Unify variable naming convention (#182)

* Renames contrasts variables in target functions

* Renames fields in "problemDef" struct

* Replaces "nbair" with "bulkIn and "nbsub" with "bulkOut"

* Renames variables in tests

* Changes "sf" to "scalefactor" in target functions

* Changes "qshift" to "qzshift" in target functions

* Tidies up "backSort.m" routine

* Renames "nba" and "nbs" to "bulkIn" and "bulkOut" respectively in target functions

* Restores use of "nba" and "nbs" as inputs in "processCustomFuncion.m" to address bug

* Renames "nba" and "nbs" to "bulkIn" and "bulkOut" respectively in utilities

* Fixes typos

* Addresses review comments and fixes bugs

* Tidies up code

3rdParty/mcmcstat/%runDram.m

@@ -71,12 +71,12 @@
 
 % Pre-processor directives for Matlab Coder.
 coder.varsize('problem.ssubs',[Inf 1],[1 0]);
-coder.varsize('problem.backgrounds',[Inf 1],[1 0]);
-coder.varsize('problem.qshifts',[Inf 1],[1 0]);
+coder.varsize('problem.backgroundParams',[Inf 1],[1 0]);
+coder.varsize('problem.qzshifts',[Inf 1],[1 0]);
 coder.varsize('problem.scalefactors',[Inf 1],[1 0]);
-coder.varsize('problem.nbairs',[Inf 1],[1 0]);
-coder.varsize('problem.nbsubs',[Inf 1],[1 0]);
-coder.varsize('problem.resolutions',[Inf 1],[1 0]);
+coder.varsize('problem.bulkIn',[Inf 1],[1 0]);
+coder.varsize('problem.bulkOut',[Inf 1],[1 0]);
+coder.varsize('problem.resolutionParams',[Inf 1],[1 0]);
 coder.varsize('problem.ssubs',[Inf 1],[1 0]);
 coder.varsize('problem.calculations.all_chis',[Inf 1],[1 0]);
 coder.varsize('problem.calculations.sum_chi',[1 1],[0 0]);

API/RATMain.m

@@ -9,12 +9,12 @@
 preAlloc = zeros(numberOfContrasts,1);
 
 problem = struct('ssubs',preAlloc,...
-                 'backgrounds',preAlloc,...
-                 'qshifts',preAlloc,...
+                 'backgroundParams',preAlloc,...
+                 'qzshifts',preAlloc,...
                  'scalefactors',preAlloc,...
-                 'nbairs',preAlloc,...
-                 'nbsubs',preAlloc,...
-                 'resolutions',preAlloc,...
+                 'bulkIn',preAlloc,...
+                 'bulkOut',preAlloc,...
+                 'resolutionParams',preAlloc,...
                  'calculations',struct('all_chis',preAlloc,'sum_chi',0),...
                  'allSubRough',preAlloc,...
                  'resample',preAlloc);

API/parseClassToStructs.m

@@ -319,12 +319,12 @@
 problemDef.contrastBulkIns = inputStruct.contrastBulkIns;
 problemDef.contrastBulkOuts = inputStruct.contrastBulkOuts;
 problemDef.contrastResolutions = contrastRes;
-problemDef.backs = inputStruct.backgroundParamValues; %inputStruct.backgrounds;       % **** note backPar workaround (todo) ****
-problemDef.shifts = inputStruct.qzshiftValues;
-problemDef.sf = inputStruct.scalefactorValues;
-problemDef.nba = inputStruct.bulkInValues;
-problemDef.nbs = inputStruct.bulkOutValues;
-problemDef.res = inputStruct.resolutionParamValues; %inputStruct.resolutions;           % **** note resolutionParam workaround (todo) ****          
+problemDef.backgroundParams = inputStruct.backgroundParamValues; %inputStruct.backgrounds;       % **** note backPar workaround (todo) ****
+problemDef.qzshifts = inputStruct.qzshiftValues;
+problemDef.scalefactors = inputStruct.scalefactorValues;
+problemDef.bulkIn = inputStruct.bulkInValues;
+problemDef.bulkOut = inputStruct.bulkOutValues;
+problemDef.resolutionParams = inputStruct.resolutionParamValues; %inputStruct.resolutions;           % **** note resolutionParam workaround (todo) ****          
 problemDef.params = inputStruct.paramValues;
 problemDef.numberOfLayers = inputStruct.numberOfLayers;
 problemDef.modelType = inputStruct.modelType;

API/parseOutToProjectClass.m

@@ -1,51 +1,52 @@
 function outProblemDef = parseOutToProjectClass(problemDefInput,outProblemStruct)
 
-
 %Reconstruct the problemDef class as an output
 %Using the outputs from the calculation(s)
 outProblemDef = problemDefInput;
 
 %(1) Parameters
-pars = outProblemStruct.params;
-for i = 1:length(pars)
-    outProblemDef.setParameterValue(i,pars(i));
+params = outProblemStruct.params;
+for i = 1:length(params)
+    outProblemDef.setParameterValue(i,params(i));
 end
 
