Get specific element from header of file?

Question

So I have data in this format:

#NUMBER OF AGES=37 MAGS= 5
#----------------------------------------------------       
#MIX-LEN  Y      Z          Zeff        [Fe/H] [a/Fe]
# 1.9380  0.3300 3.1125E-04 1.5843E-04  -1.99   0.40
#----------------------------------------------------       
#**PHOTOMETRIC SYSTEM**: SDSS (AB)
#----------------------------------------------------       
#AGE= 1.000 EEPS=276
#EEP   M/Mo    LogTeff  LogG   LogL/Lo sdss_u  sdss_g  sdss_r  sdss_i  sdss_z  
   3  0.105051  3.5416  5.3073 -2.7281 17.2434 13.9245 12.2511 11.5059 11.0920
   4  0.118159  3.5519  5.2644 -2.5931 16.5471 13.4392 11.8286 11.1502 10.7665
   5  0.133632  3.5623  5.2211 -2.4547 15.8825 12.9522 11.4091 10.7861 10.4301
   6  0.156724  3.5737  5.1745 -2.2933 15.1633 12.4008 10.9372 10.3638 10.0348
   7  0.194206  3.5861  5.1259 -2.1020 14.3673 11.7681 10.3975  9.8690  9.5654

#AGE= 1.250 EEPS=275
#EEP   M/Mo    LogTeff  LogG   LogL/Lo sdss_u  sdss_g  sdss_r  sdss_i  sdss_z  
   4  0.105349  3.5419  5.3062 -2.7248 17.2255 13.9125 12.2406 11.4972 11.0840
   5  0.118453  3.5521  5.2635 -2.5901 16.5322 13.4285 11.8194 11.1424 10.7593
   6  0.133982  3.5625  5.2202 -2.4518 15.8684 12.9418 11.4002 10.7783 10.4228
   7  0.157170  3.5739  5.1736 -2.2903 15.1503 12.3907 10.9286 10.3560 10.0274
   8  0.193935  3.5860  5.1253 -2.1021 14.3683 11.7688 10.3980  9.8694  9.5657
   9  0.233067  3.5953  5.0847 -1.9445 13.7342 11.2608  9.9652  9.4664  9.1794
  10  0.253422  3.5994  5.0635 -1.8706 13.4408 11.0263  9.7653  9.2787  8.9986
  11  0.263033  3.6012  5.0556 -1.8395 13.3177 10.9277  9.6812  9.1997  8.9225
  12  0.269548  3.6022  5.0484 -1.8175 13.2345 10.8597  9.6223  9.1439  8.8684

#AGE= 1.500 EEPS=274
#EEP   M/Mo    LogTeff  LogG   LogL/Lo sdss_u  sdss_g  sdss_r  sdss_i  sdss_z  
   5  0.107932  3.5440  5.2974 -2.6971 17.0780 13.8121 12.1528 11.4242 11.0175
   6  0.121259  3.5542  5.2549 -2.5632 16.3994 13.3328 11.7366 11.0714 10.6940
   7  0.137720  3.5647  5.2112 -2.4220 15.7312 12.8387 11.3119 10.7002 10.3502
   8  0.163277  3.5763  5.1639 -2.2544 14.9976 12.2706 10.8261 10.2628  9.9394
   9  0.199555  3.5876  5.1176 -2.0757 14.2622 11.6834 10.3250  9.8017  9.5010

And I've figured out how to read the columns (theoretically) using this:

sdss_g = []
sdss_r = []

with open ("/Users/Wilson/research/isochrones/SDSSugriz/fehm20afep4y33.SDSSugriz") as f:
   for _ in xrange(9):
        next(f)

   for line in f: 
        cols = line.split()
        g = (float(cols[6]))
        r = (float(cols[7]))
        print 'g'
        print g
        print 'r'
        print r
        sdss_g.append(g)
        sdss_r.append(r)

but this doesn't work, it gives me this error:

Traceback (most recent call last):
  File "isochronereader.py", line 18, in <module>
    g = (float(cols[6]))
IndexError: list index out of range

I'm pretty sure it's because I'm not accounting for the line space and string-formatted new title, but "list index out of range" doesn't seem to be the right indicator for that problem.

Nevertheless, I don't know how to account for the title and space in between the data and I'd like to figure that out. I'd also like to read in the AGE in each title. Because of the format of this text file I can't use genfromtxt and I can't figure out what to do, especially because the number of lines to the next new title is not uniform so I can't just read it in after a specific number of lines.

In the end, I want to be able to read in sdss_g and sdss_r and know what age each sdss_g and sdss_r element is associated with. Is there a simple way for me to do this?

The blank and commented-out lines (outside the first nine you've skipped) will still be processed, unless you add e.g. if not line or line.startswith('#'): continue. — jonrsharpe
– jonrsharpe, Commented Jul 30, 2015 at 14:50

innoSPG · Accepted Answer · 2015-07-30 15:10:23Z

2

You can do this:

sdss_g = []
sdss_r = []

with open ("/Users/Wilson/research/isochrones/SDSSugriz/fehm20afep4y33.SDSSugriz") as f:
    for line in f:
        if not line.isspace() and not line.startswith("#"):
            print line
            cols = line.split()
            g = (float(cols[6]))
            r = (float(cols[7]))
            print 'g'
            print g
            print 'r'
            print r
            sdss_g.append(g)
            sdss_r.append(r)

answered Jul 30, 2015 at 15:10

innoSPG

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Martin Evans · Accepted Answer · 2015-07-31 07:59:04Z

The CSV library could be used if the data is first split up:

import csv, re, StringIO

with open("/Users/Wilson/research/isochrones/SDSSugriz/fehm20afep4y33.SDSSugriz", "r") as f_input:
    data = f_input.read()
    lblocks = re.findall(r"#AGE=\s+?(.*?)\s+(?:.*?[\r\n]|\Z){2}(.*?(?=#AGE|\Z|^$))", data, re.S + re.M)

    for age, block in lblocks:
        csv_reader = csv.reader(StringIO.StringIO(block), delimiter=" ", skipinitialspace=True)
        print "Age:", age

        for cols in csv_reader:
            print "  sdss_g %s, sdss_r %s" % (cols[6], cols[7])

This gives the following output:

Age: 1.000
  sdss_g 13.9245, sdss_r 12.2511
  sdss_g 13.4392, sdss_r 11.8286
  sdss_g 12.9522, sdss_r 11.4091
  sdss_g 12.4008, sdss_r 10.9372
  sdss_g 11.7681, sdss_r 10.3975
Age: 1.250
  sdss_g 13.9125, sdss_r 12.2406
  sdss_g 13.4285, sdss_r 11.8194
  sdss_g 12.9418, sdss_r 11.4002
  sdss_g 12.3907, sdss_r 10.9286
  sdss_g 11.7688, sdss_r 10.3980
  sdss_g 11.2608, sdss_r 9.9652
  sdss_g 11.0263, sdss_r 9.7653
  sdss_g 10.9277, sdss_r 9.6812
  sdss_g 10.8597, sdss_r 9.6223
Age: 1.500
  sdss_g 13.8121, sdss_r 12.1528
  sdss_g 13.3328, sdss_r 11.7366
  sdss_g 12.8387, sdss_r 11.3119
  sdss_g 12.2706, sdss_r 10.8261
  sdss_g 11.6834, sdss_r 10.3250

Tested using Python 2.7

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