[SciPy-user] Array selection help

Jose Luis Gomez Dans josegomez@gmx....
Tue Feb 10 15:36:00 CST 2009

Let's say I have two 2D arrays, arr1 and arr2. The elements of arr1 contain 
different numbers (such as labels, for example), and the elements of arr2 
contain some floating point data (say, height above sea level or something 
like that). For each unique value in arr1, I want to work out the mean (... 
sum, std dev, etc) of arr2 for the overlapping region. So far, I have used 
the following code:
#Get all the unique values in arr1
U = numpy.unique ( arr1 )
#Create a dictionary with the unique values as key, and the 
#locations of elements that have that value in arr1
R =  dict (zip ( [U[i] for i in xrange(U.shape[0])], \
[ numpy.nonzero( arr1==U[i]) for i in xrange(U.shape[0]) ] ) )
#Now, calculate the eg mean of arr2 per arr1 "label"
M = dict ( zip ( R.keys(), [ numpy.mean(arr2[R[i]]) for i in R.keys() ] ) )
# So I now have a dictionary with the unique values of arr1, and the mean
# value of arr2 for those pixels.

The code is fast and I was feeling rather smug and pleased with myself about 
it :) However, when numpy.unique( arr1 ) increases, 
[ numpy.nonzero( arr1==U[i]) for i in xrange(U.shape[0]) ]  starts taking a 
long time (understandable, there are loads and loads of operations in that 
loop). At present, I can easily have numpy.unique ( arr1).shape[0] > 10000, 
so it does take a long time. 

Apart from looping through different values of arr1, can anyone think of an 
efficient way of achieving something similar to this? It doesn't have to be a 
dictionary as the output, an array or something else would do nicely. 


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