Some cython model for my research

dmask.pyx

import cython 
import numpy
#cimport numpy
cimport cython
from libc.math cimport exp, sqrt
from cython.view cimport array as cvarray
 
 
@cython.cdivision(True)
cdef inline double dgauss(double radius, double x, double spread):
    return exp(-1.0*(x-radius)**2/spread)

@cython.boundscheck(False)
@cython.wraparound(False)
cdef double dist(double[:] a , double[:] b):
    cdef double r = sqrt(
               (a[0]-b[0])**2 +
               (a[1]-b[1])**2 +
               (a[2]-b[2])**2
              )
    return r

@cython.boundscheck(False)
@cython.wraparound(False)
def makemask(double z0, double y0, double x0, double r0, double[:,:,:,:] posmap, double spread=50, outf=0,inf=0 ):
    """
        makemask(double z0, double y0, double x0, double r0, double[:,:,:,:] posmap, double spread=50, outf=0, inf=0)

        where posmap in an array of center of pixel in micro m
        outf is outside fluorescence
    """


    cdef :
        double[:] center = numpy.array([x0,y0,z0])
        double[:] cp
        int zl,yl,xl
        int ix,iy,iz
        double d
        double[:,:,:] iny
        double[:,:] inx
    zl,yl,xl,_ = numpy.shape(posmap)
    cdef :
        double [:,:,:] ze = numpy.zeros((zl,yl,xl))
        int i,zz
        int j
    for iz in range(zl):
        iny = posmap[iz]
        for iy in range(yl):
            inx = iny[iy]
            for ix in range(xl):
                cp = inx[ix]
                d= dist(cp,center)
                of = 0.0
                if d>r0 :
                    of = inf
                else :
                    of = outf
                ze[iz,iy,ix] = 1-dgauss(r0,d,spread)+of
    return numpy.array(ze)

@cython.boundscheck(False)
@cython.wraparound(False)
def makemask_doublet1(double z0, double y0, double x0, double r0, double[:,:,:,:] posmap, double thick=10, ):
    cdef :
        double[:] center = numpy.array([x0,y0,z0])
        int zl,yl,xl
        int ix,iy,iz
        double Rp = r0+thick
        double Rm = r0
        
    zl,yl,xl,_ = numpy.shape(posmap)
    cdef :
        double [:,:,:] ze = numpy.zeros((zl,yl,xl))
        int i,zz
        int j
    for iz in range(zl): 
        for iy in range(yl):
            for ix in range(xl):
                d= dist(posmap[iz,iy,ix],center)
                if d < Rp :
                    ze[iz,iy,ix] = 1
                if d < Rm :
                    ze[iz,iy,ix] = 0
    return numpy.array(ze)

@cython.boundscheck(False)
@cython.wraparound(False)
def makemask_doublet2(double z0, double y0, double x0, double r0,double z1, double y1, double x1, double r1, double[:,:,:,:] posmap, double thick=10, ):
    cdef :
        double[:] center1 = numpy.array([x0,y0,z0])
        double[:] center2 = numpy.array([x1,y1,z1])
        int zl,yl,xl
        int ix,iy,iz
        double Rp1 = r0+thick
        double Rm1 = r0
        double Rp2 = r1+thick
        double Rm2 = r1
        
    zl,yl,xl,_ = numpy.shape(posmap)
    cdef :
        double [:,:,:] ze = numpy.zeros((zl,yl,xl))
        int i,zz
        int j
    for iz in range(zl): 
        for iy in range(yl):
            for ix in range(xl):
                d1= dist(posmap[iz,iy,ix],center1)
                d2= dist(posmap[iz,iy,ix],center2)
                if d1 < Rp1 or d2< Rp2:
                    ze[iz,iy,ix] = 1
                if d1 < Rm1 or d2 < Rm2 :
                    ze[iz,iy,ix] = 0
    return numpy.array(ze)