matplotlib-users Mailing List for matplotlib

I figured it out!  I accidentally did something weird.  When I built NumPy and SciPy, I used the --user option to tell distutils to build them in my home directory. I had not realized that --user installs the packages in ~/.local/lib/python2.7/site-packages/.  I was assuming they would be installed in ~/lib/python2.7/site-packages, but I didn't notice they were "missing" until just now.  When I reinstalled NumPy and Scipy using the option --prefix=/home/cfinch and then rebuilt matplotlib, everything started working.  I didn't have to rebuild pycairo or pygtk; I just had to get everything in the same location.  This is the first I've heard of installing anything in a .local directory...why is that even an option???


Thanks for your help!



________________________________
From: Craig Finch <oa...@ya...>
To: Eric Firing <ef...@ha...>; "mat...@li..." <mat...@li...>
Sent: Wednesday, August 31, 2011 4:31 PM
Subject: Re: [Matplotlib-users] Problem with GTK backends after compiling matplotlib


I corrected the problem with the FreeType2 header file and rebuilt matplotlib from scratch, but I'm getting the same error.  Centos5 puts the file ft2build.h in /usr/lib but matplotlib looks for it in /usr/lib/freetype2.  I used this command:
PKG_CONFIG_PATH=/home/cfinch/lib/pkgconfig  python2.7 setup.py build &> build_log.txt
and got this output:


basedirlist is: ['/home/cfinch']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.0.1
                python: 2.7.2 (default, Aug 30 2011, 12:57:00) 
 [GCC 4.1.2
                        20080704 (Red Hat 4.1.2-50)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.6.1
             freetype2: 9.10.3

OPTIONAL BACKEND DEPENDENCIES
                libpng: 1.2.10
               Tkinter: no
                        * TKAgg requires
 Tkinter
              wxPython: no
                        * wxPython not found
                  Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
                        pygobject: 2.14.2
       Mac OS X native: no
                    Qt: no
                   Qt4:
 no
                 Cairo: 1.2.2

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: 1.5
                  pytz: 2010o

OPTIONAL USETEX DEPENDENCIES
                dvipng: 1.5
           ghostscript: 8.70
                 latex: 3.141592
               pdftops: 3.00

[Edit setup.cfg to suppress
 the above messages]
============================================================================
pymods ['pylab']
packages ['matplotlib', 'matplotlib.backends', 'matplotlib.backends.qt4_editor', 'matplotlib.projections', 'matplotlib.testing', 'matplotlib.testing.jpl_units', 'matplotlib.tests', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axisartist', 'matplotlib.sphinxext', 'matplotlib.numerix', 'matplotlib.numerix.mlab', 'matplotlib.numerix.ma', 'matplotlib.numerix.linear_algebra', 'matplotlib.numerix.random_array', 'matplotlib.numerix.fft', 'matplotlib.tri', 'matplotlib.delaunay']
running install
running build
running build_py

...

There are no errors in the rest of the build or install logs.  Further, I rebuild pycairo, pygtk, and matplotlib just to make sure one of them wasn't missing a freetype dependency.  Unfortunately, I am still getting exactly the same error as before.  Any other suggestions?

   Craig



________________________________
From: Eric Firing <ef...@ha...>
To: mat...@li...
Sent: Tuesday, August 30, 2011 6:19 PM
Subject: Re: [Matplotlib-users] Problem with GTK backends after compiling matplotlib

On 08/30/2011 12:14 PM, Craig Finch wrote:
> I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my
> home directory on a Centos5 system. I am trying to build
 matplotlib
> 1.0.1 in my home directory, but I am having a problem with the GTK
> backends. I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6
> in my home directory (using the libraries and headers installed in the
> default system locations). I downloaded a few pygtk examples from the
> tutorial section of their web site and ran them to verify that pygtk
> works correctly.
>
> Here is the error I get when I run a script that contains only the line
> "import matplotlib.pyplot":
>
> python2.7 test.py --verbose-helpful
> $HOME=/home/cfinch
> CONFIGDIR=/home/cfinch/.matplotlib
> matplotlib data path
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
> loaded rc file
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 1.0.1
> verbose.level helpful
>
 interactive is False
> units is False
> platform is linux2
> Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
> Traceback (most recent call last):
> File "test.py", line 1, in <module>
> import matplotlib.pyplot
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 95, in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 10, in <module>
> from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK,
> FigureCanvasGTK,\
> File
>
 "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> line 28, in <module>
> from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py",
> line 29, in <module>
> from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
> ImportError: No module named _backend_gdk
>
> Here is the beginning of my matplotlib build log, which shows that the
> build process is actually finding the GTK libraries:
>
> basedirlist is: ['/home/cfinch']
> ============================================================================
> BUILDING MATPLOTLIB
> matplotlib: 1.0.1
> python: 2.7.2 (default, Aug 30 2011, 12:57:00) [GCC 4.1.2
> 20080704 (Red Hat 4.1.2-50)]
> platform: linux2
>
> REQUIRED
 DEPENDENCIES
> numpy: 1.6.1
> freetype2: 9.10.3
> * WARNING: Could not find 'freetype2' headers in any
> * of '/home/cfinch/include', '.',
> * '/usr/include/freetype2'.

