diff --git a/API/createProject.m b/API/createProject.m index cf87c1e9d..1166cb806 100644 --- a/API/createProject.m +++ b/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 diff --git a/API/enums/calculationTypes.m b/API/enums/calculationTypes.m index eeb8d7cac..ab294b7b9 100644 --- a/API/enums/calculationTypes.m +++ b/API/enums/calculationTypes.m @@ -14,7 +14,7 @@ end enumeration - NonPolarised ('non polarised') + Normal ('normal') Domains ('domains') OilWater ('oil water') Magnetic ('magnetic') diff --git a/API/makeEmptyResultStruct.m b/API/makeEmptyResultStruct.m index a367f3e63..527fef828 100644 --- a/API/makeEmptyResultStruct.m +++ b/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 = % diff --git a/API/projectClass/customFileClass.m b/API/projectClass/customFileClass.m index 538fd90fa..19d835f07 100644 --- a/API/projectClass/customFileClass.m +++ b/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 diff --git a/API/projectClass/domainsClass.m b/API/projectClass/domainsClass.m index 928aaedab..d1acca6ce 100644 --- a/API/projectClass/domainsClass.m +++ b/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 diff --git a/API/projectClass/projectClass.m b/API/projectClass/projectClass.m index 51b6d7061..2a58e9194 100644 --- a/API/projectClass/projectClass.m +++ b/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 diff --git a/compile/fullCompile/makeCompileArgsFull.m b/compile/fullCompile/makeCompileArgsFull.m index 2c1e637f5..02182db5c 100644 --- a/compile/fullCompile/makeCompileArgsFull.m +++ b/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]); diff --git a/compile/reflectivityCalculation/makeCompileArgs.m b/compile/reflectivityCalculation/makeCompileArgs.m index 6950a9242..66ed629bf 100644 --- a/compile/reflectivityCalculation/makeCompileArgs.m +++ b/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]); diff --git a/examples/domains/README.md b/examples/domains/README.md index 7f650a5b4..027e226d8 100644 --- a/examples/domains/README.md +++ b/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 diff --git a/examples/miscellaneous/absorption/absorptionDPPC50.m b/examples/miscellaneous/absorption/absorptionDPPC50.m index f0a3ec491..75730ca62 100644 --- a/examples/miscellaneous/absorption/absorptionDPPC50.m +++ b/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).... diff --git a/examples/miscellaneous/backgroundTypes/DSPCScriptWithDataBackground.m b/examples/miscellaneous/backgroundTypes/DSPCScriptWithDataBackground.m index eac0113e7..633c07b01 100644 --- a/examples/miscellaneous/backgroundTypes/DSPCScriptWithDataBackground.m +++ b/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); diff --git a/examples/miscellaneous/backgroundTypes/DSPCScriptWithFunctionBackground.m b/examples/miscellaneous/backgroundTypes/DSPCScriptWithFunctionBackground.m index 1ccae8473..f29c79708 100644 --- a/examples/miscellaneous/backgroundTypes/DSPCScriptWithFunctionBackground.m +++ b/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); diff --git a/examples/normalReflectivity/README.md b/examples/normalReflectivity/README.md index 039c044f5..deab18b2e 100644 --- a/examples/normalReflectivity/README.md +++ b/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. diff --git a/examples/normalReflectivity/customLayers/customLayersDSPCSheet.mlx b/examples/normalReflectivity/customLayers/customLayersDSPCSheet.mlx index 6510bc6a5..fd781e046 100644 Binary files a/examples/normalReflectivity/customLayers/customLayersDSPCSheet.mlx and b/examples/normalReflectivity/customLayers/customLayersDSPCSheet.mlx differ diff --git a/examples/normalReflectivity/standardLayers/standardLayersDSPCScript.m b/examples/normalReflectivity/standardLayers/standardLayersDSPCScript.m index dbe55acfa..be94b1171 100644 --- a/examples/normalReflectivity/standardLayers/standardLayersDSPCScript.m +++ b/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; diff --git a/examples/normalReflectivity/standardLayers/standardLayersDSPCSheet.mlx b/examples/normalReflectivity/standardLayers/standardLayersDSPCSheet.mlx index 9c1e8f6bc..35248f719 100644 Binary files a/examples/normalReflectivity/standardLayers/standardLayersDSPCSheet.mlx and