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Merged
DrPaulSharp merged 4 commits into from
Apr 26, 2024
Merged

Removes code for qzshifts and undefined layers #223

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a093105
Removes code to add undefined layers
DrPaulSharp Apr 25, 2024
b2d5527
Removes "qzshift" from user-facing code
DrPaulSharp Apr 26, 2024
ea23885
Fixes build
DrPaulSharp Apr 26, 2024
0040dc7
Addresses review comments
DrPaulSharp Apr 26, 2024
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3 changes: 0 additions & 3 deletions API/makeEmptyResultStruct.m
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Expand Up @@ -36,8 +36,6 @@

backgroundParams = zeros(nContrasts,1);
coder.varsize('backgroundParams',[10000 1],[1 0]);
qzshifts = zeros(nContrasts,1);
coder.varsize('qzshifts',[10000 1],[1 0]);
scalefactors = zeros(nContrasts,1);
coder.varsize('scalefactors',[10000 1],[1 0]);
bulkIn = zeros(nContrasts,1);
Expand All @@ -52,7 +50,6 @@
coder.varsize('resample',[1 10000],[0 1]);

contrastParams = struct('backgroundParams', backgroundParams, ...
'qzshifts', qzshifts, ...
'scalefactors', scalefactors, ...
'bulkIn', bulkIn, ...
'bulkOut', bulkOut, ...
Expand Down
14 changes: 4 additions & 10 deletions API/parseOutToProjectClass.m
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Expand Up @@ -21,31 +21,25 @@
project.setScalefactor(i,'value',scalefactors(i));
end

%(4) Qzshifts
qzshifts = problemStruct.qzshifts;
for i = 1:length(qzshifts)
project.setQzshift(i,'value',qzshifts(i));
end

%(5) Bulk In
%(4) Bulk In
bulkIns = problemStruct.bulkIn;
for i = 1:length(bulkIns)
project.setBulkIn(i,'value',bulkIns(i));
end

%(6) Bulk Out
%(5) Bulk Out
bulkOuts = problemStruct.bulkOut;
for i = 1:length(bulkOuts)
project.setBulkOut(i,'value',bulkOuts(i));
end

%(7) Resolutions
%(6) Resolutions
resolutionParams = problemStruct.resolutionParams;
for i = 1:length(resolutionParams)
project.setResolutionParam(i,'value',resolutionParams(i));
end

% (8) Domain ratio
% (7) Domain ratio
if strcmpi(problemStruct.TF, calculationTypes.Domains.value)
domainRatios = problemStruct.domainRatio;
for i = 1:length(domainRatios)
Expand Down
57 changes: 22 additions & 35 deletions API/projectClass/layersClass.m
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Expand Up @@ -23,7 +23,7 @@
SLDValues {mustBeText} = 'SLD'
end

varNames = [{'Name', 'Thickness'}, SLDValues, {'Roughness','Hydration','Hydrate with'}];
varNames = [{'Name', 'Thickness'}, SLDValues, {'Roughness', 'Hydration', 'Hydrate with'}];

sz = [0 length(varNames)];
varTypes = repmat({'string'}, 1, length(varNames));
Expand All @@ -49,42 +49,29 @@
% layers.addLayer(parameters.varTable{:, 1}, 'Another layer', 1, 2, 3);
layerDetails = varargin;

if isempty(layerDetails)
% Add an empty layer
layerNum = obj.autoNameCounter;
layerName = sprintf('Layer %d',layerNum);
newRow = [{layerName}, repmat({''}, 1, obj.varCount - 2), {hydrationTypes.BulkOut.value}];

elseif length(layerDetails) == 1 && isText(layerDetails{1})
% Add an empty named layer
newRow = [layerDetails(1), repmat({''}, 1, obj.varCount - 2), {hydrationTypes.BulkOut.value}];
% Layers must be fully defined
if length(layerDetails) == (obj.varCount - 2)
% No hydration
layerDetails = [layerDetails, {'', hydrationTypes.BulkOut.value}];
elseif length(layerDetails) ~= obj.varCount
throw(exceptions.invalidNumberOfInputs(sprintf('Incorrect number of parameters for layer definition. Either %d or %d inputs are required.', obj.varCount - 2, obj.varCount)));
end

else
% Add a layer that is fully defined
if length(layerDetails) == (obj.varCount - 2)
% No hydration
layerDetails = [layerDetails, {'', hydrationTypes.BulkOut.value}];
elseif length(layerDetails) ~= obj.varCount
throw(exceptions.invalidNumberOfInputs(sprintf('Incorrect number of parameters for layer definition. Either 0, 1, %d, or %d inputs are required.', obj.varCount - 2, obj.varCount)));
end

name = layerDetails{1};
hydration = validateOption(layerDetails{end}, 'hydrationTypes', obj.invalidTypeMessage).value;

% Check that the parameter names given are real
% parameters or numbers
newRow = [name, repmat({''}, 1, obj.varCount - 2), hydration];