Freetype is a requirement, so my guess is that this is the origin of the 
problem, even though it is is showing up as a puzzling import error for 
_backend_gdk.

Eric


>
> OPTIONAL BACKEND DEPENDENCIES
> libpng: 1.2.10
> Tkinter: no
> * TKAgg requires Tkinter
> wxPython: no
> * wxPython not found
> Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
> pygobject: 2.14.2
> Mac OS X native: no
> Qt: no
> Qt4: no
> Cairo: 1.2.2
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
> datetime: present, version unknown
> dateutil: 1.5
> pytz: 2010o
>
> OPTIONAL USETEX DEPENDENCIES
> dvipng: 1.5
> ghostscript: 8.70
>
 latex: 3.141592
> pdftops: 3.00
> ------------ SNIP -----------
>
> There are no errors in the build or install logs, but I can post the
> rest of it if necessary. Also, the library _backend_gdk.so is present in
> ~/lib/python2.7/site-packages/matplotlib/backends/.
>
> Any suggestions would be appreciated!
>

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Hello,

some weeks ago, I recompiled matplotlib to get locale support for
commas, and started to get strange dimension errors while trying
to save the figure. Now here is another error that I think that
is somewhat related to it. When I try to run the script below,
savefig() gives me an IndexError:

--
from pylab import *

a1 = figure(1).add_subplot(111, polar=True)
a1.scatter([ 3.*pi/7. ], [ 0.65 ], color='black', marker='o')
a1.annotate('Target', (3.*pi/7., 0.65), xytext=(3.*pi/7., 0.7))
savefig("Radar.eps")

<...long stack...>
IndexError: Unexpected SeqBase<T> length.
---

This is in the savefig() function again, and this is related to
text, since the error disappear if I remove the annotation. But
I think I can affirm, with a great degree of certainty, that this 
happens because I recompiled matplotlib: this is an old script 
that wouldn't give me any error  before.

So, I'm probably missing some dependency, but the setup.py script
won't tell me what is missing, and the only warning I get during
compilation is the -Wstrict_prototypes one.

Actually, I am happy to find out this, since it was probably
a configuration problem that generated the errors (and matplotlib
source is ok). But if anyone can give me any clue on how to solve
this, that would be greatly appreciated.

---
José Alexandre Nalon
na...@te...

On 8/31/2011 5:48 PM, Alan G Isaac wrote:
> How can I change font properties of a legend title?


Related question: would it be a reasonable suggestion for
Legend.set_title to take a ``prop`` argument?

Alan Isaac

How can I change font properties of a legend title?

Thanks,
Alan Isaac

On Wed, Aug 31, 2011 at 3:50 PM, Alexa Villaume <ale...@gm...> wrote:

> 41, 25
>
>
>
Yes, you have it backwards.  The first axis of O3 is the rows, while the
second axis is the columns.  Keep in mind that Python and NumPy follow C
array conventions while Matlab (and IDL?) follow Fortran array conventions.

So, either transpose O3, or swap x and y in the call to contourf.

Cheers!
Ben Root

On Wed, Aug 31, 2011 at 3:45 PM, Alexa Villaume <ale...@gm...> wrote:

> #Load data in
>
> O3 = loadtxt('O3arr.txt')
>
>
> #Specify coordinates of the surface
>
> y=np.arange(-0.25, 6.0, 0.25) #The range of the ionization parameter
>
> x=np.arange(-1.0, 3.1, 0.1) #The range of the metallcity values
>
>
> #Define levels. Observed column density +- 3 sigma
>
> O3Level  = [13.936, 14.047, 14.158]
>
>
> #Contour the arrays.
>
> plt.contour(x, y, O3, O3Level)
>
> With x and y defined as they are I get a type error that says x and y
> should be the same length as the columns and rows of z, which they are. So
> I'm not sure why I get that error.


What does "print O3.shape" return?

