This is a merge.

CMakeLists.txt

@@ -57,7 +57,7 @@ else()
 endif()
 set(PDAL_UTIL_LIB_NAME pdal_util)
 set(PDAL_BOOST_LIB_NAME pdal_boost)
-#set(PDAL_ARBITER_LIB_NAME pdal_arbiter)
+set(PDAL_KAZHDAN_LIB_NAME pdal_kazhdan)
 
 set(CMAKE_INCLUDE_DIRECTORIES_PROJECT_BEFORE ON)
 
@@ -172,6 +172,7 @@ endif()
 add_subdirectory(dimbuilder)
 add_subdirectory(vendor/pdalboost)
 add_subdirectory(vendor/arbiter)
+add_subdirectory(vendor/kazhdan)
 
 if (NOT PDAL_HAVE_JSONCPP)
     add_subdirectory(vendor/jsoncpp/dist)
@@ -247,6 +248,7 @@ target_link_libraries(${PDAL_BASE_LIB_NAME}
         ${PDAL_REEXPORT}
         ${PDAL_UTIL_LIB_NAME}
         ${PDAL_ARBITER_LIB_NAME}
+        ${PDAL_KAZHDAN_LIB_NAME}
     ${JSON_CPP_LINK_TYPE}
         ${PDAL_JSONCPP_LIB_NAME}
     INTERFACE
@@ -285,6 +287,11 @@ install(DIRECTORY ${PDAL_KERNELS_DIR}
     FILES_MATCHING PATTERN "*.hpp"
     PATTERN "private" EXCLUDE
 )
+install(DIRECTORY ${PDAL_VENDOR_DIR}/nanoflann
+    DESTINATION include/pdal
+    FILES_MATCHING PATTERN "*.hpp"
+    PATTERN "private" EXCLUDE
+)
 install(DIRECTORY ${PDAL_IO_DIR}
     DESTINATION include/pdal
     FILES_MATCHING PATTERN "*.hpp"

cmake/modules/FindLASzip.cmake

@@ -54,6 +54,46 @@ FIND_LIBRARY(LASZIP_LIBRARY
   /usr/local/lib
   ${OSGEO4W_ROOT_DIR}/lib)
 
+# Comment out laszip.hpp version info
+#[[
+SET(LASZIP_VERSION_H "${LASZIP_INCLUDE_DIR}/laszip.hpp")
+IF(LASZIP_INCLUDE_DIR AND EXISTS ${LASZIP_VERSION_H})
+  SET(LASZIP_VERSION 0)
+
+  message("Looking for: ${LASZIP_INCLUDE_DIR}/laszip.hpp")
+
+  FILE(READ ${LASZIP_VERSION_H} LASZIP_VERSION_H_CONTENTS)
+
+  IF (DEFINED LASZIP_VERSION_H_CONTENTS)
+    string(REGEX REPLACE ".*#define[ \t]LASZIP_VERSION_MAJOR[ \t]+([0-9]+).*" "\\1" LASZIP_VERSION_MAJOR "${LASZIP_VERSION_H_CONTENTS}")
+    string(REGEX REPLACE ".*#define[ \t]LASZIP_VERSION_MINOR[ \t]+([0-9]+).*" "\\1" LASZIP_VERSION_MINOR "${LASZIP_VERSION_H_CONTENTS}")
+    string(REGEX REPLACE ".*#define[ \t]LASZIP_VERSION_REVISION[ \t]+([0-9]+).*"   "\\1" LASZIP_VERSION_REVISION   "${LASZIP_VERSION_H_CONTENTS}")
+
+    if(NOT ${LASZIP_VERSION_MAJOR} MATCHES "[0-9]+")
+      message(FATAL_ERROR "LASzip version parsing failed for LASZIP_VERSION_MAJOR!")
+    endif()
+    if(NOT ${LASZIP_VERSION_MINOR} MATCHES "[0-9]+")
+      message(FATAL_ERROR "LASzip version parsing failed for LASZIP_VERSION_MINOR!")
+    endif()
+    if(NOT ${LASZIP_VERSION_REVISION} MATCHES "[0-9]+")
+      message(FATAL_ERROR "LASzip version parsing failed for LASZIP_VERSION_REVISION!")
+    endif()
+
+
+    SET(LASZIP_VERSION "${LASZIP_VERSION_MAJOR}.${LASZIP_VERSION_MINOR}.${LASZIP_VERSION_REVISION}"
+      CACHE INTERNAL "The version string for LASzip library")
+
+    IF (LASZIP_VERSION VERSION_LESS LASzip_FIND_VERSION)
+      MESSAGE(FATAL_ERROR "LASzip version check failed. Version ${LASZIP_VERSION} was found, at least version ${LASzip_FIND_VERSION} is required")
+    ENDIF()
+  ELSE()
+    MESSAGE(FATAL_ERROR "Failed to open ${LASZIP_VERSION_H} file")
+  ENDIF()
+ELSE()
+  return()
+ENDIF()
+]]
+
 # Handle the QUIETLY and REQUIRED arguments and set LASZIP_FOUND to TRUE
 # if all listed variables are TRUE
 INCLUDE(FindPackageHandleStandardArgs)

doc/stages/filters.crop.rst

@@ -8,6 +8,14 @@ box (2D), polygon, or point+distance.  If more than one bounding region is
 specified, the filter will pass all input points through each bounding region,
 creating an output point set for each input crop region.
 
