Re: [Matplotlib-users] mulidimension data

[Benjamin Root]

Diego,

It isn't really clear from your description what the problem is. Is the
problem that the sub-vectors aren't all of equal lengths (i.e., a staggered
array)? Or is it that it is transposed from what you'd expect?

Ben Root

On Tue, Jun 27, 2017 at 9:07 AM, Diego Avesani 
wrote:

> Dear all Matplotlib Users,
>
> I would like to plot a multidimensional plot. I have found this script: 
> multidimension
> script
> 
> The scrip is the second one.
>
> It works perfectly. However, I have a problem with the variable data. I
> usually with data in matrix format, but this one is in a strange format:
>
> [[1.2065774590852414,
>   0.8086503430142642,
>   5.68386650687075,
>   5.299424335893731,
>   0.538429526339814],
>  [1.3499594768827485,
>   1.9507403089675424,
>   5.67760737064995,
> 
> 
> 
>
> Is a sort of vector of vectors. As a consequence, I am not able to read mu
> output data in this format.
> I usually read my data in the following way:
>
> data = np.genfromtxt(fname, skip_header=1)
>
> I would like to know how can I read my data in order to be able to use the
> script.
>
> Thanks a lot to everyone
>
>
> Diego
>
>
> 
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Re: [Matplotlib-users] plot control

[Benjamin Root]

This would seem like a bug in that package's code. The traceback shows that
it is performing its own check on the passed in kwargs, and failing to
recognize it as a valid argument. I suggest contacting the maintainers of
the "skill_metrics" package and find out from them if there is a bug in
their package. I am unfamiliar with this package, so I can't say anything
for certain.

Cheers!
Ben Root


On Wed, Apr 19, 2017 at 11:47 AM, Sudheer Joseph 
wrote:

> Dear Experts.
> I have been trying to modify plot properties of taylor diagram from below
> package. I wanted to make markerfacecolor as None( this allows me to show
> symbols which falls over another) of s as possible in normal matplotlib
> plots but I am not sure how to pass the argument in modified figure
> environment of taylor plot. If I try to use markerfacecolor option the code
> says it do not know about such option. I was also checking it is possible
> specify alpha= n so that the color intensity of symbol can be modified. But
> both options are not working or I am not putting it in proper way in such
> situation.
> Please advice if it is possible.
> Sudheer
>
> https://pypi.python.org/packages/1e/98/d6d5d9200fcec4fdbd20f0f084b6e4
> 1e176284786315449cc0c896a411e8/SkillMetrics-1.1.2.tar.gz#md5=
> 7d5e7200375b1c5e1c4fb8344624be67
>
> sm.taylor_diagram(sdev,crmsd,ccoef,markerLabel=label,markerLegend =
> 'on',markerobs='v',markerfacecolor='None',s
>...: tyleOBS='-',colOBS='r',titleobs='RAMA_SST')
> 
> ---
> ValueErrorTraceback (most recent call
> last)
>  in ()
> > 1 sm.taylor_diagram(sdev,crmsd,ccoef,markerLabel=label,markerLegend
> = 'on',markerobs='v',markerfacecolor='None',styleOBS='-',colOBS='r',
> titleobs='RAMA_SST')
>
> /usr/local/lib/python2.7/dist-packages/skill_metrics/taylor_diagram.pyc
> in taylor_diagram(*args, **kwargs)
>  71
>  72 # Get options
> ---> 73 option = get_taylor_diagram_options(CORs,**kwargs)
>  74 #print option # debug
>  75 #
>
> /usr/local/lib/python2.7/dist-packages/skill_metrics/get_taylor_diagram_options.pyc
> in get_taylor_diagram_options(*args, **kwargs)
> 177 optname = optname.lower()
> 178 if not optname in option:
> --> 179 raise ValueError('Unrecognized option: ' + optname)
> 180 else:
> 181 # Replace option value with that from arguments
>
> ValueError: Unrecognized option: markerfacecolor
>
> *** Sudheer
> Joseph Indian National Centre for Ocean Information Services Ministry of
> Earth Sciences, Govt. of India POST BOX NO: 21, IDA Jeedeemetla P.O. Via
> Pragathi Nagar,Kukatpally, Hyderabad; Pin:5000 55 Tel:+91-40-23886047
> <+91%2040%202388%206047>(O),Fax:+91-40-23895011 <+91%2040%202389%205011>(O),
> Tel:+91-40-23044600 <+91%2040%202304%204600>(R),Tel:+91-40-9440832534(Mobile)
> E-mail:sjo.in...@gmail.com;sudheer.jos...@yahoo.com Web-
> http://oppamthadathil.tripod.com **
> *
>
> 
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Re: [Matplotlib-users] Plotting speed and error when calling update() using TkAgg

