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arwelHughesarwelHughes
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Json convert (#406)
1 parent 8a4c1a3 commit e6640d3

9 files changed

Lines changed: 554 additions & 4 deletions

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‎tests/testJsonToProject/result.json‎

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‎tests/testJsonToProject/result_bayes.json‎

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‎tests/testJsonToProject/testJsonToProject.m‎

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

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

‎utilities/misc/jsonToControls.m‎

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

‎utilities/misc/jsonToProject.m‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
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for i=1:length(json_struct.parameters)
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p = json_struct.parameters(i);
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if p.name == "Substrate Roughness"
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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);
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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);
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else
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project.addParameter(p.name, p.min, p.value, p.max, p.fit, p.prior_type, p.mu, p.sigma);
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end
@@ -103,7 +103,8 @@
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end
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105105

106-
if json_struct.model == "domains"
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if json_struct.calculation == "domains"
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project.removeDomainRatio(1);
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for i=1:length(json_struct.domain_ratios)
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p = json_struct.domain_ratios(i);
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project.addDomainRatio(p.name, p.min, p.value, p.max, p.fit, p.prior_type, p.mu, p.sigma);
@@ -119,6 +120,7 @@
119120
'scalefactor', p.scalefactor, ...
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'resample', p.resample, ...
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'domainRatio', p.domain_ratio, ...
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'resolution',p.resolution, ...
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'model', p.model);
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end
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else
@@ -132,6 +134,7 @@
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'bulkOut', p.bulk_out, ...
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'scalefactor', p.scalefactor, ...
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'resample', p.resample, ...
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'resolution',p.resolution, ...
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'model', p.model);
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end
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end

‎utilities/misc/jsonToResults.m‎

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function results = jsonToResults(filename)
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% Loads in the results from a json results file, and converts it so the
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% format required for matlabRAT. The conversion mainly means converting
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% flattened array back to cells..
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% Load in the json array
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[path,filename,~] = fileparts(filename);
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file = fullfile(path, append(filename, '.json'));
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jsonRes = jsondecode(fileread(file));
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% Go through converting all arrays to cells (where the arrays have been
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% squeezed). If they are already cells, the subfunctions will just keep the
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% original..
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results.reflectivity = simArray2Cells(jsonRes.reflectivity);
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results.simulation = simArray2Cells(jsonRes.simulation);
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results.shiftedData = dataArray2Cells(jsonRes.shiftedData);
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results.backgrounds = simArray2Cells(jsonRes.backgrounds);
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results.resolutions = simArray2Cells(jsonRes.resolutions);
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results.sldProfiles = sldArray2Cells(jsonRes.sldProfiles,numel(results.reflectivity));
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results.layers = sldArray2Cells(jsonRes.layers,numel(results.reflectivity)); % Layers array is in the same format as the SLDs
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results.resampledLayers = sldArray2Cells(jsonRes.resampledLayers,numel(results.reflectivity));
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% These correctly load in as structs or arrays....
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results.calculationResults = jsonRes.calculationResults;
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results.contrastParams = jsonRes.contrastParams;
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results.fitParams = jsonRes.fitParams';
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results.fitNames = jsonRes.fitNames;
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% contrastParams.resample has the wrong shape...
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results.contrastParams.resample = results.contrastParams.resample';
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% If we have Bayes results, we have extra work to do....
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if isfield(jsonRes,'predictionIntervals')
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results.predictionIntervals = jsonRes.predictionIntervals;
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results.predictionIntervals.reflectivity = simArray2Cells(results.predictionIntervals.reflectivity);
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results.predictionIntervals.sld = simArray2Cells(results.predictionIntervals.sld);
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40+
results.confidenceIntervals = jsonRes.confidenceIntervals;
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results.dreamParams = jsonRes.dreamParams;
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results.dreamOutput = jsonRes.dreamOutput;
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results.nestedSamplerOutput = jsonRes.nestedSamplerOutput;
44+
results.chain = jsonRes.chain;
45+
end
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end
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50+
% ----------------------------------------------------------
51+
52+
function outCell = sldArray2Cells(inArray,nContrasts)
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54+
% Check we don't already have cells..
55+
if iscell(inArray)
56+
nArrays = numel(inArray);
57+
if nArrays == nContrasts % (not domains)
58+
outCell = inArray;
59+
else % ..domains - [n x 2] cell array
60+
outCell = reshape(inArray,nContrasts,2);
61+
end
62+
else
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64+
% Get number of profiles...
65+
nProfiles = size(inArray,1);
66+
67+
% Make them into cells....
68+
for i = 1:nProfiles
69+
thisSLD = inArray(i,:,:,:);
70+
thisSLD = squeeze(thisSLD); % Collapse singleton dims....
71+
outCell{i,1} = thisSLD;
72+
end
73+
74+
% If domains, reorganise the cells...
75+
if nProfiles > nContrasts
76+
outCell = transpose(reshape(outCell,nContrasts,2));
77+
end
78+
end
79+
80+
% We have an annoying automatic reshape of single layers into columns.
81+
% Fix this...
82+
for i = 1:numel(outCell)
83+
if iscolumn(outCell{i})
84+
outCell{i} = transpose(outCell{i});
85+
end
86+
end
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88+
end
89+
90+
% --------------------------------------------------------------
91+
92+
function outCell = dataArray2Cells(inArray)
93+
94+
% Check we don't already have cells..
95+
if iscell(inArray)
96+
outCell = reshape(inArray,numel(inArray),1);
97+
else
98+
99+
% Get number of profiles...
100+
nProfiles = size(inArray,1);
101+
102+
for i = 1:nProfiles
103+
thisDat = inArray(i,:,:,:);
104+
thisDat = squeeze(thisDat); % Collapse singleton dims....
105+
outCell{i,1} = thisDat;
106+
end
107+
end
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109+
end
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% --------------------------------------------------------------
112+
113+
function outCell = simArray2Cells(inArray)
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115+
% Check we don't already have cells..
116+
if iscell(inArray)
117+
outCell = inArray;
118+
else
119+
% Get 3rd dimension of array...
120+
dims = size(inArray,1);
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122+
for i = 1:dims
123+
thisArray = inArray(i,:,:);
124+
outCell{i,1} = squeeze(thisArray);
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end
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end
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end
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% ----------------------------------------------------------

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