Ben Root

I corrected the problem with the FreeType2 header file and rebuilt matplotlib from scratch, but I'm getting the same error.  Centos5 puts the file ft2build.h in /usr/lib but matplotlib looks for it in /usr/lib/freetype2.  I used this command:
PKG_CONFIG_PATH=/home/cfinch/lib/pkgconfig  python2.7 setup.py build &> build_log.txt
and got this output:


basedirlist is: ['/home/cfinch']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.0.1
                python: 2.7.2 (default, Aug 30 2011, 12:57:00)  [GCC 4.1.2
                        20080704 (Red Hat 4.1.2-50)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.6.1
             freetype2: 9.10.3

OPTIONAL BACKEND DEPENDENCIES
                libpng: 1.2.10
               Tkinter: no
                        * TKAgg requires Tkinter
              wxPython: no
                        * wxPython not found
                  Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
                        pygobject: 2.14.2
       Mac OS X native: no
                    Qt: no
                   Qt4: no
                 Cairo: 1.2.2

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: 1.5
                  pytz: 2010o

OPTIONAL USETEX DEPENDENCIES
                dvipng: 1.5
           ghostscript: 8.70
                 latex: 3.141592
               pdftops: 3.00

[Edit setup.cfg to suppress the above messages]
============================================================================
pymods ['pylab']
packages ['matplotlib', 'matplotlib.backends', 'matplotlib.backends.qt4_editor', 'matplotlib.projections', 'matplotlib.testing', 'matplotlib.testing.jpl_units', 'matplotlib.tests', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axisartist', 'matplotlib.sphinxext', 'matplotlib.numerix', 'matplotlib.numerix.mlab', 'matplotlib.numerix.ma', 'matplotlib.numerix.linear_algebra', 'matplotlib.numerix.random_array', 'matplotlib.numerix.fft', 'matplotlib.tri', 'matplotlib.delaunay']
running install
running build
running build_py

...

There are no errors in the rest of the build or install logs.  Further, I rebuild pycairo, pygtk, and matplotlib just to make sure one of them wasn't missing a freetype dependency.  Unfortunately, I am still getting exactly the same error as before.  Any other suggestions?

   Craig



________________________________
From: Eric Firing <ef...@ha...>
To: mat...@li...
Sent: Tuesday, August 30, 2011 6:19 PM
Subject: Re: [Matplotlib-users] Problem with GTK backends after compiling matplotlib

On 08/30/2011 12:14 PM, Craig Finch wrote:
> I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my
> home directory on a Centos5 system. I am trying to build matplotlib
> 1.0.1 in my home directory, but I am having a problem with the GTK
> backends. I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6
> in my home directory (using the libraries and headers installed in the
> default system locations). I downloaded a few pygtk examples from the
> tutorial section of their web site and ran them to verify that pygtk
> works correctly.
>
> Here is the error I get when I run a script that contains only the line
> "import matplotlib.pyplot":
>
> python2.7 test.py --verbose-helpful
> $HOME=/home/cfinch
> CONFIGDIR=/home/cfinch/.matplotlib
> matplotlib data path
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
> loaded rc file
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 1.0.1
> verbose.level helpful
> interactive is False
> units is False
> platform is linux2
> Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
> Traceback (most recent call last):
> File "test.py", line 1, in <module>
> import matplotlib.pyplot
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 95, in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 10, in <module>
> from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK,
> FigureCanvasGTK,\
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> line 28, in <module>
> from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py",
> line 29, in <module>
> from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
> ImportError: No module named _backend_gdk
>
> Here is the beginning of my matplotlib build log, which shows that the
> build process is actually finding the GTK libraries:
>
> basedirlist is: ['/home/cfinch']
> ============================================================================
> BUILDING MATPLOTLIB
> matplotlib: 1.0.1
> python: 2.7.2 (default, Aug 30 2011, 12:57:00) [GCC 4.1.2
> 20080704 (Red Hat 4.1.2-50)]
> platform: linux2
>
> REQUIRED DEPENDENCIES
> numpy: 1.6.1
> freetype2: 9.10.3
> * WARNING: Could not find 'freetype2' headers in any
> * of '/home/cfinch/include', '.',
> * '/usr/include/freetype2'.

Freetype is a requirement, so my guess is that this is the origin of the 
problem, even though it is is showing up as a puzzling import error for 
_backend_gdk.

Eric


>
> OPTIONAL BACKEND DEPENDENCIES
> libpng: 1.2.10
> Tkinter: no
> * TKAgg requires Tkinter
> wxPython: no
> * wxPython not found
> Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
> pygobject: 2.14.2
> Mac OS X native: no
> Qt: no
> Qt4: no
> Cairo: 1.2.2
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
> datetime: present, version unknown
> dateutil: 1.5
> pytz: 2010o
>
> OPTIONAL USETEX DEPENDENCIES
> dvipng: 1.5
> ghostscript: 8.70
> latex: 3.141592
> pdftops: 3.00
> ------------ SNIP -----------
>
> There are no errors in the build or install logs, but I can post the
> rest of it if necessary. Also, the library _backend_gdk.so is present in
> ~/lib/python2.7/site-packages/matplotlib/backends/.
>
> Any suggestions would be appreciated!
>

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On Wed, Aug 31, 2011 at 2:55 PM, Matthew Hemke <mg...@gm...> wrote:

> I have a plot canvas added to a tk interface (python 2.7.2, matplotlib
> 1.0.1) according to the recipe here:
>
>
> http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_tk.html
>
> When the window containing the plot is resized the plot shrinks, often
> leading to REALLY ugly, unreadable plots.
>
> I tried adding scrollbars to the canvas returned by get_tk_widget() and
> they connect as expected (using the yview method). Then, I set a scrollarea
> config option for the canvas.
>
> Everything seems to be working just like a tkinter canvas, but then when
> the window is resized, the plot still resizes and the scrollbars never
> activate. I was hoping the plot wouldn't resize and the scrollbars would
> activate to allow the user to scroll to see the appropriate part of the
> plot, while still keeping the plot looking pretty.
>
> Is there a way (besides editing backend_tkagg.py self.resize method) that
> would allow the scrollbars to work properly?
>
> If my question isn't clear, I can mock up some code, but it may be a bit
> lengthy, so if anyone can steer me in a better direction that would be
> great.
>
> Thanks,
>
> -Matt
>

Matt,

Currently, (if I understand the backends and the event handling correctly),
mpl makes the assumption that a window resize event directly means a figure
resize event.  Maybe these two concepts should be decoupled to allow for
interception and handling?  I don't know how much work the mpl backends have
to do to handle the various possibilities of when to scale the figures and
when to use scrollbars.  Certainly would be quite messier than the current
assumption.

Unless I am being completely unaware of current ways to implement what you
want, I would suggest filing a feature request.  In the meantime, editing
the tk backend might be your best bet.

Cheers,
Ben Root

On Tue, Aug 30, 2011 at 9:47 PM, Alexa Villaume <ale...@gm...> wrote:

> Thanks for responding, Ben. I used loadtxt() and I'm still getting a very
> strange looking contour plot. I've attached it and maybe that will be
> helpful in diagnosing what is wrong with it.
>
> I have no reason to believe that the data itself is bad since I was making
> contours in IDL with the same set.
>
> Thank you.
>
>
When I see graphing artifacts like that, the usual suspect is that the X and
Y coordinates are mixed up or something to that effect.  Could you please
post some code?

Ben Root

I have a plot canvas added to a tk interface (python 2.7.2, matplotlib 1.0.1) according to the recipe here:

http://matplotlib.sourceforge.net/examples/user_interfaces/embedding_in_tk.html

When the window containing the plot is resized the plot shrinks, often leading to REALLY ugly, unreadable plots.

I tried adding scrollbars to the canvas returned by get_tk_widget() and they connect as expected (using the yview method). Then, I set a scrollarea config option for the canvas.

Everything seems to be working just like a tkinter canvas, but then when the window is resized, the plot still resizes and the scrollbars never activate. I was hoping the plot wouldn't resize and the scrollbars would activate to allow the user to scroll to see the appropriate part of the plot, while still keeping the plot looking pretty.

Is there a way (besides editing backend_tkagg.py self.resize method) that would allow the scrollbars to work properly?

If my question isn't clear, I can mock up some code, but it may be a bit lengthy, so if anyone can steer me in a better direction that would be great.

Thanks,

-Matt

I forgot to mention the obvious solution!  Outer boundaries are ordered
anticlockwise, inner boundaries clockwise.  Calculate the area of each
boundary assuming it is ordered anticlockwise, and if the area is positive
it is an outer boundary, if negative it is an inner boundary.  I've attached
a modified version of your debug.py to show this.

This may be simpler to use than points_inside_poly, but if you have multiple
nested boundaries it could get confusing unless you know which boundary
encloses which others.

Ian Thomas

Hi,

I have a code for making graphical representations of sentences, Sentence is
represented as a bar, and under in you can represent the words. It works
fine and I have an example at the end. 

Now I wanted to add some more features to it, but I am stuck.
you can see the previous post from this link

Now, if we assign a number to each letter in a sentence and get a list of
these numbers,
[2,4,7,-7,8,6,4,4,-7,9,5,3,-7,9,5,-3,7,8,9,5,3,6,8,9,-5,3]
can I create a 1D heat map with this list as and additional bar?

First problem will be to get the range of numbers and normalize it, or we
should be able to assign a range for the heat map.

It would be great if you can help.

here is the example code.


[CODE]

text ='''World number two Nadal breezed through the first set, taking it
with breaks of serve in the fourth and sixth games.
Monfils put up more resistance in an erratic second set but his wayward
display was summed up by a double fault which sealed Nadal's victory.
The Spaniard will face a semi-final against compatriot Nicolas Almagro, who
beat Austrian Juergen Melzer 6-3 6-1.
In the women's competition, fourth seed Venus Williams booked her place in
the semi-finals with a 6-3 6-3 win over Australia's Samantha Stosur.'''
import pylab
import matplotlib



# Put text into list of sentences            
sentences = []
sentences = text.split('\n')

# Get the lenght of longest sentence-Lmax and number of sentences
Lmax=0
it = 0
for i in sentences:
      it = it + 1
      LenSen= len(i)
      if LenSen > Lmax:
            Lmax = LenSen
totalnumber = it

