matplotlib-users Mailing List for matplotlib (Page 16)

Hello,

I am trying to create a plot and I want to disable the black frame which 
is drawn around the plot automatically. I achieved this with this setting:

mp.rcParams['axes.linewidth'] = 0

The problem is now, that I would like to have the dashed axes line, too. 
Those dashed lines do appear on the top and the left of the plot, but 
not on the lower and right border. What do I have to do to plot them 
there, too?

See attached PNG.

By the way, I am impressed by the library, I was searching quite a long 
time for something like this when I was using Matlab. Great!

Regards
Paul.

Hello,

I am trying to create a plot and I want to disable the black frame which
is drawn around the plot automatically. I achieved this with this setting:

mp.rcParams['axes.linewidth'] = 0

The problem is now, that I would like to have the dashed axes line, too.
Those dashed lines do appear on the top and the left of the plot, but
not on the lower and right border. What do I have to do to plot them
there, too?

See http://purecodes.org/stuff/sample.png

By the way, I am impressed by the library, I was searching quite a long
time for something like this when I was using Matlab. Great!

Regards
Paul.

Eric Firing <efiring@...> writes:
> 
> Solution: use
> x = arange(11)
> y = arange(11)
> 
> Eric

Thanks Eric,

That has solved my problem!

Best, Juls

Gökhan SEVER wrote:
> Hello,
> 
> I am trying convert a plot written in IDL to Python using matplotlib. So 
> far, I have managed to show the image on the screen equivalent to its 
> IDL output. The only problem that I could not figure out matching the 
> colormaps between them. Please see the results on this png image: 
> http://img515.imageshack.us/img515/3951/colormaps.png
> 
> The top plot and the associated colorbar is from IDL, and the other plot 
> is using matplotlib's imshow(). I don't know how to show my lowest 
> values in the plot as white. I would be please if someone gives some 
> insight into this issue.

See 
http://matplotlib.sourceforge.net/examples/pylab_examples/image_masked.html
and in particular the use of set_under().

Eric
> 
> Thank you all.
> 
> Gökhan

Hello,

I am trying convert a plot written in IDL to Python using matplotlib. So
far, I have managed to show the image on the screen equivalent to its IDL
output. The only problem that I could not figure out matching the colormaps
between them. Please see the results on this png image:
http://img515.imageshack.us/img515/3951/colormaps.png

The top plot and the associated colorbar is from IDL, and the other plot is
using matplotlib's imshow(). I don't know how to show my lowest values in
the plot as white. I would be please if someone gives some insight into this
issue.

Thank you all.

Gökhan

Juls Night wrote:
> I'm new to matplotlib and am really enjoying using it. I'm confused by something
> though:
[...]
> The following code produces an error though (only the length of the vectors have
> been changed):
> 
> from pylab import *
> 
> x = range(11)
> y = range(11)
> 
> m,b = polyfit(x, y, 1)
> 
> plot(x, y, 'yo', x, m*x+b, '--k')

The problem is that x is a list, not an array, and m*x yields an empty 
array:

In [17]:m*x
Out[17]:[]

In [18]:m
Out[18]:0.99999999999999978

In [19]:x
Out[19]:[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]

Solution: use
x = arange(11)
y = arange(11)

Eric

I'm new to matplotlib and am really enjoying using it. I'm confused by something
though:

If I plot the following linear regression it works as expected.

from pylab import *

x = range(10)
y = range(10)

m,b = polyfit(x, y, 1)

plot(x, y, 'yo', x, m*x+b, '--k')
show()

The following code produces an error though (only the length of the vectors have
been changed):

from pylab import *

x = range(11)
y = range(11)

m,b = polyfit(x, y, 1)

plot(x, y, 'yo', x, m*x+b, '--k')
show()

I'm using:
python 2.5
matplotlib 0.98.5.2
numpy 1.3.0

Below is the error message:

Traceback (most recent call last):
  File "<stdin>", line 8, in <module>
  File "/usr/lib/python2.5/site-packages/matplotlib/pyplot.py", line 2096, in plot
    ret =  gca().plot(*args, **kwargs)
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 3277, in plot
    for line in self._get_lines(*args, **kwargs):
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 401, in
_grab_next_args
    for seg in self._plot_3_args(remaining, **kwargs):
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 340, in
_plot_3_args
    x, y, multicol = self._xy_from_xy(x, y)
  File "/usr/lib/python2.5/site-packages/matplotlib/axes.py", line 228, in
_xy_from_xy
    assert nrx == nry, 'Dimensions of x and y are incompatible'
AssertionError: Dimensions of x and y are incompatible
Unbunt Hardy 8.04

Thanks,
Juls

A quick but not necessarily accurate answer:  Don't use Python 2.6.  Use 
Python 2.5.  I don't think matplotlib has been 'certified' for 2.6 yet.

