Adds labels to plot, renames defaultProject.mat, and other refactors

API/projectClass/projectClass.m

@@ -805,9 +805,12 @@ function delete(obj)
 
         function obj = setContrastModel(obj, row, model)
             % Edits the model of an existing contrast parameter. Expects
-            % the index of contrast parameter and cell array of layer names
+            % the index of contrast parameter and cell array of layer
+            % names. Multiple models can be set simultaneously by using 
+            % an 1D array of indices or cell of strings
             %
             % project.setContrastModel(1, {'layer 1'})
+            % project.setContrastModel(1:3, {'layer 1'})
 
             % Make a different allowed list depending on whether 
             % it is custom or layers
@@ -820,7 +823,14 @@ function delete(obj)
             end
 
             % Call the setContrastModel method
-            obj.contrasts.setContrastModel(row, obj.modelType, allowedValues, model);
+             if isText(row)
+                row = {row};
+             elseif isnumeric(row) 
+                row = num2cell(row);
+             end
+             for i=1:length(row)
+                 obj.contrasts.setContrastModel(row{i}, obj.modelType, allowedValues, model);
+             end
         end
 
         % ----------------------------------------------------------------

examples/miscellaneous/bayesBenchmark/directCompare2D.m

@@ -4,15 +4,18 @@
 %Do the direct calculation first.
 %Start by converting the R1 project to 
 %the R2 case...
-[d2oproblem,controls] = r1ToProblemDef('defaultProject.mat');
+root = getappdata(0, 'root');
+d2oproblem = r1ToProjectClass(fullfile(root, 'utilities', 'misc', 'defaultR1ProjectTemplate.mat'));
+
+controls = controlsClass();
 controls.calcSldDuringFit = true;
 controls.nsTolerance = 1;
 controls.nLive = 500;
 d2oProblem.fitScalefactor = 0;
 
 
 % Run nested sampler
-controls.procedure = 'bayes';
+controls.procedure = 'ns';
 [NSProb,NSResults] = RAT(d2oproblem,controls);
 
 
@@ -22,19 +25,21 @@
 probArray = zeros(gridSize, gridSize);
 
 %Make a vector of roughness values..
-outProb = NSProb;
-minRough = outProb.paramLimits{1}(1);
-maxRough = outProb.paramLimits{1}(2);
+paramsTable = NSProb.parameters.varTable;
+minRough = paramsTable{1,2};
+maxRough = paramsTable{1,4};
 roughVector = linspace(minRough, maxRough, gridSize);
 
 %Also background...
-minBack = outProb.backgroundLimits{1}(1);
-maxBack = outProb.backgroundLimits{1}(2);
+backParsTable = NSProb.background.backgroundParams.varTable;
+minBack = backParsTable{1,2};
+maxBack = backParsTable{1,4};
 backsVector = linspace(minBack, maxBack, gridSize);
 
 % %..and scalefactor
-% minScale = outProb.scalefactorLimits{1}(1);
-% maxScale = outProb.scalefactorLimits{1}(2);
+% scalefactorTable = NSProb.scalefactors.varTable;
+% minScale = scalefactorTable{1,2};
+% maxScale = scalefactorTable{1,4};
 % scaleVector = linspace(minScale, maxScale, gridSize);
 
 
@@ -55,14 +60,15 @@
 counter = 1;
 totalGrid = gridSize^2;
 controls.procedure = 'calculate';
+controls.display = 'off';
 
 for r = 1:gridSize
     for b = 1:gridSize
         thisRough = roughVector(r);
         thisBack =  backsVector(b);
 
-        d2oproblem.params(1) = thisRough;
-        d2oproblem.backgrounds(1) = thisBack;
+        NSProb.setParameter(1,'value',thisRough);
+        NSProb.setBackgroundParam(1,'value',thisBack);
 
