Renames non-polarised TF to normal TF

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/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

examples/domains/README.md

@@ -2,7 +2,7 @@
 
 This folder contains examples of how to use RAT to analyse what are referred
 to as 'Domains TF' samples, which are those where an incoherent sum is required
-in order to calculate the reflectivity. As is the case for normal reflectivity i.e. non-polarised TF, 
+in order to calculate the reflectivity. As is the case for normal reflectivity i.e. normal TF, 
 it is possible to use either 'Standard Layers', 'Custom Layers' or 'Custom XY' models.
 
 The basic principle for all three is that there is an additional fittable 

examples/miscellaneous/absorption/absorptionDPPC50.m

@@ -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)....

examples/miscellaneous/backgroundTypes/DSPCScriptWithDataBackground.m

@@ -1,7 +1,7 @@
 % Standard Layers fit of a DSPC floating bilayer
 
 % Make the project
-problem = createProject(name='original_dspc_bilayer', calcType='non polarised', model='standard layers', geometry='substrate/liquid', absorption=false);
+problem = createProject(name='original_dspc_bilayer', calcType='normal', model='standard layers', geometry='substrate/liquid', absorption=false);
 
 % Make priors visible
 problem.showPriors(true);

examples/miscellaneous/backgroundTypes/DSPCScriptWithFunctionBackground.m

@@ -1,7 +1,7 @@
 % Standard Layers fit of a DSPC floating bilayer
 
 % Make the project
-problem = createProject(name='original_dspc_bilayer', calcType='non polarised', model='standard layers', geometry='substrate/liquid', absorption=false);
+problem = createProject(name='original_dspc_bilayer', calcType='normal', model='standard layers', geometry='substrate/liquid', absorption=false);
 
 % Make priors visible
 problem.showPriors(true);

examples/normalReflectivity/README.md

@@ -1,7 +1,7 @@
-## 'Non-polarised Target Functions' Examples
+## 'Normal Target Functions' Examples
 
 This folder contains examples of how to use RAT to analyse what are referred
-to as 'Non-polarised TF' samples. This refers to reflectivity data that does not use
+to as 'Normal TF' samples. This refers to reflectivity data that does not use
 absorption (i.e. an imaginary SLD), and is not analysed as magnetic, polarised or
 oil-water data. 
 

examples/normalReflectivity/standardLayers/standardLayersDSPCScript.m

@@ -1,7 +1,7 @@
 % Standard Layers fit of a DSPC floating bilayer
 
 % Make the project
-problem = createProject(name='original_dspc_bilayer', calcType='non polarised', model='standard layers', geometry='substrate/liquid', absorption=false);
+problem = createProject(name='original_dspc_bilayer', calcType='normal', model='standard layers', geometry='substrate/liquid', absorption=false);
 
 % Make priors visible..
 problem.showPriors = true;

targetFunctions/+domainsTF/customLayers.m

@@ -163,11 +163,11 @@
 
     % Call the core layers calculation - need to do this once for each
     % domain
-    [sldProfile1,reflect1,simul1,~,layerSld1,resampledLayer1,~] = nonPolarisedTF.coreLayersCalculation(calcAllLayers1,roughness,...
+    [sldProfile1,reflect1,simul1,~,layerSld1,resampledLayer1,~] = normalTF.coreLayersCalculation(calcAllLayers1,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
-    [sldProfile2,reflect2,simul2,shiftedData,layerSld2,resampledLayer2,~] = nonPolarisedTF.coreLayersCalculation(calcAllLayers2,roughness,...
+    [sldProfile2,reflect2,simul2,shiftedData,layerSld2,resampledLayer2,~] = normalTF.coreLayersCalculation(calcAllLayers2,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 

targetFunctions/+domainsTF/standardLayers.m

@@ -176,11 +176,11 @@
 
     % Call the core layers calculation - need to do this once for each
     % domain
-    [sldProfile1,reflect1,simul1,~,layerSld1,resampledLayer1,~] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers1,roughness,...
+    [sldProfile1,reflect1,simul1,~,layerSld1,resampledLayer1,~] = normalTF.coreLayersCalculation(thisContrastLayers1,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
-    [sldProfile2,reflect2,simul2,shiftedData,layerSld2,resampledLayer2,~] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers2,roughness,...
+    [sldProfile2,reflect2,simul2,shiftedData,layerSld2,resampledLayer2,~] = normalTF.coreLayersCalculation(thisContrastLayers2,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 

targetFunctions/+nonPolarisedTF/coreLayersCalculation.m → targetFunctions/+normalTF/coreLayersCalculation.m

