Re: [Matplotlib-users] display data in histogram

2009-11-04 Thread Matthias Michler
Hi ankita,

On Wednesday 04 November 2009 06:04:55 ankita dutta wrote:
 hi all,

 I am working on some graph stuffs and stuck at a point.

 I am trying to plot a histogram using simple :

 *import matplotlib.pyplot as plt
 .
 .
 plt.hist(x,bins=10,histtype='bar')
plt.show()
 *
 but i want to know

 1) what is the value of a particular bar in histogram and also want to
 print in on output image along with the bars ( either at top of bar or at
 bottom)*

n, bins, patches = plt.hist(...)
gives you the bin-egdes 'bins' the corresponding frequency / number of values 
per bin 'n' and the mpl-objects of the shown bars

# e.g. for top of the bar:
n, bins, patches = plt.hist(x0, bins=10, histtype='bar')
for index in xrange(len(bins)-1):
plt.text(bins[index], n[index],  %i  % (n[index]))

 *2) How to give input of 2 types of dataset in single  hist() command , so
 that i can compare 2 different dataset side by side on my output image. ( i
 dont want it on top of each other  as given by the command *histtype*:
 [ ‘barstacked’]and also i read some example in matplotlib site, but
 they are for random numbers :  something like this:

 x0 = mu + sigma*P.randn(1)
 x1 = mu + sigma*P.randn(7000)
 x2 = mu + sigma*P.randn(3000)
 P.figure()
 n, bins, patches = P.hist( [x0,x1,x2], 10, histtype='bar')

 but i need this comparision for some dataset.

I can't see any problems with placing dataset instead of x0 and x1 into this 
call.
Please notice: in that case n is a tuple and each tuple-element corresponds to 
the number of values per bin of one dataset.

Kind regards Matthias


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Re: [Matplotlib-users] basemap: Mask the ocean [SEC=UNCLASSIFIED]

2009-11-04 Thread Stephane Raynaud
Maybe using path clipping you can plot only over land like this :

--
import numpy as np
from mpl_toolkits.basemap import Basemap
import pylab as plt
import matplotlib.patches as patches
import matplotlib.transforms as transforms

ll_lat = -38.10  # extent of area of interest
ll_lon = 145.06
ur_lat = -38.00
ur_lon = 145.16

# create data points all on land
fudge = ((ll_lon+0.05,  ur_lat-0.00,   1000),
(ll_lon+0.05,  ur_lat-0.01,   2000),
(ll_lon+0.05,  ur_lat-0.02,   3000),
(ll_lon+0.05,  ur_lat-0.03,   4000),
(ll_lon+0.04,  ur_lat-0.025,  1000),
(ll_lon+0.043, ur_lat-0.036,  1),
(ll_lon+0.047, ur_lat-0.041,  2),
(ll_lon+0.07,  ur_lat-0.07,   4000),
(ll_lon+0.08,  ur_lat-0.08,   3000),
(ll_lon+0.09,  ur_lat-0.09,   2000),
(ll_lon+0.10,  ur_lat-0.10,   1000))

data = np.ones((3, len(fudge)))
for (i, (lon, lat, val)) in enumerate(fudge):
   data[0,i] = lon
   data[1,i] = lat
   data[2,i] = val

# plot the data
fig = plt.figure()
m = Basemap(projection='cyl', llcrnrlat=ll_lat, urcrnrlat=ur_lat,
  llcrnrlon=ll_lon, urcrnrlon=ur_lon, resolution='f')

# +CHANGES
coll = plt.hexbin(data[0,:], data[1,:], data[2,:], gridsize=5)
ax = plt.gca()
for n, poly in enumerate(m.coastpolygons):
type = m.coastpolygontypes[n]
if type in [1,3]:
p = patches.Polygon(np.asarray(poly).T)
p.set_color('none')
ax.add_patch(p)
m.set_axes_limits(ax=ax)
coll.set_clip_path(p)
# -CHANGES

plt.show()
--

On Wed, Nov 4, 2009 at 1:17 AM, ross.wil...@ga.gov.au wrote:



 -Original Message-
 From: Jeff Whitaker [mailto:jsw...@fastmail.fm]
 Sent: Tuesday, 3 November 2009 02:53
 To: Stephane Raynaud
 Cc: Wilson Ross; matplotlib-users@lists.sourceforge.net
 Subject: Re: [Matplotlib-users] basemap: Mask the ocean [SEC=UNCLASSIFIED]

 Stephane Raynaud wrote:
  Ross,
 
 
  one way is to mask (or remove) ocean points using the _geoslib module
  provided with basemap.
  When you create a Basemap instance, you can retrieve all its polygons
  land (continents and islands) with mymap.coastpolygons.
  Thay are stored as numpy arrays, and you can convert them to
  _geoslib.Polygon objects :
 
  poly = _geoslib.Polygon(N.asarray(coastalpoly).T)
 
  Then you loop over all Polygons and all (x,y) points and test :
 
  good_point = _geoslib.Point((x,y)).within(poly)
 
  Thanks to this method, you can choose you optimal resolution.
  You can even compute the intersection of you hexagons with coastal
  polygons using .intersection() and .area (instead of simply checking
  if the center is inside) and then reject points depending the fraction
  of the cell covered by land (or ocean).

 Following Stephane's excellent suggestion, here's a prototype Basemap
 method that checks to see if a point is on land or over water.  Ross -
 if you find it useful I'll include it in the next release.  Note that it
 will be slow for lots of points or large map regions.

 -Jeff
 --

 Yes, Stephane's approach is nice and Jeff has nicely encapsulated the
 approach. I'll put that into my bag of tricks!

 However it doesn't quite do what I want.  My data does not have any points
 in the ocean; the hex binning creates hexagonal patches that extend out into
 the ocean. As a physicist I say that's a representation artifact and leave
 it at that, but my end-users want that 'bleed' into the ocean removed.  My
 argument that they are losing data falls on deaf ears.

 Here's an even more contrived example that improves on my poor previous
 attempt to explain the problem:
 
 import numpy as np
 import matplotlib.pyplot as plt
 from mpl_toolkits.basemap import Basemap

 ll_lat = -38.10  # extent of area of interest
 ll_lon = 145.06
 ur_lat = -38.00
 ur_lon = 145.16

 # create data points all on land
 fudge = ((ll_lon+0.05,  ur_lat-0.00,   1000),
 (ll_lon+0.05,  ur_lat-0.01,   2000),
 (ll_lon+0.05,  ur_lat-0.02,   3000),
 (ll_lon+0.05,  ur_lat-0.03,   4000),
 (ll_lon+0.04,  ur_lat-0.025,  1000),
 (ll_lon+0.043, ur_lat-0.036,  1),
 (ll_lon+0.047, ur_lat-0.041,  2),
 (ll_lon+0.07,  ur_lat-0.07,   4000),
 (ll_lon+0.08,  ur_lat-0.08,   3000),
 (ll_lon+0.09,  ur_lat-0.09,   2000),
 (ll_lon+0.10,  ur_lat-0.10,   1000))

 data = np.ones((3, len(fudge)))
 for (i, (lon, lat, val)) in enumerate(fudge):
data[0,i] = lon
data[1,i] = lat
data[2,i] = val

 # plot the data
 fig = plt.figure()
 m = Basemap(projection='cyl', llcrnrlat=ll_lat, urcrnrlat=ur_lat,
llcrnrlon=ll_lon, urcrnrlon=ur_lon, resolution='f')
 plt.hexbin(data[0,:], data[1,:], data[2,:], gridsize=5)
 m.drawcoastlines(linewidth=0.5, 

[Matplotlib-users] Install problem on Mac OS 10.5

2009-11-04 Thread priggs

Hi

When I try installing matplotlib version 99.1.1 on my Mac OS 10.5 using the
DMG I receive the following error:
You cannot install matplotlib 0.99.1.1-r7813 on this volume. matplotlib
requires System Python 2.5 to install.

