RascalSoftware · alexhroom · Sep 6, 2024 · Sep 2, 2024 · Sep 2, 2024 · Sep 4, 2024
diff --git a/API/controlsClass.m b/API/controlsClass.m
diff --git a/API/parseClassToStructs.m b/API/parseClassToStructs.m
@@ -393,7 +393,8 @@
 %% Now deal with the controls class
 controls.procedure = inputControls.procedure;
 controls.parallel = inputControls.parallel;
-controls.resampleParams = inputControls.resampleParams;
+controls.resampleMinAngle = inputControls.resampleMinAngle;
+controls.resampleNPoints = inputControls.resampleNPoints;
 controls.calcSldDuringFit = inputControls.calcSldDuringFit;
 controls.display = inputControls.display;
 controls.xTolerance = inputControls.xTolerance;

diff --git a/compile/fullCompile/makeCompileArgsFull.m b/compile/fullCompile/makeCompileArgsFull.m
@@ -100,7 +100,8 @@
 ARGS_1_4 = struct;
 ARGS_1_4.procedure = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_4.parallel = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARGS_1_4.resampleParams = coder.typeof(0,[1 2]);
+ARGS_1_4.resampleMinAngle = coder.typeof(0);
+ARGS_1_4.resampleNPoints = coder.typeof(0);
 ARGS_1_4.calcSldDuringFit = coder.typeof(true);
 ARGS_1_4.display = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_4.xTolerance = coder.typeof(0);

diff --git a/compile/reflectivityCalculation/makeCompileArgs.m b/compile/reflectivityCalculation/makeCompileArgs.m
@@ -100,7 +100,8 @@
 ARGS_1_4 = struct;
 ARGS_1_4.procedure = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_4.parallel = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARGS_1_4.resampleParams = coder.typeof(0,[1 2]);
+ARGS_1_4.resampleMinAngle = coder.typeof(0);
+ARGS_1_4.resampleNPoints = coder.typeof(0);
 ARGS_1_4.calcSldDuringFit = coder.typeof(true);
 ARGS_1_4.display = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_4.xTolerance = coder.typeof(0);

diff --git a/examples/miscellaneous/absorption/absorptionDPPC50.m b/examples/miscellaneous/absorption/absorptionDPPC50.m
@@ -127,7 +127,7 @@
 
 % Now make a controls block....
 controls = controlsClass();
-controls.resampleParams(2) = 150;
+controls.resampleNPoints = 150;
 controls.parallel = 'contrasts';
 
 [problem,results] = RAT(problem,controls);

diff --git a/targetFunctions/+domainsTF/customLayers.m b/targetFunctions/+domainsTF/customLayers.m
@@ -24,7 +24,8 @@
 
     calcSld = controls.calcSldDuringFit;
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     % Pre-Allocation of output arrays...
     backgroundParams = zeros(numberOfContrasts,1);
@@ -111,7 +112,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              calcAllLayers1{i},calcAllLayers2{i});
 
@@ -132,7 +133,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              calcAllLayers1{i},calcAllLayers2{i});
 
@@ -165,7 +166,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     domainRatioIndex,backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,...
     resolutionParams,domainRatios,dataPresent,data,dataLimits,simLimits,...
-    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleParams,...
+    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,...
     useImaginary,resample,geometry,roughness,calcSld,calcAllLayers1,calcAllLayers2)
 
     % Get the domain ratio for this contrast
@@ -188,12 +189,12 @@
     [sldProfile1,reflect1,simul1,shiftedData,layerSld1,resampledLayer1,~] = nonPolarisedTF.coreLayersCalculation(calcAllLayers1,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
     [sldProfile2,reflect2,simul2,~,layerSld2,resampledLayer2,~] = nonPolarisedTF.coreLayersCalculation(calcAllLayers2,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
     % Calculate the average reflectivities....
     [reflectivity,simulation] = domainsTF.averageReflectivity(reflect1,reflect2,simul1,simul2,domainRatio);

diff --git a/targetFunctions/+domainsTF/customXY.m b/targetFunctions/+domainsTF/customXY.m
@@ -19,7 +19,8 @@
      cCustFiles, useImaginary] = extractProblemParams(problemStruct);
 
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     %Pre-Allocation...
     backgroundParams = zeros(numberOfContrasts,1);
@@ -103,7 +104,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,subRoughs(i),inputSldProfiles1{i},inputSldProfiles2{i});
 
         end
@@ -123,7 +124,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,subRoughs(i),inputSldProfiles1{i},inputSldProfiles2{i});
 
         end
@@ -155,7 +156,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     domainRatioIndex,backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,...
     resolutionParams,domainRatios,dataPresent,data,dataLimits,simLimits,...
-    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleParams,...
+    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,...
     useImaginary,roughness,sldProfile1,sldProfile2)
 
