Splitted big pyx into sub-pyx
This commit is contained in:
Guilhem Lavaux
parent
c5ad407b20
commit
8b9b72ca82
@ -8,6 +8,16 @@ add_custom_command(
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx
|
||||
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx)
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx
|
||||
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx)
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx
|
||||
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx)
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx
|
||||
@ -17,11 +27,15 @@ ENDIF(CYTHON)
|
||||
|
||||
|
||||
add_library(_cosmotool MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp)
|
||||
add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
|
||||
add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
|
||||
add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
|
||||
|
||||
SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
|
||||
|
||||
target_link_libraries(_cosmotool ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_power ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_cic ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_project ${PYTHON_LIBRARIES})
|
||||
|
||||
# Discover where to put packages
|
||||
@ -48,7 +62,7 @@ if (WIN32 AND NOT CYGWIN)
|
||||
SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
|
||||
endif (WIN32 AND NOT CYGWIN)
|
||||
|
||||
INSTALL(TARGETS _cosmotool _project
|
||||
INSTALL(TARGETS _cosmotool _project _cosmo_power _cosmo_cic
|
||||
LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
|
||||
)
|
||||
|
||||
|
||||
66
python/_cosmo_cic.pyx
Normal file
66
python/_cosmo_cic.pyx
Normal file
@ -0,0 +1,66 @@
|
||||
from libcpp cimport bool
|
||||
from libcpp cimport string as cppstring
|
||||
import numpy as np
|
||||
cimport numpy as np
|
||||
from cpython cimport PyObject, Py_INCREF
|
||||
cimport cython
|
||||
|
||||
np.import_array()
|
||||
|
||||
cdef extern from "cic.hpp" namespace "CosmoTool":
|
||||
|
||||
ctypedef float CICType
|
||||
ctypedef float Coordinates[3]
|
||||
|
||||
cdef cppclass CICParticles:
|
||||
float mass
|
||||
Coordinates coords
|
||||
|
||||
cdef cppclass CICFilter:
|
||||
|
||||
CICFilter(np.uint32_t resolution, double L) nogil
|
||||
|
||||
void resetMesh() nogil
|
||||
void putParticles(CICParticles* particles, np.uint32_t N) nogil
|
||||
void getDensityField(CICType *& field, np.uint32_t& res) nogil
|
||||
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
@cython.wraparound(False)
|
||||
def leanCic(float[:,:] particles, float L, int Resolution):
|
||||
cdef CICParticles p
|
||||
cdef CICFilter *cic
|
||||
cdef np.uint64_t i
|
||||
cdef CICType *field
|
||||
cdef np.uint32_t dummyRes
|
||||
cdef np.ndarray[np.float64_t, ndim=3] out_field
|
||||
cdef np.ndarray[np.float64_t, ndim=1] out_field0
|
||||
cdef np.float64_t[:] out_field_buf
|
||||
cdef np.uint64_t j
|
||||
|
||||
cic = new CICFilter(Resolution, L)
|
||||
cic.resetMesh()
|
||||
|
||||
if particles.shape[1] != 3:
|
||||
raise ValueError("Particles must be Nx3 array")
|
||||
|
||||
p.mass = 1
|
||||
for i in xrange(particles.shape[0]):
|
||||
p.coords[0] = particles[i,0]
|
||||
p.coords[1] = particles[i,1]
|
||||
p.coords[2] = particles[i,2]
|
||||
cic.putParticles(&p, 1)
|
||||
|
||||
field = <CICType*>0
|
||||
dummyRes = 0
|
||||
cic.getDensityField(field, dummyRes)
|
||||
|
||||
out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
|
||||
out_field0 = out_field.reshape(out_field.size)
|
||||
out_field_buf = out_field
|
||||
for j in xrange(out_field_buf.size):
|
||||
out_field_buf[j] = field[j]
|
||||
|
||||
del cic
|
||||
return out_field
|
||||
107
python/_cosmo_power.pyx
Normal file
107
python/_cosmo_power.pyx
Normal file
@ -0,0 +1,107 @@
|
||||
from libcpp cimport bool
|
||||
from libcpp cimport string as cppstring
|
||||
import numpy as np
|
||||
cimport numpy as np
|
||||
from cpython cimport PyObject, Py_INCREF
|
||||
cimport cython
|
