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Adds code to ensure parameter array indices are valid #236

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Jun 14, 2024
Merged

Adds code to ensure parameter array indices are valid #236

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ae22133
Refactors code to be more explicit about use of resolution parameters
DrPaulSharp Jun 13, 2024
751f554
Adds new routine "checkIndices.m"
DrPaulSharp Jun 13, 2024
127f2ed
Refactors "checkIndices" to be called from "parseClassToStruct"
DrPaulSharp Jun 14, 2024
14e01a8
Updates errors in "checkIndices"
DrPaulSharp Jun 14, 2024
7c73835
Addresses review comments
DrPaulSharp Jun 14, 2024
7b75cea
Fixes tests
DrPaulSharp Jun 14, 2024
3d1ce69
Restores defaults for "contrastDomainRatios"
DrPaulSharp Jun 14, 2024
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60 changes: 60 additions & 0 deletions API/checkIndices.m
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@@ -0,0 +1,60 @@
function checkIndices(problemStruct)
% Make sure that the indices provided lie within the bounds of the
% corresponding array.

numBackgroundParams = length(problemStruct.backgroundParams);
for i = 1:length(problemStruct.contrastBackgrounds)
index = problemStruct.contrastBackgrounds(i);
if index < 1 || index > numBackgroundParams
throw(exceptions.indexOutOfRange(sprintf('contrastBackgrounds(%i) is %i, which is outside the range of backgroundParams', i, index)));
end
end

numQzshifts = length(problemStruct.qzshifts);
for i = 1:length(problemStruct.contrastQzshifts)
index = problemStruct.contrastQzshifts(i);
if index < 1 || index > numQzshifts
throw(exceptions.indexOutOfRange(sprintf('contrastQzshifts(%i) is %i, which is outside the range of qzshifts', i, index)));
end
end

numScalefactors = length(problemStruct.scalefactors);
for i = 1:length(problemStruct.contrastScalefactors)
index = problemStruct.contrastScalefactors(i);
if index < 1 || index > numScalefactors
throw(exceptions.indexOutOfRange(sprintf('contrastScalefactors(%i) is %i, which is outside the range of scalefactors', i, index)));
end
end

numBulkIns = length(problemStruct.bulkIn);
for i = 1:length(problemStruct.contrastBulkIns)
index = problemStruct.contrastBulkIns(i);
if index < 1 || index > numBulkIns
throw(exceptions.indexOutOfRange(sprintf('contrastBulkIns(%i) is %i, which is outside the range of bulkIn', i, index)));
end
end

numBulkOuts = length(problemStruct.bulkOut);
for i = 1:length(problemStruct.contrastBulkOuts)
index = problemStruct.contrastBulkOuts(i);
if index < 1 || index > numBulkOuts
throw(exceptions.indexOutOfRange(sprintf('contrastBulkOuts(%i) is %i, which is outside the range of bulkOut', i, index)));
end
end

numResolutionParams = length(problemStruct.resolutionParams);
for i = 1:length(problemStruct.contrastResolutionParams)
index = problemStruct.contrastResolutionParams(i);
if (index < 1 && index ~= -1) || index > numResolutionParams
throw(exceptions.indexOutOfRange(sprintf('contrastResolutionParams(%i) is %i, which is outside the range of resolutionParams', i, index)));
end
end

numDomainRatios = length(problemStruct.domainRatio);
for i = 1:length(problemStruct.contrastDomainRatios)
index = problemStruct.contrastDomainRatios(i);
if (index < 1 && index ~= -1) || index > numDomainRatios
throw(exceptions.indexOutOfRange(sprintf('contrastDomainRatios(%i) is %i, which is outside the range of domainRatio', i, index)));
end
end

22 changes: 13 additions & 9 deletions API/parseClassToStructs.m
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Expand Up @@ -239,27 +239,29 @@

% Here we need to do the same with the contrastResolutions array
contrastResolutions = inputStruct.contrastResolutions;
resolutionNames = inputStruct.resolutionParamNames;
resolutionTypes = inputStruct.resolutionTypes;
contrastRes = zeros(1, length(contrastResolutions));

resolutionParamNames = inputStruct.resolutionParamNames;
contrastResolutionParams = zeros(1, length(contrastResolutions));

for i = 1:length(contrastResolutions)
% Check the type of the resolution that each contrast is pointing to.
% If it is a constant, point to the number of the corresponding
% resolution par. If it's data, then set it to zero
% resolution param. If it's data, then set it to -1
thisResol = contrastResolutions(i); % Which resolution
thisType = resolutionTypes{thisResol}; % What type is it?

