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.. _readers.numpy: | ||
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readers.numpy | ||
================================================================================ | ||
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PDAL has support for processing data using :ref:`filters.python`, but it is also | ||
convenient to read data from `Numpy`_ for processing in PDAL. | ||
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`Numpy`_ supports saving files with the ``save`` method, usually with the | ||
extension ``.npy``. As of PDAL 1.7.0, ``.npz`` files were not yet supported. | ||
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.. warning:: | ||
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It is untested whether the version of Python PDAL was linked against and | ||
the version that saved the ``.npy`` files can be mixed. | ||
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Array Types | ||
-------------------------------------------------------------------------------- | ||
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:ref:`readers.numpy` supports reading data in two forms: | ||
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* Arrays as named fields all of the same shape (from `laspy`_ for example) | ||
* 2-dimensional arrays | ||
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Named Field Arrays | ||
................................................................................ | ||
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`laspy`_ provides its ``.points`` Numpy array as a bunch of named fields: | ||
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:: | ||
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import laspy | ||
f = laspy.file.File('test/data/autzen/autzen.las') | ||
print (f.points[0:1]) | ||
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:: | ||
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array([ ((63608330, 84939865, 40735, 65, 73, 1, -11, 126, 7326, 245385.60820904),)], | ||
dtype=[('point', [('X', '<i4'), ('Y', '<i4'), ('Z', '<i4'), ('intensity', '<u2'), ('flag_byte', 'u1'), ('raw_classification', 'u1'), ('scan_angle_rank', 'i1'), ('user_data', 'u1'), ('pt_src_id', '<u2'), ('gps_time', '<f8')])]) | ||
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:ref:`readers.numpy` supports reading these Numpy arrays and mapping applicable | ||
names to :ref:`dimensions` names. It will try to remove ``_``, ``-``, and ``space`` from | ||
the field name and use that as a dimension name if it can match. Types are also | ||
preserved when mapped to PDAL. | ||
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Two-dimensional Arrays | ||
................................................................................ | ||
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Typical two-dimensional `Numpy`_ arrays are also supported, with options to allow | ||
you to map the values in the cells using the ``dimension`` option. Additionally, | ||
you can override the `Z` value for the entire array by using the ``assign_z`` | ||
option to set a single `Z` value for the entire point cloud. Mapping the values to the | ||
``Z`` dimension using the ``dimension`` option is also allowed. | ||
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:: | ||
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f = open('./perlin.npy', 'rb') | ||
data = np.load(f,) | ||
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data.shape | ||
(100, 100) | ||
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data.dtype | ||
dtype('float64') | ||
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In this case, the cell locations are mapped to X and Y dimensions, the cell | ||
values are mapped to ``Intensity`` using the ``dimension`` option, and the Z | ||
values are assigned to 4 using the ``assign_z`` option. | ||
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:: | ||
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pdal info perlin.npy --readers.numpy.dimension=Intensity --readers.numpy.assign_z=4 | ||
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:: | ||
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{ | ||
"filename": "perlin.npy", | ||
"pdal_version": "1.6.0 (git-version: 897afd)", | ||
"stats": | ||
{ | ||
"statistic": | ||
[ | ||
{ | ||
"average": 49.995, | ||
"count": 10000, | ||
"kurtosis": -1.201226882, | ||
"maximum": 100, | ||
"minimum": 0, | ||
"name": "X", | ||
"position": 0, | ||
"skewness": -0.0001281084091, | ||
"stddev": 29.16793715, | ||
"variance": 850.7685575 | ||
}, | ||
{ | ||
"average": 50, | ||
"count": 10000, | ||
"kurtosis": -1.1996846, | ||
"maximum": 100, | ||
"minimum": 0, | ||
"name": "Y", | ||
"position": 1, | ||
"skewness": -8.69273658e-05, | ||
"stddev": 28.87401021, | ||
"variance": 833.7084657 | ||
}, | ||
{ | ||
"average": 4, | ||
"count": 10000, | ||
"kurtosis": 9997, | ||
"maximum": 4, | ||
"minimum": 4, | ||
"name": "Z", | ||
"position": 2, | ||
"skewness": 1.844674407e+21, | ||
"stddev": 0.04000200015, | ||
"variance": 0.001600160016 | ||
}, | ||
{ | ||
"average": 0.01112664759, | ||
"count": 10000, | ||
"kurtosis": -0.5634013693, | ||
"maximum": 0.5189296418, | ||
"minimum": -0.5189296418, | ||
"name": "Intensity", | ||
"position": 3, | ||
"skewness": -0.1127124452, | ||
"stddev": 0.2024120437, | ||
"variance": 0.04097063545 | ||
} | ||
] | ||
} | ||
} | ||
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.. _`Numpy`: http://www.numpy.org/ | ||
.. _`laspy`: https://github.com/laspy/laspy | ||
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.. plugin:: | ||
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.. streamable:: | ||
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Options | ||
------- | ||
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filename | ||
npy file to read [Required] | ||
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dimension | ||
Dimension name from :ref:`dimensions` to map raster values | ||
x | ||
Dimension number (starting from 0) to map to the ``X`` PDAL :ref:`dimension <dimensions>` | ||
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y | ||
Dimension number (starting from 0) to map to the ``Y`` PDAL :ref:`dimension <dimensions>` | ||
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z | ||
Dimension number (starting from 0) to map to the ``Z`` PDAL :ref:`dimension <dimensions>` | ||
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assign_z | ||
A single value to override for ``Z`` values when ``dimension`` is used to assign the | ||
Numpy values to another dimension | ||
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.. _formatted: http://en.cppreference.com/w/cpp/string/basic_string/stof |
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Original file line number | Diff line number | Diff line change |
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@@ -1,24 +1,19 @@ | ||
set(PLANG ../plang/Invocation.cpp | ||
../plang/Environment.cpp | ||
../plang/Redirector.cpp | ||
../plang/Script.cpp) | ||
PDAL_ADD_PLUGIN(python_libname filter python | ||
FILES | ||
${PLANG} | ||
PythonFilter.cpp | ||
) | ||
target_include_directories(${python_libname} PRIVATE | ||
${PYTHON_INCLUDE_DIR} ${PDAL_JSONCPP_INCLUDE_DIR}) | ||
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target_link_libraries(${python_libname} PUBLIC | ||
${PYTHON_LIBRARY} ${CMAKE_DL_LIBS}) | ||
${PYTHON_LIBRARY} ${CMAKE_DL_LIBS} PRIVATE ${PDAL_PLANG_LIB_NAME}) | ||
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if (WITH_TESTS) | ||
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PDAL_ADD_TEST(pdal_filters_python_test | ||
FILES ../test/PythonFilterTest.cpp ${PLANG} | ||
FILES ../test/PythonFilterTest.cpp | ||
LINK_WITH ${programmable_libname} ) | ||
target_link_libraries(pdal_filters_python_test PUBLIC | ||
${PYTHON_LIBRARY} ${CMAKE_DL_LIBS}) | ||
${PYTHON_LIBRARY} ${CMAKE_DL_LIBS} PRIVATE ${PDAL_PLANG_LIB_NAME}) | ||
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endif() |
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PDAL_ADD_PLUGIN(numpy_reader reader numpy | ||
FILES | ||
NumpyReader.cpp | ||
../plang/Environment.cpp | ||
../plang/Redirector.cpp | ||
) | ||
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target_include_directories(${numpy_reader} PRIVATE | ||
${PYTHON_INCLUDE_DIR}) | ||
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target_link_libraries(${numpy_reader} PUBLIC | ||
${PYTHON_LIBRARY}) | ||
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# Install headers so Python extension | ||
# can use them later | ||
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install(DIRECTORY . | ||
DESTINATION include/pdal/io | ||
FILES_MATCHING PATTERN "*.hpp" | ||
PATTERN "CMakeFiles" EXCLUDE | ||
) | ||
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if (WITH_TESTS) | ||
PDAL_ADD_TEST(pdal_io_numpy_test | ||
FILES | ||
../test/NumpyReaderTest.cpp | ||
../plang/Environment.cpp | ||
../plang/Redirector.cpp | ||
LINK_WITH ${numpy_reader} ) | ||
target_link_libraries(pdal_io_numpy_test PUBLIC | ||
${PYTHON_LIBRARY}) | ||
endif() |
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