Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-05-17 Thread Jonathan Slavin
Matthias,

It's clear to me why apect='equal' doesn't work for you.  That option
means to give the axes equal scaling -- i.e., the ratio of length in
axis units to length in the plot is the same for both axes, so that an
axis that goes from 0 to 1 will be twice as long as one that goes from 0
to 0.5.  What is quite unclear to me is why aspect=2 should give a
result like it does.  You can get the right image, though wrong tick
labeling, if you omit the extent argument to imshow.

Jon

On Thu, 2013-05-16 at 12:43 -0700, Matthias Flor wrote:
 Hi all,
 
 it seems that I am experiencing the same problem here with imshow (rather
 than scatter) and AxesGrid. But calling imshow with aspect=False does not do
 the trick for me.
 I am trying to have two imshow subplots next to each other and a single
 colorbar at the right. The data underlying the imshow's have different x-
 and y-ranges but I want the x- and y-axis to have an aspect ratio of 1 (i.e.
 each imshow should produce a square). I've tried aspect=False,
 aspect='equal', and explicitely setting aspect=2 which should be the correct
 value. See the three images below the code example.
 
 I've also tried Grid instead of AxesGrid as suggested but I didn't manage to
 achieve good results with the colorbar in that case.
 
 I'd appreciate any help,
 
 Matthias
 
 
 
 Here's a more or less minimal code example:
 #
 import numpy as np
 import numpy.random as npr
 from scipy.interpolate import griddata
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import AxesGrid
 
 fig = figure(1, figsize=[12,10])
 
 grid = AxesGrid(fig, 111,
 nrows_ncols = (1, 2),
 axes_pad = 0.2,
 share_all = False,
 label_mode = 'L',
 cbar_location = 'right',
 cbar_mode = 'single',
 cbar_pad = 0.2
 )
 
 for i in range(2):  
 xmin, xmax = 0., 1.
 ymin, ymax = 0., 0.5
 zmin, zmax = -1., 1.
 
 # generate random data:
 N = 100
 X = xmin + (xmax-xmin)*npr.random((N,))  # x_i in [0, 1]
 Y = ymin + (ymax-ymin)*npr.random((N,))  # y_i in [0, 0.5]
 Z = zmin + (zmax-zmin)*npr.random((N,))  # z_i in [-1, 1]
 
 # generate griddata for imshow plot:
 numspaces = np.sqrt(N)
 xi = linspace(xmin, xmax, numspaces)
 yi = linspace(ymin, ymax, numspaces)
 zi = griddata((X, Y), Z, (xi[None,:], yi[:,None]), method='nearest')
 norm = matplotlib.colors.normalize(vmin=zmin, vmax=zmax)
 
 ax = grid[i]
 im = ax.imshow(zi,
 extent = [xmin,xmax,ymin,ymax],  
 norm = norm, 
 vmin = zmin,
 vmax = zmax, 
 origin = 'lower', 
 aspect = 'equal', # or False, or 'auto', or 2, or ...
 interpolation = 'nearest')
 
 ax.grid(False)
 ax.set_xlabel('x')
 ax.set_ylabel('y')
 
 # add a colorbar:
 cbar = plt.colorbar(im, cax=grid.cbar_axes[0])
 cbar.ax.set_ylabel('color level')
 
 
 And here are the three resulting images:
 
 aspect='equal':
 http://matplotlib.1069221.n5.nabble.com/file/n41075/equal.png 
 
 aspect=False:
 http://matplotlib.1069221.n5.nabble.com/file/n41075/False.png 
 
 aspect=2.:
 http://matplotlib.1069221.n5.nabble.com/file/n41075/two.png 
 
 
 
 --
 View this message in context: 
 http://matplotlib.1069221.n5.nabble.com/Squashed-axes-with-AxesGrid-tp40699p41075.html
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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-05-17 Thread Matthias Flor
Thanks for the comment, Jonathan.

