Copy icebridge files over to hdf plugin

cmake/options.cmake

@@ -27,6 +27,11 @@ option(BUILD_PLUGIN_ICEBRIDGE
 add_feature_info("Icebridge plugin" BUILD_PLUGIN_ICEBRIDGE
     "read data in the Icebridge format")
 
+option(BUILD_PLUGIN_HDF
+    "Choose if HDF support should be built" FALSE)
+add_feature_info("HDF plugin" BUILD_PLUGIN_HDF
+    "read data in the HDF format")
+
 option(BUILD_PLUGIN_MATLAB
     "Choose if Matlab support should be built" FALSE)
 add_feature_info("Matlab plugin" BUILD_PLUGIN_MATLAB

plugins/CMakeLists.txt

@@ -23,6 +23,13 @@ if(BUILD_PLUGIN_ICEBRIDGE)
     add_subdirectory(icebridge)
 endif()
 
+if(BUILD_PLUGIN_HDF)
+    if (NOT PDAL_HAVE_LIBXML2)
+        message(FATAL_ERROR "Can't build hdf plugin without libxml2")
+    endif()
+    add_subdirectory(hdf)
+endif()
+
 if(BUILD_PLUGIN_MATLAB)
     add_subdirectory(matlab)
 endif()

plugins/hdf/CMakeLists.txt

@@ -0,0 +1,22 @@
+#
+# Icebridge plugin CMake configuration
+#
+
+include (${PDAL_CMAKE_DIR}/hdf5.cmake)
+
+
+if (NOT PDAL_HAVE_HDF5)
+    message(FATAL "HDF5 not found but is required for Icebridge.")
+else()
+    PDAL_ADD_PLUGIN(libname reader hdf
+        FILES
+            io/HdfReader.cpp
+            io/Hdf5Handler.cpp
+        LINK_WITH
+            ${HDF5_LIBRARIES}
+        INCLUDES
+            ${ROOT_DIR}
+            ${LIBXML2_INCLUDE_DIR}
+    )
+
+endif()

plugins/hdf/io/Hdf5Handler.cpp

@@ -0,0 +1,152 @@
+/******************************************************************************
+* 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
+

plugins/hdf/io/Hdf5Handler.hpp

@@ -0,0 +1,119 @@
+/******************************************************************************
+* 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.
+****************************************************************************/
+
+#pragma once
+
+#include <pdal/pdal_export.hpp>  // Suppresses windows 4251 messages
+#include "H5Cpp.h"
+
+#include <memory>
+#include <vector>
+#include <string>
+#include <map>
+
+namespace pdal
+{
+
+namespace hdf5
+{
+    struct Hdf5ColumnData
+    {
+        Hdf5ColumnData(const std::string& name, const H5::PredType predType)
+            : name(name)
+            , predType(predType)
+        { }
+
+        const std::string name;
+        const H5::PredType predType;
+    };
+}
+
+class Hdf5Handler
+{
+public:
+    struct error : public std::runtime_error
+    {
+        error(const std::string& err) : std::runtime_error(err)
+        {}
+    };
+
+    Hdf5Handler();
+
+    void initialize(
+            const std::string& filename,
+            const std::vector<hdf5::Hdf5ColumnData>& columns);
+    void close();
+
+    uint64_t getNumPoints() const;
+
+    void getColumnEntries(
+            void* data,
+            const std::string& dataSetName,
+            const hsize_t numEntries,
+            const hsize_t offset) const;
+
+private:
+    struct ColumnData
+    {
+        ColumnData(
+                H5::PredType predType,
+                H5::DataSet dataSet,
+                H5::DataSpace dataSpace)
+            : predType(predType)
+            , dataSet(dataSet)
+            , dataSpace(dataSpace)
+        { }
+
+        ColumnData(H5::PredType predType)
+            : predType(predType)
+            , dataSet()
+            , dataSpace()
+        { }
+
+        H5::PredType predType;
+        H5::DataSet dataSet;
+        H5::DataSpace dataSpace;
+    };
+
+    hsize_t getColumnNumEntries(const std::string& dataSetName) const;
+    const ColumnData& getColumnData(const std::string& dataSetName) const;
+
+    std::unique_ptr<H5::H5File> m_h5File;
+    uint64_t m_numPoints;
+
+    std::map<std::string, ColumnData> m_columnDataMap;
+};
+
+} // namespace pdal
+