Re: [Matplotlib-users] how to make scatter plot and bar graphs in same figure?

2009-02-18 Thread Manuel Metz
Ryan May wrote:
 On Mon, Feb 16, 2009 at 7:22 AM, Manuel Metz mm...@astro.uni-bonn.dewrote:
 
 Attached is a very simple example that shows how to do something similar
 to scatterhist in matplotlib


 That's a nice example.  Are you going to check that into SVN?

Yes, soon ...

 Ryan
 


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Re: [Matplotlib-users] Plotting histograms with zero counts

2008-12-01 Thread Manuel Metz
Yang Zhang wrote:
 Hi, when I do:
 
hist([0,0,0], bins=10, range=(0,10))
 
 How come the single bin takes up the entire plot?  Same with just two 
 values, or anything less than 10 - the two bars take up the entire plot, 
 no matter what I plug in for range.  I'd just like 10 bins, from 0 to 9.

That's a bug in the current implementation (see also
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=503148).

mm


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Re: [Matplotlib-users] Plotting histograms with zero counts

2008-12-01 Thread Manuel Metz
Manuel Metz wrote:
 Yang Zhang wrote:
 Hi, when I do:

hist([0,0,0], bins=10, range=(0,10))

 How come the single bin takes up the entire plot?  Same with just two 
 values, or anything less than 10 - the two bars take up the entire plot, 
 no matter what I plug in for range.  I'd just like 10 bins, from 0 to 9.
 
 That's a bug in the current implementation (see also
 http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=503148).

This is fixed now on the trunk.

mm


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Re: [Matplotlib-users] Make markers in legend to appear only once

2008-12-01 Thread Manuel Metz
Alejandro Weinstein wrote:
 Hi:
 
 I am plotting using markers, in a similar way than this example:
 
 http://matplotlib.sourceforge.net/examples/pylab_examples/legend_demo2.html
 
 As you can see in the example above, the markers in the legend appear
 twice:  'green circle' 'green circle' oscillatory.
 
 Is it possible to make the markers to appear only once, like  'green
 circle' oscillatory ?

You can use the keyword numpoints in the legend method:

legend( (l2, l4), ('oscillatory', 'damped'), 'upper right', shadow=True, 
numpoints=1)

should do the job.

mm

 Regards,
 Alejandro.
 
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Re: [Matplotlib-users] Make markers in legend to appear only once

2008-12-01 Thread Manuel Metz
Alejandro Weinstein wrote:
 On Mon, Dec 1, 2008 at 7:13 AM, Manuel Metz [EMAIL PROTECTED] wrote:
 You can use the keyword numpoints in the legend method:
 
 Thank you! It did the trick.
 
 Now how you conclude that from the documentation is a mystery:
 
From the docs:
 
 numpoints: integer
 The number of points in the legend line, default is 4

Ah, that's apparently a bug in the docs, which I've fixed in the sources.

 Regards,
 Alejandro.
 
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Re: [Matplotlib-users] Make markers in legend to appear only once

2008-12-01 Thread Manuel Metz
Manuel Metz wrote:
 Alejandro Weinstein wrote:
 On Mon, Dec 1, 2008 at 7:13 AM, Manuel Metz [EMAIL PROTECTED] wrote:
 You can use the keyword numpoints in the legend method:
 Thank you! It did the trick.

 Now how you conclude that from the documentation is a mystery:

 From the docs:
 
 numpoints: integer
 The number of points in the legend line, default is 4
 
 Ah, that's apparently a bug in the docs, which I've fixed in the sources.

I have to correct myself. John Hunter applied a patch which fixed the docs.

 Regards,
 Alejandro.

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Re: [Matplotlib-users] Please help with 3d scatter plot

2008-10-27 Thread Manuel Metz
Jeremy Conlin wrote:
 I have a function (shown below) that would take a 3D numpy array and plot
 points in 3D.  I recently updated my matplotlib with the latest Enthought
 Python Distribution and now it doesn't work; I guess matplotlib changed the
 api a little bit.
 
 The first problem arises because there is no matplotlib.axes3d anymore.  I
 can't find the equivalent in the newest version.  Can someone help me figure
 this out?

The axes3d support has been completely removed in matplotlib 0.98.x

 Thanks,
 Jeremy
 
 #===
 import matplotlib.pyplot as pyplot
 import matplotlib.axes3d as p3
 
 def PlotPoints(P):
 
 
 fig = pyplot.figure()
 ax = p3.Axes3D(fig)
 ax.plot3D(P[:,0],P[:,1],P[:,2],'.')
 pyplot.show()
 return ax
 
 
 
 
 
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Re: [Matplotlib-users] Using Hex number with shape syntax

2008-08-04 Thread Manuel Metz
stuartornum wrote:
 Hi,
 
 I am just playing around with different shapes and colours at the moment, I
 have managed the standard colours like this:
 
 plot(Time, Value, 'r.')
 
 Which obviously prints a red dot.
 
 However how do use the hex colour map with the ., I have tried:
 
 plot(Time, Value, '#330066.')
 plot(Time, Value, '#330066,.')
 plot(Time, Value, '#330066' '.')
 plot(Time, Value, '#330066', '.')
 
 Not quite sure on the syntax.
 

Use the named kwarg linestyle:

   plot(Time, Value, '#330066', linestyle='.')


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Re: [Matplotlib-users] draw upper and lower limits

2008-07-31 Thread Manuel Metz
Antonino Cucchiara wrote:
 Hi,
 I have some graphs with lower and upper limits. I found a couple of 
 ideas online, but nothing like plotting symbols like arrows.
 I am using the mathtex upperarrow symbol but it is quite unconfortable 
 positioning the tex character in the righ X-Y position.
 Do you know if there is an easier way to plot arrows as markers?
 
 Thanks,
 Nino
 

Have a look at examples/pylab_examples/errorbar_limits.py. This shows 
how to plot upper/lower limits errorbars ... (if this is what you need)


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Re: [Matplotlib-users] how add axes scale to my plot?

2008-07-30 Thread Manuel Metz
sa6113 wrote:
 I am using matplotlib to draw and show my plot, now I want to know how may I
 add manual axes scale to it.
 I need to manually show the axes scale (from min to max value that I have)
 the below is some part of my code.
 .
 .
 .
 from   matplotlib.figureimport Figure
 
 self.fig = Figure(  figsize =5, 4 ))
 yLine   = self.ax.plot(  xData,  yData,  'ro-', linewidth = 2   )
 fitLine = self.ax.plot(  xData,  fitData,'bo-', linewidth = 1   )
 self.ax.set_xlabel('X')
 self.ax.set_ylabel('Y )

Maybe this is what you need:

self.ax.set_xlim(xmin, xmax)

?




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Re: [Matplotlib-users] import pylab produces rounding error

2008-07-16 Thread Manuel Metz
John Hunter wrote:
 On Wed, Jul 16, 2008 at 6:12 AM, Angela Rivera Campos [EMAIL PROTECTED] 
 wrote:
 Hi, again

 I've trying to install everything, from the begining on another machine,
 this one's running openSUSE 10.3. So I've installed the latest versions of
 numpy, scipy and matplotlib and I've discovered something new which also
 happens in the first machine, the one with openSUSE 10.2. The first time I
 imported pylab this is what I got:

 -
 from pylab import *
 /usr/lib/python2.5/site-packages/gtk-2.0/gtk/__init__.py:69: GtkWarning:
 could not open display
 
 If you cannot open the display, most likely it is because either you
 are running as root (bad, bad) or you are running over a remot
 connection (ssh) and do not have X11 forwarding properly enabled or
 configures.  If you want to use mpl with an interactive window, you
 will need to have access to the display.  The fact that you see this
 error only on the first time you import pylab is typical of exceptions
 that are thrown at module import time -- python only tries to import
 once so you see the exception only once.  To solve this, trying
 running as a normal user rather than root or sudo, and if you are on a
 remote machine, try using ssh -X to enable X11 forwarding.  We will
 need to know more about exactly what you are doing to help.

For remote access you also need to allow the remote machine to access 
the display via xhost +name on the local machine.

 So googling a bit, I've found that to avoid this error an option would be to
 add, before the pylab import, the following:

 import matplotlib
 matplotlib.use('Agg')
 This way the results floating problem disappears and I've got the correct
 tuples, though now I can't make my script show the figure I'm trying to
 plot. Is this related with matplotlibrc configuration? I haven't modified
 this file and the only lines that are not commented are

 backend  : GTKAgg
 numerix  : numpy  # numpy, Numeric or numarray

 Running my script with and without these lines with --verbose-debug, I've
 found that when they're written I get: backend agg version v2.2
 and when they are not: backend GTKAgg version 2.10.6
 
 This isn't a problem with matplotlib, but with the connection to the
 display as I mentioned above.
 Hopefully once you get the display problem sorted out, all will be
 well.  Let us know.
 
 JDH
 
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Re: [Matplotlib-users] twinx memory leak

2008-07-15 Thread Manuel Metz

John Hunter wrote:

On Mon, Jul 14, 2008 at 3:05 PM, Michael Droettboom [EMAIL PROTECTED] wrote:

I can confirm this.

Commenting out del Gcf.figs[num] in Gcf.destroy (in _pylab_helpers.py)
also seems to resolve the leak.  But I have no idea why, so I won't
commit it just yet.  I don't have much time to look deeper now.  Does
anyone (who probably understands figure management better than me) have
an idea what might cause this?


Can you post the script you are using to test -- I am a little
confused from reading this thread by whether or not twinx is
implicated.  Also, I saw that you committed some changes vis-a-vis the
twinx leak

  r5747 | mdboom | 2008-07-11 13:21:53 -0500 (Fri, 11 Jul 2008) | 2 lines

  Fix memory leak when using shared axes.

so I thought that part was resolved already...

JDH


I use a modified version of the script Laurent Oget posted (see 
attachment). Here is the output if I don't comment out PL.close(1).


~/python/test$ python looptest.py -dGTK
0 GC 69354 69354 0 13854
100 GC 84354 150 0 15163
200 GC 99354 150 0 16306
300 GC 114354 150 0 17364
400 GC 129354 150 0 18576
~/python/test$ python looptest.py -dTK
0 GC 69521 69521 0 14065
100 GC 84521 150 0 15444
200 GC 99521 150 0 16581
300 GC 114521 150 0 17719
400 GC 129521 150 0 18715
~/python/test$ python looptest.py -dPS
0 GC 59307 59307 0 7705
100 GC 59307 0 0 8037
200 GC 59307 0 0 8038
300 GC 59307 0 0 8038
400 GC 59307 0 0 8038

(so for the window-less backend PS no objects are left)

And now I commented out the line PL.close(1):

~/python/test$ python looptest.py -dGTK
0 GC 69379 69379 0 13855
100 GC 69379 0 0 14253
200 GC 69379 0 0 14253
300 GC 69379 0 0 14253
400 GC 69379 0 0 14252

Manuel
import math
import gc
import pylab as PL
from matplotlib.cbook import report_memory

def looptest():
oldlen = 0
for i in xrange(401):
fig=PL.figure(1)
ax = fig.gca()
ax=fig.add_subplot(211)
ax.set_position((0,0,0.9,0.45))
ax1=PL.twinx(ax)
t = PL.arange(1000)
st = PL.sin(t*0.01)
ax.plot(t,st)
fig.clf()

# any of these causes a memleak
#PL.close(1)
#PL.close(fig)
#PL.close()

gc.collect()
val = report_memory(i)
if i % 100 == 0:
print i, GC,
print len(gc.get_objects()), len(gc.get_objects())-oldlen,
print len(gc.garbage),
print val
oldlen = len(gc.get_objects())

looptest()-
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Re: [Matplotlib-users] twinx memory leak

2008-07-14 Thread Manuel Metz
Michael Droettboom wrote:
 Thanks for the report.  So we can diagnose this, what version of 
 matplotlib are you reporting this for?
 
 Also, you may be interested in the following FAQ (and the one following it):
 
 http://matplotlib.sourceforge.net/faq.html#LEAKS

Hi,

   I tested this with the lastest svn, and I do also see a leak. But 
it's not related to twinx, but to pylab.close(). If I just comment out 
this one line, the memleak disappears ...

Manuel

 Cheers,
 Mike
 
 laurent oget wrote:
 i forgot two imports.

 import math
 import gc
 import pylab as PL


 def looptest():
 while(1):
 fig=PL.figure(1)
 ax=fig.add_subplot(211)
 ax.set_position((0,0,0.9,0.45))
 ax1=PL.twinx(ax)
 t=range(1000)
 st=[math.sin(x*0.01) for x in t]
 ax.plot(t,st)
 fig.clf()
 PL.close(1)
 gc.collect()
 print GC
 print len(gc.get_objects())
 print len(gc.garbage)
 looptest()
 2008/7/11 laurent oget [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]:

 I think i narrowed down the memory leak i have been chasing for a
 while.
 If i remove the call to twinx i get a slow leak, which would cause
 me trouble
 after a very long time. With the call to  twinx, however i am
 losing thousands of objects
 at each loop.

 Thanks,

 Laurent


   
 import pylab as PL
 def looptest():
 while(1):
 fig=PL.figure(1)
 ax=fig.add_subplot(211)
 ax.set_position((0,0,0.9,0.45))
 ax1=PL.twinx(ax)
 t=range(1000)
 st=[math.sin(x*0.01) for x in t]
 ax.plot(t,st)
 fig.clf()
 PL.close(1)
 gc.collect()
 print GC
 print len(gc.get_objects())
 print len(gc.garbage)
 looptest()
 


 

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Re: [Matplotlib-users] twinx memory leak

2008-07-14 Thread Manuel Metz
Michael Droettboom wrote:
 Which backend?

GTK, GTKAgg, TK, but not with any backend without a window: Agg, Cairo, 
PS, PDF, SVG ...

Cheers,
   Manuel

 Cheers,
 Mike
 
 Manuel Metz wrote:
 Michael Droettboom wrote:
 Thanks for the report.  So we can diagnose this, what version of 
 matplotlib are you reporting this for?

 Also, you may be interested in the following FAQ (and the one 
 following it):

 http://matplotlib.sourceforge.net/faq.html#LEAKS

 Hi,

   I tested this with the lastest svn, and I do also see a leak. But 
 it's not related to twinx, but to pylab.close(). If I just comment out 
 this one line, the memleak disappears ...

 Manuel

 Cheers,
 Mike

 laurent oget wrote:
 i forgot two imports.

 import math
 import gc
 import pylab as PL


 def looptest():
 while(1):
 fig=PL.figure(1)
 ax=fig.add_subplot(211)
 ax.set_position((0,0,0.9,0.45))
 ax1=PL.twinx(ax)
 t=range(1000)
 st=[math.sin(x*0.01) for x in t]
 ax.plot(t,st)
 fig.clf()
 PL.close(1)
 gc.collect()
 print GC
 print len(gc.get_objects())
 print len(gc.garbage)
 looptest()
 2008/7/11 laurent oget [EMAIL PROTECTED] mailto:[EMAIL PROTECTED]:

 I think i narrowed down the memory leak i have been chasing for a
 while.
 If i remove the call to twinx i get a slow leak, which would cause
 me trouble
 after a very long time. With the call to  twinx, however i am
 losing thousands of objects
 at each loop.

 Thanks,

 Laurent


   import pylab as PL
 def looptest():
 while(1):
 fig=PL.figure(1)
 ax=fig.add_subplot(211)
 ax.set_position((0,0,0.9,0.45))
 ax1=PL.twinx(ax)
 t=range(1000)
 st=[math.sin(x*0.01) for x in t]
 ax.plot(t,st)
 fig.clf()
 PL.close(1)
 gc.collect()
 print GC
 print len(gc.get_objects())
 print len(gc.garbage)
 looptest()
 


  


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Re: [Matplotlib-users] import pylab produces rounding error

2008-07-10 Thread Manuel Metz
Angela Rivera Campos wrote:
 Hi,
 
 I'm quite a newbie on matplotlib.
 
 I'm trying to get some data from a file. I've got a function that reads 
 the data from the file and stores it in a tuple as a set of floats. When 
 I use this without importing pylab it just go well but when I do it 
 after importing this module there's a rounding and I don't get the 
 proper data:
 
 
   import myModule as m
   spc = m.Collection()
   spc.ReadCollection('file')
   sp = spc.GetCSVBlock('00074')
   sp.GetDataRecord(0)
 (0.0, 0.10001, 0.0503450001, 616.0, 
 24.818, 616.0)
 
 ---
 
   import myModule as m
   from pylab import *
   spc = m.Collection()
   spc.ReadCollection('file')
   sp = spc.GetCSVBlock('00074')
   sp.GetDataRecord(0)
 (0.0, 0.0, 0.0, 616.0, 24.0, 616.0)
 
 
 What's the problem here? What can I do to avoid it?

Try

   import pylab

instead of

   from pylab import *

Manuel


 Thanks in advance,
 
 AR
 
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Re: [Matplotlib-users] Bug: mad interference between matplotlib and openbabel

2008-06-26 Thread Manuel Metz
Hi Florian,
   you should try import pylab or import pylab as P. from pylab 
import * might overwrite some functions or methods ... if a pylab 
function/method has the same name as one in a module imported with * before.

See the following example:

#file a.py
def foo():
 print I'm a

# file b.py
def foo():
 print I'm b

# file import_ab.py
from a import *
foo()
from b import *
foo()

The output is:
I'm a
I'm b

as the function foo() is overwritten by the second import...

Manuel


Florian Koelling wrote:
 Hi folks!
 
 I' m working on a code to identify ligand's information from pdb crystal
 structures. For this purpose I use the openbabel package. I' m encoding
 the ligand's information  in smarts.
 For  checking  if the smarts are assigned correctly I 'm writing a sdf
 file (to control whether the features are placed correctly).
 
 This part works fine - but I get into deep trouble when I try to plot
 simple count statistics of my smarts, when I use the from pylab
 import* , or from pylab import matplotlib statements (trouble appears
 just after IMPORTING - I do not use a pylab function in this state of
 the program yet):
  
 Smart features are not recognized anymore, the feature coordinates are 
 shifted and  so  on -  But  I don' t know why.
 
 my code snip:
 
 
 
 
 import os
 from numpy import*
 from time import*
 
  SMARTING
 import numpy
 
 import openbabel
 from openbabel import*
 import pybel
 from pybel import*   
 
  LIGAND DETECTION
 import Bio.PDB
 from Bio.PDB import*
 import Numeric
 from Bio.PDB.StructureBuilder import *
 
 
 #from pylab import* -- RAISES THE PROBLEMS 
  
 
 def projecting_smarts(isolated_ligand, method ,color, output):


  Bio PDB- 2 get ligand coords
 parser =PDBParser()

 structure = parser.get_structure('s', isolated_ligand)
 atom = structure.get_atoms()   
 ###
 
 
 print smarting successfully started!

 mol = readfile(pdb, isolated_ligand).next()
 

 smart_list= []   

 result_acceptor = method.findall(mol)#finds acceptors


 for i in result_acceptor:#Result
 Donor= list from tuples
 list_element1 = (list(i)[0]) # - 
 resolve hierarchy
 smart_list.append(list_element1)

 print smart_list,ACCEPTOR_LIST #list of smart features
 
 
 
 
 Maybe one of you might know what to do!
 
 Thanx alot!
 
 flo
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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Re: [Matplotlib-users] Version 0.98 behavior change - scatter

2008-06-16 Thread Manuel Metz
Eric Firing wrote:
 Michael Droettboom wrote:
 As a quick-fix workaround, you can do:

 from matplotlib.pyplot import *
 p = scatter([0,1,2,3], [4,5,6,7], c ='k', alpha=0, edgecolor = 'k')
 p._alpha = 1.0
 p.set_edgecolor('k')
 show()

 But the deeper question is for the rest of the list is... what's the 
 correct behavior?  Should we just revert to what it did in 0.91, or add 
 another kwarg to set the edge alpha?
 
 I think 0.91 behavior was odd, if alpha applied only to the fill; making 
 alpha apply to everything strikes me as a bugfix, not a regression, so I 
 would not favor reverting to the old behavior.
 
 What is really needed may be some rethinking (or perhaps just 
 codification) of overall alpha handling throughout mpl, including kwargs 
 and explicit color specification.  At present it seems rather messy, for 
 understandable historical reasons, partly owing to backend quirks and 
 limitations (e.g., no alpha at all in postscript).
 
 If the kwarg strategy is chosen, then everywhere there can be an edge 
 and a face, we should support alpha= to apply to both, edgealpha= 
 for the edge alone, and facealpha= for the face.  Or something like that.

+1

 Eric
 
 Cheers,
 Mike

 S Murthy Kambhampaty wrote:
 There seems to have been a change to the behavior of the 'alpha' keyword 
 option to scatter(): where previously alpha only affected the facecolor, 
 and the edgecolor always had an alpha of 1.0, alpha now seems to affect 
 both facecolor and edgecolor.  Tested with 0.93.1 and 0.98.  Tested with 
 new API for 0.98 as well.

 ax.scatter(xSeries, ySeries, s=sY, c='k', alpha=0, edgecolor='k')

 and 

 plot1=ax.scatter(xSeries, ySeries, s=sY, c='k')
 plot1.set_alpha(0)
 plot1.set_edgecolor('k')

 Is there any way to get the old behavior using version 0.98 and forward?

 Thanks,
Murthy



   

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Re: [Matplotlib-users] How is the size value used to generate symbols?

2008-05-23 Thread Manuel Metz
Neil Crighton wrote:
 I'd like to plot values where the area of a marker is proportional to
 some value.  How is the size value given in, say:
 
 scatter(x,y,'o',s=10)
 
 used to generate the markers?  By eye it looks like the size value is
 proportional to the area (i.e. proportional to the radius squared for
 circle markers), but it would be nice to know for sure.

Hi Neil,

good eyes ;-) Have a look at the scatter documentation:

s is a size in points^2.  It is a scalar
or an array of the same length as x and y.

Manuel

 Thanks,
 Neil
 
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Re: [Matplotlib-users] hist is broken in SVN when using numpy 1.1.0.dev5077

2008-05-19 Thread Manuel Metz
Hi Glenn,

please update numpy!!! Indeed, it is the other way around: The new 
keyword-arg isn't deprecated it is *NEW* (has been added in numpy 
revision r5085, you are using r5077). Have a look at this:

http://projects.scipy.org/scipy/numpy/roadmap#Semanticchangeforhistogram

Please note that this also means a change in the semantic of the 
matplotlib hist API, see API_CHANGES.

Manuel

G Jones wrote:
 Hello,
 I am using r5186 from the SVN with numpy 1.1.0.dev5077. When I try
 hist(rand(512),arange(-128,127))
 I get:
 ---
 type 'exceptions.TypeError' Traceback (most recent call last)
 
 /home/gej/casper_work/backend/qtSpec/src/ipython console in module()
 
 /usr/lib/python2.5/site-packages/matplotlib/pyplot.py in hist(*args, **kwargs)
1688 hold(h)
1689 try:
 - 1690 ret =  gca().hist(*args, **kwargs)
1691 draw_if_interactive()
1692 except:
 
 /usr/lib/python2.5/site-packages/matplotlib/axes.py in hist(self, x,
 bins, normed, cumulative, bottom, histtype, align, orientation, width,
 log, **kwargs)
5472 if not self._hold: self.cla()
5473 n, bins = np.histogram(x, bins, range=None,
 - 5474 normed=bool(normed), new=True)
5475
5476 if cumulative:
 
 type 'exceptions.TypeError': histogram() got an unexpected keyword
 argument 'new'
 
 I guess the new keyword argument has been deprecated?
 
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Re: [Matplotlib-users] Easiest way of drawing a circle?

2008-05-08 Thread Manuel Metz
Søren Nielsen wrote:
 Hi,
 
 I'm using wxpython with matplotlib, I now have a figurecanvas embedded in my
 program and I can plot stuff using:
 
 a = self.fig.gca()
 a.plot(x,y)
 
 But what is the easiest and fastest way to draw a circle? I saw that the
 artist class has a draw_arc function.. but I don't know how to use the
 artist class with my figure canvas.. Like I can't do a.draw_arc() for
 instance ...
 
 Can anyone point me in the right direction?
 
 Thanks,
 Soren
 

from matplotlib.patches import Circle
cir = Circle( (0,0), radius=0.5)
a.add_patch(cir)

Manuel

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Re: [Matplotlib-users] Custom Pie-Like Marker In Scatter

2008-04-18 Thread Manuel Metz

Andrea Gavana wrote:

Hi All,

   I was wondering about custom markers in the scatter method, and I
thought to ask here for some suggestions.
Basically, I have 3 variables to show, which are oil, gas and water
production. I would like to define the bubble size by the sum of these
three variables (or something akin), and then I would like to be able
to split the bubble marker in 3 sections (like having a small pie
chart in place of the marker), with each section area proportional to
the value of oil, gas and water production respectively. I know this
might sound not very clear, I attach a small picture of what I mean
(the picture shows the bubble divided into 2 sections, but the purpose
is the same).
I know about custom marker, but I am not so expert with matplotlib to
be able to implement it... could someone please share some suggestion
on how to do this?

Thank you very much.

Andrea.


Hi,
as you already suggested, you have to do a little hand-work, but its not 
too hard. I attached an example, which you can use as a starting point...


Manuel


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inline: pie_example.pngimport pylab
from numpy import *

#
# first define the ratios
#

r1 = 0.2  # 20%
r2 = r1 + 0.4 # 40%

#
# define some sizes of the scatter marker
#
sizes = [60,80,120]

#
# calculate the points of the first pie marker
#
# these are just the origin (0,0) +
# some points on a circle cos,sin
#
x = [0] + cos(linspace(0, 2*math.pi*r1, 10)).tolist()
y = [0] + sin(linspace(0, 2*math.pi*r1, 10)).tolist()
xy1 = zip(x,y)

# ...
x = [0] + cos(linspace(2*math.pi*r1, 2*math.pi*r2, 10)).tolist()
y = [0] + sin(linspace(2*math.pi*r1, 2*math.pi*r2, 10)).tolist()
xy2 = zip(x,y)

x = [0] + cos(linspace(2*math.pi*r2, 2*math.pi, 10)).tolist()
y = [0] + sin(linspace(2*math.pi*r2, 2*math.pi, 10)).tolist()
xy3 = zip(x,y)


pylab.scatter( arange(3), arange(3), marker=(xy1,0), s=sizes, facecolor='blue' )
pylab.scatter( arange(3), arange(3), marker=(xy2,0), s=sizes, facecolor='green' )
pylab.scatter( arange(3), arange(3), marker=(xy3,0), s=sizes, facecolor='red' )
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Re: [Matplotlib-users] contour plot axis labels

2008-04-08 Thread Manuel Metz
Jochen Küpper wrote:
 Hi,
 
 when I create a contour plot with the following grid:
xval = [ 1.3324,  1.9971,  1.00016618]
yval = [250, 260, 270]
data = ones((3,3))
contourf(xval, yval, data)
 
 matplotlib creates a contour plot with an x-axes labels of  
 0.324, ... and adds a +1 in the lower right corner.
 Actually, it is often not visible at all.
 
 How can I set it to always use the correct values directly as labels?
 
 Greetings,
 Jochen

Hi, you can use

gca().xaxis.set_major_formatter(ScalarFormatter(useOffset=False))

see also examples/newscalarformatter_demo.py

Manuel

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Re: [Matplotlib-users] How do I widen the space for y coordinate ticks?

2008-04-03 Thread Manuel Metz
carlwenrich wrote:
 without having to increase the width of the whole chart?

Have a look at examples/major_minor_demo1.py and 
examples/major_minor_demo2.py. I guess you are looking for something 
like this ...

Manuel


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Re: [Matplotlib-users] Efficient scatter() w/ markers from plot()?

2008-03-20 Thread Manuel Metz
Ted Drain wrote:
 I need to efficiently plot a set of x,y points where each point has a
 different color.  I tried multiple calls to plot() with a single point each
 but that is way too slow.  I switched to using scatter() and passing in a
 list of colors which works great.  However, I'd really like to have the
 marker options from plot() (things like '+' and 'x') which don't work w/
 scatter.
 
 What's the easiest way to get the markers from plot() with the efficiency
 (and multi-colors) from scatter?
 
 Thanks,
 Ted
 

Hi Ted,
oh - you can use '+' and 'x' and many more markers with scatter. It's 
unfortunately just not documented in the current release but is fixed in 
the repository.

   pylab.scatter(x,y, marker=(4,2))

gives a '+', and

   pylab.scatter(x,y, marker=(4,2,math.pi/4.))

gives a 'x'. The logic is a follows:

   marker(numside, type, angle)

numside is the number of edges, i.e. 4 for a plus or a cross.

type : 0 - a filled symbol,
1 - a star-like symbol,
2 - a asterisk like symbol

angle: the symbol gets rotated by this angle

So in principle with this you can produce an endless number of different 
markers... :-)

Manuel

-- 
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   Argelander Institut fuer Astronomie
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Re: [Matplotlib-users] Point-specific colors with scatter

2008-03-14 Thread Manuel Metz
Fred Mailhot wrote:
 Hi there,
 
 I've got 4 time series that live in a 2-d space (imagine points at
 (1,1), (1,2),(2,1), and (2,2) that drift a little over time), and I'm
 using scatter() to show them. How can I plot so that each of the
 groups of points has the same colour?
 
 I've checked the docs and examples and can't seem to find quite what
 I'm looking for. A sample script or indication of where to look in the
 docs would be appreciated.
 
 Many thanks!
 Fred.


What you can do is something like this:

   x = arange(4) # just some test-data
   y = x**2

   c = ['#ff', '#cc3300', '#996600', '#66cc00'] # the color sequence

   pylab.scatter(x,y, color=c)

I think you get what you are looking for if you do this for each group 
separately.

Manuel

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Re: [Matplotlib-users] Scatter legend doesn't show markers

2008-02-23 Thread Manuel Metz
Erik Tollerud wrote:
 I use the scatter(x,y) command to make scatter plots, but I noticed
 today (on the SVN version of mpl) that when I call legend() after
 giving scatter(x,y,label='somelabel') , the legend doesn't show the
 marker symbols  - it only has a square patch colored in the color that
 was used for the scatter plot.  Is this a bug, or intended behavior?
 (and is there a work-around to show the marker symbols in the legend?)

Hi Erik,

I would say it's neither a bug nor an intended bahavior. It's just not 
implemented -- so you might call it a misbehaviour ;-)

I too hope that this will be fixed/added, since it's an issue open some 
time now (I guess since scatter was implemented !?)

Manuel

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Re: [Matplotlib-users] dashes and dpi?

2008-02-01 Thread Manuel Metz
Mark Bakker wrote:
 Alan -
 
 You started a discussion about dpi on the figures.
 Yet here you claim that 1pt = 1/72 inch.
 Is that always the case?

Yes, I that's *by definition* always the case !

pt is a point - not a dot or a pixel !!!

Point is a unit of measurement used in typography that is equal to 
1/72 inch. It is used primarily for representing the height of 
characters and the amount of space between lines, also known as leading.

   -- see http://support.microsoft.com/kb/76388

Manuel

 And why? How does mpl figure that out, if there are also different dpi
 settings?
 The plot thickens...
 
 Mark
 
 
 Alan Isaac wrote:
 
 
 Note: 1pt = 1/72 inch

 hth,
 Alan Isaac

 
 
 
 
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Re: [Matplotlib-users] Subplot Questions

2008-01-28 Thread Manuel Metz
Cheng-Kong Wu wrote:
 Dear all,
 
 I am working on sending vibration results to two
 plots: subplot(211) and subplot(212). I have the
 following questions:
 
 1. How to define the size of the figure? I will
 eventually import the figure into Microsoft Word, and
 I hope I can fit the figure into one page.

fig = pylab.figure(figsize=(6,10), dpi=96)
[...]
pylab.savefig(filename.eps, dpi=96)

,where figsize in the figure size in inches.

 2. If I want to make both the subplots square sized,
 how do I achieve it?

xylims = (-10,10) # set your axis limits here
pylab.gca().set_xlim(xylims)
pylab.gca().set_ylim(xylims)
pylab.gca().set_aspect('equal')

That's the quick-and-easy way. If the limits differ, you can create your 
own new axes instance, have a look at axes_demo.py in the examples.

Manuel

 Thanks!
 Cheng-Kong
 
 
   
 
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Re: [Matplotlib-users] [matplotlib] gscatter

2008-01-10 Thread Manuel Metz
Hi,
you are limited to 10 named symbols. But you can use much more symbols 
with scatter !!! Have a look at examples/scatter_star_symbols.py.

You can use:

   pylab.scatter(x,y,marker=(5,0))

produces a 5-sided regular polygon.

   pylab.scatter(x,y,marker=(5,1))

produces a starlike polygon

   pylab.scatter(x,y,marker=(5,2))

produces an asterisk.

You can even define your own symbols by defining the vertices of a polygon:

   verts = zip( [x1,x2,x3...], [y1,y2,y3,...])
   pylab.scatter(x,y,marker=(verts,0))

Note that there is a third, optional parameter for the marker keyword, 
ie. marker=(5,0,math.pi/4.) that defines the rotation of a symbol.

Manuel

[EMAIL PROTECTED] wrote:
 I was wondering if there exist a functino like Matlab (TM) gscatter in 
 matplot lib but I coulnd't find one.
 I also seen that in matplot lib we are limited to 10 symbols in scatter 
 while in MT we have 13 (and I have to plot 12 :)))
 is it possible to implement the new function (gscatter) and other symbols 
 ;)
 thanks
 Giorgio
 
 
 
 
 
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Re: [Matplotlib-users] [matplotlib] gscatter

2008-01-10 Thread Manuel Metz
[EMAIL PROTECTED] wrote:
 Thanks ! i didn't know that.
 Do you know also if it is possible to have something similar to a scatter 
 group ?

Sorry, but what do you mean by scatter group ?

 Thanks
 Giorgio


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Re: [Matplotlib-users] [matplotlib] gscatter

2008-01-10 Thread Manuel Metz
[EMAIL PROTECTED] wrote:
 matalb has a gscatter command that work like this
 
 GSCATTER(X,Y,G) creates a scatter plot of the vectors X and Y
 grouped by G.  Points with the same value of G are shown with
 the same color and marker.  G is a grouping variable defined as
 a vector, a cell array of strings, or a string matrix, and it
 must have the same number of rows as X and Y.  Alternatively
 G can be a cell array of grouping variables (such as {G1 G2 G3})
 to group the values in X by each unique combination of grouping
 variable values.
  
 GSCATTER(X,Y,G,CLR,SYM,SIZ) specifies the colors, markers, and
 size to use.  CLR is either a string of color specifications or
 a three-column matrix of color specifications.  SYM is a string
 of marker specifications.  Type help plot for more information.
 For example, if SYM='o+x', the first group will be plotted with a
 circle, the second with plus, and the third with x.  SIZ is a
 marker size to use for all plots.  By default, the marker is '.'.
  
 GSCATTER(X,Y,G,CLR,SYM,SIZ,DOLEG) lets you control whether legends
 are created.  Set DOLEG to 'on' (default) or 'off'.
  
 GSCATTER(X,Y,G,CLR,SYM,SIZ,DOLEG,XNAM,YNAM) specifies XNAM and
 YNAM as the names of the X and Y variables.  Each must be a
 character string.  If you omit XNAM and YNAM, GSCATTER attempts to
 determine the names of the variables passed in as the first and
 second arguments.
  
 H = GSCATTER(...) returns an array of handles to the objects
 created.
  
 Example:  Scatter plot of car data coded by country.
load carsmall
gscatter(Weight, MPG, Origin)
  
 See also grpstats, grp2idx.
 
 it's very very useful instead of doing multiple scatter and merging them 
 togheter. I think it can be easily implemented but i don't know how much 
 request there is for it.
 
 
 Giorgio
 

I don't think something like that work in matplotlib with scatter for 
the marker parameter. But it's possible to use an array of sizes and 
colors, ie.

   s = [20,30,40]
   x = arange(3)
   y = arange(3)

   scatter(x,y,s=s)

See scatter doc string:

Arguments s and c can also be given as kwargs; this is encouraged
 for readability.

 s is a size in points^2.  It is a scalar
   or an array of the same length as x and y.

 c is a color and can be a single color format string,
   or a sequence of color specifications of length N,
   or a sequence of N numbers to be mapped to colors
   using the cmap and norm specified via kwargs (see below).
   Note that c should not be a single numeric RGB or RGBA
   sequence because that is indistinguishable from an array
   of values to be colormapped. c can be a 2-D array in which
   the rows are RGB or RGBA, however.

Manuel

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Re: [Matplotlib-users] setting manual axis range?

2007-10-30 Thread Manuel Metz


Darran Edmundson wrote:
 Two simple questions:
 
 1) How does one create a simple xy plot with a user-specified y-axis 
 range?  Combination of setting kwargs ylim and autoscale_on doesn't seem 
 to do it ...

pylab.ylim( (ymin, ymax) )

or

pylab.gca().set_ylim( (ymin, ymax) )

?

 2) If I want to regenerate this plot with revised y data (but same 
 axes), what is the quickest option?  At the moment I'm doing an 
 ax.clear(), presumably tossing out everything and starting from scratch.

I do it this way - just replot everthing ...

 As always, any help is much appreciated.
 
 Cheers,
 Darran.
 

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[Matplotlib-users] facecolor and scatter

2007-10-18 Thread Manuel Metz
It seems that the keywords facecolor (or color) and alpha can not be 
used simultaniously when using scatter:


import pylab

x = pylab.npy.arange(0,10)
pylab.scatter(x,x, s=50, alpha=0.5)
pylab.scatter(x,x+0.5, facecolor='blue', s=50, alpha=0.5)
pylab.show()


The alpha value of the second call is not set correctly, but kept fix at 
alpha=1.0. Any idea ???

Manuel


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Re: [Matplotlib-users] facecolor and scatter

2007-10-18 Thread Manuel Metz
John,
svn works fine now. thanks.

John Hunter wrote:
 On 10/18/07, John Hunter [EMAIL PROTECTED] wrote:
 
 You should use the c argument for scatter -- this controls the facecolor.

 scatter(x,x+0.5, c='blue', s=50, alpha=0.5)

 This is a bit of an anachronism from matlab compatibility.
 
 This is now fixed in svn, so you can use facecolor as well.  Note that
 for constant size and color markers, plot will be significantly faster
 
   ax.plot(x, x+0.5, mfc='blue', alpha=0.5, ms=20)
 
 JDH


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Re: [Matplotlib-users] error bars on scatter plot

2007-09-13 Thread Manuel Metz
Hi,

pylab.scatter(x,y)
pylab.errorbar(x,y,yerr,linestyle='None')

if you want to use scatter, or alternatively:

pylab.errorbar(x,y,yerr,fmt='o',linestyle='None')

Manuel

Armen Nalian wrote:
 Hello,
 I was wondering where I can get an example of a scatter plot with error 
 bars.
 I have time measurements and the stds
 0   23   0.23
 1   25.1   0.21
 4   27   0.1
 7   29   0.21
 9  35   0.1
 
 
 how can I get a scatter plot with error bars? I know I can get a bar 
 plot, but I need just a symbol with error bars.
 Thank you,
 Armen
 
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Re: [Matplotlib-users] error bars on scatter plot

2007-09-13 Thread Manuel Metz
Hi,

pylab.scatter(x,y)
pylab.errorbar(x,y,yerr,linestyle='None')

if you want to use scatter, or alternatively:

pylab.errorbar(x,y,yerr,fmt='o',linestyle='None')

Manuel

Armen Nalian wrote:
 Hello,
 I was wondering where I can get an example of a scatter plot with error 
 bars.
 I have time measurements and the stds
 0   23   0.23
 1   25.1   0.21
 4   27   0.1
 7   29   0.21
 9  35   0.1
 
 
 how can I get a scatter plot with error bars? I know I can get a bar 
 plot, but I need just a symbol with error bars.
 Thank you,
 Armen
 
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Re: [Matplotlib-users] combine eps files into a ps file ?

2007-09-12 Thread Manuel Metz
On a Linux box:
   psmerge -ooutfile.ps figure1.eps figure2.eps

Anyway, I guess you need an external tool to do this ...

Manuel

Lingyun Yang wrote:
 Hi,
 
I am using matplotlib to visualize my data, but the data sometimes have
 several sets.
 Can I plot each set as usual to a EPS file, and combine these EPS file into
 a single ps file,
 each page of this ps file is only one EPS file I got before.
 
 
 Thanks.
 
 Lingyun
 
 
 
 
 
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