Tidies up code and removes unecessary routines

Author: DrPaulSharp

API/insertDataBackgroundIntoContrastData.m

@@ -12,7 +12,7 @@
 
 % Check that we have the same q
 if ~isequal(dataArray(:,1), backgroundArray(:,1))
-    error("q points must be equal for Data and Background Data");
+    throw(exceptions.invalidValue("q points must be equal for Data and Background Data"));
 end
 
 % Insert background data into columns 5 and 6 of contrast data

API/parseClassToStructs.m

@@ -193,40 +193,36 @@
 
 
 %% Deal with backgrounds and resolutions
-backgroundActions = zeros(1, length(inputStruct.contrastBackgrounds));
-for i = 1:length(inputStruct.contrastBackgrounds)
-
-    if strcmpi(inputStruct.contrastBackgroundActions{i}, actions.Add)
-        backgroundActions(i) = 1;
-    else
-        backgroundActions(i) = 2;
-    end
-
-end
+% backgroundActions = zeros(1, length(inputStruct.contrastBackgrounds));
+% for i = 1:length(inputStruct.contrastBackgrounds)
+% 
+%     if strcmpi(inputStruct.contrastBackgroundActions{i}, actions.Add)
+%         backgroundActions(i) = 1;
+%     else
+%         backgroundActions(i) = 2;
+%     end
+% 
+% end
 
 % Convert contrastBackgrounds to custom file/parameter indices
-contrastBackgrounds = inputStruct.contrastBackgrounds;
-backgroundTypes = inputStruct.backgroundTypes;
-
-backgroundParamNames = inputStruct.backgroundParamNames;
+numContrastBackgrounds = length(inputStruct.contrastBackgrounds);
 
-contrastBackgroundParams = cell(1, length(contrastBackgrounds));
-contrastBackgroundTypes = cell(1, length(contrastBackgrounds));
+contrastBackgroundParams = cell(1, numContrastBackgrounds);
+contrastBackgroundTypes = cell(1, numContrastBackgrounds);
 
-for i = 1:length(contrastBackgrounds)
+for i = 1:numContrastBackgrounds
     % Check the type of the background that each contrast is pointing to.
-    thisBack = contrastBackgrounds(i);      % Which background
-    backgroundType = backgroundTypes{thisBack};   % What type is it?
-    contrastBackgroundTypes{i} = backgroundType;
+    thisBack = inputStruct.contrastBackgrounds(i);                       % Which background
+    contrastBackgroundTypes{i} = inputStruct.backgroundTypes{thisBack};  % What type is it?
 
-    switch backgroundType
+    switch contrastBackgroundTypes{i}
 
         case allowedTypes.Constant.value
             % Background is a backgroundParam, the name of which should
             % be in the first column of backgroundValues
 
             % Find which backgroundParam this is, and set contrastBackgroundParams to this number
-            contrastBackgroundParams{i} = find(strcmpi(inputStruct.backgroundValues{thisBack,1}, backgroundParamNames));
+            contrastBackgroundParams{i} = find(strcmpi(inputStruct.backgroundValues{thisBack,1}, inputStruct.backgroundParamNames));
 
         case allowedTypes.Data.value
             % Background is in a datafile.
@@ -255,21 +251,22 @@
             contrastData = insertDataBackgroundIntoContrastData(contrastData,backgroundData);
             problemCells{2}(i) = contrastData;
 
-            % Also add the index of the data offset to the array...
-            contrastBackgroundParams{i} = find(strcmpi(backgroundDataOffset,backgroundParamNames));
-
             % Add the index of the optional data offset to contrastBackgroundParams
-            if ~isempty(backgroundDataIndex)
-                contrastBackgroundParams{i} = find(strcmpi(backgroundDataOffset,backgroundParamNames));
+            offsetIndex = find(strcmpi(backgroundDataOffset,inputStruct.backgroundParamNames));
+            if ~isempty(offsetIndex)
+                contrastBackgroundParams{i} = offsetIndex;
             end
 
         case allowedTypes.Function.value
             % Background is a background function
+            %
+            % We need the index of the custom file the function is defined
+            % in, alongside all of the function parameters.
 
-            % Get the corresponding function name...
+            % Get the corresponding function name
             backgroundFuncfileName = inputStruct.backgroundValues{thisBack,1};
 
-            % Find the index of this data name in the string array...
+            % Find the index of this function name in the custom file array
             backgroundFunctionIndex = find(strcmp(backgroundFuncfileName,inputStruct.fileNames));
 
             if isempty(backgroundFunctionIndex)
@@ -282,7 +279,7 @@
             functionParams = inputStruct.backgroundValues(thisBack,2:end);
             numDefined = length(find(~(cellfun(@(x) isequal(x,""),functionParams))));
             for n = 1:numDefined
-                backgroundParamIndex = find(strcmpi(functionParams{n},backgroundParamNames));
+                backgroundParamIndex = find(strcmpi(functionParams{n},inputStruct.backgroundParamNames));
                 contrastBackgroundParams{i}(n+1) = backgroundParamIndex;
             end
 
