Adds code to convert backgrounds to background parameters (#237)

RascalSoftware · Jun 17, 2024 · ce5a9e6 · ce5a9e6
1 parent 2257620
commit ce5a9e6
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Showing 29 changed files with 57 additions and 27 deletions.
diff --git a/API/checkIndices.m b/API/checkIndices.m
@@ -3,10 +3,10 @@ function checkIndices(problemStruct)
     % 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)));
+    for i = 1:length(problemStruct.contrastBackgroundParams)
+        index = problemStruct.contrastBackgroundParams(i);
+        if (index < 1 && index ~= -1) || index > numBackgroundParams
+            throw(exceptions.indexOutOfRange(sprintf('contrastBackgroundParams(%i) is %i, which is outside the range of backgroundParams', i, index)));
         end
     end
 

diff --git a/API/parseClassToStructs.m b/API/parseClassToStructs.m
@@ -237,6 +237,33 @@
 
 end
 
+% Convert contrastBackgrounds to parameter indices
+contrastBackgrounds = inputStruct.contrastBackgrounds;
+backgroundTypes = inputStruct.backgroundTypes;
+
+backgroundParamNames = inputStruct.backgroundParamNames;
+contrastBackgroundParams = zeros(1, length(contrastBackgrounds));
+
+for i = 1:length(contrastBackgrounds)
+    % Check the type of the background that each contrast is pointing to.
+    % If it is a constant, point to the number of the corresponding
+    % background param. If it's data, then set it to -1
+    thisBack = contrastBackgrounds(i);      % Which background
+    thisType = backgroundTypes{thisBack};   % What type is it?
+
+    if strcmpi(thisType,'data')
+        % Background is in the datafile. Set contrastBackgroundParams to -1
+        contrastBackgroundParams(i) = -1;
+    else
+        % Background is a backgroundParam, the name of which should
+        % be in the first column of backgroundValues
+        whichBackgroundParamName = inputStruct.backgroundValues{thisBack,1};
+
+        % Find which backgroundParam this is, and set contrastBackgroundParams to this number
+        contrastBackgroundParams(i) = find(strcmpi(whichBackgroundParamName,backgroundParamNames));
+    end
+end
+
 % Here we need to do the same with the contrastResolutions array
 contrastResolutions = inputStruct.contrastResolutions;
 resolutionTypes = inputStruct.resolutionTypes;
@@ -260,8 +287,7 @@
         whichResolutionParamName = inputStruct.resolutionValues{thisResol,1};
 
         % Find which resolutionParam this is, and set contrastResolutionParams to this number
-        resolutionParamNumber = find(strcmpi(whichResolutionParamName,resolutionParamNames));
-        contrastResolutionParams(i) = resolutionParamNumber;
+        contrastResolutionParams(i) = find(strcmpi(whichResolutionParamName,resolutionParamNames));
     end
 end
 
@@ -320,7 +346,7 @@
 problemStruct.numberOfContrasts = inputStruct.numberOfContrasts;
 problemStruct.geometry = inputStruct.geometry;
 problemStruct.useImaginary = inputStruct.useImaginary;
-problemStruct.contrastBackgrounds = inputStruct.contrastBackgrounds;
+problemStruct.contrastBackgroundParams = contrastBackgroundParams;
 problemStruct.contrastBackgroundActions = backgroundActions;
 problemStruct.contrastQzshifts = inputStruct.contrastQzshifts;
 problemStruct.contrastScalefactors = inputStruct.contrastScalefactors;

diff --git a/compile/fullCompile/makeCompileArgsFull.m b/compile/fullCompile/makeCompileArgsFull.m
@@ -16,7 +16,7 @@
 ARGS_1_1.numberOfContrasts = coder.typeof(0);
 ARGS_1_1.geometry = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.useImaginary = coder.typeof(true,[1 1],[0 0]);
-ARGS_1_1.contrastBackgrounds = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.contrastBackgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBackgroundActions = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastQzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastScalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);

diff --git a/compile/reflectivityCalculation/makeCompileArgs.m b/compile/reflectivityCalculation/makeCompileArgs.m
@@ -16,7 +16,7 @@
 ARGS_1_1.numberOfContrasts = coder.typeof(0);
 ARGS_1_1.geometry = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.useImaginary = coder.typeof(true,[1 1],[0 0]);
-ARGS_1_1.contrastBackgrounds = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.contrastBackgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBackgroundActions = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastQzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastScalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);

diff --git a/examples/domains/standardLayers/domainsStandardLayersScript.m b/examples/domains/standardLayers/domainsStandardLayersScript.m
@@ -55,10 +55,10 @@
     'bulk out' }; 
 
