[Solved] Plotting data from txt file

Laplace12 · (This post was last modified: Jul-06-2021, 09:10 AM by Laplace12.)

Hey! I'm trying to plot a text file that looks like this:

#0      0.4000 0.1485 2.1926  Fixed  0.0195  0.0299  64.9854 11.2706 23.7440 1.4814  1.2203  0.3871  42.1810   0.0664                 
#1      0.4000 0.1457 2.1253  Fixed  0.0185  0.0288  63.7908 11.7439 24.4653 1.4802  1.2043  0.4036  42.2980   0.0670                 
#2      0.4000 0.1429 2.1903  Fixed  0.0189  0.0299  65.3086 11.0723 23.6191 1.4004  1.1423  0.3846  42.2350   0.0677                 
#3      0.4000 0.1369 2.1734  Fixed  0.0179  0.0293  64.8133 11.0524 24.1343 1.3254  1.0651  0.3870  42.2444   0.0694                 
#4      0.4000 0.1393 2.2184  Fixed  0.0216  0.0304  67.2157  9.3551 23.4292 1.3416  1.0907  0.3780  42.1653   0.0704                 
#5      0.4000 0.1494 2.1767  Fixed  0.0217  0.0299  65.9704 10.3180 23.7115 1.5089  1.2435  0.3917  42.1547   0.0674                 
#6      0.4000 0.1499 2.1952  Fixed  0.0213  0.0304  66.1049 10.5957 23.2994 1.5131  1.2522  0.3876  42.2199   0.0672                 
#7      0.4000 0.1238 2.1880  Fixed  0.0167  0.0296  66.2869 10.5109 23.2023 1.1445  0.9037  0.3707  42.2324   0.0725                 
#8      0.4000 0.1457 2.1814  Fixed  0.0222  0.0302  66.9152  9.7170 23.3678 1.4467  1.1857  0.3872  42.1238   0.0686                 
#9      0.4000 0.1309 2.1627  Fixed  0.0169  0.0296  65.1505 11.1807 23.6688 1.2464  0.9946  0.3815  42.3048   0.0711                 
#10     0.4000 0.1226 2.2090  Fixed  0.0169  0.0304  66.6621 10.3485 22.9894 1.1272  0.8923  0.3663  42.2965   0.0740                 
#11     0.4000 0.1382 2.1704  Fixed  0.0188  0.0298  66.2671 10.7010 23.0319 1.3362  1.0828  0.3812  42.2499   0.0690                 
#12     0.4000 0.1878 2.1110  Fixed  0.0240  0.0303  62.1355 13.6391 24.2254 2.4126  2.0972  0.4406  42.1389   0.0598                 
#13     0.4000 0.1619 2.1212  Fixed  0.0213  0.0301  64.2333 11.9293 23.8374 1.7699  1.4809  0.4146  42.2166   0.0641                 
#14     0.4000 0.1529 2.1428  Fixed  0.0190  0.0299  63.9508 12.1658 23.8833 1.5838  1.3072  0.4025  42.2055   0.0651                 
#15     0.4000 0.1456 2.1313  Fixed  0.0212  0.0296  66.0905 10.2328 23.6767 1.4652  1.1931  0.3987  42.1202   0.0685                 
#16     0.4000 0.1260 2.1505  Fixed  0.0190  0.0286  66.9064  9.4892 23.6044 1.1800  0.9331  0.3777  42.1801   0.0739                 
#17     0.4000 0.1515 2.0944  Fixed  0.0212  0.0289  65.4946 10.8854 23.6201 1.5739  1.2954  0.4055  42.1221   0.0668                 
#18     0.4000 0.1725 2.1762  Fixed  0.0234  0.0320  65.5772 11.9181 22.5047 1.9533  1.6754  0.4023  42.1257   0.0619                 
#19     0.4000 0.1285 2.1495  Fixed  0.0185  0.0301  67.2668  9.9654 22.7679 1.2102  0.9621  0.3777  42.2216   0.0724                 
#20     0.4000 0.1326 2.1352  Fixed  0.0188  0.0296  66.5970 10.2232 23.1798 1.2774  1.0217  0.3851  42.2026   0.0712                 
#21     0.4000 0.1691 2.0464  Fixed  0.0229  0.0301  64.5941 11.9354 23.4705 1.9505  1.6390  0.4356  42.1784   0.0626                 
#22     0.4000 0.1354 2.0646  Fixed  0.0179  0.0294  65.9501 11.0197 23.0302 1.3295  1.0600  0.3978  42.2522   0.0695                 
#23     0.4000 0.1483 2.1130  Fixed  0.0192  0.0307  65.6120 11.5982 22.7898 1.5075  1.2344  0.3991  42.2299   0.0666                 
#24     0.4000 0.1406 2.1284  Fixed  0.0194  0.0305  66.7009 10.6242 22.6749 1.3818  1.1187  0.3895  42.2534   0.0685                 
#25     0.4000 0.1729 2.1016  Fixed  0.0218  0.0303  63.6588 12.9516 23.3896 2.0011  1.7045  0.4209  42.1136   0.0614                 
#26     0.4000 0.1447 2.1227  Fixed  0.0199  0.0300  66.5484 10.7446 22.7070 1.4448  1.1773  0.3928  42.2082   0.0671                 
#27     0.4000 0.1366 2.1660  Fixed  0.0221  0.0305  68.5456  8.9745 22.4799 1.3101  1.0596  0.3790  42.1276   0.0709                 
#28     0.4000 0.1419 2.0774  Fixed  0.0190  0.0295  65.3285 11.0722 23.5993 1.4329  1.1526  0.4071  42.2543   0.0680                 
