Removes unused fields from priors struct (#348)

* Removes unused fields from priors struct

* Moves priors into problemStruct

* Addresses review comments

3rdParty/paramonte/processParamonteRuns.m

@@ -5,7 +5,7 @@
 % 
 % controls = controlsClass();
 
-[problemStruct,problemLimits,~,controls] = parseClassToStructs(problem,controls);
+[problemStruct,problemLimits,controls] = parseClassToStructs(problem,controls);
 
 [problemStruct,fitNames] = packParams(problemStruct,problemLimits);
 

3rdParty/paramonte/runParamonte.m

@@ -15,7 +15,7 @@
 rng('default');
 
 % Split problem using the routines from RAT..
-[problemStruct,problemLimits,priors,controls] = parseClassToStructs(project,inputControls);
+[problemStruct,problemLimits,controls] = parseClassToStructs(project,inputControls);
 
 %controls.parallel = coderEnums.parallelOptions.Points;
 

API/RAT.m

@@ -61,7 +61,7 @@
 % chain               [M x nParams] double MCMC chains where M is the length of each chain
 % =================== ==================== ===============
 
-[problemStruct,problemLimits,priors,controls] = parseClassToStructs(project,controls);
+[problemStruct,problemLimits,controls] = parseClassToStructs(project,controls);
 
 % Set controls.calcSLD to 1 if we are doing customXY
 switch lower(problemStruct.modelType)
@@ -78,7 +78,7 @@
 end
 
 tic
-[problemStruct,result,bayesResults] = RATMain_mex(problemStruct,problemLimits,controls,priors);
+[problemStruct,result,bayesResults] = RATMain_mex(problemStruct,problemLimits,controls);
 
 if display
     toc

API/RATMain.m

@@ -1,4 +1,4 @@
-function [problemStruct,result,bayesResults] = RATMain(problemStruct,problemLimits,controls,priors)
+function [problemStruct,result,bayesResults] = RATMain(problemStruct,problemLimits,controls)
 coderEnums.initialise()
 
 if strcmpi(problemStruct.TF, coderEnums.calculationTypes.Domains)
@@ -29,12 +29,12 @@
             if ~strcmpi(controls.display, coderEnums.displayOptions.Off)
                 triggerEvent(coderEnums.eventTypes.Message, sprintf('\nRunning Nested Sampler\n\n'));
             end            
-            [problemStruct,result,bayesResults] = runNestedSampler(problemStruct,problemLimits,controls,priors);   
+            [problemStruct,result,bayesResults] = runNestedSampler(problemStruct,problemLimits,controls);   
         case coderEnums.procedures.Dream
             if ~strcmpi(controls.display, coderEnums.displayOptions.Off)
                 triggerEvent(coderEnums.eventTypes.Message, sprintf('\nRunning DREAM\n\n'));
             end
-            [problemStruct,result,bayesResults] = runDREAM(problemStruct,problemLimits,controls,priors);
+            [problemStruct,result,bayesResults] = runDREAM(problemStruct,problemLimits,controls);
         otherwise
             coderException(coderEnums.errorCodes.invalidOption, 'The procedure "%s" is not supported. The procedure must be one of "%s"', controls.procedure, strjoin(fieldnames(coderEnums.procedures), '", "'));
     end

API/parseClassToStructs.m

@@ -1,4 +1,4 @@
-function [problemStruct,problemLimits,priors,controls] = parseClassToStructs(project,inputControls)
+function [problemStruct,problemLimits,controls] = parseClassToStructs(project,inputControls)
 
 % Breaks up the classes into the relevant structures for inputting into C
 
@@ -13,56 +13,6 @@
     inputData{i} = [contrastData zeros(size(contrastData,1), 6-size(contrastData,2))];
 end
 