[Benjamin Root]

I am wondering if the "optimizations" you have are actually slowing you
down. I have never found myself needing to flush_events() or call update()
like that. Or to draw the artists like you are doing. Without seeing more
of the code, it is hard to judge. Have you tried using "runsnakerun" to
profile your code to find out what is actually slowing it down? I can get
60-70Hz without even trying for 3d plotting animations, and that is
probably more computation than this.

On Tue, Apr 18, 2017 at 4:50 PM, Hjalmar Turesson 
wrote:

> Thanks for the help (and sorry for the super-late reply).
>
> I just tried blitting, but it doesn't really help. I cannot exceed 20 fps.
> The problem is that I'm plotting data from a video file, so that for each
> frame I need to draw a new array (not just a foreground). I think its just
> to much data.
>
> Thanks,
> Hjalmar
>
> On Sat, Jan 7, 2017 at 3:36 PM, Thomas Caswell  wrote:
>
>> To push much past 20Hz you will want to look into blitting.  See
>> http://matplotlib.org/devdocs/api/animation_api.html for a rough
>> introduction on how to use blitting (and see the animation code for an
>> example of handling all of the corner cases).
>>
>> Tom
>>
>> On Fri, Oct 14, 2016 at 5:29 PM Hjalmar Turesson 
>> wrote:
>>
>>> That works fine. And it explains why update() only worked with the Qt
>>> backends (I tried all). The speed is still not super impressive though (~20
>>> fps), but I think I will just start skipping frames when playing at above
>>> 20 fps.
>>>
>>> Thanks,
>>> Hjalmar
>>>
>>> On Fri, Oct 14, 2016 at 10:37 AM, Thomas Caswell 
>>> wrote:
>>>
>>> Instead of `canvas.update` call `self.im.figure.canvas.draw_idle()`.
>>>
>>> IIRC `update` is part of the API inherited from Qt, not part of the API
>>> we ensure that all of the canvas objects have.
>>>
>>> Tom
>>>
>>> On Fri, Oct 7, 2016 at 4:48 PM Hjalmar Turesson 
>>> wrote:
>>>
>>> Hi all,
>>>
>>>
>>> I made a little video player using matplotlib. I need it to allow very
>>> good control over the playback speed (e.g. direction, frame-by-frame
>>> stepping and fast and slow).
>>>
>>> However, it's not very fast. Max frame rate I can achieve is 10-20 fps.
>>> I followed Basti's advice on speeding up plotting (
>>> http://bastibe.de/2013-05-30-speeding-up-matplotlib.html).
>>> This resulted in a more than 2x improvement (from <5 to 10-20 fps), but
>>> I would like to reach 40-50 fps.
>>>
>>> The core code is something like this:
>>>
>>> self.im.set_data(self.video_frame)
>>>
>>> self.text.set_text('some text')
>>>
>>>  self.ax.draw_artist(self.im)
>>>  self.ax.draw_artist(self.text)
>>>  self.im.figure.canvas.update()
>>>  self.im.figure.canvas.flush_events()
>>>
>>> video_frame is a 200 x 250 array. I tried lowering dpi from 100 to 50,
>>> but the improvement is marginal.
>>>
>>> I saw that Harden (http://www.swharden.com/wp/20
>>> 13-04-15-fixing-slow-matplotlib-in-pythonxy/) recommended using TkAgg
>>> over Qt4Agg since TkAgg is supposed to be faster.
>>> But, TkAgg doesn't play nicely with figure.canvas.update(). I get the
>>> following error:
>>> AttributeError: 'FigureCanvasTkAgg' object has no attribute 'update'
>>> It works with Qt4Agg though.
>>>
>>> Does anyone have a fix for this? Or some general advice on how to speed
>>> up playback speed?
>>>
>>> I tried with both matplotlib 1.5.1 and the current version from
>>> github 2.0.0b4+2373.gb34c55d
>>>
>>> Best regards,
>>> Hjalmar
>>> 
>>> --
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>>>
>>>
>
> 
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Re: [Matplotlib-users] accessing axis artist objects for an axes object

[Benjamin Root]

... or report it as a bug against Cartopy for not observing the pad rcParam?