But I am using System Python 2.5:
Python 2.5.1 (r251:54863, Feb  6 2009, 19:02:12) 
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type help, copyright, credits or license for more information.

Why is it not recognizing Python?

Thanks!

PS. I also tried installing from source, but got the lipo error:
src/ft2font.cpp:941: warning: control reaches end of non-void function
lipo: can't open input file:
/var/folders/eh/eh0fgkpOHKahCYCtazTUzTI/-Tmp-//ccYdEGvu.out (No such
file or directory)
error: command 'gcc' failed with exit status 1

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Re: [Matplotlib-users] Legend fails to make sample symbols for legends outside of the plot area

2009-11-04 Thread Jae-Joon Lee
On Wed, Nov 4, 2009 at 12:00 AM, Greg Novak no...@ucolick.org wrote:
 Is this the intended behavior?  How can I get complete sample lines
 when the legend lies outside the plot area?

No, this is not intended.
It seems to me that wrong clip path is set for those legend handles.
However, your code works fine with the svn version of mpl and also
with the 0.99.1.
So, maybe this is an old bug that has been fixed.
Can you check your matplotlib version and, if possible, update to newer version?
Or, if you report your version of mpl, I'll see if I can find any workaround.

-JJ

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Re: [Matplotlib-users] Legend fails to make sample symbols for legends outside of the plot area

2009-11-04 Thread Greg Novak
Indeed, my version is 98.3.  I'll update.  Thanks!
Greg

On Wed, Nov 4, 2009 at 9:03 AM, Jae-Joon Lee lee.j.j...@gmail.com wrote:
 On Wed, Nov 4, 2009 at 12:00 AM, Greg Novak no...@ucolick.org wrote:
 Is this the intended behavior?  How can I get complete sample lines
 when the legend lies outside the plot area?

 No, this is not intended.
 It seems to me that wrong clip path is set for those legend handles.
 However, your code works fine with the svn version of mpl and also
 with the 0.99.1.
 So, maybe this is an old bug that has been fixed.
 Can you check your matplotlib version and, if possible, update to newer 
 version?
 Or, if you report your version of mpl, I'll see if I can find any workaround.

 -JJ


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Re: [Matplotlib-users] cone plots

2009-11-04 Thread Jae-Joon Lee
Are you running svn version of mpl?
Also, as I said, the example is based on the patch yet to be submitted.
So, I can send you the example, but it will take me sometime to commit
the patch.
I'll give you a notice when this happen.

As far as rotating the ticks, if you're using markers, than I guess
you need a custom artist class.
So, I recommend you to just use simple lines.

Whatever path you take (even with my example), it will not be easy.
So, again, finding other plotting tool that support cone plots may be
more practical (unless someone comes up with a working example).

Regards,

-JJ



On Wed, Nov 4, 2009 at 2:44 AM, ifriad ifr...@gmail.com wrote:

 Hi,
 Thanks, I think the attached sample is good enough for me, In fact I got
 something similar except for the ticks I didn't know how to make them
 slanted, so If I can get the code for you plot this will be really great.

 I can then fine tune it to my needs.

 Thanks Ihab

 Jae-Joon Lee wrote:

 Unfortunately, I don't think something like cone plots can be easily
 done with current matplotlib.

 I guess you can define custom projection and such, as in the example below

 http://matplotlib.sourceforge.net/examples/api/custom_projection_example.html

 but this will involve some (maybe a lot) coding + some knowledge of
 mpl internals.

 With the experimental curvelinear coordinate support in axes_grid
 toolkit (and with yet-to-be-committed patch), one can draw very basic
 cone plot (see the attached). However, the current support is far from
 complete. I'm willing to make it better, but I'm afraid that this may
 not happen in a near future (likely not in this year).

