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Merge pull request #359 from agri-gaia/refactor-hdf5-core
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Refactoring in seerep_hdf5_core and seerep_core
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@jarkenau
jarkenau authored Dec 21, 2023
2 parents 793129c + 759a812 commit 83325dc
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Showing 19 changed files with 232 additions and 276 deletions.
17 changes: 10 additions & 7 deletions seerep_hdf5/seerep_hdf5_core/include/seerep_hdf5_core/hdf5_core_cameraintrinsics.h
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Expand Up @@ -40,18 +40,21 @@ class Hdf5CoreCameraIntrinsics : public Hdf5CoreGeneral
* @return true If camera intrinsics exist
* @return false If camera intrinsics do not exist
*/
bool checkCameraIntrinsicsExists(const boost::uuids::uuid& cameraintrinsics_uuid);
bool cameraIntrinsicExists(const boost::uuids::uuid& camera_intrinsic_uuid) const;

private:
const std::shared_ptr<HighFive::DataSet> generateDatasetPointer(const std::string& attribute);
const std::string getHdf5GroupPath(const std::string& id) const;
const std::string getHdf5DataSetPath(const std::string& id) const;
/**
* @brief Returns the HDF5 group path for a given camera intrinsics UUID.
*@param uuid The UUID string of a camera intrinsic.
*@return The HDF5 group path.
*/
const std::string cameraIntrinsicPath(const std::string& camera_intrinsic_uuid) const;

public:
// datatype group names in hdf5
/* HDF5 group name to store the camera instrinsics */
inline static const std::string HDF5_GROUP_CAMINTRINSICS = "cameraintrinsics";
inline static const std::string SIZE = "size";

/* HDF5 attribute names to store the camera instrinsics information */
inline static const std::string HEIGHT = "height";
inline static const std::string WIDTH = "width";
inline static const std::string DISTORTION_MODEL = "distortion_model";
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155 changes: 102 additions & 53 deletions seerep_hdf5/seerep_hdf5_core/include/seerep_hdf5_core/hdf5_core_general.h
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Expand Up @@ -43,28 +43,70 @@ class Hdf5CoreGeneral
void checkExists(const std::string& id);

/**
* @brief Checks if a DataSet or DataGroup exists in the file
* @param id The id of the DataSet or DataGroup
* @return true if the DataSet or DataGroup exists
* @brief Checks if a HDF5 path exists in the file.
*
* Wrapper around HighFive::File::exist() for logging purposes.
*
* @param path The HDF5 path to check
* @return True if the dataset exists, false otherwise.
*/
bool exists(const std::string& id);
bool exists(const std::string& path) const;

std::optional<std::string> readFrameId(const std::string& datatypeGroup, const std::string& uuid);
// ################
// Attributes
// ################
/**
* @brief Reads an attribute from an HDF5 object.
*
* @tparam T The type of the attribute to read.
* @tparam C The type of the HDF5 object to read from.
* @param object The HDF5 object to read from.
* @param attribute_name The name of the attribute to read.
* @param path The path to the HDF5 object, only used for logging.
* @return T The value of the attribute.
*/
template <typename T, class C>
T readAttributeFromHdf5(const std::string& id, const HighFive::AnnotateTraits<C>& object, std::string attributeField);
T readAttributeFromHdf5(const HighFive::AnnotateTraits<C>& object, const std::string& attribute_name,
const std::string& path);

/**
* @brief Writes an attribute to an HDF5 object.
*
* @tparam T The type of the attribute to write.
* @tparam C The type of the HDF5 object.
* @param object The HDF5 object to write the attribute to.
* @param attribute_name The name of the attribute.
* @param attribute_val The value of the attribute.
*/
template <typename T, class C>
void writeAttributeToHdf5(HighFive::AnnotateTraits<C>& object, std::string attributeField, T attributeValue);
void writeAttributeToHdf5(HighFive::AnnotateTraits<C>& object, const std::string& attribute_name, T attribute_val);

void deleteAttribute(const std::shared_ptr<HighFive::DataSet> dataSetPtr, std::string attributeField);
/**
* @brief Returns a tf2 compliant frame ID.
*
* @param frame_id The frame ID to check.
* @return The corresponding tf2 frame ID.
*/
const std::string tf2_frame_id(const std::string& frame_id) const;