     % Get the domain ratio for this contrast
@@ -175,17 +176,17 @@
 
     % Resample the sld profiles
     if ~useImaginary
-        layerSld1 = resampleLayers(sldProfile1,resampleParams);
-        layerSld2 = resampleLayers(sldProfile2,resampleParams);
+        layerSld1 = resampleLayers(sldProfile1,resampleMinAngle,resampleNPoints);
+        layerSld2 = resampleLayers(sldProfile2,resampleMinAngle,resampleNPoints);
     else
         reSLD1 = sldProfile1(:,1:2);
         imSLD1 = [sldProfile1(:,1),sldProfile1(:,3)];
 
         reSLD2 = sldProfile2(:,1:2);
         imSLD2 = [sldProfile2(:,1),sldProfile2(:,3)];
 
-        layerSld1 = resampleLayersReIm(reSLD1,imSLD1,resampleParams);
-        layerSld2 = resampleLayersReIm(reSLD2,imSLD2,resampleParams);
+        layerSld1 = resampleLayersReIm(reSLD1,imSLD1,resampleMinAngle,resampleNPoints);
+        layerSld2 = resampleLayersReIm(reSLD2,imSLD2,resampleMinAngle,resampleNPoints);
     end
 
     layerSld = {layerSld1, layerSld2};

diff --git a/targetFunctions/+domainsTF/standardLayers.m b/targetFunctions/+domainsTF/standardLayers.m
@@ -27,7 +27,8 @@
 
     calcSld = controls.calcSldDuringFit;
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     % Allocate the memory for the output arrays before the main loop
     backgroundParams = zeros(numberOfContrasts,1);
@@ -115,7 +116,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              domainContrastLayers1{i},domainContrastLayers2{i},outParameterisedLayers);
 
@@ -137,7 +138,7 @@
              backgroundParamArray,qzshiftArray,scalefactorArray,bulkInArray,...
              bulkOutArray,resolutionParamArray,domainRatioArray,dataPresent(i),...
              data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              domainContrastLayers1{i},domainContrastLayers2{i},outParameterisedLayers);
 
@@ -170,7 +171,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     domainRatioIndex,backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,...
     resolutionParams,domainRatios,dataPresent,data,dataLimits,simLimits,...
-    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleParams,...
+    repeatLayers,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,...
     useImaginary,resample,geometry,roughness,calcSld,domainContrastLayers1,...
     domainContrastLayers2,outParameterisedLayers)
 
@@ -200,12 +201,12 @@
     [sldProfile1,reflect1,simul1,shiftedData,layerSld1,resampledLayer1,~] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers1,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
     [sldProfile2,reflect2,simul2,~,layerSld2,resampledLayer2,~] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers2,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
     % Calculate the average reflectivities....
     [reflectivity,simulation] = domainsTF.averageReflectivity(reflect1,reflect2,simul1,simul2,domainRatio);

diff --git a/targetFunctions/+nonPolarisedTF/coreLayersCalculation.m b/targetFunctions/+nonPolarisedTF/coreLayersCalculation.m
@@ -2,7 +2,7 @@
     coreLayersCalculation(contrastLayers, rough, ...
     geometry, bulkIn, bulkOut, resample, calcSld, scalefactor, qzshift,...
     dataPresent, data, dataLimits, simLimits, repeatLayers,...
-    background,resolution,contrastBackgroundActions,params,parallelPoints,resampleParams,useImaginary)
+    background,resolution,contrastBackgroundActions,params,parallelPoints,resampleMinAngle,resampleNPoints,useImaginary)
 
 %   This is the main reflectivity calculation for all Layers models in the 
 %   non polarised target function. 
@@ -98,9 +98,9 @@
 % If required, then resample the SLD
 if resample == 1
     if ~useImaginary
-        layerSld = resampleLayers(sldProfile,resampleParams);
+        layerSld = resampleLayers(sldProfile,resampleMinAngle,resampleNPoints);
     else
-        layerSld = resampleLayersReIm(sldProfile,sldProfileIm,resampleParams);
+        layerSld = resampleLayersReIm(sldProfile,sldProfileIm,resampleMinAngle,resampleNPoints);
     end
     resamLayers = layerSld;
 else

diff --git a/targetFunctions/+nonPolarisedTF/customLayers.m b/targetFunctions/+nonPolarisedTF/customLayers.m
@@ -24,7 +24,8 @@
 
     calcSld = controls.calcSldDuringFit;
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     % Pre-Allocation of output arrays...
     backgroundParams = zeros(numberOfContrasts,1);
@@ -75,7 +76,7 @@
              contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              resampledLayers{i});
 
@@ -96,7 +97,7 @@
              contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              resampledLayers{i});
 
@@ -113,7 +114,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,resolutionParams,...
     dataPresent,data,dataLimits,simLimits,repeatLayers,contrastBackgroundActions,...
-    nParams,parallel,resampleParams,useImaginary,resample,geometry,roughness,...
+    nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary,resample,geometry,roughness,...
     calcSld,layer)
 
     % Extract the relevant parameter values for this contrast
@@ -130,6 +131,6 @@
      chi] = nonPolarisedTF.coreLayersCalculation(layer,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
 end
diff --git a/targetFunctions/+nonPolarisedTF/customXY.m b/targetFunctions/+nonPolarisedTF/customXY.m
@@ -19,7 +19,8 @@
      useImaginary] = extractProblemParams(problemStruct);
 
