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Merged
DrPaulSharp merged 3 commits into from
Jul 22, 2025
Merged

Refactors domain reflectivity calculations #402

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90867a5
Moves code to get domain ratios within "extractProblemParams"
DrPaulSharp Jun 30, 2025
9fb80e5
Switches naming convention in "domainsReflectivityCalculation"
DrPaulSharp Jun 30, 2025
950d2f9
Resolves seg fault
DrPaulSharp Jul 22, 2025
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2 changes: 1 addition & 1 deletion API/checkIndices.m
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Expand Up @@ -65,7 +65,7 @@ function checkIndices(problemStruct, customFiles)
numDomainRatios = length(problemStruct.domainRatios);
for i = 1:length(problemStruct.contrastDomainRatios)
index = problemStruct.contrastDomainRatios(i);
if (index < 1 && index ~= -1) || index > numDomainRatios
if index < 1 || index > numDomainRatios
throw(exceptions.indexOutOfRange(sprintf('contrastDomainRatios(%i) is %i, which is outside the range of domainRatio', i, index)));
end
end
Expand Down
4 changes: 2 additions & 2 deletions API/parseClassToStructs.m
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Expand Up @@ -202,15 +202,15 @@
if isa(project, 'domainsClass')
problemStruct.domainRatios = inputStruct.domainRatioValues;
else
problemStruct.domainRatios = ones(1,0);
problemStruct.domainRatios = zeros(1,1);
end

if isa(project, 'domainsClass') && isa(project.domainContrasts, 'domainContrastsClass')
problemStruct.numberOfDomainContrasts = inputStruct.numberOfDomainContrasts;
problemStruct.domainContrastLayers = inputStruct.domainContrastLayers;
else
problemStruct.numberOfDomainContrasts = 0;
problemStruct.domainContrastLayers = cell(1, 0);
problemStruct.domainContrastLayers = cell(1,0);
end

% Initialise the lists of fitting parameters
Expand Down
4 changes: 1 addition & 3 deletions API/projectClass/contrastsClass.m
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Expand Up @@ -85,7 +85,7 @@
contrastBackgroundActions = cell(1,nContrasts);
contrastBulkIns = ones(1,nContrasts);
contrastBulkOuts = ones(1,nContrasts);
contrastDomainRatios = zeros(1,nContrasts);
contrastDomainRatios = ones(1,nContrasts);
contrastScalefactors = ones(1,nContrasts);
contrastResolutions = ones(1,nContrasts);
resample = ones(1,nContrasts);
Expand Down Expand Up @@ -123,8 +123,6 @@

if isfield(thisContrast, 'domainRatio')
contrastDomainRatios(i) = obj.findParameterIndex(thisContrast.domainRatio, allowedNames.domainRatioNames, "domain ratio");
else
contrastDomainRatios(i) = -1;
end

contrastBackgrounds(i) = obj.findParameterIndex(thisContrast.background, allowedNames.backgroundNames, "background");
Expand Down
87 changes: 40 additions & 47 deletions targetFunctions/+domainsTF/domainsReflectivity.m
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@@ -1,7 +1,6 @@
function [reflectivity,simulation,shiftedData,backgrounds,resolutions,...
domainSldProfiles,domainLayers,domainResampledLayers,qzshifts,...
scalefactors,bulkIns,bulkOuts,subRoughs,chis...
] = domainsReflectivity(problemStruct,controls)
sldProfiles,layers,resampledLayers,qzshifts,scalefactors,bulkIns,...
bulkOuts,subRoughs,chis] = domainsReflectivity(problemStruct,controls)
% This is the main domains reflectivity calculation.
% It extracts the required parameters for the contrasts
% from the input arrays, then passes the main calculation to
Expand All @@ -11,13 +10,12 @@

% Extract parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices,...
contrastResolutionIndices, contrastDomainRatioIndices, backgroundParamValues,...
resolutionParamValues, qzshifts, scalefactors, bulkIns, bulkOuts,...
domainRatioValues, dataPresent, nParams, paramValues, resample,...
contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionIndices, backgroundParamValues, resolutionParamValues,...
qzshifts, scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent,...
nParams, paramValues, resample, contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionTypes, contrastCustomFiles, useImaginary, repeatLayers,...
data, dataLimits, simulationLimits, inputContrastLayers, layersDetails,...
customFiles, domainContrastLayers] = extractProblemParams(problemStruct);
data, dataLimits, simulationLimits, inputContrastLayers, customFiles,...
domainContrastLayers] = extractProblemParams(problemStruct);

calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
Expand All @@ -26,7 +24,6 @@
resampleNPoints = controls.resampleNPoints;

