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Merge pull request #55 from PDAL/remove-python-from-pdal-base
Remove python from pdal base
2 parents b048960 + cfe6391 commit a2f6eac

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‎.gitignore‎

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pdal/libpdalpython.cpp
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*.pyc
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_skbuild/*
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.vscode/*
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__pycache__
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build/*
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PDAL.egg-info/*
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dist/*
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*.o
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*.so
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*.dylib

‎Dockerfile‎

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FROM continuumio/miniconda3:latest
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MAINTAINER Howard Butler <[email protected]>
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RUN apt-get install -y \
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gdb && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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RUN conda update -n base -c defaults conda \
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&& conda install -y -c conda-forge \
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compilers \
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pdal \
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make ninja \
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python=3.8
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RUN git clone https://github.com/PDAL/python.git pdal-python \
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&& cd pdal-python \
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&& git checkout remove-python-from-pdal-base
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RUN cd pdal-python \
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&& pip install -e .
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ENV PDAL_DRIVER_PATH=/pdal-python/_skbuild/linux-x86_64-3.8/cmake-install/lib/
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# docker build -t pdal-python
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# docker run -t -i --cap-add=SYS_PTRACE --security-opt seccomp=unconfined pdal-python
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#gdb --args /pdal-python/_skbuild/linux-x86_64-3.8/cmake-build/pdal_filters_python_test
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‎MANIFEST.in‎

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exclude *.txt
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exclude MANIFEST.in
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include CHANGES.txt README.rst
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include CHANGES.txt README.rst pyproject.toml
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recursive-include test *.py
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recursive-include pdal *.pyx
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recursive-include pdal *.hpp
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recursive-include pdal *.cpp

‎README.rst‎

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PDAL
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================================================================================
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The PDAL Python extension allows you to process data with PDAL into `Numpy`_
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arrays. Additionally, you can use it to fetch `schema`_ and `metadata`_ from
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PDAL Python support allows you to process data with PDAL into `Numpy`_
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arrays. It supports embedding Python in PDAL pipelines with the `readers.numpy <https://pdal.io/stages/readers.numpy.html>`__
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and `filters.python <https://pdal.io/stages/filters.python.html>`__ stages, and it provides a PDAL extension module to control
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Python interaction with PDAL.
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Additionally, you can use it to fetch `schema`_ and `metadata`_ from
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PDAL operations.
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Installation
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--------------------------------------------------------------------------------
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PyPI
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................................................................................
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PDAL Python support is installable via PyPI:
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.. code-block::
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pip install PDAL
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GitHub
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................................................................................
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The repository for PDAL's Python extension is available at https://github.com/PDAL/python
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It is released independently from PDAL itself as of PDAL 1.7.
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Python support released independently from PDAL itself as of PDAL 1.7.
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Usage
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--------------------------------------------------------------------------------
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Simple
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................................................................................
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Given the following pipeline, which simply reads an `ASPRS LAS`_ file and
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sorts it by the ``X`` dimension:
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import pdal
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pipeline = pdal.Pipeline(json)
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pipeline.validate() # check if our JSON and options were good
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pipeline.loglevel = 8 #really noisy
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count = pipeline.execute()
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arrays = pipeline.arrays
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metadata = pipeline.metadata
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log = pipeline.log
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Reading using Numpy Arrays
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................................................................................
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The following more complex scenario demonstrates the full cycling between
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PDAL and Python:
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* Read a small testfile from GitHub into a Numpy array
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* Filters those arrays with Numpy for Intensity
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* Pass the filtered array to PDAL to be filtered again
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* Write the filtered array to an LAS file.
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.. code-block:: python
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data = "https://github.com/PDAL/PDAL/blob/master/test/data/las/1.2-with-color.las?raw=true"
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json = """
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{
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"pipeline": [
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{
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"type": "readers.las",
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"filename": "%s"
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}
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]
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}"""
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import pdal
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import numpy as np
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pipeline = pdal.Pipeline(json % data)
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count = pipeline.execute()
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# get the data from the first array
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# [array([(637012.24, 849028.31, 431.66, 143, 1, 1, 1, 0, 1, -9., 132, 7326, 245380.78254963, 68, 77, 88),
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# dtype=[('X', '<f8'), ('Y', '<f8'), ('Z', '<f8'), ('Intensity', '<u2'), ('ReturnNumber', 'u1'), ('NumberOfReturns', 'u1'), ('ScanDirectionFlag', 'u1'), ('EdgeOfFlightLine', 'u1'), ('Classification', 'u1'), ('ScanAngleRank', '<f4'), ('UserData', 'u1'), ('PointSourceId', '<u2'), ('GpsTime', '<f8'), ('Red', '<u2'), ('Green', '<u2'), ('Blue', '<u2')])
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arr = pipeline.arrays[0]
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print (len(arr)) # 1065 points
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# Filter out entries that have intensity < 50
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intensity = arr[arr['Intensity'] > 30]
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print (len(intensity)) # 704 points
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# Now use pdal to clamp points that have intensity
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# 100 <= v < 300, and there are 387
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clamp =u"""{
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"pipeline":[
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{
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"type":"filters.range",
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"limits":"Intensity[100:300)"
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}
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]
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}"""
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p = pdal.Pipeline(clamp, [intensity])
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count = p.execute()
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clamped = p.arrays[0]
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print (count)
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# Write our intensity data to an LAS file
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output =u"""{
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"pipeline":[
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{
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"type":"writers.las",
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"filename":"clamped.las",
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"offset_x":"auto",
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"offset_y":"auto",
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"offset_z":"auto",
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"scale_x":0.01,
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"scale_y":0.01,
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"scale_z":0.01
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}
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]
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}"""
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p = pdal.Pipeline(output, [clamped])
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count = p.execute()
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print (count)
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.. _`Numpy`: http://www.numpy.org/
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.. _`schema`: http://www.pdal.io/dimensions.html
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.. _`metadata`: http://www.pdal.io/development/metadata.html
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.. image:: https://travis-ci.org/PDAL/python.svg?branch=master
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:target: https://travis-ci.org/PDAL/python
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.. image:: https://ci.appveyor.com/api/projects/status/of4kecyahpo8892d
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:target: https://ci.appveyor.com/project/hobu/python/
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Requirements
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================================================================================
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* PDAL 1.7+
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* Python >=2.7 (including Python 3.x)
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* PDAL 2.1+
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* Python >=3.6
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* Cython (eg :code:`pip install cython`)
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* Packaging (eg :code:`pip install packaging`)
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‎debug.sh‎

