Finished early binding

This commit is contained in:
Guilhem Lavaux 2014-05-26 14:24:53 +02:00
parent ab1a181bb6
commit 6dc94056f1
4 changed files with 192 additions and 10 deletions

102
FindNumPy.cmake Normal file
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@ -0,0 +1,102 @@
# - Find the NumPy libraries
# This module finds if NumPy is installed, and sets the following variables
# indicating where it is.
#
# TODO: Update to provide the libraries and paths for linking npymath lib.
#
# NUMPY_FOUND - was NumPy found
# NUMPY_VERSION - the version of NumPy found as a string
# NUMPY_VERSION_MAJOR - the major version number of NumPy
# NUMPY_VERSION_MINOR - the minor version number of NumPy
# NUMPY_VERSION_PATCH - the patch version number of NumPy
# NUMPY_VERSION_DECIMAL - e.g. version 1.6.1 is 10601
# NUMPY_INCLUDE_DIRS - path to the NumPy include files
#============================================================================
# Copyright 2012 Continuum Analytics, Inc.
#
# MIT License
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
# distribute, sublicense, and/or sell copies of the Software, and to permit
# persons to whom the Software is furnished to do so, subject to
# the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
# OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
# ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
# OTHER DEALINGS IN THE SOFTWARE.
#
#============================================================================
# Finding NumPy involves calling the Python interpreter
if(NumPy_FIND_REQUIRED)
find_package(PythonInterp REQUIRED)
else()
find_package(PythonInterp)
endif()
if(NOT PYTHONINTERP_FOUND)
set(NUMPY_FOUND FALSE)
return()
endif()
execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
"import numpy as n; print(n.__version__); print(n.get_include());"
RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS
OUTPUT_VARIABLE _NUMPY_VALUES_OUTPUT
ERROR_VARIABLE _NUMPY_ERROR_VALUE
OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0)
if(NumPy_FIND_REQUIRED)
message(FATAL_ERROR
"NumPy import failure:\n${_NUMPY_ERROR_VALUE}")
endif()
set(NUMPY_FOUND FALSE)
return()
endif()
# Convert the process output into a list
string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES_OUTPUT})
string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES})
# Just in case there is unexpected output from the Python command.
list(GET _NUMPY_VALUES -2 NUMPY_VERSION)
list(GET _NUMPY_VALUES -1 NUMPY_INCLUDE_DIRS)
string(REGEX MATCH "^[0-9]+\\.[0-9]+\\.[0-9]+" _VER_CHECK "${NUMPY_VERSION}")
if("${_VER_CHECK}" STREQUAL "")
# The output from Python was unexpected. Raise an error always
# here, because we found NumPy, but it appears to be corrupted somehow.
message(FATAL_ERROR
"Requested version and include path from NumPy, got instead:\n${_NUMPY_VALUES_OUTPUT}\n")
return()
endif()
# Make sure all directory separators are '/'
string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS})
# Get the major and minor version numbers
string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION})
list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR)
list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR)
list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH)
string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH})
math(EXPR NUMPY_VERSION_DECIMAL
"(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}")
find_package_message(NUMPY
"Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}"
"${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}")
set(NUMPY_FOUND TRUE)

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@ -42,7 +42,7 @@ if (WIN32 AND NOT CYGWIN)
endif (WIN32 AND NOT CYGWIN) endif (WIN32 AND NOT CYGWIN)
INSTALL(TARGETS _cosmotool INSTALL(TARGETS _cosmotool
LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/flints LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
) )
INSTALL(DIRECTORY cosmotool DESTINATION ${PYTHON_SITE_PACKAGES} INSTALL(DIRECTORY cosmotool DESTINATION ${PYTHON_SITE_PACKAGES}

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@ -1,6 +1,9 @@
from libcpp cimport bool from libcpp cimport bool
import numpy as np import numpy as np
cimport numpy as np cimport numpy as np
from cpython cimport PyObject, Py_INCREF
np.import_array()
cdef extern from "loadSimu.hpp" namespace "CosmoTool": cdef extern from "loadSimu.hpp" namespace "CosmoTool":
@ -12,11 +15,11 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
np.float_t Omega_M np.float_t Omega_M
np.float_t Omega_Lambda np.float_t Omega_Lambda
np.int64_t TotalNumParticles np.int64_t TotalNumPart
np.int64_t NumParticles np.int64_t NumPart
np.int64_t *Id np.int64_t *Id
np.float_t *Pos[3] float *Pos[3]
np.float_t *Vel[3] float *Vel[3]
int *type int *type
cdef const int NEED_GADGET_ID cdef const int NEED_GADGET_ID
@ -29,23 +32,94 @@ cdef extern from "loadGadget.hpp" namespace "CosmoTool":
SimuData *loadGadgetMulti(const char *fname, int id, int flags) except + SimuData *loadGadgetMulti(const char *fname, int id, int flags) except +
cdef class Simulation: cdef class Simulation:
cdef float BoxSize cdef list positions
cdef float Hubble cdef list velocities
cdef list Position
cdef list Velocities
cdef SimuData *data cdef SimuData *data
property BoxSize:
def __get__(Simulation self):
return self.data.BoxSize
property Hubble:
def __get__(Simulation self):
return self.data.Hubble
property Omega_M:
def __get__(Simulation self):
return self.data.Omega_M
property positions:
def __get__(Simulation self):
return self.positions
property velocities:
def __get__(Simulation self):
return self.velocities
property numParticles:
def __get__(Simulation self):
return self.data.NumPart
def __cinit__(Simulation self): def __cinit__(Simulation self):
self.data = <SimuData *>0 self.data = <SimuData *>0
def __dealloc__(Simulation self): def __dealloc__(Simulation self):
if self.data != <SimuData *>0: if self.data != <SimuData *>0:
print("Clearing simulation data")
del self.data del self.data
cdef class ArrayWrapper:
cdef void* data_ptr
cdef int size
cdef set_data(self, int size, void* data_ptr):
""" Set the data of the array
This cannot be done in the constructor as it must recieve C-level
arguments.
Parameters:
-----------
size: int
Length of the array.
data_ptr: void*
Pointer to the data
"""
self.data_ptr = data_ptr
self.size = size
def __array__(self):
""" Here we use the __array__ method, that is called when numpy
tries to get an array from the object."""
cdef np.npy_intp shape[1]
shape[0] = <np.npy_intp> self.size
# Create a 1D array, of length 'size'
ndarray = np.PyArray_SimpleNewFromData(1, shape, np.NPY_FLOAT, self.data_ptr)
return ndarray
def __dealloc__(self):
""" Frees the array. This is called by Python when all the
references to the object are gone. """
pass
cdef object wrap_float_array(float *p, np.uint64_t s):
cdef np.ndarray ndarray
cdef ArrayWrapper wrapper
wrapper = ArrayWrapper()
wrapper.set_data(s, <void *>p)
ndarray = np.array(wrapper, copy=False)
ndarray.base = <PyObject*> wrapper
Py_INCREF(wrapper)
return ndarray
def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = True): def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loadVelocity = True):
cdef int flags cdef int flags
@ -62,4 +136,9 @@ def loadGadget(str filename, int snapshot_id, bool loadPosition = True, bool loa
simu = Simulation() simu = Simulation()
simu.data = data simu.data = data
if loadPosition:
simu.positions = [wrap_float_array(data.Pos[i], data.NumPart) for i in xrange(3)]
if loadVelocity:
simu.velocities = [wrap_float_array(data.Vel[i], data.NumPart) for i in xrange(3)]
return simu return simu

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@ -0,0 +1 @@
from _cosmotool import *