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DrPaulSharp merged 2 commits into from
Jul 23, 2025
Merged

Refactors "extractProblemParams" #404

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c50e56f
Refactors "extractProblemParams"
DrPaulSharp Jul 22, 2025
1211502
Corrects test file "shiftDataInputs.mat"
DrPaulSharp Jul 22, 2025
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23 changes: 17 additions & 6 deletions targetFunctions/+domainsTF/domainsReflectivity.m
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,28 @@
% Extract parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices,...
contrastResolutionIndices, backgroundParamValues, resolutionParamValues,...
qzshifts, scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent,...
nParams, paramValues, resample, contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionTypes, contrastCustomFiles, useImaginary, repeatLayers,...
data, dataLimits, simulationLimits, inputContrastLayers, customFiles,...
domainContrastLayers] = extractProblemParams(problemStruct);
dataPresent, paramValues, resample, contrastBackgroundTypes,...
contrastBackgroundActions, contrastResolutionTypes, contrastCustomFiles,...
useImaginary, repeatLayers, data, dataLimits, simulationLimits,...
inputContrastLayers, layersDetails, customFiles, domainContrastLayers...
] = extractProblemParams(problemStruct);

nParams = length(problemStruct.params);
calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
numSimulationPoints = controls.numSimulationPoints;
resampleMinAngle = controls.resampleMinAngle;
resampleNPoints = controls.resampleNPoints;

% Find the actual values from the indices given in each contrast
scalefactors = problemStruct.scalefactors(problemStruct.contrastScalefactors)';
bulkIns = problemStruct.bulkIns(problemStruct.contrastBulkIns)';
bulkOuts = problemStruct.bulkOuts(problemStruct.contrastBulkOuts)';
domainRatios = problemStruct.domainRatios(problemStruct.contrastDomainRatios)';

% qzshifts are not included as a parameter in RAT,
% so we set up dummy values for the reflectivity calculation
qzshifts = zeros(problemStruct.numberOfContrasts,1);

% Allocate the memory for the output arrays before the main loop
subRoughs = zeros(numberOfContrasts,1);
Expand Down Expand Up @@ -77,7 +88,7 @@
% parameters to all the layers in the layers list. This only
% needs to be done once, and so is done outside the contrasts
% loop
layerValues = allocateParamsToLayers(paramValues, problemStruct.layersDetails);
layerValues = allocateParamsToLayers(paramValues, layersDetails);

for i = 1:numberOfContrasts

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22 changes: 16 additions & 6 deletions targetFunctions/+normalTF/normalReflectivity.m
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Original file line number Diff line number Diff line change
Expand Up @@ -11,17 +11,27 @@
% Extract parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices,...
contrastResolutionIndices, backgroundParamValues, resolutionParamValues,...
qzshifts, scalefactors, bulkIns, bulkOuts, ~, dataPresent, nParams,...
paramValues, resample, contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionTypes, contrastCustomFiles, useImaginary, repeatLayers,...
data, dataLimits, simulationLimits, contrastLayersIndices, customFiles,...
~] = extractProblemParams(problemStruct);
dataPresent, paramValues, resample, contrastBackgroundTypes,...
contrastBackgroundActions, contrastResolutionTypes, contrastCustomFiles,...
useImaginary, repeatLayers, data, dataLimits, simulationLimits,...
contrastLayersIndices, layersDetails, customFiles, ~...
] = extractProblemParams(problemStruct);

nParams = length(problemStruct.params);
calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
numSimulationPoints = controls.numSimulationPoints;
resampleMinAngle = controls.resampleMinAngle;
resampleNPoints = controls.resampleNPoints;

% Find the actual values from the indices given in each contrast
scalefactors = problemStruct.scalefactors(problemStruct.contrastScalefactors)';
bulkIns = problemStruct.bulkIns(problemStruct.contrastBulkIns)';
bulkOuts = problemStruct.bulkOuts(problemStruct.contrastBulkOuts)';

% qzshifts are not included as a parameter in RAT,
% so we set up dummy values for the reflectivity calculation
qzshifts = zeros(problemStruct.numberOfContrasts,1);