@@ -4,7 +4,7 @@
     resolution,background,backgroundAction,params,parallelPoints,resampleMinAngle,resampleNPoints,useImaginary)
 
 %   This is the main reflectivity calculation for all Layers models in the 
-%   non polarised target function. 
+%   normal target function. 
 %
 %   The function first arranges the 
 %   roughness' in the correct order according

targetFunctions/+nonPolarisedTF/customLayers.m → targetFunctions/+normalTF/customLayers.m

@@ -1,10 +1,10 @@
 function [qzshifts,scalefactors,bulkIns,bulkOuts,...
     resolutionParams,chis,reflectivity,simulation,shiftedData,backgrounds,layerSlds,...
     sldProfiles,resampledLayers,subRoughs] = customLayers(problemStruct,problemCells,controls)
-    % The custom layers, nonPolarisedTF reflectivity calculation.
+    % The custom layers, normalTF reflectivity calculation.
     % The function extracts the relevant parameters from the input arrays,
     % allocates these on a pre-contrast basis, then calls the
-    % 'coreLayersCalculation' (the core layers nonPolarisedTF calc is
+    % 'coreLayersCalculation' (the core layers normalTF calc is
     % shared between multiple calculation types).
 
     % Extract individual cell arrays
@@ -44,7 +44,7 @@
     sldProfiles = cell(numberOfContrasts,1);
 
     % Process the custom models
-    [resampledLayers,subRoughs] = nonPolarisedTF.customLayers.processCustomFunction(contrastBulkInIndices,contrastBulkOutIndices,...
+    [resampledLayers,subRoughs] = normalTF.customLayers.processCustomFunction(contrastBulkInIndices,contrastBulkOutIndices,...
         bulkInArray,bulkOutArray,cCustFiles,numberOfContrasts,customFiles,params,useImaginary);
 
     if strcmpi(parallel, coderEnums.parallelOptions.Contrasts)
@@ -120,7 +120,7 @@
 
     % Call the core layers calculation
     [sldProfile,reflectivity,simulation,shiftedData,layerSld,resampledLayer,...
-     chi] = nonPolarisedTF.coreLayersCalculation(layer,roughness,...
+     chi] = normalTF.coreLayersCalculation(layer,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 

targetFunctions/+nonPolarisedTF/customXY.m → targetFunctions/+normalTF/customXY.m

@@ -39,7 +39,7 @@
     resampledLayers = cell(numberOfContrasts,1);
 
     % Process the custom models
-    [sldProfiles,subRoughs] = nonPolarisedTF.customXY.processCustomFunction(contrastBulkInIndices,contrastBulkOutIndices,...
+    [sldProfiles,subRoughs] = normalTF.customXY.processCustomFunction(contrastBulkInIndices,contrastBulkOutIndices,...
         bulkInArray,bulkOutArray,cCustFiles,numberOfContrasts,customFiles,params);
 
     if strcmpi(parallel, coderEnums.parallelOptions.Contrasts)

targetFunctions/+nonPolarisedTF/standardLayers.m → targetFunctions/+normalTF/standardLayers.m

