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add checks for empty flatbuffers message fields inside write function
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stop using references here so that the arguments can be null and checked inside the function
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Julian Arkenau committed Oct 13, 2022
1 parent 87b6f63 commit ee17ea5
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Showing 6 changed files with 79 additions and 80 deletions.
10 changes: 5 additions & 5 deletions seerep-hdf5/seerep-hdf5-fb/include/seerep-hdf5-fb/hdf5-fb-general.h
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,13 @@ class Hdf5FbGeneral : public seerep_hdf5_core::Hdf5CoreGeneral
// Attributes
//################
void writeAttributeMap(const std::shared_ptr<HighFive::DataSet> dataSetPtr,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::UnionMapEntry>>& attributes);
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::UnionMapEntry>>* attributes);
template <class T>
flatbuffers::Offset<flatbuffers::Vector<flatbuffers::Offset<seerep::fb::UnionMapEntry>>>
readAttributeMap(HighFive::AnnotateTraits<T>& object, flatbuffers::grpc::MessageBuilder& builder);

template <class T>
void writeHeaderAttributes(HighFive::AnnotateTraits<T>& object, const seerep::fb::Header& header);
void writeHeaderAttributes(HighFive::AnnotateTraits<T>& object, const seerep::fb::Header* header);

template <class T>
flatbuffers::Offset<seerep::fb::Header> readHeaderAttributes(flatbuffers::grpc::MessageBuilder& builder,
Expand All @@ -55,17 +55,17 @@ class Hdf5FbGeneral : public seerep_hdf5_core::Hdf5CoreGeneral
//################
void writeBoundingBoxLabeled(
const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBoxLabeled>>& boundingboxLabeled);
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBoxLabeled>>* boundingboxLabeled);

void writeBoundingBox2DLabeled(
const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBox2DLabeled>>& boundingbox2DLabeled);
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBox2DLabeled>>* boundingbox2DLabeled);

//################
// Labels General
//################
void writeLabelsGeneral(const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::LabelWithInstance>>& labelsGeneral);
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::LabelWithInstance>>* labelsGeneral);
};

} // namespace seerep_hdf5_fb
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43 changes: 23 additions & 20 deletions seerep-hdf5/seerep-hdf5-fb/include/seerep-hdf5-fb/impl/hdf5-fb-general.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -35,27 +35,30 @@ Hdf5FbGeneral::readAttributeMap(HighFive::AnnotateTraits<T>& object, flatbuffers
}

template <class T>
void Hdf5FbGeneral::writeHeaderAttributes(HighFive::AnnotateTraits<T>& object, const seerep::fb::Header& header)
void Hdf5FbGeneral::writeHeaderAttributes(HighFive::AnnotateTraits<T>& object, const seerep::fb::Header* header)
{
if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS, header.stamp()->seconds());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS).write(header.stamp()->seconds());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS, header.stamp()->nanos());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS).write(header.stamp()->nanos());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID, header.frame_id()->str());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID).write(header.frame_id()->str());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ, header.seq());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ).write(header.seq());
if (header)
{
if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS, header->stamp()->seconds());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_SECONDS).write(header->stamp()->seconds());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS, header->stamp()->nanos());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_STAMP_NANOS).write(header->stamp()->nanos());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID, header->frame_id()->str());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_FRAME_ID).write(header->frame_id()->str());

if (!object.hasAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ))
object.createAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ, header->seq());
else
object.getAttribute(seerep_hdf5_core::Hdf5CoreGeneral::HEADER_SEQ).write(header->seq());
}
}

template <class T>
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77 changes: 40 additions & 37 deletions seerep-hdf5/seerep-hdf5-fb/src/hdf5-fb-general.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,53 +11,56 @@ Hdf5FbGeneral::Hdf5FbGeneral(std::shared_ptr<HighFive::File>& file, std::shared_

