I have a text file that contains something like this:

# Comment
# Comment
# Comment
# Comment

# Comment
  Comment
# Comment

#Raw SIFs at Crack Propagation Step: 0
# Vertex, X,              Y,              Z,              K_I,            K_II,           K_III,
  0      , 2.100000e+00   , 2.000000e+00   , -1.000000e-04  , 0.000000e+00   , 0.000000e+00   , 0.000000e+00  ,
  1      , 2.100000e+00   , 2.000000e+00   , 1.699733e-01   , 8.727065e+00   , -8.696262e-04  , -1.800691e-04  ,
  2      , 2.100000e+00   , 2.000000e+00   , 3.367067e-01   , 8.907810e+00   , -2.548819e-04  , -2.789738e-04  ,

# MLS SIFs at Crack Propagation Step: 0

# MLS approximation: 
# Sample, t,             NA,             NA,              K_I,            K_II,           K_III,
# Crack front stretch: 0
  0      , 0.000000e+00   , 0.000000e+00   , 0.000000e+00   , 8.446880e+00   , -1.360875e-03  , -1.137681e-04-1.360875e-03  ,
  1      , 5.670333e-02   , 0.000000e+00   , 0.000000e+00   , 8.554168e+00   , -1.156931e-03  , -1.609628e-04  ,
  2      , 1.134067e-01   , 0.000000e+00   , 0.000000e+00   , 8.648241e+00   , -9.755573e-04  , -1.981679e-04  ,

# more comments
  more comments
# more comments

# Raw SIFs at Crack Propagation Step: 1
# Vertex, X,              Y,              Z,              K_I,            K_II,           K_III,
  0      , 2.186139e+00   , 2.000000e+00   , -1.688418e-03  , 0.000000e+00   , 0.000000e+00   , 0.000000e+00   ,
  1      , 2.192003e+00   , 2.000000e+00   , 1.646902e-01   , 9.571022e+00   , 4.770358e-03   , -7.809699e-03  ,
  2      , 2.196234e+00   , 2.000000e+00   , 3.319183e-01   , 9.693934e+00   , -9.634989e-03  , -4.455937e-03  ,

# MLS SIFs at Crack Propagation Step: 1

# MLS approximation: 
# Sample, t,             NA,             NA,              K_I,            K_II,           K_III,
# Crack front stretch: 0
   0      , 0.000000e+00   , 0.000000e+00   , 0.000000e+00   , 9.402031e+00   , 2.097959e-02   , -1.066071e-02  ,
   1      , 5.546786e-02   , 0.000000e+00   , 0.000000e+00   , 9.467541e+00   , 1.443546e-02   , -9.256367e-03  ,
   2      , 1.109357e-01   , 0.000000e+00   , 0.000000e+00   , 9.525021e+00   , 8.554051e-03   , -8.001627e-03  ,

As you can see, the lines without the # symbol contains the data I would like to plot. I've only shown you a short portion of step 0 and step 1, but there are around 20 steps in this file. And in each step, there are two types of data: RAW SIFS and MLS SIFS. In the Python GUI, I would like to give the inputter several options on how they want the graphs to look like:
1) Raw, MLS, or both?
2) What steps do they want to see on the graph? (ex. odd steps [1,3,5...], block steps [ like 1-5, 6-10, 11-15...], etc.)
3) If they want RAW SIFS, what values do they want for the x-axis (vertex, X, Y, or Z)?
4) Have KI, KII, and KIII in one graph; in 3 seperate graphs; or other combinations?

So far, I plotted a line graph of: vertex (1st column) versus K_I (5th column), vertex (1st column) versus K_II (6th column), and vertex (1st column) versus K_III (7th kevin). In the end, I plotted the 20 steps of RAW SIFS for vertex vs K_I with 20 curves all in one graph. Then, another graph of the 20 steps of RAW SIFS for vertex vs K_II, and another one for K_III. Similarly, I plotted the 20 steps of **MLS SIFS **for vertex vs K_I with 20 curves all in one graph. Then, another graph of the 20 steps of **MLS SIFS **for vertex vs K_II, and another one for K_III. I also incuded lightening shades of color for each graph.

