Re: [Matplotlib-users] two scales in the same plot

[Ondrej Certik]

On Fri, Apr 24, 2009 at 1:10 PM, Sandro Tosi  wrote:
> Hi Ondrej,
> nice to see you here :)

Nice to see you too! :)

>
> On Fri, Apr 24, 2009 at 22:02, Ondrej Certik  wrote:
>> Hi,
>>
>> is there a way to have one plot with two functions, one using some
>> scale, the other one a different scale and show for example one scale
>> on the left, the other scale on the right?
>
> sure, twinx() is what you're looking for; here is a simple example:
>
> import matplotlib.pyplot as plt
> import numpy as np
> x = np.arange(0., np.e, 0.01)
> y1 = np.exp(-x)
> y2 = np.log(x)
> fig = plt.figure()
> ax1 = fig.add_subplot(111)
> ax1.plot(x, y1)
> ax1.set_ylabel('Y values for exp(-x)')
> ax2 = ax1.twinx()
> ax2.plot(x, y2, 'r')
> ax2.set_xlim([0,np.e])
> ax2.set_ylabel('Y values for ln(x)')
> ax2.set_xlabel('Same X for both exp(-x) and ln(x)')
>
> The values on X has to be of the same scale, tough, else the graph
> would look really weird.

Thanks a lot for the code. That worked. I was meeting some deadline,
so I forgot to reply that it worked.

Thanks Ryan and Jouni as well!

Ondrej

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Re: [Matplotlib-users] Font size and savefig

[Thomas Robitaille]

Hi Jae-Jong and John,

Thanks for your replies! While experimenting with this to send  
screenshots, I realized that my default backend was set to MacOSX, not  
WXAgg. The WXAgg output to the screen actually agrees with the PNG  
output in terms of font sizes. But the font sizes differ between the  
MacOSX and WXAgg backends. Attached are screenshots using the MacOSX  
and WXAgg backends. You can see the font size is different. Is this a  
bug?


Thanks,

Thomas


<><>

On 29 Apr 2009, at 00:24, Jae-Joon Lee wrote:

On Tue, Apr 28, 2009 at 11:09 PM, John Hunter   
wrote:
If you want the relative fontsizes in the figure window and saved  
figure to

agree, pass the same "dpi" to the figure command and savefig command.


John,
I thought the font size (which is specified in points) is independent
of dpi, i.e., font size in "pixel" actually scales with the dpi. I
think it should be filed as a bug if the relative font size depends on
the dpi.

Anyhow, I just did a quick test and the (relative) font size does not
seem to vary with dpi.

Thomas,
What version of mpl are you using?
With the mpl from the svn trunk, I don't see any significant change as
you described.
The WxAgg figure and the png output are actually drawn by an identical
backend, so there should be no significant difference. There can be
some subtle difference due to different dpi, but I don't see a
difference as large as 30%. Can you post a some sample images? i.e., a
screenshot of WxAgg figure and the png output.

I can see that the text in pdf output occupies a bit larger area than
png (when usetex=False), but, to me, this seems to be due to different
amount of kernings (it seems that no kerning is applied for pdf text)
instead of different font size.

So, can you first check if the difference goes away when you use same
dpi as John suggested? And if that is the case, can you try the latest
svn and check if the relative font size still depends on the dpi?

Regards,

-JJ


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Re: [Matplotlib-users] Pixel Position of X/Y Axis

[Jae-Joon Lee]

You may use the bbox attribute of the axes.
For example,  ax.bbox.extents gives you the x,y coordinates of the
lowerleft and topright corners.

-JJ

On Wed, Apr 29, 2009 at 4:06 PM, Mark Larsen  wrote:
> It's been a while, please allow me to bump this...
>
>> Sorry.  I use matplotlib to create PNGs graphics for display on a
>> web-page.  I want to make the plots zoom-able.  I'll use javascript to
>> capture the pixel positions of the user's selected zoom region on the
>> PNG plot.  I'll then translate this into the coordinate system on the
>> plot and redraw it with a new x, y range.  I'm having trouble
>> translating the initial axises into the pixel positions (essentially
>> where they are on the PNG image).
>>
>> For example, I use the following code to map point positions from the
>> coordinate system to pixel positions.  I use an img map  to
>> provide interaction with the actual lines.
>>
>> [CODE]
>>
>> lineObj = plt.plot(Xs,Ys,marker='o')[0]
>> path, affine = lineObj._transformed_path.get_transformed_points_and_affine()
>> path = affine.transform_path(path)
>> for real,pixel in zip(lineObj.get_xydata(),path.vertices):
>>  ## write  tag  for each point
>>
>> [/CODE]
>>
>> I'd like to get information similar to this for the axis of the plot.
>>
>> Thanks.
>>
>
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Re: [Matplotlib-users] Fixed patch relative to axes

[Eric Firing]

Thomas Robitaille wrote:
> Thanks!
> 
> Is there an easy way to keep a reference to patches? I notice that for 
> example
> 
> p = ax.add_patch(Circle((0.5,0.5),radius=0.5))
> 
> does not work (p is not a reference to the patch). Is there a way to 
> keep a reference so I can update the properties of the patch at a later 
> time?

Split the command up:
p = Circle(...)
ax.add_patch(p, ...)

(add_* could be modified to return the reference; maybe this would be 
worthwhile.)


