[Numpy-discussion] np.genfromtxt StopIteration Error

[Bennet Fauber]

What happens if you use this?

for txtfile in filesList:
    data = np.genfromtxt(txtfile, dtype=str, usecols=(1),
        skip_header=27, skip_footer=1, encoding=None)
print(data)

That pulls one file name from filesList, stuffs the name into txtfile,
which is then provided to genfromtxt().

The point is that genfromtxt() wants one thing; you have to give it
one thing.  The above gives it one thing, but runs it for however many
things are in the filesList.

Does that help?

On Fri, Oct 11, 2019 at 2:41 PM Stephen P. Molnar
<s.molnar at sbcglobal.net> wrote:
>
> 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
> >>
> >> _______________________________________________
> >> NumPy-Discussion mailing list
> >> NumPy-Discussion at python.org
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> >
>
> --
> Stephen P. Molnar, Ph.D.
> www.molecular-modeling.net
> 614.312.7528 (c)
> Skype:  smolnar1
>
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