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Fix slow C3DFileAdpaterReading issue #1698 #1730

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merged 10 commits into from
May 25, 2017
Merged

Fix slow C3DFileAdpaterReading issue #1698 #1730

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46385eb
Added timing to C3DFileAdapter testing
May 25, 2017
9b827ad
Add a protected convenience constructor to create a DataTable with th…
May 25, 2017
3acb82c
Provide a convenience constructor for TimeSeriesTable_ to be filled f…
May 25, 2017
a1ee753
Speedup C3DFileAdapter::extendRead() by exploiting the new TimeSeries…
May 25, 2017
eb4136d
To access member of template class need to disambiguate with this->
May 25, 2017
b99762f
Fix typo and clarify comment.
May 25, 2017
eb0ed3c
Add more details about why derive class implementations of the conven…
May 25, 2017
eff1881
Address size_t->int warning and clarify comments.
May 25, 2017
3e5b56a
Make nf an int and use marker_nrow for number of marker frames.
May 25, 2017
26b8135
Address size_t -> int loss warning.
May 25, 2017
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173 changes: 94 additions & 79 deletions OpenSim/Common/C3DFileAdapter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -69,13 +69,19 @@ C3DFileAdapter::extendRead(const std::string& fileName) const {
reader->Update();
auto acquisition = reader->GetOutput();

EventTable event_table{};
auto events = acquisition->GetEvents();
for (auto it = events->Begin();
it != events->End();
++it) {
auto et = *it;
event_table.push_back({ et->GetLabel(),
et->GetTime(),
et->GetFrame(),
et->GetDescription() });
}

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Is there a particular reason for moving this?

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I thought it read better to get the events first, which are then added to both the marker and force tables that are created in the two code blocks below. I also thought I might be able to extract the start time for the acquisition at some point.

OutputTables tables{};
auto& marker_table = *(new TimeSeriesTableVec3{});
auto& force_table = *(new TimeSeriesTableVec3{});
tables.emplace(_markers,
std::shared_ptr<TimeSeriesTableVec3>(&marker_table));
tables.emplace(_forces,
std::shared_ptr<TimeSeriesTableVec3>(&force_table));

auto marker_pts = btk::PointCollection::New();

Expand All @@ -88,45 +94,51 @@ C3DFileAdapter::extendRead(const std::string& fileName) const {
}

if(marker_pts->GetItemNumber() != 0) {
marker_table.
updTableMetaData().
setValueForKey("DataRate",
std::to_string(acquisition->GetPointFrequency()));

marker_table.
updTableMetaData().
setValueForKey("Units",
acquisition->GetPointUnit());

ValueArray<std::string> marker_labels{};
for(auto it = marker_pts->Begin();
it != marker_pts->End();
++it) {
marker_labels.
upd().
push_back(SimTK::Value<std::string>((*it)->GetLabel()));
}
int marker_nrow = marker_pts->GetFrontItem()->GetFrameNumber();
int marker_ncol = marker_pts->GetItemNumber();

TimeSeriesTableVec3::DependentsMetaData marker_dep_metadata{};
marker_dep_metadata.setValueArrayForKey("labels", marker_labels);
marker_table.setDependentsMetaData(marker_dep_metadata);
std::vector<double> marker_times(marker_nrow);
SimTK::Matrix_<SimTK::Vec3> marker_matrix(marker_nrow, marker_ncol);

std::vector<std::string> marker_labels{};
for (auto it = marker_pts->Begin(); it != marker_pts->End(); ++it) {
marker_labels.push_back(SimTK::Value<std::string>((*it)->GetLabel()));
}

double time_step{1.0 / acquisition->GetPointFrequency()};
for(int f = 0;
f < marker_pts->GetFrontItem()->GetFrameNumber();
++f) {
for(int f = 0; f < marker_nrow; ++f) {
SimTK::RowVector_<SimTK::Vec3> row{marker_pts->GetItemNumber()};
int m{0};
for(auto it = marker_pts->Begin();
it != marker_pts->End();
++it) {
for(auto it = marker_pts->Begin(); it != marker_pts->End(); ++it) {
auto pt = *it;
row[m++] = SimTK::Vec3{pt->GetValues().coeff(f, 0),
pt->GetValues().coeff(f, 1),
pt->GetValues().coeff(f, 2)};
}
marker_table.appendRow(0 + f * time_step, row);

marker_matrix.updRow(f) = row;
marker_times[f] = 0 + f * time_step; //TODO: 0 should be start_time
}