         [outProblem,results] = RAT(d2oproblem,controls);
         thisChi = results.calculationResults.sumChi;
@@ -105,9 +111,9 @@
 scaleDist = squeeze(scaleDist);
 %figure(2); clf; contour(backsVector, scaleVector, scaleDist)
 scaleDist = sum(scaleDist,2);
-scaleDist = [scaleVector(:) scaleDist(:)];
-figure(3); subplot(1,2,3); hold on
-plot(scaleDist(:,1), scaleDist(:,2),'linewidth',2);
+% scaleDist = [scaleVector(:) scaleDist(:)];
+% figure(3); subplot(1,2,3); hold on
+% plot(scaleDist(:,1), scaleDist(:,2),'linewidth',2);
 % % scaleDist = [scaleVector(:) scaleDist(:)];
 % 
 % 

examples/miscellaneous/bayesBenchmark/directCompare3D.m

@@ -1,16 +1,16 @@
 %Comparison of MCMC, NS and direct calculation.
 clear
-useSaved = true;
+useSaved = false;
 
 %Do the direct calculation first.
 %Start by converting the R1 project to 
 %the R2 case...
-d2oproblem = r1ToProjectClass('defaultProject.mat');
-
+root = getappdata(0, 'root');
+d2oproblem = r1ToProjectClass(fullfile(root, 'utilities', 'misc', 'defaultR1ProjectTemplate.mat'));
 d2oproblem.setScalefactor(1,'min',0.07);
 d2oproblem.setScalefactor(1,'max',0.13);
 
-controls = controlsDef();
+controls = controlsClass();
 controls.calcSldDuringFit = true;
 [outProb,results] = RAT(d2oproblem,controls);
 figure(1); clf
@@ -19,9 +19,7 @@
 fprintf('Chi squared in %d \n',thisChisq);
 
 % Run MCMC
-controls.procedure = 'bayes';
-controls.nsimu = 50000;
-controls.repeats = 3;
+controls.procedure = 'dream';
 [bayesProb,bayesResults] = RAT(d2oproblem,controls);
 
 %Use a 30 x 30 grid.
@@ -84,9 +82,7 @@
 
 %%
 if useSaved
-    probArray = load('probArray.mat');
-    probArray = probArray.probArray;
-
+    probArray = load('probArray.mat').probArray;
 else
 
     [problemStruct,problemLimits,priors,controls] = parseClassToStructs(d2oproblem,controls);
@@ -107,15 +103,15 @@
                 problemStruct.fitParams(2) = thisBack;
                 problemStruct.fitParams(3) = thisScale;
                 problemStruct = unpackParams(problemStruct,controls.checks);
-                [problem,results] = reflectivity_calculation(problemStruct,problemLimits,controls);
+                results = reflectivityCalculation(problemStruct,problemLimits,controls);
 
 %                 d2oproblem.setParameter(1,'value',thisRough);
 %                 d2oproblem.setBackgroundParam(1,'value',thisBack);
 %                 d2oproblem.setScalefactor(1,'value',thisScale);
 % 
 %                 [outProblem,results] = RAT(d2oproblem,controls);
 
-                thisChi = problem.calculations.sumChi;
+                thisChi = results.calculationResults.sumChi;
                 probArray(r,b,s) = exp(-thisChi/2);
                 percent = (counter/totalGrid)*100;
                 fprintf('Calculated %1.1f percent \n',percent);

tests/testProjectClass.m

@@ -522,6 +522,13 @@ function testContrast(testCase)
             testCase.verifyEqual(testCase.project.contrasts.contrasts{1}.model, {'Hydrogenated Heads', 'Deuterated Heads'}, 'setContrastModel method not working');
             testCase.project.setContrastModel('Another Bilayer', {'Deuterated Heads', 'Hydrogenated Heads'});
             testCase.verifyEqual(testCase.project.contrasts.contrasts{1}.model, {'Deuterated Heads', 'Hydrogenated Heads'}, 'setContrastModel method not working');
+            testCase.project.addContrast('First Bilayer');
+            testCase.project.setContrastModel(1:2, {'Deuterated Heads'});
+            testCase.verifyEqual(testCase.project.contrasts.contrasts{1}.model, {'Deuterated Heads'}, 'setContrastModel method not working');
+            testCase.verifyEqual(testCase.project.contrasts.contrasts{2}.model, {'Deuterated Heads'}, 'setContrastModel method not working');
+            testCase.project.setContrastModel({'First Bilayer', 'Another Bilayer'}, {'Hydrogenated Heads'});
+            testCase.verifyEqual(testCase.project.contrasts.contrasts{1}.model, {'Hydrogenated Heads'}, 'setContrastModel method not working');
+            testCase.verifyEqual(testCase.project.contrasts.contrasts{2}.model, {'Hydrogenated Heads'}, 'setContrastModel method not working');
             testCase.verifyError(@() testCase.project.setContrastModel(3, {}), exceptions.indexOutOfRange.errorID)
             testCase.verifyError(@() testCase.project.setContrastModel('Bilayer', {}), exceptions.nameNotRecognised.errorID);
         end

