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Adding some SubjectOnDisk fields and a binding for unwrapEulerAngles #222

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merged 3 commits into from
Sep 28, 2024
Merged

Adding some SubjectOnDisk fields and a binding for unwrapEulerAngles #222

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deb01b1
Adding a binding for unwrapEulerAngles
keenon Sep 27, 2024
46eaef0
Threading through some new SubjectOnDisk values to help with aggregat…
keenon Sep 27, 2024
69ff638
Adding a data quality enum to SubjectOnDisk
keenon Sep 28, 2024
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187 changes: 187 additions & 0 deletions dart/biomechanics/SubjectOnDisk.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -181,6 +181,118 @@ MissingGRFReason missingGRFReasonFromProto(proto::MissingGRFReason reason)
return notMissingGRF;
}

BasicTrialType basicTrialTypeFromProto(proto::BasicTrialType type)
{
switch (type)
{
case proto::BasicTrialType::treadmill:
return treadmill;
case proto::BasicTrialType::overground:
return overground;
case proto::BasicTrialType::staticTrial:
return staticTrial;
case proto::BasicTrialType::other:
return other;
case proto::BasicTrialType_INT_MIN_SENTINEL_DO_NOT_USE_:
return other;
break;
case proto::BasicTrialType_INT_MAX_SENTINEL_DO_NOT_USE_:
return other;
break;
}
return other;
}

proto::BasicTrialType basicTrialTypeToProto(BasicTrialType type)
{
switch (type)
{
case treadmill:
return proto::BasicTrialType::treadmill;
case overground:
return proto::BasicTrialType::overground;
case staticTrial:
return proto::BasicTrialType::staticTrial;
case other:
return proto::BasicTrialType::other;
}
return proto::BasicTrialType::other;
}

DataQuality dataQualityFromProto(proto::DataQuality quality)
{
switch (quality)
{
case proto::DataQuality::pilotData:
return pilotData;
case proto::DataQuality::experimentalData:
return experimentalData;
case proto::DataQuality::internetData:
return internetData;
case proto::DataQuality_INT_MIN_SENTINEL_DO_NOT_USE_:
return internetData;
break;
case proto::DataQuality_INT_MAX_SENTINEL_DO_NOT_USE_:
return internetData;
break;
}
return internetData;
}

proto::DataQuality dataQualityToProto(DataQuality quality)
{
switch (quality)
{
case pilotData:
return proto::DataQuality::pilotData;
case experimentalData:
return proto::DataQuality::experimentalData;
case internetData:
return proto::DataQuality::internetData;
}
return proto::DataQuality::pilotData;
}

DetectedTrialFeature detectedTrialFeatureFromProto(
proto::DetectedTrialFeature feature)
{
switch (feature)
{
case proto::DetectedTrialFeature::walking:
return walking;
case proto::DetectedTrialFeature::running:
return running;
case proto::DetectedTrialFeature::unevenTerrain:
return unevenTerrain;
case proto::DetectedTrialFeature::flatTerrain:
return flatTerrain;
case proto::DetectedTrialFeature_INT_MIN_SENTINEL_DO_NOT_USE_:
return walking;
break;
case proto::DetectedTrialFeature_INT_MAX_SENTINEL_DO_NOT_USE_:
return walking;
break;
}
return walking;
}

proto::DetectedTrialFeature detectedTrialFeatureToProto(
DetectedTrialFeature feature)
{
switch (feature)
{
case walking:
return proto::DetectedTrialFeature::walking;
case running:
return proto::DetectedTrialFeature::running;
case unevenTerrain:
return proto::DetectedTrialFeature::unevenTerrain;
case flatTerrain:
return proto::DetectedTrialFeature::flatTerrain;
}
return proto::DetectedTrialFeature::walking;
}

SubjectOnDisk::SubjectOnDisk(const std::string& path)
: mPath(path), mLoadedAllFrames(false)
{
Expand Down Expand Up @@ -1490,6 +1602,12 @@ std::vector<MissingGRFReason> SubjectOnDisk::getMissingGRF(int trial)
return mHeader->mTrials[trial]->mMissingGRFReason;
}

