[Numpy-discussion] loadtxt and missing values

[Sean Arms]

Keith Goodman wrote:
> On Thu, Mar 6, 2008 at 12:36 PM,  <caver_sean at ou.edu> wrote:
>
>   
>>  Proposed solution:
>>  -------------------------
>>
>>  It's probably not the best way (noob, that's me), but this situation could be fixed by:
>>
>>  1) add a fill keyword to loadtxt such that
>>
>>  def loadtxt(...,fill=-999):
>>
>>  2) add the following after the line "vals = line.split(delimiter)" (line 713 in core/numeric.py , numpy 1.0.4)
>>
>>  ======================
>>        for j in range(0,len(vals)):
>>            if vals[j] != '':
>>                pass
>>            else:
>>                vals[j]=fill
>>  ======================
>>
>>
>>  Testing: -------------------------
>>
>>  Load an 18,000 line ascii dataset, 22 float variables on each line, skipping the first column (its a time stamp).
>>
>>  Timings using %timeit in ipython:
>>
>>  Reading an ascii file with no missing values using the current version of loadtxt:
>>  ***10 loops, best of 3: 704 ms per loop
>>
>>  Reading an ascii file with no missing values using the proposed changes to loadtxt:
>>  ***10 loops, best of 3: 802 ms per loop
>>
>>  The changes do create a slight performance hit for those who use loadtxt to read in nicely behaving ascii data.  If this is an issue, could a loadtxt2 function be added?
>>     
>
> I haven't used loadtxt so I don't have an opinion on changing it. But
> would this be faster instead of a for loop?
>
> vals = [(z, fill)[z is ''] for z in vals]
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>   
Your suggestion appears to be about 2 ms faster (but still ~100 ms 
slower than the unaltered loadtxt).