我正在尝试将一些 Python/Numpy 代码转换为 Cython 以加快速度。这是我的代码:
cimport numpy as np
import numpy as np
from numpy import *
import pylab as pl
from pylab import *
from scipy import integrate
def myc_rb_e2f(np.ndarray[double,ndim=1] y = np.zeros(7),double t, double k,double d):
M = y[0]
E = y[1]
CD = y[2]
CE = y[3]
R = y[4]
RP = y[5]
RE = y[6]
cdef double S = 0.01
if t > 300.0:
S = 5.0
#if t > 400
#S = 0.01
cdef double t1 = k[0]*S/(k[7]+S)
cdef double t2 = k[1]*(M/(k[14]+M))*(E/(k[15]+E))
cdef double t3 = k[5]*M/(k[14]+M)
cdef double t4 = k[11]*CD*RE/(k[16]+RE)
cdef double t5 = k[12]*CE*RE/(k[17]+RE)
cdef double t6 = k[2]*M/(k[14]+M)
cdef double t7 = k[3]*S/(k[7]+S)
cdef double t8 = k[6]*E/(k[15]+E)
cdef double t9 = k[13]*RP/(k[18]+RP)
cdef double t10 = k[9]*CD*R/(k[16]+R)
cdef double t11 = k[10]*CE*R/(k[17]+R)
dM = t1-d[0]*M
dE = t2+t3+t4+t5-k[8]*R*E-d[1]*E
dCD = t6+t7-d[2]*CD
dCE = t8-d[3]*CE
dR = k[4]+t9-k[8]*R*E-t10-t11-d[4]*R
dRP = t10+t11+t4+t5-t9-d[5]*RP
dRE = k[8]*R*E-t4-t5-d[6]*RE
dy = [dM,dE,dCD,dCE,dR,dRP,dRE]
return dy
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
cdef int i
for i in range (0,5000):
k[0] = 1.+0.1*randn(1)
k[1] = 0.15+0.05*randn(1)
k[2] = 0.2+0.05*randn(1)
k[3] = 0.2+0.05*randn(1)
k[4] = 0.35+0.05*randn(1)
k[5] = 0.001+0.0001*randn(1)
k[6] = 0.5+0.05*randn(1)
k[7] = 0.3+0.05*randn(1)
k[8] = 30.+5.*randn(1)
k[9] = 18.+3.*randn(1)
k[10] = 18.+3.*randn(1)
k[11] = 18.+3.*randn(1)
k[12] = 18.+3.*randn(1)
k[13] = 3.6+0.5*randn(1)
k[14] = 0.15+0.05*randn(1)
k[15] = 0.15+0.05*randn(1)
k[16] = 0.92+0.1*randn(1)
k[17] = 0.92+0.1*randn(1)
k[18] = 0.01+0.001*randn(1)
d[0] = 0.7+0.05*randn(1)
d[1] = 0.25+0.025*randn(1)
d[2] = 1.5+0.05*randn(1)
d[3] = 1.5+0.05*randn(1)
d[4] = 0.06+0.01*randn(1)
d[5] = 0.06+0.01*randn(1)
d[6] = 0.03+0.005*randn(1)
r = integrate.odeint(myc_rb_e2f,y0,t,args=(k,d))
E_simulated[:,i] = r[:,1]
for i in range(0,10000):
E_avg[i] = sum(E_simulated[i,:])/5000.
pl.plot(t,E_avg,'-ro')
pl.show()
我在尝试编译时遇到了很多错误:
Error compiling Cython file:
------------------------------------------------------------
...
dy = [dM,dE,dCD,dCE,dR,dRP,dRE]
return dy
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:48:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:52:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:53:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:54:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:55:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:56:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:57:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:1:0: Buffer vars not allowed in module scope
An exception has occurred, use %tb to see the full traceback.
SystemExit: error: command 'gcc' failed with exit status 1
%run setup.py build_ext --inplace
running build_ext
cythoning myc_rb_e2f_pyx.pyx to myc_rb_e2f_pyx.c
building 'myc_rb_e2f_pyx' extension
C:\Python27\Scripts\gcc.exe -mno-cygwin -mdll -O -Wall -DMS_WIN64 -IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -c myc_rb_e2f_pyx.c -o build\temp.win-amd64-2.7\Release\myc_rb_e2f_pyx.o
Error compiling Cython file:
------------------------------------------------------------
...
dy = [dM,dE,dCD,dCE,dR,dRP,dRE]
return dy
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:48:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:52:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:53:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
t = np.linspace(0.,3000.,10000.)
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:54:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:55:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:56:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:57:31: Buffer types only allowed as function local variables
Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
^
------------------------------------------------------------
myc_rb_e2f_pyx.pyx:1:0: Buffer vars not allowed in module scope
An exception has occurred, use %tb to see the full traceback.
SystemExit: error: command 'gcc' failed with exit status 1
任何人都可以帮助我解决我在声明数组时出错的地方吗？
请您参考如下方法:
错误信息很清楚:缓冲区类型的变量在顶层是不允许的。将所有从 t 的声明开始的代码放在一个函数中，比如说 main，然后调用它。