On Wed, Sep 7, 2016 at 12:59 PM, Hearne, Mike <mhea...@usgs.gov> wrote:

> It turns out that the Cartopy gridline labels are NOT tick labels, but
> Text objects managed by the Gridliner class.   I think I'm just going
> to draw the grid line labels myself.
>
> On Wed, Sep 7, 2016 at 9:04 AM, Benjamin Root <ben.v.r...@gmail.com>
> wrote:
> > Hmm, strange. Well, I know this works in mplot3d (we have a test for it)
> >
> > for i, tick in enumerate(ax.yaxis.get_major_ticks()):
> > tick.set_pad(tick.get_pad() - i * 5)
> >
> > A bit silly, but it is how you can have labels anywhere you want
> relative to
> > the ticks.
> >
> >
> > On Wed, Sep 7, 2016 at 11:47 AM, Hearne, Mike <mhea...@usgs.gov> wrote:
> >>
> >> I couldn't find an rcParams property called "tickpad".  I did find
> >> "xtick.major.pad", which was set to 4.0.  Setting it to a negative
> >> value has no effect.  xtick.minor.pad doesn't do anything either.
> >>
> >> On Wed, Sep 7, 2016 at 8:32 AM, Benjamin Root <ben.v.r...@gmail.com>
> >> wrote:
> >> > I think you do that by setting a negative tickpad value in the
> rcParams.
> >> >
> >> > On Wed, Sep 7, 2016 at 11:28 AM, Hearne, Mike <mhea...@usgs.gov>
> wrote:
> >> >>
> >> >> Thomas - I hate to be obtuse, but did you mean to imply that the
> xaxis
> >> >> and yaxis properties of an Axes object are AxisArtist objects?
> >> >> IPython tells me that they are XAxis and YAxis objects. From
> >> >> inspecting the GitHub repo, it seems that these are child classes of
> >> >> the Axis object.
> >> >>
> >> >> I suppose I should ask the question addressing the problem I actually
> >> >> have:  How do I render the tick (map) labels *inside* a Cartopy map
> >> >> instead of *outside*?
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Mike
> >> >>
> >> >> On Tue, Sep 6, 2016 at 5:03 PM, Thomas Caswell <tcasw...@gmail.com>
> >> >> wrote:
> >> >> > ax.xaxis or ax.yaxis
> >> >> >
> >> >> > axes_grid is an alternative to the default Axes/Axis classes.
> >> >> >
> >> >> > Tom
> >> >> >
> >> >> >
> >> >> > On Tue, Sep 6, 2016, 19:53 Hearne, Mike <mhea...@usgs.gov> wrote:
> >> >> >>
> >> >> >> Python: 3.5
> >> >> >> Matplotlib: 1.5.2
> >> >> >>
> >> >> >> I'm trying to invert the tick labels on a Cartopy map, and I found
> >> >> >> this Matplotlib example:
> >> >> >>
> >> >> >> ax.axis[:].invert_ticklabel_direction()
> >> >> >>
> >> >> >> found here:
> >> >> >> http://matplotlib.org/mpl_toolkits/axes_grid/users/
> axisartist.html
> >> >> >>
> >> >> >> My problem is that any Axes object (or child class thereof) that
> >> >> >> I've
> >> >> >> experimented with says that the axis attribute is a *method*, not
> a
> >> >> >> sequence as I infer from the above example.
> >> >> >>
> >> >> >> How do I get the axisartists for a bog-standard Axes instance?
> >> >> >>
> >> >> >> Thanks in advance,
> >> >> >>
> >> >> >> Mike
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> 
> --
> >> >> >> ___
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> >> >> >> Matplotlib-users@lists.sourceforge.net
> >> >> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >> >>
> >> >>
> >> >>
> >> >> 
> --
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> >> >
> >> >
> >
> >
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Re: [Matplotlib-users] accessing axis artist objects for an axes object

