matplotlib-users

[Matplotlib-users] direct plot fromfile?

[manouchk <man...@gm...>]

Hi,

Data file I use usually have a first line or more with comments and sometimes 
column with text. I used to use gnuplot that does skip au
which  with 
I wondering if there is an hidden possibilty to plot more or less directly 
from file.

imagine the file :
col1 col2 col3 col4 col5 col6
T3-4B 450 100 4.31 1.44 0
T3-4B 450 200 5.56 2.06 0
T3-4B 450 500 6.03 2.09 0
T3-4A 450 5000 9.71 2.16 0

that would be a function that plots column number 3 and 4 skipping first line 
and ignoring first column (that would put zeros in the array for example)
It could have a syntax like that one:
plotfromfile(file="data",using=(3,4),skippingline=1,ignorecolumn=[1])

is there a function in pylab that I missed and that already does something 
similar?

Re: [Matplotlib-users] direct plot fromfile?

[manouchk <man...@gm...>]

Le Mercredi 05 Avril 2006 11:36, manouchk a =E9crit=A0:
I made a mistake with my mail. Just correcting it, sorry for inconvenience.

Hi,

Data file I use usually have a first line or more with comments and sometim=
es=20
column with text. I used to use gnuplot that now automatically skips rows t=
hat=20
does not contain numbers (before one should use every n to skip n forst lin=
e)=20
and handle well files that have column without number.
using column 3 and 4 from a file to plot is done using using 3:3.
I wondering if there is an hidden possibilty to plot more or less directly=
=20
from file as in gnuplot.

imagine the file :
col1 col2 col3 col4 col5 col6
T3-4B 450 100 4.31 1.44 0
T3-4B 450 200 5.56 2.06 0
T3-4B 450 500 6.03 2.09 0
T3-4A 450 5000 9.71 2.16 0

that would be a function that plots column number 3 and 4 skipping first li=
ne=20
and ignoring first column (that would put zeros in the array for example)
A fonction that would do that could look like that one:
plotfromfile(file=3D"data",using=3D(3,4),skippingline=3D1,ignorecolumn=3D[1=
])

is there a function in pylab I missed and that already does something=20
similar?

Re: [Matplotlib-users] direct plot fromfile?

[Ryan K. <rya...@gm...>]

I don't know much about using Matplotlib apart from Scipy, but
scipy.io.read_array seems to handle this without a problem.  I copied
and pasted your example data into a file I called datafile.txt
(attached).  Then I basically did:
from scipy.io import read_array
data=3Dread_array('datafile.txt')

It does it's best with the first row and column:
In [4]: data[0,:]
Out[4]: array([ 1.,  2.,  3.,  4.,  5.,  6.])

In [5]: data[:,0]
Out[5]: array([ 1.,  3.,  3.,  3.,  3.])

but if you throw them away, you basically have what you want:
In [6]: data[1:,1:]
Out[6]:
array([[  4.50000000e+02,   1.00000000e+02,   4.31000000e+00,
          1.44000000e+00,   0.00000000e+00],
       [  4.50000000e+02,   2.00000000e+02,   5.56000000e+00,
          2.06000000e+00,   0.00000000e+00],
       [  4.50000000e+02,   5.00000000e+02,   6.03000000e+00,
          2.09000000e+00,   0.00000000e+00],
       [  4.50000000e+02,   5.00000000e+03,   9.71000000e+00,
          2.16000000e+00,   0.00000000e+00]])

You could also do it with low-level Python io and text processing if
you don't have Scipy:
f=3Dopen('datafile.txt')
text=3Df.readlines()
text=3Dtext[1:]#eliminates first row
cleantext=3D[row.replace('\n','') for row in text]
matstring=3D[row.split(' ') for row in cleantext]
almostdone=3D[row[1:] for row in matstring]#eliminates first column

at that point you have a nested list of strings:
[['450', '100', '4.31', '1.44', '0'],
 ['450', '200', '5.56', '2.06', '0'],
 ['450', '500', '6.03', '2.09', '0'],
 ['450', '5000', '9.71', '2.16', '0']]

which you have to convert to an array.  With NumPy you could do:
stringmat=3Darray(almostdone)
stringmat.astype('f')

which produces
array([[450, 100, 4.31, 1.44, 0],
       [450, 200, 5.56, 2.06, 0],
       [450, 500, 6.03, 2.09, 0],
       [450, 5000, 9.71, 2.16, 0]], dtype=3D(string,4))

if you are using someother numerix, you may need to handle this last
step slightly differently.  If nothing else, you could iterate over
the nested list and call float on each element to get a nest list of
float values.

