[Numpy-discussion] np.genfromtxt StopIteration Error

[Stephen P. Molnar]

Thanks for the reply.

Keep in mind that i am a Chemist, not an IT person. I used to be a 
marginally proficient FORTRAN II user in the ancient past.

I tried running your code. Please see my comments/questing below:

On 10/11/2019 01:12 PM, Bennet Fauber wrote:
> I think genfromtxt() wants a filename as the first argument, and you
> have to tell it the entries in the file are strings not numerics.
>
> test.py
> ------------------------------------------
> import os
> import glob
> import numpy as np
>
> fileList = []
> filesList = []
>
> for files in glob.glob("*.log"):
>      fileName, fileExtension = os.path.splitext(files)
>      fileList.append(fileName)
>      filesList.append(files)
>
> print('fileList = ', fileList)
> print('filesList = ', filesList
>
> fname = '/tmp/foo.txt'
There is no '/temp/foo.txt' Where did it come from in your example?
> print('fname = ', fname)
> data = np.genfromtxt(fname, dtype=str)
> print(data)
> ------------------------------------------
>
> Contents of /tmp/foo.txt
> ------------------------------------------
> 15-7.log
> 18-7.log
> 14-7.log
> C-VX3.log
> ------------------------------------------
>
> Sample run
I'm using python 3.7.3, should this make a difference?
>
> $ python --version
> Python 2.7.15+
>
> $ python t.py
> ('fileList = ', ['15-7', '18-7', '14-7', 'C-VX3'])
> ('filesList = ', ['15-7.log', '18-7.log', '14-7.log', 'C-VX3.log'])
> ('fname = ', '/tmp/foo.txt')
> ['15-7.log' '18-7.log' '14-7.log' 'C-VX3.log']
>
> Is that any help?
if I use data = np.genfromtxt('14-7.log', dtype=str, usecols=(1), 
skip_header=27, skip_footer=1, encoding=None) with a specific file name. 
in this example 14-7, I get the resutt I desired:

# 14-7
-9.960902669
-8.979504781
-8.942611364
-8.915523010
-8.736508831
-8.663387139
-8.410739711
-8.389146347
-8.296798909
-8.168454106
-8.127990818
-8.127103774
-7.979090739
-7.941872682
-7.900766215
-7.881485228
-7.837826485
-7.815909505
-7.722540286
-7.720346742

so, my question is; why the StopIteration error message in my original 
query? Why is the dcrtipt not iterating over the log files?

Sorry to be so dense.


>
> On Fri, Oct 11, 2019 at 12:41 PM Stephen P. Molnar
> <s.molnar at sbcglobal.net> wrote:
>> I have been fighting with the genfromtxt function in numpy for a while now and am trying a slightly different approach.
>>
>> Here is the code:
>>
>>
>> import os
>> import glob
>> import numpy as np
>>
>> fileList = []
>> filesList = []
>>
>> for files in glob.glob("*.log"):
>> ?????? fileName, fileExtension = os.path.splitext(files)
>> ?????? fileList.append(fileName)
>> ?????? filesList.append(files)
>>
>> print('fileList = ', fileList)
>> print('filesList = ', filesList)
>>
>> fname = filesList
>> print('fname = ', fname)
>> data = np.genfromtxt(fname, usecols=(1), skip_header=27, skip_footer=1, encoding=None)
>> print(data)
>>
>> np.savetxt('fileList.dG', data, fmt='%12.9f', header='${d}')
>> print(data.dG)
>>
>> I am using the Spyder IDE which has a variable explorer which shows:
>>
>> filesList = ['C-VX3.log', '18-7.log', '14-7.log', '15-7.log']
>> fileList = ['C-VX3', '18-7', '14-7', '15-7']
>>
>> so the lists that genfromtxt needs are being generated.
>>
>> Goggling 'numpy genfromtxt stopiteration error' does not seem to address this problem. At least, I didn't find plaything that I thought applied.
>>
>> I would greatly appreciate some assistance here.
>>
>> Thanks is advance.
>>
>> --
>> Stephen P. Molnar, Ph.D.
>> www.molecular-modeling.net
>> 614.312.7528 (c)
>> Skype:  smolnar1
>>
>> _______________________________________________
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-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1