Merge branch 'master' into ept-zstandard-updates

doc/development/writing-filter.rst

@@ -65,7 +65,13 @@ elements - the filter name, description, and a link to documentation.
 
 PDAL requires that filter names always begin with ``filters.``, and end with a
 string that uniquely identifies the filter. The description will be displayed
-to users of the PDAL CLI (``pdal --drivers``).
+to users of the PDAL CLI (``pdal --drivers``).  When making a shared plugin,
+the name of the shared library must correspond with the name of the filter
+provided here.  The name of the generated shared object must be
+
+::
+
+    libpdal_plugin_filter_<filter name>.<shared library extension>
 
 Next, we pass the following to the ``CREATE_SHARED_STAGE`` macro, passing in
 the name of the stage and the ``PluginInfo`` struct.

doc/development/writing-reader.rst

@@ -60,6 +60,14 @@ to the main PDAL installation.  The macro is supplied with the class name
 of the plugin and a PluginInfo object.  The PluginInfo objection includes
 the name of the plugin, a description, and a link to documentation.
 
+When making a shared plugin,
+the name of the shared library must correspond with the name of the reader
+provided here.  The name of the generated shared object must be
+
+::
+
+    libpdal_plugin_reader_<reader name>.<shared library extension>
+
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
    :lines: 8-15

doc/development/writing-writer.rst

@@ -79,6 +79,13 @@ to create a SHARED stage, which means it will be external to the main PDAL
 installation.  When using the macro, we specify the name of the Stage and
 the PluginInfo struct we defined earlier.
 
+When making a shared plugin, the name of the shared library must
+correspond with the name of the writer
+provided here.  The name of the generated shared object must be
+
+::
+    libpdal_plugin_writer_<writer name>.<shared library extension>
+
 .. literalinclude:: ../../examples/writing-writer/MyWriter.cpp
    :language: cpp
    :lines: 20-31

doc/project/docker.rst

@@ -8,7 +8,7 @@ Building Docker Containers for PDAL
 PDAL's :ref:`repository <source>` is linked to `DockerHub`_ for automatic
 building of `Docker`_ containers. PDAL keeps three Docker containers current.
 
-* ``pdal/dependencies:latest`` -- PDAL's dependencies
+* ``pdal/ubuntu-dependencies:latest`` -- PDAL's dependencies
 * ``pdal/pdal:latest`` -- PDAL master
 * ``pdal/pdal:1.5`` -- PDAL maintenance branch
 
@@ -22,7 +22,7 @@ building of `Docker`_ containers. PDAL keeps three Docker containers current.
 .. note::
 
     Containers are built upon the `Dependencies`_ container, but the
-    `Dependencies`_ container is not pinned to specific Xenial or PDAL release
+    `Dependencies`_ container is not pinned to specific Bionic or PDAL release
     times. It corresponds to where ever the ``dependencies`` tag of the PDAL
     source tree at https://github.com/PDAL/PDAL resides
 
@@ -34,7 +34,7 @@ Dependencies
 The PDAL dependencies Docker container is used by both the latest and release
 branch Docker containers. The dependencies container is also used during
 :ref:`integration` testing by Travis. It is built using the Dockerfile at
-https://github.com/PDAL/PDAL/blob/master/scripts/docker/dependencies/Dockerfile
+https://github.com/PDAL/PDAL/blob/master/scripts/docker/ubuntu/dependencies/Dockerfile
 
 The ``pdal/dependencies:latest`` image is regenerated by force-pushing a tag of
 the SHA you wish to use to have `DockerHub`_ build.
@@ -46,10 +46,10 @@ the SHA you wish to use to have `DockerHub`_ build.
 
 .. note::
 
-    The dependencies container is currently built upon `Ubuntu Xenial`_. When
+    The dependencies container is currently built upon `Ubuntu Bionic`_. When
     the next Ubuntu LTS is released, the PDAL project will likely move to it.
 