Eric

> 
> Cheers,
> 
> Thomas
> 
> On 29 Apr 2009, at 21:13, Eric Firing wrote:
> 
>> Thomas Robitaille wrote:
>>> Hi,
>>> Is there an easy way to draw a patch or a patchcollection such that 
>>> it  always stays at the same relative position in a set of axes, 
>>> rather  than at the same pixel position? So for example, I would want 
>>> to plot  it at (0.1,0.1) relative to the axes, and if I zoom in I 
>>> would still  want it to stay at (0.1,0.1)
>>
>> With ipython -pylab:
>>
>> ax = gca()
>> ax.fill([0.1, 0.2, 0.15], [0.1, 0.1, 0.15], transform=ax.transAxes)
>> draw()
>>
>> then pan, zoom at will.
>>
>> Eric
>>
> 


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Re: [Matplotlib-users] Fixed patch relative to axes

[Thomas Robitaille]

Thanks!

Is there an easy way to keep a reference to patches? I notice that for  
example

p = ax.add_patch(Circle((0.5,0.5),radius=0.5))

does not work (p is not a reference to the patch). Is there a way to  
keep a reference so I can update the properties of the patch at a  
later time?

Cheers,

Thomas

On 29 Apr 2009, at 21:13, Eric Firing wrote:

> Thomas Robitaille wrote:
>> Hi,
>> Is there an easy way to draw a patch or a patchcollection such that  
>> it  always stays at the same relative position in a set of axes,  
>> rather  than at the same pixel position? So for example, I would  
>> want to plot  it at (0.1,0.1) relative to the axes, and if I zoom  
>> in I would still  want it to stay at (0.1,0.1)
>
> With ipython -pylab:
>
> ax = gca()
> ax.fill([0.1, 0.2, 0.15], [0.1, 0.1, 0.15], transform=ax.transAxes)
> draw()
>
> then pan, zoom at will.
>
> Eric
>


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Re: [Matplotlib-users] Fixed patch relative to axes

[Eric Firing]

Thomas Robitaille wrote:
> Hi,
> 
> Is there an easy way to draw a patch or a patchcollection such that it  
> always stays at the same relative position in a set of axes, rather  
> than at the same pixel position? So for example, I would want to plot  
> it at (0.1,0.1) relative to the axes, and if I zoom in I would still  
> want it to stay at (0.1,0.1)

With ipython -pylab:

ax = gca()
ax.fill([0.1, 0.2, 0.15], [0.1, 0.1, 0.15], transform=ax.transAxes)
draw()

then pan, zoom at will.

Eric


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[Matplotlib-users] Fixed patch relative to axes

[Thomas Robitaille]

Hi,

Is there an easy way to draw a patch or a patchcollection such that it  
always stays at the same relative position in a set of axes, rather  
than at the same pixel position? So for example, I would want to plot  
it at (0.1,0.1) relative to the axes, and if I zoom in I would still  
want it to stay at (0.1,0.1)

Thanks for any advice,

Thomas

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Re: [Matplotlib-users] Integrating matplotlib into a GUI

[Gökhan SEVER]

Hi Gary,

Could you please give some information on how Traits compare to Wx or
Qt? What are Traits' limits? I haven't started writing anything on GUI
level yet, but spending time to understand the Traits way.

Thank you.

Gökhan



On Wed, Apr 29, 2009 at 11:10 AM, Gary Pajer  wrote:
> On Sun, Apr 26, 2009 at 6:41 PM, Gökhan SEVER  wrote:
>> Hello,
>>
>> Thanks for the pointer Bryan. I also seen Gael's tutorial
>> (http://gael-varoquaux.info/computers/traits_tutorial/index.html)
>>
>> To me, it seems much easier to use Traits, instead of learning WX or QT.
>
> It is.  I had spent hours learning Tk, Wx, and Qt looking for a
> "practical" gui solution ... but then I found Traits and I haven't
> looked back.
>
>> They are still confusing to me, and seemingly Traits is there to help me
>> implement what I have had in my mind for a while.
>>
>> Gökhan
>>
>>
>> On Sun, Apr 26, 2009 at 2:52 AM, Bryan Cole  wrote:
>>>
>>> > I know wxPython or PyQt seems way to go on this issue. But (there is
>>> > always this but :) there is Chaco on the Enthought side and with
>>> > nicely and simply integration with Traits and Traits UI.
>>> >
>>> > Are there anybody in the group that design a similar tool for their
>>> > scientific data analysis needs? Could I get some insight into this?
>>> > Any recommendations or pointers? Why's and why not's?
>>>
>>> You can integrate matplotlib plots into a Traits app. I wrote this
>>> recipe:
>>>
>>> http://www.scipy.org/Cookbook/EmbeddingInTraitsGUI
>>>
>>> Both Chaco and Matplotlib are excellent. If you want multiple
>>> interactive elements in your plot (drag-able labels, cursors etc.),
>>> Chaco is probably the best bet. However, for quick data-exploration
>>> apps, I find matplotlib quicker to set up (it's defaults "just work",
>>> whereas Chaco takes a bit more preparation).
>>>
>>> Either way, Traits is indispensable.
>>>
>>> BC
>>>
>>> >
>>> > Thank you
>>> >
>>> > Gökhan
>>> >
>>> > --
>>> > Crystal Reports - New Free Runtime and 30 Day Trial
>>> > Check out the new simplified licensign option that enables unlimited
>>> > royalty-free distribution of the report engine for externally facing
>>> > server and web deployment.
>>> > http://p.sf.net/sfu/businessobjects
>>> > ___ Matplotlib-users mailing
>>> > list Matplotlib-users@lists.sourceforge.net
>>> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>>
>>>
>>>
>>>
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>>
>>
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>>
>>
>

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[Matplotlib-users] matplotlib for Python 2.6

[R. Padraic Springuel]

Is there a Windows installer file for matplotlib for Python 2.6?  I 
couldn't find one on the download page, but have to admit to being in 
something of a hurry and so didn't look too hard.

--

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Research Assistant
Department of Physics and Astronomy
University of Maine
Bennett 309
Office Hours: By appointment only


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Re: [Matplotlib-users] Pixel Position of X/Y Axis

[Mark Larsen]

It's been a while, please allow me to bump this...