+The provided bounding regions are assumed to have the same spatial reference
+as the points unless the option `a_srs` provides an explicit spatial reference
+for bounding regions.
+If the point input consists of multiple point views with differing
+spatial references, one is chosen at random and assumed to be the
+spatial reference of the input bounding region.  In this case a warning will
+be logged.
+
 Example
 -------
 
@@ -46,3 +54,8 @@ point
 
 distance
   Distance in units of common X, Y, and Z :ref:`dimensions` to crop circle or sphere in combination with ``point``.
+
+a_srs
+  Indicates the spatial reference of the bounding regions.  If not provided,
+  it is assumed that the spatial reference of the bounding region matches
+  that of the points (if possible).

doc/stages/filters.pmf.rst

@@ -52,6 +52,12 @@ Notes
   extra iteration. This parameter can have a strongly negative impact on
   computation performance.
 
+* ``exponential`` is used to control the rate of growth of morphological window
+  sizes toward ``max_window_size``. Linear growth preserves gradually changing
+  topographic features well, but demands considerable compute time. The default
+  behavior is to grow the window sizes exponentially, thus reducing the number
+  of iterations.
+
 * This filter will mark all returns deemed to be ground returns with a
   classification value of 2 (per the LAS specification). To extract only these
   returns, users can add a :ref:`range filter<filters.range>` to the pipeline.
@@ -71,27 +77,27 @@ Notes
 Options
 -------------------------------------------------------------------------------
 
-max_window_size
-  Maximum window size. [Default: **33**]
-
-slope
-  Slope. [Default: **1.0**]
-
-max_distance
-  Maximum distance. [Default: **2.5**]
-
-initial_distance
-  Initial distance. [Default: **0.15**]
-
 cell_size
   Cell Size. [Default: **1**]
 
-approximate
-  Use approximate algorithm? [Default: **false**]
-  
+exponential
+  Use exponential growth for window sizes? [Defualt: **true**]
+
 ignore
   Optional range of values to ignore.
+
+initial_distance
+  Initial distance. [Default: **0.15**]
 
 last
   Consider only last returns (when return information is available)? [Default:
   **true**]
+
+max_distance
+  Maximum distance. [Default: **2.5**]
+
+max_window_size
+  Maximum window size. [Default: **33**]
+
+slope
+  Slope. [Default: **1.0**]

doc/stages/filters.poisson.rst

@@ -4,14 +4,26 @@
 filters.poisson
 ===============================================================================
 
-The Poisson filter passes data through the Point Cloud Library (`PCL`_) Poisson
-surface reconstruction algorithm.
-
-Poisson is an implementation of the method described in [Kazhdan2006]_.
+The poisson filter passes data Mischa Kazhdan's poisson surface reconstruction
+algorithm. [Kazhdan2006]_  It creates a watertight surface from the original
+point set by creating an entirely new point set representing the imputed
+isosurface.  The algorithm requires normal vectors to each point in order
+to run.  If the x, y and z normal dimensions are present in the input point
+set, they will be used by the algorithm.  If they don't exist, the poisson
+filter will invoke the PDAL normal filter to create them before running.
+
+The poisson algorithm will usually create a larger output point set
+than the input point set.  Because the algorithm constructs new points, data
+associated with the original points set will be lost, as the algorithm has
+limited ability to impute associated data.  However, if color dimensions
+(red, green and blue) are present in the input, colors will be reconstruced
+in the output point set.
 
 .. [Kazhdan2006] Kazhdan, Michael, Matthew Bolitho, and Hugues Hoppe. "Poisson surface reconstruction." Proceedings of the fourth Eurographics symposium on Geometry processing. Vol. 7. 2006.
 
-.. _`PCL`: http://www.pointclouds.org
+This integration of the algorithm with PDAL only supports a limited set of
+the options available to the implementation.  If you need support for further
+options, please let us know.
 
 Example
 -------------------------------------------------------------------------------
@@ -23,12 +35,10 @@ Example
         "dense.las",
         {
           "type":"filters.poisson",
-          "depth":"8",
-          "point_weight":"4"
         },
         {
-          "type":"writers.las",
-          "filename":"thinned.las",
+          "type":"writers.ply",
+          "filename":"isosurface.ply",
         }
       ]
     }
@@ -37,8 +47,12 @@ Example
 Options
 -------------------------------------------------------------------------------
 
+density
+  Write an estimate of neighborhood density for each point in the output
+  set.
+
 depth
-  Maximum depth of the tree used for reconstruction. [Default: **8**]
+  Maximum depth of the tree used for reconstruction. The output is sentsitve
+  to this parameter.  Increase if the results appear unsatisfactory.
+  [Default: **8**]
 
-point_weight
-  Importance of interpolation of point samples in the screened Poisson equation. [Default: **4.0**]

doc/tutorial/python-filtering.rst

@@ -33,9 +33,8 @@ be a very quick way to prototype a tool that identified specific points
 we would like to filter.
 