 Of course, you can try to plot everything  (axes boundary, ticks,
 ticklabels etc.) manually if you want, and maybe this is the best way
 currently available.

 Regards,

 -JJ

 On Sat, Oct 31, 2009 at 4:15 AM, ifriad ifr...@gmail.com wrote:

 Hi,
 Does any one knows how to do those cone plots,

 I am attaching a sample plot.

 Thanks Ihab
 http://old.nabble.com/file/p26140834/cone.png cone.png
 --
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Re: [Matplotlib-users] Location matplotlibrc file on my Mac

2009-11-04 Thread PHobson



 -Original Message-
 From: Tony S Yu [mailto:ton...@mit.edu]
 Sent: Tuesday, November 03, 2009 1:11 PM
 To: Paul Hobson
 Cc: Matplotlib Users
 Subject: Re: [Matplotlib-users] Location matplotlibrc file on my Mac


 (Paul, I hope you don't mind if I bring this bump this back to the
 list).
 
 Apparently I skimmed your original email and didn't see that you tried
 putting the file in your working directory. That should work. (My
 original response is still appropriate for a global rc file.)
 
 As suggested on the mpl website (specifically:
 http://matplotlib.sourceforge.net/users/customizing.html
 ), you can try printing out the path of the rc file being used by
 adding the following to your script:
 
   import matplotlib
   print matplotlib.matplotlib_fname()
 
 Also, you may want to check that the working directory is where you
 think it is. For example, if you run a script from the terminal as:
 
 $ python ~/path/to/file.py
 
 Your working directory is '~' and not '~/path/to/'---so matplotlibrc
 file located in the same directory as file.py would not be in the
 working directory.
 
 Otherwise, I have no idea why the matplotlibrc is not being found in
 the working directory.
 
 Best,
 -Tony

I won't mention how long it had been so I had done this, but I had to move the 
file to /Users/paul/.matplotlib in Terminal since Mac OSX won't let you do that 
in Finder (sigh). This made everything work splendidly. I even got it to work 
in the present working directory (not sure how I was messing that up earlier).

Thanks so much, Tony.

Paul M. Hobson  
Senior Staff Engineer
-- 
Geosyntec Consultants 
55 SW Yamhill St, Ste 200
Portland, OR 97204
Phone: (503) 222-9518
Web:   www.geosyntec.com


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Re: [Matplotlib-users] Drawing a single contour line

2009-11-04 Thread Brendan Arnold
Ah, I was a little confused by what you wrote John (I though I had to
access contour through the axes object and the meaning of R, F, dR was
a little unclear..) however using the 'levels' keyword now works. i.e.

plt.contour(x, y, z, levels=[0])

Incidentally, this keyword (levels) is not documented at
http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.contour
and in fact the documentation implies that contour(kx, ky, z, [0])
should work when it does not.

Perhaps the docs could be updated to reflect this?

Brendan

On Tue, Nov 3, 2009 at 2:19 PM, Brendan Arnold brendanarn...@gmail.com wrote:
 Hi again,

 Thanks for the responses, however neither work, the error still
 persists. Here are more details...

 Traceback (most recent call last):
  File C:\Program Files\Python\2.5\lib\lib-tk\Tkinter.py, line 1403,
 in __call__
    return self.func(*args)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\backends\backend_tkagg.py,
 line 212, in resize
    self.show()
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\backends\backend_tkagg.py,
 line 215, in draw
    FigureCanvasAgg.draw(self)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\backends\backend_agg.py,
 line 314, in draw
    self.figure.draw(self.renderer)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\artist.py, line 46, in
 draw_wrapper
    draw(artist, renderer, *kl)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\figure.py, line 773, in
 draw
    for a in self.axes: a.draw(renderer)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\artist.py, line 46, in
 draw_wrapper
    draw(artist, renderer, *kl)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\axes.py, line 1735, in
 draw
    a.draw(renderer)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\text.py, line 515, in
 draw
    bbox, info = self._get_layout(renderer)
  File C:\Program
 Files\Python\2.5\lib\site-packages\matplotlib\text.py, line 257, in
 _get_layout
    if key in self.cached: return self.cached[key]
 TypeError: unhashable type: 'numpy.ndarray'

 matplotlib.__version__
 '0.99.1'
 numpy.__version__
 '1.3.0'

