Hi Stephen, Is this not what your original question to this list was about? See https://mail.python.org/pipermail/numpy-discussion/2019-October/080130.html and replies. I still believe that you _can't_ give genfromtxt file names in an iterable. The iterable input is only inteded to contain the contents of a single file, probably as if read using `f.readlines()`. Genfromtxt seems to read data from at most one file with each call. Regards,
AndrĂ¡s On Fri, Oct 11, 2019 at 8:41 PM Stephen P. Molnar <s.mol...@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.mol...@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@python.org > >> https://mail.python.org/mailman/listinfo/numpy-discussion > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion@python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > > > > -- > Stephen P. Molnar, Ph.D. > www.molecular-modeling.net > 614.312.7528 (c) > Skype: smolnar1 > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@python.org > https://mail.python.org/mailman/listinfo/numpy-discussion _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@python.org https://mail.python.org/mailman/listinfo/numpy-discussion