/// This returns the user supplied enum of type 'DataQuality'
DataQuality SubjectOnDisk::getQuality()
{
return mHeader->getQuality();
}

int SubjectOnDisk::getNumProcessingPasses()
{
return mHeader->mPasses.size();
Expand Down Expand Up @@ -3193,6 +3311,17 @@ void SubjectOnDiskTrial::setMissingGRFReason(
mMissingGRFReason = missingGRFReason;
}

std::vector<bool> SubjectOnDiskTrial::getHasManualGRFAnnotation()
{
return mHasManualGRFAnnotation;
}

void SubjectOnDiskTrial::setHasManualGRFAnnotation(
std::vector<bool> hasManualGRFAnnotation)
{
mHasManualGRFAnnotation = hasManualGRFAnnotation;
}

void SubjectOnDiskTrial::setCustomValues(
std::vector<Eigen::MatrixXs> customValues)
{
Expand Down Expand Up @@ -3250,6 +3379,27 @@ std::vector<ForcePlate> SubjectOnDiskTrial::getForcePlates()
return mForcePlates;
}

void SubjectOnDiskTrial::setBasicTrialType(BasicTrialType type)
{
mBasicTrialType = type;
}

BasicTrialType SubjectOnDiskTrial::getBasicTrialType()
{
return mBasicTrialType;
}

void SubjectOnDiskTrial::setDetectedTrialFeatures(
std::vector<DetectedTrialFeature> features)
{
mDetectedTrialFeatures = features;
}

std::vector<DetectedTrialFeature> SubjectOnDiskTrial::getDetectedTrialFeatures()
{
return mDetectedTrialFeatures;
}

std::shared_ptr<SubjectOnDiskTrialPass> SubjectOnDiskTrial::addPass()
{
mTrialPasses.push_back(std::make_shared<SubjectOnDiskTrialPass>());
Expand Down Expand Up @@ -3305,6 +3455,19 @@ void SubjectOnDiskTrial::read(const proto::SubjectOnDiskTrialHeader& proto)
mMissingGRFReason.push_back(
missingGRFReasonFromProto(proto.missing_grf_reason(i)));
}
mHasManualGRFAnnotation.clear();
for (int i = 0; i < proto.has_manual_grf_annotation_size(); i++)
{
mHasManualGRFAnnotation.push_back(proto.has_manual_grf_annotation(i));
}

mBasicTrialType = basicTrialTypeFromProto(proto.trial_type());
mDetectedTrialFeatures.clear();
for (int i = 0; i < proto.detected_trial_feature_size(); i++)
{
mDetectedTrialFeatures.push_back(
detectedTrialFeatureFromProto(proto.detected_trial_feature(i)));
}

// ///////////////////////////////////////////////////////////////////////////
// // Raw sensor observations, which are shared across processing passes
Expand Down Expand Up @@ -3378,6 +3541,16 @@ void SubjectOnDiskTrial::write(proto::SubjectOnDiskTrialHeader* proto)
proto->add_missing_grf_reason(
missingGRFReasonToProto(mMissingGRFReason[i]));
}
for (int i = 0; i < mHasManualGRFAnnotation.size(); i++)
{
proto->add_has_manual_grf_annotation(mHasManualGRFAnnotation[i]);
}
proto->set_trial_type(basicTrialTypeToProto(mBasicTrialType));
for (int i = 0; i < mDetectedTrialFeatures.size(); i++)
{
proto->add_detected_trial_feature(
detectedTrialFeatureToProto(mDetectedTrialFeatures[i]));
}

// ///////////////////////////////////////////////////////////////////////////
// // Raw sensor observations, which are shared across processing passes
Expand Down Expand Up @@ -3547,6 +3720,17 @@ SubjectOnDiskHeader& SubjectOnDiskHeader::setNotes(const std::string& notes)
return *this;
}

SubjectOnDiskHeader& SubjectOnDiskHeader::setQuality(DataQuality quality)
{
mDataQuality = quality;
return *this;
}

DataQuality SubjectOnDiskHeader::getQuality()
{
return mDataQuality;
}

std::shared_ptr<SubjectOnDiskPassHeader>
SubjectOnDiskHeader::addProcessingPass()
{
Expand Down Expand Up @@ -3782,6 +3966,7 @@ void SubjectOnDiskHeader::write(dart::proto::SubjectOnDiskHeader* header)
{
header->add_exo_dof_index(index);
}
header->set_data_quality(dataQualityToProto(mDataQuality));

if (!header->IsInitialized())
{
Expand Down Expand Up @@ -3926,6 +4111,8 @@ void SubjectOnDiskHeader::read(const dart::proto::SubjectOnDiskHeader& proto)
{
mExoDofIndices.push_back(proto.exo_dof_index(i));
}