% Must be a parameter name or number . . .
for i = 2:(obj.varCount - 2)
newRow{i} = obj.findParameter(layerDetails{i}, paramNames);
end

% . . . (apart from the penultimate column which can also be empty or NaN)
if ~(strcmpi(layerDetails{obj.varCount - 1}, '') || any(isnan(layerDetails{obj.varCount - 1})))
newRow{obj.varCount - 1} = obj.findParameter(layerDetails{obj.varCount - 1}, paramNames);
end
name = layerDetails{1};
hydration = validateOption(layerDetails{end}, 'hydrationTypes', obj.invalidTypeMessage).value;

% Check that the parameter names given are real
% parameters or numbers
newRow = [name, repmat({''}, 1, obj.varCount - 2), hydration];

% Must be a parameter name or number . . .
for i = 2:(obj.varCount - 2)
newRow{i} = obj.findParameter(layerDetails{i}, paramNames);
end

% . . . (apart from the penultimate column which can also be empty or NaN)
if ~(strcmpi(layerDetails{obj.varCount - 1}, '') || any(isnan(layerDetails{obj.varCount - 1})))
newRow{obj.varCount - 1} = obj.findParameter(layerDetails{obj.varCount - 1}, paramNames);
end

obj.addRow(newRow{:});
Expand Down
57 changes: 13 additions & 44 deletions API/projectClass/projectClass.m
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Expand Up @@ -22,7 +22,6 @@
bulkOut % parametersClass object
background % backgroundsClass object
scalefactors % parametersClass object
qzshifts % parametersClass object
resolution % resolutionClass object
contrasts % contrastsClass object
data % dataClass object
Expand All @@ -41,10 +40,14 @@
protectedParameters
end

properties (SetAccess = immutable, Hidden)
qzshifts = parametersClass('Qz shift 1',-1e-4,0,1e-4,false,priorTypes.Uniform,0,Inf)
end

properties(Access = protected, Constant, Hidden)
classes = struct(name = ["parameters", "bulkIn", "bulkOut", "scalefactors", "qzshifts", "backgroundParams", "resolutionParams", "domainRatio", "layers", "customFile", "backgrounds", "resolutions", "data", "contrast"], ...
addRoutine = ["addParameter", "addBulkIn", "addBulkOut", "addScalefactor", "addQzshift", "addBackgroundParam", "addResolutionParam", "addDomainRatio", "addLayer", "addCustomFile", "addBackground", "addResolution", "addData", "addContrast"], ...
removeRoutine = ["removeParameter", "removeBulkIn", "removeBulkOut", "removeScalefactor", "removeQzshift", "removeBackgroundParam", "removeResolutionParam", "removeDomainRatio", "removeLayer", "removeCustomFile", "removeBackground", "removeResolution", "removeData", "removeContrast"]);
classes = struct(name = ["parameters", "bulkIn", "bulkOut", "scalefactors", "backgroundParams", "resolutionParams", "domainRatio", "layers", "customFile", "backgrounds", "resolutions", "data", "contrast"], ...
addRoutine = ["addParameter", "addBulkIn", "addBulkOut", "addScalefactor", "addBackgroundParam", "addResolutionParam", "addDomainRatio", "addLayer", "addCustomFile", "addBackground", "addResolution", "addData", "addContrast"], ...
removeRoutine = ["removeParameter", "removeBulkIn", "removeBulkOut", "removeScalefactor", "removeBackgroundParam", "removeResolutionParam", "removeDomainRatio", "removeLayer", "removeCustomFile", "removeBackground", "removeResolution", "removeData", "removeContrast"])
end

methods
Expand Down Expand Up @@ -113,9 +116,6 @@
% Initialise scalefactors table
obj.scalefactors = parametersClass('Scalefactor 1',0.02,0.23,0.25,false,priorTypes.Uniform,0,Inf);

% Initialise qzshifts table
obj.qzshifts = parametersClass('Qz shift 1',-1e-4,0,1e-4,false,priorTypes.Uniform,0,Inf);

% Initialise backgrounds object
backgroundParams = parametersClass('Background Param 1',1e-7,1e-6,1e-5,false,priorTypes.Uniform,0,Inf);
backgrounds = {'Background 1',allowedTypes.Constant.value,'Background Param 1','','','',''};
Expand Down Expand Up @@ -176,13 +176,10 @@ function delete(obj)
% (4) Scalefactors
obj.scalefactors.showPriors = showFlag;

% (5) Qz shifts
obj.qzshifts.showPriors = showFlag;

% (6) Backgrounds (parameters table)
% (5) Backgrounds (parameters table)
obj.background.backgroundParams.showPriors = showFlag;

% (7) Resolutions (parameters table)
% (6) Resolutions (parameters table)
obj.resolution.resolutionParams.showPriors = showFlag;

end
Expand Down Expand Up @@ -723,37 +720,9 @@ function delete(obj)
obj.scalefactors.setParameter(varargin{:});
end


