Unifies the indices used by python and cpp to be same with matlab

Author: StephenNneji

.github/workflows/runTests.yml

@@ -36,7 +36,7 @@ jobs:
   build_and_test_mex:
     strategy:
       matrix:
-        platform: [windows-latest, ubuntu-latest, macos-15-intel, macos-latest]
+        platform: [windows-latest, ubuntu-22.04, macos-15-intel, macos-latest]
     runs-on: ${{ matrix.platform }}
     needs: [build_cpp]
 

examples/miscellaneous/alternativeLanguages/customBilayer.cpp

@@ -13,6 +13,8 @@ extern "C" {
 
     LIB_EXPORT void customBilayer(std::vector<double>& params, std::vector<double>& bulkIn, std::vector<double>& bulkOut, int contrast, std::vector<double>& output, double* outputSize, double* rough)
     {
+        # Note - The first contrast number is 1 (not 0) so be careful if you use 
+        # this variable for array indexing. 
         double subRough = params[0];
         double oxideThick = params[1];
         double oxideHydration = params[2];
@@ -65,9 +67,9 @@ extern "C" {
 
         // Manually deal with hydration for layers in
         // this example.
-        double oxSLD = (oxideHydration * bulkOut[contrast]) + ((1 - oxideHydration) * oxideSLD);
-        double headSLD = (headHydration * bulkOut[contrast]) + ((1 - headHydration) * SLDhead);
-        double tailSLD = (bilayerHydration * bulkOut[contrast]) + ((1 - bilayerHydration) * SLDtail);
+        double oxSLD = (oxideHydration * bulkOut[contrast-1]) + ((1 - oxideHydration) * oxideSLD);
+        double headSLD = (headHydration * bulkOut[contrast-1]) + ((1 - headHydration) * SLDhead);
+        double tailSLD = (bilayerHydration * bulkOut[contrast-1]) + ((1 - bilayerHydration) * SLDtail);
 
         // Make the layers
         // oxide...
@@ -77,7 +79,7 @@ extern "C" {
 
         // Water...
         output.push_back(waterThick);
-        output.push_back(bulkOut[contrast]);
+        output.push_back(bulkOut[contrast-1]);
         output.push_back(bilayerRough);
 
         // Heads...

examples/miscellaneous/alternativeLanguages/customBilayer.py

@@ -2,6 +2,8 @@
 import numpy as np
 
 def customBilayer(params, bulk_in, bulk_out, contrast):
+    # Note - The first contrast number is 1 (not 0) so be careful if you use 
+    # this variable for array indexing. 
     params = params
     bulk_in = bulk_in
     bulk_out = bulk_out
@@ -58,13 +60,13 @@ def customBilayer(params, bulk_in, bulk_out, contrast):
 
     # Manually deal with hydration for layers in
     # this example.
-    oxSLD = (oxide_hydration * bulk_out[contrast]) + ((1 - oxide_hydration) * oxide_SLD)
-    headSLD = (headHydration * bulk_out[contrast]) + ((1 - headHydration) * SLDhead)
-    tailSLD = (bilayerHydration * bulk_out[contrast]) + ((1 - bilayerHydration) * SLDtail)   
+    oxSLD = (oxide_hydration * bulk_out[contrast-1]) + ((1 - oxide_hydration) * oxide_SLD)
+    headSLD = (headHydration * bulk_out[contrast-1]) + ((1 - headHydration) * SLDhead)
+    tailSLD = (bilayerHydration * bulk_out[contrast-1]) + ((1 - bilayerHydration) * SLDtail)   
 
     # Make the layers
     oxide = [oxide_thick, oxSLD, sub_rough]
-    water = [waterThick, bulk_out[contrast], bilayerRough]
+    water = [waterThick, bulk_out[contrast-1], bilayerRough]
     head = [headThick, headSLD, bilayerRough]
     tail = [tailThick, tailSLD, bilayerRough]
 

targetFunctions/+domainsTF/processCustomFunction.m

@@ -21,8 +21,8 @@
             [output1, subRoughs(i)] = callMatlabFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 1);
             [output2, ~] = callMatlabFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 2);
         else
-            [output1, subRoughs(i)] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i-1, 0);
-            [output2, ~] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i-1, 1);
+            [output1, subRoughs(i)] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 1);
+            [output2, ~] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 2);
         end
 
         % If SLD is real, add dummy imaginary column

targetFunctions/+normalTF/processCustomFunction.m

@@ -16,7 +16,7 @@
         if isnan(str2double(functionHandle))
             [output, subRoughs(i)] = callMatlabFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 0);
         else
-            [output, subRoughs(i)] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i-1, -1);
+            [output, subRoughs(i)] = callCppFunction(functionHandle, paramValues, bulkIns(i), bulkOuts, i, 0);
         end
 
         % If SLD is real, add dummy imaginary column

targetFunctions/common/customModelFunctions/callCppFunction.m

@@ -51,7 +51,7 @@
         bulkOutArray = coder.ceval('convertPtr2Vector', coder.ref(bulkOut), numel(bulkOut));
 
         % domain should either before 0 or 1. A value less than zero indicates no domains
-        if (domains < 0)
+        if (domains < 1)
             coder.ceval(['std::mem_fn<void(std::vector<double>&, std::vector<double>&, std::vector<double>&, int, ' ...
                         'std::vector<double>&, double*, double*)>(&CallbackInterface::invoke)'], ...
                          callback, paramsArray, bulkInArray, bulkOutArray, contrast, outArray, ...