 PDAL has three different ways to manipulate data with Python. The first is
-:ref:`filters.python`, which we will be using in this tutorial. The
-second is :ref:`filters.`, which allows you to keep or remove points
-given a Python filtering operation. The third is the Python extension at
+:ref:`filters.python`, which we will be using in this tutorial.
+The second is the Python extension at
 https://pypi.python.org/pypi/PDAL that allows you to utilize PDAL processing
 operations in your own Python programs.
 
@@ -75,12 +74,11 @@ running.
 Python Filter
 -------------------------------------------------------------------------------
 
-Through the use of the :ref:`filters.python` and :ref:`filters.`
-filters, PDAL allows the use of Python and |NumPy| to process point cloud
-data. This can be very useful in prototyping situations, where PDAL can provide
-convenient data access and the processing logic of software that is still
-taking shape can be constructed with the rapid prototyping tools that Python
-can provide.
+Through the use of the :ref:`filters.python`, PDAL allows the use of Python and
+|NumPy| to process point cloud data. This can be very useful in prototyping
+situations, where PDAL can provide convenient data access and the processing
+logic of software that is still taking shape can be constructed with the rapid
+prototyping tools that Python can provide.
 
 
 .. code-block:: python
@@ -112,7 +110,7 @@ can provide.
         # Print our dict to stdout
         print output
 
-        # filters. must return True to tell
+        # filters.python must return True to tell
         # PDAL it successfully completed
         return True
 
@@ -221,7 +219,7 @@ three standard deviations:
         # Print our dict to stdout
         print output
 
-        # filters. must return True to tell
+        # filters.python must return True to tell
         # PDAL it successfully completed
         return True
 

doc/tutorial/writing-reader.rst

@@ -33,15 +33,7 @@ These methods are required to fulfill the specs for defining a new plugin.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.hpp
    :language: cpp
-   :lines: 20
-   :linenos:
-
-``getDefaultDimensions`` returns a list of :ref:`dimensions` that the
-reader provides.
-
-.. literalinclude:: ../../examples/writing-reader/MyReader.hpp
-   :language: cpp
-   :lines: 23-25
+   :lines: 21-23
    :linenos:
 
 ``m_stream`` is used to process the input, while ``m_index`` is used to track
@@ -111,16 +103,7 @@ dimension MyData.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 31-40
-   :linenos:
-
-This method returns the list of :ref:`dimensions` that the reader can
-provide.
-
-
-.. literalinclude:: ../../examples/writing-reader/MyReader.cpp
-   :language: cpp
-   :lines: 42-46
+   :lines: 31-35
    :linenos:
 
 This method is called when the Reader is ready for use.  It will only be
@@ -129,7 +112,7 @@ processed.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 49-62
+   :lines: 37-50
    :linenos:
 
 This is a helper function, which will convert a string value into the type
@@ -139,7 +122,7 @@ strings to doubles when reading from the input stream.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 65
+   :lines: 53
    :linenos:
 
 This method is the main processing method for the reader.  It takes a
@@ -152,15 +135,15 @@ PointView object.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 74-76
+   :lines: 62-64
    :linenos:
 
 In preparation for reading the file, we prepare to skip some header lines.  In
 our case, the header is only a single line.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 77-82
+   :lines: 65-70
    :linenos:
 
 Here we begin our main loop.  In our example file, the first line is a header,
@@ -171,18 +154,17 @@ sure we are skipping the header lines here before moving on.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 85-94
+   :lines: 73-82
    :linenos:
 
 Here we take the line we read in the for block header, split it, and make sure
 that we have the proper number of fields.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 96-109
+   :lines: 84-97
    :linenos:
 
-
 Here we take the values we read and put them into the PointView object.  The
 X and Y fields are simply converted from the file and put into the respective
 fields.  MyData is done likewise with the custom dimension we defined.  The Z
@@ -195,7 +177,7 @@ each iteration of the loop), and the dimension value.
 
 .. literalinclude:: ../../examples/writing-reader/MyReader.cpp
    :language: cpp
-   :lines: 111-113
+   :lines: 99-101
    :linenos:
 
 Finally, we increment the nextId and make a call into the progress callback

doc/tutorial/writing-writer.rst

@@ -58,7 +58,7 @@ that corresponds to the data field for easier lookup.
 As mentioned, there cen be additional configurations done as needed.
 
 
-The header
+The source
 -------------------------------------------------------------------------------
 
 We will start with a full listing of the writer source.