#29     0.4000 0.1461 2.0880  Fixed  0.0223  0.0293  66.8589  9.7719 23.3692 1.4844  1.2068  0.4041  42.1765   0.0684                 
#30     0.4000 0.1644 2.1231  Fixed  0.0223  0.0299  65.3076 11.5743 23.1181 1.7942  1.5126  0.4064  42.1303   0.0633                 
#31     0.4000 0.1411 2.1044  Fixed  0.0199  0.0300  67.0179 10.4432 22.5389 1.3901  1.1253  0.3918  42.1674   0.0688                 
#32     0.4000 0.1646 2.1427  Fixed  0.0251  0.0306  66.3990 10.3496 23.2514 1.8036  1.5215  0.4077  42.0829   0.0648                 
#33     0.4000 0.1589 2.1114  Fixed  0.0223  0.0304  66.1828 11.0755 22.7417 1.7011  1.4206  0.4060  42.1118   0.0649                 
#34     0.4000 0.1523 2.0527  Fixed  0.0218  0.0291  65.6313 10.7024 23.6663 1.6114  1.3211  0.4180  42.1892   0.0671                 
#35     0.4000 0.1522 2.1521  Fixed  0.0198  0.0305  65.4273 11.5670 23.0057 1.5576  1.2895  0.3936  42.2862   0.0650                 
#36     0.4000 0.1301 2.0665  Fixed  0.0188  0.0295  66.7894 10.0438 23.1668 1.2761  1.0041  0.3999  42.1965   0.0724                 
#37     0.4000 0.1285 2.1273  Fixed  0.0180  0.0299  67.1615 10.2937 22.5448 1.2168  0.9663  0.3806  42.2621   0.0726                 
#38     0.4000 0.1367 2.1016  Fixed  0.0195  0.0294  66.7871 10.2103 23.0025 1.3310  1.0664  0.3923  42.1630   0.0698                 
#39     0.4000 0.1958 2.0671  Fixed  0.0277  0.0317  63.9121 12.8755 23.2124 2.6789  2.3509  0.4535  42.0563   0.0588                 
#40     0.4000 0.1315 2.0868  Fixed  0.0186  0.0288  66.4101 10.2574 23.3325 1.2705  1.0084  0.3921  42.2757   0.0715                 
#41     0.4000 0.1653 2.0615  Fixed  0.0225  0.0304  65.4340 11.6680 22.8980 1.8472  1.5490  0.4227  42.1883   0.0635                 
#42     0.4000 0.1709 2.0562  Fixed  0.0215  0.0298  63.7508 12.9209 23.3284 1.9813  1.6762  0.4299  42.1492   0.0620                 
#43     0.4000 0.1347 2.1474  Fixed  0.0180  0.0300  66.1287 10.9189 22.9524 1.3008  1.0446  0.3841  42.2772   0.0700                 
#44     0.4000 0.1352 2.0543  Fixed  0.0178  0.0294  65.6570 11.1316 23.2114 1.3374  1.0626  0.4034  42.2764   0.0696                 
#45     0.4000 0.1642 2.0722  Fixed  0.0233  0.0307  66.0989 11.1780 22.7231 1.8240  1.5301  0.4190  42.1244   0.0640                 
#46     0.4000 0.1650 2.0688  Fixed  0.0235  0.0300  65.4304 11.1399 23.4297 1.8424  1.5452  0.4230  42.1477   0.0638                 
#47     0.4000 0.1549 2.0342  Fixed  0.0202  0.0292  64.6196 11.8704 23.5100 1.6630  1.3677  0.4222  42.2095   0.0653                 
#48     0.4000 0.1770 2.0805  Fixed  0.0253  0.0308  65.1282 11.6274 23.2445 2.1167  1.8093  0.4329  42.1227   0.0617                 
#49     0.4000 0.1734 2.0832  Fixed  0.0266  0.0307  65.9513 10.7070 23.3416 2.0332  1.7295  0.4289  42.0954   0.0627                 
#50     0.4000 0.1077 2.1400  Fixed  0.0162  0.0291  67.6514  9.4889 22.8597 0.9908  0.7600  0.3672  42.3381   0.0804                 
#51     0.4000 0.1151 2.1446  Fixed  0.0181  0.0299  68.1800  9.0882 22.7318 1.0691  0.8307  0.3735  42.2072   0.0784                 
#52     0.4000 0.1449 2.1191  Fixed  0.0202  0.0295  65.8096 10.6812 23.5092 1.4621  1.1885  0.3994  42.1852   0.0677                 
#53     0.4000 0.1452 2.1133  Fixed  0.0229  0.0298  67.6496  9.4322 22.9182 1.4607  1.1900  0.3969  42.1365   0.0689                 
#54     0.4000 0.1404 2.0963  Fixed  0.0201  0.0294  65.9752 10.3499 23.6749 1.4074  1.1345  0.4012  42.2226   0.0698                 
#55     0.4000 0.1847 2.0944  Fixed  0.0254  0.0305  63.6377 12.5124 23.8499 2.3246  2.0121  0.4377  42.1622   0.0607                 
#56     0.4000 0.1424 2.1103  Fixed  0.0206  0.0292  66.2297 10.2403 23.5300 1.4232  1.1512  0.3989  42.2029   0.0692                 
#57     0.4000 0.1797 2.1408  Fixed  0.0234  0.0313  63.8664 12.8094 23.3242 2.1499  1.8519  0.4214  42.1289   0.0606                 
#58     0.4000 0.1312 2.1708  Fixed  0.0237  0.0297  68.5779  7.9633 23.4588 1.2490  0.9971  0.3817  42.1462   0.0739                 
#59     0.4000 0.1516 2.0907  Fixed  0.0200  0.0295  64.7978 11.5618 23.6403 1.5822  1.2986  0.4099  42.1454   0.0664