> Sorry.  I use matplotlib to create PNGs graphics for display on a
> web-page.  I want to make the plots zoom-able.  I'll use javascript to
> capture the pixel positions of the user's selected zoom region on the
> PNG plot.  I'll then translate this into the coordinate system on the
> plot and redraw it with a new x, y range.  I'm having trouble
> translating the initial axises into the pixel positions (essentially
> where they are on the PNG image).
>
> For example, I use the following code to map point positions from the
> coordinate system to pixel positions.  I use an img map  to
> provide interaction with the actual lines.
>
> [CODE]
>
> lineObj = plt.plot(Xs,Ys,marker='o')[0]
> path, affine = lineObj._transformed_path.get_transformed_points_and_affine()
> path = affine.transform_path(path)
> for real,pixel in zip(lineObj.get_xydata(),path.vertices):
>  ## write  tag  for each point
>
> [/CODE]
>
> I'd like to get information similar to this for the axis of the plot.
>
> Thanks.
>

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Re: [Matplotlib-users] fill_between and masked array

[Eric Firing]

John Hunter wrote:
> 
> 
> On Wed, Apr 29, 2009 at 11:03 AM, John Hunter  > wrote:
> 
> 
> ...but I'd like more feedback from the author or users of
> fill_between
> before committing that change.  (That, and Eric Firing can
> probably find
> a much more efficient way to do the masked array manipulation... ;)
> 
> 
> I'm working on a patch for this nowbut I would also like Eric to
> take a look when I am done since I am a masked array dummy
> 

John,

The way you did it looked OK; but since I was looking at it, I went 
ahead and did some rearranging and condensation to try to make the whole 
thing (not just the mask handling) read better. I doubt there are any 
significant performance differences, but I did not test that. I also 
added a subplot to the fill_between.py demo to illustrate the mask 
handling.  Then I noticed a flaw in the demo plots, and added a note 
about it.  See revision 7071.

Eric

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Re: [Matplotlib-users] last tick label not showing up

[Erik Thompson]

Matthias,

Thanks for your help.  When I did ax.set_xlim((0.0, 120.0)) the 180 tick
showed up although ugly on some plots because there was missing data at the
180 degrees mark.

I then copied all the datapoints from the -180 degrees into new 180 degree
data points (they are the supposed to be the same) and everything works well
now.

Erik Thompson
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Re: [Matplotlib-users] last tick label not showing up

[Jae-Joon Lee]

On Wed, Apr 29, 2009 at 12:21 PM, Matthias Michler
 wrote:
> where the last tick is out of the xlimits. Could this be the case for your
> example, too?
> Nevertheless the question still would be: Is this a bug in the handling of
> xticks and their corresponding labels?


get_majorticklocs (and similar methods) does not return the locations
of the ticks that will be plotted. It simply returns the tick values
generated by the locator instance. And among them, only those within
the axis limits will be drawn. My guess is that this was a design
decision, not a bug.

The following is a related post which includes some code snippets that
can be used to retrieve tick locations inside the axis limits.

http://www.nabble.com/eliminating-the-top-tick-on-an-axis-to19446256.html#a19446256

Regards,

-JJ

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Re: [Matplotlib-users] last tick label not showing up

[Matthias Michler]

Hello Erik,

I can reproduce your problem (mpl 0.98.6svn) with the following little 
example:

import matplotlib.pyplot as plt
ax = plt.axes()
ax.set_xlim((0.0, .))
print ax.xaxis.get_majorticklocs()
plt.show()

where the last tick is out of the xlimits. Could this be the case for your 
example, too?
Nevertheless the question still would be: Is this a bug in the handling of 
xticks and their corresponding labels?

best regards Matthias

On Wednesday 29 April 2009 18:07:17 Erik Thompson wrote:
> How do I get the final "180" tick label to show up on my plots on the far
> right of my x axis (or top of the y axis).
>
> When I do: print ax.xaxis.get_majorticklocs() it returns:
> [   0.   20.   40.   60.   80.  100.  120.]
>
> and I have a label for each of those locations:
> ax.xaxis.set_ticklabels(["-180", "-120", "-60", "0", "60", "120", "180"])
>
> For some reason the final "180" tick label doesn't display.
>
> Thanks,
> Erik Thompson



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Re: [Matplotlib-users] Integrating matplotlib into a GUI

[Gary Pajer]

On Sun, Apr 26, 2009 at 6:41 PM, Gökhan SEVER  wrote:
> Hello,
>
> Thanks for the pointer Bryan. I also seen Gael's tutorial
> (http://gael-varoquaux.info/computers/traits_tutorial/index.html)
>
> To me, it seems much easier to use Traits, instead of learning WX or QT.

It is.  I had spent hours learning Tk, Wx, and Qt looking for a
"practical" gui solution ... but then I found Traits and I haven't
looked back.