 Layer3 = {'Layer 3',...         % Name of the layer
-    'L2 thick',...              % Layer thickness
-    'L2 SLD',...                % Layer SLD
-    'L2 Rough',...              % Layer roughness
-    'L2 Hydr',...               % hydration (precent)
+    'L3 thick',...              % Layer thickness
+    'L3 SLD',...                % Layer SLD
+    'L3 Rough',...              % Layer roughness
+    'L3 Hydr',...               % hydration (precent)
     'bulk out' };
 
 problem.addLayerGroup({Layer1, Layer2, Layer3});

diff --git a/targetFunctions/common/backSort.m b/targetFunctions/common/backSort.m
@@ -1,12 +1,12 @@
-function [outBackgroundParam,outQzshift,outScalefactor,outBulkIn,outBulkOut,outResolutionParam] = backSort(contrastBackgrounds,contrastQzshifts,contrastScalefactors,contrastBulkIns,contrastBulkOuts,contrastResolutionParams,backgroundParams,qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams)
+function [outBackgroundParam,outQzshift,outScalefactor,outBulkIn,outBulkOut,outResolutionParam] = backSort(contrastBackgroundParams,contrastQzshifts,contrastScalefactors,contrastBulkIns,contrastBulkOuts,contrastResolutionParams,backgroundParams,qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams)
     % Distributes the background and shift values among the different contrasts
     %
     % USAGE::
     %
     %    [backgroundParams,qzshift,scalefactor,bulkIn,bulkOut,resolutionParams] = backsort(contrastBackgrounds,contrastQzshifts,contrastScalefactors,contrastBulkIns,contrastBulkOuts,contrastResolutions,backs,qzshifts,scalefactor,bulkIn,bulkOut,res)
     %
     % INPUTS:
-    %    * contrastBackgrounds: Which background value is associated with each contrast
+    %    * contrastBackgroundParams: Which background value is associated with each contrast
     %    * contrastQzshifts: Which qz_shift value is associated with each contrast
     %    * contrastScalefactors: Which scalefactor value is associated with each contrast
     %    * contrastBulkIns: Which BulkIn value is associated with each contrast
@@ -27,8 +27,12 @@
     %    * outBulkOut: list of actual bulkOut values for each contrast
     %    * outResolution: list of actual resolution parameter for each contrast  
 
-        outBackgroundParam = backgroundParams(contrastBackgrounds);
-
+        if contrastBackgroundParams ~= -1
+            outBackgroundParam = backgroundParams(contrastBackgroundParams);
+        else
+            outBackgroundParam = -1;     % Negative value means we have a data background.
+        end
+
         outQzshift = qzshifts(contrastQzshifts);
 
         outScalefactor = scalefactors(contrastScalefactors);

diff --git a/targetFunctions/common/extractProblemParams.m b/targetFunctions/common/extractProblemParams.m
@@ -1,12 +1,12 @@
-function [numberOfContrasts, geometry, contrastBackgrounds, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
+function [numberOfContrasts, geometry, contrastBackgroundParams, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
 contrastResolutionParams, contrastDomainRatios, backgroundParams, qzshifts, scalefactors, bulkIn, bulkOut, resolutionParams, domainRatio,...
 dataPresent, nParams, params, numberOfLayers, resample, contrastBackgroundActions, contrastCustomFiles, useImaginary] = extractProblemParams(problemStruct)
 
