matplotlib-users Mailing List for matplotlib

Pau,

linewidth=xx (or lw=xx) does that job in scatter plots.  Also see
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.scatterthough
really it isn't very clear and I found it out by accident

Regards,
Ian

----
Ian Bell
Graduate Research Assistant
Herrick Labs
Purdue University
email: ib...@pu...
cell: (607)227-7626


On Tue, May 3, 2011 at 2:27 PM, Pau <vim...@go...> wrote:

> thanks!
>
> I wish there was something similar to markeredgewidth in scatter, though
>
> But it's doing what I wanted, thanks
>
> Pau
>
> On 3 May 2011 19:21, Buchholz, Greg <gbu...@in...> wrote:
> >    Maybe you want to use the "scatter" procedure?
> >
> >
> http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_demo.html?highlight=scatter
> >
> http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.scatter
> >
> >
> >> -----Original Message-----
> >> From: Pau [mailto:vim...@go...]
> >> Sent: Tuesday, May 03, 2011 10:04 AM
> >> To: matplotlib
> >> Subject: [Matplotlib-users] Use a variable for the ms option in the
> >> plot function
> >>
> >> Hello,
> >>
> >> I am looking for a way to feed
> >>
> >> R=log(M)
> >>
> >> to plot in the ms field ("HERE" in the example):
> >>
> >> plot(X, Y, \
> >>                           marker='o', mec='black',ms=HERE,ls='None',\
> >>                           mfc='red',alpha=0.9,mew=2,antialiased=True)
> >>
> >>
> >> thanks,
> >>
> >> Pau
> >>
> >> -----------------------------------------------------------------------
> >> -------
> >> WhatsUp Gold - Download Free Network Management Software
> >> The most intuitive, comprehensive, and cost-effective network
> >> management toolset available today.  Delivers lowest initial
> >> acquisition cost and overall TCO of any competing solution.
> >> http://p.sf.net/sfu/whatsupgold-sd
> >> _______________________________________________
> >> Matplotlib-users mailing list
> >> Mat...@li...
> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
>
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

THANKS!!

I am not a native speaker and sometimes I find it very hard to find a
keyword to look for...

that tip was excellent, thank you a lot

On 3 May 2011 22:27, Buchholz, Greg <gbu...@in...> wrote:
>> From: Pau [mailto:vim...@go...]
>>
>> PS: I thought I would probably give a better example
>>
>> The goal is to have all the data files plotted in a single graph
>
> import glob
>
> for filename in glob.glob('*.dat'):
>    if 'e' in set(filename): #or whatever
>        #do something for files that have an 'e' in their name
>    else:
>        #do something else
>    loadtxt(filename) #yada, yada, yada
>    scatter() #etc.
>

> From: Pau [mailto:vim...@go...]
> 
> PS: I thought I would probably give a better example
> 
> The goal is to have all the data files plotted in a single graph

import glob

for filename in glob.glob('*.dat'):
    if 'e' in set(filename): #or whatever
        #do something for files that have an 'e' in their name
    else:
        #do something else
    loadtxt(filename) #yada, yada, yada
    scatter() #etc.

On 5/3/2011 2:37 PM, Pau wrote:
> I am afraid that I know the answer to the question: use python
>
> But my problem is that I do not really know python.

Fortunately, the documentation is excellent:
http://docs.python.org/library/glob.html

hth,
Alan Isaac

would it be easier to have all data in a single file and then tell
matplotlib to plot different parts of that file?

The file would look like:

.
.
.
  13.0576 -66.6586  -9.6419  34.1672  1.445e+05  4962
  13.0576 -55.4192  44.0864  16.7687  1.445e+05  4963
  13.0576 65.0328  -38.8888  -215.3602  1.445e+05  4964
  13.0576 -110.7375  -0.1741  -91.9251  5.459e+04  4512
.
.
.

The fifth column is what defines the transition between a file and the next one

How can I tell matplotlib to plot those data first with a certain
color and then the next data with a different color?


