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
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_______________________________________________
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
