add simple readers.hdf test based on autzen

plugins/hdf/CMakeLists.txt

@@ -21,8 +21,10 @@ else()
     )
 
     if (WITH_TESTS)
-        PDAL_ADD_TEST(hdftest
+        PDAL_ADD_TEST(pdal_io_hdf_reader_test
             FILES test/HdfReadertest.cpp
-            LINK_WITH ${libname})
+            LINK_WITH ${libname}
+            INCLUDES
+                ${NLOHMANN_INCLUDE_DIR})
     endif()
 endif()

plugins/hdf/io/HdfReader.cpp

@@ -1,5 +1,5 @@
 /******************************************************************************
-* Copyright (c) 2014, Connor Manning, connor@hobu.co
+* Copyright (c) 2020, Ryan Pals, ryan@hobu.co
 *
 * All rights reserved.
 *
@@ -45,8 +45,8 @@ namespace pdal
 static PluginInfo const s_info
 {
     "readers.hdf",
-    "HDF Reader (WIP)",
-    "http://pdal.io/"
+    "HDF Reader",
+    "http://pdal.io/stages/readers.hdf.html"
 };
 
 CREATE_SHARED_STAGE(HdfReader, s_info)
@@ -80,20 +80,7 @@ point_count_t HdfReader::read(PointViewPtr view, point_count_t count)
 
     PointId nextId = startId;
     uint8_t *buf = nullptr;
-    // for(uint64_t pi = 0; pi < m_hdf5Handler.getNumPoints(); pi++) {
-    //     int index = 0;
-    //     for(auto info : m_infos) {
-    //         // auto info = m_infos.at(0);
-    //         int bufIndex = pi % m_hdf5Handler.getChunkSize();
-    //         if(bufIndex == 0) {
-    //             buf = m_hdf5Handler.getNextChunk(index);
-    //         }
-    //         uint8_t *p = buf + bufIndex*point_size;
-    //         view->setField(info.id, info.pdal_type, nextId, (void*) p);
-    //         index++;
-    //     }
-    //     nextId++;
-    // }
+
     int index = 0;
     log()->get(LogLevel::Info) << "num infos: " << m_infos.size() << std::endl;
     log()->get(LogLevel::Info) << "num points: " << m_hdf5Handler.getNumPoints() << std::endl;
@@ -130,10 +117,8 @@ void HdfReader::initialize()
         log()->get(LogLevel::Info) << "Key: " << key << ", Val: " << value <<std::endl;
     }
 
-    // Data are WGS84 (4326) with ITRF2000 datum (6656)
-    // See http://nsidc.org/data/docs/daac/icebridge/ilvis2/index.html for
-    // background
-    setSpatialReference(SpatialReference("EPSG:4326"));
+    // ICESat-2 datasets are EPSG:7912
+    setSpatialReference(SpatialReference("EPSG:7912"));
 }
 
 void HdfReader::done(PointTableRef table)

plugins/hdf/io/HdfReader.hpp

@@ -1,5 +1,5 @@
 /******************************************************************************
-* Copyright (c) 2014, Connor Manning, connor@hobu.co
+* Copyright (c) 2020, Ryan Pals, ryan@hobu.co
 *
 * All rights reserved.
 *

plugins/hdf/test/HdfReadertest.cpp

@@ -39,50 +39,11 @@
 #include <pdal/PipelineManager.hpp>
 #include <pdal/StageFactory.hpp>
 #include <pdal/util/FileUtils.hpp>
-
+#include <nlohmann/json.hpp>
 #include "Support.hpp"
 
 using namespace pdal;
 