-%% Put the priors into their own array
-priors.params = inputStruct.paramPriors;
-priors.backgroundParams = inputStruct.backgroundParamPriors;
-priors.scalefactors = inputStruct.scalefactorPriors;
-priors.qzshifts = inputStruct.qzshiftPriors;
-priors.bulkIns = inputStruct.bulkInPriors;
-priors.bulkOuts = inputStruct.bulkOutPriors;
-priors.resolutionParams = inputStruct.resolutionParamPriors;
-if isa(project, 'domainsClass')
-    priors.domainRatios = inputStruct.domainRatioPriors;
-else
-    priors.domainRatios = cell(0,1);
-end
-
-priorFields = fieldnames(priors);
-totalNumber = 0;
-for i=1:length(priorFields)
-    totalNumber = totalNumber + size(priors.(priorFields{i}), 1);
-end
-
-priorsCell = cell(totalNumber,4);
-cellCount = 1;
-
-for i=1:length(priorFields)
-    currentPrior = priorFields{i};
-    for j = 1:size(priors.(currentPrior), 1)
-        priorsCell{cellCount,1} = priors.(currentPrior){j}{1};
-
-        % Check prior type.....
-        thisType = priors.(currentPrior){j}{2};
-
-        if strcmpi(thisType, priorTypes.Uniform.value)
-            priorType = 1;
-        elseif strcmpi(thisType, priorTypes.Gaussian.value)
-            priorType = 2;
-        else
-            priorType = 3;
-        end
-        priorsCell{cellCount,2} = priorType;
-
-        priorsCell{cellCount,3} = priors.(currentPrior){j}{3};
-        priorsCell{cellCount,4} = priors.(currentPrior){j}{4};
-        cellCount = cellCount + 1;
-    end
-end
-
-priors.priorNames = priorsCell(:, 1);
-priors.priorValues = cell2mat(priorsCell(:, 2:end));
-
-
 %% Deal with backgrounds and resolutions
 
 % Convert contrastBackgrounds to custom file/parameter indices
@@ -277,6 +227,52 @@
 problemStruct.fitLimits = [];
 problemStruct.otherLimits = [];
 
+%% Put the priors into their fields
+
+priorFields = {"paramPriors", "backgroundParamPriors", ...
+               "scalefactorPriors","qzshiftPriors", "bulkInPriors", ...
+               "bulkOutPriors", "resolutionParamPriors"};
+
+if isa(project, 'domainsClass')
+    priorFields{end+1} = "domainRatioPriors";
+end
+
+totalNumber = 0;
+for i=1:length(priorFields)
+    totalNumber = totalNumber + size(inputStruct.(priorFields{i}), 1);
+end
+
+priorsCell = cell(totalNumber,4);
+cellCount = 1;
+
+for i=1:length(priorFields)
+    currentPrior = priorFields{i};
+    for j = 1:size(inputStruct.(currentPrior), 1)
+        priorsCell{cellCount,1} = inputStruct.(currentPrior){j}{1};
+
+        % Check prior type
+        thisType = inputStruct.(currentPrior){j}{2};
+
+        if strcmpi(thisType, priorTypes.Uniform.value)
+            priorType = 1;
+        elseif strcmpi(thisType, priorTypes.Gaussian.value)
+            priorType = 2;
+        else
+            priorType = 3;
+        end
+        priorsCell{cellCount,2} = priorType;
+
+        priorsCell{cellCount,3} = inputStruct.(currentPrior){j}{3};
+        priorsCell{cellCount,4} = inputStruct.(currentPrior){j}{4};
+        cellCount = cellCount + 1;
+    end
+end
+
+problemStruct.priorNames = priorsCell(:, 1);
+problemStruct.priorValues = cell2mat(priorsCell(:, 2:end));
+
+%% Add structs for parameter names and fits
+
 % Record lists of parameter names
 problemStruct.names.params = inputStruct.paramNames;
 problemStruct.names.backgroundParams = inputStruct.backgroundParamNames;
@@ -292,7 +288,7 @@
 end
 problemStruct.names.contrasts = inputStruct.contrastNames;
 