% Allocate the memory for the output arrays before the main loop
subRoughs = zeros(numberOfContrasts,1);
Expand Down Expand Up @@ -57,7 +67,7 @@
% parameters to all the layers in the layers list. This only
% needs to be done once, and so is done outside the contrasts
% loop
layerValues = allocateParamsToLayers(paramValues, problemStruct.layersDetails);
layerValues = allocateParamsToLayers(paramValues, layersDetails);

for i = 1:numberOfContrasts

Expand Down
35 changes: 6 additions & 29 deletions targetFunctions/common/extractProblemParams.m
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
function [numberOfContrasts, geometry, contrastBackgroundParams,...
contrastResolutionParams, backgroundParams, resolutionParams, qzshifts,...
scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent, nParams, params,...
resample, contrastBackgroundTypes, contrastBackgroundActions, contrastResolutionTypes,...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits,...
contrastLayers, customFiles, domainContrastLayers] = extractProblemParams(problemStruct)
contrastResolutionParams, backgroundParams, resolutionParams, dataPresent,...
params, resample, contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionTypes, contrastCustomFiles, useImaginary, repeatLayers,...
data, dataLimits, simulationLimits, contrastLayers, layersDetails, customFiles,...
domainContrastLayers] = extractProblemParams(problemStruct)

resample = problemStruct.resample;
data = problemStruct.data;
Expand All @@ -21,34 +21,11 @@
contrastResolutionTypes = problemStruct.contrastResolutionTypes;
backgroundParams = problemStruct.backgroundParams;
resolutionParams = problemStruct.resolutionParams;
nParams = length(problemStruct.params);
params = problemStruct.params;
contrastLayers = problemStruct.contrastLayers;
layersDetails = problemStruct.layersDetails;
customFiles = problemStruct.customFiles;
contrastCustomFiles = problemStruct.contrastCustomFiles;
domainContrastLayers = problemStruct.domainContrastLayers;


% qzshifts are not included as a parameter in RAT, so we set up dummy
% values for the reflectivity calculation
contrastQzshifts = ones(1,problemStruct.numberOfContrasts);
qzshiftValues = 0.0;

contrastScalefactors = problemStruct.contrastScalefactors;
contrastBulkIns = problemStruct.contrastBulkIns;
contrastBulkOuts = problemStruct.contrastBulkOuts;
contrastDomainRatios = problemStruct.contrastDomainRatios;

scalefactorValues = problemStruct.scalefactors;
bulkInValues = problemStruct.bulkIns;
bulkOutValues = problemStruct.bulkOuts;
domainRatioValues = problemStruct.domainRatios;

% Find the actual values from the indices given in each contrast
qzshifts = qzshiftValues(contrastQzshifts)';
scalefactors = scalefactorValues(contrastScalefactors)';
bulkIns = bulkInValues(contrastBulkIns)';
bulkOuts = bulkOutValues(contrastBulkOuts)';
domainRatios = domainRatioValues(contrastDomainRatios)';

end
19 changes: 6 additions & 13 deletions tests/domainsTFReflectivityCalculation/testDomainsReflectivityCalculations.m
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Expand Up @@ -254,28 +254,20 @@ function testCheckIndices(testCase)
end

function testExtractProblemParams(testCase)
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams, backgroundParams, resolutionParams,...
~, scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent, nParams, params, resample, backgroundTypes, backgroundActions, resolutionTypes,...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers, customFiles, domainContrastLayers...
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams,...
backgroundParams, resolutionParams, dataPresent, params, resample,...
backgroundTypes, backgroundActions, resolutionTypes, contrastCustomFiles,...
useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers,...
layersDetails, customFiles, domainContrastLayers...
] = extractProblemParams(testCase.problemStruct);

testScalefactors = testCase.problemStruct.scalefactors(testCase.problemStruct.contrastScalefactors)';
testBulkIns = testCase.problemStruct.bulkIns(testCase.problemStruct.contrastBulkIns)';
testBulkOuts = testCase.problemStruct.bulkOuts(testCase.problemStruct.contrastBulkOuts)';
testDomainRatios = testCase.problemStruct.domainRatios(testCase.problemStruct.contrastDomainRatios)';