Yeah, I did not expect aspect='equal' to work but I tried it anyway ;-)
Removing the extent argument indeed produces a very nice output but I have
not tried yet to also get the tick labels right. Instead, I have now
reverted back to matplotlib.pylab's subplots method and an extra axes for
the colorbar (see code below just in case somebody else can use that). With
some fiddling with spacing it looks ok now. It's just a mess to produce
differently sized figures but I probably won't need to do that.

Best, Matthias


http://matplotlib.1069221.n5.nabble.com/file/n41080/2imshow%2B1colorbar.png 
###
import numpy as np
import numpy.random as npr
from scipy.interpolate import griddata
import matplotlib.pyplot as plt

fig, axes = plt.subplots(nrows=1, ncols=2, figsize=[12,5])

for ax in axes:
xmin, xmax = 0., 1.
ymin, ymax = 0., 0.5
zmin, zmax = -1., 1.

# create random data:
N = 100
X = xmin + (xmax-xmin)*npr.random((N,))  # x_i in [0, 1]
Y = ymin + (ymax-ymin)*npr.random((N,))  # y_i in [0, 0.5]
Z = zmin + (zmax-zmin)*npr.random((N,))  # z_i in [-1, 1]

# generate griddata for contour plot:
numspaces = np.sqrt(N)
xi = linspace(xmin, xmax, numspaces)
yi = linspace(ymin, ymax, numspaces)
zi = griddata((X, Y), Z, (xi[None,:], yi[:,None]), method='nearest')
norm = matplotlib.colors.normalize(vmin=zmin, vmax=zmax)

im = ax.imshow(zi,
extent = [xmin,xmax,ymin,ymax],  
norm = norm, 
vmin = zmin,
vmax = zmax, 
origin = 'lower', 
aspect = 2., 
interpolation = 'nearest')

ax.grid(False)
ax.set_xlabel('x')
ax.set_ylabel('y')

# add a colorbar:
fig.subplots_adjust(left=0.05, bottom=0.2, right=0.8, top=0.95, wspace=0.2,
hspace=0.2)
cbar_ax = fig.add_axes([0.85, 0.2, 0.03, 0.75])
fig.colorbar(im, cax=cbar_ax)
cbar_ax.set_ylabel('color level')
fig.subplots_adjust(left=0.05, bottom=0.2, right=0.8, top=0.95, wspace=0.2,
hspace=0.2)
##



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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-05-16 Thread Matthias Flor
Hi all,

it seems that I am experiencing the same problem here with imshow (rather
than scatter) and AxesGrid. But calling imshow with aspect=False does not do
the trick for me.
I am trying to have two imshow subplots next to each other and a single
colorbar at the right. The data underlying the imshow's have different x-
and y-ranges but I want the x- and y-axis to have an aspect ratio of 1 (i.e.
each imshow should produce a square). I've tried aspect=False,
aspect='equal', and explicitely setting aspect=2 which should be the correct
value. See the three images below the code example.

I've also tried Grid instead of AxesGrid as suggested but I didn't manage to
achieve good results with the colorbar in that case.

I'd appreciate any help,

Matthias



Here's a more or less minimal code example:
#
import numpy as np
import numpy.random as npr
from scipy.interpolate import griddata
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import AxesGrid

fig = figure(1, figsize=[12,10])

grid = AxesGrid(fig, 111,
nrows_ncols = (1, 2),
axes_pad = 0.2,
share_all = False,
label_mode = 'L',
cbar_location = 'right',
cbar_mode = 'single',
cbar_pad = 0.2
)

for i in range(2):  
xmin, xmax = 0., 1.
ymin, ymax = 0., 0.5
zmin, zmax = -1., 1.

