Skip to content

Improvements for XsensDataReader #4063

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

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
+581 −316
Open

Improvements for XsensDataReader #4063

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
5 changes: 4 additions & 1 deletion OpenSim/Common/FileAdapter.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -166,9 +166,12 @@ class TableMissingHeader : public Exception {
public:
TableMissingHeader(const std::string& file,
size_t line,
const std::string& func) :
const std::string& func,
const std::string& message = "") :
Exception(file, line, func) {
std::string msg = "Table does not have metadata for 'header'.";
if(!message.empty())
msg += " " + message;

addMessage(msg);
}
Expand Down
225 changes: 118 additions & 107 deletions OpenSim/Common/Test/testXsensDataReader.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -37,113 +37,124 @@ PacketCounter<tab>SampleTimeFine<tab>Year<tab>Month<tab>Day<tab>Second<tab>UTC_N
06951<tab><tab><tab><tab><tab><tab><tab><tab><tab><tab><tab><tab><tab><tab>2.657654<tab>5.012634<tab>-7.581414<tab>0.392058<tab>0.353193<tab>-0.712047<tab>-0.114258<tab>-0.155518<tab>0.913330<tab>0.387756<tab>0.877453<tab>0.282349<tab>0.716718<tab>-0.479624<tab>0.506238<tab>0.579621<tab>0.006068<tab>-0.814863
*/

