Script to convert Matlab slices and index to numpy array notation

Question

I am porting some Matlab code to Python. In this code there are many instances of a large matrix being sliced in many different ways, eg M(2:45,13:18), M(:12,:), V(4), V(:27), etc. It is technically possible to convert this to numpy notation manually, by replacing the parentheses with square brackets and substracting 1 to all indices (except after :) but it is incredibly tedious and there is a very high probability that I will make a typo at some point.

I tried automating this but my grep/awk/parsing skills are not good enough. Is there a script out there that will do the job?

While basic indexing is similar enough, indexing with lists/arrays, what numpy docs call advanced indexing is different. You have to use np.ix_ to get similar 'block' indexing. — hpaulj
– hpaulj, Commented Oct 8, 2022 at 15:55
Cris Luengo: noted, but whether the input Matlab is valid is not really my issue to solve. I'm confident that my actual inputs will be valid, and I was just wondering hoe to automate the conversion. Thanks anyway. — Mathieu
– Mathieu, Commented Oct 9, 2022 at 18:04
Still, it makes no sense to translate V(:27) because it means nothing in MATLAB. — Cris Luengo
– Cris Luengo, Commented Oct 9, 2022 at 21:07

PlainRavioli · Accepted Answer · 2022-10-09 23:41:01Z

1

Assuming you have your matlab code in a string, you can format it in Python. You could do this with regex match replacement:

import re

def format_indexers(match):
    # Format any "(x:y:z)" into python format
    ret = match[0].replace("(", "[").replace(")", "]") # replace brackets
    ret = re.sub(r"(\[|,)(\d+)", lambda x: x[1] +  str(int(x[2]) - 1) , ret) # replaces numbers by decremented ones
    return ret    

s = "M(2:45,13:18), M(:12,:), V(4), V(:27)"

# Searches expressions between parenthesis and apply format_indexers to found matches
re.sub(r"\(.*\)", format_indexers, s)

outputs:

'M[1:45,12:18], M[:12,:], V[3], V[:27]'

edited Oct 9, 2022 at 23:41

answered Oct 8, 2022 at 13:07

PlainRavioli

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6 Comments

Mathieu Over a year ago

Thanks, I'll look into it. But note that M(2:45) should become M[1:45], since Matlab slices are end-inclusive.

PlainRavioli Over a year ago

Oh right I misunderstood the "except after :" part

Mathieu Over a year ago

Based on your example I got something working (see my new comment). What is the correct etiquette? Should I accept your answer and leave mine, or accept mine and upvote yours? Not sure what is called for. Thanks anyway.

PlainRavioli Over a year ago

I don't know in this case ahah, but your output is the same as me now, isn't it ?

Mathieu Over a year ago

My bad, I hadn't realized that you edited your original answer. Thanks again.

|

Mathieu · Accepted Answer · 2022-10-09 20:51:08Z

0

Here is another take based on PlainRavioli's original answer:

INPUT = 'M(2:45,13:18) M(:12,:) V(4) V(:27)'

import re

def my_replace(m):
    m = m.group()
    a, m = m[0], m[2:-1]
    m = m.split(',')
    for k in range(len(m)):
        if ':' in m[k]:
            m[k] = m[k].split(':')
            if m[k][0]:
                m[k][0] = str(int(m[k][0])-1)
            m[k] = ':'.join(m[k])
        else:
            m[k] = str(int(m[k])-1)
    m = ','.join(m)
    m = a + '[' + m + ']'
    return m

OUT = re.sub('\\w\\(\d*:?\d*(,\d*:?\d*)?\\)', my_replace, INPUT)
    
print(OUT)
# yields:  M[1:45,12:18] M[:12,:] V[3] V[:27]

edited Oct 9, 2022 at 20:51

answered Oct 9, 2022 at 18:01

Mathieu

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1 Comment

Cris Luengo Over a year ago

You’d have to look for end in indexing and translate that correctly too. Some indexing doesn’t translate at all, for example a(end+1)=1 you can’t do in Python. And special indexing would be translated wrong with this program, a([1,2,3],[3,5,2]) does something very different from the similar-looking Python code. Be careful!

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