// Create the data
auto& marker_table = *new
TimeSeriesTableVec3(marker_times, marker_matrix, marker_labels);

marker_table.
updTableMetaData().
setValueForKey("DataRate",
std::to_string(acquisition->GetPointFrequency()));

marker_table.
updTableMetaData().
setValueForKey("Units",
acquisition->GetPointUnit());

marker_table.updTableMetaData().setValueForKey("events", event_table);

tables.emplace(_markers,
std::shared_ptr<TimeSeriesTableVec3>(&marker_table));
}

// This is probably the right way to get the raw forces data from force
Expand Down Expand Up @@ -174,57 +186,37 @@ C3DFileAdapter::extendRead(const std::string& fileName) const {
}

if(fp_force_pts->GetItemNumber() != 0) {
force_table.
updTableMetaData().
setValueForKey("CalibrationMatrices", std::move(fpCalMatrices));

force_table.
updTableMetaData().
setValueForKey("Corners", std::move(fpCorners));

force_table.
updTableMetaData().
setValueForKey("Origins", std::move(fpOrigins));

force_table.
updTableMetaData().
setValueForKey("Types", std::move(fpTypes));

force_table.
updTableMetaData().
setValueForKey("DataRate",
std::to_string(acquisition->GetAnalogFrequency()));

ValueArray<std::string> labels{};
std::vector<std::string> labels{};
ValueArray<std::string> units{};
for(int fp = 1; fp <= fp_force_pts->GetItemNumber(); ++fp) {
auto fp_str = std::to_string(fp);

labels.upd().push_back(SimTK::Value<std::string>("f" + fp_str));
labels.push_back(SimTK::Value<std::string>("f" + fp_str));
auto force_unit = acquisition->GetPointUnits().
at(_unit_index.at("force"));
units.upd().push_back(SimTK::Value<std::string>(force_unit));

labels.upd().push_back(SimTK::Value<std::string>("m" + fp_str));
labels.push_back(SimTK::Value<std::string>("m" + fp_str));
auto moment_unit = acquisition->GetPointUnits().
at(_unit_index.at("moment"));
units.upd().push_back(SimTK::Value<std::string>(moment_unit));

labels.upd().push_back(SimTK::Value<std::string>("p" + fp_str));
labels.push_back(SimTK::Value<std::string>("p" + fp_str));
auto position_unit = acquisition->GetPointUnits().
at(_unit_index.at("marker"));
units.upd().push_back(SimTK::Value<std::string>(position_unit));
}
TimeSeriesTableVec3::DependentsMetaData force_dep_metadata{};
force_dep_metadata.setValueArrayForKey("labels", labels);
force_dep_metadata.setValueArrayForKey("units", units);
force_table.setDependentsMetaData(force_dep_metadata);

const int nf = fp_force_pts->GetFrontItem()->GetFrameNumber();

std::vector<double> force_times(nf);
SimTK::Matrix_<SimTK::Vec3> force_matrix(nf, labels.size());

double time_step{1.0 / acquisition->GetAnalogFrequency()};
for(int f = 0;
f < fp_force_pts->GetFrontItem()->GetFrameNumber();
++f) {
SimTK::RowVector_<SimTK::Vec3>

for(int f = 0; f < nf; ++f) {
SimTK::RowVector_<SimTK::Vec3>
row{fp_force_pts->GetItemNumber() * 3};
int col{0};
for(auto fit = fp_force_pts->Begin(),
Expand All @@ -247,23 +239,46 @@ C3DFileAdapter::extendRead(const std::string& fileName) const {
(*pit)->GetValues().coeff(f, 2)};
++col;
}
force_table.appendRow(0 + f * time_step, row);
force_matrix.updRow(f) = row;
force_times[f] = 0 + f * time_step; //TODO: 0 should be start_time
}
}

EventTable event_table{};
auto events = acquisition->GetEvents();
for(auto it = events->Begin();
it != events->End();
++it) {
auto et = *it;
event_table.push_back({et->GetLabel(),
et->GetTime(),
et->GetFrame(),
et->GetDescription()});
}
marker_table.updTableMetaData().setValueForKey("events", event_table);
auto& force_table =
*(new TimeSeriesTableVec3(force_times, force_matrix, labels));

TimeSeriesTableVec3::DependentsMetaData force_dep_metadata
= force_table.getDependentsMetaData();

