Splitted big pyx into sub-pyx
This commit is contained in:
Guilhem Lavaux
parent
c5ad407b20
commit
8b9b72ca82
@ -3,12 +3,22 @@ set(CMAKE_SHARED_MODULE_PREFIX)
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include_directories(${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src ${CMAKE_SOURCE_DIR}/python)
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IF(CYTHON)
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add_custom_command(
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add_custom_command(
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OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp
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COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx
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DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmotool.pyx)
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add_custom_command(
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add_custom_command(
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OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp
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COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx
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DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_power.pyx)
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add_custom_command(
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OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp
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COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx
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DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmo_cic.pyx)
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add_custom_command(
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OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp
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COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx
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DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp )
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@ -17,11 +27,15 @@ ENDIF(CYTHON)
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add_library(_cosmotool MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmotool.cpp)
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add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
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add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
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add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
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SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Bsymbolic-functions")
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target_link_libraries(_cosmotool ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
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target_link_libraries(_cosmo_power ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
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target_link_libraries(_cosmo_cic ${CosmoTool_local} ${PYTHON_LIBRARIES} ${GSL_LIBRARIES})
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target_link_libraries(_project ${PYTHON_LIBRARIES})
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# Discover where to put packages
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@ -48,7 +62,7 @@ if (WIN32 AND NOT CYGWIN)
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SET_TARGET_PROPERTIES(_cosmotool PROPERTIES SUFFIX ".pyd")
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endif (WIN32 AND NOT CYGWIN)
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INSTALL(TARGETS _cosmotool _project
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INSTALL(TARGETS _cosmotool _project _cosmo_power _cosmo_cic
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LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
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)
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66
python/_cosmo_cic.pyx
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66
python/_cosmo_cic.pyx
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@ -0,0 +1,66 @@
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from libcpp cimport bool
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from libcpp cimport string as cppstring
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import numpy as np
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cimport numpy as np
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from cpython cimport PyObject, Py_INCREF
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cimport cython
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np.import_array()
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cdef extern from "cic.hpp" namespace "CosmoTool":
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ctypedef float CICType
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ctypedef float Coordinates[3]
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cdef cppclass CICParticles:
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float mass
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Coordinates coords
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cdef cppclass CICFilter:
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CICFilter(np.uint32_t resolution, double L) nogil
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void resetMesh() nogil
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void putParticles(CICParticles* particles, np.uint32_t N) nogil
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void getDensityField(CICType *& field, np.uint32_t& res) nogil
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@cython.boundscheck(False)
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@cython.cdivision(True)
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@cython.wraparound(False)
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def leanCic(float[:,:] particles, float L, int Resolution):
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cdef CICParticles p
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cdef CICFilter *cic
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cdef np.uint64_t i
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cdef CICType *field
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cdef np.uint32_t dummyRes
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cdef np.ndarray[np.float64_t, ndim=3] out_field
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cdef np.ndarray[np.float64_t, ndim=1] out_field0
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cdef np.float64_t[:] out_field_buf
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cdef np.uint64_t j
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cic = new CICFilter(Resolution, L)
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cic.resetMesh()
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if particles.shape[1] != 3:
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raise ValueError("Particles must be Nx3 array")
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p.mass = 1
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for i in xrange(particles.shape[0]):
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p.coords[0] = particles[i,0]
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p.coords[1] = particles[i,1]
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p.coords[2] = particles[i,2]
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cic.putParticles(&p, 1)
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field = <CICType*>0
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dummyRes = 0
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cic.getDensityField(field, dummyRes)
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out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
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out_field0 = out_field.reshape(out_field.size)
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out_field_buf = out_field
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for j in xrange(out_field_buf.size):
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out_field_buf[j] = field[j]
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del cic
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return out_field
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107
python/_cosmo_power.pyx
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107
python/_cosmo_power.pyx
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@ -0,0 +1,107 @@
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from libcpp cimport bool
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from libcpp cimport string as cppstring
