Added utilities for saving and loading RasCAL2 files....

API/controlsClass.m

@@ -440,11 +440,8 @@
             fwrite(fileID, true, 'uchar');
             fclose(fileID);
         end
-    end
-
-    %------------------------- Display Methods --------------------------
-    methods (Access = protected)
-        function groups = getPropertyGroups(obj)
+
+        function dispPropList = getAvailableFields(obj)
             masterPropList = struct('parallel', {obj.parallel},...
                 'procedure', {obj.procedure},...
                 'display', {obj.display},...
@@ -499,20 +496,29 @@
                 'boundHandling',...
                 'adaptPCR'};
 
+
+            dispPropList = masterPropList;
+            if strcmpi(obj.procedure, 'calculate')
+                dispPropList = rmfield(masterPropList, [deCell, simplexCell, nsCell, dreamCell, {'updatePlotFreq','updateFreq'}]);
+            elseif strcmpi(obj.procedure, 'simplex')
+                dispPropList = rmfield(masterPropList, [deCell, nsCell, dreamCell]);
+            elseif strcmpi(obj.procedure, 'de')
+                dispPropList = rmfield(masterPropList, [simplexCell, nsCell, dreamCell]);
+                % Add the update back...
+            elseif strcmpi(obj.procedure, 'ns')
+                dispPropList = rmfield(masterPropList, [simplexCell, deCell, dreamCell, {'updatePlotFreq','updateFreq'}]);
+            elseif strcmpi(obj.procedure, 'dream')
+                dispPropList = rmfield(masterPropList, [simplexCell, deCell, nsCell, {'updatePlotFreq','updateFreq'}]);
+            end
+        end
+    end
+
+    %------------------------- Display Methods --------------------------
+    methods (Access = protected)
+        function groups = getPropertyGroups(obj)
+
             if isscalar(obj)
-                dispPropList = masterPropList;
-                if strcmpi(obj.procedure, 'calculate')
-                    dispPropList = rmfield(masterPropList, [deCell, simplexCell, nsCell, dreamCell, {'updatePlotFreq','updateFreq'}]);
-                elseif strcmpi(obj.procedure, 'simplex')
-                    dispPropList = rmfield(masterPropList, [deCell, nsCell, dreamCell]);
-                elseif strcmpi(obj.procedure, 'de')
-                    dispPropList = rmfield(masterPropList, [simplexCell, nsCell, dreamCell]);
-                    % Add the update back...
-                elseif strcmpi(obj.procedure, 'ns')
-                    dispPropList = rmfield(masterPropList, [simplexCell, deCell, dreamCell, {'updatePlotFreq','updateFreq'}]);
-                elseif strcmpi(obj.procedure, 'dream')
-                    dispPropList = rmfield(masterPropList, [simplexCell, deCell, nsCell, {'updatePlotFreq','updateFreq'}]);
-                end
+                dispPropList = obj.getAvailableFields();
                 groups = matlab.mixin.util.PropertyGroup(dispPropList);
             else
                 groups = getPropertyGroups@matlab.mixin.CustomDisplay(obj);

tests/testJsonToProject/testJsonToProject.m

@@ -15,14 +15,24 @@
             'DSPC_standard_layers'}
 
         resultFile = {'result', ...
-            'result_bayes'}
+                      'result_bayes_dream', ...
+                      'result_bayes_ns'}
+
+        controlsParams = {{'calculate', 'numSimulationPoints', 100},...
+                          {'simplex' 'xTolerance', 19},...
+                          {'de' 'populationSize', 200},...
+                          {'ns' 'nLive', 19},...
+                          {'dream' 'nSamples', 200}}
+        r2Tests = {{'normalReflectivity', 'standardLayers', 'standardLayersDSPCScript'},...
+                   {'domains', 'customLayers', 'domainsCustomLayersScript'},...
+                   {'domains', 'customXY', 'domainsCustomXYScript'}}
     end
 
     methods(TestClassSetup)
         function addDataPath(testCase)
             import matlab.unittest.fixtures.PathFixture
             path = fullfile(getappdata(0, 'root'), 'tests', 'testJsonToProject');
-            testCase.applyFixture(PathFixture(path))  
+            testCase.applyFixture(PathFixture(path));
         end
         function setWorkingFolder(testCase)
             import matlab.unittest.fixtures.WorkingFolderFixture;
@@ -48,19 +58,15 @@ function testJsonResultConversion(testCase, resultFile)
             resultsToJson(result, "test.json");
             result2 = jsonToResults("test.json");
 