#Set the image properties
pylab.rcParams['figure.figsize']       = [Lmax/20, totalnumber]
pylab.rcParams['figure.subplot.left']  = 0.2 # Left margin
pylab.rcParams['figure.subplot.right'] = 1.0-0.04 # Right margin
pylab.rcParams['font.size'] = 7

# Axes range from 0 to 1 for x-axis (simplifying calls to .axhspan()) and 
# 20 down to 0 for Y-values because that's convenient for this example
ax = [0, 1, totalnumber+1, 0] # [xlo, xhi,   ylo, yhi]


# printer is a drawing module
def printer(searchterm, Input,start,end,xstart,color):
      lens = len(searchterm)
      while True:
             inDex = Input.find(searchterm, start,end)
             if inDex == -1:
                   break
             inDex = float(inDex)
             inDS=inDex/Lmax
             inDE=(inDex+lens)/Lmax
             matplotlib.pyplot.axhspan(it+xstart,it+0.2+xstart, xmin=inDS,
xmax=inDE, ec='k', fc=color)
             # if search string not found, find() returns -1
             # search is complete, break out of the while loop

             # move to next possible start position
             inDex= int(inDex)
             start = inDex + 1
it=0      
for i in sentences:
      it = it+1
      LenSen= len(i)
      LenF = float(LenSen)
      matplotlib.pyplot.axhspan(it+0.2,it+0.4, xmin=0, xmax=LenF/Lmax,
ec='k', fc='r') #creates sentence bar
      pylab.text(-0.2, it+0.4, 'sentence'+str(it)+' with spaces') # create
the sentence bar 
      printer(' ', i, 1, LenSen,0.2,'b')    #blue represents the spaces on
sentence bar
      printer('the', i, 1, LenSen,0,'y') #above sentence bar, yellow
represents 'the'
      pylab.text(-0.2, it+0.2, 'the')



pylab.axis(ax)
matplotlib.pyplot.title("Analysis")

matplotlib.pyplot.xticks((),()) # No labels for X-axis
matplotlib.pyplot.yticks((),()) # No labels for Y-axis
pylab.show()

[CODE]
-- 
View this message in context: http://old.nabble.com/1D-heat-map-tp32374379p32374379.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

On 08/31/2011 06:45 AM, Jeffrey Blackburne wrote:
> Hi,
>
> Are the edges of the rectangles returned by plt.bar() supposed to conform to the 'lines.solid_joinstyle' rcParam? If not, is there another method for specifying that joinstyle?
>
> I have not been able to change the joinstyle using this method in versions 1.0.0 (linux, gtkagg and tkagg) or 1.0.1 (os x, tkagg). I can send a minimal example script if requested.
>

The bar rectangles are Patch object outlines, not Line2D objects, and 
solid_joinstyle is not presently supported by patches, as far as I can see.

Eric

> -Jeff
>

On 30 August 2011 18:23, Tijs de Kler <tij...@sa...> wrote:

> Im trying to use the tricontourf function in matplotlib to reduce the
> complexity of an unstructured dataset into contours.
> The resulting contours are retrieved from the path by the to_polygon()
> function, but i have some trouble distinguishing inner boundaries on the
> polygons, while plot.show() clearly doesn't
>
> Using Matplotlib 1.01, and the attached code, I get one level, consisting
> of 2 polygons, where the first is the outer boundary, and the second should
> be the inner boundary.
> The figure shown by show() correctly displays a square with a inner square
> cut-out. However i cannot distinguish between inner and outer boundaries in
> the list of polygons that to_polygon() returns.
>
> Is there a trick how the plot functions distinguish inner boundaries?
> Calculating for each polygon if it is contained in other polygons will
> become complicated with a large number of polygons: As far as i can tell
> this would be checking if the starting point of each polygon is contained in
> any of the other polygons. Is there a simpler method i missed?
>

Matplotlib includes a function to determine if a set of points is within a
polygon, called points_inside_poly.  For an example see
http://matplotlib.sourceforge.net/faq/howto_faq.html#test-whether-a-point-is-inside-a-polygon
That is about as simple as it gets from a user's perspective!

Since you ask about tricks in plot functions, no there aren't any.
Rendering functions don't explicitly determine if a contour polygon is an
inner or outer boundary.  Usually a sweep algorithm is performed across all
points to construct the triangulation of the polygons as it progresses.  You
could extract the inner/outer-ness of each boundary from such an algorithm
but it would be overkill for what you want to do.

Ian Thomas

Hi,

Are the edges of the rectangles returned by plt.bar() supposed to conform to the 'lines.solid_joinstyle' rcParam? If not, is there another method for specifying that joinstyle?

