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Merge pull request #10 from YichiDanielSong/mm-fixes 

Import cython bind
fixes-turtlebasket
Mattia Montanari 2020-05-21 17:53:08 +01:00 committed by GitHub
parent 0bb555f0a1 d090fafe02
commit 4c0580cc75
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GPG Key ID: 4AEE18F83AFDEB23
6 changed files with 277 additions and 5 deletions
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35
.gitignore vendored
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@ -176,6 +176,41 @@ sysinfo.txt
# Office # Office
~*.pptx ~*.pptx
#Cython https://github.com/cython/cython/blob/master/.gitignore
*.pyc
*.pyo
__pycache__
*.o
.*cache*/
*/cython/*.c
/TEST_TMP/
/build/
/cython_build/
/wheelhouse*/
!tests/build/
/dist/
.gitrev
.coverage
*.patch
*.diff
*.orig
*.prof
*.rej
*.log
*.dep
*.swp
*~
callgrind.out.*
.ipynb_checkpoints
# Jetbrains IDE project files
/.idea
/*.iml
# Pytest # Pytest
.cache .cache
.pytest_cache .pytest_cache

8
CMakeLists.txt
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@ -9,21 +9,21 @@
# # # #
# This file is part of openGJK. # # This file is part of openGJK. #
# # # #
# openGJK is free software: you can redistribute it and/or modify # # OpenGJK is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by # # it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or # # the Free Software Foundation, either version 3 of the License, or #
# any later version. # # any later version. #
# # # #
# openGJK is distributed in the hope that it will be useful, # # OpenGJK is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of # # but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The #
# GNU General Public License for more details. # # GNU General Public License for more details. #
# # # #
# You should have received a copy of the GNU General Public License # # You should have received a copy of the GNU General Public License #
# along with openGJK. If not, see <https://www.gnu.org/licenses/>. # # along with OpenGJK. If not, see <https://www.gnu.org/licenses/>. #
# # # #
# openGJK: open-source Gilbert-Johnson-Keerthi algorithm # # openGJK: open-source Gilbert-Johnson-Keerthi algorithm #
# Copyright (C) Mattia Montanari 2018 - 2019 # # Copyright (C) Mattia Montanari 2018 - 2020 #
# http://iel.eng.ox.ac.uk/?page_id=504 # # http://iel.eng.ox.ac.uk/?page_id=504 #
# # # #
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #

44
examples/cython/openGJK_cython.pxd Normal file
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@ -0,0 +1,44 @@
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# ##### # # # #
# #### ##### ###### # # # # # # # #
# # # # # # ## # # # # # #
# # # # # ##### # # # # #### # ### #
# # # ##### # # # # # # # # # # #
# # # # # # ## # # # # # # #
# #### # ###### # # ##### ##### # # #
# #
# This file is part of openGJK. #
# #
# OpenGJK is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# OpenGJK is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with OpenGJK. If not, see <https://www.gnu.org/licenses/>. #
# #
# openGJK: open-source Gilbert-Johnson-Keerthi algorithm #
# Copyright (C) Mattia Montanari 2018 - 2020 #
# http://iel.eng.ox.ac.uk/?page_id=504 #
# #
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# Declare C function and data types
cdef extern from "openGJK.h":
struct bd:
int numpoints
double s[3]
double ** coord
struct simplex:
int nvrtx
double vrtx[4][3]
int wids[4]
double lambdas[4]
double gjk(bd bd1, bd bd2, simplex *s)