I suggest
  (1) uninstall Python 2.6 and numpy for 2.6.
  (2) Install Python 2.5 and numpy for 2.5

 (3) Install matplotlib for 2.5





Constantine <ck...@gm...> 
07/04/2009 10:19 AM

To
mat...@li...
cc

Subject
[Matplotlib-users] Installing Matplotlib






Hi,

sorry to bother you. This may be a trivial question for experienced 
Matplotlib users. I am trying to install Matplotlib under Windows XP but 
with no success. I am not familiar with Python or any of the other 
packages and I've never used Matplotlib before. I followed the 
instructions in the Matplotlib User's Manual and I have installed in the 
following sequence 1) Python(x,y)-2.1.12, 2) python-2.6.1.msi and 3) 
numpy-1.3.0-win32-superpack-python2.6.exe. Can anyone advise me on what to 
do next?

Thanks,
Constantine 
 



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Hi,

sorry to bother you. This may be a trivial question for experienced
Matplotlib users. I am trying to install Matplotlib under Windows XP but
with no success. I am not familiar with Python or any of the other packages
and I've never used Matplotlib before. I followed the instructions in the
Matplotlib User's Manual and I have installed in the following sequence 1)
Python(x,y)-2.1.12, 2) python-2.6.1.msi and 3)
numpy-1.3.0-win32-superpack-python2.6.exe. Can anyone advise me on what to
do next?

Thanks,
Constantine

j bai wrote:
> Hi,  P.Romero,
> Please let me know if you get this working.   I am trying to do the same 
> type of 2 axes bar chart.  but I got error message.  
> I am using regular  bar ().  
> the following is the email i sent a week ago.   Eric, I did use the 
> twinx(), but it gave errors.
>  
> thanks in advance.  
> 
> Hi, everyone, 
> I am a matplotlib beginner.  I am trying to do a chart with 2 y axes 
> using twinx()
> I keep getting error message  "malformed header from script. Bad 
> header=    is masked in one or more l: test.cgi"  when I do two bar 
> charts on two axes.  if I do one bar chart and one line chart, I wouldnt 
> get the error.  
> if I refresh the web page, the chart would show up. 
> the following is my code.  
> 
>         ...
>         ax = self.fig.add_axes( self.rectMain, axisbg=self.axesBG)
>         ticks = self.setTickInterval( 10, 0, buybackDataobj.sharesMax)
>         ind = na.array(range(len(
> buybackDataobj.quarters)))
>         majorFormatter = FormatStrFormatter('%2.1f')
>         ax.yaxis.set_major_locator(MultipleLocator( ticks ) )
>         ax.yaxis.set_major_formatter(majorFormatter)
>          bar(ind, buybackDataobj.shares, self.barwidth, 
> color=self.draw.color['DarkGreen'] ) 

Try making that ax.bar(...)


>         
>         t = arange(0, float(buybackDataobj.sharesMax), ticks )
>         ax.set_ylim(0, buybackDataobj.sharesMax * 1.1)
>         ax.set_xlim(0, ind[-1] + self.barwidth*2)
>         ax.set_ylabel("Value Bought " + buybackDataobj.scale, fontsize = 
> self.fontsize )
>  
>         ax.set_xticks(ind + self.barwidth)
>  
>         ax.set_xticklabels( buybackDataobj.quarters, fontsize = 
> self.fontsize)
>         setp( ax.get_xticklabels(), rotation = self.rotation, 
> horizontalalignment='center', family=
> 'sans-serif', fontsize = self.xaxisfs )
> 
>              if buybackDataobj.charttype == 'sells':
> 
>                 ax2 = twinx()
>                 #ax2.plot(ind + self.barwidth/2, buybackDataobj.sells, 
> ls='-', marker ='.', ms=11, c='#FF3300')  //  I wouldnt get the error 
> message if I do this 
> plot                                                                                      
> 
>                 bar(ind + self.barwidth, buybackDataobj.sells, 
> self.barwidth, color='#FF3300' )  // malformed header from script. Bad 
> header=    is masked in one or more l: test.cgi 

And make that one ax2.bar(...).


