[AstroPy] question on matplotlib's loadtxt

Grigoris Maravelias gr.maravelias@gmail....
Fri Nov 4 11:19:41 CDT 2011


Hello!

I forgot to mention that I call this through a script ...

If I use this:
x, y, z = numpy.loadtxt('test.test', unpack=True,usecols=(0,1,3))

without specifying dtype (as float are default) it works.

But if I try to use it then it fails:

In [7]: dt = dtype({'names':['n1','n2','n3'],'formats':[float,float,float]})

In [8]: x, y, z = loadtxt('test.test', unpack=True, usecols=(0,1,2) , 
dtype=dt)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/home/.../<ipython console> in <module>()

ValueError: too many values to unpack


And I get the same even for 2 variables (as Erin's proposal without the 
strings):

In [23]: s,d = 
loadtxt('test.test',unpack=True,dtype=[('x','f8'),('y','f8')], 
usecols=[0,1])
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)

/home/.../<ipython console> in <module>()

ValueError: too many values to unpack



Derek, I checked the version of numpy and it is 1.3.0 - So I suppose it 
should be due to the version only?



Regards

Grigoris


On 11/04/2011 05:35 PM, Erin Sheldon wrote:
> This is the proper syntax, and works for me on your file:
>
>    loadtxt('tmp/test.txt',dtype=[('x','f8'),('s','S5')], usecols=[0,5])
>
> You need to give a proper dtype with full field description.
>
> -e
>
> On Fri, Nov 4, 2011 at 11:14 AM, Derek Homeier
> <derek@astro.physik.uni-goettingen.de>  wrote:
>> Hi Grigoris,
>>
>>> Hello to all!  I would like to ask about an error I face with
>>> matplotlib's loadtxt...
>>>
>>> Suppose that we have a file (called "test.test") with 6 columns like:
>>>
>>> 1496548.  862.235400937  14.008  0  20110523.201416  tth*g
>>> 1690289.  919.424007603  13.875  0  20110523.221527  hgf4
>>> 1667241.  996.262754039  13.890  0  20110524.001639  nb.mj
>>> 739181.6  881.1753527  14.774  0  20110524.010203  vbfhg
>>>
>>> When I use
>>> x, y = loadtxt('test.test', unpack=True, usecols=(0,1), dtype=(float,float))
>>>
>>> it prints normally the first and second column.
>>> If I add another column like:
>>>
>>> x, y, z = loadtxt('test.test', unpack=True,usecols=(0,1,3),
>>> dtype=(float,float,float))
>>>
>>> the output is this:
>>>    File "/usr/lib/python2.7/site-packages/numpy/lib/io.py", line 584, in
>>> loadtxt
>>>      dtype = np.dtype(dtype)
>>> TypeError: data type not understood
>>>
>> I don't quit understand that part, I admit - dtype only takes a single type or pairs of names and
>> types, so it would seem the first case actually only worked by accident:
>>
>> In [193]: np.dtype((float,float))
>> Out[193]: dtype('float64')
>>
>> I have no idea how it interprets the second float, but as you see it has no effect anyway.
>> You could in fact get the same result with 'usecols=[0,1,3], dtype=float'
>> which will simply apply the dtype to all columns (and is the default already...).
>>> Even if I use a dictionary, like:
>>> dt = dtype({'names':['n1','n2','n3'],'formats':[float,float,float]})
>>> x, y, z = loadtxt('test.test', unpack=True, usecols=(0,1,2) , dtype=dt)
>>>
>>> the output is the same as previous.
>>>
>> No things are getting strange - the above is the correct (and I think, only) way to
>> define dtypes with different formats -
>> np.dtype([('n1',float),('n2',float),('n3',float)])
>> would be equivalent. As there is no error on the first line (i.e., dt is a valid dtype),
>> this seems to be a bug in loadtxt. Could you check what happens if you try the
>> above without the 'unpack' option? Should return a structured array with the 3
>> fields 'n1','n2','n3'...
>> Also (as loadtxt is actually part of numpy), which is your installed version of numpy
>> (numpy.__version__ or np.__version__, you may have to re-import it as pylab
>> unfortunately imports everything into one namespace). I recall that there have
>> been issues with unpacking structured arrays prior to 1.6 or 1.6.1.
>>
>>> Additionaly, when I am trying to load the last column as strings:
>>> x, y = loadtxt('test.test', delimiter='  ', unpack=True,usecols=(0,5),
>>> dtype=(float,'S5'))
>>>
>>> I get this error:
>>>    File "/usr/lib/python2.7/site-packages/numpy/lib/io.py", line 584, in
>>> loadtxt
>>>      dtype = np.dtype(dtype)
>>> ValueError: mismatch in size of old and new data-descriptor
>>>
>>>
>>> What am I doing wrong ? I am sorry if it is something really obvious ...
>>> but I am unable to find it...
>> Similar problem - this ought to work with dtype=[('n1', 'f'), ('n6','S5')] ; but it might
>> be broken in the same way as above - if you can update to numpy 1.6.x, you
>> should hopefully be set.
>>
>> HTH,
>>                                                 Derek
>>
>>
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>
>


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