// add units to the dependent meta data
force_dep_metadata.setValueArrayForKey("units", units);
force_table.setDependentsMetaData(force_dep_metadata);

force_table.
updTableMetaData().
setValueForKey("CalibrationMatrices", std::move(fpCalMatrices));

force_table.
updTableMetaData().
setValueForKey("Corners", std::move(fpCorners));

force_table.
updTableMetaData().
setValueForKey("Origins", std::move(fpOrigins));

force_table.
updTableMetaData().
setValueForKey("Types", std::move(fpTypes));

force_table.
updTableMetaData().
setValueForKey("DataRate",
std::to_string(acquisition->GetAnalogFrequency()));

tables.emplace(_forces,
std::shared_ptr<TimeSeriesTableVec3>(&force_table));

force_table.updTableMetaData().setValueForKey("events", event_table);
}

return tables;
}
Expand Down
33 changes: 27 additions & 6 deletions OpenSim/Common/DataTable.h
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Original file line number Diff line number Diff line change
Expand Up @@ -661,7 +661,8 @@ class DataTable_ : public AbstractDataTable {
// No "labels". So no operation.
}
_depData.resize(1, depRow.size());
} else
}
else
_depData.resizeKeep(_depData.nrow() + 1, _depData.ncol());

_depData.updRow(_depData.nrow() - 1) = depRow;
Expand Down Expand Up @@ -1158,6 +1159,28 @@ class DataTable_ : public AbstractDataTable {
}

protected:
/** Convenience constructor to efficiently populate a DataTable from
known data. This is primarily useful for reading in large data tables
without having to reallocate and copy memory. NOTE derived tables
must validate the table according to the needs of the concrete type.
The virtual validateRow() overridden by derived types cannot be
invoked here - that is by the base class. A derived class must perform
its own validation by invoking its own validateRow() implementation. */
DataTable_(const std::vector<ETX>& indVec,
const SimTK::Matrix_<ETY>& depData,
const std::vector<std::string>& labels) {
OPENSIM_THROW_IF(indVec.size() != depData.nrow(), InvalidArgument,
"Length of independent column does not match number of rows of "
"dependent data.");
OPENSIM_THROW_IF(labels.size() != depData.ncol(), InvalidArgument,
"Number of labels does not match number of columns of "
"dependent data.");

setColumnLabels(labels);
_indData = indVec;
_depData = depData;
}

// Implement toString.
std::string toString_impl(std::vector<int> rows = {},
std::vector<int> cols = {},
Expand Down Expand Up @@ -1452,11 +1475,9 @@ class DataTable_ : public AbstractDataTable {

for(const std::string& key : _dependentsMetaData.getKeys()) {
OPENSIM_THROW_IF(numCols !=
_dependentsMetaData.
getValueArrayForKey(key).size(),
IncorrectMetaDataLength, key, numCols,
_dependentsMetaData.
getValueArrayForKey(key).size());
_dependentsMetaData.getValueArrayForKey(key).size(),
IncorrectMetaDataLength, key, numCols,
_dependentsMetaData.getValueArrayForKey(key).size());
}
}

Expand Down
6 changes: 6 additions & 0 deletions OpenSim/Common/Test/testC3DFileAdapter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,14 @@ void compare_tables(const OpenSim::TimeSeriesTableVec3& table1,

void test(const std::string filename) {
using namespace OpenSim;

std::clock_t startTime = std::clock();
auto tables = C3DFileAdapter::read(filename);

std::cout << "\nC3DFileAdapter '" << filename << "' read time = "
<< 1.e3*(std::clock() - startTime) / CLOCKS_PER_SEC
<< "ms\n" << std::endl;

auto& marker_table = tables.at("markers");
auto& force_table = tables.at("forces");

Expand Down
24 changes: 24 additions & 0 deletions OpenSim/Common/TimeSeriesTable.h
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,30 @@ class TimeSeriesTable_ : public DataTable_<double, ETY> {
TimeSeriesTable_& operator=(const TimeSeriesTable_&) = default;
TimeSeriesTable_& operator=(TimeSeriesTable_&&) = default;
~TimeSeriesTable_() = default;

/** Convenience constructor to efficiently populate a time series table
from available data. This is primarily useful for constructing with large
data read in from file without having to reallocate and copy memory.*/
TimeSeriesTable_(const std::vector<double>& indVec,
const SimTK::Matrix_<ETY>& depData,
const std::vector<std::string>& labels) :
DataTable_<double, ETY>(indVec, depData, labels) {
try {
// Perform the validation of the data of this TimeSeriesTable
this->validateDependentsMetaData();
for (size_t i = 0; i < indVec.size(); ++i) {
this->validateRow(i, indVec[i], depData.row(int(i)));
}
}
catch (std::exception& x) {
// wipe out the data loaded if any
this->_indData.clear();
this->_depData.clear();
this->removeDependentsMetaDataForKey("labels");
throw;
}
}

#ifndef SWIG
using DataTable_<double, ETY>::DataTable_;
using DataTable_<double, ETY>::operator=;
Expand Down