@@ -369,7 +366,7 @@
 problemStruct.useImaginary = inputStruct.useImaginary;
 problemStruct.contrastBackgroundParams = contrastBackgroundParams;
 problemStruct.contrastBackgroundTypes = contrastBackgroundTypes;
-problemStruct.contrastBackgroundActions = backgroundActions;
+problemStruct.contrastBackgroundActions = inputStruct.contrastBackgroundActions;
 problemStruct.contrastQzshifts = inputStruct.contrastQzshifts;
 problemStruct.contrastScalefactors = inputStruct.contrastScalefactors;
 problemStruct.contrastBulkIns = inputStruct.contrastBulkIns;

API/projectClass/backgroundsClass.m

@@ -1,6 +1,6 @@
 classdef backgroundsClass < handle
     % Backgrounds are defined in a two stage process. Firstly we define the
-    % actual fitted parameters. These are held in a 'ParametersClass'
+    % actual fitted parameters. These are held in a 'Parameters'
     % table. Then, we group these into the backgrounds themselves using a
     % multiTypeTable. So, we can then use the background parameters to
     % either define background as constant, data or a function. 

compile/fullCompile/makeCompileArgsFull.m

@@ -21,7 +21,7 @@
 ARGS_1_1.contrastBackgroundParams = coder.typeof({ARG},[1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBackgroundTypes = coder.typeof({ARG},[1 maxArraySize],[0 1]);
-ARGS_1_1.contrastBackgroundActions = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.contrastBackgroundActions = coder.typeof({ARG},[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]);
 ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);

compile/reflectivityCalculation/makeCompileArgs.m

@@ -21,7 +21,7 @@
 ARGS_1_1.contrastBackgroundParams = coder.typeof({ARG},[1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastBackgroundTypes = coder.typeof({ARG},[1 maxArraySize],[0 1]);
-ARGS_1_1.contrastBackgroundActions = coder.typeof(0,[1 maxArraySize],[0 1]);
+ARGS_1_1.contrastBackgroundActions = coder.typeof({ARG},[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]);
 ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);

targetFunctions/+domainsTF/customLayers.m

@@ -82,7 +82,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes{i},contrastBackgroundActions(i), ...
+             contrastBackgroundTypes{i},contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              calcAllLayers1{i},calcAllLayers2{i});
@@ -104,7 +104,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes{i},contrastBackgroundActions(i), ...
+             contrastBackgroundTypes{i},contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              calcAllLayers1{i},calcAllLayers2{i});

targetFunctions/+domainsTF/customXY.m

@@ -75,7 +75,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes{i},contrastBackgroundActions(i), ...
+             contrastBackgroundTypes{i},contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,subRoughs(i),inputSldProfiles1{i},inputSldProfiles2{i});
 
@@ -96,7 +96,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes,contrastBackgroundActions(i), ...
+             contrastBackgroundTypes,contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,subRoughs(i),inputSldProfiles1{i},inputSldProfiles2{i});
 

targetFunctions/+domainsTF/reflectivityCalculation.m

@@ -87,7 +87,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes{i},contrastBackgroundActions(i), ...
+             contrastBackgroundTypes{i},contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              domainContrastLayers1{i},domainContrastLayers2{i},outParameterisedLayers);
@@ -110,7 +110,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundTypes{i},contrastBackgroundActions(i), ...
+             contrastBackgroundTypes{i},contrastBackgroundActions{i}, ...
              customFiles,nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              domainContrastLayers1{i},domainContrastLayers2{i},outParameterisedLayers);

targetFunctions/+domainsTF/standardLayers.m

@@ -41,25 +41,21 @@
 % If calc SLD flag is set, then calculate the SLD profile
 if calcSld
 
+    thisSldLays = theseLayers;
+
     % If we need them both, we process real and imaginary parts of the SLD
-    % seperately...
+    % separately
     if useImaginary
         thisSldLays = [theseLayers(:,1:2) theseLayers(:,4:end)];
         thisSldLaysIm = [theseLayers(:,1) theseLayers(:,3:end)];
-    else
-        thisSldLays = theseLayers;
-        thisSldLaysIm = [0 0]; % Dummy value for coder
-    end
-    
-    sldProfile = makeSLDProfiles(bulkIn,bulkOut,thisSldLays,ssubs,repeatLayers);
 
-    % If we have imaginary, we are also
-    % going to need an SLD profile for the imaginary part
-    if useImaginary
         % Note bulkIn and bulkOut = 0 since there is never any imaginary part for
         % the bulk phases..
         sldProfileIm = makeSLDProfiles(0,0,thisSldLaysIm,ssubs,repeatLayers);
     end
+    
+    sldProfile = makeSLDProfiles(bulkIn,bulkOut,thisSldLays,ssubs,repeatLayers);
+
 end
 
 % If required, then resample the SLD