> They are still confusing to me, and seemingly Traits is there to help me
> implement what I have had in my mind for a while.
>
> Gökhan
>
>
> On Sun, Apr 26, 2009 at 2:52 AM, Bryan Cole  wrote:
>>
>> > I know wxPython or PyQt seems way to go on this issue. But (there is
>> > always this but :) there is Chaco on the Enthought side and with
>> > nicely and simply integration with Traits and Traits UI.
>> >
>> > Are there anybody in the group that design a similar tool for their
>> > scientific data analysis needs? Could I get some insight into this?
>> > Any recommendations or pointers? Why's and why not's?
>>
>> You can integrate matplotlib plots into a Traits app. I wrote this
>> recipe:
>>
>> http://www.scipy.org/Cookbook/EmbeddingInTraitsGUI
>>
>> Both Chaco and Matplotlib are excellent. If you want multiple
>> interactive elements in your plot (drag-able labels, cursors etc.),
>> Chaco is probably the best bet. However, for quick data-exploration
>> apps, I find matplotlib quicker to set up (it's defaults "just work",
>> whereas Chaco takes a bit more preparation).
>>
>> Either way, Traits is indispensable.
>>
>> BC
>>
>> >
>> > Thank you
>> >
>> > Gökhan
>> >
>> > --
>> > Crystal Reports - New Free Runtime and 30 Day Trial
>> > Check out the new simplified licensign option that enables unlimited
>> > royalty-free distribution of the report engine for externally facing
>> > server and web deployment.
>> > http://p.sf.net/sfu/businessobjects
>> > ___ Matplotlib-users mailing
>> > list Matplotlib-users@lists.sourceforge.net
>> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>>
>>
>>
>>
>> --
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Re: [Matplotlib-users] fill_between and masked array

[John Hunter]

On Wed, Apr 29, 2009 at 11:03 AM, John Hunter  wrote:

>
>> ...but I'd like more feedback from the author or users of fill_between
>> before committing that change.  (That, and Eric Firing can probably find
>> a much more efficient way to do the masked array manipulation... ;)
>
>
> I'm working on a patch for this nowbut I would also like Eric to take a
> look when I am done since I am a masked array dummy



Here's the diff I just committed::
Index: lib/matplotlib/axes.py
===
--- lib/matplotlib/axes.py  (revision 7069)
+++ lib/matplotlib/axes.py  (working copy)
@@ -5832,6 +5832,26 @@
 self._process_unit_info(xdata=x, ydata=y1, kwargs=kwargs)
 self._process_unit_info(ydata=y2)

+if where is None:
+where = np.ones(len(x), np.bool)
+else:
+where = np.asarray(where)
+
+maskedx = isinstance(x, np.ma.MaskedArray)
+maskedy1 = isinstance(y1, np.ma.MaskedArray)
+maskedy2 = isinstance(y2, np.ma.MaskedArray)
+
+if (maskedx or maskedy1 or maskedy2):
+if maskedx:
+where = where & (~x.mask)
+
+if maskedy1:
+where = where & (~y1.mask)
+
+if maskedy2:
+where = where & (~y2.mask)
+
+
 # Convert the arrays so we can work with them
 x = np.asarray(self.convert_xunits(x))
 y1 = np.asarray(self.convert_yunits(y1))
@@ -5843,10 +5863,7 @@
 if not cbook.iterable(y2):
 y2 = np.ones_like(x)*y2

-if where is None:
-where = np.ones(len(x), np.bool)

-where = np.asarray(where)
 assert( (len(x)==len(y1)) and (len(x)==len(y2)) and
len(x)==len(where))

 polys = []
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Re: [Matplotlib-users] fill_between and masked array

[John Hunter]

On Wed, Apr 29, 2009 at 10:56 AM, Michael Droettboom wrote:

> I don't believe fill_between directly supports missing values -- but it
> does have the where parameter for this purpose.
>
> We could also be smarter about how "where" is generated when none is
> provided:
>
>if where is None:
>where = (~np.ma.getmaskarray(x) & ~np.ma.getmaskarray(y1) &
> ~np.ma.getmaskarray(y2))
>
> ...but I'd like more feedback from the author or users of fill_between
> before committing that change.  (That, and Eric Firing can probably find
> a much more efficient way to do the masked array manipulation... ;)


I'm working on a patch for this nowbut I would also like Eric to take a
look when I am done since I am a masked array dummy

JDH
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Re: [Matplotlib-users] fill_between and masked array

[Michael Droettboom]

I don't believe fill_between directly supports missing values -- but it 
does have the where parameter for this purpose.

We could also be smarter about how "where" is generated when none is 
provided:

if where is None:
where = (~np.ma.getmaskarray(x) & ~np.ma.getmaskarray(y1) &
 ~np.ma.getmaskarray(y2))

...but I'd like more feedback from the author or users of fill_between 
before committing that change.  (That, and Eric Firing can probably find 
a much more efficient way to do the masked array manipulation... ;)

Mike

Andres Luhamaa wrote:
> Hello,
> I try to do fill_between two arrays, that have missing value (masked 
> arrays). Following code shows behaviour that seems not correct. Images 
> what I expect the result to be (by omitting the missing value) and 
> what I get by plotting the whole arrays.
>
> import pylab
> import numpy as np
> edatmax=np.array([10,4,6,9,np.nan,9,10])
> edatmax=np.ma.masked_array(edatmax,np.isnan(edatmax))
> edatmin=np.array([8,4,5,1,np.nan,8,5])
> edatmin=np.ma.masked_array(edatmin,np.isnan(edatmin))
> xtelg=np.arange(edatmax.size)
> xtelg=np.ma.masked_array(xtelg,np.isnan(edatmin))
> pylab.plot(edatmax,"gx")
> pylab.plot(edatmin,"r+")
> # comment out to see better
> pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3')
> # comment in to see better
> #pylab.fill_between(xtelg[:4],edatmax[:4],edatmin[:4],facecolor='green',alpha='0.3')
>  
>
> #pylab.fill_between(xtelg[5:],edatmax[5:],edatmin[5:],facecolor='green',alpha='0.3')
>  
>
> pylab.show()
>
> Version of matplotlib is current cvs.
>
> Best regards,
> Andres
>
> 
>
>
> 
>
> 
>
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Operations and Engineering Division
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Operated by AURA for NASA


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Re: [Matplotlib-users] fill_between and masked array

[John Hunter]

On Wed, Apr 29, 2009 at 6:40 AM, Andres Luhamaa wrote:

> Hello,
> I try to do fill_between two arrays, that have missing value (masked
> arrays). Following code shows behaviour that seems not correct. Images what
> I expect the result to be (by omitting the missing value) and what I get by
> plotting the whole arrays.
>
> import pylab
> import numpy as np
> edatmax=np.array([10,4,6,9,np.nan,9,10])
> edatmax=np.ma.masked_array(edatmax,np.isnan(edatmax))
> edatmin=np.array([8,4,5,1,np.nan,8,5])
> edatmin=np.ma.masked_array(edatmin,np.isnan(edatmin))
> xtelg=np.arange(edatmax.size)
> xtelg=np.ma.masked_array(xtelg,np.isnan(edatmin))
> pylab.plot(edatmax,"gx")
> pylab.plot(edatmin,"r+")
> # comment out to see better
> pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3')
> # comment in to see better
>
> #pylab.fill_between(xtelg[:4],edatmax[:4],edatmin[:4],facecolor='green',alpha='0.3')
>
> #pylab.fill_between(xtelg[5:],edatmax[5:],edatmin[5:],facecolor='green',alpha='0.3')
> pylab.show()
>
> Version of matplotlib is current cvs.
>


fill_between does not currently support masked arrays, but I think we could
easily extend it to support the mask using the existing support for the
"where" kwarg.  For now, does this behave like you expect?

  valid = ~(edatmax.mask & edatmax.mask )
  pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3',
where=valid)

JDH
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Re: [Matplotlib-users] fill_between and masked array

[John Hunter]

On Wed, Apr 29, 2009 at 10:54 AM, John Hunter  wrote:

>
>
> fill_between does not currently support masked arrays, but I think we could
> easily extend it to support the mask using the existing support for the
> "where" kwarg.  For now, does this behave like you expect?
>
>   valid = ~(edatmax.mask & edatmax.mask )
>   pylab.fill_between(xtelg,edatmax,edatmin,facecolor='green',alpha='0.3',
> where=valid)
>
>

Oops -- meant

 valid = ~(edatmin.mask & edatmax.mask )

JDH
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Re: [Matplotlib-users] Interactive backends very (suprisingly?) slow for multiple subplots

[Adam]

On Wed, Apr 29, 2009 at 9:22 AM, John Hunter  wrote:
>
>
> On Wed, Apr 29, 2009 at 9:50 AM, Adam  wrote:
>>
>> I would like to have access to the command line while simultaneously
>> being able to interact with and/or display plots.  I think this is
>> what ipython does by default when you pass it a thread keyword
>> (-pylab, -qt4thread, etc.).  I had some trouble getting ipython to
>> work correctly, but I think that had to do with passing the thread
>> keyword before/after some other keywords.
>
> From your previous posts, I think you may have been be using ipython
> incorrectly, ie mixing ipython -pylab with the matplotlib use directive.
> Start with a canconical simple script, eg::
>
>     import matplotlib.pyplot as plt
>
>     plt.figure(1)
>     plt.plot([1,2,3])
>
>     plt.figure(2)
>     plt.plot([4,5,6])
>
>     plt.show()
>
> and set your matplotlibrc to backend to TkAgg.  Start ipython with::
>
>   > ipython -pylab
>
> and run your test script with::
>
>   In [61]: run test.py
>
> If that works, close everything down and set your backend to QtAgg and try
> running it again in the same way and let us know what happens.  It should
> just work.  I'm suspecting in that as you were testing and trying a lot of
> things, you got yourself into a situation where multiple GUIs were competing
> for attention.
>
>> Part of my question that I hope makes sense: Is there a way to unblock
>> the command line without closing the plot window when using an
>> interactive backend?
>
> Yes, that makes sense, and basically you need to either use TkAgg from a
> regular python shell, use ipython in pylab mode with any supported backend,
> or use a GUI shell.  ipython also has support for embedding in GUI shells.
> See also
>
>   http://matplotlib.sourceforge.net/users/shell.html
>
> JDH
>
Thanks John.  I think you answered my questions completely now.

FWIW, I was not using matplotlib.use() with ipython, I was using it
when calling 'python test.py' on the command line.  My mistake with
ipython was using an import command before -pylab, i.e.:
ipython -i -c "import pyfits,matplotlib" -pylab

which does not work, whereas
ipython -pylab -i -c "import pyfits,matplotlib"

does.


Thanks for the help!

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Re: [Matplotlib-users] Histogram of 2D Data

[John Hunter]

On Wed, Apr 29, 2009 at 9:59 AM, marcog  wrote:

>
> Hi
>
> I have a set of 2 dimensional data that I would like to form a histogram
> of.
> Each data point is defined by an x and y variable. So essentially what I
> would like to obtain is a "row" of histograms as produced by the plot.hist
> function, stacking them next to one another in a single 3D plot. For
> example, something like [1], but I don't need it to be interpolated.
>
> [1] http://www.mathworks.com/matlabcentral/fx_files/14205/1/hist.jpg




hexbin may be what you are looking for, which does a 2D colormapped
histogram, with an optional reduce function so you can specify the intensity
function over the bins


http://matplotlib.sourceforge.net/api/axes_api.html#matplotlib.axes.Axes.hexbin
  http://matplotlib.sourceforge.net/examples/pylab_examples/hexbin_demo.html

http://matplotlib.sourceforge.net/examples/pylab_examples/hexbin_demo2.html

JDH
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Re: [Matplotlib-users] Font size and savefig

[John Hunter]

On Tue, Apr 28, 2009 at 11:24 PM, Jae-Joon Lee  wrote:

> On Tue, Apr 28, 2009 at 11:09 PM, John Hunter  wrote:
> > If you want the relative fontsizes in the figure window and saved figure
> to
> > agree, pass the same "dpi" to the figure command and savefig command.
>
> John,
> I thought the font size (which is specified in points) is independent
> of dpi, i.e., font size in "pixel" actually scales with the dpi. I
> think it should be filed as a bug if the relative font size depends on
> the dpi.
>
> Anyhow, I just did a quick test and the (relative) font size does not
> seem to vary with dpi.