 Python version 2.5

 the code in full is as follows,

 import matplotlib
 import numpy as np
 import matplotlib.cm as cm
 import matplotlib.mlab as mlab
 import matplotlib.pyplot as plt

 # Set some model parameters
 model_points = 1
 t0 = 0.38
 t1 = 0.32*t0
 t2 = 0.5*t1

 def energy(kx, ky):
    '''Energy function, evetually this will be provided by raw data
 from WIEN2k'''
    return -2*t0*(np.cos(kx)+np.cos(ky)) \
        + 4*t1*np.cos(kx)*np.cos(ky) \
        - 2*t2*(np.cos(2*kx)+np.cos(2*ky))

 def shift_energy_up(energy_val, dE):
    '''Shifts the energy according to a gap'''
    return energy_val + np.sqrt(energy_val**2 + dE**2)

 def shift_energy_dn(energy_val, dE):
    '''Shifts the energy down according to an energy'''
    return energy_val - np.sqrt(energy_val**2 + dE**2)

 kx = np.arange(0, 2*np.pi, 2*np.pi/np.sqrt(model_points))
 ky = np.arange(0, 2*np.pi, 2*np.pi/np.sqrt(model_points))
 mgx, mgy = np.meshgrid(kx, ky)
 z = energy(mgx, mgy)

 # Set the ticks to go outwards
 matplotlib.rcParams['xtick.direction'] = 'out'
 matplotlib.rcParams['ytick.direction'] = 'out'

 plt.figure()
 CS = plt.contour(kx, ky, z, [0, 0])
 plt.clabel(CS, inline=1, fontsize=10)
 plt.title('Simplest default with labels')
 plt.show()


 kind regards,

 Brendan

 On Mon, Nov 2, 2009 at 9:33 PM, Pierre de Buyl pdeb...@ulb.ac.be wrote:
 From memory, you just need to make a length one list

 contour(z, [i])

 Pierre

 Le 2 nov. 09 à 22:19, Brendan Arnold a écrit :

 Hi there,

 I can draw a single contour line in MATLAB using

 contour(z, [i i])

 however,

 contour(z, [i, i])

 using matplotlib gives an error. In fact any plot that plots a single
 line (i.e. contour(z, 1)) also gives an error as follows,

 TypeError: unhashable type: 'numpy.ndarray'

 How do I draw a single contour line using matplotlib?

 regards,

 Brendan


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[Matplotlib-users] How do I change where MPL looks for Latex?

2009-11-04 Thread PHobson
I know support for the usetex feature is limited, but I think (*hope*) that 
this is purely an MPL question and not out of the scope and annoying to the 
members of the group.

I like to use the fourier.sty package since I like the Utopia font and it's 
math font is particularly nice. But MPL is using this Latex installation:
/sw/share/texmf-dist/tex/latex/
which has no fourier package, and raises predictable errors when I set
text.latex.preamble :  \usepackage{fourier}

But I only use and maintain this one:
/usr/local/texlive/2008/texmf-dist/tex/latex/
(fourier and many other packages I like)

Is there a way to tell MPL to use my preferred Latex directory, or should I 
update and maintain the one it currently searches?

Mac OS 10.5
MPL 0.99.1

Many thanks,

Paul M. Hobson  
Senior Staff Engineer
-- 
Geosyntec Consultants 
55 SW Yamhill St, Ste 200
Portland, OR 97204
Phone: (503) 222-9518
Web:   www.geosyntec.com




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Re: [Matplotlib-users] How do I change where MPL looks for Latex?