-            props = properties(result);
+            props = fieldnames(result);
             for i = 1:length(props)
                 testCase.verifyEqual(result.(props{i}), result2.(props{i}));
             end
        end
 
-       function testJsonControlsConversion(testCase)
+       function testJsonControlsConversion(testCase, controlsParams)
             controls = controlsClass();
-            controls.numSimulationPoints = 100;
-            controls.xTolerance = 19;
-            controls.populationSize = 200;
-            controls.nLive = 140;
-            controls.nSamples = 200;
+            controls.setProcedure(controlsParams{1}, controlsParams{2:end});
 
             controlsToJson(controls, "test.json");
             controls2 = jsonToControls("test.json");
@@ -69,6 +75,52 @@ function testJsonControlsConversion(testCase)
             for i = 1:length(props)
                 testCase.verifyEqual(controls.(props{i}), controls2.(props{i}));
             end
+       end
+
+       function testR2Conversion(testCase, r2Tests)
+            scriptName = r2Tests{3};
+            outFolder = ['save_' scriptName];
+
+            copyfile(fullfile(getappdata(0, 'root'), 'examples', r2Tests{1}, r2Tests{2}), ...
+                     fullfile(pwd))
+            evalc(scriptName);
+
+            controls = controlsClass();
+            controls.display = 'off';
+            [project, result] =  RAT(problem, controls);
+
+            saveR2(outFolder,  project, result, controls)
+            testCase.verifyEqual(exist(fullfile(pwd, outFolder, 'results.json'), 'file'), 2)
+            testCase.verifyEqual(exist(fullfile(pwd, outFolder, 'project.json'), 'file'), 2)
+            testCase.verifyEqual(exist(fullfile(pwd, outFolder, 'controls.json'), 'file'), 2)
+            for i=1:project.customFile.rowCount
+                customFile = project.customFile.varTable{i, 2};
+                testCase.verifyEqual(exist(fullfile(pwd, outFolder, customFile), 'file'), 2)
+            end
+
+            [project2, result2] = loadR2(outFolder);
+            % verifies the problem name, model type and geometry
+            testCase.verifyEqual(project.experimentName, project2.experimentName);
+            testCase.verifyEqual(project.modelType, project2.modelType);
+            testCase.verifyEqual(project.geometry, project2.geometry);
+
+            % verifies the count of problem properties
+            testCase.verifyEqual(project.contrasts.numberOfContrasts, project2.contrasts.numberOfContrasts);
+            testCase.verifyEqual(project.parameters.rowCount, project2.parameters.rowCount);
+            testCase.verifyEqual(project.bulkOut.rowCount, project2.bulkOut.rowCount);
+            testCase.verifyEqual(project.background.backgrounds.rowCount, project2.background.backgrounds.rowCount);
+            testCase.verifyEqual(project.data.rowCount, project2.data.rowCount);
+            testCase.verifyEqual(project.scalefactors.rowCount, project2.scalefactors.rowCount);
+            if isa(project.layers, 'layersClass')
+                testCase.verifyEqual(project.layers.rowCount, project2.layers.rowCount);
+            end
+            testCase.verifyEqual(project.bulkIn.rowCount, project2.bulkIn.rowCount);
+
+            props = fieldnames(result);
+            for i = 1:length(props)
+                testCase.verifyEqual(result.(props{i}), result2.(props{i}));
+            end
+            close all
         end
     end
 

utilities/misc/controlsToJson.m

@@ -2,7 +2,7 @@
 function controlsToJson(controls,filename)
 
 % Saves the current controls block as a json..
-encoded = jsonencode(controls,ConvertInfAndNaN=false);
+encoded = jsonencode(controls.getAvailableFields(),ConvertInfAndNaN=false);
 