Here is the code I written so far:

# helper function to parse a data block 
def parse_SIF(lines): 
    SIF = [] 
    while lines: 
        line = lines.pop(0).lstrip() 
        if line == '' or line.startswith('#') or line.startswith('[-1.000000e+00'):
            if line.startswith('# Raw SIFs at') or line.startswith('# MLS SIFs at'):
                lines.insert(0, line)
                break
            continue  
        data = line.split(',') 
        # pick only columns 0, 4, 5, 6 and 
        # convert to appropiate numeric format 
        # and append to list for current SIF and step 
        SIF.append([int(data[0]), float(data[4]), float(data[5]), float(data[6])]) 
    return SIF 

# your global data structure - nested lists 
raw = [] 
mls = []

# read whole file into one list - ok if data is not large 
with open('C:\Users\Documents\edge_cracked_crack_propag_3D_hpGFEM_mesh_11x11x3.crp') as fptr: 
    lines = fptr.readlines() 

# global parse routine - call helper function to parse data blocks 
while lines: 
    line = lines.pop(0) 
    if line.startswith('#'): 
        if line.find('Raw SIFs at Crack Propagation Step:') > -1: 
            raw.append(parse_SIF(lines)) 
        if line.find('MLS SIFs at Crack Propagation Step:') > -1: 
            mls.append(parse_SIF(lines))

# show results for data 
#from pprint import pprint
#for raw_step, mls_step in zip(raw, mls): 
#    print 'raw:'
#    pprint(raw_step) 
#    print 'mls:' 
#    pprint(mls_step)

from pylab import *
import matplotlib.pyplot as plt 

blues = plt.get_cmap('Blues') # this returns a colormap 
reds = plt.get_cmap('Reds') 
greens = plt.get_cmap('Greens')

for i, raw_step in enumerate(raw): 
    raw_step = zip(*raw_step)
    Raw_Vertex, Raw_KI, Raw_KII, Raw_KIII = raw_step[0], raw_step[1], raw_step[2], raw_step[3]

    figure(1)
    plot(Raw_Vertex, Raw_KI, 'o-', color = blues(3*(1 - float(i)/(len(raw)-0.1)))) # blues(x) returns a color for each x between 0.0 and 1.0 
    grid(True)
    title('Raw SIFs')
    xlabel('Vertex')
    ylabel('K_I')

    figure(2)
    plot(Raw_Vertex, Raw_KII, 'o-', color = greens(3*(1 - float(i)/(len(raw)-0.1)))) 
    grid(True)
    title('Raw SIFs')
    xlabel('Vertex')
    ylabel('K_II')

    figure(3)
    plot(Raw_Vertex, Raw_KIII, 'o-', color = reds(3*(1 - float(i)/(len(raw)-0.1)))) 
    grid(True)
    title('Raw SIFs')
    xlabel('Vertex')
    ylabel('K_III')

show()


for i, mls_step in enumerate(mls): 
    mls_step = zip(*mls_step)
    MLS_Vertex, MLS_KI, MLS_KII, MLS_KIII = mls_step[0], mls_step[1], mls_step[2], mls_step[3]

    figure(4)
    plot(MLS_Vertex, MLS_KI, 'o-', color = blues(3*(1 - float(i)/(len(mls)-0.1)))) 
    grid(True)
    title('MLS SIFs')
    xlabel('Vertex')
    ylabel('K_I')

    figure(5)
    plot(MLS_Vertex, MLS_KII, 'o-', color = greens(3*(1 - float(i)/(len(mls)-0.1))))
    grid(True)
    title('MLS SIFs')
    xlabel('Vertex')
    ylabel('K_II')

    figure(6)
    plot(MLS_Vertex, MLS_KIII, 'o-', color = reds(3*(1 - float(i)/(len(mls)-0.1)))) 
    grid(True)
    title('MLS SIFs')
    xlabel('Vertex')
    ylabel('K_III')

show()

Pictures of the 6 graphs are here:

raw_vertex_KI
raw_vertex_KIIraw_vertex_KIIImls_vertex_KImls_vertex_KIImls_vertex_KIII

How do I go about writing the code to give inputters those 4 options and then plotting what they want? Any help is greatly appreciated!

I would starting working with the Enthought Tool Suite. Their TraitsUI (and now the new Enaml framework) are worth investing the time into. They allow for really simple GUI's that are interactive from the door. In your case, it would be as simple as having a checkbox and when the user changes the value, the plot data in your chaco plot (chaco is a matplotlib wrapper for interactive plotting) would just change to whatever plot you waned. In fact, it would be easy to have all the plots on the same screen and the user can merely readjust the view to get one out of the frame for example.

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