# generate random data:
N = 100
X = xmin + (xmax-xmin)*npr.random((N,))  # x_i in [0, 1]
Y = ymin + (ymax-ymin)*npr.random((N,))  # y_i in [0, 0.5]
Z = zmin + (zmax-zmin)*npr.random((N,))  # z_i in [-1, 1]

# generate griddata for imshow plot:
numspaces = np.sqrt(N)
xi = linspace(xmin, xmax, numspaces)
yi = linspace(ymin, ymax, numspaces)
zi = griddata((X, Y), Z, (xi[None,:], yi[:,None]), method='nearest')
norm = matplotlib.colors.normalize(vmin=zmin, vmax=zmax)

ax = grid[i]
im = ax.imshow(zi,
extent = [xmin,xmax,ymin,ymax],  
norm = norm, 
vmin = zmin,
vmax = zmax, 
origin = 'lower', 
aspect = 'equal', # or False, or 'auto', or 2, or ...
interpolation = 'nearest')

ax.grid(False)
ax.set_xlabel('x')
ax.set_ylabel('y')

# add a colorbar:
cbar = plt.colorbar(im, cax=grid.cbar_axes[0])
cbar.ax.set_ylabel('color level')


And here are the three resulting images:

aspect='equal':
http://matplotlib.1069221.n5.nabble.com/file/n41075/equal.png 

aspect=False:
http://matplotlib.1069221.n5.nabble.com/file/n41075/False.png 

aspect=2.:
http://matplotlib.1069221.n5.nabble.com/file/n41075/two.png 



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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-03-22 Thread Sterling Smith
Steven,

Did you mean to switch back to AxesGrid?  I thought you said that it was fixed 
with Grid.

-Sterling

On Mar 22, 2013, at 9:30AM, Steven Boada wrote:

 Well... I jumped the gun. To better illustrate the problem(s) I am having, I 
 wrote a simple script that doesn't work...
 
 import pylab as pyl
 from mpl_toolkits.axes_grid1 import AxesGrid
 
 # make some data
 xdata = pyl.random(100) * 25.
 ydata = pyl.random(100) * 8.
 colordata = pyl.random(100) * 3.
 
 # make us a figure
 F = pyl.figure(1,figsize=(5.5,3.5))
 grid = AxesGrid(F, 111,
nrows_ncols=(1,2),
axes_pad = 0.1,
add_all=True,
share_all = True,
cbar_mode = 'each',
cbar_location = 'top')
 
 # Plot!
 sc1 = grid[0].scatter(xdata, ydata, c=colordata, s=50, cmap='spectral')
 sc2 = grid[1].scatter(xdata, ydata, c=colordata, s=50, cmap='spectral')
 
 # Add colorbars
 grid.cbar_axes[0].colorbar(sc1)
 grid.cbar_axes[1].colorbar(sc2)
 
 grid[0].set_xlim(0,25)
 grid[0].set_ylim(0,8)
 
 pyl.show()
 
 
 And you get some squashed figures... I'll attach a png.
 
 Thanks again.
 
 Steven
 
 On Fri Mar 22 10:49:44 2013, Steven Boada wrote:
 
 Thanks JJ!
 
 That did fix my problem, but I can't say I understand what the
 difference is. Why does Axesgrid make them squashed while just Grid
 works?
 
 
 On Thu Mar 21 22:28:34 2013, Jae-Joon Lee wrote:
 
 It is not clear what your problem is.
 AxesGrid implicitly assumes aspect=1 for each axes. So, I guess your
 y-limits are smaller (in its span) than x-limits.
 If you don't want this behavior, there is no need of using the
 AxesGrid. Rather use Grid, or simply subplots.
 
 import matplotlib.pyplot as plt
 from mpl_toolkits.axes_grid1 import Grid
 
 F = plt.figure(1,(5.5,3.5))
 grid = Grid(F, 111,
 nrows_ncols=(1,3),
 axes_pad = 0.1,
 add_all=True,
 label_mode = 'L',
 )
 
 If this is not the answer you're looking for, I recommend you to post
 a complete but simple script that reproduces your problem and describe
 the problem more explicitly.
 
 Regards,
 
 -JJ
 
 
 On Fri, Mar 22, 2013 at 6:03 AM, Steven Boada bo...@physics.tamu.edu
 mailto:bo...@physics.tamu.edu wrote:
 
 Heya List,
 
 See attached image for what I mean.
 