Hmm, I must have been confused.  In older versions of mpl, as you increased
the dpi the fonts looked larger in relation to the rest of the figure, and
that is what I was remembering.  I just ran a few tests and they do scale as
expected, so sorry for the noise
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[Matplotlib-users] Histogram of 2D Data

[marcog]

Hi

I have a set of 2 dimensional data that I would like to form a histogram of.
Each data point is defined by an x and y variable. So essentially what I
would like to obtain is a "row" of histograms as produced by the plot.hist
function, stacking them next to one another in a single 3D plot. For
example, something like [1], but I don't need it to be interpolated.

[1] http://www.mathworks.com/matlabcentral/fx_files/14205/1/hist.jpg

Thanks!
Marco
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Re: [Matplotlib-users] Interactive backends very (suprisingly?) slow for multiple subplots

[Adam]

On Wed, Apr 29, 2009 at 8:29 AM, John Hunter  wrote:
>
>
> On Wed, Apr 29, 2009 at 9:07 AM, keflavich  wrote:
>>
>> Since there don't seem to be any forthcoming answers, I have a somewhat
>> different question.  In the matplotlib FAQ, it states that using 'show()'
>> puts you in the GUI mainloop
>> (http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show).  However,
>> using plot commands on the ipython command line does not shut down the
>> command line generally.  I gathered from some googling that this is
>> because
>> ipython starts up the matplotlib graphics in a different 'thread', but I
>> don't understand how this is done and most of what I've seen says it is
>> bad.
>
> most GUI mainloops are blocking, so after you start them you cannot issue
> more commands from an interactive shell.  Either you need to run a GUI
> shell, or in the case of ipython run the GUI in a separate thread.  One
> exception to this is tkinter (tkagg), which plays nicely with a standard
> python shell.  I understand that recent versions of pygtk work also w/o
> running the mainloop in a separate thread, but I haven't dug into the
> details.

OK, that's very helpful.

>> So, my question now: How can I exit the GUI mainloop without closing the
>> graphics windows?
>
> This question doesn't really make sense to me.  Perhaps you can clearly
> describe your use case (what you need to do) rather than the proposed
> solutions.

I would like to have access to the command line while simultaneously
being able to interact with and/or display plots.  I think this is
what ipython does by default when you pass it a thread keyword
(-pylab, -qt4thread, etc.).  I had some trouble getting ipython to
work correctly, but I think that had to do with passing the thread
keyword before/after some other keywords.

Part of my question that I hope makes sense: Is there a way to unblock
the command line without closing the plot window when using an
interactive backend?

Thanks, and sorry about the misunderstandings / lack of clarity,
Adam

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Re: [Matplotlib-users] Interactive backends very (suprisingly?) slow for multiple subplots

[John Hunter]

On Wed, Apr 29, 2009 at 9:07 AM, keflavich  wrote:

>
> Since there don't seem to be any forthcoming answers, I have a somewhat
> different question.  In the matplotlib FAQ, it states that using 'show()'
> puts you in the GUI mainloop
> (http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show).  However,
> using plot commands on the ipython command line does not shut down the
> command line generally.  I gathered from some googling that this is because
> ipython starts up the matplotlib graphics in a different 'thread', but I
> don't understand how this is done and most of what I've seen says it is
> bad.
>

most GUI mainloops are blocking, so after you start them you cannot issue
more commands from an interactive shell.  Either you need to run a GUI
shell, or in the case of ipython run the GUI in a separate thread.  One
exception to this is tkinter (tkagg), which plays nicely with a standard
python shell.  I understand that recent versions of pygtk work also w/o
running the mainloop in a separate thread, but I haven't dug into the
details.


>
> So, my question now: How can I exit the GUI mainloop without closing the
> graphics windows?
>

This question doesn't really make sense to me.  Perhaps you can clearly
describe your use case (what you need to do) rather than the proposed
solutions.

JDH
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Re: [Matplotlib-users] Interactive backends very (suprisingly?) slow for multiple subplots

[keflavich]

Since there don't seem to be any forthcoming answers, I have a somewhat
different question.  In the matplotlib FAQ, it states that using 'show()'
puts you in the GUI mainloop
(http://matplotlib.sourceforge.net/faq/howto_faq.html#use-show).  However,
using plot commands on the ipython command line does not shut down the
command line generally.  I gathered from some googling that this is because
ipython starts up the matplotlib graphics in a different 'thread', but I
don't understand how this is done and most of what I've seen says it is bad.

So, my question now: How can I exit the GUI mainloop without closing the
graphics windows?

Thanks,
Adam
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Re: [Matplotlib-users] Matplotlib documentation

[John Hunter]

On Wed, Apr 29, 2009 at 2:55 AM, Gökhan SEVER  wrote:

>
> I would like discuss these point before start working on other api
> functions and classes. Also need some explanation about them, since
> pyplot is composed of functions but some other api's are mixed with
> classes and functions.
>
> Please, contact me of the list so I can send the modified pyploy_rst.api.


Hey Gökhan -- thanks for working on this.  We are very happy to have
documentation contributions.  I don't feel strongly about how the pyplot rst
file is generated, whether by extending Sphinx, using a script, or simply
hand editing it.  I'm actually incline toward the latter, because it would
probably be nice to have some simple description in the section header, eg::

  acorr - autocorrelation plots
  =

as we do on the main page.  Part of the sphinx philosophy is that "hand
edited" documentation cannot be fully replaced by autogenerated
documentaiton, and this may be a reasonable place to do some hand editing.

