Json convert

tests/testJsonToProject/testJsonToProject.m

@@ -13,6 +13,9 @@
             'DSPC_custom_layers', ...
             'DSPC_custom_XY', ...
             'DSPC_standard_layers'}
+
+        resultFile = {'result', ...
+            'result_bayes'}
     end
 
     methods(TestClassSetup)
@@ -28,9 +31,44 @@ function setWorkingFolder(testCase)
     end
 
     % test that JSON to Project successfully converts projects
-    methods (Test, ParameterCombination='exhaustive')
+    methods (Test)
         function testJsonConversion(testCase, file)
-            jsonToProject(append(file, ".json"));
+            project = jsonToProject(append(file, ".json"));
+            projectToJson(project, "test.json");
+            project2 = jsonToProject("test.json");
+
+            props = properties(project);
+            for i = 1:length(props)
+                testCase.verifyEqual(project.(props{i}), project2.(props{i}));
+            end
+        end
+
+       function testJsonResultConversion(testCase, resultFile)
+            result = jsonToResults(append(resultFile, ".json"));
+            resultsToJson(result, "test.json");
+            result2 = jsonToResults("test.json");
+
+            props = properties(result);
+            for i = 1:length(props)
+                testCase.verifyEqual(result.(props{i}), result2.(props{i}));
+            end
+       end
+
+       function testJsonControlsConversion(testCase)
+            controls = controlsClass();
+            controls.numSimulationPoints = 100;
+            controls.xTolerance = 19;
+            controls.populationSize = 200;
+            controls.nLive = 140;
+            controls.nSamples = 200;
+
+            controlsToJson(controls, "test.json");
+            controls2 = jsonToControls("test.json");
+
+            props = properties(controls);
+            for i = 1:length(props)
+                testCase.verifyEqual(controls.(props{i}), controls2.(props{i}));
+            end
         end
     end
 

utilities/misc/controlsToJson.m

@@ -0,0 +1,14 @@
+
+function controlsToJson(controls,filename)
+
+% Saves the current controls block as a json..
+encoded = jsonencode(controls,ConvertInfAndNaN=false);
+encoded = replace(encoded,'Infinity','Inf');
+
+[path,filename,~] = fileparts(filename);
+fid = fullfile(path, append(filename, '.json'));
+fid = fopen(fid,'w');
+fprintf(fid,'%s',encoded);
+fclose(fid);
+
+end

utilities/misc/jsonToControls.m

@@ -0,0 +1,17 @@
+
+function controls = jsonToControls(filename)
+
+% Loads in a controls json, and contructs the controlsClass from it...
+
+% Load the file...
+jsonControls = jsondecode(fileread(filename));
+
+% Make a controlsClass()
+controls = controlsClass();
+
+fieldNames = fieldnames(jsonControls);
+for i = 1:length(fieldNames)
+    controls.(fieldNames{i}) = jsonControls.(fieldNames{i});
+end
+
+end

utilities/misc/jsonToProject.m

@@ -23,7 +23,7 @@
 for i=1:length(json_struct.parameters)
     p = json_struct.parameters(i);
     if p.name == "Substrate Roughness"
-        project.setParameter(i, 'min', p.min, 'value', p.value, 'max', p.max, 'fit', p.fit, 'prior', p.prior_type, 'mu', p.mu, 'sigma', p.sigma);
+        project.setParameter(1, 'min', p.min, 'value', p.value, 'max', p.max, 'fit', p.fit, 'prior', p.prior_type, 'mu', p.mu, 'sigma', p.sigma);
     else
         project.addParameter(p.name, p.min, p.value, p.max, p.fit, p.prior_type, p.mu, p.sigma);
     end
@@ -103,7 +103,8 @@
 end
 
 
-if json_struct.model == "domains"
+if json_struct.calculation == "domains"
+    project.removeDomainRatio(1);
     for i=1:length(json_struct.domain_ratios)
         p = json_struct.domain_ratios(i);
         project.addDomainRatio(p.name, p.min, p.value, p.max, p.fit, p.prior_type, p.mu, p.sigma);
@@ -119,6 +120,7 @@
         'scalefactor', p.scalefactor, ...
         'resample', p.resample, ...
         'domainRatio', p.domain_ratio, ...
+        'resolution',p.resolution, ...
         'model', p.model);
     end
 else
@@ -132,6 +134,7 @@
         'bulkOut', p.bulk_out, ...
         'scalefactor', p.scalefactor, ...
         'resample', p.resample, ...
+        'resolution',p.resolution, ...
         'model', p.model);
     end
 end

utilities/misc/jsonToResults.m

@@ -0,0 +1,130 @@
+
+function results = jsonToResults(filename)
+
+% Loads in the results from a json results file, and converts it so the
+% format required for matlabRAT. The conversion mainly means converting
+% flattened array back to cells..
+
+% Load in the json array
+[path,filename,~] = fileparts(filename);
+file = fullfile(path, append(filename, '.json'));
+jsonRes = jsondecode(fileread(file));
+
+% Go through converting all arrays to cells (where the arrays have been
+% squeezed). If they are already cells, the subfunctions will just keep the
+% original..
+results.reflectivity = simArray2Cells(jsonRes.reflectivity);
+results.simulation = simArray2Cells(jsonRes.simulation);
+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));
+
+% These correctly load in as structs or arrays....
+results.calculationResults = jsonRes.calculationResults;
+results.contrastParams = jsonRes.contrastParams;
+results.fitParams = jsonRes.fitParams';
+results.fitNames = jsonRes.fitNames;
+
+% contrastParams.resample has the wrong shape...
+results.contrastParams.resample = results.contrastParams.resample';
+
+% If we have Bayes results, we have extra work to do....
+if isfield(jsonRes,'predictionIntervals')
+    results.predictionIntervals = jsonRes.predictionIntervals;
+    results.predictionIntervals.reflectivity = simArray2Cells(results.predictionIntervals.reflectivity);
+    results.predictionIntervals.sld = simArray2Cells(results.predictionIntervals.sld);
+
+    results.confidenceIntervals = jsonRes.confidenceIntervals;
+    results.dreamParams = jsonRes.dreamParams;
+    results.dreamOutput = jsonRes.dreamOutput;
+    results.nestedSamplerOutput = jsonRes.nestedSamplerOutput;
+    results.chain = jsonRes.chain;
+end
+
+end
+
+
+% ----------------------------------------------------------
+
+function outCell = sldArray2Cells(inArray,nContrasts)
+
+% 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);
+    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;
+    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});
+    end
+end
+
+end
+
+% --------------------------------------------------------------
+
+function outCell = dataArray2Cells(inArray)
+
+% Check we don't already have cells..
+if iscell(inArray)
+    outCell = reshape(inArray,numel(inArray),1);
+else
+
+    % Get number of profiles...
+    nProfiles = size(inArray,1);
+
+    for i = 1:nProfiles
+        thisDat = inArray(i,:,:,:);
+        thisDat = squeeze(thisDat); % Collapse singleton dims....
+        outCell{i,1} = thisDat;
+    end
+end
+
+end
+
+% --------------------------------------------------------------
+
+function outCell = simArray2Cells(inArray)
+
+% Check we don't already have cells..
+if iscell(inArray)
+    outCell = inArray;
+else
+    % Get 3rd dimension of array...
+    dims = size(inArray,1);
+
+    for i = 1:dims
+        thisArray = inArray(i,:,:);
+        outCell{i,1} = squeeze(thisArray);
+    end
+end
+
+end
+
+% ----------------------------------------------------------