 Here is the grid creation bit. I can't seem to figure out what
 might be causing such a problem.
 
 F = pyl.figure(1,(5.5,3.5))
 grid = AxesGrid(F, 111,
 nrows_ncols=(1,3),
 axes_pad = 0.1,
 add_all=True,
 label_mode = 'L',
 aspect=True)
 
 Should be simple enough right?
 
 --
 
 Steven Boada
 
 Doctoral Student
 Dept of Physics and Astronomy
 Texas AM University
 bo...@physics.tamu.edu mailto:bo...@physics.tamu.edu
 
 
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 Texas AM University
 bo...@physics.tamu.edu
 
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 Screen Shot 2013-03-22 at 11.27.19 
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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-03-22 Thread Steven Boada
Sorry y'all. I can see the confusion.

I started with AxesGrid -- squashed.

JJ suggested Grid and that fixes the scaling problems.

I realized that using just plain Grid doesn't give me the nice controls 
over the colorbars (which I would like to have), so I wrote a simple 
script and emailed it back out. That did include AxesGrid.

According to the manual ( 
http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1 
)...

aspect
By default (False), widths and heights of axes in the grid are scaled 
independently. If True, they are scaled according to their data limits 
(similar to aspect parameter in mpl).

Which I read as it should scale the widths and heights should not be 
squashed. But what Ben is telling me (thanks for the explanation) is 
that isn't true. Seems like there is something simple I am just missing.

Sorry for that bit of confusion.

Steven

On Fri Mar 22 11:39:46 2013, Benjamin Root wrote:


 On Fri, Mar 22, 2013 at 12:30 PM, Steven Boada bo...@physics.tamu.edu
 mailto:bo...@physics.tamu.edu wrote:

 Well... I jumped the gun. To better illustrate the problem(s) I am
 having, I wrote a simple script that doesn't work...

 import pylab as pyl
 from mpl_toolkits.axes_grid1 import AxesGrid

 # make some data
 xdata = pyl.random(100) * 25.
 ydata = pyl.random(100) * 8.
 colordata = pyl.random(100) * 3.

 # make us a figure
 F = pyl.figure(1,figsize=(5.5,3.5)__)
 grid = AxesGrid(F, 111,
 nrows_ncols=(1,2),
 axes_pad = 0.1,
 add_all=True,
 share_all = True,
 cbar_mode = 'each',
 cbar_location = 'top')

 # Plot!
 sc1 = grid[0].scatter(xdata, ydata, c=colordata, s=50,
 cmap='spectral')
 sc2 = grid[1].scatter(xdata, ydata, c=colordata, s=50,
 cmap='spectral')

 # Add colorbars
 grid.cbar_axes[0].colorbar(__sc1)
 grid.cbar_axes[1].colorbar(__sc2)

 grid[0].set_xlim(0,25)
 grid[0].set_ylim(0,8)

 pyl.show()


 And you get some squashed figures... I'll attach a png.

 Thanks again.

 Steven


 You used AxesGrid again, not Grid.  AxesGrid implicitly applies an
 aspect='equal' to the subplots.  This means that a unit of distance on
 the x-axis takes the same amount of space as the same unit of distance
 on the y-axis.  In your example, the x axis goes from 0 to 25, while
 the y-axis goes from 0 to 8.  When aspect='equal', the y-axis will
 then be about a third the size of the x-axis, because the y-limits are
 about a third the size of the x-limits.

 Ben Root


--

Steven Boada

Doctoral Student
Dept of Physics and Astronomy
Texas AM University
bo...@physics.tamu.edu

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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-03-22 Thread Jody Klymak
...and did aspect=False not give you what you want?  

From what I can see 
http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1

contradicts itself, and the chart is correct and the description below 
incorrect.

FWIW, I would expect the default to be False as well, but who am I to say?

Cheers,   Jody

On Mar 22, 2013, at  9:52 AM, Steven Boada bo...@physics.tamu.edu wrote:

 Sorry y'all. I can see the confusion.
 
 I started with AxesGrid -- squashed.
 