void Hdf5FbGeneral::writeAttributeMap(
const std::shared_ptr<HighFive::DataSet> dataSetPtr,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::UnionMapEntry>>& attributes)
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::UnionMapEntry>>* attributes)
{
for (auto attribute : attributes)
if (attributes)
{
if (attribute->value_type() == seerep::fb::Datatypes_Boolean)
for (auto attribute : *attributes)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Boolean*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_Integer)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Integer*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_Double)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Double*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_String)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::String*>(attribute->value())->data()->str());
}
else
{
std::stringstream errorMsg;
errorMsg << "type " << attribute->value_type() << " of attribute " << attribute->key()->c_str()
<< " not implemented in hdf5-io.";
BOOST_LOG_SEV(m_logger, boost::log::trivial::severity_level::error) << errorMsg.str();
throw std::invalid_argument(errorMsg.str());
if (attribute->value_type() == seerep::fb::Datatypes_Boolean)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Boolean*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_Integer)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Integer*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_Double)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::Double*>(attribute->value())->data());
}
else if (attribute->value_type() == seerep::fb::Datatypes_String)
{
writeAttributeToHdf5(*dataSetPtr, attribute->key()->str(),
static_cast<const seerep::fb::String*>(attribute->value())->data()->str());
}
else
{
std::stringstream errorMsg;
errorMsg << "type " << attribute->value_type() << " of attribute " << attribute->key()->c_str()
<< " not implemented in hdf5-io.";
BOOST_LOG_SEV(m_logger, boost::log::trivial::severity_level::error) << errorMsg.str();
throw std::invalid_argument(errorMsg.str());
}
}
}
}

void Hdf5FbGeneral::writeBoundingBoxLabeled(
const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBoxLabeled>>& boundingboxLabeled)
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBoxLabeled>>* boundingboxLabeled)
{
if (!boundingboxLabeled.size() == 0)
if (boundingboxLabeled && boundingboxLabeled->size() != 0)
{
std::string id = datatypeGroup + "/" + uuid;

std::vector<std::string> labels;
std::vector<std::vector<double>> boundingBoxes;
std::vector<std::string> instances;
for (auto label : boundingboxLabeled)
for (auto label : *boundingboxLabeled)
{
labels.push_back(label->labelWithInstance()->label()->str());
std::vector<double> box{ label->bounding_box()->point_min()->x(), label->bounding_box()->point_min()->y(),
Expand Down Expand Up @@ -86,16 +89,16 @@ void Hdf5FbGeneral::writeBoundingBoxLabeled(

void Hdf5FbGeneral::writeBoundingBox2DLabeled(
const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBox2DLabeled>>& boundingbox2DLabeled)
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::BoundingBox2DLabeled>>* boundingbox2DLabeled)
{
std::string id = datatypeGroup + "/" + uuid;

if (!boundingbox2DLabeled.size() == 0)
if (boundingbox2DLabeled && boundingbox2DLabeled->size() != 0)
{
std::vector<std::string> labels;
std::vector<std::vector<double>> boundingBoxes;
std::vector<std::string> instances;
for (auto label : boundingbox2DLabeled)
for (auto label : *boundingbox2DLabeled)
{
labels.push_back(label->labelWithInstance()->label()->str());
std::vector<double> box{ label->bounding_box()->point_min()->x(), label->bounding_box()->point_min()->y(),
Expand Down Expand Up @@ -123,15 +126,15 @@ void Hdf5FbGeneral::writeBoundingBox2DLabeled(

void Hdf5FbGeneral::writeLabelsGeneral(
const std::string& datatypeGroup, const std::string& uuid,
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::LabelWithInstance>>& labelsGeneral)
const flatbuffers::Vector<flatbuffers::Offset<seerep::fb::LabelWithInstance>>* labelsGeneral)
{
std::string id = datatypeGroup + "/" + uuid;

if (labelsGeneral.size() != 0)
if (labelsGeneral && labelsGeneral->size() != 0)
{
std::vector<std::string> labels;
std::vector<std::string> instances;
for (auto label : labelsGeneral)
for (auto label : *labelsGeneral)
{
labels.push_back(label->label()->str());