b/examples/normalReflectivity/standardLayers/standardLayersDSPCSheet.mlx differ diff --git a/targetFunctions/+domainsTF/customLayers.m b/targetFunctions/+domainsTF/customLayers.m index ab5ca06c2..439e0581f 100644 --- a/targetFunctions/+domainsTF/customLayers.m +++ b/targetFunctions/+domainsTF/customLayers.m @@ -158,11 +158,11 @@ % 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); diff --git a/targetFunctions/+domainsTF/standardLayers.m b/targetFunctions/+domainsTF/standardLayers.m index 48bc2dfbc..e2f8e10aa 100644 --- a/targetFunctions/+domainsTF/standardLayers.m +++ b/targetFunctions/+domainsTF/standardLayers.m @@ -166,11 +166,11 @@ % 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); diff --git a/targetFunctions/+nonPolarisedTF/+customLayers/processCustomFunction.m b/targetFunctions/+normalTF/+customLayers/processCustomFunction.m similarity index 100% rename from targetFunctions/+nonPolarisedTF/+customLayers/processCustomFunction.m rename to targetFunctions/+normalTF/+customLayers/processCustomFunction.m diff --git a/targetFunctions/+nonPolarisedTF/+customXY/processCustomFunction.m b/targetFunctions/+normalTF/+customXY/processCustomFunction.m similarity index 100% rename from targetFunctions/+nonPolarisedTF/+customXY/processCustomFunction.m rename to targetFunctions/+normalTF/+customXY/processCustomFunction.m diff --git a/targetFunctions/+nonPolarisedTF/coreLayersCalculation.m b/targetFunctions/+normalTF/coreLayersCalculation.m similarity index 100% rename from targetFunctions/+nonPolarisedTF/coreLayersCalculation.m rename to targetFunctions/+normalTF/coreLayersCalculation.m diff --git a/targetFunctions/+nonPolarisedTF/customLayers.m b/targetFunctions/+normalTF/customLayers.m similarity index 94% rename from targetFunctions/+nonPolarisedTF/customLayers.m rename to targetFunctions/+normalTF/customLayers.m index d6ed31512..0c7440d90 100644 --- a/targetFunctions/+nonPolarisedTF/customLayers.m +++ b/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,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 parameters from problemStruct @@ -37,7 +37,7 @@ 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) @@ -113,7 +113,7 @@ % 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); diff --git a/targetFunctions/+nonPolarisedTF/customXY.m b/targetFunctions/+normalTF/customXY.m similarity index 97% rename from targetFunctions/+nonPolarisedTF/customXY.m rename to targetFunctions/+normalTF/customXY.m index 39cd9473b..776d98f19 100644 --- a/targetFunctions/+nonPolarisedTF/customXY.m +++ b/targetFunctions/+normalTF/customXY.m @@ -31,7 +31,7 @@ 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) diff --git a/targetFunctions/+nonPolarisedTF/standardLayers.m b/targetFunctions/+normalTF/standardLayers.m similarity index 98% rename from targetFunctions/+nonPolarisedTF/standardLayers.m rename to targetFunctions/+normalTF/standardLayers.m index f57d181a1..b5a135803 100644 --- a/targetFunctions/+nonPolarisedTF/standardLayers.m +++ b/targetFunctions/+normalTF/standardLayers.m @@ -124,7 +124,7 @@ % 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); diff --git a/targetFunctions/reflectivityCalculation.m b/targetFunctions/reflectivityCalculation.m index 400a8d0de..66e585b26 100644 --- a/targetFunctions/reflectivityCalculation.m +++ b/targetFunctions/reflectivityCalculation.m @@ -7,7 +7,7 @@ % (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 % @@ -21,7 +21,7 @@ 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,controls); + subRoughs] = normalTF.standardLayers(problemStruct,controls); case coderEnums.modelTypes.CustomLayers [qzshifts,scalefactors,bulkIns,bulkOuts,... resolutionParams,chis,reflectivity,simulation,shiftedData,... backgrounds,layerSlds,sldProfiles,resampledLayers,... - subRoughs] = nonPolarisedTF.customLayers(problemStruct,controls); + subRoughs] = normalTF.customLayers(problemStruct,controls); case coderEnums.modelTypes.CustomXY [qzshifts,scalefactors,bulkIns,bulkOuts,... resolutionParams,chis,reflectivity,simulation,shiftedData,... backgrounds,layerSlds,sldProfiles,resampledLayers,... - subRoughs] = nonPolarisedTF.customXY(problemStruct,controls); + subRoughs] = normalTF.customXY(problemStruct,controls); otherwise error('The model