[Numpy-discussion] fast method to to count a particular value in a large matrix

Benjamin Root ben.root@ou....
Sat Feb 4 14:35:08 CST 2012

On Saturday, February 4, 2012, Naresh Pai <npai@uark.edu> wrote:
> I am somewhat new to Python (been coding with Matlab mostly). I am trying
> simplify (and expedite) a piece of code that is currently a bottleneck in
a larger
> code.
> I have a large array (7000 rows x 4500 columns) titled say, abc, and I am
> to find a fast method to count the number of instances of each unique
value within
> it. All unique values are stored in a variable, say, unique_elem. My
current code
> is as follows:
> import numpy as np
> #allocate space for storing element count
> elem_count = zeros((len(unique_elem),1))
> #loop through and count number of unique_elem
> for i in range(len(unique_elem)):
>    elem_count[i]= np.sum(reduce(np.logical_or,(abc== x for x
in [unique_elem[i]])))
> This loop is bottleneck because I have about 850 unique elements and it
> about 9-10 minutes. Can you suggest a faster way to do this?
> Thank you,
> Naresh

no.unique() can return indices and reverse indices.  It would be trivial to
histogram the reverse indices using np.histogram().

Does that help?

Ben Root
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