/**
* @brief Reads a tf2 compliant frame ID from an HDF5 object.
*
* @tparam C The type of the HDF5 object to read from.
* @param object The HDF5 object to read from.
* @param frame_field The name of HDF5 attribute to read the frame ID from.
* @param id The path to the HDF5 object, only used for logging.
* @return The frame ID as a string.
*/
template <class C>
std::string readFrameId(const std::string& id, const HighFive::AnnotateTraits<C>& object,
const std::string& frame_field);
std::string readFrameId(const HighFive::AnnotateTraits<C>& object, const std::string& frame_field,
const std::string& path);

/**
* @brief Writes a tf2 compliant frame ID to an HDF5 object.
*
* @tparam C The type of the HDF5 object to write to.
* @param object The HDF5 object to write to.
* @param frame_field The name of the HDF5 attribute to write the frame ID to.
* @param frame_id The frame ID to write.
*/
template <class C>
void writeFrameId(HighFive::AnnotateTraits<C>& object, const std::string& frame_field, const std::string& frame_id);

Expand Down Expand Up @@ -94,14 +136,6 @@ class Hdf5CoreGeneral
template <class T>
void writeHeader(HighFive::AnnotateTraits<T>& object, seerep_core_msgs::Header header);

/*
* @brief Corrects a frame_id to be valid for tf2.
*
* @param [in] frame_id frame_id to check
* @param [out] frame_id which complies with tf2
*/
const std::string tf2_frame_id(std::string frame_id);

/**
* @brief Read header from a group within an hd5f file
*
Expand Down Expand Up @@ -161,59 +195,72 @@ class Hdf5CoreGeneral
void writeVersion(const std::string& version);
const std::optional<std::string> readVersion();

// ################
// Geodetic Coordinates
// ################
/**
* @brief Writes Geodetic location of the project to its HDF5 file.
* @brief Writes a geodetic coordinate to an HDF5 file.
*
* Note: The data is written to the root group of the HDF5 file, since the geo-reference applies to complete project.
*
* @param geocoords seerep_core_msgs Geodetic Coordinates object.
* @param geo_coordinates The geodetic coordinate to write to the file.
*/
void writeGeodeticLocation(const seerep_core_msgs::GeodeticCoordinates geocoords);
void writeGeodeticLocation(const seerep_core_msgs::GeodeticCoordinates& geo_coordinates);

/**
* @brief Read Geodetic location of the project from its HDF5 file.
* @brief Reads a geodetic coodrinate from HDF5 file.
*
* Note: The data is expected to be stored in the root group of the HDF5 file.
*
* @return std::optional<seerep_core_msgs::GeodeticCoordinates> Optional return of Geodetic Coordinates
* @return std::optional<seerep_core_msgs::GeodeticCoordinates> Geodetic coordinate if available, empty optional otherwise.
*/
std::optional<seerep_core_msgs::GeodeticCoordinates> readGeodeticLocation();

// ################
// Hdf5
// ################
/**
* @brief Get a shared pointer to a hdf5 group
* @brief Returns a shared pointer to an HDF5 group object.
*
* @param hdf5GroupPath path to the data group
* @param create create a new group if the group path can't be found?
* @return std::shared_ptr<HighFive::Group> shared pointer to the group
* @param group_path The path to the HDF5 group.
* @param create If true, the group will be created if it does not already exist.
* @return std::shared_ptr<HighFive::Group> A shared pointer to the HDF5 group object. Nullptr if the group does not
* exist and create is false.
*/
std::shared_ptr<HighFive::Group> getHdf5Group(const std::string& hdf5GroupPath, bool create = true);
std::shared_ptr<HighFive::Group> getHdf5Group(const std::string& group_path, bool create = true);