-.. _`Ubuntu Xenial`: http://releases.ubuntu.com/16.04/
+.. _`Ubuntu Bionic`: http://releases.ubuntu.com/18.04/
 
 Maintenance
 ================================================================================

doc/stages/filters.stats.rst

@@ -11,6 +11,14 @@ The output of the stats filter is metadata that can be stored by writers or
 used through the PDAL API.  Output from the stats filter can also be
 quickly obtained in JSON format by using the command "pdal info --stats".
 
+.. note::
+
+The filter can compute both sample and population statistics.  For kurtosis,
+the filter can also compute standard and excess kurtosis.  However, only
+a single value is reported for each statistic type in metadata, and that is
+the sample statistic, rather than the population statistic.  For kurtosis
+the sample excess kurtosis is reported.  This seems to match the behavior
+of many other software packages.
 
 Example
 ................................................................................

filters/ColorinterpFilter.cpp

@@ -215,7 +215,7 @@ void ColorinterpFilter::filter(PointView& view)
         }
         else
         {
-             double threshold = (m_stdDevThreshold * summary.stddev());
+             double threshold = (m_stdDevThreshold * summary.sampleStddev());
              m_min = median - threshold;
              m_max = median + threshold;
 

filters/HAGFilter.cpp

@@ -36,7 +36,7 @@
 
 #include <pdal/KDIndex.hpp>
 
-#include "private/delaunator-decl.hpp"
+#include "private/delaunator.hpp"
 
 #include <string>
 #include <vector>

filters/OverlayFilter.cpp

@@ -36,7 +36,6 @@
 
 #include <vector>
 
-#include <pdal/QuadIndex.hpp>
 #include <pdal/GDALUtils.hpp>
 #include <pdal/util/ProgramArgs.hpp>
 
@@ -53,26 +52,6 @@ static StaticPluginInfo const s_info
 
 CREATE_STATIC_STAGE(OverlayFilter, s_info)
 
-struct OGRDataSourceDeleter
-{
-    template <typename T>
-    void operator()(T* ptr)
-    {
-        if (ptr)
-            ::OGR_DS_Destroy(ptr);
-    }
-};
-
-struct OGRFeatureDeleter
-{
-    template <typename T>
-    void operator()(T* ptr)
-    {
-        if (ptr)
-            ::OGR_F_Destroy(ptr);
-    }
-};
-
 
 void OverlayFilter::addArgs(ProgramArgs& args)
 {
@@ -105,7 +84,7 @@ void OverlayFilter::prepared(PointTableRef table)
 void OverlayFilter::ready(PointTableRef table)
 {
     m_ds = OGRDSPtr(OGROpen(m_datasource.c_str(), 0, 0),
-            OGRDataSourceDeleter());
+            [](void *p){ if (p) ::OGR_DS_Destroy(p); });
     if (!m_ds)
         throwError("Unable to open data source '" + m_datasource + "'");
 
@@ -119,8 +98,13 @@ void OverlayFilter::ready(PointTableRef table)
     if (!m_lyr)
         throwError("Unable to select layer '" + m_layer + "'");
 
+    auto featureDeleter = [](void *p)
+    {
+        if (p)
+            ::OGR_F_Destroy(p);
+    };
     OGRFeaturePtr feature = OGRFeaturePtr(OGR_L_GetNextFeature(m_lyr),
-        OGRFeatureDeleter());
+        featureDeleter);
 
     int field_index(1); // default to first column if nothing was set
     if (m_column.size())
@@ -133,23 +117,12 @@ void OverlayFilter::ready(PointTableRef table)
     do
     {
         OGRGeometryH geom = OGR_F_GetGeometryRef(feature.get());
-        OGRwkbGeometryType t = OGR_G_GetGeometryType(geom);
         int32_t fieldVal = OGR_F_GetFieldAsInteger(feature.get(), field_index);
 
-        if (!(t == wkbPolygon ||
-            t == wkbMultiPolygon ||
-            t == wkbPolygon25D ||
-            t == wkbMultiPolygon25D))
-        {
-            throwError("Geometry is not Polygon or MultiPolygon!");
-        }
-
-        // Don't think Polygon meets criteria for implicit move ctor.
         m_polygons.push_back(
             { Polygon(geom, table.anySpatialReference()), fieldVal} );
 