 [path,filename,~] = fileparts(filename);
 fid = fullfile(path, append(filename, '.json'));

utilities/misc/jsonToResults.m

@@ -18,9 +18,9 @@
 results.shiftedData = dataArray2Cells(jsonRes.shiftedData);
 results.backgrounds = simArray2Cells(jsonRes.backgrounds);
 results.resolutions = simArray2Cells(jsonRes.resolutions);
-results.sldProfiles = sldArray2Cells(jsonRes.sldProfiles,numel(results.reflectivity));
-results.layers = sldArray2Cells(jsonRes.layers,numel(results.reflectivity));    % Layers array is in the same format as the SLDs
-results.resampledLayers = sldArray2Cells(jsonRes.resampledLayers,numel(results.reflectivity));
+results.sldProfiles = sldArray2Cells(jsonRes.sldProfiles);
+results.layers = sldArray2Cells(jsonRes.layers);    % Layers array is in the same format as the SLDs
+results.resampledLayers = sldArray2Cells(jsonRes.resampledLayers);
 
 % These correctly load in as structs or arrays....
 results.calculationResults = jsonRes.calculationResults;
@@ -35,7 +35,7 @@
 if isfield(jsonRes,'predictionIntervals')
     results.predictionIntervals = jsonRes.predictionIntervals;
     results.predictionIntervals.reflectivity = simArray2Cells(results.predictionIntervals.reflectivity);
-    results.predictionIntervals.sld = simArray2Cells(results.predictionIntervals.sld);
+    results.predictionIntervals.sld = sldArray2Cells(results.predictionIntervals.sld);
 
     results.confidenceIntervals = jsonRes.confidenceIntervals;
     results.dreamParams = jsonRes.dreamParams;
@@ -49,42 +49,33 @@
 
 % ----------------------------------------------------------
 
-function outCell = sldArray2Cells(inArray,nContrasts)
+function outCell = sldArray2Cells(inArray)
 
 % Check we don't already have cells..
 if iscell(inArray)
-    nArrays = numel(inArray);
-    if nArrays == nContrasts % (not domains)
-        outCell = inArray;
-    else  % ..domains - [n x 2] cell array
-        outCell = reshape(inArray,nContrasts,2);
+    row = size(inArray, 1); 
+    if iscell(inArray{1})
+        col = size(inArray{1}, 1);
+    else
+        col = size(inArray(1),1);
     end
-else
-
-    % Get number of profiles...
-    nProfiles = size(inArray,1);
-
-    % Make them into cells....
-    for i = 1:nProfiles
-        thisSLD = inArray(i,:,:,:);
-        thisSLD = squeeze(thisSLD); % Collapse singleton dims....
-        outCell{i,1} = thisSLD;
+    outCell = cell(row, col);
+    for i=1:row
+        for j=1:col
+            outCell{i, j} = squeeze(inArray{i}{j});
+        end
     end
-
-    % If domains, reorganise the cells...
-    if nProfiles > nContrasts
-        outCell = transpose(reshape(outCell,nContrasts,2));
-    end
-end
-
-% We have an annoying automatic reshape of single layers into columns.
-% Fix this...
-for i = 1:numel(outCell)
-    if iscolumn(outCell{i})
-        outCell{i} = transpose(outCell{i});
+else
+    dims = size(inArray);
+    row = dims(1);
+    col = dims(2);
+    outCell = cell(row, col);
+    for i=1:row
+        for j=1:col
+            outCell{i, j} = reshape(inArray(i, j, :, :), dims(3:end));
+        end
     end
 end
-
 end
 