 JJ suggested Grid and that fixes the scaling problems.
 
 I realized that using just plain Grid doesn't give me the nice controls 
 over the colorbars (which I would like to have), so I wrote a simple 
 script and emailed it back out. That did include AxesGrid.
 
 According to the manual ( 
 http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1 
 )...
 
 aspect
 By default (False), widths and heights of axes in the grid are scaled 
 independently. If True, they are scaled according to their data limits 
 (similar to aspect parameter in mpl).
 
 Which I read as it should scale the widths and heights should not be 
 squashed. But what Ben is telling me (thanks for the explanation) is 
 that isn't true. Seems like there is something simple I am just missing.
 
 Sorry for that bit of confusion.
 
 Steven
 
 On Fri Mar 22 11:39:46 2013, Benjamin Root wrote:
 
 
 On Fri, Mar 22, 2013 at 12:30 PM, Steven Boada bo...@physics.tamu.edu
 mailto:bo...@physics.tamu.edu wrote:
 
Well... I jumped the gun. To better illustrate the problem(s) I am
having, I wrote a simple script that doesn't work...
 
import pylab as pyl
from mpl_toolkits.axes_grid1 import AxesGrid
 
# make some data
xdata = pyl.random(100) * 25.
ydata = pyl.random(100) * 8.
colordata = pyl.random(100) * 3.
 
# make us a figure
F = pyl.figure(1,figsize=(5.5,3.5)__)
grid = AxesGrid(F, 111,
nrows_ncols=(1,2),
axes_pad = 0.1,
add_all=True,
share_all = True,
cbar_mode = 'each',
cbar_location = 'top')
 
# Plot!
sc1 = grid[0].scatter(xdata, ydata, c=colordata, s=50,
cmap='spectral')
sc2 = grid[1].scatter(xdata, ydata, c=colordata, s=50,
cmap='spectral')
 
# Add colorbars
grid.cbar_axes[0].colorbar(__sc1)
grid.cbar_axes[1].colorbar(__sc2)
 
grid[0].set_xlim(0,25)
grid[0].set_ylim(0,8)
 
pyl.show()
 
 
And you get some squashed figures... I'll attach a png.
 
Thanks again.
 
Steven
 
 
 You used AxesGrid again, not Grid.  AxesGrid implicitly applies an
 aspect='equal' to the subplots.  This means that a unit of distance on
 the x-axis takes the same amount of space as the same unit of distance
 on the y-axis.  In your example, the x axis goes from 0 to 25, while
 the y-axis goes from 0 to 8.  When aspect='equal', the y-axis will
 then be about a third the size of the x-axis, because the y-limits are
 about a third the size of the x-limits.
 
 Ben Root
 
 
 --
 
 Steven Boada
 
 Doctoral Student
 Dept of Physics and Astronomy
 Texas AM University
 bo...@physics.tamu.edu
 
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--
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http://web.uvic.ca/~jklymak/





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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-03-22 Thread Steven Boada
Hey Jody et al.

Yeah aspect = False does the trick. Thanks for the help trouble 
shooting.

Steven

On Fri Mar 22 11:59:45 2013, Jody Klymak wrote:
 ...and did aspect=False not give you what you want?

  From what I can see 
 http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1

 contradicts itself, and the chart is correct and the description below 
 incorrect.

 FWIW, I would expect the default to be False as well, but who am I to say?

 Cheers,   Jody

 On Mar 22, 2013, at  9:52 AM, Steven Boada bo...@physics.tamu.edu wrote:

 Sorry y'all. I can see the confusion.

 I started with AxesGrid -- squashed.

 JJ suggested Grid and that fixes the scaling problems.

 I realized that using just plain Grid doesn't give me the nice controls
 over the colorbars (which I would like to have), so I wrote a simple
 script and emailed it back out. That did include AxesGrid.

 According to the manual (
 http://matplotlib.org/mpl_toolkits/axes_grid/users/overview.html#axes-grid1
 )...

 aspect
 By default (False), widths and heights of axes in the grid are scaled
 independently. If True, they are scaled according to their data limits
 (similar to aspect parameter in mpl).