 %(2) Backgrounds
-backs = outProblemStruct.backs;
-for i = 1:length(backs)
-    outProblemDef.setBackgroundParamValue(i,backs(i));
+backgroundParams = outProblemStruct.backgroundParams;
+for i = 1:length(backgroundParams)
+    outProblemDef.setBackgroundParamValue(i,backgroundParams(i));
 end
 
 %(3) Scalefactors
-scales = outProblemStruct.sf;
-for i = 1:length(scales)
-    outProblemDef.setScalefactor(i,'value',scales(i));
+scalefactors = outProblemStruct.scalefactors;
+for i = 1:length(scalefactors)
+    outProblemDef.setScalefactor(i,'value',scalefactors(i));
 end
 
 %(4) Qzshifts
-% shifts = outProblemStruct.shifts;
-% outProblemDef.qzshifts = shifts;
+qzshifts = outProblemStruct.qzshifts;
+for i = 1:length(qzshifts)
+    outProblemDef.setQzshift(i,'value',qzshifts(i));
+end
 
-%(4) Nbairs
-nbairs = outProblemStruct.nba;
-for i = 1:length(nbairs)
-    outProblemDef.setBulkIn(i,'value',nbairs(i));
+%(5) Bulk In
+bulkIns = outProblemStruct.bulkIn;
+for i = 1:length(bulkIns)
+    outProblemDef.setBulkIn(i,'value',bulkIns(i));
 end
 
-%(5) Nbsubs
-nbsubs = outProblemStruct.nbs;
-for i = 1:length(nbsubs)
-    outProblemDef.setBulkOut(i,'value',nbsubs(i));
+%(6) Bulk Out
+bulkOuts = outProblemStruct.bulkOut;
+for i = 1:length(bulkOuts)
+    outProblemDef.setBulkOut(i,'value',bulkOuts(i));
 end
 
-%(5) Resolutions
-resol = outProblemStruct.res;
-for i = 1:length(resol)
-    outProblemDef.setResolutionParam(i,'value',resol(i));
+%(7) Resolutions
+resolutionParams = outProblemStruct.resolutionParams;
+for i = 1:length(resolutionParams)
+    outProblemDef.setResolutionParam(i,'value',resolutionParams(i));
 end
 
-% (6) Domain ratio
+% (8) Domain ratio
 if strcmpi(outProblemStruct.TF,'domains')
     domainRatios = outProblemStruct.domainRatio;
     for i = 1:length(domainRatios)

compile/fullCompile/makeCompileArgsFull.m

@@ -23,12 +23,12 @@
 ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.backs = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.shifts = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.sf = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.nba = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.nbs = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.res = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.bulkIn = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.bulkOut = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.resolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.params = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.numberOfLayers = coder.typeof(0);
 ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);

compile/reflectivityCalculation/makeCompileArgs.m

@@ -23,12 +23,12 @@
 ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.backs = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.shifts = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.sf = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.nba = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.nbs = coder.typeof(0,[1 maxArraySize],[0 1]);
-ARGS_1_1.res = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.bulkIn = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.bulkOut = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.resolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.params = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.numberOfLayers = coder.typeof(0);
 ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);

minimisers/generalUtils/checkBounds.m

@@ -9,23 +9,23 @@
 
 fitWhichBacks = problem.fitBackgrounds;
 fittingBacks = problem.backs(find(fitWhichBacks));
-fittingBacksConstr = problem.backs_constr(find(fitWhichBacks),:);
+fittingBacksConstr = problem.backgroundParamLimits(find(fitWhichBacks),:);
 fittingBacksNames = problem.backgroundParamNames(find(fitWhichBacks));
 
 fitWhichScales = problem.fitScalefactor;
 fittingScales = problem.scalefac(find(fitWhichScales));
-fittingScalesConstr = problem.scale_constr(find(fitWhichScales),:);
-fittingScalesNames = problem.scalesNames(find(fitWhichScales));
+fittingScalesConstr = problem.scalefactorLimits(find(fitWhichScales),:);
+fittingScalesNames = problem.scalefactorNames(find(fitWhichScales));
 
 fitWhichShifts = problem.fitQzshift;
-fittingShifts = problem.shifts_horisontal(find(fitWhichShifts));
-fittingShiftsConstr = problem.shifts_constr(find(fitWhichShifts),:);
-fittingShiftsNames = problem.shiftsNames(find(fitWhichShifts));
+fittingShifts = problem.qzshifts(find(fitWhichShifts));
+fittingShiftsConstr = problem.qzshiftLimit(find(fitWhichShifts),:);
+fittingShiftsNames = problem.qzshiftNames(find(fitWhichShifts));
 
 fitWhichNbas = problem.fitBulkIn;
-fittingNbas = problem.nba(find(fitWhichNbas));
-fittingNbaConstr = problem.nbairs_constr(find(fitWhichNbas),:);
-fittingNbaNames = problem.nbaNames(find(fitWhichNbas));
+fittingNbas = problem.bulkIn(find(fitWhichNbas));
+fittingNbaConstr = problem.bulkInLimits(find(fitWhichNbas),:);
+fittingNbaNames = problem.bulkInNames(find(fitWhichNbas));
 
 
 fittingParams = [fittingParams(:) ; fittingBacks(:) ; fittingScales(:) ; fittingShifts(:) ; fittingNbas(:)];