[Benjamin Root]

Hmm, strange. Well, I know this works in mplot3d (we have a test for it)

for i, tick in enumerate(ax.yaxis.get_major_ticks()):
tick.set_pad(tick.get_pad() - i * 5)

A bit silly, but it is how you can have labels anywhere you want relative
to the ticks.


On Wed, Sep 7, 2016 at 11:47 AM, Hearne, Mike <mhea...@usgs.gov> wrote:

> I couldn't find an rcParams property called "tickpad".  I did find
> "xtick.major.pad", which was set to 4.0.  Setting it to a negative
> value has no effect.  xtick.minor.pad doesn't do anything either.
>
> On Wed, Sep 7, 2016 at 8:32 AM, Benjamin Root <ben.v.r...@gmail.com>
> wrote:
> > I think you do that by setting a negative tickpad value in the rcParams.
> >
> > On Wed, Sep 7, 2016 at 11:28 AM, Hearne, Mike <mhea...@usgs.gov> wrote:
> >>
> >> Thomas - I hate to be obtuse, but did you mean to imply that the xaxis
> >> and yaxis properties of an Axes object are AxisArtist objects?
> >> IPython tells me that they are XAxis and YAxis objects. From
> >> inspecting the GitHub repo, it seems that these are child classes of
> >> the Axis object.
> >>
> >> I suppose I should ask the question addressing the problem I actually
> >> have:  How do I render the tick (map) labels *inside* a Cartopy map
> >> instead of *outside*?
> >>
> >> Thanks,
> >>
> >> Mike
> >>
> >> On Tue, Sep 6, 2016 at 5:03 PM, Thomas Caswell <tcasw...@gmail.com>
> wrote:
> >> > ax.xaxis or ax.yaxis
> >> >
> >> > axes_grid is an alternative to the default Axes/Axis classes.
> >> >
> >> > Tom
> >> >
> >> >
> >> > On Tue, Sep 6, 2016, 19:53 Hearne, Mike <mhea...@usgs.gov> wrote:
> >> >>
> >> >> Python: 3.5
> >> >> Matplotlib: 1.5.2
> >> >>
> >> >> I'm trying to invert the tick labels on a Cartopy map, and I found
> >> >> this Matplotlib example:
> >> >>
> >> >> ax.axis[:].invert_ticklabel_direction()
> >> >>
> >> >> found here:
> >> >> http://matplotlib.org/mpl_toolkits/axes_grid/users/axisartist.html
> >> >>
> >> >> My problem is that any Axes object (or child class thereof) that I've
> >> >> experimented with says that the axis attribute is a *method*, not a
> >> >> sequence as I infer from the above example.
> >> >>
> >> >> How do I get the axisartists for a bog-standard Axes instance?
> >> >>
> >> >> Thanks in advance,
> >> >>
> >> >> Mike
> >> >>
> >> >>
> >> >>
> >> >> 
> --
> >> >> ___
> >> >> 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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Re: [Matplotlib-users] accessing axis artist objects for an axes object

[Benjamin Root]

I think you do that by setting a negative tickpad value in the rcParams.

On Wed, Sep 7, 2016 at 11:28 AM, Hearne, Mike  wrote:

> Thomas - I hate to be obtuse, but did you mean to imply that the xaxis
> and yaxis properties of an Axes object are AxisArtist objects?
> IPython tells me that they are XAxis and YAxis objects. From
> inspecting the GitHub repo, it seems that these are child classes of
> the Axis object.
>
> I suppose I should ask the question addressing the problem I actually
> have:  How do I render the tick (map) labels *inside* a Cartopy map
> instead of *outside*?
>
> Thanks,
>
> Mike
>
> On Tue, Sep 6, 2016 at 5:03 PM, Thomas Caswell  wrote:
> > ax.xaxis or ax.yaxis
> >
> > axes_grid is an alternative to the default Axes/Axis classes.
> >
> > Tom
> >
> >
> > On Tue, Sep 6, 2016, 19:53 Hearne, Mike  wrote:
> >>
> >> Python: 3.5
> >> Matplotlib: 1.5.2
> >>
> >> I'm trying to invert the tick labels on a Cartopy map, and I found
> >> this Matplotlib example:
> >>
> >> ax.axis[:].invert_ticklabel_direction()
> >>
> >> found here:
> >> http://matplotlib.org/mpl_toolkits/axes_grid/users/axisartist.html
> >>
> >> My problem is that any Axes object (or child class thereof) that I've
> >> experimented with says that the axis attribute is a *method*, not a
> >> sequence as I infer from the above example.
> >>
> >> How do I get the axisartists for a bog-standard Axes instance?
> >>
> >> Thanks in advance,
> >>
> >> Mike
> >>
> >>
> >> 
> --
> >> ___
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> >> Matplotlib-users@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
> 
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Re: [Matplotlib-users] Fw: Matplotlib Figure margin transparancy

[Benjamin Root]

The other reason why this message never got posted is because this message
was sent to the now defunct mailing list hosted by sourceforge. The mailing
list moved about a year ago (I think) to python.org. You will have to
subscribe in order to post unmoderated.

https://mail.python.org/mailman/listinfo/matplotlib-users

Ben Root

On Wed, Aug 10, 2016 at 4:25 AM, Jens Nielsen 
wrote:

> At least for me gmail put your mail in the spam folder.
>
> Anyway the inline backend is actually from in IPython/Jupyter and not in
> matplotlib. I think they have changed the default a couple of times and had
> the transparent as a default earlier but changed it. Looking at the current
> master it looks like they are respecting the matplotlib default colors
> from the matplotlib rc params. Can you please check which version on
> IPython and Jupyter you are running.
>
> You can change the matplotlib rc parameters as described in the docs
> http://matplotlib.org/users/customizing.html#customizing-matplotlib but
> the default ones should be white.
>
> best
> Jens
>
> On Wed, 10 Aug 2016 at 05:06 Sudheer Joseph 
> wrote:
>
>> Hi,
>> I have send below query to matplotlib user group recently but did not get
>> posted so far. Can you please tell me is there is any thin wrong with the
>> message?
>> With best regards,
>> Sudheer
>>
>> >
>> > Dear Expert,
>> > Recently after up-gradation of matplotlib and ubuntu
>> 16.04 I am
>> > getting transparent figure axis when using the "linux color scheme"
>> > option in ipython qtconsole. May I know if there is a way to fix this
>> issue?. I
>> > wanted to keep black screen as it reduces eye strain.
>> >
>> > ipython qtconsole --matplotlib inline
>> >
>> > If I save the image i am able to get axis properly but to see on screen
>> as the
>> > axis is not plotted with white background the black axis line and
>> labels are not
>> > visible. Earlier I used to get figures as attached in second figure.
>> > Earlier Satus which I am looking for below link
>> > https://drive.google.com/open?id=0B3heUQNme7G5ZmVlUHpRakZxUlk
>> > Present status without boarder below link
>> >
>> >
>> > https://drive.google.com/open?id=0B3heUQNme7G5VkhZWHhiUnpfWDg
>> >
>> > Kindly suggest a solution
>> > with best regards,
>> > Sudheer
>> >
>>
>> 
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Re: [Matplotlib-users] Matplotlib & Basemap / What is the Best Graphical Back-end for Raster Data Display (.png) ?

[Benjamin Root]

AGG is used for image handling, particularly for handling transforms,
scaling, interpolation and such. The AxesImage object that you get from
calling imshow() is handled through the AGG library. This is true
regardless of the backend being used because it is based in the AxesImage
class (and others). An SVG of a plot that used imshow() has raster data in
it that comes from AGG (and you can choose to rasterize other things, as
well). Cairo still needs the image buffer.

So, the distinction is the use of the AGG library, and the use of the AGG
backend. The AGG library is required, but the AGG backend is not (but
highly recommended).

I will admit that I didn't have this distinction very clear in my own head
until very recently when reviewing some PRs that reworked the image
handling architecture. I hope that clears it up for you, too.