It sounds like you have a combined mpl and cgi problem here; maybe an 
exception in mpl is triggering a cgi error.  "malformed header from 
script" is not coming from mpl.  "is masked in one or more" probably is, 
but you need to see the whole traceback to find out what the problem is.

So as a matter of strategy, separate the mpl from the cgi; make sure 
your script runs without error in standalone mode.  Stick to purely or 
mostly OO style.  You probably want to start with something like

import matplotlib
matplotlib.use("agg")
import pyplot as plt  # e.g. if you want to use "fig = plt.figure()"

This makes sure you are using a non-interactive backend.

See 
http://matplotlib.sourceforge.net/faq/howto_faq.html#matplotlib-in-a-web-application-server

Eric


>                 ax2.set_xticklabels(buybackDataobj.quarters, visible=False )
>                 ax2.set_ylim(buybackDataobj.sellsMin * 0.75, 
> buybackDataobj.sellsMax * 1.1)
>                 ax2.set_ylabel("Insider Selling $" + 
> buybackDataobj.sellsScale, verticalalignment='center', fontsize = 
> self.fontsize)
> 
>                 setp( ax2.get_yticklabels(), rotation = 0, 
> horizontalalignment='left', family='sans-serif', fontsize=self.fontsize )
>            





> .............
> 
> 
> On Mon, Apr 6, 2009 at 3:44 PM, Eric Firing <ef...@ha... 
> <mailto:ef...@ha...>> wrote:
> 
>     P.Romero wrote:
>      > Is it possible to create a colorbar with different scales on each
>     side?
>      >
>      >
>      >
>      > Example:
>      >
>      >  a temperature colorbar with celcius values on the left side and
>      > farenheit values on the right side.
>      >
>      >
>      >
>      > If so, how could this be done?
> 
>     A colorbar is just an axes object with some customization of the ticks
>     and labels, and with a pcolor plot inside.  You could get your second
>     scale using a technique similar to the twinx and twiny Axes methods; you
>     can then use set_xlim or set_ylim so that the Fahrenheit range on the
>     new axes matches the Celcius range on the old one.
> 
>     To get started, look at the source for the twinx/twiny methods.
> 
>     Eric
> 
>      >
>      >
>      >
>      > Please help,
>      >
>      > Thanks,
>      >
>      > P.Romero
>      >
>      >
>      >
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Hi,  P.Romero,
Please let me know if you get this working.   I am trying to do the same
type of 2 axes bar chart.  but I got error message.
I am using regular  bar ().
the following is the email i sent a week ago.   Eric, I did use the twinx(),
but it gave errors.

thanks in advance.

Hi, everyone,
I am a matplotlib beginner.  I am trying to do a chart with 2 y axes using
twinx()
I keep getting error message  "malformed header from script. Bad header=
is masked in one or more l: test.cgi"  when I do two bar charts on two
axes.  if I do one bar chart and one line chart, I wouldnt get the error.
if I refresh the web page, the chart would show up.
the following is my code.

        ...
        ax = self.fig.add_axes( self.rectMain, axisbg=self.axesBG)
        ticks = self.setTickInterval( 10, 0, buybackDataobj.sharesMax)
        ind = na.array(range(len(buybackDataobj.quarters)))
        majorFormatter = FormatStrFormatter('%2.1f')
        ax.yaxis.set_major_locator(MultipleLocator( ticks ) )
        ax.yaxis.set_major_formatter(majorFormatter)
         bar(ind, buybackDataobj.shares, self.barwidth,
color=self.draw.color['DarkGreen'] )

        t = arange(0, float(buybackDataobj.sharesMax), ticks )
        ax.set_ylim(0, buybackDataobj.sharesMax * 1.1)
        ax.set_xlim(0, ind[-1] + self.barwidth*2)
        ax.set_ylabel("Value Bought " + buybackDataobj.scale, fontsize =
self.fontsize )

        ax.set_xticks(ind + self.barwidth)

        ax.set_xticklabels( buybackDataobj.quarters, fontsize =
self.fontsize)
        setp( ax.get_xticklabels(), rotation = self.rotation,
horizontalalignment='center', family=
'sans-serif', fontsize = self.xaxisfs )

             if buybackDataobj.charttype == 'sells':

                ax2 = twinx()
                #ax2.plot(ind + self.barwidth/2, buybackDataobj.sells,
ls='-', marker ='.', ms=11, c='#FF3300')  //  I wouldnt get the error
message if I do this
plot