-template <typename T>
-void checkDimension(const PointView& data, std::size_t index,
-    Dimension::Id dim, T expected)
-{
-    T actual = data.getFieldAs<T>(dim, index);
-    EXPECT_FLOAT_EQ((float)expected, (float)actual);
-}
-
-void checkPoint(
-        const PointView& data,
-        std::size_t index,
-        float time,
-        float latitude,
-        float longitude,
-        float elevation,
-        int xmtSig,
-        int rcvSig,
-        float azimuth,
-        float pitch,
-        float roll,
-        float gpsPdop,
-        float pulseWidth,
-        float relTime)
-{
-    using namespace Dimension;
-    checkDimension(data, index, Id::OffsetTime, time);
-    checkDimension(data, index, Id::Y, latitude);
-    checkDimension(data, index, Id::X, longitude);
-    checkDimension(data, index, Id::Z, elevation);
-    checkDimension(data, index, Id::StartPulse, xmtSig);
-    checkDimension(data, index, Id::ReflectedPulse, rcvSig);
-    checkDimension(data, index, Id::Azimuth, azimuth);
-    checkDimension(data, index, Id::Pitch, pitch);
-    checkDimension(data, index, Id::Roll, roll);
-    checkDimension(data, index, Id::Pdop, gpsPdop);
-    checkDimension(data, index, Id::PulseWidth, pulseWidth);
-    checkDimension(data, index, Id::GpsTime, relTime);
-}
-
 std::string getFilePath()
 {
     return Support::datapath("hdf/autzen.h5");
@@ -95,59 +56,19 @@ TEST(HdfReaderTest, testRead)
     EXPECT_TRUE(reader);
 
     Option filename("filename", getFilePath());
-    std::cout << getFilePath() << std::endl;
-    Option dataset("dataset", "/autzen");
+
+    NL::json j = {{ "X" ,"autzen/X"}, {"Y" , "autzen/Y"},  {"Z" , "autzen/Z" }};
+    Option dataset("map", j.dump());
+
     Options options(filename);
     options.add(dataset);
     reader->setOptions(options);
 
     PointTable table;
     reader->prepare(table);
     PointViewSet viewSet = reader->execute(table);
-    // EXPECT_EQ(viewSet.size(), 1u);
+    EXPECT_EQ(viewSet.size(), 1u);
     PointViewPtr view = *viewSet.begin();
-//     EXPECT_EQ(view->size(), 2u);
-
-//     checkPoint(
-//             *view,
-//             0,
-//             1414375e2f,      // time
-//             82.60531f,       // latitude
-//             -58.59381f,      // longitude
-//             18.678f,         // elevation
-//             2408,            // xmtSig
-//             181,             // rcvSig
-//             49.91f,          // azimuth
-//             -4.376f,         // pitch
-//             0.608f,          // roll
-//             2.9f,            // gpsPdop
-//             20.0f,           // pulseWidth
-//             0.0f);           // relTime
-
-//     checkPoint(
-//             *view,
-//             1,
-//             1414375e2f,      // time
-//             82.60528f,       // latitude
-//             -58.59512f,      // longitude
-//             18.688f,         // elevation
-//             2642,            // xmtSig
-//             173,             // rcvSig
-//             52.006f,         // azimuth
-//             -4.376f,         // pitch
-//             0.609f,          // roll
-//             2.9f,            // gpsPdop
-//             17.0f,           // pulseWidth
-//             0.0f);           // relTime
-}
-
-// TEST(HdfReaderTest, testPipeline)
-// {
-//     PipelineManager manager;
-
-//     manager.readPipeline(Support::configuredpath("hdf/pipeline.json"));
-
-//     point_count_t numPoints = manager.execute();
-//     EXPECT_EQ(numPoints, 2u);
-//     FileUtils::deleteFile(Support::datapath("hdf/outfile.txt"));
-// }
+    EXPECT_EQ(view->size(), 1065u);
+    Support::check_p0_p1_p2(*view); 
+}

scripts/conda/osx.sh

@@ -20,6 +20,7 @@ CFLAGS= CXXFLAGS= CC=/usr/bin/cc CXX=/usr/bin/c++ cmake   -G "$CONFIG"  \
         -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} \
         -DBUILD_PLUGIN_PGPOINTCLOUD=ON \
         -DBUILD_PLUGIN_NITF=ON \
+        -DBUILD_PLUGIN_HDF=ON \
         -DBUILD_PLUGIN_ICEBRIDGE=ON \
         -DBUILD_PLUGIN_TILEDB=ON \
         -DBUILD_PLUGIN_RDBLIB=ON \