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     %Pre-Allocation...
     backgroundParams = zeros(numberOfContrasts,1);
@@ -72,7 +73,7 @@
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},...
              repeatLayers{i},contrastBackgroundActions(i),nParams,parallel,...
-             resampleParams,useImaginary,subRoughs(i),sldProfiles{i});
+             resampleMinAngle,resampleNPoints,useImaginary,subRoughs(i),sldProfiles{i});
         end
 
     else
@@ -90,7 +91,7 @@
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},...
              repeatLayers{i},contrastBackgroundActions(i),nParams,parallel,...
-             resampleParams,useImaginary,subRoughs(i),sldProfiles{i});
+             resampleMinAngle,resampleNPoints,useImaginary,subRoughs(i),sldProfiles{i});
 
         end
 
@@ -105,7 +106,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,resolutionParams,...
     dataPresent,data,dataLimits,simLimits,repeatLayers,contrastBackgroundActions,...
-    nParams,parallel,resampleParams,useImaginary,roughness,sldProfile)
+    nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary,roughness,sldProfile)
 
     % Extract the relevant parameter values for this contrast
     % from the input arrays.
@@ -118,11 +119,11 @@
 
     % Resample the layers
     if ~useImaginary
-        layerSld = resampleLayers(sldProfile,resampleParams);
+        layerSld = resampleLayers(sldProfile,resampleMinAngle,resampleNPoints);
     else
         reSLD = sldProfile(:,1:2);
         imSLD = [sldProfile(:,1),sldProfile(:,3)];
-        layerSld = resampleLayersReIm(reSLD,imSLD,resampleParams);
+        layerSld = resampleLayersReIm(reSLD,imSLD,resampleMinAngle,resampleNPoints);
     end
 
     resampledLayer = layerSld;

diff --git a/targetFunctions/+nonPolarisedTF/standardLayers.m b/targetFunctions/+nonPolarisedTF/standardLayers.m
@@ -25,7 +25,8 @@
 
     calcSld = controls.calcSldDuringFit;
     parallel = controls.parallel;
-    resampleParams = controls.resampleParams;
+    resampleMinAngle = controls.resampleMinAngle;
+    resampleNPoints = controls.resampleNPoints;
 
     % Allocate the memory for the output arrays before the main loop
     backgroundParams = zeros(numberOfContrasts,1);
@@ -81,7 +82,7 @@
              contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              contrastLayers{i},outParameterisedLayers);
 
@@ -102,7 +103,7 @@
              contrastResolutionParamIndices(i),backgroundParamArray,qzshiftArray,...
              scalefactorArray,bulkInArray,bulkOutArray,resolutionParamArray,...
              dataPresent(i),data{i},dataLimits{i},simLimits{i},repeatLayers{i},...
-             contrastBackgroundActions(i),nParams,parallel,resampleParams,...
+             contrastBackgroundActions(i),nParams,parallel,resampleMinAngle,resampleNPoints,...
              useImaginary,resample(i),geometry,subRoughs(i),calcSld,...
              contrastLayers{i},outParameterisedLayers);
 
@@ -119,7 +120,7 @@
     qzshiftIndex,scalefactorIndex,bulkInIndex,bulkOutIndex,resolutionParamIndex,...
     backgroundParams,qzshifts,scalefactors,bulkIns,bulkOuts,resolutionParams,...
     dataPresent,data,dataLimits,simLimits,repeatLayers,contrastBackgroundActions,...
-    nParams,parallel,resampleParams,useImaginary,resample,geometry,roughness,...
+    nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary,resample,geometry,roughness,...
     calcSld,contrastLayers,outParameterisedLayers)
 
     % Extract the relevant parameter values for this contrast
@@ -141,6 +142,6 @@
      chi] = nonPolarisedTF.coreLayersCalculation(thisContrastLayers,roughness,...
      geometry,bulkInValue,bulkOutValue,resample,calcSld,scalefactorValue,qzshiftValue,...
      dataPresent,data,dataLimits,simLimits,repeatLayers,backgroundParamValue,...
-     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleParams,useImaginary);
+     resolutionParamValue,contrastBackgroundActions,nParams,parallel,resampleMinAngle,resampleNPoints,useImaginary);
 
 end
diff --git a/targetFunctions/common/resampleLayers/resampleLayers.m b/targetFunctions/common/resampleLayers/resampleLayers.m
@@ -1,4 +1,4 @@
-function newSLD = resampleLayers(sldProfile,resampleParams)
+function newSLD = resampleLayers(sldProfile,minAngle, nPoints)
 
 
 % Function handle for adaptive resampling
@@ -10,11 +10,6 @@
 xstart = x(1);
 xend = x(end);
 
-% Keep points and minangle as constants for now
-% will fix later
-minAngle = resampleParams(1);
-nPoints = resampleParams(2);
-
 newX = linspace(xstart,xend,100);
 out = adaptive(sldProfile, [xstart xend], minAngle*pi, nPoints);
 yy = out{1};