Merge remote-tracking branch 'origin/master' into issue-1922

HOWTORELEASE.txt

@@ -143,3 +143,28 @@ Release Process
     ::
 
         http://upload.osgeo.org/cgi-bin/osgeo4w-promote.sh
+
+12) Update Alpine package
+
+  - The PDAL Alpine package lives at
+    https://github.com/alpinelinux/aports/blob/master/testing/pdal/APKBUILD.
+    Pull requests can be made against the alpinelinux/aports repository. If the
+    build configuration alone is changing, with no version increase, simply
+    increment the build number `pkgrel`. If the `pkgver` is changing, then
+    reset `pkgrel` to 0.
+  - Pull requests should have a commit message of the following form
+    `testing/pdal: <description>`.
+
+13) Update Conda package
+
+  - For PDAL releases that bump version number, but do not change dependencies
+    or build configurations, the `regro-cf-autotick-bot` should automatically
+    create a pull request at https://github.com/conda-forge/pdal-feedstock.
+    Once the builds succeed, the PR can be merged and the updated package will
+    soon be available in the `conda-forge` channel. If the PR does not build
+    successfully, updates to the PR can be pushed to the bot's branch. Version
+    bumps should reset the build number to zero.
+  - Updates that alter the build configuration but do not bump the version
+    number should be submitted as PRs from a fork of the
+    https://github.com/conda-forge/pdal-feedstock repository. In these cases,
+    the build number should be incremented.

apps/CMakeLists.txt

@@ -76,14 +76,14 @@ if(UNIX OR APPLE)
         DESTINATION
             "${PDAL_OUTPUT_BIN_DIR}/"
         FILE_PERMISSIONS
-            OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
+	    OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
             WORLD_READ WORLD_EXECUTE)
 
     install(PROGRAMS "${PDAL_OUTPUT_BIN_DIR}/pdal-config"
         DESTINATION
             "${CMAKE_INSTALL_PREFIX}/bin"
         PERMISSIONS
-            OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
+            OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
             WORLD_READ WORLD_EXECUTE)
 
 elseif(WIN32)
@@ -95,14 +95,14 @@ elseif(WIN32)
          DESTINATION
             "${PDAL_OUTPUT_BIN_DIR}/"
          FILE_PERMISSIONS
-            OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
+            OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
             WORLD_READ WORLD_EXECUTE)
 
     install(PROGRAMS "${PDAL_OUTPUT_BIN_DIR}/pdal-config.bat"
         DESTINATION
             "${CMAKE_INSTALL_PREFIX}/bin"
         PERMISSIONS
-            OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
+            OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE
             WORLD_READ WORLD_EXECUTE)
 
 endif()

apps/pdal.cpp

@@ -73,7 +73,6 @@ class App
     void outputOptions();
     void outputOptions(const std::string& stageName,std::ostream& strm);
     void addArgs(ProgramArgs& args);
-    std::string findKernel();
 
     std::ostream& m_out;
 
@@ -114,7 +113,7 @@ void App::outputHelp(const ProgramArgs& args)
     // Load all kernels so that we can report the names.
     StageFactory f;
     PluginManager<Kernel>::loadAll();
-    outputCommands("  -");
+    outputCommands("  - ");
     m_out << std::endl;
     m_out << "See http://pdal.io/apps/ for more detail" << std::endl;
 }
@@ -160,7 +159,6 @@ void App::outputDrivers()
     }
     else
     {
-
         Json::Value array(Json::arrayValue);
         for (auto name : stages)
         {
@@ -172,9 +170,7 @@ void App::outputDrivers()
             node["link"] = link;
             array.append(node);
         }
-
         m_out << array;
-
     }
 }
 
@@ -183,8 +179,13 @@ void App::outputCommands(const std::string& leader)
 {
     StageFactory f;
     PluginManager<Kernel>::loadAll();
+    std::string kernelbase("kernels.");
     for (auto name : PluginManager<Kernel>::names())
+    {
+        if (Utils::startsWith(name, kernelbase))
+            name = name.substr(kernelbase.size());
         m_out << leader << name << std::endl;
+    }
 }
 
 
@@ -200,7 +201,6 @@ void App::outputOptions(std::string const& stageName, std::ostream& strm)
         return;
     }
 
-
     ProgramArgs args;
     s->addAllArgs(args);
 
@@ -226,7 +226,6 @@ void App::outputOptions(std::string const& stageName, std::ostream& strm)
         object[stageName] = array;
 
         strm  << object;
-
     }
 }
 
@@ -245,7 +244,8 @@ void App::outputOptions()
             outputOptions(n, m_out);
             m_out << std::endl;
         }
-    } else
+    }
+    else
     {
         std::ostringstream strm;
         Json::Value options (Json::arrayValue);
@@ -260,7 +260,6 @@ void App::outputOptions()
 
             strm.str("");
         }
-
         m_out << options;
     }
 }
@@ -303,35 +302,6 @@ int main(int argc, char* argv[])
 }
 
