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Add missing fields in ExpData HDF5 I/O
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Closes #2589
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@dweindl
dweindl committed Nov 23, 2024
1 parent f42cc16 commit fa61a77
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Showing 2 changed files with 95 additions and 2 deletions.
3 changes: 1 addition & 2 deletions include/amici/hdf5.h
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Original file line number Diff line number Diff line change
Expand Up @@ -182,8 +182,7 @@ void writeSimulationExpData(
void writeSimulationExpData(
ExpData const& edata, std::string const& hdf5Filename,
std::string const& hdf5Location
);

);

/**
* @brief Check whether an attribute with the given name exists
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94 changes: 94 additions & 0 deletions src/hdf5.cpp
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Expand Up @@ -195,6 +195,47 @@ std::unique_ptr<ExpData> readSimulationExpData(
));
}

if (locationExists(file, hdf5Root + "/parameters")) {
edata->parameters = getDoubleDataset1D(file, hdf5Root + "/parameters");

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}

if (locationExists(file, hdf5Root + "/x0")) {
edata->x0 = getDoubleDataset1D(file, hdf5Root + "/x0");

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}

if (locationExists(file, hdf5Root + "/sx0")) {
edata->sx0 = getDoubleDataset1D(file, hdf5Root + "/sx0");

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}

if (locationExists(file, hdf5Root + "/pscale")) {
auto pscaleInt = getIntDataset1D(file, hdf5Root + "/pscale");
edata->pscale.resize(pscaleInt.size());

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for (int i = 0; (unsigned)i < pscaleInt.size(); ++i)
edata->pscale[i] = static_cast<ParameterScaling>(pscaleInt[i]);
}

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if (locationExists(file, hdf5Root + "/plist")) {
edata->plist = getIntDataset1D(file, hdf5Root + "/plist");

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}

if (locationExists(
file, hdf5Root + "/reinitialization_state_idxs_presim"
)) {
edata->reinitialization_state_idxs_presim = getIntDataset1D(
file, hdf5Root + "/reinitialization_state_idxs_presim"
);

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}

if (locationExists(file, hdf5Root + "/reinitialization_state_idxs_sim")) {
edata->reinitialization_state_idxs_sim = getIntDataset1D(
file, hdf5Root + "/reinitialization_state_idxs_sim"
);

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}

if (attributeExists(file, hdf5Root, "tstart")) {
edata->tstart_ = getDoubleScalarAttribute(file, hdf5Root, "tstart");

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}

return edata;
}

Expand Down Expand Up @@ -262,6 +303,59 @@ void writeSimulationExpData(
file.getId(), hdf5Location.c_str(),
"reinitializeFixedParameterInitialStates", &int_attr, 1
);

if (!edata.parameters.empty())
createAndWriteDouble1DDataset(
file, hdf5Location + "/parameters", edata.parameters

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);

if (!edata.x0.empty())
createAndWriteDouble1DDataset(file, hdf5Location + "/x0", edata.x0);

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if (!edata.sx0.empty())
createAndWriteDouble1DDataset(file, hdf5Location + "/sx0", edata.sx0);

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std::vector<int> int_buffer;

if (!edata.pscale.empty()) {
int_buffer.resize(edata.pscale.size());

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for (int i = 0; (unsigned)i < edata.pscale.size(); i++)
int_buffer[i] = static_cast<int>(edata.pscale[i]);
createAndWriteInt1DDataset(file, hdf5Location + "/pscale", int_buffer);

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}

if (!edata.plist.empty()) {
int_buffer.resize(edata.plist.size());

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for (int i = 0; (unsigned)i < edata.plist.size(); i++)
int_buffer[i] = static_cast<int>(edata.plist[i]);
createAndWriteInt1DDataset(file, hdf5Location + "/plist", int_buffer);

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}

if (!edata.reinitialization_state_idxs_presim.empty()) {
int_buffer.resize(edata.reinitialization_state_idxs_presim.size());
for (int i = 0;
(unsigned)i < edata.reinitialization_state_idxs_presim.size(); i++)
int_buffer[i]
= static_cast<int>(edata.reinitialization_state_idxs_presim[i]);
createAndWriteInt1DDataset(
file, hdf5Location + "/reinitialization_state_idxs_presim",

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int_buffer
);
}

if (!edata.reinitialization_state_idxs_sim.empty()) {
int_buffer.resize(edata.reinitialization_state_idxs_sim.size());
for (int i = 0;
(unsigned)i < edata.reinitialization_state_idxs_sim.size(); i++)
int_buffer[i]
= static_cast<int>(edata.reinitialization_state_idxs_sim[i]);
createAndWriteInt1DDataset(
file, hdf5Location + "/reinitialization_state_idxs_sim", int_buffer

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);
}

H5LTset_attribute_double(
file.getId(), hdf5Location.c_str(), "tstart", &edata.tstart_, 1
);
}

void writeReturnData(
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