-% Also need to deal with the checks...
+% Record lists of parameter fits
 problemStruct.checks.params = inputStruct.fitParam;
 problemStruct.checks.backgroundParams = inputStruct.fitBackgroundParam;
 problemStruct.checks.scalefactors = inputStruct.fitScalefactor;

compile/fullCompile/makeCompileArgsFull.m

@@ -8,7 +8,7 @@
 maxDataSize = 10000;
 
 ARGS = cell(1,1);
-ARGS{1} = cell(4,1);
+ARGS{1} = cell(3,1);
 ARGS_1_1 = struct;
 ARGS_1_1.TF = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.resample = coder.typeof(0,[1 maxArraySize],[0 1]);
@@ -63,6 +63,9 @@
 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]);
+ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
+ARGS_1_1.priorNames = coder.typeof({ARG}, [maxArraySize 1],[1 0]);
+ARGS_1_1.priorValues = coder.typeof(0, [maxArraySize 3], [1 0]);
 ARGS_1_1_names = struct;
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1_names.params = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
@@ -127,74 +130,5 @@
 ARGS_1_3.adaptPCR = coder.typeof(true);
 ARGS_1_3.IPCFilePath = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS{1}{3} = coder.typeof(ARGS_1_3);
-ARGS_1_4 = struct;
-ARG_20 = cell([1 4]);
-ARG_20{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_20{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_20{3} = coder.typeof(0);
-ARG_20{4} = coder.typeof(0);
-ARG_20 = coder.typeof(ARG_20,[1 4]);
-ARG_20 = ARG_20.makeHeterogeneous();
-ARGS_1_4.params = coder.typeof({ARG_20}, [maxArraySize 1],[1 0]);
-ARG_21 = cell([1 4]);
-ARG_21{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_21{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_21{3} = coder.typeof(0);
-ARG_21{4} = coder.typeof(0);
-ARG_21 = coder.typeof(ARG_21,[1 4]);
-ARG_21 = ARG_21.makeHeterogeneous();
-ARGS_1_4.backgroundParams = coder.typeof({ARG_21}, [maxArraySize 1],[1 0]);
-ARG_22 = cell([1 4]);
-ARG_22{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_22{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_22{3} = coder.typeof(0);
-ARG_22{4} = coder.typeof(0);
-ARG_22 = coder.typeof(ARG_22,[1 4]);
-ARG_22 = ARG_22.makeHeterogeneous();
-ARGS_1_4.scalefactors = coder.typeof({ARG_22}, [maxArraySize 1],[1 0]);
-ARG_23 = cell([1 4]);
-ARG_23{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_23{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_23{3} = coder.typeof(0);
-ARG_23{4} = coder.typeof(0);
-ARG_23 = coder.typeof(ARG_23,[1 4]);
-ARG_23 = ARG_23.makeHeterogeneous();
-ARGS_1_4.qzshifts = coder.typeof({ARG_23}, [maxArraySize 1],[1 0]);
-ARG_24 = cell([1 4]);
-ARG_24{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_24{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_24{3} = coder.typeof(0);
-ARG_24{4} = coder.typeof(0);
-ARG_24 = coder.typeof(ARG_24,[1 4]);
-ARG_24 = ARG_24.makeHeterogeneous();
-ARGS_1_4.bulkIns = coder.typeof({ARG_24}, [maxArraySize 1],[1 0]);
-ARG_25 = cell([1 4]);
-ARG_25{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_25{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_25{3} = coder.typeof(0);
-ARG_25{4} = coder.typeof(0);
-ARG_25 = coder.typeof(ARG_25,[1 4]);
-ARG_25 = ARG_25.makeHeterogeneous();
-ARGS_1_4.bulkOuts = coder.typeof({ARG_25}, [maxArraySize 1],[1 0]);
-ARG_26 = cell([1 4]);
-ARG_26{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_26{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_26{3} = coder.typeof(0);
-ARG_26{4} = coder.typeof(0);
-ARG_26 = coder.typeof(ARG_26,[1 4]);
-ARG_26 = ARG_26.makeHeterogeneous();
-ARGS_1_4.resolutionParams = coder.typeof({ARG_26}, [maxArraySize 1],[1 0]);
-ARG_27 = cell([1 4]);
-ARG_27{1} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_27{2} = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG_27{3} = coder.typeof(0);
-ARG_27{4} = coder.typeof(0);
-ARG_27 = coder.typeof(ARG_27,[1 4]);
-ARG_27 = ARG_27.makeHeterogeneous();
-ARGS_1_4.domainRatios = coder.typeof({ARG_27}, [maxArraySize 1],[1 0]);
-ARG_28 = coder.typeof('X',[1 Inf],[0 1]);
-ARGS_1_4.priorNames = coder.typeof({ARG_28}, [maxArraySize 1],[1 0]);
-ARGS_1_4.priorValues = coder.typeof(0, [maxArraySize 3], [1 0]);
-ARGS{1}{4} = coder.typeof(ARGS_1_4);
 
