[Numpy-discussion] numarray speed problem

Humufr humufr at yahoo.fr
Tue Sep 20 08:45:01 CDT 2005


Hello,

I have a problem with numarray and especially the function numarray.all.

I want to compare two files to do this I read the files with a function 
readcol2 who can put them in a list or numarray format (string or 
numerical).

I'm doing a comparaison on each line of the file.
If I'm using the array format and the numarray.all function, that take 
forever to do the comparaison for 2 big files. If I'm using python list 
object, it's very fast. I think there are some problem or at least some 
improvement to do. If I understand correctly the goal of numarray, it 
has been write to speed up some part of python but here it slow down a lot.

An very simple sample to see the effect is at the bottom of this mail.

Thanks for numarray, I hope to not bother you. My comments are more to 
improve numarray than other things. I have been able to find the problem 
so no I can avoied it.

H.




def 
readcol(fname,comments='%',columns=None,delimiter=None,dep=0,arraytype='list'):
    """
    Load ASCII data from fname into an array and return the array.
   
    The data must be regular, same number of values in every row
   
    fname can be a filename or a file handle.
   

    Input:

    - Fname : the name of the file to read

    Optionnal input:
   
    - comments : a string to indicate the charactor to delimit the domments.
   
                 the default is the matlab character '%'.
   
    - columns : list or tuple ho contains the columns to use.
   
    - delimiter : a string to delimit the columns

    - dep : an integer to indicate from which line you want to begin

            to use the file (useful to avoid the descriptions lines)

    - arraytype : a string to indicate which kind of array you want ot
   
                  have: numeric array (numeric) or character array 
(numstring) or list (list). By default it's the

                  list mode used
         
         

    matfile data is not currently supported, but see
    Nigel Wade's matfile ftp://ion.le.ac.uk/matfile/matfile.tar.gz

    Example usage:

    x,y = transpose(readcol('test.dat'))  # data in two columns

    X = readcol('test.dat')    # a matrix of data

    x = readcol('test.dat')    # a single column of data

    x = readcol('test.dat,'#') # the character use like a comment 
delimiter is '#'

    initial function from pylab (J.Hunter). Change by myself for my 
specific need

    """
    from numarray import array,transpose

    fh = file(fname)

    X = []
    numCols = None
    nline = 0
    if columns is None:
        for line in fh:
            nline += 1
            if dep is not None and nline <= dep: continue
            line = line[:line.find(comments)].strip()
            if not len(line): continue
            if arraytype=='numeric':
                row = [float(val) for val in line.split(delimiter)]
            else:
                row = [val.strip() for val in line.split(delimiter)]
            thisLen = len(row)
            if numCols is not None and thisLen != numCols:
                raise ValueError('All rows must have the same number of 
columns')
            X.append(row)
    else:
        for line in fh:
            nline +=1
            if dep is not None and nline <= dep: continue
            line = line[:line.find(comments)].strip()
            if not len(line): continue
            row = line.split(delimiter)
            if arraytype=='numeric':
                row = [float(row[i-1]) for i in columns]
            elif arraytype=='numstring':
                row = [row[i-1].strip() for i in columns]
            else:
                row = [row[i-1].strip() for i in columns]
            thisLen = len(row)
       
            if numCols is not None and thisLen != numCols:
                raise ValueError('All rows must have the same number of 
columns')
            X.append(row)

    if arraytype=='numeric':
        X = array(X)
        r,c = X.shape
        if r==1 or c==1:
            X.shape = max([r,c]),
    elif arraytype == 'numstring':
        import numarray.strings               # pb if numeric+pylab
        X = numarray.strings.array(X)
        r,c = X.shape
        if r==1 or c==1:
            X.shape = max([r,c]),
       
    return X


-------------------------------------------
files_test_creation.py

-------------------------------------------

f1 = file('test1.dat','w')
for i in range(10000):
    f1.write(str(i)+'   '+str(i+1)+'   '+str(i+2)+'\n')
   
f1.close()


f2 = file('test2.dat','w')
for i in range(10000):
    f2.write(str(i)+'   '+str(i+1)+'   '+str(i+2)+'\n')
   
f2.close()

-------------------------------------------
numarray_pb_sample.py

-------------------------------------------

import numarray
data1 = 
readcol2.readcol('test1.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='numstring')
data2 = 
readcol2.readcol('test2.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='numstring')

#or in non string array form  (same result)
## data1 = 
readcol2.readcol('test1.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='numeric')
## data2 = 
readcol2.readcol('test2.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='numeric')

for a_i in range(data1.shape[0]):
    for b_i in range(data2.shape[0]):
        if numarray.all(data1[a_i,:] == data2[b_i,:]):
            print a_i,b_i

-------------------------------------------
python_list_sample.py

-------------------------------------------

data1 = 
readcol2.readcol('test1.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='list')
data2 = 
readcol2.readcol('test2.dat',columns=[1,2,3],comments='#',delimiter='  
',dep=1,arraytype='list')

for a_i in range(len(data1)):
    for b_i in  range(len(data2)):
        if data1[a_i] == data2[b_i]:
            print a_i,b_i


 





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