 %Extract individual parameters from problem
 
 numberOfContrasts = problemStruct.numberOfContrasts;
 geometry = problemStruct.geometry;
-contrastBackgrounds = problemStruct.contrastBackgrounds;
+contrastBackgroundParams = problemStruct.contrastBackgroundParams;
 contrastBackgroundActions = problemStruct.contrastBackgroundActions;
 contrastQzshifts = problemStruct.contrastQzshifts;
 contrastScalefactors = problemStruct.contrastScalefactors;

diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/testDomainsReflectivityCalculations.m b/tests/domainsTFReflectivityCalculation/testDomainsReflectivityCalculations.m
@@ -227,10 +227,10 @@ function testCheckIndices(testCase)
 
             % Test Background Param Error
             testInput = testCase.problemStruct;
-            testInput.contrastBackgrounds(1) = 0;
+            testInput.contrastBackgroundParams(1) = 0;
             testCase.verifyError(@() checkIndices(testInput), exceptions.indexOutOfRange.errorID);
             testInput = testCase.problemStruct;
-            testInput.contrastBackgrounds(1) = 4;
+            testInput.contrastBackgroundParams(1) = 4;
             testCase.verifyError(@() checkIndices(testInput), exceptions.indexOutOfRange.errorID);
 
             % Test Qzshift Error
@@ -296,13 +296,13 @@ function testParseCells(testCase)
         end        
 
         function testExtractProblemParams(testCase)
-            [numberOfContrasts, geometry, contrastBackgrounds, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
+            [numberOfContrasts, geometry, contrastBackgroundParams, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
             contrastResolutionParams, contrastDomainRatios, backgroundParams, qzshifts, scalefactors, bulkIn, bulkOut, resolutionParams, domainRatio,...
             dataPresent, nParams, params, numberOfLayers, resample, backgroundParamsType, contrastCustomFiles, useImaginary] = extractProblemParams(testCase.problemStruct);
 
             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(contrastBackgrounds, testCase.problemStruct.contrastBackgrounds, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
+            testCase.verifyEqual(contrastBackgroundParams, testCase.problemStruct.contrastBackgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastQzshifts, testCase.problemStruct.contrastQzshifts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastScalefactors, testCase.problemStruct.contrastScalefactors, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastBulkIns, testCase.problemStruct.contrastBulkIns, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);

diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m b/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m
@@ -227,10 +227,10 @@ function testCheckIndices(testCase)
 
             % Test Background Param Error
             testInput = testCase.problemStruct;
-            testInput.contrastBackgrounds(1) = 0;
+            testInput.contrastBackgroundParams(1) = 0;
             testCase.verifyError(@() checkIndices(testInput), exceptions.indexOutOfRange.errorID);
             testInput = testCase.problemStruct;
-            testInput.contrastBackgrounds(1) = 4;
+            testInput.contrastBackgroundParams(1) = 4;
             testCase.verifyError(@() checkIndices(testInput), exceptions.indexOutOfRange.errorID);
 
             % Test Qzshift Error
@@ -296,13 +296,13 @@ function testParseCells(testCase)
         end        
 
         function testExtractProblemParams(testCase)
-            [numberOfContrasts, geometry, contrastBackgrounds, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
+            [numberOfContrasts, geometry, contrastBackgroundParams, contrastQzshifts, contrastScalefactors, contrastBulkIns, contrastBulkOuts,...
             contrastResolutionParams, contrastDomainRatios, backgroundParams, qzshifts, scalefactors, bulkIn, bulkOut, resolutionParams, domainRatio,...
             dataPresent, nParams, params, numberOfLayers, resample, backgroundParamsType, contrastCustomFiles, useImaginary] = extractProblemParams(testCase.problemStruct);
 
             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(contrastBackgrounds, testCase.problemStruct.contrastBackgrounds, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
+            testCase.verifyEqual(contrastBackgroundParams, testCase.problemStruct.contrastBackgroundParams, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastQzshifts, testCase.problemStruct.contrastQzshifts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastScalefactors, testCase.problemStruct.contrastScalefactors, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);
             testCase.verifyEqual(contrastBulkIns, testCase.problemStruct.contrastBulkIns, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance);

diff --git a/tests/testProjectConversion/DSPCBilayerProjectClass.mat b/tests/testProjectConversion/DSPCBilayerProjectClass.mat
diff --git a/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat b/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat