Skip to content

Remove ReturnData::nx, ReturnData::nxtrue #2966

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dweindl merged 2 commits into from
Oct 6, 2025
Merged

Remove ReturnData::nx, ReturnData::nxtrue #2966

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e4f1f44
Remove `ReturnData::nx`, `ReturnData::nxtrue`
dweindl Oct 6, 2025
777c2bb
Merge branch 'main' into nxrdata
dweindl Oct 6, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 0 additions & 13 deletions include/amici/rdata.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -468,19 +468,6 @@ class ReturnData : public ModelDimensions {
*/
int status = AMICI_NOT_RUN;

/**
* @brief Number of state variables.
*
* (alias `nx_rdata`, kept for backward compatibility)
*/
int nx{0};

/**
* Number of state variables in the unaugmented system
* (alias nxtrue_rdata, kept for backward compatibility)
*/
int nxtrue{0};

/** Number of parameters w.r.t. which sensitivities were requested */
int nplist{0};

Expand Down
4 changes: 2 additions & 2 deletions include/amici/serialization.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -208,8 +208,8 @@ void serialize(
) {
ar& dynamic_cast<amici::ModelDimensions&>(r);
ar & r.id;
ar & r.nx;
ar & r.nxtrue;
ar & r.nx_rdata;
ar & r.nxtrue_rdata;
ar & r.nplist;
ar & r.nmaxevent;
ar & r.nt;
Expand Down
6 changes: 3 additions & 3 deletions models/model_calvetti_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_dirac_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_events_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_jakstat_adjoint_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_nested_events_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_neuron_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_robertson_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
6 changes: 3 additions & 3 deletions models/model_steadystate_py/main.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
12 changes: 6 additions & 6 deletions python/sdist/amici/numpy.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -265,12 +265,12 @@ def __init__(self, rdata: ReturnDataPtr | ReturnData):
)
self._field_dimensions = {
"ts": [rdata.nt],
"x": [rdata.nt, rdata.nx],
"x0": [rdata.nx],
"x_ss": [rdata.nx],
"sx": [rdata.nt, rdata.nplist, rdata.nx],
"sx0": [rdata.nplist, rdata.nx],
"sx_ss": [rdata.nplist, rdata.nx],
"x": [rdata.nt, rdata.nx_rdata],
"x0": [rdata.nx_rdata],
"x_ss": [rdata.nx_rdata],
"sx": [rdata.nt, rdata.nplist, rdata.nx_rdata],
"sx0": [rdata.nplist, rdata.nx_rdata],
"sx_ss": [rdata.nplist, rdata.nx_rdata],
# observables
"y": [rdata.nt, rdata.ny],
"sigmay": [rdata.nt, rdata.ny],
Expand Down
8 changes: 4 additions & 4 deletions src/hdf5.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,7 @@ void writeReturnData(

if (!rdata.x.empty())
createAndWriteDouble2DDataset(
file, hdf5Location + "/x", rdata.x, rdata.nt, rdata.nx
file, hdf5Location + "/x", rdata.x, rdata.nt, rdata.nx_rdata
);

if (!rdata.y.empty())
Expand Down Expand Up @@ -463,13 +463,13 @@ void writeReturnData(

if (!rdata.sx0.empty())
createAndWriteDouble2DDataset(
file, hdf5Location + "/sx0", rdata.sx0, rdata.nplist, rdata.nx
file, hdf5Location + "/sx0", rdata.sx0, rdata.nplist, rdata.nx_rdata
);

if (!rdata.sx.empty())
createAndWriteDouble3DDataset(
file, hdf5Location + "/sx", rdata.sx, rdata.nt, rdata.nplist,
rdata.nx
rdata.nx_rdata
);

if (!rdata.sy.empty())
Expand Down Expand Up @@ -699,7 +699,7 @@ void writeReturnDataDiagnosis(

if (!rdata.J.empty())
createAndWriteDouble2DDataset(
file, hdf5Location + "/J", rdata.J, rdata.nx, rdata.nx
file, hdf5Location + "/J", rdata.J, rdata.nx_rdata, rdata.nx_rdata
);

if (!rdata.x_ss.empty())
Expand Down
6 changes: 3 additions & 3 deletions src/main.template.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,14 +78,14 @@ int main() {

std::cout << "State sensitivities for timepoint " << rdata->ts[i_time]
<< std::endl; // nt x nplist x nx
for (int i_state = 0; i_state < rdata->nx; ++i_state) {
for (int i_state = 0; i_state < rdata->nx_rdata; ++i_state) {
std::cout << "\td(" << state_ids[i_state] << ")/d("
<< parameter_ids[model->plist(i_nplist)] << ") = ";

// rdata->sx is a flat 3D array in row-major ordering
std::cout << rdata->sx
[i_time * rdata->nplist * rdata->nx
+ i_nplist * rdata->nx + i_state];
[i_time * rdata->nplist * rdata->nx_rdata
+ i_nplist * rdata->nx_rdata + i_state];
std::cout << std::endl;
}

Expand Down
38 changes: 18 additions & 20 deletions src/rdata.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,8 +37,6 @@ ReturnData::ReturnData(
)
: ModelDimensions(model_dimensions_)
, ts(std::move(ts_))
, nx(nx_rdata)
, nxtrue(nxtrue_rdata)
, nplist(plist_.size())
, nmaxevent(nmaxevent_)
, nt(ts.size())
Expand Down Expand Up @@ -135,7 +133,7 @@ void ReturnData::initializeFullReporting(bool quadratic_llh) {
sigmaz.resize(nmaxevent * nz, 0.0);

rz.resize(nmaxevent * nz, 0.0);
x.resize(nt * nx, 0.0);
x.resize(nt * nx_rdata, 0.0);
w.resize(nt * nw, 0.0);

preeq_numsteps.resize(3, 0);
Expand All @@ -159,17 +157,17 @@ void ReturnData::initializeFullReporting(bool quadratic_llh) {
}
}

x0.resize(nx, getNaN());
x_ss.resize(nx, getNaN());
x0.resize(nx_rdata, getNaN());
x_ss.resize(nx_rdata, getNaN());

if (sensi >= SensitivityOrder::first) {
sx0.resize(nx * nplist, getNaN());
sx_ss.resize(nx * nplist, getNaN());
sx0.resize(nx_rdata * nplist, getNaN());
sx_ss.resize(nx_rdata * nplist, getNaN());

if (sensi_meth == SensitivityMethod::forward
|| sensi >= SensitivityOrder::second) {
// for second order we can fill in from the augmented states
sx.resize(nt * nx * nplist, 0.0);
sx.resize(nt * nx_rdata * nplist, 0.0);
sz.resize(nmaxevent * nz * nplist, 0.0);
srz.resize(nmaxevent * nz * nplist, 0.0);
}
Expand Down Expand Up @@ -339,7 +337,7 @@ void ReturnData::getDataOutput(
int it, Model& model, SolutionState const& sol, ExpData const* edata
) {
if (!x.empty()) {
model.fx_rdata(slice(x, it, nx), sol.x);
model.fx_rdata(slice(x, it, nx_rdata), sol.x);
}
if (!w.empty())
model.getExpression(slice(w, it, nw), ts[it], sol.x);
Expand Down Expand Up @@ -378,7 +376,7 @@ void ReturnData::getDataSensisFSA(
) {
if (!sx.empty()) {
model.fsx_rdata(
gsl::span<realtype>(&sx.at(it * nplist * nx), nplist * nx), sol.sx,
gsl::span<realtype>(&sx.at(it * nplist * nx_rdata), nplist * nx_rdata), sol.sx,
sol.x
);
}
Expand Down Expand Up @@ -652,14 +650,14 @@ void ReturnData::invalidate(int const it_start) {
invalidateSLLH();

if (!x.empty())
std::fill(x.begin() + nx * it_start, x.end(), getNaN());
std::fill(x.begin() + nx_rdata * it_start, x.end(), getNaN());
if (!y.empty())
std::fill(y.begin() + ny * it_start, y.end(), getNaN());
if (!w.empty())
std::fill(w.begin() + nw * it_start, w.end(), getNaN());

if (!sx.empty())
std::fill(sx.begin() + nx * nplist * it_start, sx.end(), getNaN());
std::fill(sx.begin() + nx_rdata * nplist * it_start, sx.end(), getNaN());
if (!sy.empty())
std::fill(sy.begin() + ny * nplist * it_start, sy.end(), getNaN());
}
Expand Down Expand Up @@ -729,10 +727,10 @@ void ReturnData::applyChainRuleFactorToSimulationResults(Model const& model) {
&& sensi_meth == SensitivityMethod::adjoint) {
if (!sx.empty() && !x.empty())
for (int ip = 0; ip < nplist; ++ip)
for (int ix = 0; ix < nxtrue; ++ix)
for (int ix = 0; ix < nxtrue_rdata; ++ix)
for (int it = 0; it < nt; ++it)
sx.at(ix + nxtrue * (ip + it * nplist))
= x.at(it * nx + nxtrue + ip * nxtrue + ix);
sx.at(ix + nxtrue_rdata * (ip + it * nplist))
= x.at(it * nx_rdata + nxtrue_rdata + ip * nxtrue_rdata + ix);

if (!sy.empty() && !y.empty())
for (int ip = 0; ip < nplist; ++ip)
Expand Down Expand Up @@ -789,14 +787,14 @@ void ReturnData::applyChainRuleFactorToSimulationResults(Model const& model) {
val *= pcoefficient[ip];
};

chain_rule(sx, nxtrue, nx, nt);
chain_rule(sx, nxtrue_rdata, nx_rdata, nt);
chain_rule(sy, nytrue, ny, nt);
chain_rule(ssigmay, nytrue, ny, nt);
chain_rule(sz, nztrue, nz, nmaxevent);
chain_rule(ssigmaz, nztrue, nz, nmaxevent);
chain_rule(srz, nztrue, nz, nmaxevent);
chain_rule(sx0, nxtrue, nx, 1);
chain_rule(sx_ss, nxtrue, nx, 1);
chain_rule(sx0, nxtrue_rdata, nx_rdata, 1);
chain_rule(sx_ss, nxtrue_rdata, nx_rdata, 1);
}

if (o2mode == SecondOrderMode::full) {
Expand Down Expand Up @@ -843,7 +841,7 @@ void ReturnData::applyChainRuleFactorToSimulationResults(Model const& model) {
}
};

chain_rule(sx, nxtrue, nx, nt);
chain_rule(sx, nxtrue_rdata, nx_rdata, nt);
chain_rule(sy, nytrue, ny, nt);
chain_rule(ssigmay, nytrue, ny, nt);
chain_rule(sz, nztrue, nz, nmaxevent);
Expand Down Expand Up @@ -883,7 +881,7 @@ void ReturnData::applyChainRuleFactorToSimulationResults(Model const& model) {
}
};

chain_rule(sx, nxtrue, nx, nt);
chain_rule(sx, nxtrue_rdata, nx_rdata, nt);
chain_rule(sy, nytrue, ny, nt);
chain_rule(ssigmay, nytrue, ny, nt);
chain_rule(sz, nztrue, nz, nmaxevent);
Expand Down
2 changes: 1 addition & 1 deletion tests/cpp/testfunctions.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -307,7 +307,7 @@ void verifyReturnDataSensitivities(H5::H5File const& file, std::string const& re
expected = hdf5::getDoubleDataset3D(file, resultPath + "/sx", m, n, o);
for(int ip = 0; ip < model->nplist(); ++ip)
checkEqualArray(&expected[ip * model->nt() * model->nxtrue_rdata],
&rdata->sx[ip * model->nt() * rdata->nx],
&rdata->sx[ip * model->nt() * rdata->nx_rdata],
model->nt() * model->nxtrue_rdata, atol, rtol, "sx");
} else {
ASSERT_TRUE(rdata->sx.empty());
Expand Down
4 changes: 2 additions & 2 deletions tests/cpp/unittests/testSerialization.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,8 @@ void checkReturnDataEqual(
ASSERT_EQ(r.id, s.id);
ASSERT_EQ(r.np, s.np);
ASSERT_EQ(r.nk, s.nk);
ASSERT_EQ(r.nx, s.nx);
ASSERT_EQ(r.nxtrue, s.nxtrue);
ASSERT_EQ(r.nx_rdata, s.nx_rdata);
ASSERT_EQ(r.nxtrue_rdata, s.nxtrue_rdata);
ASSERT_EQ(r.nx_solver, s.nx_solver);
ASSERT_EQ(r.nx_solver_reinit, s.nx_solver_reinit);
ASSERT_EQ(r.ny, s.ny);
Expand Down
Loading