111
examples/cython/openGJK_cython.pyx Normal file
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@ -0,0 +1,111 @@
#!python
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# ##### # # # #
# #### ##### ###### # # # # # # # #
# # # # # # ## # # # # # #
# # # # # ##### # # # # #### # ### #
# # # ##### # # # # # # # # # # #
# # # # # # ## # # # # # # #
# #### # ###### # # ##### ##### # # #
# #
# This file is part of openGJK. #
# #
# OpenGJK is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# OpenGJK is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with OpenGJK. If not, see <https://www.gnu.org/licenses/>. #
# #
# openGJK: open-source Gilbert-Johnson-Keerthi algorithm #
# Copyright (C) Mattia Montanari 2018 - 2020 #
# http://iel.eng.ox.ac.uk/?page_id=504 #
# #
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# cython: language_level=3
# distutils: sources = ../../src/openGJK.c
# distutils: include_dirs = ../../include/openGJK
cimport openGJK_cython
import numpy as np
from libc.stdlib cimport free, malloc
from cpython.mem cimport PyMem_Malloc, PyMem_Free
# Create Python function
def pygjk(bod1, bod2):
# Declare data types
cdef:
simplex s
bd bd1
bd bd2
double dist2
# Convert 1D array to 2D, if any
if bod1.ndim < 2:
bod1 = np.append([bod1], [[1.,1.,1.]], axis = 0)
bd1.numpoints = np.size(bod1,0) - 1
else:
bd1.numpoints = np.size(bod1,0)
if bod2.ndim < 2:
bod2 = np.append([bod2], [[1.,1.,1.]], axis = 0)
bd2.numpoints = np.size(bod2,0) - 1
else:
bd2.numpoints = np.size(bod2,0)
# Allocate memory for bodies
bd1.coord = <double **> malloc(bd1.numpoints * sizeof(double *))
if not bd1.coord:
raise NameError('Not enough memory for bd1.coord')
for i in range(0, bd1.numpoints):
bd1.coord[i] = <double *> malloc(3 * sizeof(double))
if not bd1.coord[i]:
raise NameError('Not enough memory for bd1.coord[]')
bd2.coord = <double **> malloc(bd2.numpoints * sizeof(double *))
if not bd2.coord:
raise NameError('Not enough memory for bd2.coord')
for j in range(0, bd2.numpoints):
bd2.coord[j] = <double *> malloc(3 * sizeof(double))
if not bd2.coord[j]:
raise NameError('Not enough memory for bd2.coord[]')
# Create numpy-array MemoryView
cdef:
double [:,:] narr1 = bod1
double [:,:] narr2 = bod2
# Assign coordinate values
for i in range(0, bd1.numpoints):
for j in range(0,3):
bd1.coord[i][j] = narr1[i,j]
for i in range(0, bd2.numpoints):
for j in range(0,3):
bd2.coord[i][j] = narr2[i,j]
# Call C function
dist2 = gjk(bd1, bd2, &s)
# Free the memory
for ii in range(0, bd1.numpoints):
free(bd1.coord[ii])
free(bd1.coord)
for jj in range(0, bd2.numpoints):
free(bd2.coord[jj])
free(bd2.coord)
return dist2

38
examples/cython/pygjk_trial.py Normal file
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@ -0,0 +1,38 @@
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# ##### # # # #
# #### ##### ###### # # # # # # # #
# # # # # # ## # # # # # #
# # # # # ##### # # # # #### # ### #
# # # ##### # # # # # # # # # # #
# # # # # # ## # # # # # # #
# #### # ###### # # ##### ##### # # #
# #
# This file is part of openGJK. #
# #
# OpenGJK is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# OpenGJK is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with OpenGJK. If not, see <https://www.gnu.org/licenses/>. #
# #
# openGJK: open-source Gilbert-Johnson-Keerthi algorithm #
# Copyright (C) Mattia Montanari 2018 - 2020 #
# http://iel.eng.ox.ac.uk/?page_id=504 #
# #
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
import numpy as np
import openGJK_cython as opengjk
a = np.array([[1.,1.,1.],[1.,1.,1.]])
b = np.array([[11.,1.,1.],[1.,1.,1.]])
d = opengjk.pygjk(a,b)
print(d)

44
examples/cython/setup.py Normal file
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@ -0,0 +1,44 @@
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
# ##### # # # #
# #### ##### ###### # # # # # # # #
# # # # # # ## # # # # # #
# # # # # ##### # # # # #### # ### #
# # # ##### # # # # # # # # # # #
# # # # # # ## # # # # # # #
# #### # ###### # # ##### ##### # # #
# #
# This file is part of openGJK. #
# #
# OpenGJK is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# any later version. #
# #
# OpenGJK is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See The #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with OpenGJK. If not, see <https://www.gnu.org/licenses/>. #
# #
# openGJK: open-source Gilbert-Johnson-Keerthi algorithm #
# Copyright (C) Mattia Montanari 2018 - 2020 #
# http://iel.eng.ox.ac.uk/?page_id=504 #
# #
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
from setuptools import Extension, setup
from Cython.Build import cythonize
exts = Extension(
"openGJK_cython",
sources = ["openGJK_cython.pyx"],
extra_compile_args=['-I../../include/','-fopenmp'],
extra_link_args=['-fopenmp'],
)
setup(
name='openGJK-cython-version',
ext_modules = cythonize( [exts] )
)