% Allocate the memory for the output arrays before the main loop
domainRatios = zeros(numberOfContrasts,1);
subRoughs = zeros(numberOfContrasts,1);
chis = zeros(numberOfContrasts,1);

Expand All @@ -35,21 +32,20 @@
shiftedData = cell(numberOfContrasts,1);
backgrounds = cell(numberOfContrasts,1);
resolutions = cell(numberOfContrasts,1);

domainSldProfiles = cell(numberOfContrasts,2);
domainLayers = cell(numberOfContrasts,2);
domainResampledLayers = cell(numberOfContrasts,2);

sldProfiles = cell(numberOfContrasts,1);
layers = cell(numberOfContrasts,1);
resampledLayers = cell(numberOfContrasts,1);
sldProfiles = cell(numberOfContrasts,2);
layers = cell(numberOfContrasts,2);
resampledLayers = cell(numberOfContrasts,2);

contrastLayers1 = cell(numberOfContrasts,1);
contrastLayers2 = cell(numberOfContrasts,1);

contrastSlds1 = cell(numberOfContrasts,1);
contrastSlds2 = cell(numberOfContrasts,1);

domainSldProfiles = cell(numberOfContrasts,1);
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@StephenNneji StephenNneji Jul 22, 2025

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I guess the reason for the name flip is to sync this function with the normal? but its confusing to see the domiains... variables have a single column. Don't know if we can rename to something else

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@DrPaulSharp DrPaulSharp Jul 22, 2025

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Yes, that's the reason I switched them. For matlab coder we have to have them as a variable with up to two columns so I'm not sure there's much we can do.

domainLayers = cell(numberOfContrasts,1);
domainResampledLayers = cell(numberOfContrasts,1);

for i = 1:numberOfContrasts

shiftedData{i} = zeros(1,3);
Expand All @@ -63,17 +59,12 @@
contrastSlds1{i} = zeros(1,3);
contrastSlds2{i} = zeros(1,3);

domainLayers{i,1} = zeros(1,6);
domainLayers{i,2} = zeros(1,6);
layers{i,1} = zeros(1,6);
layers{i,2} = zeros(1,6);

domainResampledLayers{i,1} = zeros(1,6);
domainResampledLayers{i,2} = zeros(1,6);
resampledLayers{i,1} = zeros(1,6);
resampledLayers{i,2} = zeros(1,6);

% Get the domain ratio for this contrast
if isempty(contrastDomainRatioIndices(i))
contrastDomainRatioIndices(i) = 1;
end
domainRatios(i) = domainRatioValues(contrastDomainRatioIndices(i));
end

%% Obtain model specific parameters
Expand All @@ -86,7 +77,7 @@
% 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, layersDetails);
layerValues = allocateParamsToLayers(paramValues, problemStruct.layersDetails);

for i = 1:numberOfContrasts

Expand Down Expand Up @@ -145,12 +136,13 @@
data{i},dataLimits{i},simulationLimits{i},numSimulationPoints);

[reflectivity{i},simulation{i},shiftedData{i},...
sldProfiles{i},layers{i},resampledLayers{i},...
chis(i)] = contrastCustomXYCalculation(bulkIns(i),...
bulkOuts(i),domainRatios(i),shiftedData{i},simulationXData,...
dataIndices,backgrounds{i},resolutions{i},...
contrastBackgroundActions{i},nParams,parallel,resampleMinAngle,...
resampleNPoints,subRoughs(i),contrastSlds1{i},contrastSlds2{i});
domainSldProfiles{i},domainLayers{i},...
domainResampledLayers{i},chis(i)...
] = contrastCustomXYCalculation(bulkIns(i),bulkOuts(i),...
domainRatios(i),shiftedData{i},simulationXData,dataIndices,...
backgrounds{i},resolutions{i},contrastBackgroundActions{i},...
nParams,parallel,resampleMinAngle,resampleNPoints,...
subRoughs(i),contrastSlds1{i},contrastSlds2{i});

end

Expand All @@ -168,12 +160,13 @@
data{i},dataLimits{i},simulationLimits{i},numSimulationPoints);