TEST_CASE("XsensDataReader")
{
XsensDataReaderSettings readerSettings;
std::vector<std::string> imu_names{ "shank", "thigh" };
std::vector<std::string> file_names{ "000_00B421AF", "000_00B4227B" };
// Programmatically add items to Map, write to xml
for (int index = 0; index < (int)imu_names.size(); ++index) {
ExperimentalSensor nextSensor(file_names[index], imu_names[index]);
readerSettings.append_ExperimentalSensors(nextSensor);
}
readerSettings.updProperty_trial_prefix() = "MT_012005D6_031-";
readerSettings.print("reader2xml.xml");
// read xml we wrote into a new XsensDataReader to readTrial
XsensDataReader reconstructFromXML(XsensDataReaderSettings("reader2xml.xml"));
DataAdapter::OutputTables tables = reconstructFromXML.read("./");
std::string folder = readerSettings.get_data_folder();
std::string trial = readerSettings.get_trial_prefix();
// Write tables to sto files
// Accelerations
const TimeSeriesTableVec3& accelTableTyped =
reconstructFromXML.getLinearAccelerationsTable(tables);
STOFileAdapterVec3::write(accelTableTyped, folder + trial + "accelerations.sto");
const SimTK::RowVectorView_<SimTK::Vec3>& rvv = accelTableTyped.getRowAtIndex(0);
SimTK::Vec3 fromTable = accelTableTyped.getRowAtIndex(0)[0];
SimTK::Vec3 fromFile = SimTK::Vec3{ 3.030769, 5.254238, -7.714005 };
double tolerance = SimTK::Eps;
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// test last row as well to make sure all data is read correctly,
// size is as expected
size_t numRows = accelTableTyped.getIndependentColumn().size();
fromTable = accelTableTyped.getRowAtIndex(numRows - 1)[0];
fromFile = SimTK::Vec3{ 2.657654, 5.012634, -7.581414 };
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Magenometer
const TimeSeriesTableVec3& magTableTyped =
reconstructFromXML.getMagneticHeadingTable(tables);
STOFileAdapterVec3::write(magTableTyped, folder + trial + "magnetometers.sto");
fromTable = magTableTyped.getRowAtIndex(0)[0];
fromFile = SimTK::Vec3{ -0.045410, -0.266113, 0.897217 };
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Gyro
const TimeSeriesTableVec3& gyroTableTyped =
reconstructFromXML.getAngularVelocityTable(tables);
STOFileAdapterVec3::write(gyroTableTyped, folder + trial + "gyros.sto");
fromTable = gyroTableTyped.getRowAtIndex(0)[0];
fromFile = SimTK::Vec3{ 0.005991, -0.032133, 0.022713 };
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Orientation
const TimeSeriesTableQuaternion& quatTableTyped =
reconstructFromXML.getOrientationsTable(tables);
STOFileAdapterQuaternion::write(quatTableTyped, folder + trial + "quaternions.sto");
SimTK::Quaternion quat = quatTableTyped.getRowAtIndex(0)[1];
// Convert back to orientation matrix and compare with gold standard data in file
//-0.444898<tab>0.895542<tab>0.008444
// 0.333934<tab>0.157132<tab>0.929407
// 0.830996<tab>0.416311<tab>-0.368959
std::vector<double> rotationVectorInFile{ -0.444898,0.895542,0.008444,
0.333934,0.157132,0.929407,
0.830996,0.416311,-0.368959 };
SimTK::Rotation rot;
rot.setRotationFromQuaternion(quat);
tolerance = 1e-6; // empirically determined due to conversion back and forth
for (int i = 0; i < 3; ++i){
for (int j = 0; j < 3; ++j) {
// Matrix is stored column major
ASSERT_EQUAL(rotationVectorInFile[i * 3 + j], rot[j][i], tolerance);
TEST_CASE("XsensDataReader") {
SECTION("Full Set Basic Processing") {
XsensDataReaderSettings readerSettings;
std::vector<std::string> imu_names{"shank", "thigh"};
std::vector<std::string> file_names{"000_00B421AF", "000_00B4227B"};
// Programmatically add items to Map, write to xml
for (int index = 0; index < (int)imu_names.size(); ++index) {
ExperimentalSensor nextSensor(file_names[index], imu_names[index]);
readerSettings.append_ExperimentalSensors(nextSensor);
}
readerSettings.updProperty_trial_prefix() = "MT_012005D6_031-";
readerSettings.print("reader2xml.xml");
// read xml we wrote into a new XsensDataReader to readTrial
XsensDataReader reconstructFromXML(
XsensDataReaderSettings("reader2xml.xml"));
DataAdapter::OutputTables tables = reconstructFromXML.read("./");
std::string folder = readerSettings.get_data_folder();
std::string trial = readerSettings.get_trial_prefix();
// Write tables to sto files
// Accelerations
const TimeSeriesTableVec3& accelTableTyped =
reconstructFromXML.getLinearAccelerationsTable(tables);
STOFileAdapterVec3::write(
accelTableTyped, folder + trial + "accelerations.sto");
const SimTK::RowVectorView_<SimTK::Vec3>& rvv =
accelTableTyped.getRowAtIndex(0);
SimTK::Vec3 fromTable = accelTableTyped.getRowAtIndex(0)[0];
SimTK::Vec3 fromFile = SimTK::Vec3{3.030769, 5.254238, -7.714005};
double tolerance = SimTK::Eps;
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// test last row as well to make sure all data is read correctly,
// size is as expected
size_t numRows = accelTableTyped.getIndependentColumn().size();
fromTable = accelTableTyped.getRowAtIndex(numRows - 1)[0];
fromFile = SimTK::Vec3{2.657654, 5.012634, -7.581414};
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Magenometer
const TimeSeriesTableVec3& magTableTyped =
reconstructFromXML.getMagneticHeadingTable(tables);
STOFileAdapterVec3::write(
magTableTyped, folder + trial + "magnetometers.sto");
fromTable = magTableTyped.getRowAtIndex(0)[0];
fromFile = SimTK::Vec3{-0.045410, -0.266113, 0.897217};
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Gyro
const TimeSeriesTableVec3& gyroTableTyped =
reconstructFromXML.getAngularVelocityTable(tables);
STOFileAdapterVec3::write(gyroTableTyped, folder + trial + "gyros.sto");
fromTable = gyroTableTyped.getRowAtIndex(0)[0];
fromFile = SimTK::Vec3{0.005991, -0.032133, 0.022713};
ASSERT_EQUAL(fromTable, fromFile, tolerance);
// Orientation
const TimeSeriesTableQuaternion& quatTableTyped =
reconstructFromXML.getOrientationsTable(tables);
STOFileAdapterQuaternion::write(
quatTableTyped, folder + trial + "quaternions.sto");
SimTK::Quaternion quat = quatTableTyped.getRowAtIndex(0)[1];
// Convert back to orientation matrix and compare with gold standard
// data in file
//-0.444898<tab>0.895542<tab>0.008444
// 0.333934<tab>0.157132<tab>0.929407
// 0.830996<tab>0.416311<tab>-0.368959
std::vector<double> rotationVectorInFile{-0.444898, 0.895542, 0.008444,
0.333934, 0.157132, 0.929407, 0.830996, 0.416311, -0.368959};
SimTK::Rotation rot;
rot.setRotationFromQuaternion(quat);
tolerance =
1e-6; // empirically determined due to conversion back and forth
for (int i = 0; i < 3; ++i) {
for (int j = 0; j < 3; ++j) {
// Matrix is stored column major
ASSERT_EQUAL(
rotationVectorInFile[i * 3 + j], rot[j][i], tolerance);
}
}
}
// Now test the case where only orientation data is available, rest is missing
XsensDataReaderSettings readOrientationsOnly;
ExperimentalSensor nextSensor("000_00B421ED", "test");
readOrientationsOnly.append_ExperimentalSensors(nextSensor);
readOrientationsOnly.updProperty_trial_prefix() = "MT_012005D6-000_sit_to_stand-";
DataAdapter::OutputTables tables2 =
XsensDataReader(readOrientationsOnly).read("./");
const TimeSeriesTableVec3& accelTable2 =
reconstructFromXML.getLinearAccelerationsTable(tables2);
ASSERT(accelTable2.getNumRows() ==0);
ASSERT(tables2.at(IMUDataReader::MagneticHeading)->getNumRows() == 0);
ASSERT(tables2.at(IMUDataReader::AngularVelocity)->getNumRows() == 0);
// Now a file with extra comment in header as reported by user, has 3 rows
XsensDataReaderSettings readerSettings3;
ExperimentalSensor nextSensor2("test1_00B421E6", "test");
readerSettings3.append_ExperimentalSensors(nextSensor2);
DataAdapter::OutputTables tables3 =
XsensDataReader(readerSettings3).read("./");
auto accelTable3 = tables3.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable3->getNumRows() == 3);
//
// Now a file with latest format
XsensDataReaderSettings readerSettings4;
ExperimentalSensor nextSensor4("MT_01200454_000-000_00B40DE4", "test");
readerSettings4.append_ExperimentalSensors(nextSensor4);
DataAdapter::OutputTables tables4 =
XsensDataReader(readerSettings4).read("./");
auto accelTable4 = tables4.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable4->getNumRows() == 4);