I have not been able to change the joinstyle using this method in versions 1.0.0 (linux, gtkagg and tkagg) or 1.0.1 (os x, tkagg). I can send a minimal example script if requested.

-Jeff

On 08/31/2011 04:01 AM, Trevor J Christensen wrote:
> In preparing to upgrade from 0.99 to 1.0.1, I was reading the online
> documentation about the various backends. I do not see a TkAgg backend
> listed. Is that because there is no longer a backend for Tk? Has support
> for Tk been dropped in 1.0.1? Or has it not yet been added to the
> documentation?
>
> Trevor

Trevor,

Where did you expect to find it, but not see it?

Eric

Dear Trevor,

I am using 1.0.1 and the TkAgg backend with no problems.  I'm not sure why you can't find the documentation.  It is listed in the faq as a viable backend.

Chad



________________________________
From: Trevor J Christensen <tr...@jc...>
To: mat...@li...
Sent: Wednesday, August 31, 2011 9:01 AM
Subject: [Matplotlib-users] Matplotlib 1.0.1 Tk backend


In preparing to upgrade from 0.99 to 1.0.1, I was reading the online documentation about the various backends.  I do not see a TkAgg backend listed.  Is that because there is no longer a backend for Tk?  Has support for Tk been dropped in 1.0.1?  Or has it not yet been added to the documentation?

Trevor

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In preparing to upgrade from 0.99 to 1.0.1, I was reading the online documentation about the various backends. I do not see a TkAgg backend listed. Is that because there is no longer a backend for Tk? Has support for Tk been dropped in 1.0.1? Or has it not yet been added to the documentation? 

Trevor 

On Tuesday, August 30, 2011, Katie Boyle <kat...@gm...> wrote:
> Hi Ben,
>
> I'm using mpl 0.99 on Ubuntu 10.10, and whether I use contour or contourf
I get a plot that is laying in the X-Y plane with contour loops extending
into the +z direction. The contour plot itself looks right (if I could get
it to be 2D instead of 3D), it's just its orientation and non-planarity that
pose problems.
>
> Cheers,
> Katie
>

Posting an image would be very helpful.  In addition, I don't think v0.99
supports what you are trying to do.  But perhaps the image would make things
clearer.

Ben Root

Hi Ben,

I'm using mpl 0.99 on Ubuntu 10.10, and whether I use contour or contourf I
get a plot that is laying in the X-Y plane with contour loops extending into
the +z direction. The contour plot itself looks right (if I could get it to
be 2D instead of 3D), it's just its orientation and non-planarity that pose
problems.

Cheers,
Katie


On Tue, Aug 30, 2011 at 5:22 PM, Benjamin Root <ben...@ou...> wrote:

>
>
> On Tuesday, August 30, 2011, Katie Boyle <kat...@gm...> wrote:
> > Hi All,
> >
> > I have a 2D grid comprised of 100 nodes in X, 300 nodes in Z, and a
> single node in Y. I have a scalar value defined at each node point.
> >
> > I want to display this planar grid in 3D by first rendering a contour
> plot (no problems there) and then rotating it such that it plots as a
> vertical sheet when viewed in 3D. Right now it is automatically forced to
> reside in the X-Y plane, but I want it to reside in the X-Z plane. Here is
> an excerpt from my code:
> >
> > fig = plt.figure(figsize=(25,20))
> > ax = Axes3D(fig)
> > ax.contourf(xx, yy, zz, 100, cmp = plt.cm.jet,zdir='y',extend3D=False)
> > plt.hold(True)
> > ax.bar3d(5000, 625, 1500, 1, 1, 1, color='r')
> > ax.set_xlabel("X [m]")
> > ax.set_ylabel("Y [m]")
> > ax.set_zlabel("Z [m]")
> > plt.savefig("Feature.png",dpi=200)
> >
> > I think the 'zdir' flag is supposed to do this exact task, but setting it
> to 'y' seems to have no effect on my plot. Also, the plot is being extended
> into 3D even though I set the extend3D flag to False. Can anyone tell me
> what I'm doing wrong?
> >
> > Cheers!
> >
>
> What version of mpl are you using?  I don't think those kwargs were added
> until the upcoming release, v1.1.0.  Does the graph look right if you do
> just contour?
>
> Plus, from the top of my head, I don't think extend3d works for contourf
> (but I could be wrong).
>
> Ben Root