type "%s" is not supported', modelType); diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat index 6bca1bdf3..ad483ce40 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat and b/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat differ diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat index f73a7707f..68f099645 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat and b/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat differ diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat index 599333a48..7f8b13053 100644 Binary files a/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat and b/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat deleted file mode 100644 index ff6e176b9..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat deleted file mode 100644 index d6870bd31..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat deleted file mode 100644 index 47b0ffdf7..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat deleted file mode 100644 index 5f2d8a53c..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat deleted file mode 100644 index b069dccaa..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat deleted file mode 100644 index 47cc71d77..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat deleted file mode 100644 index 16984745e..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat deleted file mode 100644 index ef305805c..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat deleted file mode 100644 index da19973fd..000000000 Binary files a/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat and /dev/null differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXY.m b/tests/normalTFReflectivityCalculation/DPPCCustomXY.m similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXY.m rename to tests/normalTFReflectivityCalculation/DPPCCustomXY.m diff --git a/tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXYScript.m b/tests/normalTFReflectivityCalculation/DPPCCustomXYScript.m similarity index 98% rename from tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXYScript.m rename to tests/normalTFReflectivityCalculation/DPPCCustomXYScript.m index 0c11267a9..80c11021e 100644 --- a/tests/nonPolarisedTFReflectivityCalculation/DPPCCustomXYScript.m +++ b/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/'); %% diff --git a/tests/nonPolarisedTFReflectivityCalculation/DPPCStandardLayers.m b/tests/normalTFReflectivityCalculation/DPPCStandardLayers.m similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/DPPCStandardLayers.m rename to tests/normalTFReflectivityCalculation/DPPCStandardLayers.m diff --git a/tests/nonPolarisedTFReflectivityCalculation/c_PLP0016596.dat b/tests/normalTFReflectivityCalculation/c_PLP0016596.dat similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/c_PLP0016596.dat rename to tests/normalTFReflectivityCalculation/c_PLP0016596.dat diff --git a/tests/nonPolarisedTFReflectivityCalculation/c_PLP0016601.dat b/tests/normalTFReflectivityCalculation/c_PLP0016601.dat similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/c_PLP0016601.dat rename to tests/normalTFReflectivityCalculation/c_PLP0016601.dat diff --git a/tests/nonPolarisedTFReflectivityCalculation/c_PLP0016607.dat b/tests/normalTFReflectivityCalculation/c_PLP0016607.dat similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/c_PLP0016607.dat rename to tests/normalTFReflectivityCalculation/c_PLP0016607.dat diff --git a/tests/nonPolarisedTFReflectivityCalculation/customBilayer.m b/tests/normalTFReflectivityCalculation/customBilayer.m similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/customBilayer.m rename to tests/normalTFReflectivityCalculation/customBilayer.m diff --git a/tests/normalTFReflectivityCalculation/customLayersInputs.mat b/tests/normalTFReflectivityCalculation/customLayersInputs.mat new file mode 100644 index 000000000..f2a034cca Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customLayersInputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/customLayersOutputs.mat b/tests/normalTFReflectivityCalculation/customLayersOutputs.mat new file mode 100644 index 000000000..74d82bb61 Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customLayersOutputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/customLayersTFParams.mat b/tests/normalTFReflectivityCalculation/customLayersTFParams.mat new file mode 100644 index 000000000..2032b812d Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customLayersTFParams.mat differ diff --git a/tests/normalTFReflectivityCalculation/customXYInputs.mat b/tests/normalTFReflectivityCalculation/customXYInputs.mat new file mode 100644 index 000000000..183807c0e Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customXYInputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/customXYOutputs.mat b/tests/normalTFReflectivityCalculation/customXYOutputs.mat new file mode 100644 index 000000000..336d1ad88 Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customXYOutputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/customXYTFParams.mat b/tests/normalTFReflectivityCalculation/customXYTFParams.mat new file mode 100644 index 000000000..76dd51a1f Binary files /dev/null and b/tests/normalTFReflectivityCalculation/customXYTFParams.mat differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/dppc.mat b/tests/normalTFReflectivityCalculation/dppc.mat similarity index 100% rename from tests/nonPolarisedTFReflectivityCalculation/dppc.mat rename to tests/normalTFReflectivityCalculation/dppc.mat diff --git a/tests/nonPolarisedTFReflectivityCalculation/makeInputsAndOutputs.m b/tests/normalTFReflectivityCalculation/makeInputsAndOutputs.m similarity index 83% rename from tests/nonPolarisedTFReflectivityCalculation/makeInputsAndOutputs.m rename to tests/normalTFReflectivityCalculation/makeInputsAndOutputs.m index f88f6eb82..532b4796d 100644 --- a/tests/nonPolarisedTFReflectivityCalculation/makeInputsAndOutputs.m +++ b/tests/normalTFReflectivityCalculation/makeInputsAndOutputs.m @@ -20,7 +20,7 @@ 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,problemLimits,controls); @@ -38,12 +38,12 @@ 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,controls); + resampledLayers,subRoughs] = normalTF.customLayers(problemStruct,controls); TFParams.qzshifts = qzshifts; TFParams.scalefactors = scalefactors; @@ -61,7 +61,7 @@ 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 @@ -80,7 +80,7 @@ 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,problemLimits,controls); @@ -98,12 +98,12 @@ 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,controls); + resampledLayers, subRoughs] = normalTF.customXY(problemStruct,controls); TFParams.qzshifts = qzshifts; TFParams.scalefactors = scalefactors; @@ -121,7 +121,7 @@ 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 @@ -140,7 +140,7 @@ 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,problemLimits,controls); @@ -158,12 +158,12 @@ 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,controls); + resampledLayers,subRoughs] = normalTF.standardLayers(problemStruct,controls); TFParams.qzshifts = qzshifts; TFParams.scalefactors = scalefactors; @@ -181,7 +181,7 @@ 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 diff --git a/tests/nonPolarisedTFReflectivityCalculation/orsoDSPCCustomLayers.m b/tests/normalTFReflectivityCalculation/orsoDSPCCustomLayers.m similarity index 98% rename from tests/nonPolarisedTFReflectivityCalculation/orsoDSPCCustomLayers.m rename to tests/normalTFReflectivityCalculation/orsoDSPCCustomLayers.m index a145975c6..82044eb60 100644 --- a/tests/nonPolarisedTFReflectivityCalculation/orsoDSPCCustomLayers.m +++ b/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/'); %% % % diff --git a/tests/normalTFReflectivityCalculation/standardLayersInputs.mat b/tests/normalTFReflectivityCalculation/standardLayersInputs.mat new file mode 100644 index 000000000..d02cb9719 Binary files /dev/null and b/tests/normalTFReflectivityCalculation/standardLayersInputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/standardLayersOutputs.mat b/tests/normalTFReflectivityCalculation/standardLayersOutputs.mat new file mode 100644 index 000000000..b527c64d9 Binary files /dev/null and b/tests/normalTFReflectivityCalculation/standardLayersOutputs.mat differ diff --git a/tests/normalTFReflectivityCalculation/standardLayersTFParams.mat b/tests/normalTFReflectivityCalculation/standardLayersTFParams.mat