matplotlib-users Mailing List for matplotlib

On Sun, Apr 30, 2006 at 08:48:06AM -1000, Eric Firing wrote:
> It might not be complicated, but forget about using imshow--it is for 
> image data, which are inherently evenly spaced.  Pcolor and pcolormesh 
> don't have this limitation.  Note that Zij will give the color of the 
> box with diagonal corners (Xij, Yij) and (Xi+1,j+1, Yi+1,j+1), so if Z 
> has the same dimensions as X and Y, the last row and column will not be 
> shown.  If your input data are intended to give the (x,y) positions of 
> the centers of regions rather than the corners, then you will need to do 
> some sort of regridding of Z, or shifting of your X and Y points, in 
> order to get everything exactly right with pcolor and pcolormesh.
> 
> The attached script and sample data file show how you can put the data 
> from your ascii file into X, Y, and Z arrays, and plot them using pcolor 
> or pcolormesh.  This is for the simple case in which treating x and y as 
> corners is good enough. Note that the grid does not have to form 
> rectangular cells; they can be quadrilaterals.  I illustrated this in 
> the sample file by shifting one point.
> 
> Eric
> 
> 
> 

> 1.0 1.0 1.1
> 1.0 1.5 1.2
> 1.0 2.5 1.1
> 1.0 4.0 1.0
> 1.0 4.5 1.0
> 2.0 1.0 1.2
> 2.0 1.5 1.3
> 2.5 2.9 1.4
> 2.0 4.0 1.1
> 2.0 4.5 1.1
> 3.0 1.0 1.0
> 3.0 1.5 1.3
> 3.0 2.5 1.5
> 3.0 4.0 1.2
> 3.0 4.5 1.2
> 4.0 1.0 1.0
> 4.0 1.5 1.3
> 4.0 2.5 1.5
> 4.0 4.0 1.2
> 4.0 4.5 1.2

> #!/usr/bin/env python
> 
> from pylab import subplot, show
> from pylab import nx as N
> 
> fname = 'xyz.asc'
> nx, ny = (4,5)
> 
> lines = open(fname).readlines()
> a_list = [[float(field) for field in line.split()] for line in lines]
> a = N.array(a_list)
> 
> X = N.reshape(a[:,0], (nx, ny))
> Y = N.reshape(a[:,1], (nx, ny))
> Z = N.reshape(a[:,2], (nx, ny))
> 
> ax = subplot(1,2,1)
> ax.pcolor(X,Y,Z, shading='flat')
> 
> ax = subplot(1,2,2)
> ax.pcolormesh(X,Y,Z, shading='flat')
> 
> show()

Unfortunately, I couldn't even get this example to work. It was some
sort of error related to pcolor not being a method of subplot, or
something like that (sorry, I don't have the exact error message with
me right now).

Essentially, it seems to me that the above example *would* in
principle work, though it's still going to take me a while to get
things working. I have a thesis to turn in on Friday, or else I would
keep playing with it until I got it to work. As it is, I'm going to
have to do without it (luckily, I can use the program that's exporting
the data to make my plots, I just think they're ugly).

Perhaps in the next few weeks I'll play with it some more and write up
the results if I get it working well.

Thanks for all the responses,

Mike

Michael V. De Palatis wrote:
> On Sat, Apr 29, 2006 at 08:41:48AM -1000, Eric Firing wrote:
> 
>>How easy it is to do this depends on your ascii file format, and how the 
>>data are organized in it.  Are the points in order? e.g.
>>
>>x0, y0, z00
>>x0, y1, z01
>>x0, y2, z02
>>x1, y0, z10
>>x1, y1, z11
>>x1, y2, z12
> 
> 
> This is precisely the ordering.
> 
> 
>>Are the values space-delimited, or comma-delimited, or in some other
>>format?
> 
> 
> The values are space-delimited. The way I am reading them in is with
> readline, then splitting the resulting string and appending to a list
> of x, y, and z values.
> 
> 
>>Is the grid uniform in the sense that all the x-intervals are the same 
>>and all the y-intervals are the same?
> 
> 
> Unfortunately, the grid is not uniform. From the responses I have been
> getting thus far, it's looking like this is going to be far more
> complicated than I had hoped...

It might not be complicated, but forget about using imshow--it is for 
image data, which are inherently evenly spaced.  Pcolor and pcolormesh 
don't have this limitation.  Note that Zij will give the color of the 
box with diagonal corners (Xij, Yij) and (Xi+1,j+1, Yi+1,j+1), so if Z 
has the same dimensions as X and Y, the last row and column will not be 
shown.  If your input data are intended to give the (x,y) positions of 
the centers of regions rather than the corners, then you will need to do 
some sort of regridding of Z, or shifting of your X and Y points, in 
order to get everything exactly right with pcolor and pcolormesh.