2009-11-04 Thread John Hunter
On Wed, Nov 4, 2009 at 11:25 AM,  phob...@geosyntec.com wrote:
 I know support for the usetex feature is limited, but I think (*hope*) that 
 this is purely an MPL question and not out of the scope and annoying to the 
 members of the group.

 I like to use the fourier.sty package since I like the Utopia font and it's 
 math font is particularly nice. But MPL is using this Latex installation:
 /sw/share/texmf-dist/tex/latex/
 which has no fourier package, and raises predictable errors when I set
 text.latex.preamble :  \usepackage{fourier}

 But I only use and maintain this one:
 /usr/local/texlive/2008/texmf-dist/tex/latex/
 (fourier and many other packages I like)

This looks like a UNIX PATH issue -- mpl will use the version of latex
it finds first in your PATH, so if you want it to find
/usr/local/texlive/2008/texmf-dist/tex/latex/, put the directory
containing that latex ahead of the fink one (/sw)

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Re: [Matplotlib-users] How do I change where MPL looks for Latex?

2009-11-04 Thread PHobson
 On Wed, Nov 4, 2009 at 11:25 AM,  phob...@geosyntec.com wrote:
  I know support for the usetex feature is limited, but I think
 (*hope*) that this is purely an MPL question and not out of the scope
 and annoying to the members of the group.
 
  I like to use the fourier.sty package since I like the Utopia font
 and it's math font is particularly nice. But MPL is using this Latex
 installation:
  /sw/share/texmf-dist/tex/latex/
  which has no fourier package, and raises predictable errors when I
 set
  text.latex.preamble :  \usepackage{fourier}
 
  But I only use and maintain this one:
  /usr/local/texlive/2008/texmf-dist/tex/latex/
  (fourier and many other packages I like)

From: John Hunter [mailto:jdh2...@gmail.com]
Sent: Wednesday, November 04, 2009 9:33 AM
 This looks like a UNIX PATH issue -- mpl will use the version of latex
 it finds first in your PATH, so if you want it to find
 /usr/local/texlive/2008/texmf-dist/tex/latex/, put the directory
 containing that latex ahead of the fink one (/sw)

Thanks, John. Looks like I can take from here. I'll add my Texlive directory to 
near the top of the path.

-paul

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[Matplotlib-users] mplot3d: bar3d + colormap somehow?

2009-11-04 Thread qubax
Greetings.

I would like to make a mplot3d.bar3d plot where the colour indicates
the value of the element. Like: negative values blue, positive red,
zero green. From what i see i can only give all bars the same 
color ... Is there a way around it?

I know that this is currently done in mayavi, but mayavi also
seems to be tons slower.

thanks for any help

with best regards,
q

-- 
The king who needs to remind his people of his rank, is no king.

To gain that which is worth having, it may be necessary to lose everything else.

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Re: [Matplotlib-users] Drawing a single contour line

2009-11-04 Thread Eric Firing
John Hunter wrote:
 On Wed, Nov 4, 2009 at 11:16 AM, Brendan Arnold brendanarn...@gmail.com 
 wrote:
 Ah, I was a little confused by what you wrote John (I though I had to
 access contour through the axes object and the meaning of R, F, dR was
 a little unclear..) however using the 'levels' keyword now works. i.e.

 plt.contour(x, y, z, levels=[0])

 Incidentally, this keyword (levels) is not documented at
 http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.contour
 and in fact the documentation implies that contour(kx, ky, z, [0])
 should work when it does not.

But it does work, as it should:

x = arange(5)
y = arange(7)
X, Y = meshgrid(x,y)
z = X+Y
contour(X, Y, z, [5])


Drop the above into ipython -pylab.

Eric


 Perhaps the docs could be updated to reflect this?
 
 Thanks for the heads up -- I updated the docstring in svn HEAD
 
 Sorry the original example was confusing -- I cut and pasted from some
 code I was working on, and forgot to import the mindreading module
 
 JDH
 
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