code conversion from matlab to python

Question

I am converting matlab file to python code. my matlab file is :

function [q,len] = curve_to_q(p)

[n,N] = size(p);
for i = 1:n
    v(i,:) = gradient(p(i,:),1/(N)); 
end

len = sum(sqrt(sum(v.*v)))/N;
v = v/len;
for i = 1:N
    L(i) = sqrt(norm(v(:,i)));
    if L(i) > 0.0001
        q(:,i) = v(:,i)/L(i);
    else
        q(:,i) = v(:,i)*0.0001;
    end
end

converted code is :

from __future__ import division
import numpy as np
from scipy.io import loadmat,savemat
import os

def curve_to_q(p):
    n, N = p.shape # nargout=2
    for i in range(1, (n +1)):
        v[(i -1), :] = np.gradient(p[(i -1), :], 1 / (N))
    len_ = np.sum(np.sqrt(np.sum(v.np.dot(v)))) / N
    v = v / len_
    for i in range(1, (N +1)):
        L[(i -1)] = sqrt(norm(v[:, (i -1)]))
        if L[(i -1)] > 0.0001:
            q[:, (i -1)] = v[:, (i -1)] / L[(i -1)]
        else:
            q[:, (i -1)] = v[:, (i -1)] * 0.0001
    return q, len_

But, there seems to be problem in

len_ = np.sum(np.sqrt(np.sum(v.np.dot(v)))) / N

and

L[(i -1)] = sqrt(norm(v[:, (i -1)]))

how can i make it proper conversion to python?

First off, you don't define initialize v anywhere in curve_to_q, which could be causing problems. Same for L. If v is an array, you should be using *, not np.dot, and if v is a matrix, you should be using np.multiply (because you want .*, which is elementwise multiplication, not matrix multiplication). — senshin
– senshin, Commented Jan 9, 2014 at 7:49
@ShinTakezou : I do not able to understand that how np.sum(v.np.dot(v))) will work in python? — sam
– sam, Commented Jan 9, 2014 at 8:46

Luke · Accepted Answer · 2014-01-09 12:37:10Z

Working with numpy, it is better to initialise all arrays as numpy arrays rather than python arrays (lists of lists) and then converting to numpy at the time of execution. So for the first step I'd put in v = np.zeros(n, N) to initialise. This should fix your second problem.

The next step is to make your code more readable. Remove N+1/i-1, etc. L doesn't need to be a list - only the current value is ever used, so change it to a local variable rather than a list.

In matlab: v.*v is not the dot product, it is the element by element multiplication of the two arrays. Further, when you try to take the dot product of v with itself, v is not square, so it won't work. However, we can use the dot product with the transpose to simplify this step.

The code below should help. The first sum in the matlab code sums across the 'first array dimension' (I forget which one this is) - so you'll have to check that v_squared_sum has the same dimensions in both languages.

def curve_to_q(p):
    n, N = p.shape # nargout=2
    v = np.zeros((n, N))
    for i in range(n):
        v[i, :] = np.gradient(p[i, :], 1 / N)
    v_squared_sum = v.dot(v.transpose()) # 1 x (n or N) array
    len_ = np.sum(np.sqrt(v_squared_sum)) / N
    v = v / len_
    for i in range(N):
        L = sqrt(norm(v[:, i]))
            q[:, i] = v[:, i] / max(L, 0.0001)
    return q, len_

TheBlackCat · Accepted Answer · 2015-02-05 09:52:48Z

0

Your first problem is that in Matlab, sum sums over the last dimension by default, while in numpy, np.sum sums over the flattened array by default.

Matlab

>> sum([5,5,5;5,5,5])
ans = 
    10 10 10

Python:

>>> np.sum([[5,5,5],[5,5,5]])
30

You would need something like this in python:

>>> np.sum([[5,5,5],[5,5,5]], axis=0)
array([10, 10, 10])

The second problem is that you need np.sqrt and np.norm, not sqrt and norm.

answered Feb 5, 2015 at 9:52

TheBlackCat

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