                bar(ind + self.barwidth, buybackDataobj.sells,
self.barwidth, color='#FF3300' )  // malformed header from script. Bad
header=    is masked in one or more l: test.cgi
                ax2.set_xticklabels(buybackDataobj.quarters, visible=False )
                ax2.set_ylim(buybackDataobj.sellsMin * 0.75,
buybackDataobj.sellsMax * 1.1)
                ax2.set_ylabel("Insider Selling $" +
buybackDataobj.sellsScale, verticalalignment='center', fontsize =
self.fontsize)

                setp( ax2.get_yticklabels(), rotation = 0,
horizontalalignment='left', family='sans-serif', fontsize=self.fontsize )

.............


On Mon, Apr 6, 2009 at 3:44 PM, Eric Firing <ef...@ha...> wrote:

> P.Romero wrote:
> > Is it possible to create a colorbar with different scales on each side?
> >
> >
> >
> > Example:
> >
> >  a temperature colorbar with celcius values on the left side and
> > farenheit values on the right side.
> >
> >
> >
> > If so, how could this be done?
>
> A colorbar is just an axes object with some customization of the ticks
> and labels, and with a pcolor plot inside.  You could get your second
> scale using a technique similar to the twinx and twiny Axes methods; you
> can then use set_xlim or set_ylim so that the Fahrenheit range on the
> new axes matches the Celcius range on the old one.
>
> To get started, look at the source for the twinx/twiny methods.
>
> Eric
>
> >
> >
> >
> > Please help,
> >
> > Thanks,
> >
> > P.Romero
> >
> >
> > ------------------------------------------------------------------------
> >
> >
> ------------------------------------------------------------------------------
> > This SF.net email is sponsored by:
> > High Quality Requirements in a Collaborative Environment.
> > Download a free trial of Rational Requirements Composer Now!
> > http://p.sf.net/sfu/www-ibm-com
> >
> >
> > ------------------------------------------------------------------------
> >
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> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>
>
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>

In regards to my previous example, the lambda function magic is unnecessary, instead of:

gobject.idle_add(lambda iter=animate(): iter.next())

It is simply adequate to do:

gobject.idle_add(animate().next)

Which is much simpler. My apologies for over coding the solution.

-- Nathaniel

I don't know who I should notify about this, but I've found a fix for simple animation. If one uses the code found here: http://matplotlib.sourceforge.net/examples/animation/simple_anim_gtk.html it works okay, but if you try to move the window it freezes, and you can't use anything on the toolbar. Really annoying, and why not quite a bug, its definitely undesirable behavior. So I've found a very simple fix that leaves the gui reasonably interactive and the window is freely movable. It centers around using a python generator and the yield statement. Calling "yield some_variable" in a function causes execution to stop at that point until the generator's next() method is called, this allows us to "pause" the execution of the animate() function and return control the gui thread. As it currently stands, once animate() is called it executes until completion, never allowing gui events to be handled, hence the freezing. The solution is changing too lines of
 code, note that this is for the GTK example but the same principle should be applicable to the other backends. Note that there are extra explanatory comments that could be removed when posting the actual example.
 
-- Nathaniel

"""
A simple example of an animated plot using a gtk backend
"""
import time
import numpy as np
import matplotlib
matplotlib.use('GTKAgg') # do this before importing pylab

import matplotlib.pyplot as plt

fig = plt.figure()

ax = fig.add_subplot(111)

def animate():
    tstart = time.time()                  # for profiling
    x = np.arange(0, 2*np.pi, 0.01)       # x-array
    line, = ax.plot(x, np.sin(x))

    for i in np.arange(1,200):
        line.set_ydata(np.sin(x+i/10.0))  # update the data
        fig.canvas.draw()                 # redraw the canvas

        # Here is generator magic that stops execution of animate() till the generators next() method is called
        yield True                        # continue animating 
    print 'FPS:' , 200/(time.time()-tstart)
    raise SystemExit

import gobject
print 'adding idle'

# This is some lambda and python magic:
# Python only evaluates defaults for arguments once, 
# so the first call to this lambda function sets iter to the generator made (automagically) from the animate() function.
# Each subsequent call to the lambda function calls iter.next() which restarts(unpauses) execution of the animate() function,
# until it yeilds again, at which point control goes back to the gui
# These calls are done when the gui is idle, hence why we are registering an idle callback,
gobject.idle_add(lambda iter=animate(): iter.next())

print 'showing'
plt.show()