if strcmpi(thisType,'data')
% Resolution is in the datafile. Set contrastRes to zero
contrastRes(i) = -1;
% Resolution is in the datafile. Set contrastResolutionParams to -1
contrastResolutionParams(i) = -1;
else
% Resolution is a resolutionParam, the name of which should
% be in the first column of resolutionValues
whichResolutionParamName = inputStruct.resolutionValues{thisResol,1};

% Find which resolutionParam this is, and set contrastRes to this number
resolutionParamNumber = find(strcmpi(whichResolutionParamName,resolutionNames));
contrastRes(i) = resolutionParamNumber;
% Find which resolutionParam this is, and set contrastResolutionParams to this number
resolutionParamNumber = find(strcmpi(whichResolutionParamName,resolutionParamNames));
contrastResolutionParams(i) = resolutionParamNumber;
end
end

Expand Down Expand Up @@ -324,7 +326,7 @@
problemStruct.contrastScalefactors = inputStruct.contrastScalefactors;
problemStruct.contrastBulkIns = inputStruct.contrastBulkIns;
problemStruct.contrastBulkOuts = inputStruct.contrastBulkOuts;
problemStruct.contrastResolutions = contrastRes;
problemStruct.contrastResolutionParams = contrastResolutionParams;
problemStruct.backgroundParams = inputStruct.backgroundParamValues; %inputStruct.backgrounds; % **** note backPar workaround (todo) ****
problemStruct.qzshifts = inputStruct.qzshiftValues;
problemStruct.scalefactors = inputStruct.scalefactorValues;
Expand Down Expand Up @@ -358,6 +360,8 @@
problemStruct.fitLimits = [];
problemStruct.otherLimits = [];

% Make sure the indices cannot lie outside of the arrays
checkIndices(problemStruct)

%% Now deal with the controls class
controls.procedure = inputControls.procedure;
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2 changes: 2 additions & 0 deletions API/projectClass/contrastsClass.m
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Expand Up @@ -116,6 +116,8 @@

if isfield(thisContrast, 'domainRatio')
contrastDomainRatios(i) = find(strcmpi(thisContrast.domainRatio,allowedNames.domainRatioNames));
else
contrastDomainRatios(i) = -1;
end

contrastBackgrounds(i) = find(strcmpi(thisContrast.background,allowedNames.backgroundNames));
Expand Down
2 changes: 1 addition & 1 deletion compile/fullCompile/makeCompileArgsFull.m
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Expand Up @@ -22,7 +22,7 @@
ARGS_1_1.contrastScalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
Expand Down
2 changes: 1 addition & 1 deletion compile/reflectivityCalculation/makeCompileArgs.m
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Expand Up @@ -22,7 +22,7 @@
ARGS_1_1.contrastScalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
Expand Down
2 changes: 1 addition & 1 deletion examples/domains/customXY/domainsCustomXYMain.m
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Expand Up @@ -24,7 +24,7 @@
problem.addBulkOut('SLD H2O', -0.6e-6, -0.56e-6, -0.5e-6);

% Add the custom file...
problem.addCustomFile('Domain Layer','domainsXY','matlab',pwd);
problem.addCustomFile('Domain Layer','domainsXY.m','matlab',pwd);

% Make a contrast
problem.addContrast('name', 'D2O',...
Expand Down
8 changes: 4 additions & 4 deletions targetFunctions/+domainsTF/customLayers.m
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Expand Up @@ -17,11 +17,11 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, contrastDomainRatioIndices, backgroundParamArray,...
contrastResolutionParamIndices, contrastDomainRatioIndices, backgroundParamArray,...
qzshiftArray, scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray,...
domainRatioArray, dataPresent, nParams, params, ~, resample,...
contrastBackgroundActions, cCustFiles, useImaginary] = extractProblemParams(problemStruct);

calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
resampleParams = controls.resampleParams;
Expand Down Expand Up @@ -107,7 +107,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand All @@ -128,7 +128,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand Down
6 changes: 3 additions & 3 deletions targetFunctions/+domainsTF/customXY.m
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Expand Up @@ -13,7 +13,7 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, ~, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, contrastDomainRatioIndices, backgroundParamArray,...
contrastResolutionParamIndices, contrastDomainRatioIndices, backgroundParamArray,...
qzshiftArray, scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray,...
domainRatioArray, dataPresent, nParams, params, ~, ~, contrastBackgroundActions,...
cCustFiles, useImaginary] = extractProblemParams(problemStruct);
Expand Down Expand Up @@ -99,7 +99,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand All @@ -119,7 +119,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand Down
6 changes: 3 additions & 3 deletions targetFunctions/+domainsTF/standardLayers.m
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Expand Up @@ -20,7 +20,7 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, contrastDomainRatioIndices, backgroundParamArray,...
contrastResolutionParamIndices, contrastDomainRatioIndices, backgroundParamArray,...
qzshiftArray, scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray,...
domainRatioArray, dataPresent, nParams, params, ~, resample,...
contrastBackgroundActions, ~, useImaginary] = extractProblemParams(problemStruct);
Expand Down Expand Up @@ -111,7 +111,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand All @@ -133,7 +133,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),contrastDomainRatioIndices(i),...
contrastResolutionParamIndices(i),contrastDomainRatioIndices(i),...
backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
Expand Down
8 changes: 4 additions & 4 deletions targetFunctions/+nonPolarisedTF/customLayers.m
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Expand Up @@ -17,11 +17,11 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, ~, backgroundParamArray, qzshiftArray,...
contrastResolutionParamIndices, ~, backgroundParamArray, qzshiftArray,...
scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray, ~,...
dataPresent, nParams, params, ~, resample, contrastBackgroundActions, cCustFiles,...
useImaginary] = extractProblemParams(problemStruct);

calcSld = controls.calcSldDuringFit;
parallel = controls.parallel;
resampleParams = controls.resampleParams;
Expand Down Expand Up @@ -72,7 +72,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
contrastBackgroundActions(i),nParams,parallel,resampleParams,...
Expand All @@ -93,7 +93,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
contrastBackgroundActions(i),nParams,parallel,resampleParams,...
Expand Down
6 changes: 3 additions & 3 deletions targetFunctions/+nonPolarisedTF/customXY.m
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Expand Up @@ -13,7 +13,7 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, ~, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, ~, backgroundParamArray, qzshiftArray,...
contrastResolutionParamIndices, ~, backgroundParamArray, qzshiftArray,...
scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray, ~,...
dataPresent, nParams, params, ~, ~, contrastBackgroundActions, cCustFiles,...
useImaginary] = extractProblemParams(problemStruct);
Expand Down Expand Up @@ -68,7 +68,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},...
repeatLayers{i},contrastBackgroundActions(i),nParams,parallel,...
Expand All @@ -86,7 +86,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i),...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},...
repeatLayers{i},contrastBackgroundActions(i),nParams,parallel,...
Expand Down
6 changes: 3 additions & 3 deletions targetFunctions/+nonPolarisedTF/standardLayers.m
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Expand Up @@ -18,7 +18,7 @@
% Extract individual parameters from problemStruct
[numberOfContrasts, geometry, contrastBackgroundIndices, contrastQzshiftIndices,...
contrastScalefactorIndices, contrastBulkInIndices, contrastBulkOutIndices,...
contrastResolutionIndices, ~, backgroundParamArray, qzshiftArray,...
contrastResolutionParamIndices, ~, backgroundParamArray, qzshiftArray,...
scalefactorArray, bulkInArray, bulkOutArray, resolutionParamArray, ~,...
dataPresent, nParams, params, ~, resample, contrastBackgroundActions, ~,...
useImaginary] = extractProblemParams(problemStruct);
Expand Down Expand Up @@ -78,7 +78,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i), ...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
contrastBackgroundActions(i),nParams,parallel,resampleParams,...
Expand All @@ -99,7 +99,7 @@
] = contrastCalculation(contrastBackgroundIndices(i),...
contrastQzshiftIndices(i),contrastScalefactorIndices(i),...
contrastBulkInIndices(i),contrastBulkOutIndices(i), ...
contrastResolutionIndices(i),backgroundParamArray,qzshiftArray,...
contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
contrastBackgroundActions(i),nParams,parallel,resampleParams,...
Expand Down
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