/**
* @brief Get a shared pointer to a hdf5 data set specified by the hdf5DataSetPath
* @brief Returns a shared pointer to a HighFive::DataSet object for the given dataset path.
*
* @tparam T type of the dataset
* @param hdf5DataSetPath path to the dataset
* @param dataSpace the data space to specify the dimensions of the dataset
* @return std::shared_ptr<HighFive::DataSet> shared pointer to the data set
* @param dataset_path The path to the dataset.
* @return std::shared_ptr<HighFive::DataSet> A shared pointer to the dataset object. Nullptr if the dataset does not exist.
*/
std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& dataset_path);

/**
* @brief Returns a shared pointer to a HighFive::DataSet object for the given dataset path and data space.
*
* A new dataset will be created if it does not already exist.
*
* @tparam T The data type of the dataset.
* @param dataset_path The path to the dataset.
* @param dataspace The data space of the dataset.
* @return std::shared_ptr<HighFive::DataSet> A shared pointer to the HighFive dataset object.
*/
template <class T>
std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& hdf5DataSetPath, HighFive::DataSpace& dataSpace);
std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& dataset_path,
const HighFive::DataSpace& dataspace);

/**
* @brief Get a shared pointer to a hdf5 data set specified by the hdf5DataSetPath
* @brief Get a shared pointer to a HighFive::Dataset object for the given path, dataspace, and properties.
*
* @tparam T type of the dataset
* @param hdf5DataSetPath path to the dataset
* @param dataSpace the data space to specify the dimensions of the dataset
* @param createProps properties for creation of the dataset
* @return std::shared_ptr<HighFive::DataSet> shared pointer to the data set
* A new dataset will be created if it does not already exist.
*
* @tparam T The datatype of the dataset.
* @param dataset_path The path to the dataset.
* @param dataspace The dataspace of the dataset.
* @param properties The properties of the dataset.
* @return std::shared_ptr<HighFive::DataSet> A shared pointer to the HDF5 dataset.
*/
template <class T>
std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& hdf5DataSetPath, HighFive::DataSpace& dataSpace,
HighFive::DataSetCreateProps& createProps);
std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& dataset_path,
const HighFive::DataSpace& dataspace,
const HighFive::DataSetCreateProps& properties);

std::shared_ptr<HighFive::DataSet> getHdf5DataSet(const std::string& hdf5DataSetPath);
/**
* @brief get the labels of a group/dataset matching the general prefix (label type) and return the labels matching
* the specified type. Also extract the category from the postfix
Expand Down Expand Up @@ -268,7 +315,9 @@ class Hdf5CoreGeneral
protected:
std::shared_ptr<HighFive::File> m_file;
std::shared_ptr<std::mutex> m_write_mtx;
boost::log::sources::severity_logger<boost::log::trivial::severity_level> m_logger;

/* The logger does not change the state of the object, thus we can make it mutable, to use it in const functions */
mutable boost::log::sources::severity_logger<boost::log::trivial::severity_level> m_logger;
};

} // namespace seerep_hdf5_core
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63 changes: 27 additions & 36 deletions seerep_hdf5/seerep_hdf5_core/include/seerep_hdf5_core/impl/hdf5_core_general.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -3,40 +3,40 @@
namespace seerep_hdf5_core
{
template <typename T, class C>
T Hdf5CoreGeneral::readAttributeFromHdf5(const std::string& id, const HighFive::AnnotateTraits<C>& object,
std::string attributeField)
T Hdf5CoreGeneral::readAttributeFromHdf5(const HighFive::AnnotateTraits<C>& object, const std::string& attribute_name,
const std::string& path)
{
T attributeValue;
if (object.hasAttribute(attributeField))
T attribute_value;
if (object.hasAttribute(attribute_name))
{
object.getAttribute(attributeField).read(attributeValue);
object.getAttribute(attribute_name).read(attribute_value);
}
else
{
throw std::invalid_argument("id " + id + " has no attribute " + attributeField);
throw std::invalid_argument("Path: " + path + " has no attribute:" + attribute_name);
}
return attributeValue;
return attribute_value;
}

template <typename T, class C>
void Hdf5CoreGeneral::writeAttributeToHdf5(HighFive::AnnotateTraits<C>& object, std::string attributeField,
T attributeValue)
void Hdf5CoreGeneral::writeAttributeToHdf5(HighFive::AnnotateTraits<C>& object, const std::string& attribute_name,
T attribute_val)
{
if (object.hasAttribute(attributeField))
if (object.hasAttribute(attribute_name))
{
object.getAttribute(attributeField).write(attributeValue);
object.getAttribute(attribute_name).write(attribute_val);
}
else
{
object.createAttribute(attributeField, attributeValue);
object.createAttribute(attribute_name, attribute_val);
}
}