P.Romero wrote:
> Jeff,
> I've attached a test script and my data file.
> Unfortunately, the method that Im using to create the data set isn't very
> portable (the data is being imported from an external program), so sending
> my .npz file is the best I can do.
>
> The gaps are about 5 pixels, and create an offset from where the contours
> end to where the basemap hits the edge of the plot.
>
> Please let me know if there's something in my data set that could be causing
> this, or if its an issue with basemap.
>
> Thanks,
> P.Romero 
>   

Pablo:  The extend of your map projection region is

m.ymin, m.ymax = 0.0 1812318.63167

whereas Y.min(), Y.max() = -28762.6317985 1780259.69866.

The reason you get the gap along the top edge is that the data doesn't 
extend all the way to the northern boundary of the map region.  Just 
shrink your map region a little bit and it will go away.

-Jeff
> -----Original Message-----
> From: Jeff Whitaker [mailto:js...@fa...] 
> Sent: 2009-04-06 6:13 AM
> To: P.Romero
> Cc: mat...@li...
> Subject: Re: [Matplotlib-users] problem with basemap & my data arrays, gap
> around plot edge
>
> P.Romero wrote:
>   
>> Hi,
>>
>> Im having a problem with contourf & basemap;
>>
>> theres a fairly wide gap showing up around the top&left edges of my plot.
>>
>> Im trying to do the following:
>>
>> Import numpy as np
>>
>> Z=my_data( .)
>>
>> m=basemap( . )
>>
>> X,Y=m(*np.meshgrid(Z.lon,Z.lat))
>>
>> Znp=Z.filled
>>
>> cs=m.contourf(X,Y,Znp)
>>
>> using this method, Im experiencing a strange gap around the left&top 
>> edges of the plot.
>>
>> It seems as if the contour data is not aligning correctly with the 
>> basemap, or is somehow 'falling short' of filling in the entire area.
>>
>> Ive used this same method to plot other contour plots and have never 
>> experienced this type of gap (using the same version of 
>> basemap/matplotlib/numpy/etc.).
>>
>> Im not sure if there's something wrong with the way Im creating my 
>> data, or if this is a problem with basemap.
>>
>> In either case, can someone please provide me with some help figuring 
>> out why that gap is appearing?
>>
>> Ive attached an npz file with my 3 arrays: X,Y,Znp.
>>
>> Ive also attached a png image of my output, where the gap is clearly 
>> evident around the left&top edges.
>>
>> Thanks,
>>
>> P.Romero
>>
>>     
>
> Pablo: Please include a working example that creates your example plot.
>
> -Jeff
>   


-- 
Jeffrey S. Whitaker         Phone  : (303)497-6313
Meteorologist               FAX    : (303)497-6449
NOAA/OAR/PSD  R/PSD1        Email  : Jef...@no...
325 Broadway                Office : Skaggs Research Cntr 1D-113
Boulder, CO, USA 80303-3328 Web    : http://tinyurl.com/5telg

P.Romero wrote:
> Is it possible to create a colorbar with different scales on each side?
> 
>  
> 
> Example:
> 
>  a temperature colorbar with celcius values on the left side and 
> farenheit values on the right side.
> 
>  
> 
> If so, how could this be done?

A colorbar is just an axes object with some customization of the ticks 
and labels, and with a pcolor plot inside.  You could get your second 
scale using a technique similar to the twinx and twiny Axes methods; you 
can then use set_xlim or set_ylim so that the Fahrenheit range on the 
new axes matches the Celcius range on the old one.

To get started, look at the source for the twinx/twiny methods.

Eric

> 
>  
> 
> Please help,
> 
> Thanks,
> 
> P.Romero
> 
> 
> ------------------------------------------------------------------------
> 
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Hi,

I am having trouble installing Basemap. I followed the directions in the
README file included in the archive (and posted at
http://matplotlib.sourceforge.net/basemap/doc/html/users/installing.html).
After successfully installing the GEOS library (also included), I cd to the
"top level basemap directory" and run the command "python setup.py install."
The install fails, with multiple compile errors related to src/_proj.c.

However, it appears that 
lib/python2.5/site-packages/numpy/core/include/numpy/__multiarray_a
pi.h also produces errors, so I suspect it may have to do with gcc...

