No longer segfaults - wip

PDAL · Feb 7, 2020 · b079046 · b079046
1 parent 1dc6ce3
commit b079046
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Showing 3 changed files with 39 additions and 15 deletions.
diff --git a/plugins/hdf/io/Hdf5Handler.cpp b/plugins/hdf/io/Hdf5Handler.cpp
@@ -63,11 +63,15 @@ using namespace hdf5;
 
 
 Hdf5Handler::Hdf5Handler()
-    : m_numPoints(0)
+    : m_chunkOffset(0)
+    , m_numPoints(0)
     , m_columnDataMap()
-    , m_chunkOffset(0)
 { }
 
+void Hdf5Handler::setLog(pdal::LogPtr log) {
+    m_logger = log;
+}
+
 DimInfo::DimInfo(
     const std::string& dimName,
     H5::IntType int_type)
@@ -121,12 +125,12 @@ void Hdf5Handler::initialize(
         if(dimensionality != 1)
             throw error("Only 1-dimensional arrays are supported.");
     } else {
-        std::cout << "Dataset not chunked; proceeding to read one element at a time" << std::endl;
+        m_logger->get(LogLevel::Warning) << "Dataset not chunked; proceeding to read 1024 elements at a time" << std::endl;
         m_chunkSize = 1024;
     }
-    std::cout << "Chunk size: " << m_chunkSize << std::endl;
-    std::cout << "Num points: " << m_numPoints << std::endl;
-    std::cout << "Number of dataspace dimensions: " << m_dspace.getSimpleExtentNdims() << std::endl;
+    m_logger->get(LogLevel::Warning) << "Chunk size: " << m_chunkSize << std::endl;
+    m_logger->get(LogLevel::Warning) << "Num points: " << m_numPoints << std::endl;
+    m_logger->get(LogLevel::Warning) << "Number of dataspace dimensions: " << m_dspace.getSimpleExtentNdims() << std::endl;
     H5::DataType dtype = m_dset.getDataType();
     H5T_class_t vauge_type = dtype.getClass();
 
@@ -153,7 +157,8 @@ void Hdf5Handler::initialize(
     }
     // m_buf = malloc(dtype.getSize() * m_chunkSize); //TODO free
     m_buf = malloc(dtype.getSize() * m_chunkSize); //TODO free
-    std::cout << "Chunk offset: " << m_chunkOffset << std::endl;
+    m_data.resize(m_chunkSize*dtype.getSize());
+    m_logger->get(LogLevel::Warning) << "Chunk offset: " << m_chunkOffset << std::endl;
     // dspace.selectElements(H5S_SELECT_SET, m_chunkSize, &m_chunkOffset);
     // dspace.selectHyperslab(H5S_SELECT_SET, &m_chunkSize, &m_chunkOffset);
     // H5::DataSpace mspace( 1, &m_chunkOffset);
@@ -165,17 +170,30 @@ void Hdf5Handler::close()
     m_h5File->close();
 }
 
+// void *Hdf5Handler::getNextChunk() {
+//     void *buf = malloc(m_dset.getDataType().getSize() * m_chunkSize);
+//     m_logger->get(LogLevel::Warning) << "chunk size: " << m_chunkSize << ", chunk offset: "
+//         << m_chunkOffset << std::endl;
+//     m_dspace.selectHyperslab(H5S_SELECT_SET, &m_chunkSize, &m_chunkOffset);
+//     m_dset.read(buf, m_dset.getDataType(), H5::DataSpace::ALL, m_dspace);
+//     // m_dset.read(m_buf, m_dset.getDataType());
+//     m_chunkOffset += m_chunkSize;
+//     return buf;
+// }
+
 void *Hdf5Handler::getNextChunk() {
-    void *buf = malloc(m_dset.getDataType().getSize() * m_chunkSize);
-    std::cout << "chunk size: " << m_chunkSize << ", chunk offset: "
-        << m_chunkOffset << std::endl;
+    // m_logger->get(LogLevel::Warning) << "chunk size: " << m_chunkSize << ", chunk offset: "
+    //     << m_chunkOffset << std::endl;
     m_dspace.selectHyperslab(H5S_SELECT_SET, &m_chunkSize, &m_chunkOffset);
-    m_dset.read(buf, m_dset.getDataType(), H5::DataSpace::ALL, m_dspace);
-    // m_dset.read(m_buf, m_dset.getDataType());
+    m_dset.read(m_data.data(),
+                m_dset.getDataType(),
+                H5::DataSpace::ALL,
+                m_dspace );
     m_chunkOffset += m_chunkSize;
-    return buf;
+    return m_data.data();
 }
 
+
 uint64_t Hdf5Handler::getNumPoints() const
 {
     return m_numPoints;

diff --git a/plugins/hdf/io/Hdf5Handler.hpp b/plugins/hdf/io/Hdf5Handler.hpp
@@ -36,6 +36,7 @@
 
 #include <pdal/pdal_export.hpp>  // Suppresses windows 4251 messages
 #include <pdal/Dimension.hpp>
+#include <pdal/Log.hpp>
 #include "H5Cpp.h"
 
 #include <memory>
@@ -125,6 +126,7 @@ class Hdf5Handler
             const hsize_t numEntries,
             const hsize_t offset) const;
     hsize_t m_chunkSize;
+    void setLog(pdal::LogPtr log);
 
 private:
     struct ColumnData
@@ -155,10 +157,12 @@ class Hdf5Handler
     const ColumnData& getColumnData(const std::string& dataSetName) const;
     void *m_buf;
     void *m_nextVal;
+    std::vector<uint8_t> m_data;
     // hsize_t m_chunkSize;
     H5::DataSet m_dset;
     H5::DataSpace m_dspace;
     hsize_t m_chunkOffset;
+    pdal::LogPtr m_logger;
 
     std::unique_ptr<H5::H5File> m_h5File;
     uint64_t m_numPoints;

diff --git a/plugins/hdf/io/HdfReader.cpp b/plugins/hdf/io/HdfReader.cpp
@@ -114,10 +114,12 @@ void HdfReader::addDimensions(PointLayoutPtr layout)
 void HdfReader::ready(PointTableRef table)
 {
     std::cout << "HdfReader::ready" << std::endl;
+    m_hdf5Handler.setLog(log());
     try
     {
         // m_hdf5Handler.initialize(m_filename, hdf5Columns);
         // m_hdf5Handler.initialize(m_filename);
+        m_hdf5Handler.initialize(m_filename, m_dimName, m_datasetName);
     }
     catch (const Hdf5Handler::error& err)
     {
@@ -275,8 +277,8 @@ void HdfReader::initialize()
     {
         throwError("Invalid metadata file: '" + m_metadataFile + "'");
     }
-    m_hdf5Handler.initialize(m_filename, m_dimName, m_datasetName);
-
+    // m_hdf5Handler.initialize(m_filename, m_dimName, m_datasetName);
+    // m_hdf5Handler.setLog(log());
     // Data are WGS84 (4326) with ITRF2000 datum (6656)
     // See http://nsidc.org/data/docs/daac/icebridge/ilvis2/index.html for
     // background