On Tuesday, August 30, 2011, Katie Boyle <kat...@gm...> wrote:
> Hi All,
>
> I have a 2D grid comprised of 100 nodes in X, 300 nodes in Z, and a single
node in Y. I have a scalar value defined at each node point.
>
> I want to display this planar grid in 3D by first rendering a contour plot
(no problems there) and then rotating it such that it plots as a vertical
sheet when viewed in 3D. Right now it is automatically forced to reside in
the X-Y plane, but I want it to reside in the X-Z plane. Here is an excerpt
from my code:
>
> fig = plt.figure(figsize=(25,20))
> ax = Axes3D(fig)
> ax.contourf(xx, yy, zz, 100, cmp = plt.cm.jet,zdir='y',extend3D=False)
> plt.hold(True)
> ax.bar3d(5000, 625, 1500, 1, 1, 1, color='r')
> ax.set_xlabel("X [m]")
> ax.set_ylabel("Y [m]")
> ax.set_zlabel("Z [m]")
> plt.savefig("Feature.png",dpi=200)
>
> I think the 'zdir' flag is supposed to do this exact task, but setting it
to 'y' seems to have no effect on my plot. Also, the plot is being extended
into 3D even though I set the extend3D flag to False. Can anyone tell me
what I'm doing wrong?
>
> Cheers!
>

What version of mpl are you using?  I don't think those kwargs were added
until the upcoming release, v1.1.0.  Does the graph look right if you do
just contour?

Plus, from the top of my head, I don't think extend3d works for contourf
(but I could be wrong).

Ben Root

Hi All,

I have a 2D grid comprised of 100 nodes in X, 300 nodes in Z, and a single
node in Y. I have a scalar value defined at each node point.

I want to display this planar grid in 3D by first rendering a contour plot
(no problems there) and then rotating it such that it plots as a vertical
sheet when viewed in 3D. Right now it is automatically forced to reside in
the X-Y plane, but I want it to reside in the X-Z plane. Here is an excerpt
from my code:

fig = plt.figure(figsize=(25,20))
ax = Axes3D(fig)
ax.contourf(xx, yy, zz, 100, cmp = plt.cm.jet,zdir='y',extend3D=False)
plt.hold(True)
ax.bar3d(5000, 625, 1500, 1, 1, 1, color='r')
ax.set_xlabel("X [m]")
ax.set_ylabel("Y [m]")
ax.set_zlabel("Z [m]")
plt.savefig("Feature.png",dpi=200)

I think the 'zdir' flag is supposed to do this exact task, but setting it to
'y' seems to have no effect on my plot. Also, the plot is being extended
into 3D even though I set the extend3D flag to False. Can anyone tell me
what I'm doing wrong?

Cheers!

On 08/30/2011 12:14 PM, Craig Finch wrote:
> I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my
> home directory on a Centos5 system. I am trying to build matplotlib
> 1.0.1 in my home directory, but I am having a problem with the GTK
> backends. I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6
> in my home directory (using the libraries and headers installed in the
> default system locations). I downloaded a few pygtk examples from the
> tutorial section of their web site and ran them to verify that pygtk
> works correctly.
>
> Here is the error I get when I run a script that contains only the line
> "import matplotlib.pyplot":
>
> python2.7 test.py --verbose-helpful
> $HOME=/home/cfinch
> CONFIGDIR=/home/cfinch/.matplotlib
> matplotlib data path
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
> loaded rc file
> /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
> matplotlib version 1.0.1
> verbose.level helpful
> interactive is False
> units is False
> platform is linux2
> Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
> Traceback (most recent call last):
> File "test.py", line 1, in <module>
> import matplotlib.pyplot
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py",
> line 95, in <module>
> new_figure_manager, draw_if_interactive, show = pylab_setup()
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py",
> line 25, in pylab_setup
> globals(),locals(),[backend_name])
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py",
> line 10, in <module>
> from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK,
> FigureCanvasGTK,\
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py",
> line 28, in <module>
> from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
> File
> "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py",
> line 29, in <module>
> from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
> ImportError: No module named _backend_gdk
>
> Here is the beginning of my matplotlib build log, which shows that the
> build process is actually finding the GTK libraries:
>
> basedirlist is: ['/home/cfinch']
> ============================================================================
> BUILDING MATPLOTLIB
> matplotlib: 1.0.1
> python: 2.7.2 (default, Aug 30 2011, 12:57:00) [GCC 4.1.2
> 20080704 (Red Hat 4.1.2-50)]
> platform: linux2
>
> REQUIRED DEPENDENCIES
> numpy: 1.6.1
> freetype2: 9.10.3
> * WARNING: Could not find 'freetype2' headers in any
> * of '/home/cfinch/include', '.',
> * '/usr/include/freetype2'.

Freetype is a requirement, so my guess is that this is the origin of the 
problem, even though it is is showing up as a puzzling import error for 
_backend_gdk.