template <class C>
std::string Hdf5CoreGeneral::readFrameId(const std::string& uuid, const HighFive::AnnotateTraits<C>& object,
const std::string& frame_field)
std::string Hdf5CoreGeneral::readFrameId(const HighFive::AnnotateTraits<C>& object, const std::string& frame_field,
const std::string& path)
{
return tf2_frame_id(readAttributeFromHdf5<std::string>(uuid, object, frame_field));
return tf2_frame_id(readAttributeFromHdf5<std::string>(object, frame_field, path));
}

template <class C>
Expand All @@ -48,30 +48,21 @@ void Hdf5CoreGeneral::writeFrameId(HighFive::AnnotateTraits<C>& object, const st

template <class T>
std::shared_ptr<HighFive::DataSet> Hdf5CoreGeneral::getHdf5DataSet(const std::string& hdf5DataSetPath,
HighFive::DataSpace& dataSpace)
const HighFive::DataSpace& dataSpace)
{
HighFive::DataSetCreateProps emptyProps;
return getHdf5DataSet<T>(hdf5DataSetPath, dataSpace, emptyProps);
return getHdf5DataSet<T>(hdf5DataSetPath, dataSpace, HighFive::DataSetCreateProps());
}

template <class T>
std::shared_ptr<HighFive::DataSet> Hdf5CoreGeneral::getHdf5DataSet(const std::string& hdf5DataSetPath,
HighFive::DataSpace& dataSpace,
HighFive::DataSetCreateProps& createProps)
std::shared_ptr<HighFive::DataSet> Hdf5CoreGeneral::getHdf5DataSet(const std::string& dataset_path,
const HighFive::DataSpace& dataspace,
const HighFive::DataSetCreateProps& properties)
{
try
{
checkExists(hdf5DataSetPath);
BOOST_LOG_SEV(m_logger, boost::log::trivial::severity_level::trace)
<< "hdf5 group" << hdf5DataSetPath << " already exists!";
return std::make_shared<HighFive::DataSet>(m_file->getDataSet(hdf5DataSetPath));
}
catch (std::invalid_argument const& e)
if (exists(dataset_path))
{
BOOST_LOG_SEV(m_logger, boost::log::trivial::severity_level::trace)
<< "hdf5 group " << hdf5DataSetPath << " does not exist! Creating a new group";
return std::make_shared<HighFive::DataSet>(m_file->createDataSet<T>(hdf5DataSetPath, dataSpace, createProps));
return std::make_shared<HighFive::DataSet>(m_file->getDataSet(dataset_path));
}
return std::make_shared<HighFive::DataSet>(m_file->createDataSet<T>(dataset_path, dataspace, properties));
}

template <class T>
Expand All @@ -92,9 +83,9 @@ void Hdf5CoreGeneral::readHeader(const std::string& id, HighFive::AnnotateTraits
std::string uuidproject_str = std::filesystem::path(m_file->getName()).filename().stem();
header.uuidProject = boost::lexical_cast<boost::uuids::uuid>(uuidproject_str);

header.timestamp.seconds = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(id, object, HEADER_STAMP_SECONDS);
header.timestamp.nanos = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(id, object, HEADER_STAMP_NANOS);
header.frameId = Hdf5CoreGeneral::readFrameId(id, object, HEADER_FRAME_ID);
header.sequence = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(id, object, HEADER_SEQ);
header.timestamp.seconds = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(object, HEADER_STAMP_SECONDS, id);
header.timestamp.nanos = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(object, HEADER_STAMP_NANOS, id);
header.frameId = Hdf5CoreGeneral::readFrameId(object, HEADER_FRAME_ID, id);
header.sequence = Hdf5CoreGeneral::readAttributeFromHdf5<int32_t>(object, HEADER_SEQ, id);
}
} // namespace seerep_hdf5_core
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