Full compile of some minimizers (#161)

* Some initial corrections to DREAM for compile

* Most 'screener' identified problems with DREAM resolved

* All issues found via 'coder.screener('RATMain')' now cleared

* Fixed assignment problem in Gelman

* Most compile issues now cleared

* Fixed pre-allocation issue in refPrcentileconfInts

* Full compile working with Bayes commented out. Most Bayes issues theared though...

* Half way through re-configuring 'bayesOutputs' to be more sensible

* Cleared up to output structs. Now rationalising 'bayesOutputs'

* Almost compiles. A slight problem with assignment size of 'sldXdata' when assigning outputs in 'runDREAM'

* Fixes so the code compiles

* Dream now runs to completion, but this has messed up the outputs (ref_yVals{n})

* Full compile now working correctly

* Fixes unit test and removes unneeded files

* Addresses review comments

* Fixes kmeans

---------

Co-authored-by: arwelHughes <[email protected]>

Author: StephenNneji

.gitignore

@@ -41,3 +41,4 @@ __pycache__/
 *.dll
 *.lib
 *.dylib
+*.prj

3rdParty/paramonte/pmLogFunction.m

@@ -30,7 +30,7 @@
 
             problem = unpackparams(problem,control);
 
-            [outProblem,results] = reflectivityCalculationWrapper(problem,cells,limits,control);
+            [outProblem,results] = reflectivityCalculation(problem,cells,limits,control);
             chi = outProblem.calculations.sum_chi;
             logFuncVal = -chi/2;
 

3rdParty/paramonte/processParamonteRuns.m

@@ -47,7 +47,7 @@
 bayesOutputs.data = problemDefCells{2};
 bayesOutputs.results.mean = mean(unscaledChain);
 
-[problemDef,outProblemStruct,result,bayesResults] = processBayes_newMethod(bayesOutputs,allProblem);
+[problemDef,outProblemStruct,result,bayesResults] = processBayes(bayesOutputs,allProblem);
 
 
 result = parseResultToStruct(outProblemStruct,result);

3rdParty/paramonte/runParamonte.m

@@ -130,7 +130,7 @@
 % output.bestPars = mean(unscaledChain);
 % output.data = data;
 % 
-% [problemDef,outProblem,result,bayesResults] = processBayes_newMethod(output,outProblem);
+% [problemDef,outProblem,result,bayesResults] = processBayes(output,outProblem);
 
 % pmpdOut = pmpd;
 

API/RAT.m

@@ -79,7 +79,7 @@
 end
 
 tic
-[outProblemStruct,problem,result,bayesResults] = RATMain(problemDef,problemDefCells,problemDefLimits,controls,priors);
+[outProblemStruct,problem,result,bayesResults] = RATMain_mex(problemDef,problemDefCells,problemDefLimits,controls,priors);
 sendTextOutput(sprintf('\n'));
 
 if ~strcmpi(controls.display,'off')
@@ -92,7 +92,7 @@
     originalProc = controls.proc;
     controls.calcSld = 1;
     controls.proc = 'calculate';
-    [outProblemStruct,problem,result,~] = RATMain(outProblemStruct,problemDefCells,problemDefLimits,controls,priors);
+    [outProblemStruct,problem,result,~] = RATMain_mex(outProblemStruct,problemDefCells,problemDefLimits,controls,priors);
     controls.proc = originalProc;
 end
 

API/RATMain.m

@@ -1,7 +1,10 @@
 function [outProblemDef,problem,results,bayesResults] = RATMain(problemDef,problemDefCells,problemDefLimits,controls,priors)
 
 
-result = cell(6,1);
+result = cell(1,1);
+result{1} = {1};
+results = repmat(result,1,6);
+
 numberOfContrasts = problemDef.numberOfContrasts;
 preAlloc = zeros(numberOfContrasts,1);
 
@@ -13,22 +16,31 @@
                  'nbsubs',preAlloc,...
                  'resolutions',preAlloc,...
                  'calculations',struct('all_chis',preAlloc,'sum_chi',0),...
-                 'allSubRough',preAlloc);
+                 'allSubRough',preAlloc,...
+                 'resample',preAlloc);
 
-% Make empty bayes results even though we may not fill it (for output purposes)
-bayesResults.res = [];
-bayesResults.chain = [];
-bayesResults.s2chain = [];
-bayesResults.ssChain = [];
-bayesResults.bestPars = [];
+if strcmpi(problemDef.TF,'domains')
+    domains = true;
+else
+    domains = false;
+end
+bayesResults = makeEmptyBayesResultsStruct(1e3, problemDef.numberOfContrasts, domains, controls.nChains);
+% bayesResults = struct('bayesRes',[],...
+%     'chain',[],...
+%     's2chain',[],...
+%     'ssChain',[],...
+%     'bestPars_Mean',[],...
+%     'bestFitsMean',[],...
+%     'predLims',[],...
+%     'parConfInts',[]);
 
 outProblemDef = problemDef;
 
