Address feedback

doc/stages/readers.hdf.rst

@@ -48,15 +48,26 @@ properly mapped and then outputs a LAS file.
     ]
 
 
-This example reads the X, Y, and Z coordinates from the ICESAT2
-ATL03 format and converts them into a LAS file.
-
 .. note::
     All dimensions must be simple numeric HDF datasets with
     equal lengths. Compound types, enum types, string types,
     etc. are not supported.
 
 
+.. warning::
+    The HDF reader does not set an SRS.
+
+
+Common Use Cases
+----------------
+
+A common use case for this data is reading NASA's ICESAT2 data.
+This example reads the X, Y, and Z coordinates from the ICESAT2
+ATL03 format and converts them into a LAS file.
+
+.. note::
+    ICESAT2 data use EPSG:7912.
+
 .. code-block:: json
 
     [
@@ -85,9 +96,6 @@ Options
 
 .. include:: reader_opts.rst
 
-map
+dimensions
   A JSON map with PDAL dimension names as the keys and HDF dataset paths as the values.
 
-metadata
-  TBD
-

plugins/hdf/io/Hdf5Handler.cpp

@@ -76,7 +76,7 @@ DimInfo::DimInfo(
 
 void Hdf5Handler::initialize(
         const std::string& filename,
-        const NL::json& map)
+        const std::map<std::string,std::string>& map)
 {
     try
     {
@@ -89,8 +89,11 @@ void Hdf5Handler::initialize(
     int index = 0;
     std::vector<hsize_t> m_chunkOffset;
 
-    for(const auto& [dimName, datasetName] : map.items()) {
+    for( auto const& entry : map) {
+        std::string const& dimName = entry.first;
+        std::string const& datasetName = entry.second;
         hsize_t chunkSize;
+
         m_logger->get(LogLevel::Info) << "Opening dataset '"
             << datasetName << "' with dimension name '" << dimName
             << "'" << std::endl;
@@ -150,7 +153,7 @@ void Hdf5Handler::close()
 
 uint8_t *Hdf5Handler::getNextChunk(int index) {
     hsize_t elementsRemaining = m_numPoints - m_chunkOffsets.at(index);
-    hsize_t chunkSize = m_dimInfos.at(0).chunkSize;
+    hsize_t chunkSize = m_dimInfos.at(index).chunkSize;
     hsize_t selectionSize = std::min(elementsRemaining, chunkSize);
 
     H5::DataSpace memspace(1, &selectionSize);

plugins/hdf/io/Hdf5Handler.hpp

@@ -72,7 +72,7 @@ class Hdf5Handler
 public:
     void initialize(
             const std::string& filename,
-            const NL::json& map);
+            const std::map<std::string,std::string>& map);
     void close();
 
     uint8_t *getNextChunk(int index);

plugins/hdf/io/HdfReader.cpp

@@ -130,40 +130,38 @@ bool HdfReader::processOne(PointRef& point)
 
 void HdfReader::addArgs(ProgramArgs& args)
 {
-    args.add("map", "Map of HDF path to PDAL dimension", m_pathDimMap);
+    args.add("dimensions", "Map of HDF path to PDAL dimension", m_pathDimJson);
 }
 
 void HdfReader::initialize()
 {
-    for(const auto& [key, value] : m_pathDimMap.items()) {
-        log()->get(LogLevel::Info) << "Key: " << key << ", Val: " << value <<std::endl;
-    }
-    validateMap();
-
-    // ICESat-2 datasets are EPSG:7912
-    setSpatialReference(SpatialReference("EPSG:7912"));
+    parseDimensions();
 }
 
-void HdfReader::validateMap()
+void HdfReader::parseDimensions()
 {
     log()->get(LogLevel::Info) << "**JSON map**" << std::endl;
-    log()->get(LogLevel::Info) << m_pathDimMap << std::endl;
+    log()->get(LogLevel::Info) << m_pathDimJson << std::endl;
 
-    if(m_pathDimMap.is_null()) {
+    if(m_pathDimJson.is_null()) {
         throw pdal_error("Required option 'map' was not set");
-    } else if(!m_pathDimMap.is_object()) {
-        throw pdal_error("Option 'map' must be a JSON object, not a " +
-            std::string(m_pathDimMap.type_name()));
+    } else if(!m_pathDimJson.is_object()) {
+        throw pdal_error("Option 'dimensions' must be a JSON object, not a " +
+            std::string(m_pathDimJson.type_name()));
     }
 
-    for(auto& [dimName, datasetName] : m_pathDimMap.items()) {
+    for(auto& entry : m_pathDimJson.items()) {
+        std::string dimName = entry.key();
+        auto datasetName = entry.value();
         log()->get(LogLevel::Info) << "Key: " << dimName << ", Value: "
             << datasetName << ", Type: " << datasetName.type_name() << std::endl;
 
         if(!datasetName.is_string()) {
-            throw pdal_error("Every value in 'map' must be a string. Key '"
+            throw pdal_error("Every value in 'dimensions' must be a string. Key '"
                 + dimName + "' has value with type '" +
                 std::string(datasetName.type_name()) + "'");
+        } else {
+            m_pathDimMap[dimName] = datasetName;
         }
     }
 }
@@ -174,9 +172,4 @@ void HdfReader::done(PointTableRef table)
 }
 
 
-bool HdfReader::eof()
-{
-    return m_index >= m_hdf5Handler->getNumPoints();
-}
-
 } // namespace pdal

plugins/hdf/io/HdfReader.hpp

@@ -63,16 +63,16 @@ class PDAL_DLL HdfReader : public pdal::Reader, public pdal::Streamable
     std::unique_ptr<Hdf5Handler> m_hdf5Handler;
     point_count_t m_index;
 
-    virtual void addDimensions(PointLayoutPtr layout);
-    virtual void addArgs(ProgramArgs& args);
-    virtual void initialize();
-    virtual void ready(PointTableRef table);
-    virtual point_count_t read(PointViewPtr view, point_count_t count);
-    virtual bool processOne(PointRef& point);
-    virtual void done(PointTableRef table);
-    virtual bool eof();
+    virtual void addDimensions(PointLayoutPtr layout) override;
+    virtual void addArgs(ProgramArgs& args) override;
+    virtual void initialize() override;
+    virtual void ready(PointTableRef table) override;
+    virtual point_count_t read(PointViewPtr view, point_count_t count) override;
+    virtual bool processOne(PointRef& point) override;
+    virtual void done(PointTableRef table) override;
 
-    NL::json m_pathDimMap;
+    NL::json m_pathDimJson;
+    std::map<std::string,std::string> m_pathDimMap;
     Dimension::IdList m_idlist;
     struct BufferInfo {
         BufferInfo(const hdf5::DimInfo& info);
@@ -82,7 +82,7 @@ class PDAL_DLL HdfReader : public pdal::Reader, public pdal::Streamable
     std::vector<BufferInfo> m_info;
     // std::vector<std::unique_ptr<hdf5::DimInfo>> m_infos;
     // std::vector<uint8_t *> m_bufs;
-    void validateMap();
+    void parseDimensions();
 
     HdfReader& operator=(const HdfReader&);   // Not implemented.
     HdfReader(const HdfReader&);              // Not implemented.