[reflectivity{i},simulation{i},shiftedData{i},...
sldProfiles{i},layers{i},resampledLayers{i},...
chis(i)] = contrastCustomXYCalculation(bulkIns(i),...
bulkOuts(i),domainRatios(i),shiftedData{i},simulationXData,...
dataIndices,backgrounds{i},resolutions{i},...
contrastBackgroundActions{i},nParams,parallel,resampleMinAngle,...
resampleNPoints,subRoughs(i),contrastSlds1{i},contrastSlds2{i});
domainSldProfiles{i},domainLayers{i},...
domainResampledLayers{i},chis(i)...
] = contrastCustomXYCalculation(bulkIns(i),bulkOuts(i),...
domainRatios(i),shiftedData{i},simulationXData,dataIndices,...
backgrounds{i},resolutions{i},contrastBackgroundActions{i},...
nParams,parallel,resampleMinAngle,resampleNPoints,...
subRoughs(i),contrastSlds1{i},contrastSlds2{i});

end

Expand All @@ -195,7 +188,7 @@
data{i},dataLimits{i},simulationLimits{i},numSimulationPoints);

[reflectivity{i},simulation{i},shiftedData{i},...
sldProfiles{i},layers{i},resampledLayers{i},...
domainSldProfiles{i},domainLayers{i},domainResampledLayers{i},...
chis(i)] = contrastLayersCalculation(bulkIns(i),bulkOuts(i),...
domainRatios(i),shiftedData{i},simulationXData,dataIndices,...
backgrounds{i},resolutions{i},repeatLayers(i),...
Expand All @@ -220,7 +213,7 @@
data{i},dataLimits{i},simulationLimits{i},numSimulationPoints);

[reflectivity{i},simulation{i},shiftedData{i},...
sldProfiles{i},layers{i},resampledLayers{i},...
domainSldProfiles{i},domainLayers{i},domainResampledLayers{i},...
chis(i)] = contrastLayersCalculation(bulkIns(i),bulkOuts(i),...
domainRatios(i),shiftedData{i},simulationXData,dataIndices,...
backgrounds{i},resolutions{i},repeatLayers(i),...
Expand All @@ -236,18 +229,18 @@

for i = 1:numberOfContrasts
for j = 1:2
domainSldProfiles{i,j} = sldProfiles{i}{j};
domainLayers{i,j} = layers{i}{j};
domainResampledLayers{i,j} = resampledLayers{i}{j};
sldProfiles{i,j} = domainSldProfiles{i}{j};
layers{i,j} = domainLayers{i}{j};
resampledLayers{i,j} = domainResampledLayers{i}{j};
end
end

% Remove dummy imaginary column if present
if ~useImaginary
for i=1:numberOfContrasts
for j = 1:2
domainLayers{i,j}(:,3) = [];
domainResampledLayers{i,j}(:,3) = [];
layers{i,j}(:,3) = [];
resampledLayers{i,j}(:,3) = [];
end
end
end
Expand Down
8 changes: 4 additions & 4 deletions targetFunctions/+normalTF/normalReflectivity.m
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Expand Up @@ -10,12 +10,12 @@

% Extract parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices,...
contrastResolutionIndices, ~, backgroundParamValues, resolutionParamValues,...
contrastResolutionIndices, backgroundParamValues, resolutionParamValues,...
qzshifts, scalefactors, bulkIns, bulkOuts, ~, dataPresent, nParams,...
paramValues, resample, contrastBackgroundTypes, contrastBackgroundActions,...
contrastResolutionTypes, contrastCustomFiles, useImaginary, repeatLayers,...
data, dataLimits, simulationLimits, contrastLayersIndices, layersDetails,...
customFiles, ~] = extractProblemParams(problemStruct);
data, dataLimits, simulationLimits, contrastLayersIndices, customFiles,...
~] = extractProblemParams(problemStruct);

calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
Expand Down Expand Up @@ -57,7 +57,7 @@
% 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, layersDetails);
layerValues = allocateParamsToLayers(paramValues, problemStruct.layersDetails);

