Renames target functions and minimisers (#176)

* Renames "standardTF" to "nonPolarisedTF"

* Tidies up Paramonte functions

* Tidies up code in minimisers

* Renames "NSMain" as "NS"

* Updates paths

* Addresses review comments

Author: DrPaulSharp

3rdParty/paramonte/pmLogFunction.m

@@ -16,21 +16,16 @@
 
         function logFuncVal = get(obj,pars)
 
-            problem = obj.problemDef;
-            control = obj.controls;
-            cells = obj.problemDefCells;
-            limits = obj.problemDefLimits;
-            priors = obj.priors;
-            
+            problem = obj.problemDef;            
             problem.fitpars = pars;
 
-            if obj.scaled 
+            if obj.scaled
                 problem = unscalePars(problem);
             end
 
-            problem = unpackparams(problem,control);
+            problem = unpackparams(problem,obj.controls);
 
-            [outProblem,results] = reflectivityCalculation_mex(problem,cells,limits,control);
+            [outProblem,~] = reflectivityCalculation_mex(problem,obj.problemDefCells,obj.controls);
             chi = outProblem.calculations.sum_chi;
             logFuncVal = -chi/2;
 
@@ -42,14 +37,10 @@
             % Now apply the priors where necessary. 
             priorfun = @(th,mu,sig) sum(((th-mu)./sig).^2);
 
-            val = priorfun(problem.fitpars,priors(:,1),priors(:,2));
-
-            logFuncVal = logFuncVal + val;
+            val = priorfun(problem.fitpars,obj.priors(:,1),obj.priors(:,2));
 
-            %end
-            
+            logFuncVal = logFuncVal + val;           
 
         end   
     end
 end
-    

3rdParty/paramonte/pmPars.m

@@ -1,20 +1,15 @@
 classdef pmPars < handle
 
-
-properties
-
-    covMat = []
-    delayedRejectionCount = []
-    name = ''
-    scalefactor = 1e-3
-    chainSize = 10000
-    chainTrim = 0.25    % Use only the last part of chain...
-    mpi = false;
-
-end
-
-
-
-
+    properties
+    
+        covMat = []
+        delayedRejectionCount = []
+        name = ''
+        scalefactor = 1e-3
+        chainSize = 10000
+        chainTrim = 0.25    % Use only the last part of chain...
+        mpi = false;
+    
+    end
 
 end

3rdParty/paramonte/processParamonteRuns.m

@@ -1,16 +1,13 @@
-
-function [outProblemDef,result,pmpd] = processFits(problem,controls,chainName,chainTrim)
+function [outProblemDef,result,pmpd] = processParamonteRuns(problem,controls,chainName,chainTrim)
 
 % problem = load(name);
 % problem = problem.twentyMNProblem;
 % 
 % controls = controlsClass();
 
-[problemDef,problemDefCells,problemDefLimits,priors,controls] = parseClassToStructs(problem,controls);
-problemDefInput = problemDef;
+[problemDef,problemDefCells,problemDefLimits,~,controls] = parseClassToStructs(problem,controls);
 
 [problemDef,fitNames] = packparams(problemDef,problemDefCells,problemDefLimits,controls.checks);
-nDims = length(problemDef.fitpars);
 
 pm = paramonte();
 pmpd = pm.ParaDRAM();
@@ -50,7 +47,6 @@
 [problemDef,outProblemStruct,result,bayesResults] = processBayes(bayesOutputs,allProblem);
 bayesResults.chain = unscaledChain;
 
-
 result = parseResultToStruct(outProblemStruct,result);
 
 if isfield(problemDef,'fitpars')

3rdParty/paramonte/runParamonte.m

@@ -40,7 +40,7 @@
 logFunc.NDIM = nDims;
 logFunc.scaled = true;
 
-% Create a paraMonte object
+% Create a paramonte object
 pm = paramonte();
 
 % create a ParaDRAM simulation object

3rdParty/paramonte/scalePars.m

@@ -1,10 +1,11 @@
 function problem = scalePars(problem)
 
-
 limits = problem.fitconstr;
 vals = problem.fitpars;
 
 scaled = (vals(:) - limits(:,1))./(limits(:,2)-limits(:,1));
 
 problem.fitpars = scaled;
-%problem.unscaledPars = vals;
+%problem.unscaledPars = vals;
+
+end

3rdParty/paramonte/unscalePars.m

@@ -5,4 +5,6 @@
 
 unscaled = (scaled.*(limits(:,2)-limits(:,1)))+limits(:,1);
 
-problem.fitpars = unscaled;
+problem.fitpars = unscaled;
+
+end

addPaths.m

@@ -37,7 +37,7 @@
     fullfile(root,'minimisers','DE');
     %fullfile(root,'minimisers','mcmcstat_new');
     %fullfile(root,'minimisers','mcmcstat_new','src');
-    fullfile(root,'minimisers','NSMain');
+    fullfile(root,'minimisers','NS');
 
     fullfile(root,'targetFunctions' );
     fullfile(root,'targetFunctions','common');
@@ -50,7 +50,7 @@
     fullfile(root,'targetFunctions','common','resampleLayers');
     fullfile(root,'targetFunctions','common','resolutionFunctions','simpleGaussian'); 
 
-    fullfile(root,'tests','standardTFReflectivityCalculation');
+    fullfile(root,'tests','nonPolarisedTFReflectivityCalculation');
     fullfile(root,'tests','domainsTFReflectivityCalculation');
     fullfile(root,'tests','testCommonFunctions');
     fullfile(root,'tests','testProjectConversion');

compile/reflectivityCalculation/setCompilePaths.m

@@ -1,4 +1,4 @@
-function setCompilePaths(which)
+function setCompilePaths()
 
 % This function sets the paths for compiling, depending on whether a mex
 % file of source code is being generated.

minimisers/DREAM/diagnostics/raftery.m

@@ -103,7 +103,7 @@
         q = 0.0;
         i1 = find(runs == 0); i2 = find(runs == 1);
         ct1 = size(i1);   ct2 = size(i2);
-        if (ct1+ct2 ~= n), error('raftery needs 0s and 1s in runs'); end;
+        if (ct1+ct2 ~= n), error('raftery needs 0s and 1s in runs'); end
         work = runs;
         q = sum(runs);
         q = q/n;

minimisers/DREAM/functions/DREAM.m

@@ -193,7 +193,7 @@
 
 
         % Store the model simulations (if appropriate)
-        storeDREAMResults ( DREAMPar , fx , Meas_info , 'a+' );
+        storeDREAMResults(DREAMPar,fx,Meas_info,'a+');
     end
 
     % Check whether we update the crossover values