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Added utilities for saving and loading RasCAL2 files.... #431

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e68ef7f
Added a simple 'saveR2' utility
arwelHughes Feb 3, 2026
604cad4
Added loadR2 utility
arwelHughes Feb 3, 2026
a1ff04e
Remove extra files
StephenNneji Feb 13, 2026
7ead514
Fix bug in controls and result json conversion, adds comments
StephenNneji Feb 20, 2026
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42 changes: 24 additions & 18 deletions API/controlsClass.m
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Original file line number Diff line number Diff line change
Expand Up @@ -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},...
Expand Down Expand Up @@ -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);
Expand Down
67 changes: 60 additions & 7 deletions tests/testJsonToProject/testJsonToProject.m
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Expand Up @@ -16,13 +16,22 @@

resultFile = {'result', ...
'result_bayes'}

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;
Expand Down Expand Up @@ -54,13 +63,9 @@ function testJsonResultConversion(testCase, resultFile)
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");
Expand All @@ -69,6 +74,54 @@ 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();
[~, project, result] = evalc('RAT(problem, controls);');
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@abuts abuts Feb 25, 2026

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Suggestion:
I can vageuly understand and accept why one would use evalc in 85, though IMHO function handle would be much better. But in 88! Why?
Why to use:

[~, project, result] =  evalc('RAT(problem, controls);');

instead of just:

 [project, result] =  RAT(problem, controls);

It works faster and much more clear code.


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);
props = properties(project);
for i = 1:length(props)
% verifies the problem name, model type and geometry
Comment on lines +101 to +102
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@abuts abuts Feb 25, 2026 •
edited
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Request if I understand it correctly:
I am puzzled. Why this loop? Nothing inside it depends on i or props -- you just run the same check 16 times. Should loop be removed?

All prop check is correctly perfromed at rows 120-124.

Test between for and end partially repeats 120-124 but ok, this way of testing may be more beneficial or clear, but why to run it in a loop?

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);
end

props = properties(result);
for i = 1:length(props)
testCase.verifyEqual(result.(props{i}), result2.(props{i}));
end
close all
end
end

Expand Down
2 changes: 1 addition & 1 deletion utilities/misc/controlsToJson.m
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Expand Up @@ -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'));
Expand Down
65 changes: 38 additions & 27 deletions utilities/misc/jsonToResults.m
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Expand Up @@ -53,37 +53,48 @@

% 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);
col = size(inArray(1),1);
outCell = cell(row, col);
for i=1:row
for j=1:col
outCell{i, j} = squeeze(inArray{i}{j});
end
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});
row = size(inArray, 1);
col = size(inArray(1),1);
outCell = cell(row, col);
for i=1:row
for j=1:col
outCell{i, j} = squeeze(inArray(i, j, :, :));
end
end
end
%
% % 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

Expand Down
40 changes: 40 additions & 0 deletions utilities/misc/loadR2.m
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@@ -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
53 changes: 52 additions & 1 deletion utilities/misc/resultsToJson.m
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Expand Up @@ -2,13 +2,64 @@
function resultsToJson(results,filename)

% Encodes the results into a json file...
tmpResults = struct();
for fn = fieldnames(results)'
tmpResults.(fn{1}) = results.(fn{1});
end

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);

encoded = jsonencode(tmpResults,ConvertInfAndNaN=false);
encoded = strrep(encoded, '"[', '[');
encoded = strrep(encoded, ']"', ']');

encoded = jsonencode(results,ConvertInfAndNaN=false);

[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 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
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