new file mode 100644 index 000000000..74ea3a249 Binary files /dev/null and b/tests/normalTFReflectivityCalculation/standardLayersTFParams.mat differ diff --git a/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m b/tests/normalTFReflectivityCalculation/testReflectivityCalculations.m similarity index 97% rename from tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m rename to tests/normalTFReflectivityCalculation/testReflectivityCalculations.m index 92b21c323..2f5680e58 100644 --- a/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m +++ b/tests/normalTFReflectivityCalculation/testReflectivityCalculations.m @@ -3,7 +3,7 @@ % testReflectivityCalculations Class based unit tests for RAT API, the % reflectivity calculation and pre- and post-processing routines. % -% We are using the test cases for a non-polarised TF reflectivity +% We are using the test cases for a normal TF reflectivity % calculation to test the routines. We consider standard layers, custom % layers and custom XY examples. For the reflectivity calculation itself, % we consider the serial and parallel versions (both points and contrasts), @@ -61,7 +61,7 @@ methods (TestClassSetup, ParameterCombination='sequential') function addDataPath(testCase) import matlab.unittest.fixtures.PathFixture - path = fullfile(getappdata(0, 'root'), 'tests', 'nonPolarisedTFReflectivityCalculation'); + path = fullfile(getappdata(0, 'root'), 'tests', 'normalTFReflectivityCalculation'); testCase.applyFixture(PathFixture(path)) end @@ -168,7 +168,7 @@ function testReflectivityCalculation(testCase, parallel, useCompiled) testCase.verifyEqual(result, testCase.expectedResultStruct, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance); end - function testNonPolarisedTFReflectivityCalculation(testCase, parallel, TFFile) + function testNormalTFReflectivityCalculation(testCase, parallel, TFFile) testCase.controls.parallel = parallel; % Choose the appropriate routine for each test case @@ -176,15 +176,15 @@ function testNonPolarisedTFReflectivityCalculation(testCase, parallel, TFFile) case 'standardLayersTFParams.mat' [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,chis,reflectivity,... simulation,shiftedData,backgrounds,layerSLDs,SLDProfiles,resampledLayers,... - subRoughs] = nonPolarisedTF.standardLayers(testCase.problemStruct,testCase.controls); + subRoughs] = normalTF.standardLayers(testCase.problemStruct,testCase.controls); case 'customLayersTFParams.mat' [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,chis,reflectivity,... simulation,shiftedData,backgrounds,layerSLDs,SLDProfiles,resampledLayers,... - subRoughs] = nonPolarisedTF.customLayers(testCase.problemStruct,testCase.controls); + subRoughs] = normalTF.customLayers(testCase.problemStruct,testCase.controls); case 'customXYTFParams.mat' [qzshifts,scalefactors,bulkIn,bulkOut,resolutionParams,chis,reflectivity,... simulation,shiftedData,backgrounds,layerSLDs,SLDProfiles,resampledLayers,... - subRoughs] = nonPolarisedTF.customXY(testCase.problemStruct,testCase.controls); + subRoughs] = normalTF.customXY(testCase.problemStruct,testCase.controls); end testCase.verifyEqual(qzshifts, testCase.TFQzshifts, 'RelTol', testCase.tolerance, 'AbsTol', testCase.absTolerance); diff --git a/tests/testContrastsClass.m b/tests/testContrastsClass.m index 1974b6ffc..4aba9b211 100644 --- a/tests/testContrastsClass.m +++ b/tests/testContrastsClass.m @@ -78,7 +78,7 @@ methods (TestClassSetup) function readClassData(testCase) import matlab.unittest.fixtures.PathFixture - path = fullfile(getappdata(0, 'root'), 'tests', 'nonPolarisedTFReflectivityCalculation'); + path = fullfile(getappdata(0, 'root'), 'tests', 'normalTFReflectivityCalculation'); testCase.applyFixture(PathFixture(path)) % Read in the data used in the example calculation diff --git a/tests/testCreateProject.m b/tests/testCreateProject.m index 02ea9d3a6..4a62ca87b 100644 --- a/tests/testCreateProject.m +++ b/tests/testCreateProject.m @@ -9,8 +9,8 @@ calculationType = {calculationTypes.Domains, ... calculationTypes.Magnetic, ... calculationTypes.MagneticDomains, ... - calculationTypes.NonPolarised, ... - calculationTypes.NonPolarised, ... + calculationTypes.Normal, ... + calculationTypes.Normal, ... calculationTypes.OilWater ... } SLDValues = {{'SLD'}, ... diff --git a/tests/testCustomFileClass.m b/tests/testCustomFileClass.m index 0083d8003..f5a7a5bea 100644 --- a/tests/testCustomFileClass.m +++ b/tests/testCustomFileClass.m @@ -27,8 +27,8 @@ {2, 'language', supportedLanguages.Python, 'filename', 'model.m', 'functionName', 'modelFunc', 'name', 'New Model', 'path', pwd},... } expectedRow = {["New Model", "DPPCCustomXY.m", "DPPCCustomXY", string(supportedLanguages.Matlab.value), "../../"],... - ["DPPC Model", "model.m", "model", string(supportedLanguages.Matlab.value), "tests/nonPolarisedTFReflectivityCalculation/"],... - ["DSPC Model", "customBilayer.m", "customBilayer", string(supportedLanguages.Python.value), "tests/nonPolarisedTFReflectivityCalculation/"],... + ["DPPC Model", "model.m", "model", string(supportedLanguages.Matlab.value), "tests/normalTFReflectivityCalculation/"],... + ["DSPC Model", "customBilayer.m", "customBilayer", string(supportedLanguages.Python.value), "tests/normalTFReflectivityCalculation/"],... ["New Model", "model.m", "modelFunc", string(supportedLanguages.Python.value), pwd],... } invalidInputData = {{'DPPC Model', 'name', 42},... @@ -52,7 +52,7 @@ methods (TestClassSetup) function addDataPath(testCase) import matlab.unittest.fixtures.PathFixture - path = fullfile(getappdata(0, 'root'), 'tests', 'nonPolarisedTFReflectivityCalculation'); + path = fullfile(getappdata(0, 'root'), 'tests', 'normalTFReflectivityCalculation'); testCase.applyFixture(PathFixture(path)) end @@ -77,8 +77,8 @@ function initialiseCustomFileClass(testCase) % "DPPCCustomXY.m" and "orsoDSPCCustomLayers.m" testCase.exampleClass = customFileClass(); - testCase.exampleClass.varTable(1,:) = {'DPPC Model', 'DPPCCustomXY.m', 'DPPCCustomXY', 'matlab', 'tests/nonPolarisedTFReflectivityCalculation/'}; - testCase.exampleClass.varTable(2,:) = {'DSPC Model', 'customBilayer.m', 'customBilayer', 'matlab', 'tests/nonPolarisedTFReflectivityCalculation/'}; + testCase.exampleClass.varTable(1,:) = {'DPPC Model', 'DPPCCustomXY.m', 'DPPCCustomXY', 'matlab', 'tests/normalTFReflectivityCalculation/'}; + testCase.exampleClass.varTable(2,:) = {'DSPC Model', 'customBilayer.m', 'customBilayer', 'matlab', 'tests/normalTFReflectivityCalculation/'}; testCase.numRows = height(testCase.exampleClass.varTable); testCase.numCols = width(testCase.exampleClass.varTable); @@ -356,7 +356,7 @@ function testToStructEmpty(testCase) emptyClass = customFileClass(); fileStruct = emptyClass.toStruct(); testCase.verifyClass(fileStruct, 'struct'); - testCase.verifyEqual(fileStruct.files, {}); + testCase.verifyEmpty(fileStruct.files); end function testToStructWrapper(testCase) diff --git a/tests/testDomainsClass.m b/tests/testDomainsClass.m index 659b3cb8e..b9f8409f6 100644 --- a/tests/testDomainsClass.m +++ b/tests/testDomainsClass.m @@ -91,13 +91,13 @@ function testConversion(testCase) testCase.verifyEqual(testCase.project.calculationType, calculationTypes.Domains.value, 'Calculation Type not set correctly'); testCase.verifyTrue(testCase.project.contrasts.domainsCalc, 'Calculation Type not set correctly') - nonPolarised = testCase.project.toProjectClass(); - testCase.verifyClass(nonPolarised, 'projectClass') - testCase.verifyEqual(nonPolarised.experimentName, testCase.project.experimentName, 'Experiment name not copied correctly'); - testCase.verifyEqual(nonPolarised.calculationType, calculationTypes.NonPolarised.value, 'Calculation Type not set correctly'); - testCase.verifyFalse(nonPolarised.contrasts.domainsCalc, 'Calculation Type not set correctly') - testCase.verifyEqual(nonPolarised.parameters, testCase.project.parameters, 'Parameters not copied correctly'); - testCase.verifyEqual(nonPolarised.layers, testCase.project.layers, 'Layers not copied correctly'); + normal = testCase.project.toProjectClass(); + testCase.verifyClass(normal, 'projectClass') + testCase.verifyEqual(normal.experimentName, testCase.project.experimentName, 'Experiment name not copied correctly'); + testCase.verifyEqual(normal.calculationType, calculationTypes.Normal.value, 'Calculation Type not set correctly'); + testCase.verifyFalse(normal.contrasts.domainsCalc, 