On 3 May 2011 21:38, Pau <vim...@go...> wrote:
> PS: I thought I would probably give a better example
>
>
> In a directory I have these files:
>
>
> 2537.dat
> 5043.dat
> 5075.dat
> 7581.dat
> 1.009e+04.dat
> 1.551e+04.dat
> 1.805e+04.dat
> 2.056e+04.dat
> 4.955e+04.dat
> 5.209e+04.dat
> 5.459e+04.dat
> 5.462e+04.dat
> 1.445e+05.dat
> 1.47e+05.dat
> 5.016e+05.dat
> 5.041e+05.dat
> 5.067e+05.dat
> 5.171e+05.dat
> 5.196e+05.dat
> 5.511e+05.dat
> 5.537e+05.dat
> 5.562e+05.dat
> 8.842e+05.dat
> 1.465e+06.dat
>
> I would like to plot them with matplotlib like this:
>
> -----------------------------------------------------------
> X = cluster[:, 1]  # Column 2
> Y = cluster[:, 2]  # Column 3
> M = cluster[:, 4]  # Column 5
> Radius = log(M)
>
>
> ylabel ('Y (pc)', size=18)
>
> scatter(X, Y, s=Radius,\
>        marker='o', color='red',\
>        edgecolors='black',\
>        alpha=0.9,antialiased=True)
>
> xlabel ('X (pc)', size=18)
> -----------------------------------------------------------
>
> where
>
> "cluster" runs from the first data file to the last one and
> "color" changes from one data file to the next one
>
> The goal is to have all the data files plotted in a single graph
>
> How could I do this?
>
> Thanks a lot
>
> P.
>
>
> On 3 May 2011 20:37, Pau <vim...@go...> wrote:
>> Hello,
>>
>> I am afraid that I know the answer to the question: use python
>>
>> But my problem is that I do not really know python. I just started and
>> I can do some nice plots with matplotlib but I don't really know
>> python.
>>
>> I am now running into a snag. I have different directories with
>> different number of data files
>>
>> Directory 1 ---> data1.dat data2.dat data3.dat data4.dat data5.dat
>> Directory 2 ---> data1.dat data2.dat data3.dat
>>
>> The number of files is huge, I do not want to run this one by one per hand.
>>
>> I am trying to do this with a shell script which actually prepares the
>> data files but I do not know how to tell matplotlib from the shell
>> script that the number of files is different and that it should use
>> different colours for different files.
>>
>> I can explain this in much more detail if needed, but I wanted to hear
>> a first impression.
>>
>> thanks,
>>
>> Pau
>>
>

PS: I thought I would probably give a better example


In a directory I have these files:


2537.dat
5043.dat
5075.dat
7581.dat
1.009e+04.dat
1.551e+04.dat
1.805e+04.dat
2.056e+04.dat
4.955e+04.dat
5.209e+04.dat
5.459e+04.dat
5.462e+04.dat
1.445e+05.dat
1.47e+05.dat
5.016e+05.dat
5.041e+05.dat
5.067e+05.dat
5.171e+05.dat
5.196e+05.dat
5.511e+05.dat
5.537e+05.dat
5.562e+05.dat
8.842e+05.dat
1.465e+06.dat

I would like to plot them with matplotlib like this:

-----------------------------------------------------------
X = cluster[:, 1]  # Column 2
Y = cluster[:, 2]  # Column 3
M = cluster[:, 4]  # Column 5
Radius = log(M)


ylabel ('Y (pc)', size=18)

scatter(X, Y, s=Radius,\
        marker='o', color='red',\
        edgecolors='black',\
        alpha=0.9,antialiased=True)

xlabel ('X (pc)', size=18)
-----------------------------------------------------------

where

"cluster" runs from the first data file to the last one and
"color" changes from one data file to the next one

The goal is to have all the data files plotted in a single graph

How could I do this?

Thanks a lot

P.


On 3 May 2011 20:37, Pau <vim...@go...> wrote:
> Hello,
>
> I am afraid that I know the answer to the question: use python
>
> But my problem is that I do not really know python. I just started and
> I can do some nice plots with matplotlib but I don't really know
> python.
>
> I am now running into a snag. I have different directories with
> different number of data files
>
> Directory 1 ---> data1.dat data2.dat data3.dat data4.dat data5.dat
> Directory 2 ---> data1.dat data2.dat data3.dat
>
> The number of files is huge, I do not want to run this one by one per hand.
>
> I am trying to do this with a shell script which actually prepares the
> data files but I do not know how to tell matplotlib from the shell
> script that the number of files is different and that it should use
> different colours for different files.
>
> I can explain this in much more detail if needed, but I wanted to hear
> a first impression.
>
> thanks,
>
> Pau
>

Hello,

I am afraid that I know the answer to the question: use python

But my problem is that I do not really know python. I just started and
I can do some nice plots with matplotlib but I don't really know
python.

