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Unifies the indices used by python and cpp to be same with matlab #430

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Merged
StephenNneji merged 2 commits into from
Feb 3, 2026
+18 −14
Merged

Unifies the indices used by python and cpp to be same with matlab #430

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0f754f4
Unifies the indices used by python and cpp to be same with matlab
StephenNneji Feb 2, 2026
ecd6aa5
Addresses review comments
StephenNneji Feb 3, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/runTests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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]

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10 changes: 6 additions & 4 deletions examples/miscellaneous/alternativeLanguages/customBilayer.cpp
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Expand Up @@ -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];
Expand Down Expand Up @@ -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...
Expand All @@ -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...
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10 changes: 6 additions & 4 deletions examples/miscellaneous/alternativeLanguages/customBilayer.py
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Expand Up @@ -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
Expand Down Expand Up @@ -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]

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4 changes: 2 additions & 2 deletions targetFunctions/+domainsTF/processCustomFunction.m
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion targetFunctions/+normalTF/processCustomFunction.m
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions targetFunctions/common/customModelFunctions/callCppFunction.m
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Expand Up @@ -50,8 +50,8 @@
bulkOutArray = coder.opaque('std::vector<double>');
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)
% domain should either be 1 or 2. A value less than 1 indicates no domains
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, ...
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