% -----------------------------------------------------------------
% Editing of qzshifts block

function obj = addQzshift(obj, varargin)
% Adds a new qz shift parameter. Expects the name
% of qz shift, min, value, max, and if fit is off or on
%
% project.addQzshift('Qz shift 2', -0.2e-4, 0, 2e-4, false);
obj.qzshifts.addParameter(varargin{:});
end

function obj = removeQzshift(obj, varargin)
% Removes specified qz shift parameter. Expects the name/index
% of qz shift parameter to remove
%
% project.removeQzshift(2);
obj.qzshifts.removeParameter(varargin{:});
end

function obj = setQzshift(obj, varargin)
% Edits an existing qz shift parameter. Expects the index of
% qz shift parameter to edit and key-value pairs
%
% project.setScalefactor(1, 'name','Qz shift 1', 'value', 0.0001);
obj.qzshifts.setParameter(varargin{:});
end



% -----------------------------------------------------------------
% editing of custom models block
% Editing of custom models block

function obj = addCustomFile(obj, varargin)
% Adds a new custom file parameter. Expects a parameter name, filename,
Expand Down Expand Up @@ -990,8 +959,8 @@ function writeScript(obj, options)
fprintf(fileID, "\n");

% Add all parameters based on a parametersClass
paramClasses = ["bulkIn", "bulkOut", "scalefactors", "qzshifts", "background", "resolution"];
paramSubclasses = ["", "", "", "", "backgroundParams", "resolutionParams"];
paramClasses = ["bulkIn", "bulkOut", "scalefactors", "background", "resolution"];
paramSubclasses = ["", "", "", "backgroundParams", "resolutionParams"];

if isprop(obj, 'domainRatio')
paramClasses(end + 1) = "domainRatio";
Expand Down
1 change: 0 additions & 1 deletion targetFunctions/+domainsTF/reflectivityCalculation.m
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Expand Up @@ -100,7 +100,6 @@

% Package everything into one array for tidy output
contrastParams.backgroundParams = backgroundParams;
contrastParams.qzshifts = qzshifts;
contrastParams.scalefactors = scalefactors;
contrastParams.bulkIn = bulkIns;
contrastParams.bulkOut = bulkOuts;
Expand Down
1 change: 0 additions & 1 deletion targetFunctions/+nonPolarisedTF/reflectivityCalculation.m
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Expand Up @@ -97,7 +97,6 @@

% Package everything into structs for tidy output
contrastParams.backgroundParams = backgroundParams;
contrastParams.qzshifts = qzshifts;
contrastParams.scalefactors = scalefactors;
contrastParams.bulkIn = bulkIns;
contrastParams.bulkOut = bulkOuts;
Expand Down
1 change: 0 additions & 1 deletion targetFunctions/reflectivityCalculation.m
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Expand Up @@ -21,7 +21,6 @@
preAlloc = zeros(numberOfContrasts,1);

contrastParams = struct('backgroundParams',preAlloc,...
'qzshifts',preAlloc,...
'scalefactors',preAlloc,...
'bulkIn',preAlloc,...
'bulkOut',preAlloc,...
Expand Down
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20 changes: 2 additions & 18 deletions tests/testLayersClass.m
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Expand Up @@ -12,8 +12,7 @@

properties (TestParameter)
% Cell arrays for adding layers
layerInput = {{'Named Layer'},...
{'Oxide Names Layer',...
layerInput = {{'Oxide Names Layer',...
'Oxide thick',...
'Oxide SLD',...
'Substrate Roughness'},...
Expand All @@ -26,8 +25,7 @@
{'Oxide Indices Layer', 2, 3, 1},...
{'Water Indices Layer', 13, 14, 8, 15, hydrationTypes.BulkOut.value}
}
addedLayer = {{'Named Layer','','','','',hydrationTypes.BulkOut.value},...
{'Oxide Names Layer',...
addedLayer = {{'Oxide Names Layer',...
'Oxide thick',...
'Oxide SLD',...
'Substrate Roughness',...
Expand Down Expand Up @@ -171,20 +169,6 @@ function testAddLayer(testCase, layerInput, addedLayer)
testCase.verifyEqual(testCase.exampleClass.varTable, expectedTable, 'addLayer does not work correctly');
end

function testAddLayerEmpty(testCase)
% Test adding a layer to the layers class, with no input
% parameters.
% We can add a layer with no parameters, just a layer name, or
% a fully defined layer, which consists of either a length
% four or length six cell array
newLayer = {'Layer 1','','','','',hydrationTypes.BulkOut.value};
expectedTable = [testCase.exampleClass.varTable; newLayer];

testCase.exampleClass.addLayer(testCase.parameterNames);

testCase.verifyEqual(testCase.exampleClass.varTable, expectedTable, 'addLayer does not work correctly');
end

function testAddLayerInvalidFullLayer(testCase)
% Test adding a layer to the layers class.
% If we use an invalid set of layer parameters it should raise
Expand Down
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