Some relevant information...
Python 2.5.2 (r252:60911, Oct  5 2008, 19:24:49) 
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy; import matplotlib
>>> print numpy.__version__, matplotlib.__version__
1.1.1 0.98.3

...And the last few errors when trying to install...
src/_proj.c:3563: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘__pyx_PyInt_AsUnsignedLongLong’
src/_proj.c:3585: error: expected ‘)’ before ‘*’ token
src/_proj.c:3600: error: expected ‘)’ before ‘*’ token
src/_proj.c:3615: error: expected ‘)’ before ‘*’ token
src/_proj.c:3630: error: expected ‘)’ before ‘*’ token
src/_proj.c:3645: error: expected ‘)’ before ‘*’ token
src/_proj.c:3660: error: expected ‘)’ before ‘*’ token
src/_proj.c:3675: error: expected ‘)’ before ‘*’ token
src/_proj.c:3690: error: expected ‘)’ before ‘*’ token
src/_proj.c:3705: error: expected ‘)’ before ‘*’ token
src/_proj.c:3720: error: expected ‘)’ before ‘*’ token
src/_proj.c:3735: error: expected ‘)’ before ‘*’ token
error: Command "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2
-Wall -Wstrict-prototypes -fPIC -Isrc
-I/home/jtamir/lib/python2.5/site-packages/numpy/core/include
-I/home/jtamir/include/python2.5 -c src/_proj.c -o
build/temp.linux-i686-2.5/src/_proj.o" failed with exit status 1

Any idea how to proceed?

Thanks,
Jon

-- 
View this message in context: http://www.nabble.com/Basemap-Installation-Errors-tp22915617p22915617.html
Sent from the matplotlib - users mailing list archive at Nabble.com.

Is it possible to create a colorbar with different scales on each side?

 

Example:

 a temperature colorbar with celcius values on the left side and farenheit
values on the right side.

 

If so, how could this be done?

 

Please help,

Thanks,

P.Romero

Jeff,
I've attached a test script and my data file.
Unfortunately, the method that Im using to create the data set isn't very
portable (the data is being imported from an external program), so sending
my .npz file is the best I can do.

The gaps are about 5 pixels, and create an offset from where the contours
end to where the basemap hits the edge of the plot.

Please let me know if there's something in my data set that could be causing
this, or if its an issue with basemap.

Thanks,
P.Romero 

-----Original Message-----
From: Jeff Whitaker [mailto:js...@fa...] 
Sent: 2009-04-06 6:13 AM
To: P.Romero
Cc: mat...@li...
Subject: Re: [Matplotlib-users] problem with basemap & my data arrays, gap
around plot edge

P.Romero wrote:
>
> Hi,
>
> Im having a problem with contourf & basemap;
>
> theres a fairly wide gap showing up around the top&left edges of my plot.
>
> Im trying to do the following:
>
> Import numpy as np
>
> Z=my_data( .)
>
> m=basemap( . )
>
> X,Y=m(*np.meshgrid(Z.lon,Z.lat))
>
> Znp=Z.filled
>
> cs=m.contourf(X,Y,Znp)
>
> using this method, Im experiencing a strange gap around the left&top 
> edges of the plot.
>
> It seems as if the contour data is not aligning correctly with the 
> basemap, or is somehow 'falling short' of filling in the entire area.
>
> Ive used this same method to plot other contour plots and have never 
> experienced this type of gap (using the same version of 
> basemap/matplotlib/numpy/etc.).
>
> Im not sure if there's something wrong with the way Im creating my 
> data, or if this is a problem with basemap.
>
> In either case, can someone please provide me with some help figuring 
> out why that gap is appearing?
>
> Ive attached an npz file with my 3 arrays: X,Y,Znp.
>
> Ive also attached a png image of my output, where the gap is clearly 
> evident around the left&top edges.
>
> Thanks,
>
> P.Romero
>

Pablo: Please include a working example that creates your example plot.

-Jeff

On Monday 06 April 2009 20:15:47 Jouni K. Seppänen wrote:
> Chaitanya Krishna <ic...@gm...> writes:
> > That is, when I use pylab.ylabel(r'$V [A^{3}]$') I don't get any space
> > in between V and [.
>
> Like TeX, matplotlib ignores spaces in math mode and uses spacing
> derived from the usual roles of the symbols. You need to use an explicit
> command to add space.
>
> > I also tried using the math mode spacing for Latex, So, if I try to do
> > pylab.ylabel(r'$V\;[A^{3}]$'), I only get V and not even A^3.
>
> On the current trunk, and on the v0_98_5 maintenance branch, that works
> fine. At least the following spacing commands seem to work: r'$a\ b$',
> r'$a\,b$', r'$a\;b$', r'$a\!b$' (negative space) and r'$a\quad b$' work.
> Perhaps you can update to a newer version of matplotlib?