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import numpy as np
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cimport numpy as np
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from cpython cimport PyObject, Py_INCREF
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cimport cython
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np.import_array()
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cdef extern from "cosmopower.hpp" namespace "CosmoTool":
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cdef enum CosmoFunction "CosmoTool::CosmoPower::CosmoFunction":
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POWER_EFSTATHIOU "CosmoTool::CosmoPower::POWER_EFSTATHIOU",
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HU_WIGGLES "CosmoTool::CosmoPower::HU_WIGGLES",
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HU_BARYON "CosmoTool::CosmoPower::HU_BARYON",
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OLD_POWERSPECTRUM,
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POWER_BARDEEN "CosmoTool::CosmoPower::POWER_BARDEEN",
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POWER_SUGIYAMA "CosmoTool::CosmoPower::POWER_SUGIYAMA",
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POWER_BDM,
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POWER_TEST
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cdef cppclass CosmoPower:
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double n
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double K0
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double V_LG_CMB
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double CMB_VECTOR[3]
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double h
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double SIGMA8
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double OMEGA_B
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double OMEGA_C
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double omega_B
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double omega_C
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double Theta_27
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double OMEGA_0
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double Omega
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double beta
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double OmegaEff
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double Gamma0
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double normPower
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CosmoPower()
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void setFunction(CosmoFunction)
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void updateCosmology()
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void updatePhysicalCosmology()
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void normalize()
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void setNormalization(double)
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double power(double)
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cdef class CosmologyPower:
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cdef CosmoPower power
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def __init__(self,**cosmo):
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self.power = CosmoPower()
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self.power.OMEGA_B = cosmo['omega_B_0']
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self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
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self.power.h = cosmo['h']
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if 'ns' in cosmo:
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self.power.n = cosmo['ns']
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assert self.power.OMEGA_C > 0
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self.power.updateCosmology()
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def normalize(self,s8):
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self.power.SIGMA8 = s8
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self.power.normalize()
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def setFunction(self,funcname):
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cdef CosmoFunction f
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f = POWER_EFSTATHIOU
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if funcname=='EFSTATHIOU':
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f = POWER_EFSTATHIOU
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elif funcname=='HU_WIGGLES':
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f = HU_WIGGLES
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elif funcname=='HU_BARYON':
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f = HU_BARYON
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elif funcname=='BARDEEN':
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f = POWER_BARDEEN
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elif funcname=='SUGIYAMA':
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f = POWER_SUGIYAMA
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self.power.setFunction(f)
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cdef double _compute(self, double k):
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k *= self.power.h
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return self.power.power(k)
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def compute(self, k):
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cdef np.ndarray out
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cdef double kval
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cdef tuple i
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if isinstance(k, np.ndarray):
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out = np.empty(k.shape, dtype=np.float64)
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for i,kval in np.ndenumerate(k):
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out[i] = self._compute(kval)
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return out
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else:
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return self._compute(k)
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@ -7,64 +7,6 @@ cimport cython
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np.import_array()
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cdef extern from "cosmopower.hpp" namespace "CosmoTool":
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cdef enum CosmoFunction "CosmoTool::CosmoPower::CosmoFunction":
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POWER_EFSTATHIOU "CosmoTool::CosmoPower::POWER_EFSTATHIOU",
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HU_WIGGLES "CosmoTool::CosmoPower::HU_WIGGLES",
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HU_BARYON "CosmoTool::CosmoPower::HU_BARYON",
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OLD_POWERSPECTRUM,
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POWER_BARDEEN "CosmoTool::CosmoPower::POWER_BARDEEN",
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POWER_SUGIYAMA "CosmoTool::CosmoPower::POWER_SUGIYAMA",
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POWER_BDM,
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POWER_TEST
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cdef cppclass CosmoPower:
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double n
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double K0
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double V_LG_CMB
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double CMB_VECTOR[3]
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double h
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double SIGMA8
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double OMEGA_B
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double OMEGA_C
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double omega_B
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double omega_C
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double Theta_27
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double OMEGA_0
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double Omega
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double beta
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double OmegaEff
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double Gamma0
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double normPower
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CosmoPower()
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void setFunction(CosmoFunction)
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void updateCosmology()
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void updatePhysicalCosmology()