Ryan




On 4/5/06, manouchk <man...@gm...> wrote:
> Le Mercredi 05 Avril 2006 11:36, manouchk a =E9crit:
> I made a mistake with my mail. Just correcting it, sorry for inconvenienc=
e.
>
> Hi,
>
> Data file I use usually have a first line or more with comments and somet=
imes
> column with text. I used to use gnuplot that now automatically skips rows=
 that
> does not contain numbers (before one should use every n to skip n forst l=
ine)
> and handle well files that have column without number.
> using column 3 and 4 from a file to plot is done using using 3:3.
> I wondering if there is an hidden possibilty to plot more or less directl=
y
> from file as in gnuplot.
>
> imagine the file :
> col1 col2 col3 col4 col5 col6
> T3-4B 450 100 4.31 1.44 0
> T3-4B 450 200 5.56 2.06 0
> T3-4B 450 500 6.03 2.09 0
> T3-4A 450 5000 9.71 2.16 0
>
> that would be a function that plots column number 3 and 4 skipping first =
line
> and ignoring first column (that would put zeros in the array for example)
> A fonction that would do that could look like that one:
> plotfromfile(file=3D"data",using=3D(3,4),skippingline=3D1,ignorecolumn=3D=
[1])
>
> is there a function in pylab I missed and that already does something
> similar?
>
>
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Re: [Matplotlib-users] direct plot fromfile?

[John H. <jdh...@ac...>]

>>>>> "manouchk" =3D=3D manouchk  <man...@gm...> writes:

    manouchk> Le Mercredi 05 Avril 2006 11:36, manouchk a =E9crit=A0: I
    manouchk> made a mistake with my mail. Just correcting it, sorry
    manouchk> for inconvenience.

    manouchk> Hi,

    manouchk> Data file I use usually have a first line or more with
    manouchk> comments and sometimes column with text. I used to use
    manouchk> gnuplot that now automatically skips rows that does not
    manouchk> contain numbers (before one should use every n to skip n
    manouchk> forst line) and handle well files that have column
    manouchk> without number.  using column 3 and 4 from a file to
    manouchk> plot is done using using 3:3.  I wondering if there is
    manouchk> an hidden possibilty to plot more or less directly from
    manouchk> file as in gnuplot.



    manouchk> imagine the file : col1 col2 col3 col4 col5 col6 T3-4B
    manouchk> 450 100 4.31 1.44 0 T3-4B 450 200 5.56 2.06 0 T3-4B 450
    manouchk> 500 6.03 2.09 0 T3-4A 450 5000 9.71 2.16 0

    manouchk> that would be a function that plots column number 3 and
    manouchk> 4 skipping first line and ignoring first column (that
    manouchk> would put zeros in the array for example) A fonction
    manouchk> that would do that could look like that one:
    manouchk> plotfromfile(file=3D"data",using=3D(3,4),skippingline=3D1,i=
gnorecolumn=3D[1])

The latest matplotlib release includes some enhancements to the load
function to allow you to skip rows and extract certain columns.  It
also allows you to pass in converter functions to convert certain
columns to floating point numbers, eg for dates.  See
examples/load_demo.py for a full example.  Here is an example
skipping the header and extracting the 3rd and 4th column:

  from pylab import figure, load, show
  x, y =3D load('test.dat', skiprows=3D1, usecols=3D(2,3), unpack=3DTrue)
  fig =3D figure()
  ax =3D fig.add_subplot(111)
  ax.plot(x,y)
  show()


JDH

Re: [Matplotlib-users] direct plot fromfile?

[Jean-Luc M. <jea...@fr...>]

> is there a function in pylab I missed and that already does something 
> similar?


try something like that :

import Numeric,pylab,string

def plotfromfile(file="data",using=(3,4),skippingline=1):
	f=open(file,'r')
	for i in range(skippingline):
		f.readlines()
	res=Numeric.array([[string.atof(x)] for x in 
string.split(y)[using[0]:using[-1]+1] for y in f.readlines()])
	
	for u in using :
		pylab.plot(res[:,u])
	pylab.show()


Warning : not tested
Jean-Luc