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Merged
StephenNneji merged 2 commits into from
Jan 7, 2025
Merged

Adds script to generate tutorial example data #302

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0c9992d
Adds script to generate tutorial example data
StephenNneji Jan 2, 2025
dc6fed8
Addresses review comments
StephenNneji Jan 7, 2025
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82 changes: 82 additions & 0 deletions examples/tutorialFiles/twoContrastExample.m
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% Full Example
problem = projectClass('DSPC monolayers');% Define the parameters:
Parameters = {
% Name min val max fit?
{'Tails Thickness', 10, 20, 30, true};
{'Heads Thickness', 3, 11, 16, true};
{'Tails Roughness', 2, 5, 9, true};
{'Heads Roughness', 2, 5, 9, true};
{'Deuterated Tails SLD', 4e-6, 6e-6, 2e-5, true};
{'Hydrogenated Tails SLD', -0.6e-6, -0.4e-6, 0, true};
{'Deuterated Heads SLD', 1e-6, 3e-6, 8e-6, true};
{'Hydrogenated Heads SLD', 0.1e-6, 1.4e-6, 3e-6, true};
{'Heads Hydration', 0, 0.3, 0.5, true};
};

problem.addParameterGroup(Parameters);
H_Heads = {'Hydrogenated Heads',...
'Heads Thickness',...
'Hydrogenated Heads SLD',...
'Heads Roughness',...
'Heads Hydration',...
'bulk out' };

D_Heads = {'Deuterated Heads',...
'Heads Thickness',...
'Deuterated Heads SLD',...
'Heads Roughness',...
'Heads Hydration',...
'bulk out' };

D_Tails = {'Deuterated Tails',...
'Tails Thickness',...
'Deuterated Tails SLD',...
'Tails Roughness'};

H_Tails = {'Hydrogenated Tails',...
'Tails Thickness',...
'Hydrogenated Tails SLD',...
'Tails Roughness'};

problem.addLayerGroup({H_Heads; D_Heads; H_Tails; D_Tails});
problem.setBackgroundParamName(1, 'Backs Value ACMW'); % Use existing backsPar
problem.setBackgroundParamValue(1, 5.5e-6);
problem.addBackgroundParam('Backs Value D2O', 1e-8, 2.8e-6, 1e-5);
problem.addBackground('Background D2O', 'constant', 'Backs Value D2O');
problem.setBackground(1, 'name', 'Background ACMW', 'source', 'Backs Value ACMW');
problem.addBulkOut('SLD ACMW', -1e-6, 0.0, 1e-6, true);

root = getappdata(0, 'root');
dataPath = '/examples/miscellaneous/convertRascal1Project/';
d13ACM = readmatrix(fullfile(root, dataPath, 'd13acmw20.dat'));
d70d2O = readmatrix(fullfile(root, dataPath, 'd70d2o20.dat'));
problem.addData('H-tail / D-head / ACMW', d13ACM);
problem.addData('D-tail / H-head / D2O', d70d2O);

problem.addContrast('name', 'D-tail/H-Head/D2O',...
'background', 'Background D2O',...
'resolution', 'Resolution 1',...
'scalefactor', 'Scalefactor 1',...
'BulkOut', 'SLD D2O',...
'BulkIn', 'SLD Air',...
'data', 'D-tail / H-head / D2O');

problem.addContrast('name', 'H-tail/D-Head/ACMW',...
'background', 'Background ACMW',...
'resolution', 'Resolution 1',...
'scalefactor', 'Scalefactor 1',...
'BulkOut', 'SLD ACMW',...
'BulkIn', 'SLD Air',...
'data', 'H-tail / D-head / ACMW');
problem.setContrastModel(1, {'Deuterated Tails','Hydrogenated Heads'});
problem.setContrastModel(2, {'Hydrogenated Tails','Deuterated Heads'});

problem.setBackgroundParam(1,'fit', true);
problem.setBackgroundParam(2,'fit', true);
problem.setScalefactor(1,'fit', true);
problem.setBulkOut(1,'fit', true);

%% Save problem
[path, ~, ~] = fileparts(mfilename("fullpath"));
save([path filesep 'twoContrastExample.mat'], 'problem');

Binary file modified examples/tutorialFiles/twoContrastExample.mat
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17 changes: 15 additions & 2 deletions tests/testExamples.m
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Expand Up @@ -16,9 +16,11 @@
['miscellaneous' filesep 'backgroundTypes'],...
['miscellaneous' filesep 'bayesBenchmark'],...
['miscellaneous' filesep 'roundRobin'],...
['miscellaneous' filesep 'convertRascal1Project']};
['miscellaneous' filesep 'convertRascal1Project'],...
'tutorialFiles'};
exampleLiveScriptFile = {'domainsStandardLayersSheet', 'domainsCustomLayersSheet',...
'domainsCustomXYSheet', 'bayesBenchmark', 'convertRascal'}
'domainsCustomXYSheet', 'bayesBenchmark', 'convertRascal'};
tutorialFiles = {'twoContrastExample'};
% exampleLiveScriptFile = {'domainsStandardLayersSheet', 'domainsCustomLayerSheet', 'domainsCustomXYSheet',...
% 'customLayersDSPCSheet', 'standardLayersDSPCSheet', 'customXYDSPCSheet',...
% 'roundRobin', 'bayesBenchmark', 'convertRascal'}
Expand Down Expand Up @@ -140,6 +142,17 @@ function testLiveScriptExamples(testCase, exampleLiveScriptFile)
close all;
end

function testTutorialFiles(testCase, tutorialFiles)
% runs the example live script file
testExamples.setupCurrentDir(testCase, tutorialFiles)
problem1 = load('twoContrastExample.mat');
problem1 = problem1.problem;
evalc(tutorialFiles);
problem2 = load('twoContrastExample.mat');
problem2 = problem2.problem;
testCase.verifyEqual(problem1, problem2, 'twoContrastExample.mat is not correctly updated. Update the mat file by manually running twoContrastExample.m');
end
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@DrPaulSharp DrPaulSharp Jan 7, 2025

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What happens if this test fails after the evalc, and is then re-run. Presumerably, the problem saved to twoContrastExample.mat is incorrect and the test will always fail?

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@StephenNneji StephenNneji Jan 7, 2025

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The original 'twoContrastExample.mat' is never changed as the test is run in a temp directory


function testWriteScript(testCase, exampleScriptFile)
% Test that a the example projectClass objects can be written
% to a script that can regenerate the object
Expand Down