If you go this route, update the pyplot module, the developer's guide and
the boilerplate.py script (it lives besides setup.py and is a script to
generate part of pyplot) so that when developers add a new function to
pyplot they know to update the api docs as well.

You may want to move further discussion over to the developers list.  Any
changes you want to make should be posted as an svn diff to the developers
list.  If you don't get immediate attention, also post it as a patch to the
sourceforge site, and reply to the developers list with a link to the patch
-- see

  http://matplotlib.sourceforge.net/faq/howto_faq.html#contributing-howto

Thanks!
JDH
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Re: [Matplotlib-users] Another Gnuplot style question

[Matthias Michler]

Hello Eric, Hello list,

a year ago I also encountered the problem of "one file - one figure" of the 
plotfile function. I would like to propose an addional functionality of using 
one figure and several files in plotfile, because sometimes I don't want to 
read data myself. I added a patch including the following changes:
- added a new keywordargument to plotfile 'use_cf': If use_cf isTrue plotfile 
uses fig = gcf() instead of fig = figure() to suppress opening of a new 
figure and therewith allowing to use the user preferred figure
- added a further new keyword argument 'names' to set x/ylabels in the case 
there are no names in the csv-file

Furthermore I attached the modified plotfile_demo.py 
(examples/pylab_examples/plotfile_demo.py) and some new data 
(examples/data/data_x_x2_x3.csv).

Could this be useful?

Thanks in advance for any comments.

best regards
Matthias

On Wednesday 29 April 2009 09:20:17 Eric Firing wrote:
> Joseph Smidt wrote:
> > Okay, I am another gnuplot user trying to migrate over to matplotlib.
> > I like what I see, but there are a couple things that are very easy to
> > do in Gnuplot that I can't figure out how to do with matplotlib.
> >
> > I have a file with 3 columns of data called data.txt that looks like:
> >
> > 0.  1. 1.0
> > 0.0634  1.0655  1.1353
> > 0.1269  1.1353  1.28899916094
> > 0.1903  1.2097  1.46345358199
> > 0.2538  1.2889 1.6615188369
> > 0.3173  1.3734 1.88639043926
> > ...
> >
> > I can plot this data, 2 versus 1 and 3 versus 1, very easily on the
> > same plot, with a legend, with log y values, and only for the xrange
> > between 2 and 3 with gnuplot:
> >
> > set log y
> > set xrange[2:3]
> > plot 'data.txt' u 1:2 w l t 'apples', 'data.txt' u 1:3 w l t 'oranges'
> >
> > Now, how do I do that same thing with matplotlob?  Ie:
> >
> > 1. Both graphs overlayed on the same plot.
> > 2. Semilogy. (log y values),
> > 3. Only ploy for x in the range 2-3.
> > 4. Legend for the two graphs on same plot.
>
> Something like this:
>
> import numpy as np
> import matplotlib.pyplot as plt
>
> x, apples, oranges = np.loadtxt('data.txt', unpack=True)
> plt.semilogy(x, apples, label='apples')
> plt.semilogy(x, oranges, label='oranges')
> plt.legend()
> plt.gca().set_xlim(2, 3)
> plt.show()
>
> There are many possible variations and styles.  The basic point is to
> separate reading in the data from plotting it.  Plotfile won't do what
> you want because it is designed to make separate subplots instead of
> plotting multiple lines on a single axes.  Maybe doing the latter would
> be at least as useful, if not more, and could be enabled as an option
> with one more kwarg.
>
> Eric
>
> > I have spent time looking through the documentation but I can't find
> > anyway to do this is any straightforward way.  plotfile() looks
> > promising, but I can't seem to make it do the above.  Thanks in
> > advance.
> >
> >  Joseph Smidt
>
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Index: lib/matplotlib/pyplot.py
===
--- lib/matplotlib/pyplot.py	(revision 7068)
+++ lib/matplotlib/pyplot.py	(working copy)
@@ -1447,8 +1447,8 @@
 draw_if_interactive()
 return ret
 
-def plotfile(fname, cols=(0,), plotfuncs=None,
- comments='#', skiprows=0, checkrows=5, delimiter=',',
+def plotfile(fname, cols=(0,), plotfuncs=None, use_cf=False,
+ comments='#', skiprows=0, checkrows=5, delimiter=',', names=None,
  **kwargs):
 """
 Plot the data in *fname*
@@ -1473,9 +1473,12 @@
 vector as you use in the *plotfuncs* dictionary, eg., integer
 column numbers in both or column names in both.
 
-*comments*, *skiprows*, *checkrows*, and *delimiter* are all passed on to
-:func:`matplotlib.pylab.csv2rec` to load the data into a record array.
+*use_cf* : use current figure instead of a new figure for plotting
 
+*comments*, *skiprows*, *checkrows*, *delimiter*, and *names* are all
+passed on to :func:`matplotlib.pylab.csv2rec` to load the data into a
+record array. 
+
 kwargs are passed on to plotting functions.
 
 Example usage::
@@ -1484,17 +1487,21 @@
   plotfile(fname, (0,1,3))
 
   # plot using column names; specify an alternate plot type for volume
-  plotfile(fname, ('date', 'volume', 'adj_close'), plo

Re: [Matplotlib-users] Another Gnuplot style question

[Joseph Smidt]

Thanks everyone, this is exactly what I wanted.