-        feature = OGRFeaturePtr(OGR_L_GetNextFeature(m_lyr),
-            OGRFeatureDeleter());
+        feature = OGRFeaturePtr(OGR_L_GetNextFeature(m_lyr), featureDeleter);
     }
     while (feature);
 }
@@ -176,27 +149,23 @@ void OverlayFilter::spatialReferenceChanged(const SpatialReference& srs)
 bool OverlayFilter::processOne(PointRef& point)
 {
     for (const auto& poly : m_polygons)
-        if (poly.geom.covers(point))
+    {
+        double x = point.getFieldAs<double>(Dimension::Id::X);
+        double y = point.getFieldAs<double>(Dimension::Id::Y);
+        if (poly.geom.contains(x, y))
             point.setField(m_dim, poly.val);
+    }
     return true;
 }
 
 
 void OverlayFilter::filter(PointView& view)
 {
-    QuadIndex idx(view);
-
-    for (const auto& poly : m_polygons)
+    PointRef point(view, 0);
+    for (PointId id = 0; id < view.size(); ++id)
     {
-        PointIdList ids = idx.getPoints(poly.geom.bounds());
-
-        PointRef point(view, 0);
-        for (PointId id : ids)
-        {
-            point.setPointId(id);
-            if (poly.geom.covers(point))
-                point.setField(m_dim, poly.val);
-        }
+        point.setPointId(id);
+        processOne(point);
     }
 }
 

filters/SkewnessBalancingFilter.cpp

@@ -67,7 +67,7 @@ std::set<PointId> SkewnessBalancingFilter::processGround(PointViewPtr view)
     point_count_t n1(0);
     double delta, delta_n, term1, M1, M2, M3;
     M1 = M2 = M3 = 0.0;
-    std::vector<double> skewness;
+    std::vector<double> skewness(view->size());
     for (PointId i = 0; i < view->size(); ++i)
     {
         double z = view->getFieldAs<double>(Dimension::Id::Z, i);
@@ -83,14 +83,15 @@ std::set<PointId> SkewnessBalancingFilter::processGround(PointViewPtr view)
     }
 
     PointId j(0);
-    for (PointId i = view->size() - 1; i >= 0; --i)
+    PointId i(view->size());
+    do
     {
         if (skewness[i] <= 0)
         {
             j = i;
             break;
         }
-    }
+    } while (--i != 0);
 
     std::set<PointId> groundIdx;
     for (PointId i = 0; i <= j; ++i)
@@ -105,13 +106,16 @@ std::set<PointId> SkewnessBalancingFilter::processGround(PointViewPtr view)
 
 PointViewSet SkewnessBalancingFilter::run(PointViewPtr input)
 {
+    PointViewSet viewSet;
+    if (!input->size())
+        return viewSet;
+
     bool logOutput = log()->getLevel() > LogLevel::Debug1;
     if (logOutput)
         log()->floatPrecision(8);
 
     auto idx = processGround(input);
 
-    PointViewSet viewSet;
     if (!idx.empty())
     {
         // set the classification label of ground returns as 2

filters/StatsFilter.cpp

@@ -68,24 +68,24 @@ void Summary::extractMetadata(MetadataNode &m)
     m.add("maximum", maximum(), "maximum");
     m.add("average", average(), "average");
 
-    double std = stddev();
+    double std = sampleStddev();
     if (!std::isinf(std) && !std::isnan(std))
         m.add("stddev", std, "standard deviation");
 
-    double v = variance();
+    double v = sampleVariance();
     if (!std::isinf(v) && !std::isnan(v))
         m.add("variance", v, "variance");
     m.add("name", m_name, "name");
 
     if (m_advanced)
     {
-        double k = kurtosis();
+        double k = sampleExcessKurtosis();
         if (!std::isinf(k) && !std::isnan(k))
             m.add("kurtosis", k, "kurtosis");
 
-        double sk = skewness();
+        double sk = sampleSkewness();
         if (!std::isinf(sk) && !std::isnan(sk))
-            m.add("skewness", skewness(), "skewness");
+            m.add("skewness", sampleSkewness(), "skewness");
     }
 
     if (m_enumerate == Enumerate)