I am now running into a snag. I have different directories with
different number of data files

Directory 1 ---> data1.dat data2.dat data3.dat data4.dat data5.dat
Directory 2 ---> data1.dat data2.dat data3.dat

The number of files is huge, I do not want to run this one by one per hand.

I am trying to do this with a shell script which actually prepares the
data files but I do not know how to tell matplotlib from the shell
script that the number of files is different and that it should use
different colours for different files.

I can explain this in much more detail if needed, but I wanted to hear
a first impression.

thanks,

Pau

thanks!

I wish there was something similar to markeredgewidth in scatter, though

But it's doing what I wanted, thanks

Pau

On 3 May 2011 19:21, Buchholz, Greg <gbu...@in...> wrote:
>    Maybe you want to use the "scatter" procedure?
>
> http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_demo.html?highlight=scatter
> http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.scatter
>
>
>> -----Original Message-----
>> From: Pau [mailto:vim...@go...]
>> Sent: Tuesday, May 03, 2011 10:04 AM
>> To: matplotlib
>> Subject: [Matplotlib-users] Use a variable for the ms option in the
>> plot function
>>
>> Hello,
>>
>> I am looking for a way to feed
>>
>> R=log(M)
>>
>> to plot in the ms field ("HERE" in the example):
>>
>> plot(X, Y, \
>>                           marker='o', mec='black',ms=HERE,ls='None',\
>>                           mfc='red',alpha=0.9,mew=2,antialiased=True)
>>
>>
>> thanks,
>>
>> Pau
>>
>> -----------------------------------------------------------------------
>> -------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> Matplotlib-users mailing list
>> Mat...@li...
>> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>

    Maybe you want to use the "scatter" procedure?

http://matplotlib.sourceforge.net/examples/pylab_examples/scatter_demo.html?highlight=scatter
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.scatter


> -----Original Message-----
> From: Pau [mailto:vim...@go...]
> Sent: Tuesday, May 03, 2011 10:04 AM
> To: matplotlib
> Subject: [Matplotlib-users] Use a variable for the ms option in the
> plot function
> 
> Hello,
> 
> I am looking for a way to feed
> 
> R=log(M)
> 
> to plot in the ms field ("HERE" in the example):
> 
> plot(X, Y, \
>                           marker='o', mec='black',ms=HERE,ls='None',\
>                           mfc='red',alpha=0.9,mew=2,antialiased=True)
> 
> 
> thanks,
> 
> Pau
> 
> -----------------------------------------------------------------------
> -------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Hello,

I am looking for a way to feed

R=log(M)

to plot in the ms field ("HERE" in the example):

plot(X, Y, \
                          marker='o', mec='black',ms=HERE,ls='None',\
                          mfc='red',alpha=0.9,mew=2,antialiased=True)


thanks,

Pau

Thank you very much,
it works very well now.
Cheers.

Emanuele Passera

Software Engineer

Tele-Rilevamento Europa - T.R.E. srl
Via Vittoria Colonna, 7
20149 Milano – Italia
Tel.: +39.02.4343.121 - Fax: +39.02.4343.1230
ema...@tr... - www.treuropa.com


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This communication, that may contain confidential and/or legally privileged
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Opinions, conclusions and other information contained in this message, that
do not relate to the official business of this firm, shall be considered as
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communication is subject to the terms and conditions provided by the
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On Thu, Apr 21, 2011 at 5:38 PM, Emanuele Passera <
ema...@tr...> wrote:

> Hello everybody,
>
> I am experiencing a strange behavior with the scatter() function when
> using different figure canvas y dimensions in inches.
>
> Executing the code listed below, I obtain good images when using some
> dimensions
> and totally white images when using others.
> I have attached the input data buffers and the resulting images too.
>
> #!/usr/bin/python
>
> import numpy as n
> import pylab as p
>
> def scatterFun(x, y, data, yCanvasDimInches, imageName):
>     """ This function draws a scatterogram for the input data. """
>     canvasObj = p.figure(figsize=(8, yCanvasDimInches), dpi=100)
>     axisObj = canvasObj.add_axes([0, 0, 1, 1])
>     axisObj.scatter(x, y, 10, data, 'o')
>     canvasObj.savefig(imageName, dpi=100)
>     p.close()
>
>
> # data buffer files
> yPosFile = "/users/lelepass/python/test_scatter/yPos"
> xPosFile = "/users/lelepass/python/test_scatter/xPos"
> dataFile = "/users/lelepass/python/test_scatter/data"
> # loading data
> s = file(dataFile, 'rb').read()
> data = n.fromstring(s, 'f')
> s = file(yPosFile, 'rb').read()
> y = n.fromstring(s, 'd')
> s = file(xPosFile, 'rb').read()
> x = n.fromstring(s, 'd')
>
> # scatterogram generation
> scatterFun(x, y, data, 6, "pippo1.png")
> scatterFun(x, y, data, 6.01, "pippo2.png")
> scatterFun(x, y, data, 6.015, "pippo3.png")
> scatterFun(x, y, data, 6.02, "pippo4.png")
> scatterFun(x, y, data, 6.028, "pippo5.png")
> scatterFun(x, y, data, 6.03, "pippo6.png")
>
> Can anyone help me ?
>
> I use
> Linux openSUSE 11.3 (x86_64)
> Linux sat1 2.6.34.7-0.7-default #1 SMP 2010-12-13 11:13:53 +0100 x86_64
> x86_64 x86_64 GNU/Linux
> Python       2.6.5
> numpy        1.5.1
> matplotlib   1.0.1 with backend Agg v2.2
>
> On the same system descripted above linking matplotlib from svn
> matplotlib-matplotlib-v1.0.1-756-g3c43d83.tar.gz instead of the installed
> one,
> all the images are white.
>
> If it can be of some help this strange behavior does not appear with a
> system
> Linux Ubuntu 9.10
> Linux joshua 2.6.28-11-server #42-Ubuntu SMP Fri Apr 17 02:48:10 UTC 2009
> i686 GNU/Linux
> Python       2.6.4
> numpy        1.3.0
> matplotlib   0.99.0 with backend Agg v2.2
>
> Executing the script with verbosity I get the subsequent output
>
> $HOME=/users/lelepass
> CONFIGDIR=/users/lelepass/.matplotlib
>
> Bad key "numerix" on line 30 in
> /users/lelepass/.matplotlib/matplotlibrc.
> You probably need to get an updated matplotlibrc file from
> http://matplotlib.sf.net/_static/matplotlibrc or from the matplotlib
> source
> distribution
> matplotlib data path /usr/lib64/python2.6/site-packages/matplotlib/mpl-data
> loaded rc file /users/lelepass/.matplotlib/matplotlibrc
> matplotlib version 1.0.1
> verbose.level helpful
> interactive is False
> units is True
> platform is linux2
> Using fontManager instance from /users/lelepass/.matplotlib/fontList.cache
> backend agg version v2.2
> findfont: Matching
> :family=sans-serif:style=normal:variant=normal:weight=normal:stretch=normal:size=medium
> to Bitstream Vera Sans
> (/usr/lib64/python2.6/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf)
> with score of 0.000000
>
>
> Thank you all.
> Bye.
>
> Emanuele Passera
>
> Software Engineer
>
> Tele-Rilevamento Europa - T.R.E. srl
> Via Vittoria Colonna, 7
> 20149 Milano – Italia
> Tel.: +39.02.4343.121 - Fax: +39.02.4343.1230
> ema...@tr... - www.treuropa.com
>
>
> --
> This communication, that may contain confidential and/or legally privileged
> information, is intended solely for the use of the intended addressees.
> Opinions, conclusions and other information contained in this message, that
> do not relate to the official business of this firm, shall be considered as
> not given or endorsed by it. Every opinion or advice contained in this
> communication is subject to the terms and conditions provided by the
> agreement governing the engagement with such a client. If you have received
> this communication in error, please notify us immediately by responding to
> this email and then delete it from your system. Any use, disclosure, copying
> or distribution of the contents of this communication by a not-intended
> recipient or in violation of the purposes of this communication is strictly
> prohibited and may be unlawful.
>  --
>

Hello,

I've been trying to animate some plots with the qt backend and run into 
a couple of problems.

Firstly,
I'd like to be able to update the axis limits in an automated fashion as 
the data changes size.

Secondly,
Resizing figures appears to redraw everything _but_ items with the 
animation flag.  The is causing me problems when the animation is paused 
or the frames are occurring slow enough such that there is a noticable 
period where the my lines disappear.

I've sort of solved both of these problems but the solutions seem 
hackish.  In particular updating the axis limits is slowing the 
animation by 25% and toggling the animated field using the qt events 
just feels like its asking for trouble.

Below is the qt animation example with my solutions.  Adjust the size of 
the plot after the animation finishes to see the effect of the resize 
hack.  I would be grateful if anyone could suggest some improvements.

Thanks,
Gerald.

# For detailed comments on animation and the techniqes used here, see

# the wiki entry http://www.scipy.org/Cookbook/Matplotlib/Animations

import os

import sys

#import matplotlib

#matplotlib.use('Qt4Agg')

from matplotlib.figure import Figure

from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas

from PyQt4 import QtCore, QtGui

ITERS = 100

import numpy as np

import time

class BlitQT(FigureCanvas):

     def __init__(self):

         FigureCanvas.__init__(self, Figure())

         self.ax = self.figure.add_subplot(111)

         #self.ax.grid()

         self.draw()

         self.old_size = self.ax.bbox.width, self.ax.bbox.height

         self.ax_background = self.copy_from_bbox(self.ax.bbox)

         self.cnt = 0

         self.x = np.arange(0,2*np.pi,0.01)

         self.sin_line, = self.ax.plot(self.x, np.sin(self.x), animated=True)

         self.cos_line, = self.ax.plot(self.x, np.cos(self.x), animated=True)

         self.draw()

         self.old_limits = self.ax.get_xlim(),self.ax.get_ylim()

         self.tstart = time.time()

         self.maintimer = self.startTimer(10)

     ## HACK for disapearing objects on resize

     def resizeEvent(self,evt):

         super(BlitQT,self).resizeEvent(evt)

         self.sin_line.set_animated(False)

     def paintEvent(self,evt):

         super(BlitQT,self).paintEvent(evt)

         self.sin_line.set_animated(True)

     def timerEvent(self, evt):

         current_size = self.ax.bbox.width, self.ax.bbox.height

         if self.old_size != current_size:

             self.old_size = current_size

             #self.ax.clear()

             #self.ax.grid()

             self.draw()

             self.ax_background = self.copy_from_bbox(self.ax.bbox)

         self.restore_region(self.ax_background)

         # update the data

         self.sin_line.set_ydata(np.sin(self.x+self.cnt/10.0)*self.cnt/100.0)

         self.cos_line.set_ydata(np.cos(self.x+self.cnt/10.0)*self.cnt/100.0)

         ## HACK for updating axis limits

         self.ax.relim()

         self.ax.autoscale_view()

         current_limits = self.ax.get_xlim(),self.ax.get_ylim()

         if self.old_limits != current_limits:

             self.old_limits = current_limits

             self.draw()

             self.ax_background = self.copy_from_bbox(self.ax.bbox)

             self.blit(self.figure.bbox)

          

         # just draw the animated artist

         self.ax.draw_artist(self.sin_line)

         self.ax.draw_artist(self.cos_line)

         # just redraw the axes rectangle

         self.blit(self.ax.bbox)

         if self.cnt == 0:

             # TODO: this shouldn't be necessary, but if it is excluded the

             # canvas outside the axes is not initially painted.

             self.draw()

         if self.cnt==ITERS:

             # print the timing info and quit

             print 'FPS:' , ITERS/(time.time()-self.tstart)

             #sys.exit()

             self.killTimer(self.maintimer)

         else:

             self.cnt += 1

app = QtGui.QApplication(sys.argv)

widget = BlitQT()

widget.show()

sys.exit(app.exec_())

A colleague posed an interesting challenge:
How to do a filled plot having the y-axis in logarithm?
I think I can do it with creating patches myself an adding it to the 
axis, but isn't there anything built-in?

Best regards,
Michael