It is also possible to mix math mode and non-math mode. 

ylabel(r'$V$ [\AA$^3$]')

(also note that units by convention are not italic...)

Best regards
Troels Kofoed Jacobsen

Chaitanya Krishna <ic...@gm...> writes:

> That is, when I use pylab.ylabel(r'$V [A^{3}]$') I don't get any space
> in between V and [.

Like TeX, matplotlib ignores spaces in math mode and uses spacing
derived from the usual roles of the symbols. You need to use an explicit
command to add space.

> I also tried using the math mode spacing for Latex, So, if I try to do
> pylab.ylabel(r'$V\;[A^{3}]$'), I only get V and not even A^3.

On the current trunk, and on the v0_98_5 maintenance branch, that works
fine. At least the following spacing commands seem to work: r'$a\ b$',
r'$a\,b$', r'$a\;b$', r'$a\!b$' (negative space) and r'$a\quad b$' work.
Perhaps you can update to a newer version of matplotlib?

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

A B <pyt...@gm...> writes:

> I have the following code and am wondering whether there is a more
> efficient way to plot multiple curves. Maybe somehow accumulating the
> data into a single variable, then calling plot once ... Thanks for any
> ideas.
>
> for ofile in files:
>     d = mlab.csv2rec(ofile, names = ['date','field'])
>     ax.plot(d['date'], d['field'])

You can give multiple x,y pairs to plot, so perhaps something like

data = [mlab.csv2rec(f, names=['date','field']) for f in files]
data = [[x['date'],x['field']] for x in data]
ax.plot(*np.concatenate(data))

would work. But I don't know if it's really any more efficient. For
large plots, you may want to take a look at collections:

http://matplotlib.sourceforge.net/api/collections_api.html#matplotlib.collections.LineCollection

-- 
Jouni K. Seppänen
http://www.iki.fi/jks

Hi,

I found a minor bug, feel free to ignore it :) . If the vertical scale 
of a plot has numbers ~1E-6 the ylabel won't be visible. Example script:

#-------------------------------------------
import matplotlib.pyplot as plt
import numpy as np

x = np.arange(-10.0,10.0,0.1)
plt.plot(x,1E-6*np.sin(x))
plt.ylabel("Y Label")
plt.show()
#-------------------------------------------

The workaround is of course simple, just adjust figure.subplot.left.

Ubuntu 8.10, matplotlib svn (rev. 7032).

JLS

There are a few ways to do that depending on exactly what you want.

>From your script, you may just clip your image.

im = imshow(Z, extent=(-1, 1, -1, 1))
im.set_clip_path(Circle((0,0),1, transform=ax.transData))

(Note the use of extent keyword in imshow)

Or,

You can use polar coordinate with pcolormesh for image display. But
your data need to be defined in the polar coordinate, unlike your
script.

# function defined in polar coordinate
def func5(theta, r):
    y = r*np.sin(theta)
    theta=np.arcsin(y)
    return np.cos(theta)


R=1.
n_theta, n_r = 360, 100

# cooridnates of the mesh
theta = np.linspace(0, 2*np.pi, n_theta+1)
r = np.linspace(0., R, n_r + 1)

dr, dtheta = r[1]-r[0], theta[1]-theta[0]

# cooridnate for the data point
theta_d = np.arange(dtheta/2., 2*np.pi, dtheta)
r_d = np.arange(dr/2., R, dr)


TT, RR = meshgrid(theta_d, r_d)
Z = func5(TT, RR)

ax=subplot(1,1,1, projection="polar", aspect=1.)
ax.pcolormesh(theta, r, Z)