||||
|
||||
np.import_array()
|
||||
|
||||
cdef extern from "cosmopower.hpp" namespace "CosmoTool":
|
||||
|
||||
cdef enum CosmoFunction "CosmoTool::CosmoPower::CosmoFunction":
|
||||
POWER_EFSTATHIOU "CosmoTool::CosmoPower::POWER_EFSTATHIOU",
|
||||
HU_WIGGLES "CosmoTool::CosmoPower::HU_WIGGLES",
|
||||
HU_BARYON "CosmoTool::CosmoPower::HU_BARYON",
|
||||
OLD_POWERSPECTRUM,
|
||||
POWER_BARDEEN "CosmoTool::CosmoPower::POWER_BARDEEN",
|
||||
POWER_SUGIYAMA "CosmoTool::CosmoPower::POWER_SUGIYAMA",
|
||||
POWER_BDM,
|
||||
POWER_TEST
|
||||
|
||||
cdef cppclass CosmoPower:
|
||||
double n
|
||||
double K0
|
||||
double V_LG_CMB
|
||||
|
||||
double CMB_VECTOR[3]
|
||||
double h
|
||||
double SIGMA8
|
||||
double OMEGA_B
|
||||
double OMEGA_C
|
||||
double omega_B
|
||||
double omega_C
|
||||
double Theta_27
|
||||
double OMEGA_0
|
||||
double Omega
|
||||
double beta
|
||||
double OmegaEff
|
||||
double Gamma0
|
||||
double normPower
|
||||
|
||||
|
||||
CosmoPower()
|
||||
void setFunction(CosmoFunction)
|
||||
void updateCosmology()
|
||||
void updatePhysicalCosmology()
|
||||
void normalize()
|
||||
void setNormalization(double)
|
||||
double power(double)
|
||||
|
||||
cdef class CosmologyPower:
|
||||
|
||||
cdef CosmoPower power
|
||||
|
||||
def __init__(self,**cosmo):
|
||||
|
||||
self.power = CosmoPower()
|
||||
self.power.OMEGA_B = cosmo['omega_B_0']
|
||||
self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
|
||||
self.power.h = cosmo['h']
|
||||
if 'ns' in cosmo:
|
||||
self.power.n = cosmo['ns']
|
||||
|
||||
assert self.power.OMEGA_C > 0
|
||||
|
||||
self.power.updateCosmology()
|
||||
|
||||
def normalize(self,s8):
|
||||
self.power.SIGMA8 = s8
|
||||
self.power.normalize()
|
||||
|
||||
|
||||
def setFunction(self,funcname):
|
||||
cdef CosmoFunction f
|
||||
|
||||
f = POWER_EFSTATHIOU
|
||||
|
||||
if funcname=='EFSTATHIOU':
|
||||
f = POWER_EFSTATHIOU
|
||||
elif funcname=='HU_WIGGLES':
|
||||
f = HU_WIGGLES
|
||||
elif funcname=='HU_BARYON':
|
||||
f = HU_BARYON
|
||||
elif funcname=='BARDEEN':
|
||||
f = POWER_BARDEEN
|
||||
elif funcname=='SUGIYAMA':
|
||||
f = POWER_SUGIYAMA
|
||||
|
||||
self.power.setFunction(f)
|
||||
|
||||
cdef double _compute(self, double k):
|
||||
k *= self.power.h
|
||||
return self.power.power(k)
|
||||
|
||||
def compute(self, k):
|
||||
cdef np.ndarray out
|
||||
cdef double kval
|
||||
cdef tuple i
|
||||
|
||||
if isinstance(k, np.ndarray):
|
||||
out = np.empty(k.shape, dtype=np.float64)
|
||||
for i,kval in np.ndenumerate(k):
|
||||
out[i] = self._compute(kval)
|
||||
return out
|
||||
else:
|
||||
return self._compute(k)
|
||||
|
||||
@ -7,64 +7,6 @@ cimport cython
|
||||
|
||||
np.import_array()
|
||||
|
||||
cdef extern from "cosmopower.hpp" namespace "CosmoTool":
|
||||
|
||||
cdef enum CosmoFunction "CosmoTool::CosmoPower::CosmoFunction":
|
||||
POWER_EFSTATHIOU "CosmoTool::CosmoPower::POWER_EFSTATHIOU",
|
||||
HU_WIGGLES "CosmoTool::CosmoPower::HU_WIGGLES",
|
||||
HU_BARYON "CosmoTool::CosmoPower::HU_BARYON",
|
||||
OLD_POWERSPECTRUM,
|
||||
POWER_BARDEEN "CosmoTool::CosmoPower::POWER_BARDEEN",
|
||||
POWER_SUGIYAMA "CosmoTool::CosmoPower::POWER_SUGIYAMA",
|
||||
POWER_BDM,
|
||||
POWER_TEST
|
||||
|
||||
cdef cppclass CosmoPower:
|
||||
double n
|
||||
double K0
|
||||
double V_LG_CMB
|
||||
|
||||
double CMB_VECTOR[3]
|
||||
double h
|
||||
double SIGMA8
|
||||
double OMEGA_B
|
||||
double OMEGA_C
|
||||
double omega_B
|
||||
double omega_C
|
||||
double Theta_27
|
||||
double OMEGA_0
|
||||
double Omega
|
||||
double beta
|
||||
double OmegaEff
|
||||
double Gamma0
|
||||
double normPower
|
||||
|
||||
|
||||
CosmoPower()
|
||||
void setFunction(CosmoFunction)
|
||||
void updateCosmology()
|
||||
void updatePhysicalCosmology()
|
||||
void normalize()
|
||||
void setNormalization(double)
|
||||
double power(double)
|
||||
|
||||
cdef extern from "cic.hpp" namespace "CosmoTool":
|
||||
|
||||
ctypedef float CICType
|
||||
