[Tutor] plotting in python

[Emile van Sebille]

On 11/30/2011 1:08 PM stm atoc said...
> Hi there,
>
> I have a question regarding plotting with Python.
>
> I have the following python script:
>
> # coding: utf-8
> from pylab import *
> import numpy
>
> filename='ourtest_out.list'
>
> fh=open(filename)
> line=fh.readline()
> fh.close
>
> z=array([ float(val) for val in line.split()[1:] ])
>
>
> a = numpy.loadtxt(filename,skiprows=3)
> N=100
> t = a[:,0]
> nu = a[0:,1:N+1]
> #Conc = a[1:,N+1:]
> Conc = a[1:,N+1:]
>
> levels=arange(-10,1)
> levels=levels[-3]-levels
> t=t/360.
>
> figure()
> plot(Conc[0],z)
>
> xlabel('C')
> ylabel('z')
> #show()
> savefig('Conc.png')
> close()
>
> #########nu
> figure()
> lw = 2.0 #linewidth
> dpi = 96
>
> levels=arange(-10,1)
> levels=levels[-3]-levels
> plot(nu[0],z)
> xlabel('nu')
> ylabel('z')
> savefig('nu.png')
> close()
>
>
> --------However, once I run the program (run.py)
>
> I have error like this:
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
> /Users/…./run.py in<module>()
>       24
>       25 figure()
> --->  26 plot(Conc[0],z)
>       27
>       28 xlabel('C')
>
> /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/pyplot.py
> in plot(*args, **kwargs)
>     2284         ax.hold(hold)
>     2285     try:
> ->  2286         ret = ax.plot(*args, **kwargs)
>     2287         draw_if_interactive()
>     2288     finally:
>
> /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
> in plot(self, *args, **kwargs)
>     3781         lines = []
>     3782
> ->  3783         for line in self._get_lines(*args, **kwargs):
>     3784             self.add_line(line)
>     3785             lines.append(line)
>
> /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
> in _grab_next_args(self, *args, **kwargs)
>      315                 return
>      316             if len(remaining)<= 3:
> -->  317                 for seg in self._plot_args(remaining, kwargs):
>      318                     yield seg
>      319                 return
>
> /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
> in _plot_args(self, tup, kwargs)
>      292             x = np.arange(y.shape[0], dtype=float)
>      293
> -->  294         x, y = self._xy_from_xy(x, y)
>      295
>      296         if self.command == 'plot':
>
> /Library/Frameworks/EPD64.framework/Versions/7.1/lib/python2.7/site-packages/matplotlib/axes.py
> in _xy_from_xy(self, x, y)
>      232         y = np.atleast_1d(y)
>      233         if x.shape[0] != y.shape[0]:
> -->  234             raise ValueError("x and y must have same first dimension")
>      235         if x.ndim>  2 or y.ndim>  2:
>      236             raise ValueError("x and y can be no greater than 2-D")
>
> ValueError: x and y must have same first dimension
>
>
> -------So, What would you suggest?

Looking over the traceback and code, it would appear the error is saying 
that there is an inconsistency with the arguments expected vs the 
arguments passed, which appears in this case to relate to ...

plot(Conc[0],z)

... which derives its parameters from the two lines ...

z=array([ float(val) for val in line.split()[1:] ])

... and ...

a = numpy.loadtxt(filename,skiprows=3)


So, I'd conclude that I'd need a better understanding of how to use the 
functions plot, array and numpy.loadtext.  Neither plot nor array are 
python builtins nor defined within your script, so they're likely 
brought in from ...

from pylab import *

... which is generally not something you want to do except when first 
starting to experiment and learn a new module, and then I'd keep things 
to the interactive interpreter for testing and discovery.  This form of 
import is generally thought of as polluting the namespace and may allow 
library specific names to mask python builtins.  For example. suppose a 
module 'xyz' contains a special 'print' function.  Executing 'from xyz 
import *' would shadow the python builtin print function essentially 
making it inaccessible.  It's possible (although unlikely in the case of 
pylab specifically) that any python builtins that are used in your 
script have been replaced with pylab versions.  A better technique is to 
simply import pylab and refer to its functions as pylab.xyz so that no 
ambiguity is possible.

So, read up on pylab, find their support list [1], and follow up there. 
  We focus mainly on getting you far enough along with python basics and 
generally leave specific library support to the library authors and 
support groups.

HTH

Emile


[1] start at http://www.scipy.org/Mailing_Lists