 end

compile/reflectivityCalculation/makeCompileArgs.m

@@ -63,6 +63,9 @@
 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]);
+ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
+ARGS_1_1.priorNames = coder.typeof({ARG}, [maxArraySize 1],[1 0]);
+ARGS_1_1.priorValues = coder.typeof(0, [maxArraySize 3], [1 0]);
 ARGS_1_1_names = struct;
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1_names.params = coder.typeof({ARG}, [1 maxArraySize],[0 1]);

minimisers/DREAM/runDREAM.m

@@ -1,4 +1,4 @@
-function [outProblemStruct,result,bayesResults] = runDREAM(problemStruct,problemLimits,controls,priors)
+function [outProblemStruct,result,bayesResults] = runDREAM(problemStruct,problemLimits,controls)
 
 
 % Make an empty struct for bayesResults to hold the outputs of the
@@ -33,7 +33,8 @@
 [problemStruct,fitParamNames] = packParams(problemStruct,problemLimits);
 
 % Get the priors for the fitted parameters...
-priorList = getFittedPriors(fitParamNames,priors,problemStruct.fitLimits);
+priorList = getFittedPriors(fitParamNames, problemStruct.priorNames, ...
+                            problemStruct.priorValues, problemStruct.fitLimits);
 
 % Put all the RAT parameters together into one array...
 ratInputs.problemStruct = problemStruct;

minimisers/NS/runNestedSampler.m

@@ -1,4 +1,4 @@
-function  [problemStruct,result,bayesResults] = runNestedSampler(problemStruct,problemLimits,controls,inPriors)
+function  [problemStruct,result,bayesResults] = runNestedSampler(problemStruct,problemLimits,controls)
 
 [problemStruct,fitNames] = packParams(problemStruct,problemLimits);
 
@@ -17,10 +17,11 @@
 end
 bayesResults = makeEmptyBayesResultsStruct(numberOfContrasts, domains, numberOfChains);
 
-%Deal with priors.
-priorList = getFittedPriors(fitNames,inPriors,problemStruct.fitLimits);
+% Deal with priors.
+priorList = getFittedPriors(fitNames, problemStruct.priorNames, ...
+                            problemStruct.priorValues, problemStruct.fitLimits);
 
-%Tuning Parameters
+% Tuning Parameters
 model.ssfun = @nsIntraFun;
 nLive = controls.nLive;
 tolerance = controls.nsTolerance;

minimisers/DREAM/getFittedPriors.m → minimisers/generalUtils/getFittedPriors.m

@@ -1,8 +1,4 @@
-function priorFitList = getFittedPriors(paramNames,priors,fitLimits)
-
-% Get the list of all the priors..
-priorNames = priors.priorNames;
-priorValues = priors.priorValues;
+function priorFitList = getFittedPriors(paramNames,priorNames,priorValues,fitLimits)
 
 % Find the values for fitParams
 numberOfParams = length(paramNames);