParams
 
     R = zeros(nChains,nChains);
     coder.varsize('R',[1e4 1e4],[1 1]);
@@ -157,7 +118,7 @@
                                'R', R);
 
     % -------------------------------------------------------------------
-    % (5) bayesResults.dreamOutput
+    % (4) bayesResults.dreamOutput
 
     allChains = [1 1 1];
     coder.varsize('allChains',[1e4 50 50],[1 1 1]);
@@ -186,7 +147,7 @@
                                 'CR', CR);
 
     % -------------------------------------------------------------------
-    % (6) bayesResults.nestedSamplerOutput
+    % (5) bayesResults.nestedSamplerOutput
 
     % Nested Sampler
     LogZ = 0;
@@ -201,15 +162,14 @@
         nestSamples,'postSamples',postSamples);
 
     % ------------------------------------------------------------------
-    % (7) chain
+    % (6) chain
 
     chain = [0 0];
     coder.varsize('chain',[1e6 1e3],[1 1]);
 
     % -------------------------------------------------------------------
     % Make the final structure...
-    bayesResults = struct('bestFitMean',bestFitMean,...
-                          'predictionIntervals', predictionIntervals,...
+    bayesResults = struct('predictionIntervals', predictionIntervals,...
                           'confidenceIntervals', confidenceIntervals,...
                           'dreamParams', dreamParams,...
                           'dreamOutput', dreamOutput,...

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/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/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
diff --git a/utilities/plotting/bayesShadedPlot.m b/utilities/plotting/bayesShadedPlot.m
@@ -65,8 +65,8 @@ function bayesShadedPlot(problem,result,varargin)
 sldXdata = pLims.sldXData;
 
 % Get the reflectivities for mean...
-bestRefMean = result.bestFitMean.reflectivity;
-bestSldMean = result.bestFitMean.sld;
+bestRefMean = result.reflectivity;
+bestSldMean = result.sldProfiles;
 
 shiftedData = result.shiftedData;
 numberOfContrasts = length(shiftedData);