The attached script and sample data file show how you can put the data 
from your ascii file into X, Y, and Z arrays, and plot them using pcolor 
or pcolormesh.  This is for the simple case in which treating x and y as 
corners is good enough. Note that the grid does not have to form 
rectangular cells; they can be quadrilaterals.  I illustrated this in 
the sample file by shifting one point.

Eric

>>>>> "giandomenico" == giandomenico sica <gia...@po...> writes:

    giandomenico> Thanks for the message.  I know networkx having used
    giandomenico> it in the early development of the project.  It's a
    giandomenico> good package but is missing of some basic functions
    giandomenico> that I need to use, related to the analysis of
    giandomenico> graphs. Since my programming skills are quite weak,
    giandomenico> I'm not able to supply this lack through usual
    giandomenico> python programming code.  Best, Nico

I've CCd Aric Hagberg, one of the networkx developers. If you describe
the missing features, he might be able to help add them to networkx.
I believe he has also applied network theory to healthcare, though in
the epidemiology domain.

JDH

Original post below

From: gia...@po...
Subject: [Matplotlib-users] CFC: An Atlas of Linguistic Graphs
To: mat...@li...
Date: Sun, 30 Apr 2006 18:44:13 +0200
X-Spambayes-Classification: ham; 0.00

I'm a researcher in graph theory and networks.
I'm working about a project connected with the theory and the applications of
linguistic graphs, which are mathematical structures useful to represent
languages and consequently to manage the organization of data in different
kinds of scientific fields.
At the present I'm developing an application of these graphs to medicine,
specifically related to the ontology of clinical diseases.
And now to the purpose of this message, which is to ask if someone in this list
can be interested in collaborating with me about the construction of an open
source software useful to represent, to analyse and to compare linguistic
graphs.
I've developed the project but don't have the necessary programming skills to
proceed with the creation of the code.
The software would be distributed in public domain and the collaboration would
be free and voluntary.
I really hope that someone can be interested.
In the case, please feel free to contact me by using my private e-mail address.
I'll be pleased to send the complete documentation related to the project.
Really many thanks.

All the best,
Giandomenico Sica

Faculty of Philosophy
Leiden University
gia...@po...

Publications
http://www.polimetrica.com/polimetrica/view/people/Sica,_Giandomenico.html

1st World Congress and School on Universal Logic
http://www.uni-log.org



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Thanks for the message.
I know networkx having used it in the early development of the project.
It's a good package but is missing of some basic functions that I need to use,
related to the analysis of graphs. Since my programming skills are quite weak,
I'm not able to supply this lack through usual python programming code.
Best,
Nico

Quoting John Hunter <jdh...@ac...>:

>>>>>> "giandomenico" == giandomenico sica 
>>>>>> <gia...@po...> writes:
>    giandomenico> graphs.  I've developed the project but don't have
>    giandomenico> the necessary programming skills to proceed with the
>    giandomenico> creation of the code.  The software would be
>    giandomenico> distributed in public domain and the collaboration
>
> A useful starting point would be networkx, a python graph/network
> package.  It also can use matplotlib to display them :-)
>
>  http://networkx.sf.net
>
> JDH
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

>>>>> "giandomenico" == giandomenico sica <gia...@po...> writes:
    giandomenico> graphs.  I've developed the project but don't have
    giandomenico> the necessary programming skills to proceed with the
    giandomenico> creation of the code.  The software would be
    giandomenico> distributed in public domain and the collaboration

A useful starting point would be networkx, a python graph/network
package.  It also can use matplotlib to display them :-)

  http://networkx.sf.net

JDH

I'm a researcher in graph theory and networks.
I'm working about a project connected with the theory and the applications of
linguistic graphs, which are mathematical structures useful to represent
languages and consequently to manage the organization of data in different
kinds of scientific fields.
At the present I'm developing an application of these graphs to medicine,
specifically related to the ontology of clinical diseases.
And now to the purpose of this message, which is to ask if someone in this list
can be interested in collaborating with me about the construction of an open
source software useful to represent, to analyse and to compare linguistic
graphs.
I've developed the project but don't have the necessary programming skills to
proceed with the creation of the code.
The software would be distributed in public domain and the collaboration would
be free and voluntary.
I really hope that someone can be interested.
In the case, please feel free to contact me by using my private e-mail address.
I'll be pleased to send the complete documentation related to the project.
Really many thanks.

All the best,
Giandomenico Sica

Faculty of Philosophy
Leiden University
gia...@po...

Publications
http://www.polimetrica.com/polimetrica/view/people/Sica,_Giandomenico.html

1st World Congress and School on Universal Logic
http://www.uni-log.org