tests/testProjectClassToR1.m

@@ -24,7 +24,7 @@ function defineVariables(testCase)
             testCase.inputStandardProjectClass = 'DSPCBilayerProjectClass.mat';
             testCase.inputStandardStruct = 'DSPCBilayerStructInput.mat';
             testCase.outputStandardStruct = 'DSPCBilayerStructOutput.mat';
-            testCase.defaultProject = 'defaultProject.mat';
+            testCase.defaultProject = 'defaultR1ProjectTemplate.mat';
             testCase.outputCustomStruct = 'monolayerVolumeModel.mat';
             testCase.inputCustomProjectClass = 'monolayerVolumeModelProjectClass.mat';
             testCase.modelFile = 'monolayerVolumeCustomLayerModel.m';

utilities/misc/projectClassToR1.m

@@ -4,7 +4,7 @@
 % outputs r1 struct. The optional arguments are:
 %
 % r1Problem (struct):    The r1 struct which is updated with equivalent projectClass values. 
-%                        [default] defaultProject.mat.
+%                        [default] defaultR1ProjectTemplate.mat.
 % dirName (char):        The directory where the files are saved. 
 %                        [default] newDirectory.
 % dirPath (char):        The path where the new directory is created. 
@@ -28,7 +28,7 @@
     r1Problem = pars.r1Problem;
     if isfield(r1Problem,'empty')
         % load default project if r1Problem not provided
-        r1Problem = load('defaultProject.mat').problem;
+        r1Problem = load('defaultR1ProjectTemplate.mat').problem;
     end
 
     if ~exist(fullName,'dir') && saveTheProject

utilities/plotting/bayesShadedPlot.m

@@ -44,6 +44,8 @@ function bayesShadedPlot(problem, result, options)
 subplot(1,2,1)
 set(gca,'YScale','log','XScale','log');
 hold on; box on
+xlabel('$\textrm{Q}_{z} (\AA^{-1})$', 'Interpreter', 'Latex') 
+ylabel('Reflectivity', 'Interpreter', 'Latex')
 
 for i = 1:numberOfContrasts
 
@@ -92,6 +94,8 @@ function bayesShadedPlot(problem, result, options)
 
 % Now plot the SLDs
 subplot(1,2,2); hold on; box on
+xlabel('$\textrm{Z} (\AA)$','Interpreter','Latex') 
+ylabel('$\textrm{SLD} (\AA^{-2})$','Interpreter','Latex') 
 
 if ~isDomains
 

utilities/plotting/plotRefSLDHelper.m

@@ -41,6 +41,8 @@ function plotRefSLDHelper(data, noDelay, linearX, q4, showErrorBar, showGrid, sh
        set(gca,'YGrid','on','XGrid','on');
     end   
     hold on
+    xlabel('$\textrm{Q}_{z} (\AA^{-1})$', 'Interpreter', 'Latex') 
+    ylabel('Reflectivity', 'Interpreter', 'Latex') 
     lines = cell(numberOfContrasts, 1);
     mult = 1;
     q4Data = 1;
@@ -80,6 +82,8 @@ function plotRefSLDHelper(data, noDelay, linearX, q4, showErrorBar, showGrid, sh
          set(gca,'YGrid','on','XGrid','on');
     end
     hold on
+    xlabel('$\textrm{Z} (\AA)$','Interpreter','Latex') 
+    ylabel('$\textrm{SLD} (\AA^{-2})$','Interpreter','Latex') 
     nColumns = size(data.sldProfiles, 2);
     lines = cell(numberOfContrasts * nColumns, 1);
     names = cell(numberOfContrasts * nColumns, 1);