 %Decide what we are doing....
 action = controls.proc;
 switch lower(action)
     case 'calculate' %Just a single reflectivity calculation
-        [problem,results] = reflectivityCalculationWrapper(problemDef,problemDefCells,problemDefLimits,controls);
+        [problem,results] = reflectivityCalculation(problemDef,problemDefCells,problemDefLimits,controls);
         outProblemDef = problemDef;
     case 'simplex'
         if ~strcmpi(controls.display,'off')
@@ -40,11 +52,11 @@
             sendTextOutput(sprintf('\nRunning Differential Evolution\n\n'));
         end
         [outProblemDef,problem,results] = runDE(problemDef,problemDefCells,problemDefLimits,controls);
-    case 'ns'
-        if ~strcmpi(controls.display,'off')
-            sendTextOutput(sprintf('\nRunning Nested Sampler\n\n'));
-        end            
-        [outProblemDef,problem,results,bayesResults] = runNestedSampler(problemDef,problemDefCells,problemDefLimits,controls);   
+%     case 'ns'
+%         if ~strcmpi(controls.display,'off')
+%             sendTextOutput(sprintf('\nRunning Nested Sampler\n\n'));
+%         end            
+%         [outProblemDef,problem,results,bayesResults] = runNestedSampler(problemDef,problemDefCells,problemDefLimits,controls);   
     case 'dream'
         if ~strcmpi(controls.display,'off')
             sendTextOutput(sprintf('\nRunning DREAM\n\n'));

API/parseClassToStructs.m

@@ -202,15 +202,27 @@
     currentPrior = priorFields{i};
     for j = 1:size(priors.(currentPrior), 1)
         allPriors{cellCount,1} = priors.(currentPrior){j}{1};
-        allPriors{cellCount,2} = priors.(currentPrior){j}{2};
-        allPriors{cellCount,3} = num2str(priors.(currentPrior){j}{3});
-        allPriors{cellCount,4} = num2str(priors.(currentPrior){j}{4});
+       
+        % Check prior type.....
+        thisType = priors.(currentPrior){j}{2};
+
+        if strcmpi(thisType,'uniform')
+            priorType = 1;
+        elseif strcmpi(thisType,'gaussian')
+            priorType = 2;
+        else
+            priorType = 3;
+        end
+        allPriors{cellCount,2} = priorType;
+
+        allPriors{cellCount,3} = priors.(currentPrior){j}{3};
+        allPriors{cellCount,4} = priors.(currentPrior){j}{4};
         cellCount = cellCount + 1;
     end
 end
 
 priors.priorNames = allPriors(:, 1);
-priors.priorVals = allPriors(:, 2:end);
+priors.priorVals = cell2mat(allPriors(:, 2:end));   % Note move to double now for this...
 
 
 %% Split up the contrastBacks array

API/parseResultToStruct.m

@@ -8,7 +8,9 @@
 result.allLayers = results{6};      % Resampled layers
 
 result.calculationResults = problem.calculations;
-problem = rmfield(problem,'calculations');
+
+% For compile, we can't remove a field, so just clear it for now...
+%problem = rmfield(problem,'calculations');
 result.contrastParams = problem;
 
-end
+end

API/textProgressBar.m

@@ -2,6 +2,8 @@ function textProgressBar(curm,pct)
 
 persistent lastNchar
 
+strDotsMax = 40;
+
 if strcmpi(curm,'init')
     %fprintf('\n');
     lastNchar = 0;
@@ -18,12 +20,16 @@ function textProgressBar(curm,pct)
 end
 
 %curm = 'progress';
-progressmsg=[183-uint8((1:40)<=(pct*40)).*(183-'*') ''];
-%curmtxt=sprintf('% 9.3g\n',curm(1:min(end,20),1));
-progressmsg=sprintf('\n %s %5.1f%% [%s]',curm,(pct*100),progressmsg);
-fprintf('%s%s',repmat(char(8),1,lastNchar),progressmsg);
+
+nDots = floor(pct * strDotsMax);
+progressmsg = ['[' repmat('*',1,nDots) repmat('.',1,strDotsMax-nDots) ']'];
+
+% progressmsg=[183-uint16((1:40)<=(pct*40)).*(183-'*') ''];
+% %curmtxt=sprintf('% 9.3g\n',curm(1:min(end,20),1));
+progressmsg=sprintf('\n %s %5.1f%% %s',curm,(pct*100),progressmsg);
+
+fprintf('%s%s',repmat(sprintf('\b'),1,lastNchar),progressmsg);
 drawnow
 lastNchar=length(progressmsg);
 
 end
-

addPaths.m

@@ -27,6 +27,7 @@
     eventCompilePath;
     fullfile(root,'compile','customWrapper');
     fullfile(root,'compile','reflectivityCalculation');
+    fullfile(root,'compile','fullCompile');
     fullfile(root,'compile','simplex');
     fullfile(root,'compile');