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8 changes: 4 additions & 4 deletions seerep-hdf5/seerep-hdf5-fb/src/hdf5-fb-image.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -73,10 +73,10 @@ void Hdf5FbImage::writeImage(const std::string& id, const seerep::fb::Image& ima
}

data_set_ptr->write(tmp);
writeHeaderAttributes(*data_set_ptr, *image.header());
writeHeaderAttributes(*data_set_ptr, image.header());

writeBoundingBox2DLabeled(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, *image.labels_bb());
writeLabelsGeneral(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, *image.labels_general());
writeBoundingBox2DLabeled(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, image.labels_bb());
writeLabelsGeneral(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, image.labels_general());

m_file->flush();
}
Expand All @@ -86,7 +86,7 @@ void Hdf5FbImage::writeImageBoundingBox2DLabeled(const std::string& id,
{
const std::scoped_lock lock(*m_write_mtx);

writeBoundingBox2DLabeled(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, *bb2dLabeledStamped.labels_bb());
writeBoundingBox2DLabeled(seerep_hdf5_core::Hdf5CoreImage::HDF5_GROUP_IMAGE, id, bb2dLabeledStamped.labels_bb());
}

std::optional<flatbuffers::grpc::Message<seerep::fb::Image>> Hdf5FbImage::readImage(const std::string& id,
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8 changes: 4 additions & 4 deletions seerep-hdf5/seerep-hdf5-fb/src/hdf5-fb-point.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -39,11 +39,11 @@ void Hdf5FbPoint::writePoint(const std::string& id, const seerep::fb::PointStamp
}

data_set_ptr->write(data);
writeHeaderAttributes(*data_set_ptr, *point->header());
writeHeaderAttributes(*data_set_ptr, point->header());

writeAttributeMap(data_set_ptr, *point->attribute());
writeAttributeMap(data_set_ptr, point->attribute());

writeLabelsGeneral(seerep_hdf5_core::Hdf5CorePoint::HDF5_GROUP_POINT, id, *point->labels_general());
writeLabelsGeneral(seerep_hdf5_core::Hdf5CorePoint::HDF5_GROUP_POINT, id, point->labels_general());

m_file->flush();
}
Expand All @@ -60,7 +60,7 @@ void Hdf5FbPoint::writeAdditionalPointAttributes(const seerep::fb::AttributesSta
std::shared_ptr<HighFive::DataSet> data_set_ptr =
std::make_shared<HighFive::DataSet>(m_file->getDataSet(hdf5DatasetRawDataPath));

writeAttributeMap(data_set_ptr, *attributeStamped.attribute());
writeAttributeMap(data_set_ptr, attributeStamped.attribute());
}
catch (const std::exception& e)
{
Expand Down
13 changes: 3 additions & 10 deletions seerep-hdf5/seerep-hdf5-fb/src/hdf5-fb-pointcloud.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -43,19 +43,12 @@ void Hdf5FbPointCloud::writePointCloud2(const std::string& id, const seerep::fb:
writeAttributeToHdf5<uint32_t>(*dataGroupPtr, seerep_hdf5_core::Hdf5CorePointCloud::ROW_STEP, cloud.row_step());
writeAttributeToHdf5<bool>(*dataGroupPtr, seerep_hdf5_core::Hdf5CorePointCloud::IS_DENSE, cloud.is_dense());

writeHeaderAttributes(*dataGroupPtr, *cloud.header());
writeHeaderAttributes(*dataGroupPtr, cloud.header());

writePointFieldAttributes(*dataGroupPtr, *cloud.fields());

if (cloud.labels_bb() != nullptr)
{
writeBoundingBoxLabeled(seerep_hdf5_core::Hdf5CorePointCloud::HDF5_GROUP_POINTCLOUD, id, *cloud.labels_bb());
}

if (cloud.labels_general() != nullptr)
{
writeLabelsGeneral(seerep_hdf5_core::Hdf5CorePointCloud::HDF5_GROUP_POINTCLOUD, id, *cloud.labels_general());
}
writeBoundingBoxLabeled(seerep_hdf5_core::Hdf5CorePointCloud::HDF5_GROUP_POINTCLOUD, id, cloud.labels_bb());
writeLabelsGeneral(seerep_hdf5_core::Hdf5CorePointCloud::HDF5_GROUP_POINTCLOUD, id, cloud.labels_general());

CloudInfo info = getCloudInfo(cloud);

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