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This file was deleted.

‎pdal/CMakeLists.txt‎

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cmake_minimum_required(VERSION 3.11.0)
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project(pdal)
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# macros for creating targets
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include(${PROJECT_SOURCE_DIR}/macros.cmake NO_POLICY_SCOPE)
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set(CMAKE_CXX_STANDARD 11)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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set(CMAKE_CXX_EXTENSIONS OFF)
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set(CMAKE_BUILD_TYPE "Release")
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enable_testing()
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# Python-finding settings
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set(Python3_FIND_STRATEGY "LOCATION")
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set(Python3_FIND_REGISTRY "LAST")
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set(Python3_FIND_FRAMEWORK "LAST")
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find_package(Python3 COMPONENTS Interpreter Development NumPy REQUIRED)
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# find PDAL. Require 2.1+
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find_package(PDAL 2.1 REQUIRED)
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if(SKBUILD)
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find_package(PythonExtensions REQUIRED)
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find_package(Cython REQUIRED)
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message(STATUS "The project is built using scikit-build")
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endif()
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execute_process(
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COMMAND
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${Python3_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('Py_ENABLE_SHARED'))"
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OUTPUT_VARIABLE Py_ENABLE_SHARED
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OUTPUT_STRIP_TRAILING_WHITESPACE
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)
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#execute_process(
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# COMMAND
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# ${Python3_EXECUTABLE} -c "from distutils import sysconfig; print(sysconfig.get_config_var('LDSHARED').split(' ', 1)[1])"
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# OUTPUT_VARIABLE PYTHON_LDSHARED
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# OUTPUT_STRIP_TRAILING_WHITESPACE
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#)
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#if (NOT Py_ENABLE_SHARED)
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# message(STATUS "Python ${Python3_EXECUTABLE} is statically linked")
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# if (APPLE)
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# # conda gives us -bundle, which isn't valid
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# message(STATUS "Removing extra -bundle argument from sysconfig.get_config_var('LDSHARED')")
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# string(REPLACE "-bundle" "" PYTHON_LDSHARED "${PYTHON_LDSHARED}")
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# string(STRIP ${PYTHON_LDSHARED} PYTHON_LDSHARED)
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# endif()
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# # set(Python3_LIBRARIES ${PYTHON_LDSHARED})
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# message(STATUS "Setting Python3_LIBRARIES to '${Python3_LIBRARIES}' due to static Python")
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#endif()
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set(EXTENSION_SRC
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PyArray.cpp
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PyArray.hpp
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PyDimension.hpp
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PyPipeline.cpp
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PyPipeline.hpp)
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set(extension "libpdalpython")
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add_cython_target(${extension} libpdalpython.pyx CXX PY3)
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add_library(${extension} MODULE ${EXTENSION_SRC} libpdalpython)
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target_include_directories( ${extension}
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PRIVATE
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.
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${PDAL_INCLUDE_DIRS}
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${Python3_INCLUDE_DIRS}
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${Python3_NumPy_INCLUDE_DIRS})
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target_link_libraries(${extension} ${PDAL_LIBRARIES})
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python_extension_module(${extension})
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install(TARGETS ${extension} LIBRARY DESTINATION ${PROJECT_NAME})
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PDAL_PYTHON_ADD_PLUGIN(numpy_reader reader numpy
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FILES
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./io/NumpyReader.cpp
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./io/NumpyReader.hpp
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./plang/Invocation.cpp
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./plang/Environment.cpp
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./plang/Redirector.cpp
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./plang/Script.cpp
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LINK_WITH
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${PDAL_LIBRARIES}
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${Python3_LIBRARIES}
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${CMAKE_DL_LIBS}
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SYSTEM_INCLUDES