 
-std::string App::findKernel()
-{
-    StringList loadedKernels;
-
-    auto kernelSurname = [](const std::string& name)
-    {
-        StringList names = Utils::split2(name, '.');
-        return names.size() == 2 ? names[1] : std::string();
-    };
-
-    StageFactory f(true);
-    // Discover available kernels without plugins, and test to see if
-    // the positional option 'command' is a valid kernel
-    loadedKernels = PluginManager<Kernel>::names();
-    for (auto& name : loadedKernels)
-        if (m_command == kernelSurname(name))
-            return name;
-
-    // Force loading of plugins.
-    StageFactory f2(false);
-    loadedKernels = PluginManager<Kernel>::names();
-    for (auto& name : loadedKernels)
-        if (m_command == kernelSurname(name))
-            return name;
-
-    return std::string();
-}
-
-
 int App::execute(StringList& cmdArgs, LogPtr& log)
 {
     ProgramArgs args;
@@ -374,12 +344,13 @@ int App::execute(StringList& cmdArgs, LogPtr& log)
     if (!m_command.empty())
     {
         int ret = 0;
-        std::string name(findKernel());
-        if (name.size())
+        std::string name("kernels." + m_command);
+
+        Kernel *kernel = PluginManager<Kernel>::createObject(name);
+        if (kernel)
         {
             if (m_help)
                 cmdArgs.push_back("--help");
-            Kernel *kernel = PluginManager<Kernel>::createObject(name);
             // This shouldn't throw.  If it does, it's something awful, so
             // not cleaning up seems inconsequential.
             log->setLeader("pdal " + m_command);

cmake/cpack.cmake

@@ -32,12 +32,13 @@ list(APPEND CPACK_SOURCE_IGNORE_FILES "Makefile")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "CMakeFiles")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "CTestTestfile.cmake")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/test/data/local/")
+list(APPEND CPACK_SOURCE_IGNORE_FILES "/test/unit/TestConfig.hpp")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/doc/doxygen/")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/doc/build/")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/doc/presentations/")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/doc/_static/logo/dongle/")
 list(APPEND CPACK_SOURCE_IGNORE_FILES "/cmake/examples/")
-list(APPEND CPACK_SOURCE_IGNORE_FILES "/include/pdal/pdal_defines.h")
+list(APPEND CPACK_SOURCE_IGNORE_FILES "pdal_features.hpp")
 list(APPEND CPACK_SOURCE_IGNORE_FILES ".gz2")
 list(APPEND CPACK_SOURCE_IGNORE_FILES ".bz2")
 

cmake/modules/FindGEOS.cmake

@@ -162,6 +162,19 @@ IF (GEOS_INCLUDE_DIR AND GEOS_LIBRARY)
    SET(GEOS_FOUND TRUE)
 ENDIF (GEOS_INCLUDE_DIR AND GEOS_LIBRARY)
 
+if (NOT GEOS_INCLUDE_DIR OR NOT GEOS_LIBRARY)
+  include(SelectLibraryConfigurations)
+  select_library_configurations(GEOS)
+  include(FindPackageHandleStandardArgs)
+  find_package_handle_standard_args(GEOS REQUIRED_VARS GEOS_LIBRARY GEOS_INCLUDE_DIR)
+  if(GEOS_FOUND)
+    set(GEOS_INCLUDE_DIRS ${GEOS_INCLUDE_DIR})
+    if(NOT GEOS_LIBRARIES)
+      set(GEOS_LIBRARIES ${GEOS_LIBRARY})
+    endif()
+  endif()
+endif()
+
 IF (GEOS_FOUND)
 
    IF (NOT GEOS_FIND_QUIETLY)

dimbuilder/CMakeLists.txt

@@ -31,11 +31,10 @@ target_include_directories(dimbuilder PRIVATE
 PDAL_TARGET_COMPILE_SETTINGS(dimbuilder)
 target_link_libraries(dimbuilder
     PRIVATE
-        ${EXECINFO_LIBRARY})
+        ${EXECINFO_LIBRARY}
+        ${CMAKE_DL_LIBS}
+)
 if (PDAL_HAVE_JSONCPP)
     target_link_libraries(dimbuilder ${JSON_CPP_LINK_TYPE}
         ${PDAL_JSONCPP_LIB_NAME})
 endif()
-if (UNIX AND NOT APPLE)
-    target_link_libraries(dimbuilder PRIVATE  ${CMAKE_DL_LIBS})
-endif()

doc/faq.rst

@@ -11,7 +11,7 @@ FAQ
   The proper spelling of the project name is PDAL, in uppercase. It is
   pronounced to rhyme with "GDAL".
 
-  .. it is properly pronounced like the dog though :)
+  .. it is properly pronounced like the dog though :) -- hobu
 |
 * Why do I get the error "Couldn't create ... stage of type ..."?
 
@@ -44,6 +44,8 @@ FAQ
   sizes before PDAL can process the data. Furthermore, some operations
   (notably :ref:`DEM creation<writers.gdal>`) can use large amounts of
   additional memory during processing before the output can be written.
+  Depending on the operation, PDAL will attempt operate in "stream mode" to
+  limit memory consumption when possible.
 |
 * What is PDAL's relationship to PCL?
 