ctypedef float Coordinates[3]
|
||||
|
||||
cdef cppclass CICParticles:
|
||||
float mass
|
||||
Coordinates coords
|
||||
|
||||
cdef cppclass CICFilter:
|
||||
|
||||
CICFilter(np.uint32_t resolution, double L) nogil
|
||||
|
||||
void resetMesh() nogil
|
||||
void putParticles(CICParticles* particles, np.uint32_t N) nogil
|
||||
void getDensityField(CICType *& field, np.uint32_t& res) nogil
|
||||
|
||||
cdef extern from "loadSimu.hpp" namespace "CosmoTool":
|
||||
|
||||
cdef cppclass SimuData:
|
||||
@ -409,100 +351,3 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision =
|
||||
|
||||
return _PySimulationAdaptor(wrap_simudata(data, flags))
|
||||
|
||||
|
||||
cdef class CosmologyPower:
|
||||
|
||||
cdef CosmoPower power
|
||||
|
||||
def __init__(self,**cosmo):
|
||||
|
||||
self.power = CosmoPower()
|
||||
self.power.OMEGA_B = cosmo['omega_B_0']
|
||||
self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
|
||||
self.power.h = cosmo['h']
|
||||
if 'ns' in cosmo:
|
||||
self.power.n = cosmo['ns']
|
||||
|
||||
assert self.power.OMEGA_C > 0
|
||||
|
||||
self.power.updateCosmology()
|
||||
|
||||
def normalize(self,s8):
|
||||
self.power.SIGMA8 = s8
|
||||
self.power.normalize()
|
||||
|
||||
|
||||
def setFunction(self,funcname):
|
||||
cdef CosmoFunction f
|
||||
|
||||
f = POWER_EFSTATHIOU
|
||||
|
||||
if funcname=='EFSTATHIOU':
|
||||
f = POWER_EFSTATHIOU
|
||||
elif funcname=='HU_WIGGLES':
|
||||
f = HU_WIGGLES
|
||||
elif funcname=='HU_BARYON':
|
||||
f = HU_BARYON
|
||||
elif funcname=='BARDEEN':
|
||||
f = POWER_BARDEEN
|
||||
elif funcname=='SUGIYAMA':
|
||||
f = POWER_SUGIYAMA
|
||||
|
||||
self.power.setFunction(f)
|
||||
|
||||
cdef double _compute(self, double k):
|
||||
k *= self.power.h
|
||||
return self.power.power(k)
|
||||
|
||||
def compute(self, k):
|
||||
cdef np.ndarray out
|
||||
cdef double kval
|
||||
cdef tuple i
|
||||
|
||||
if isinstance(k, np.ndarray):
|
||||
out = np.empty(k.shape, dtype=np.float64)
|
||||
for i,kval in np.ndenumerate(k):
|
||||
out[i] = self._compute(kval)
|
||||
return out
|
||||
else:
|
||||
return self._compute(k)
|
||||
|
||||
@cython.boundscheck(False)
|
||||
@cython.cdivision(True)
|
||||
@cython.wraparound(False)
|
||||
def leanCic(float[:,:] particles, float L, int Resolution):
|
||||
cdef CICParticles p
|
||||
cdef CICFilter *cic
|
||||
cdef np.uint64_t i
|
||||
cdef CICType *field
|
||||
cdef np.uint32_t dummyRes
|
||||
cdef np.ndarray[np.float64_t, ndim=3] out_field
|
||||
cdef np.ndarray[np.float64_t, ndim=1] out_field0
|
||||
cdef np.float64_t[:] out_field_buf
|
||||
cdef np.uint64_t j
|
||||
|
||||
cic = new CICFilter(Resolution, L)
|
||||
cic.resetMesh()
|
||||
|
||||
if particles.shape[1] != 3:
|
||||
raise ValueError("Particles must be Nx3 array")
|
||||
|
||||
p.mass = 1
|
||||
for i in xrange(particles.shape[0]):
|
||||
p.coords[0] = particles[i,0]
|
||||
p.coords[1] = particles[i,1]
|
||||
p.coords[2] = particles[i,2]
|
||||
cic.putParticles(&p, 1)
|
||||
|
||||
field = <CICType*>0
|
||||
dummyRes = 0
|
||||
cic.getDensityField(field, dummyRes)
|
||||
|
||||
out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
|
||||
out_field0 = out_field.reshape(out_field.size)
|
||||
out_field_buf = out_field
|
||||
for j in xrange(out_field_buf.size):
|
||||
out_field_buf[j] = field[j]
|
||||
|
||||
del cic
|
||||
return out_field
|
||||
|
||||
@ -1,9 +1,16 @@
|
||||
from _cosmotool import *
|
||||
from _project import *
|
||||
from _cosmo_power import *
|
||||
from _cosmo_cic import *
|
||||
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
|
||||
from .borg import read_borg_vol
|
||||
from .cic import cicParticles
|
||||
try:
|
||||
import pyopencl
|
||||
from .cl_cic import cl_CIC_Density
|
||||
except:
|
||||
print("No opencl support")
|
||||
|
||||
from .simu import loadRamsesAll, simpleWriteGadget, SimulationBare
|
||||
from .timing import time_block, timeit, timeit_quiet
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user