mDataQuality = dataQualityFromProto(proto.data_quality());
}

void SubjectOnDiskHeader::writeSensorsFrame(
Expand Down
18 changes: 18 additions & 0 deletions dart/biomechanics/SubjectOnDisk.hpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -347,6 +347,8 @@ class SubjectOnDiskTrial
void setOriginalTrialEndTime(s_t endTime);
std::vector<MissingGRFReason> getMissingGRFReason();
void setMissingGRFReason(std::vector<MissingGRFReason> missingGRFReason);
std::vector<bool> getHasManualGRFAnnotation();
void setHasManualGRFAnnotation(std::vector<bool> hasManualGRFAnnotation);
void setCustomValues(std::vector<Eigen::MatrixXs> customValues);
void setMarkerNamesGuessed(bool markersGuessed);
std::vector<std::map<std::string, Eigen::Vector3s>> getMarkerObservations();
Expand All @@ -361,6 +363,10 @@ class SubjectOnDiskTrial
void setExoTorques(std::map<int, Eigen::VectorXs> exoTorques);
void setForcePlates(std::vector<ForcePlate> forcePlates);
std::vector<ForcePlate> getForcePlates();
void setBasicTrialType(BasicTrialType type);
BasicTrialType getBasicTrialType();
void setDetectedTrialFeatures(std::vector<DetectedTrialFeature> features);
std::vector<DetectedTrialFeature> getDetectedTrialFeatures();
std::shared_ptr<SubjectOnDiskTrialPass> addPass();
std::vector<std::shared_ptr<SubjectOnDiskTrialPass>> getPasses();
void read(const proto::SubjectOnDiskTrialHeader& proto);
Expand All @@ -373,6 +379,7 @@ class SubjectOnDiskTrial
std::vector<std::string> mTrialTags;
std::vector<std::shared_ptr<SubjectOnDiskTrialPass>> mTrialPasses;
std::vector<MissingGRFReason> mMissingGRFReason;
std::vector<bool> mHasManualGRFAnnotation;
// This is true if we guessed the marker names, and false if we got them from
// the uploaded user's file, which implies that they got them from human
// observations.
Expand All @@ -385,6 +392,9 @@ class SubjectOnDiskTrial
s_t mOriginalTrialStartTime;
s_t mOriginalTrialEndTime;

BasicTrialType mBasicTrialType;
std::vector<DetectedTrialFeature> mDetectedTrialFeatures;

///////////////////////////////////////////////////////////////////////////
// Recovered proto summaries, for incremental loading of Frames
///////////////////////////////////////////////////////////////////////////
Expand Down Expand Up @@ -453,6 +463,8 @@ class SubjectOnDiskHeader
SubjectOnDiskHeader& setSubjectTags(std::vector<std::string> subjectTags);
SubjectOnDiskHeader& setHref(const std::string& sourceHref);
SubjectOnDiskHeader& setNotes(const std::string& notes);
SubjectOnDiskHeader& setQuality(DataQuality quality);
DataQuality getQuality();
std::shared_ptr<SubjectOnDiskPassHeader> addProcessingPass();
std::vector<std::shared_ptr<SubjectOnDiskPassHeader>> getProcessingPasses();
std::shared_ptr<SubjectOnDiskTrial> addTrial();
Expand Down Expand Up @@ -512,6 +524,9 @@ class SubjectOnDiskHeader
// This is exoskeleton data
std::vector<int> mExoDofIndices;

// This is the user supplied quality of the data
DataQuality mDataQuality;

friend class SubjectOnDisk;
friend struct Frame;
friend struct FramePass;
Expand Down Expand Up @@ -627,6 +642,9 @@ class SubjectOnDisk
/// include `notMissingGRF`.
std::vector<MissingGRFReason> getMissingGRF(int trial);

/// This returns the user supplied enum of type 'DataQuality'
DataQuality getQuality();

int getNumProcessingPasses();

ProcessingPassType getProcessingPassType(int processingPass);
Expand Down
23 changes: 23 additions & 0 deletions dart/biomechanics/enums.hpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,29 @@ enum MissingGRFReason
extendedToNearestPeakForce
};

enum BasicTrialType
{
treadmill,
overground,
staticTrial,
other
};

enum DetectedTrialFeature
{
walking,
running,
unevenTerrain,
flatTerrain
};

enum DataQuality
{
pilotData,
experimentalData,
internetData
};

enum MissingGRFStatus
{
no = 0, // no will cast to `false`
Expand Down
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