I want to be able to plot all columns (except for the numbering and 'Fixed' ones), but I suppose the problem is that the indices aren't consistent in the file. I want to plot stuff from the file in the y-axis, leaving x as a defined range. I tried creating a dataframe:

df = pd.read_csv(out)
print(df)
x = range(0, 80)
y = df[:,1]
df.plot(x, y)

with this error:

Traceback (most recent call last):

  File "<ipython-input-7-f8159069ae40>", line 1, in <module>
    runfile('C:/.../Python scripts/palsfit_output.py', wdir='C:/.../Python scripts')

  File "C:\...\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 710, in runfile
    execfile(filename, namespace)

  File "C:\...\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "C:/.../Python scripts/palsfit_output.py", line 156, in <module>
    y = df[:,1]

  File "C:\...\Anaconda3\lib\site-packages\pandas\core\frame.py", line 1964, in __getitem__
    return self._getitem_column(key)

  File "C:\...\Anaconda3\lib\site-packages\pandas\core\frame.py", line 1971, in _getitem_column
    return self._get_item_cache(key)

  File "C:\...\Anaconda3\lib\site-packages\pandas\core\generic.py", line 1643, in _get_item_cache
    res = cache.get(item)

TypeError: unhashable type: 'slice'

And using plt.plot:

with open(out) as file:
    data = file.read()
    print(data)

x = range(0,80)
print(x)
y = data[:,5]
print(y)
plt.plot(x,y, c='r', label='data')
plt.legend()
plt.show()

with an error:

Traceback (most recent call last):

  File "<ipython-input-10-f8159069ae40>", line 1, in <module>
    runfile('C:/.../Python scripts/palsfit_output.py', wdir='C:/.../Python scripts')

  File "C:\...\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 710, in runfile
    execfile(filename, namespace)

  File "C:\...\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile
    exec(compile(f.read(), filename, 'exec'), namespace)

  File "C:/.../Python scripts/palsfit_output.py", line 168, in <module>
    y = data[:,5]

TypeError: string indices must be integers

I assume the error is in that the file is not spaced consistently, and thus reading columns doesn't work. How can this be fixed?

Laplace12 · Jul-06-2021, 07:14 AM

I've now changed the composition of the values so that I have everything in a list. Now what I'd have to do is stack every 8th value into a column somehow, if that's possible, or create a loop to calculate the averages of every 8th value etc. The output is now this:

[['#0'], ['0.4000'], ['0.1500'], ['1.5187'], ['Fixed'], ['Fixed'], ['0.0473'], ['76.2093'], ['8.8510'], ['14.9398'], ['1.3789'], ['0.9853'], ['0.5720'], ['40.4648'], ['0.0551'], ['#1'], ['0.4000'], ['0.1500'], ['1.5094'], ['Fixed'], ['Fixed'], ['0.0450'], ['74.3954'], ['9.9777'], ['15.6269'], ['1.3704'], ['0.9724'], ['0.5760'], ['40.5128'], ['0.0545'], ['#2'], ['0.4000'], ['0.1500'], ['1.5491'], ['Fixed'], ['Fixed'], ['0.0468'], ['74.7040'], ... ['Fixed'], ['Fixed'], ['0.0536'], ['77.1376'], ['8.7556'], ['14.1069'], ['1.2754'], ['0.9602'], ['0.4889'], ['40.5042'], ['0.0548']]

(with this code):

my_file = open(out, "r")
content = my_file.read()

content_list = content.split()
my_file.close()

myList = content_list
myList = [i.split('\n') for i in myList] 
del myList[0:10]
print(myList)

So now I'd have to calculate averages of every 8th value, as well as plot them. I suppose it's easier this way: is there a method to stack the values into columns somehow, is the only option loop over the values? Any help is greatly appreciated!

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[Solved] Plotting data from txt file

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