 % --------------------------------------------------------------

utilities/misc/loadR2.m

@@ -0,0 +1,40 @@
+
+function [problem,varargout] = loadR2(dirName)
+    % Loads in a RasCAL2 project.
+    %
+    % Examples
+    % --------
+    % >>> project = loadR2("r2_example");  % Load project from a given directory
+    % >>> [project, results] = loadR2("r2_example");  % Load project and result
+    %
+    % Parameters
+    % ----------
+    % dirName : string or char array
+    %    The path of the R2 project folder.
+    %
+    % Returns
+    % -------
+    % project : projectClass
+    %    An instance of the ``projectClass`` which should be equivalent to the given R2 problem.
+    % results : struct
+    %    An optional output. A struct which contains the R2 results if present.
+
+    arguments
+        dirName {mustBeTextScalar, mustBeNonempty}
+    end
+    % Load the project.
+    projectFile = fullfile(dirName,'project.json');
+    problem = jsonToProject(projectFile);
+
+    % If there is a second output, also load results.
+    if nargout > 1
+        resultsFile = fullfile(dirName, 'results.json');
+        if exist(resultsFile, 'file') == 2
+            varargout{1} = jsonToResults(resultsFile);
+        else
+            varargout{1} = struct();
+            warning("result.json was not found in the project.");
+        end
+    end
+
+end

utilities/misc/resultsToJson.m

@@ -2,13 +2,84 @@
 function resultsToJson(results,filename)
 
 % Encodes the results into a json file...
+tmpResults = struct();
+for fn = fieldnames(results)'
+   tmpResults.(fn{1}) = results.(fn{1});
+end
 
-encoded = jsonencode(results,ConvertInfAndNaN=false);
+tmpResults.reflectivity = correctCellArray(tmpResults.reflectivity);
+tmpResults.simulation = correctCellArray(tmpResults.simulation);
+tmpResults.shiftedData = correctCellArray(tmpResults.shiftedData);
+tmpResults.backgrounds = correctCellArray(tmpResults.backgrounds);
+tmpResults.resolutions = correctCellArray(tmpResults.resolutions );
+tmpResults.sldProfiles = makeCellJson(tmpResults.sldProfiles);
+tmpResults.layers = makeCellJson(tmpResults.layers);
+tmpResults.resampledLayers = makeCellJson(tmpResults.resampledLayers);
+
+for prop = {'dreamOutput', 'nestedSamplerOutput', 'confidenceIntervals'}
+    if isfield(tmpResults, prop{1})
+        for fn = fieldnames(tmpResults.(prop{1}))'
+            tmpResults.(prop{1}).(fn{1}) = correctRowArray(tmpResults.(prop{1}).(fn{1}));
+        end
+    end
+end
+
+if isfield(tmpResults,'predictionIntervals')
+    tmpResults.predictionIntervals.reflectivity = correctCellArray(tmpResults.predictionIntervals.reflectivity);
+    tmpResults.predictionIntervals.sld = makeCellJson(tmpResults.predictionIntervals.sld);
+    tmpResults.predictionIntervals.sampleChi = correctRowArray(tmpResults.predictionIntervals.sampleChi);
+end
+
+encoded = jsonencode(tmpResults,ConvertInfAndNaN=false);
+encoded = strrep(encoded, ']"', ']');
+encoded = strrep(encoded, '"[', '[');
 
 [path,filename,~] = fileparts(filename);
 fid = fullfile(path, append(filename, '.json'));
 fid = fopen(fid,'w');
 fprintf(fid,'%s',encoded);
 fclose(fid);
 
+end
+
+function outputArray = makeCellJson(cellArray)
+    % The jsonencode function flattens 2d cell arrays this is a workaround to
+    % avoid flattening by converting to a string array with is not flattened. 
+    [row, col] = size(cellArray, [1, 2]);
+    outputArray = strings([row, col]);
+    for i=1:row
+        for j=1:col
+            entry = cellArray{i, j};
+            if size(entry, 1) == 1
+                entry = {entry};
+            end
+            if col == 1
+                entry = {entry};
+            end
+            outputArray(i, j) = jsonencode(entry);
+        end
+    end
+    if row == 1
+        outputArray = {outputArray};
+    end
+
+end
+
+function array = correctRowArray(array)
+    % Corrects row array so its written as 2D array in json 
+    if isa(array, "double") && size(array, 1) == 1 && size(array, 2) > 1
+        array = {array};
+    end
+end
+
+function cellArray = correctCellArray(cellArray)
+    % Corrects array with single row so its written as 2D array in json 
+    [row, col] = size(cellArray, [1, 2]);
+    for i=1:row
+        for j=1:col
+            if size(cellArray{i, j}, 1) == 1
+               cellArray{i, j} = {cellArray{i, j}};
+            end
+        end
+    end
 end