trjhtr

I need to benchmark a code in cython for which I have written a code to find the centroid of 1000 simulated Gaussian images. When executed, it takes 1.58 seconds to run. But when I wrote a pure python code even it took around 1.5 seconds for execution.

Yes, I have made use of numpy modules in both. Could someone please take a look at the cython code? how can I improve the speed of the cython code?

from scipy.interpolate import UnivariateSpline
import matplotlib.pyplot as plt
import pylab as pl
import random
import math
import time
cimport cython
import numpy as np
@cython.boundscheck(False)
@cython.wraparound(False)
def gaussian_2D_distribution(x,y,int mean_x,int mean_y,double sigma):
 #cdef double[:,:]f
 f = np.exp((-0.5*(np.square(x-mean_x) + np.square(y-mean_y))/sigma))/(sigma*np.sqrt(2*math.pi));
 return f

def Centroid2(x,y,f):
 temp_x = np.multiply(x,f)
 temp_y = np.multiply(y,f)
 X_c = (temp_x.sum()/f.sum());
 Y_c = -((temp_y.sum()/f.sum())+1);
 return(X_c,Y_c);

@cython.boundscheck(False)
@cython.wraparound(False)
def benchmark_func(int no_of_frames):
 cdef:
 int i
 double start
 double end
 #int shift[10000][2]
 double Centroid[10000][2]
 #---------------------------------------------Creating Matrices--------------------------------------------------------#
 start = time.time()
 a = np.arange(-50,50,1);
 x = np.matlib.repmat(a,100 ,1);
 y = x.transpose();
 f = np.zeros([no_of_frames,100,100])

 print "Done stage 1 ..."
 #---------------------------------------Creating Gaussian Images------------------------------------------------------#
 shift = np.zeros([no_of_frames,2])
 shift[:,0] = 15
 shift[:,1] = 25

 for i in range(int (no_of_frames)):
 #shift[i][0] = random.randint(-50,50)
 #shift[i][1] = random.randint(-50,50)
 f[i,:,:] = gaussian_2D_distribution(x,y,shift[i][0],shift[i][1],0.1)
 f[i,:,:]= np.flip(f[i,:,:],0)

 print "Done stage 2 ..."
 #---------------------------------------To find the centroid----------------------------------------------------------#

 #start = time.time()
 for i in range(int (no_of_frames)):
 Centroid[i][:] = Centroid2(x,y,f[i])
 end = time.time()

 #print Centroid[2]
 print(end - start),
 print "seconds"
 print "Done stage 3 ..."
 return Centroid