'Calculation Type not set correctly') + testCase.verifyEqual(normal.parameters, testCase.project.parameters, 'Parameters not copied correctly'); + testCase.verifyEqual(normal.layers, testCase.project.layers, 'Layers not copied correctly'); end function testModelType(testCase) diff --git a/tests/testProjectClass.m b/tests/testProjectClass.m index dcbccb2c4..597b1cece 100644 --- a/tests/testProjectClass.m +++ b/tests/testProjectClass.m @@ -82,10 +82,10 @@ function testCreation(testCase) % Tests project class can be created and the experiment name is set correctly newProject = projectClass(); testCase.verifyEqual(newProject.experimentName, '', 'Experiment name not set correctly'); - testCase.verifyEqual(newProject.calculationType, calculationTypes.NonPolarised.value, 'Calculation Type not set correctly'); + testCase.verifyEqual(newProject.calculationType, calculationTypes.Normal.value, 'Calculation Type not set correctly'); newProject = projectClass('New experiment'); testCase.verifyEqual(newProject.experimentName, 'New experiment', 'Experiment name not set correctly'); - testCase.verifyEqual(newProject.calculationType, calculationTypes.NonPolarised.value, 'Calculation Type not set correctly'); + testCase.verifyEqual(newProject.calculationType, calculationTypes.Normal.value, 'Calculation Type not set correctly'); testCase.verifyError(@() projectClass(1), 'MATLAB:validators:mustBeTextScalar') end @@ -107,7 +107,7 @@ function testConversion(testCase) % Tests project class can be converted to domains class and % the properties are copied over testCase.verifyClass(testCase.project, 'projectClass') - testCase.verifyEqual(testCase.project.calculationType, calculationTypes.NonPolarised.value, 'Calculation Type not set correctly'); + testCase.verifyEqual(testCase.project.calculationType, calculationTypes.Normal.value, 'Calculation Type not set correctly'); testCase.verifyFalse(testCase.project.contrasts.domainsCalc, 'Calculation Type not set correctly') domains = testCase.project.toDomainsClass(); @@ -293,7 +293,7 @@ function testLayers(testCase) function testLayersExceptions(testCase) % Ensure layers are not defined for a custom model, % and the routines modifying the layers raise an error - customProject = projectClass('custom project', calculationTypes.NonPolarised, modelTypes.CustomLayers); + customProject = projectClass('custom project', calculationTypes.Normal, modelTypes.CustomLayers); testCase.verifyEmpty(customProject.layers); testCase.verifyError(@() customProject.addLayerGroup({{'New Layer'}, {'Another Layer'}}), exceptions.invalidProperty.errorID) testCase.verifyError(@() customProject.addLayer('New Layer'), exceptions.invalidProperty.errorID) @@ -557,7 +557,7 @@ function testToStruct(testCase) projectStruct = testCase.project.toStruct(); testCase.verifyEqual(projectStruct.experimentName, testCase.project.experimentName, 'toStruct method not working'); testCase.verifyEqual(projectStruct.geometry, testCase.project.geometry, 'toStruct method not working'); - testCase.verifyEqual(projectStruct.TF, calculationTypes.NonPolarised.value, 'toStruct method not working'); + testCase.verifyEqual(projectStruct.TF, calculationTypes.Normal.value, 'toStruct method not working'); testCase.verifyEqual(projectStruct.paramNames, {'Substrate Roughness'}, 'toStruct method not working'); testCase.verifyEqual(projectStruct.backgroundNames, testCase.project.background.backgrounds.varTable{:, 1}, 'toStruct method not working'); testCase.verifyEqual(projectStruct.backgroundTypes, testCase.project.background.backgrounds.varTable{:, 2}, 'toStruct method not working'); diff --git a/tests/testProjectConversion/DSPCBilayerProjectClass.mat b/tests/testProjectConversion/DSPCBilayerProjectClass.mat index 47a688549..bf6333671 100644 Binary files a/tests/testProjectConversion/DSPCBilayerProjectClass.mat and b/tests/testProjectConversion/DSPCBilayerProjectClass.mat differ diff --git a/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat b/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat index d8c22e709..dbeb9a0e7 100644 Binary files a/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat and b/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat differ