Looking for suggestions on improving numpy code
robert.kern at gmail.com
Mon Feb 25 18:11:33 CET 2008
David Lees wrote:
> I am starting to use numpy and have written a hack for reading in a
> large data set that has 8 columns and millions of rows. I want to read
> and process a single column. I have written the very ugly hack below,
> but am sure there is a more efficient and pythonic way to do this. The
> file is too big to read by brute force and select a column, so it is
> read in chunks and the column selected. Things I don't like in the code:
> 1. Performing a transpose on a large array
Transposition is trivially fast in numpy. It does not copy any memory.
> 2. Uncertainty about numpy append efficiency
Rest assured that it's slow. Appending to lists is fast since lists preallocate
memory according to a scheme such that the amortized cost of appending elements
is O(1). We don't quite have that luxury in numpy.
> Is there a way to directly read every n'th element from the file into an
Since this is a regular binary file, you can memory map the file.
M = 1000000
N = 8
column = 2
m = numpy.memmap('testcase.bin', dtype=numpy.int16, shape=(M,N))
z = m[:,column] * sf
You may want to ask future numpy questions on the numpy mailing list.
"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco
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