-- 

Joseph Smidt 

Physics and Astronomy
4129 Frederick Reines Hall
Irvine, CA 92697-4575
Office: 949-824-3269

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Re: [Matplotlib-users] Matplotlib documentation

[Gökhan SEVER]

Hello,

About two months ago I was asking how to implement the following
functionality for matplotlib documentation. Well today I figured it
out :) I was busy with some other school work not been thinking for
over twom months :P

"Is there a way to get functions separately listed under each bookmark
listing in the pdf file? For example if I go IV Matplotlib API section
from the bookmarks menu and click the matplotlib.pyplot seb-menu I
would like to see the function names listed. In addition to module
indexing (where keywords highlighted back to original names) this
would be a nice feature to add the pdf documentation."

Enough said, here is what I did. (Thanks to Georg Brandl of Sphinx)
(As of now the latest svn checkout 0.98.6svn_rev__7068 although
__revision__ says: 6887, and with Sphinx 0.6.1)

I have modified the pyplot_api.rst as follows:


.. automodule:: matplotlib.pyplot
   :undoc-members:
   :show-inheritance:


acorr
=
.. autofunction:: acorr

annotate

.. autofunction:: annotate

and other 121 manual entries. (The new PDF file is 12 pages more than
original file.) While I was adding the function names I thought of
myself that these could be done via a little program. I mean before
Sphinx visit --in this case pyplot.py function names might read into a
list and following this an appropriate rst file could be created (and
this is also apply for the other api documentation as well). Or
another way, these could be added to Sphinx as a feature, that is to
say read function names and read docstrings, create figures etc.. and
make a subsection for each item via a special syntax.

The first method eliminates having a pre-written pyplot_api.rst file
since this could be created via a short python script.

I would like discuss these point before start working on other api
functions and classes. Also need some explanation about them, since
pyplot is composed of functions but some other api's are mixed with
classes and functions.

Please, contact me of the list so I can send the modified pyploy_rst.api.

Gökhan

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Re: [Matplotlib-users] Another Gnuplot style question

[Eric Firing]

Joseph Smidt wrote:
> Okay, I am another gnuplot user trying to migrate over to matplotlib.
> I like what I see, but there are a couple things that are very easy to
> do in Gnuplot that I can't figure out how to do with matplotlib.
> 
> I have a file with 3 columns of data called data.txt that looks like:
> 
> 0.  1. 1.0
> 0.0634  1.0655  1.1353
> 0.1269  1.1353  1.28899916094
> 0.1903  1.2097  1.46345358199
> 0.2538  1.2889 1.6615188369
> 0.3173  1.3734 1.88639043926
> ...
> 
> I can plot this data, 2 versus 1 and 3 versus 1, very easily on the
> same plot, with a legend, with log y values, and only for the xrange
> between 2 and 3 with gnuplot:
> 
> set log y
> set xrange[2:3]
> plot 'data.txt' u 1:2 w l t 'apples', 'data.txt' u 1:3 w l t 'oranges'
> 
> Now, how do I do that same thing with matplotlob?  Ie:
> 
> 1. Both graphs overlayed on the same plot.
> 2. Semilogy. (log y values),
> 3. Only ploy for x in the range 2-3.
> 4. Legend for the two graphs on same plot.

Something like this:

import numpy as np
import matplotlib.pyplot as plt

x, apples, oranges = np.loadtxt('data.txt', unpack=True)
plt.semilogy(x, apples, label='apples')
plt.semilogy(x, oranges, label='oranges')
plt.legend()
plt.gca().set_xlim(2, 3)
plt.show()

There are many possible variations and styles.  The basic point is to 
separate reading in the data from plotting it.  Plotfile won't do what 
you want because it is designed to make separate subplots instead of 
plotting multiple lines on a single axes.  Maybe doing the latter would 
be at least as useful, if not more, and could be enabled as an option 
with one more kwarg.

Eric

> 
> I have spent time looking through the documentation but I can't find
> anyway to do this is any straightforward way.  plotfile() looks
> promising, but I can't seem to make it do the above.  Thanks in
> advance.
> 
>  Joseph Smidt
> 


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Re: [Matplotlib-users] Another Gnuplot style question

[Sandro Tosi]

On Wed, Apr 29, 2009 at 08:20, Joseph Smidt  wrote:
> 1. Both graphs overlayed on the same plot.
> 2. Semilogy. (log y values),
> 3. Only ploy for x in the range 2-3.
> 4. Legend for the two graphs on same plot.

a simple example:

In [2]: import numpy as np

In [3]: import matplotlib.pyplot as plt

In [16]: data = np.random.rand(10,3)

In [17]: data
Out[17]:
array([[ 0.00669083,  0.4421283 ,  0.46697081],
   [ 0.18093819,  0.11669917,  0.70887601],
   [ 0.11659791,  0.96514955,  0.07389404],
   [ 0.95616662,  0.30350482,  0.10036185],
   [ 0.14197553,  0.10560376,  0.2964961 ],
   [ 0.74705585,  0.21806946,  0.37095176],
   [ 0.1551145 ,  0.76093425,  0.878701  ],
   [ 0.44315466,  0.3625146 ,  0.06750168],
   [ 0.96109656,  0.88401174,  0.59215722],
   [ 0.46190334,  0.39079641,  0.5958516 ]])

In [28]: plt.semilogy(data[:,0], data[:,1], label='first dataset')
Out[28]: []

In [29]: plt.semilogy(data[:,0], data[:,2], label='second dataset')
Out[29]: []

In [30]: plt.xlim([0.2, 0.8]) # limit x to 0.2..0.8
Out[30]: (0.20001, 0.80004)

In [31]: plt.legend()
Out[31]: 

In [32]: plt.show()

> I have spent time looking through the documentation but I can't find
> anyway to do this is any straightforward way.  plotfile() looks
> promising, but I can't seem to make it do the above.  Thanks in
> advance.

to load data from file you can try

matplotlib.mlab.csv2rec

Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi

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