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${PDAL_INCLUDE_DIRS}
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${Python3_INCLUDE_DIRS}
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${Python3_NumPy_INCLUDE_DIRS}
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COMPILE_OPTIONS
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${PYTHON_LINK_LIBRARY}
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)
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# Download and unpack googletest at configure time
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configure_file(test/gtest/CMakeLists.txt.in googletest-download/CMakeLists.txt)
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execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
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RESULT_VARIABLE result
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download )
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if(result)
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message(FATAL_ERROR "CMake step for googletest failed: ${result}")
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endif()
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execute_process(COMMAND ${CMAKE_COMMAND} --build .
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RESULT_VARIABLE result
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download )
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if(result)
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message(FATAL_ERROR "Build step for googletest failed: ${result}")
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endif()
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# Prevent overriding the parent project's compiler/linker
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# settings on Windows
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set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
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# Add googletest directly to our build. This defines
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# the gtest and gtest_main targets.
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add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/googletest-src
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${CMAKE_CURRENT_BINARY_DIR}/googletest-build
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EXCLUDE_FROM_ALL)
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PDAL_PYTHON_ADD_PLUGIN(python_filter filter python
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FILES
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./filters/PythonFilter.cpp
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./filters/PythonFilter.hpp
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./plang/Invocation.cpp
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./plang/Environment.cpp
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./plang/Redirector.cpp
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./plang/Script.cpp
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LINK_WITH
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${PDAL_LIBRARIES}
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${Python3_LIBRARIES}
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${CMAKE_DL_LIBS}
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SYSTEM_INCLUDES
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${PDAL_INCLUDE_DIRS}
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${Python3_INCLUDE_DIRS}
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${Python3_NumPy_INCLUDE_DIRS}
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COMPILE_OPTIONS
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${PYTHON_LINK_LIBRARY}
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)
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PDAL_PYTHON_ADD_TEST(pdal_io_numpy_test
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FILES
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./test/NumpyReaderTest.cpp
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./test/Support.cpp
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./plang/Invocation.cpp
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./plang/Environment.cpp
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./plang/Redirector.cpp
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./plang/Script.cpp
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LINK_WITH
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${numpy_reader}
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${Python3_LIBRARIES}
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${PDAL_LIBRARIES}
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${CMAKE_DL_LIBS}
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SYSTEM_INCLUDES
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${PDAL_INCLUDE_DIRS}
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${Python3_INCLUDE_DIRS}
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${Python3_NumPy_INCLUDE_DIRS}
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)
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PDAL_PYTHON_ADD_TEST(pdal_filters_python_test
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FILES
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./test/PythonFilterTest.cpp
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./test/Support.cpp
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./plang/Invocation.cpp
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./plang/Environment.cpp
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./plang/Redirector.cpp
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./plang/Script.cpp
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LINK_WITH
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${python_filter}
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${Python3_LIBRARIES}
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${PDAL_LIBRARIES}
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${CMAKE_DL_LIBS}
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SYSTEM_INCLUDES
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${PDAL_INCLUDE_DIRS}
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${Python3_INCLUDE_DIRS}
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${Python3_NumPy_INCLUDE_DIRS}
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)

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