Eric


>
> OPTIONAL BACKEND DEPENDENCIES
> libpng: 1.2.10
> Tkinter: no
> * TKAgg requires Tkinter
> wxPython: no
> * wxPython not found
> Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
> pygobject: 2.14.2
> Mac OS X native: no
> Qt: no
> Qt4: no
> Cairo: 1.2.2
>
> OPTIONAL DATE/TIMEZONE DEPENDENCIES
> datetime: present, version unknown
> dateutil: 1.5
> pytz: 2010o
>
> OPTIONAL USETEX DEPENDENCIES
> dvipng: 1.5
> ghostscript: 8.70
> latex: 3.141592
> pdftops: 3.00
> ------------ SNIP -----------
>
> There are no errors in the build or install logs, but I can post the
> rest of it if necessary. Also, the library _backend_gdk.so is present in
> ~/lib/python2.7/site-packages/matplotlib/backends/.
>
> Any suggestions would be appreciated!
>

I successfully built Python 2.7.2, NumPy 1.61, and Scipy 0.9.0 in my home directory on a Centos5 system.  I am trying to build matplotlib 1.0.1 in my home directory, but I am having a problem with the GTK backends.  I also built pycairo 1.2.2, pygobject 2.14.2, and pygtk 2.10.6 in my home directory (using the libraries and headers installed in the default system locations).  I downloaded a few pygtk examples from the tutorial section of their web site and ran them to verify that pygtk works correctly.

Here is the error I get when I run a script that contains only the line "import matplotlib.pyplot":

python2.7 test.py --verbose-helpful
$HOME=/home/cfinch
CONFIGDIR=/home/cfinch/.matplotlib
matplotlib data path /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data
loaded rc file /home/cfinch/.local/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
matplotlib version 1.0.1
verbose.level helpful
interactive is False
units is False
platform is linux2
Using fontManager instance from /home/cfinch/.matplotlib/fontList.cache
Traceback (most recent call last):
  File "test.py", line 1, in <module>
    import matplotlib.pyplot
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/pyplot.py", line 95, in <module>
    new_figure_manager, draw_if_interactive, show = pylab_setup()
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/__init__.py", line 25, in pylab_setup
    globals(),locals(),[backend_name])
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtkagg.py", line 10, in <module>
    from matplotlib.backends.backend_gtk import gtk, FigureManagerGTK, FigureCanvasGTK,\
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gtk.py", line 28, in <module>
    from matplotlib.backends.backend_gdk import RendererGDK, FigureCanvasGDK
  File "/home/cfinch/.local/lib/python2.7/site-packages/matplotlib/backends/backend_gdk.py", line 29, in <module>
    from matplotlib.backends._backend_gdk import pixbuf_get_pixels_array
ImportError: No module named _backend_gdk


Here is the beginning of my matplotlib build log, which shows that the build process is actually finding the GTK libraries:

basedirlist is: ['/home/cfinch']
============================================================================
BUILDING MATPLOTLIB
            matplotlib: 1.0.1
                python: 2.7.2 (default, Aug 30 2011, 12:57:00)  [GCC 4.1.2
                        20080704 (Red Hat 4.1.2-50)]
              platform: linux2

REQUIRED DEPENDENCIES
                 numpy: 1.6.1
             freetype2: 9.10.3
                        * WARNING: Could not find 'freetype2' headers in any
                        * of '/home/cfinch/include', '.',
                        * '/usr/include/freetype2'.

OPTIONAL BACKEND DEPENDENCIES
                libpng: 1.2.10
               Tkinter: no
                        * TKAgg requires Tkinter
              wxPython: no
                        * wxPython not found
                  Gtk+: gtk+: 2.10.4, glib: 2.12.3, pygtk: 2.10.6,
                        pygobject: 2.14.2
       Mac OS X native: no
                    Qt: no
                   Qt4: no
                 Cairo: 1.2.2

OPTIONAL DATE/TIMEZONE DEPENDENCIES
              datetime: present, version unknown
              dateutil: 1.5
                  pytz: 2010o

OPTIONAL USETEX DEPENDENCIES
                dvipng: 1.5
           ghostscript: 8.70
                 latex: 3.141592
               pdftops: 3.00
------------ SNIP -----------

There are no errors in the build or install logs, but I can post the rest of it if necessary.  Also, the library _backend_gdk.so is present in ~/lib/python2.7/site-packages/matplotlib/backends/.

Any suggestions would be appreciated!

Hey Matplotlib users,

Im trying to use the tricontourf function in matplotlib to reduce the complexity of an unstructured dataset into contours.
The resulting contours are retrieved from the path by the to_polygon() function, but i have some trouble distinguishing inner boundaries on the 
polygons, while plot.show() clearly doesn't

Using Matplotlib 1.01, and the attached code, I get one level, consisting of 2 polygons, where the first is the outer boundary, and the second should 
be the inner boundary.
The figure shown by show() correctly displays a square with a inner square cut-out. However i cannot distinguish between inner and outer boundaries in 
the list of polygons that to_polygon() returns.

Is there a trick how the plot functions distinguish inner boundaries? Calculating for each polygon if it is contained in other polygons will become 
complicated with a large number of polygons: As far as i can tell this would be checking if the starting point of each polygon is contained in any of 
the other polygons. Is there a simpler method i missed?

Thanks in advance,
Tijs de Kler