testCase.verifyEqual(numberOfContrasts, testCase.problemStruct.numberOfContrasts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(geometry, testCase.problemStruct.geometry, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastBackgroundParams, testCase.problemStruct.contrastBackgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastResolutionParams, testCase.problemStruct.contrastResolutionParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(backgroundParams, testCase.problemStruct.backgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(resolutionParams, testCase.problemStruct.resolutionParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(scalefactors, testScalefactors, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(bulkIns, testBulkIns, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(bulkOuts, testBulkOuts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(domainRatios, testDomainRatios, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(dataPresent, testCase.problemStruct.dataPresent, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(nParams, length(testCase.problemStruct.params), 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(params, testCase.problemStruct.params, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(resample, testCase.problemStruct.resample, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(backgroundTypes, testCase.problemStruct.contrastBackgroundTypes, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
Expand All @@ -288,6 +280,7 @@ function testExtractProblemParams(testCase)
testCase.verifyEqual(dataLimits, testCase.problemStruct.dataLimits, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(simulationLimits, testCase.problemStruct.simulationLimits, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastLayers, testCase.problemStruct.contrastLayers, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(layersDetails, testCase.problemStruct.layersDetails, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(customFiles, testCase.problemStruct.customFiles, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(domainContrastLayers, testCase.problemStruct.domainContrastLayers, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);

Expand Down
19 changes: 6 additions & 13 deletions tests/normalTFReflectivityCalculation/testReflectivityCalculations.m
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Expand Up @@ -268,28 +268,20 @@ function testCheckIndices(testCase)
end

function testExtractProblemParams(testCase)
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams, backgroundParams, resolutionParams,...
~, scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent, nParams, params, resample, backgroundTypes, backgroundActions, resolutionTypes,...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers, customFiles, domainContrastLayers...
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams,...
backgroundParams, resolutionParams, dataPresent, params, resample,...
backgroundTypes, backgroundActions, resolutionTypes, contrastCustomFiles,...
useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers,...
layersDetails, customFiles, domainContrastLayers...
] = extractProblemParams(testCase.problemStruct);

testScalefactors = testCase.problemStruct.scalefactors(testCase.problemStruct.contrastScalefactors)';
testBulkIns = testCase.problemStruct.bulkIns(testCase.problemStruct.contrastBulkIns)';
testBulkOuts = testCase.problemStruct.bulkOuts(testCase.problemStruct.contrastBulkOuts)';
testDomainRatios = testCase.problemStruct.domainRatios(testCase.problemStruct.contrastDomainRatios)';

testCase.verifyEqual(numberOfContrasts, testCase.problemStruct.numberOfContrasts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(geometry, testCase.problemStruct.geometry, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastBackgroundParams, testCase.problemStruct.contrastBackgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastResolutionParams, testCase.problemStruct.contrastResolutionParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(backgroundParams, testCase.problemStruct.backgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(resolutionParams, testCase.problemStruct.resolutionParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(scalefactors, testScalefactors, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(bulkIns, testBulkIns, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(bulkOuts, testBulkOuts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(domainRatios, testDomainRatios, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(dataPresent, testCase.problemStruct.dataPresent, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(nParams, length(testCase.problemStruct.params), 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(params, testCase.problemStruct.params, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(resample, testCase.problemStruct.resample, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(backgroundTypes, testCase.problemStruct.contrastBackgroundTypes, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
Expand All @@ -302,6 +294,7 @@ function testExtractProblemParams(testCase)
testCase.verifyEqual(dataLimits, testCase.problemStruct.dataLimits, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(simulationLimits, testCase.problemStruct.simulationLimits, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(contrastLayers, testCase.problemStruct.contrastLayers, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(layersDetails, testCase.problemStruct.layersDetails, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(customFiles, testCase.problemStruct.customFiles, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
testCase.verifyEqual(domainContrastLayers, testCase.problemStruct.domainContrastLayers, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
end
Expand Down
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