 Which I read as it should scale the widths and heights should not be
 squashed. But what Ben is telling me (thanks for the explanation) is
 that isn't true. Seems like there is something simple I am just missing.

 Sorry for that bit of confusion.

 Steven

 On Fri Mar 22 11:39:46 2013, Benjamin Root wrote:


 On Fri, Mar 22, 2013 at 12:30 PM, Steven Boada bo...@physics.tamu.edu
 mailto:bo...@physics.tamu.edu wrote:

 Well... I jumped the gun. To better illustrate the problem(s) I am
 having, I wrote a simple script that doesn't work...

 import pylab as pyl
 from mpl_toolkits.axes_grid1 import AxesGrid

 # make some data
 xdata = pyl.random(100) * 25.
 ydata = pyl.random(100) * 8.
 colordata = pyl.random(100) * 3.

 # make us a figure
 F = pyl.figure(1,figsize=(5.5,3.5)__)
 grid = AxesGrid(F, 111,
 nrows_ncols=(1,2),
 axes_pad = 0.1,
 add_all=True,
 share_all = True,
 cbar_mode = 'each',
 cbar_location = 'top')

 # Plot!
 sc1 = grid[0].scatter(xdata, ydata, c=colordata, s=50,
 cmap='spectral')
 sc2 = grid[1].scatter(xdata, ydata, c=colordata, s=50,
 cmap='spectral')

 # Add colorbars
 grid.cbar_axes[0].colorbar(__sc1)
 grid.cbar_axes[1].colorbar(__sc2)

 grid[0].set_xlim(0,25)
 grid[0].set_ylim(0,8)

 pyl.show()


 And you get some squashed figures... I'll attach a png.

 Thanks again.

 Steven


 You used AxesGrid again, not Grid.  AxesGrid implicitly applies an
 aspect='equal' to the subplots.  This means that a unit of distance on
 the x-axis takes the same amount of space as the same unit of distance
 on the y-axis.  In your example, the x axis goes from 0 to 25, while
 the y-axis goes from 0 to 8.  When aspect='equal', the y-axis will
 then be about a third the size of the x-axis, because the y-limits are
 about a third the size of the x-limits.

 Ben Root


 --

 Steven Boada

 Doctoral Student
 Dept of Physics and Astronomy
 Texas AM University
 bo...@physics.tamu.edu

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Steven Boada

Doctoral Student
Dept of Physics and Astronomy
Texas AM University
bo...@physics.tamu.edu

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Re: [Matplotlib-users] Squashed axes with AxesGrid

2013-03-21 Thread Jae-Joon Lee
It is not clear what your problem is.
AxesGrid implicitly assumes aspect=1 for each axes. So, I guess your
y-limits are smaller (in its span) than x-limits.
If you don't want this behavior, there is no need of using the AxesGrid.
Rather use Grid, or simply subplots.

import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import Grid

F = plt.figure(1,(5.5,3.5))
grid = Grid(F, 111,
nrows_ncols=(1,3),
axes_pad = 0.1,
add_all=True,
label_mode = 'L',
)

If this is not the answer you're looking for, I recommend you to post a
complete but simple script that reproduces your problem and describe the
problem more explicitly.

Regards,

-JJ


On Fri, Mar 22, 2013 at 6:03 AM, Steven Boada bo...@physics.tamu.eduwrote:

 Heya List,

 See attached image for what I mean.

 Here is the grid creation bit. I can't seem to figure out what might be
 causing such a problem.

 F = pyl.figure(1,(5.5,3.5))
 grid = AxesGrid(F, 111,
 nrows_ncols=(1,3),
 axes_pad = 0.1,
 add_all=True,
 label_mode = 'L',
 aspect=True)

 Should be simple enough right?

 --

 Steven Boada

 Doctoral Student
 Dept of Physics and Astronomy
 Texas AM University
 bo...@physics.tamu.edu



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