Renames non-polarised calculation to normal calculation (#281)

Author: StephenNneji

API/createProject.m

@@ -7,10 +7,10 @@
     % absorption terms are included in the refractive index.
     % All of the arguments are optional.
     %
-    % project = createProject(name='New experiment', calc='non polarised');
+    % project = createProject(name='New experiment', calc='normal');
     arguments
         options.name {mustBeTextScalar} = ''
-        options.calcType = calculationTypes.NonPolarised
+        options.calcType = calculationTypes.Normal
         options.model = modelTypes.StandardLayers
         options.geometry = geometryOptions.AirSubstrate
         options.absorption {mustBeA(options.absorption,'logical')} = false

API/enums/calculationTypes.m

@@ -14,7 +14,7 @@
     end
 
     enumeration
-        NonPolarised ('non polarised')
+        Normal ('normal')
         Domains ('domains')
         OilWater ('oil water')
         Magnetic ('magnetic')

API/makeEmptyResultStruct.m

@@ -4,7 +4,7 @@
     %
     % nParams = number of fitted parameters
     % nContrasts = number of contrasts
-    % nDomains = number of domains - 1 for non-polarised, 2 for domains
+    % nDomains = number of domains - 1 for normal, 2 for domains
     %
     % result = 
     % 

API/projectClass/customFileClass.m

@@ -237,7 +237,7 @@ function displayTable(obj)
             % Convert the custom files class to a struct
             %
             % customFiles.toStruct()
-            fileStruct.files = {};
+            fileStruct.files = cell(1, 0);
             fileStruct.fileIdentifiers = {};
             numberOfFiles = obj.rowCount;      
             if numberOfFiles > 0

API/projectClass/domainsClass.m

@@ -53,10 +53,10 @@
             % Alias of the converter routine from domainsClass to
             % projectClass.
             % This routine takes the currently defined project and
-            % converts it to a nonPolarised calculation, preserving all
+            % converts it to a normal calculation, preserving all
             % currently defined properties.
             %
-            % nonPolarisedProject = project.toProjectClass();
+            % normalProject = project.toProjectClass();
             projectObj = obj.projectClass();
         end
 
@@ -245,11 +245,11 @@
         function projectObj = projectClass(obj)
             % Converter routine from domainsClass to projectClass.
             % This routine takes the currently defined project and
-            % converts it to a nonPolarised calculation, preserving all
+            % converts it to a normal calculation, preserving all
             % currently defined properties.
             %
-            % nonPolarisedProject = project.projectClass();
-            projectObj = projectClass(obj.experimentName, calculationTypes.NonPolarised, obj.modelType, obj.geometry, obj.absorption);
+            % normalProject = project.projectClass();
+            projectObj = projectClass(obj.experimentName, calculationTypes.Normal, obj.modelType, obj.geometry, obj.absorption);
             projectObj = copyProperties(obj, projectObj);
 
             % Need to treat contrasts separately due to changes in the

API/projectClass/projectClass.m

@@ -64,7 +64,7 @@
             % project = projectClass('New experiment');
             arguments
                 experimentName {mustBeTextScalar} = ''
-                calculationType = calculationTypes.NonPolarised
+                calculationType = calculationTypes.Normal
                 modelType = modelTypes.StandardLayers
                 geometry = geometryOptions.AirSubstrate
                 absorption {mustBeA(absorption,'logical')} = false

compile/fullCompile/makeCompileArgsFull.m

@@ -50,7 +50,7 @@
 ARG = coder.typeof(0,[1 10],[1 1]);
 ARGS_1_1.layersDetails = coder.typeof({ARG}, [maxArraySize 1],[1 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARGS_1_1.customFiles = coder.typeof({ARG}, [1 maxArraySize], [1 1]);
+ARGS_1_1.customFiles = coder.typeof({ARG}, [1 maxArraySize], [0 1]);
 ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastCustomFiles = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastDomainRatios = coder.typeof(0,[1 maxArraySize],[0 1]);

compile/reflectivityCalculation/makeCompileArgs.m

@@ -50,7 +50,7 @@
 ARG = coder.typeof(0,[1 10],[1 1]);
 ARGS_1_1.layersDetails = coder.typeof({ARG}, [maxArraySize 1],[1 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARGS_1_1.customFiles = coder.typeof({ARG}, [1 maxArraySize], [1 1]);
+ARGS_1_1.customFiles = coder.typeof({ARG}, [1 maxArraySize], [0 1]);
 ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastCustomFiles = coder.typeof(0,[1 maxArraySize],[0 1]);
 ARGS_1_1.contrastDomainRatios = coder.typeof(0,[1 maxArraySize],[0 1]);

examples/domains/README.md

@@ -2,7 +2,7 @@
 
 
 % Set up the initial project....
-problem = createProject(name = 'DPPC_50_3pcBins', calcType = 'non polarised',...
+problem = createProject(name = 'DPPC_50_3pcBins', calcType = 'normal',...
     model = 'custom layers', geometry = 'substrate/liquid', absorption = true);
 
 % Add the required parameters (substrate reference as already there by default)....