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void normalize()
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void setNormalization(double)
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double power(double)
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cdef extern from "cic.hpp" namespace "CosmoTool":
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ctypedef float CICType
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ctypedef float Coordinates[3]
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cdef cppclass CICParticles:
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float mass
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Coordinates coords
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cdef cppclass CICFilter:
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CICFilter(np.uint32_t resolution, double L) nogil
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void resetMesh() nogil
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void putParticles(CICParticles* particles, np.uint32_t N) nogil
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void getDensityField(CICType *& field, np.uint32_t& res) nogil
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cdef extern from "loadSimu.hpp" namespace "CosmoTool":
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cdef cppclass SimuData:
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@ -409,100 +351,3 @@ def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision =
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return _PySimulationAdaptor(wrap_simudata(data, flags))
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cdef class CosmologyPower:
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cdef CosmoPower power
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def __init__(self,**cosmo):
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self.power = CosmoPower()
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self.power.OMEGA_B = cosmo['omega_B_0']
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self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0']
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self.power.h = cosmo['h']
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if 'ns' in cosmo:
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self.power.n = cosmo['ns']
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assert self.power.OMEGA_C > 0
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self.power.updateCosmology()
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def normalize(self,s8):
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self.power.SIGMA8 = s8
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self.power.normalize()
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def setFunction(self,funcname):
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cdef CosmoFunction f
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f = POWER_EFSTATHIOU
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if funcname=='EFSTATHIOU':
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f = POWER_EFSTATHIOU
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elif funcname=='HU_WIGGLES':
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f = HU_WIGGLES
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elif funcname=='HU_BARYON':
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f = HU_BARYON
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elif funcname=='BARDEEN':
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f = POWER_BARDEEN
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elif funcname=='SUGIYAMA':
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f = POWER_SUGIYAMA
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self.power.setFunction(f)
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cdef double _compute(self, double k):
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k *= self.power.h
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return self.power.power(k)
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def compute(self, k):
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cdef np.ndarray out
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cdef double kval
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cdef tuple i
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if isinstance(k, np.ndarray):
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out = np.empty(k.shape, dtype=np.float64)
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for i,kval in np.ndenumerate(k):
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out[i] = self._compute(kval)
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return out
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else:
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return self._compute(k)
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@cython.boundscheck(False)
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@cython.cdivision(True)
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@cython.wraparound(False)
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def leanCic(float[:,:] particles, float L, int Resolution):
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cdef CICParticles p
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cdef CICFilter *cic
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cdef np.uint64_t i
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cdef CICType *field
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cdef np.uint32_t dummyRes
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cdef np.ndarray[np.float64_t, ndim=3] out_field
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cdef np.ndarray[np.float64_t, ndim=1] out_field0
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cdef np.float64_t[:] out_field_buf
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cdef np.uint64_t j
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cic = new CICFilter(Resolution, L)
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cic.resetMesh()
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if particles.shape[1] != 3:
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raise ValueError("Particles must be Nx3 array")
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p.mass = 1
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for i in xrange(particles.shape[0]):
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p.coords[0] = particles[i,0]
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p.coords[1] = particles[i,1]
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p.coords[2] = particles[i,2]
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cic.putParticles(&p, 1)
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field = <CICType*>0
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dummyRes = 0
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cic.getDensityField(field, dummyRes)
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out_field = np.empty((dummyRes, dummyRes, dummyRes), dtype=np.float64)
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out_field0 = out_field.reshape(out_field.size)
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out_field_buf = out_field
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for j in xrange(out_field_buf.size):
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out_field_buf[j] = field[j]
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del cic
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return out_field
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@ -1,9 +1,16 @@
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from _cosmotool import *
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from _project import *
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from _cosmo_power import *
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from _cosmo_cic import *
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from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
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from .borg import read_borg_vol
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from .cic import cicParticles
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from .cl_cic import cl_CIC_Density
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try:
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import pyopencl
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from .cl_cic import cl_CIC_Density
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except:
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print("No opencl support")
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from .simu import loadRamsesAll, simpleWriteGadget, SimulationBare
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from .timing import time_block, timeit, timeit_quiet
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