for i = 1:numberOfContrasts

Expand Down
14 changes: 8 additions & 6 deletions targetFunctions/common/extractProblemParams.m
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@@ -1,7 +1,9 @@
function [numberOfContrasts, geometry, contrastBackgroundParams,...
contrastResolutionParams, contrastDomainRatios, backgroundParams, resolutionParams, qzshifts, scalefactors, bulkIns, bulkOuts,...
domainRatios, dataPresent, nParams, params, resample, contrastBackgroundTypes, contrastBackgroundActions, contrastResolutionTypes,...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers, layersDetails, customFiles, domainContrastLayers] = extractProblemParams(problemStruct)
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)

resample = problemStruct.resample;
data = problemStruct.data;
Expand All @@ -17,16 +19,13 @@
contrastBackgroundActions = problemStruct.contrastBackgroundActions;
contrastResolutionParams = problemStruct.contrastResolutionParams;
contrastResolutionTypes = problemStruct.contrastResolutionTypes;
contrastDomainRatios = problemStruct.contrastDomainRatios;
backgroundParams = problemStruct.backgroundParams;
resolutionParams = problemStruct.resolutionParams;
nParams = length(problemStruct.params);
params = problemStruct.params;
contrastLayers = problemStruct.contrastLayers;
customFiles = problemStruct.customFiles;
contrastCustomFiles = problemStruct.contrastCustomFiles;
layersDetails = problemStruct.layersDetails;
domainRatios = problemStruct.domainRatios;
domainContrastLayers = problemStruct.domainContrastLayers;


Expand All @@ -38,15 +37,18 @@
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
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6 changes: 3 additions & 3 deletions tests/domainsTFReflectivityCalculation/makeDomainsInputsAndOutputs.m
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Expand Up @@ -42,7 +42,7 @@
% (c) TF Parameters
[reflectivity,simulation,shiftedData,backgrounds,resolutions,sldProfiles,...
layers,resampledLayers,qzshifts,scalefactors,bulkIn,bulkOut,subRoughs,chis...
] = normalTF.normalReflectivity(problemStruct,controls);
] = domainsTF.domainsReflectivity(problemStruct,controls);

TFParams.reflectivity = reflectivity;
TFParams.simulation = simulation;
Expand Down Expand Up @@ -99,7 +99,7 @@
% (c) TF Parameters
[reflectivity,simulation,shiftedData,backgrounds,resolutions,sldProfiles,...
layers,resampledLayers,qzshifts,scalefactors,bulkIn,bulkOut,subRoughs,chis...
] = normalTF.normalReflectivity(problemStruct,controls);
] = domainsTF.domainsReflectivity(problemStruct,controls);

TFParams.reflectivity = reflectivity;
TFParams.simulation = simulation;
Expand Down Expand Up @@ -155,7 +155,7 @@
% (c) TF Parameters
[reflectivity,simulation,shiftedData,backgrounds,resolutions,sldProfiles,...
layers,resampledLayers,qzshifts,scalefactors,bulkIn,bulkOut,subRoughs,chis...
] = normalTF.normalReflectivity(problemStruct,controls);
] = domainsTF.domainsReflectivity(problemStruct,controls);

TFParams.reflectivity = reflectivity;
TFParams.simulation = simulation;
Expand Down
9 changes: 4 additions & 5 deletions tests/domainsTFReflectivityCalculation/testDomainsReflectivityCalculations.m
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Expand Up @@ -254,26 +254,26 @@ function testCheckIndices(testCase)
end

function testExtractProblemParams(testCase)
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams, contrastDomainRatios, backgroundParams, resolutionParams,...
[numberOfContrasts, geometry, contrastBackgroundParams, contrastResolutionParams, backgroundParams, resolutionParams,...
~, scalefactors, bulkIns, bulkOuts, domainRatios, dataPresent, nParams, params, resample, backgroundTypes, backgroundActions, resolutionTypes,...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers, layersDetails, customFiles, domainContrastLayers...
contrastCustomFiles, useImaginary, repeatLayers, data, dataLimits, simulationLimits, contrastLayers, 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(contrastDomainRatios, testCase.problemStruct.contrastDomainRatios, '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, testCase.problemStruct.domainRatios, '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);
Expand All @@ -288,7 +288,6 @@ 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
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