// Now a file exported from MTManager2020.0.2
XsensDataReaderSettings readerSettings5;
ExperimentalSensor nextSensor5("MT_01200312-002-000_00B474BA", "test");
readerSettings5.append_ExperimentalSensors(nextSensor5);
XsensDataReader reader5(readerSettings5);
DataAdapter::OutputTables tables5 = reader5.read("./");
auto accelTable5 = tables5.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable5->getNumRows() == 5);
//const TimeSeriesTableQuaternion& quatTable5 =
// reader5.getOrientationsTable(tables5);
// STOFileAdapterQuaternion::write(quatTable5, "2020-0-2-quaternions.sto");
SECTION("Only Orientation") {
// Now test the case where only orientation data is available, rest is
// missing
XsensDataReaderSettings readOrientationsOnly;
ExperimentalSensor nextSensor("000_00B421ED", "test");
readOrientationsOnly.append_ExperimentalSensors(nextSensor);
readOrientationsOnly.updProperty_trial_prefix() =
"MT_012005D6-000_sit_to_stand-";
DataAdapter::OutputTables tables2 =
XsensDataReader(readOrientationsOnly).read("./");
const auto accelTable2 = tables2.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable2->getNumRows() == 0);
ASSERT(tables2.at(IMUDataReader::MagneticHeading)->getNumRows() == 0);
ASSERT(tables2.at(IMUDataReader::AngularVelocity)->getNumRows() == 0);
// Now a file with extra comment in header as reported by user, has 3
// rows
XsensDataReaderSettings readerSettings3;
ExperimentalSensor nextSensor2("test1_00B421E6", "test");
readerSettings3.append_ExperimentalSensors(nextSensor2);
DataAdapter::OutputTables tables3 =
XsensDataReader(readerSettings3).read("./");
auto accelTable3 = tables3.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable3->getNumRows() == 3);
}
SECTION("Exported with Current (2022-2025) Format") {
// Now a file with latest format
XsensDataReaderSettings readerSettings4;
ExperimentalSensor nextSensor4("MT_01200454_000-000_00B40DE4", "test");
readerSettings4.append_ExperimentalSensors(nextSensor4);
DataAdapter::OutputTables tables4 =
XsensDataReader(readerSettings4).read("./");
auto accelTable4 = tables4.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable4->getNumRows() == 4);
}
SECTION("Exported from MTManager2020.0.2") {
// Now a file exported from MTManager2020.0.2
XsensDataReaderSettings readerSettings5;
ExperimentalSensor nextSensor5("MT_01200312-002-000_00B474BA", "test");
readerSettings5.append_ExperimentalSensors(nextSensor5);
XsensDataReader reader5(readerSettings5);
DataAdapter::OutputTables tables5 = reader5.read("./");
auto accelTable5 = tables5.at(XsensDataReader::LinearAccelerations);
ASSERT(accelTable5->getNumRows() == 5);
}
}
Loading
Loading