-JJ






On Mon, Apr 6, 2009 at 6:35 AM, Lorenzo Isella <lor...@gm...> wrote:
> Hello,
> So maybe a couple of images can help.
> Using the code
>
>
> #!/usr/bin/env python
> """
> See pcolor_demo2 for a much faster way of generating pcolor plots
> """
> from __future__ import division
> from pylab import *
>
> def func3(x,y):
>   return (1- x/2 + x**5 + y**3)*exp(-x**2-y**2)
>
>
> def func4(x,y):
>   theta=arcsin(y)
>   return cos(theta)
>
>
> # make these smaller to increase the resolution
> dx, dy = 0.05, 0.05
>
> x = arange(-1.0, 1.0, dx)
> y = arange(-1.0, 1.0, dy)
> X,Y = meshgrid(x, y)
>
> Z = func4(X, Y)
>
> print "Z is, ", Z
>
> ax = subplot(111)
> im = imshow(Z, cmap=cm.jet)
> #im.set_interpolation('nearest')
> #im.set_interpolation('bicubic')
> im.set_interpolation('bilinear')
> #ax.set_image_extent(-3, 3, -3, 3)
>
> show()
>
> I can get the attached image.png, but what I am really after is
> image2.png (the same quantity plotted on a circular domain!). How can
> I achieve that (without using scissors on an existing image?).
> This is what I meant from start.
> Cheers
>
> Lorenzo
>
>
>
>
> 2009/4/3 Jae-Joon Lee <lee...@gm...>:
>> I'm afraid that I'm still confused and there seems to be not much
>> thing I can help..
>>
>> You're considering a circle, but you already have your function in a
>> cartesian coordinate. I'm not sure why you can't just plot in a
>> cartesian coordinate? (in other words, what is wrong with your
>> original script?)
>>
>> There is an "set_image_extent" call in your original script (although
>> commented out). Maybe what you're trying to do is simply
>>
>>  im = imshow(Z, cmap=cm.jet, extent=(-3, 3, -3, 3))
>>
>> I'm not sure it would be relevant, but if you have your function or
>> data in  (r, theta) coordinate, one simple way is just to use the
>> polar axes with pcolormesh method.
>>
>>  n_theta, n_r = 100, 50
>>  theta = np.linspace(0, 2*np.pi, n_theta+1)
>>  r = np.linspace(0., 1., n_r + 1)
>>  data = np.arange(0., n_theta*n_r).reshape(n_r, n_theta)
>>  ax=subplot(1,1,1, projection="polar", aspect=1.)
>>  ax.pcolormesh(theta, r, data)
>>
>>
>>
>> -JJ
>>
>
>
>
> --
> Life is what happens to you while you're busy making other plans.
>

The easiest solution would be to use a proxy(?) artist.
For example,


  l1, = plot(x, y, "bo") # original points
  l2, = plot(xnew, ynew, "b-") # interpolated line

  l3, = plot(x, y, "bo-") # just for the legend
  l3.remove() # remove the line from the axes so that it is not drawn.

  legend([ll3], ["bo-"])

IHTH,

-JJ



On Mon, Apr 6, 2009 at 3:01 AM, Sahar <sa...@cm...> wrote:
> I want to plot smooth line between data points (Excel like) and I can do it
> with with 2 lines:
>
> Original data points as circles, for instance: plot(x, y, 'bo')
> Spline of these points as line: plot(xnew, ynew, 'b-')
>
> The only problem with this is the legend - I get either 'o' or '---' but not
> the required 'o-----o'.
>
>
> Thanks for any suggestions,
>
>
>
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>

P.Romero wrote:
>
> Hi,
>
> Im having a problem with contourf & basemap;
>
> theres a fairly wide gap showing up around the top&left edges of my plot.
>
> Im trying to do the following:
>
> Import numpy as np
>
> Z=my_data( …)
>
> m=basemap( … )
>
> X,Y=m(*np.meshgrid(Z.lon,Z.lat))
>
> Znp=Z.filled
>
> cs=m.contourf(X,Y,Znp)
>
> using this method, Im experiencing a strange gap around the left&top 
> edges of the plot.
>
> It seems as if the contour data is not aligning correctly with the 
> basemap, or is somehow ‘falling short’ of filling in the entire area.
>
> Ive used this same method to plot other contour plots and have never 
> experienced this type of gap (using the same version of 
> basemap/matplotlib/numpy/etc.).
>
> Im not sure if there’s something wrong with the way Im creating my 
> data, or if this is a problem with basemap.
>
> In either case, can someone please provide me with some help figuring 
> out why that gap is appearing?
>
> Ive attached an npz file with my 3 arrays: X,Y,Znp.
>
> Ive also attached a png image of my output, where the gap is clearly 
> evident around the left&top edges.
>
> Thanks,
>
> P.Romero
>

Pablo: Please include a working example that creates your example plot.

-Jeff