@@ -133,7 +133,7 @@
 
     % Call the core layers calculation
     [sldProfile,reflectivity,simulation,shiftedData,layerSld,resampledLayer,...
-     chi] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers,roughness,...
+     chi] = normalTF.coreLayersCalculation(thisContrastLayers,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,shiftedData,simLimits,repeatLayers,...
      resolutionParamValue,background,backgroundAction,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 

targetFunctions/reflectivityCalculation.m

@@ -7,21 +7,21 @@
 % (i.e. 'Target function' is required, and call the relevant routines.
 % The types of available target functions are:*
 %
-% * non polarised  - The main basic target function type, for non polarised neutrons (or x-rays) with non-absorbing samples. Different model types are specified in sub functions from here.
+% * normal     - The main basic target function type, for non polarised neutrons (or x-rays) with non-absorbing samples. Different model types are specified in sub functions from here.
 %
-% * oil water      - Target function for oil-water samples
+% * oil water  - Target function for oil-water samples
 %
-% * domains        - Target function for samples consisting of domains which are larger than the beam lateral coherence length.
+% * domains    - Target function for samples consisting of domains which are larger than the beam lateral coherence length.
 %
-% * magnetic       - Target function for cases for polarised neutrons with polarisation analysis.
+% * magnetic   - Target function for cases for polarised neutrons with polarisation analysis.
 %                       
 
 % Decide which target function we are calling and call the relevant routines
 targetFunction = problemStruct.TF;
 modelType = problemStruct.modelType;
 
 switch targetFunction
-    case coderEnums.calculationTypes.NonPolarised      
+    case coderEnums.calculationTypes.Normal      
 
         switch lower(modelType)
 
@@ -30,21 +30,21 @@
                 [qzshifts,scalefactors,bulkIns,bulkOuts,...
                  resolutionParams,chis,reflectivity,simulation,shiftedData,...
                  backgrounds,layerSlds,sldProfiles,resampledLayers,...
-                 subRoughs] = nonPolarisedTF.standardLayers(problemStruct,problemCells,controls);
+                 subRoughs] = normalTF.standardLayers(problemStruct,problemCells,controls);
 
             case coderEnums.modelTypes.CustomLayers
 
                 [qzshifts,scalefactors,bulkIns,bulkOuts,...
                  resolutionParams,chis,reflectivity,simulation,shiftedData,...
                  backgrounds,layerSlds,sldProfiles,resampledLayers,...
-                 subRoughs] = nonPolarisedTF.customLayers(problemStruct,problemCells,controls);
+                 subRoughs] = normalTF.customLayers(problemStruct,problemCells,controls);
 
             case coderEnums.modelTypes.CustomXY
 
                 [qzshifts,scalefactors,bulkIns,bulkOuts,...
                  resolutionParams,chis,reflectivity,simulation,shiftedData,...
                  backgrounds,layerSlds,sldProfiles,resampledLayers,...
-                 subRoughs] = nonPolarisedTF.customXY(problemStruct,problemCells,controls);
+                 subRoughs] = normalTF.customXY(problemStruct,problemCells,controls);
 
             otherwise
                 error('The model type "%s" is not supported', modelType);

tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXYScript.m → tests/normalTFReflectivityCalculation/DPPCCustomXYScript.m

@@ -34,7 +34,7 @@
 
 %%
 % Now add the custom file to the project..
-project.addCustomFile('DPPC Model','DPPCCustomXY.m','matlab','tests/nonPolarisedTFReflectivityCalculation/');
+project.addCustomFile('DPPC Model','DPPCCustomXY.m','matlab','tests/normalTFReflectivityCalculation/');
 
 
 %% 

tests/nonPolarisedTFReflectivityCalculation/makeInputsAndOutputs.m → tests/normalTFReflectivityCalculation/makeInputsAndOutputs.m

@@ -21,7 +21,7 @@
 inputs.controlsInput = controlsInput;
 inputs.controls = controls;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customLayersInputs'],'inputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/customLayersInputs'],'inputs');
 
 % (b) Outputs
 resultStruct = reflectivityCalculation(problemStruct,problemCells,problemLimits,controls);
@@ -39,12 +39,12 @@
 outputs.project = project;
 outputs.result = result;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs'],'outputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/customLayersOutputs'],'outputs');
 
