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/******************************************************************************
* Copyright (c) 2014, Connor Manning, connor@hobu.co
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following
* conditions are met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in
* the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Hobu, Inc. or Flaxen Geo Consulting nor the
* names of its contributors may be used to endorse or promote
* products derived from this software without specific prior
* written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
* FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
* COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
* INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
* BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
* OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
* AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
* OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
* OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
* OF SUCH DAMAGE.
****************************************************************************/
#include "Hdf5Handler.hpp"
#include <pdal/util/FileUtils.hpp>
#include <pdal/pdal_types.hpp>
namespace pdal
{
using namespace hdf5;
Hdf5Handler::Hdf5Handler()
: m_numPoints(0)
, m_columnDataMap()
{ }
void Hdf5Handler::initialize(
const std::string& filename,
const std::vector<Hdf5ColumnData>& columns)
{
try
{
m_h5File.reset(new H5::H5File(filename, H5F_ACC_RDONLY));
}
catch (const H5::FileIException&)
{
throw error("Could not open HDF5 file '" + filename + "'.");
}
try
{
// Open each HDF5 DataSet and its corresponding DataSpace.
for (const auto& col : columns)
{
const std::string dataSetName = col.name;
const H5::PredType predType = col.predType;
const H5::DataSet dataSet = m_h5File->openDataSet(dataSetName);
const H5::DataSpace dataSpace = dataSet.getSpace();
m_columnDataMap.insert(std::make_pair(
dataSetName,
ColumnData(predType, dataSet, dataSpace)));
// Does not check whether all the columns are the same length.
m_numPoints = (std::max)((uint64_t)getColumnNumEntries(dataSetName),
m_numPoints);
}
}
catch (const H5::Exception&)
{
throw error("Could not initialize data set information.");
}
}
void Hdf5Handler::close()
{
m_h5File->close();
}
uint64_t Hdf5Handler::getNumPoints() const
{
return m_numPoints;
}
void Hdf5Handler::getColumnEntries(
void* data,
const std::string& dataSetName,
const hsize_t numEntries,
const hsize_t offset) const
{
try
{
const ColumnData& columnData(getColumnData(dataSetName));
columnData.dataSpace.selectHyperslab(
H5S_SELECT_SET,
&numEntries,
&offset);
const hsize_t outOffset = 0;
const H5::DataSpace outSpace(1, &numEntries);
outSpace.selectHyperslab(H5S_SELECT_SET, &numEntries, &outOffset);
columnData.dataSet.read(
data,
columnData.predType,
outSpace,
columnData.dataSpace);
}
catch (const H5::Exception&)
{
throw error("Could not read from dataset.");
}
}
hsize_t
Hdf5Handler::getColumnNumEntries(const std::string& dataSetName) const
{
hsize_t entries = 0;
getColumnData(dataSetName).dataSpace.getSimpleExtentDims(&entries);
return entries;
}
const Hdf5Handler::ColumnData&
Hdf5Handler::getColumnData(const std::string& dataSetName) const
{
const auto columnDataIt(m_columnDataMap.find(dataSetName));
if (columnDataIt == m_columnDataMap.end())
{
throw error("Could not retrieve column data.");
}
return columnDataIt->second;
}
} // namespace pdal
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