@@ -72,7 +74,7 @@ FAQ
 |
 * Are there any command line tools in PDAL similar to LAStools?
 
-  Yes. The ``pdal`` command provides a wide range of features which go
+  Yes. The :ref:`pdal <apps>` command provides a wide range of features which go
   far beyond basic LIDAR data processing. Additionally, PDAL is licensed
   under an open source license (this applies to the whole library and
   all command line tools).
@@ -88,3 +90,19 @@ FAQ
   focus on usability and readability. You will find that the ``pdal``
   command has several well-organized subcommands such as ``info``
   or ``translate`` (see :ref:`apps`).
+
+* I get GeoTIFF errors. What can I do about them?
+
+  ::
+
+    (readers.las Error) Geotiff directory contains key 0 with short entry and more than one value.
+
+  If :ref:`readers.las` is outputting error messages about GeoTIFF, this means
+  the keys that were written into your file were incorrect or at least not
+  readable by `libgeotiff`_. Rewrite the file using PDAL to fix the issue:
+
+  ::
+
+    pdal translate badfile.las goodfile.las --writers.las.forward=all
+
+.. _`libgeotiff`: https://trac.osgeo.org/geotif

doc/stages/filters.delaunay.rst

@@ -15,7 +15,7 @@ dimensions of the point cloud.
 
 .. _Geogram: http://alice.loria.fr/software/geogram/doc/html/index.html
 
-.. embed::
+.. plugin::
 
 Example
 -------

filters/FerryFilter.cpp

@@ -80,7 +80,7 @@ void FerryFilter::initialize()
             throwError("Can't ferry two source dimensions to the same "
                 "destination dimension.");
         toNames.push_back(s[1]);
-        m_dims.emplace_back( s[0], s[1] );
+        m_dims.emplace_back(s[0], s[1]);
     }
 }
 
@@ -90,7 +90,11 @@ void FerryFilter::addDimensions(PointLayoutPtr layout)
     for (auto& info : m_dims)
     {
         const Dimension::Id fromId = layout->findDim(info.m_fromName);
-        const Dimension::Type fromType = layout->dimType(fromId);
+        // Dimensions being created with the "=>Dim" syntax won't have
+        // be in the layout, so we have to assign a default type.
+        Dimension::Type fromType = layout->dimType(fromId);
+        if (fromType == Dimension::Type::None)
+            fromType = Dimension::Type::Double;
 
         info.m_toId = layout->registerOrAssignDim(info.m_toName, fromType);
     }

filters/ReprojectionFilter.cpp

@@ -62,7 +62,6 @@ ReprojectionFilter::ReprojectionFilter()
     , m_in_ref_ptr(NULL)
     , m_out_ref_ptr(NULL)
     , m_transform_ptr(NULL)
-    , m_errorHandler(new gdal::ErrorHandler())
 {}
 
 

filters/ReprojectionFilter.hpp

@@ -42,11 +42,6 @@
 namespace pdal
 {
 
-namespace gdal
-{
-    class ErrorHandler;
-}
-
 class PDAL_DLL ReprojectionFilter : public Filter, public Streamable
 {
 public:
@@ -74,7 +69,6 @@ class PDAL_DLL ReprojectionFilter : public Filter, public Streamable
     ReferencePtr m_in_ref_ptr;
     ReferencePtr m_out_ref_ptr;
     TransformPtr m_transform_ptr;
-    gdal::ErrorHandler* m_errorHandler;
 
     ReprojectionFilter& operator=(const ReprojectionFilter&); // not implemented
     ReprojectionFilter(const ReprojectionFilter&); // not implemented

io/BpfCompressor.hpp

@@ -37,7 +37,7 @@
 #include <stdexcept>
 #include <ostream>
 
-#include <pdal/pdal_internal.hpp>
+#include <pdal/pdal_features.hpp>
 #include <pdal/util/Charbuf.hpp>
 #include <pdal/util/OStream.hpp>
 

io/BpfReader.cpp

@@ -36,9 +36,12 @@
 
 #include <climits>
 
-#include <zlib.h>
-
 #include <pdal/Options.hpp>
+#include <pdal/pdal_features.hpp>
+
+#ifdef PDAL_HAVE_ZLIB
+#include <zlib.h>
+#endif
 
 namespace pdal
 {

io/GeotiffSupport.cpp

@@ -45,6 +45,7 @@ PDAL_C_START
 // aren't exported.
 char PDAL_DLL * GTIFGetOGISDefn(GTIF*, GTIFDefn*);
 int PDAL_DLL GTIFSetFromOGISDefn(GTIF*, const char*);
+void VSIFree(void *data);
 
 PDAL_C_END
 
@@ -146,7 +147,10 @@ GeotiffSrs::GeotiffSrs(const std::vector<uint8_t>& directoryRec,
     {
         char *wkt = GTIFGetOGISDefn(ctx.gtiff, &sGTIFDefn);
         if (wkt)
+        {
             m_srs.set(wkt);
+            VSIFree(wkt);
+        }
     }
 }