 % (c) TF Parameters
 [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,...
  chis,reflectivity,simulation,shiftedData,backgrounds,layerSlds,sldProfiles,...
- resampledLayers,subRoughs] = nonPolarisedTF.customLayers(problemStruct,problemCells,controls);
+ resampledLayers,subRoughs] = normalTF.customLayers(problemStruct,problemCells,controls);
 
 TFParams.qzshifts = qzshifts;
 TFParams.scalefactors = scalefactors;
@@ -62,7 +62,7 @@
 TFParams.sldProfiles = sldProfiles;
 TFParams.resampledLayers = resampledLayers;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams'],'TFParams');
+save([root filesep 'tests/normalTFReflectivityCalculation/customLayersTFParams'],'TFParams');
 
 %% 2. Custom XY.
 % (a) Inputs
@@ -82,7 +82,7 @@
 inputs.controlsInput = controlsInput;
 inputs.controls = controls;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customXYInputs'],'inputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/customXYInputs'],'inputs');
 
 % (b) Outputs
 resultStruct = reflectivityCalculation(problemStruct,problemCells,problemLimits,controls);
@@ -100,12 +100,12 @@
 outputs.project = project;
 outputs.result = result;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customXYOutputs'],'outputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/customXYOutputs'],'outputs');
 
 % (c) TF Parameters
 [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,...
  chis,reflectivity,simulation,shiftedData,backgrounds,layerSlds,sldProfiles,...
- resampledLayers, subRoughs] = nonPolarisedTF.customXY(problemStruct,problemCells,controls);
+ resampledLayers, subRoughs] = normalTF.customXY(problemStruct,problemCells,controls);
 
 TFParams.qzshifts = qzshifts;
 TFParams.scalefactors = scalefactors;
@@ -123,7 +123,7 @@
 TFParams.sldProfiles = sldProfiles;
 TFParams.resampledLayers = resampledLayers;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/customXYTFParams'],'TFParams');
+save([root filesep 'tests/normalTFReflectivityCalculation/customXYTFParams'],'TFParams');
 
 %% 3. Standard Layers
 % (a) Inputs
@@ -144,7 +144,7 @@
 inputs.controlsInput = controlsInput;
 inputs.controls = controls;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs'],'inputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/standardLayersInputs'],'inputs');
 
 % (b) Outputs
 resultStruct = reflectivityCalculation(problemStruct,problemCells,problemLimits,controls);
@@ -162,12 +162,12 @@
 outputs.project = project;
 outputs.result = result;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs'],'outputs');
+save([root filesep 'tests/normalTFReflectivityCalculation/standardLayersOutputs'],'outputs');
 
 % (c) TF Parameters
 [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,...
  chis,reflectivity,simulation,shiftedData,backgrounds,layerSlds,sldProfiles,...
- resampledLayers,subRoughs] = nonPolarisedTF.standardLayers(problemStruct,problemCells,controls);
+ resampledLayers,subRoughs] = normalTF.standardLayers(problemStruct,problemCells,controls);
 
 TFParams.qzshifts = qzshifts;
 TFParams.scalefactors = scalefactors;
@@ -185,7 +185,7 @@
 TFParams.sldProfiles = sldProfiles;
 TFParams.resampledLayers = resampledLayers;
 
-save([root filesep 'tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams'],'TFParams');
+save([root filesep 'tests/normalTFReflectivityCalculation/standardLayersTFParams'],'TFParams');
 
 %% 4. Converting between RAT and RASCAL
 

tests/nonPolarisedTFReflectivityCalculation/orsoDSPCCustomLayers.m → tests/normalTFReflectivityCalculation/orsoDSPCCustomLayers.m

@@ -71,7 +71,7 @@
 % 
 % Add the custom file to the project....
 
-project.addCustomFile('DSPC Model','customBilayer.m','matlab','tests/nonPolarisedTFReflectivityCalculation/');
+project.addCustomFile('DSPC Model','customBilayer.m','matlab','tests/normalTFReflectivityCalculation/');
 %% 
 % 
 %