Cheers!
Ben Root


On Thu, Mar 3, 2016 at 10:05 AM, Jerzy Karczmarczuk <
jerzy.karczmarc...@unicaen.fr> wrote:

> Le 03/03/2016 15:43, Benjamin Root a écrit :
> > Matplotlib will not work at all without AGG. Even the AGG-less
> > backends still use AGG for image handling (imshow() and such).
>
> Is it so? I never found such strong statement in the docs.
>
> 1. SVG backend produces vector graphics, no rasterisation in principle,
> so why AGG?
> 2. Cairo uses its own engine. Why AGG?
> 3. Image (PNG) "production" from curves, etc. uses AntiGrain, but if
> imshow() shows an image which is just a pixel array, there is no
> manipulation needing AGG, an element (triple RGB) becomes a pixel, and
> that's it.
>
> Jerzy Karczmarczuk
>
>
>
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Re: [Matplotlib-users] Matplotlib & Basemap / What is the Best Graphical Back-end for Raster Data Display (.png) ?

[Benjamin Root]

Matplotlib will not work at all without AGG. Even the AGG-less backends
still use AGG for image handling (imshow() and such).

We can not guarantee that matplotlib would work with agg 2.5, as that is
the GPL'ed version. We develop against a patched 2.4 branch of AGG (which
is BSD-licensed), which is distributed with our source, and is built as
part of our build process. Have you tried building matplotlib directly from
our source without a system install of AGG?

Cheers
Ben Root


On Thu, Mar 3, 2016 at 6:34 AM, Claude Falbriard  wrote:

> Dear colleagues,
>
> I like to receive an advice about the best back-end choice for Matplotlib
> & Basemap to generate large .png images in a background processing mode.
> Having issues with the pre-compiled "Agg" package which does not work
> under my machine architecture. Also not able to recompile the Agg 2.5
> package as its build throws an error at the build script autogen.sh.
> Error:
>
> ./configure: line 15546: syntax error near unexpected token `$SDL_VERSION,'
> ./configure: line 15546: `AM_PATH_SDL($SDL_VERSION,'
>
> When bypassing this line it runs into another dependency which is blocking
> the make install process.
>
> libtool: link: cannot find the library
> `../src/platform/X11/libaggplatformX11.la' or unhandled argument
> `../src/platform/X11/libaggplatformX11.la'
> Makefile:1166: recipe for target 'aa_demo' failed
> make[1]: *** [aa_demo] Error 1
> make[1]: Leaving directory '/data/Downloads/agg/agg-2.5/examples'
> Makefile:481: recipe for target 'install-recursive' failed
> make: *** [install-recursive] Error 1
>
> I do not plan to use any interactive access, so my guess is that excluding
> X11 libraries should work OK.
>
> My test showed that the  "Cairo" package is working fine, but its quality
> (vector oriented) is not as good compared to the Agg raster display. Case
> the "Agg"
> is not able to install on my machine, is there an alternate graphical
> back-end available under SuSE environments?
>
> Regards,
>
> *Claude Falbriard*
> Certified IT Specialist L2 - Middleware
> --
> *Phone:*55-13-99662-5703 | *Mobile:*55-13-98117-3316
> *E-mail:* *clau...@br.ibm.com* 
>
>
>
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Re: [Matplotlib-users] Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault

[Benjamin Root]

Sorry, forgot to post the link: https://pypi.python.org/pypi/faulthandler/

On Wed, Feb 24, 2016 at 3:33 PM, Benjamin Root <ben.v.r...@gmail.com> wrote:

> Could you try using faulthandler and post the traceback please? That'll
> help us isolate the problem better.
>
> Ben Root
>
> On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard <clau...@br.ibm.com>
> wrote:
>
>> Dear colleagues,
>>
>>  I've done a build from source of latest *Matplotlib* package and
>> deployed it at our IBM z13 machine (s390x). It uses the current release
>> 1.5.1.
>> During the unit tests I found an issue with a test case from NOAA which
>> uses a* pcolormesh* draw function with *basemap*.
>>
>> Example 2: Plot data from an NWW3 GRiB2 file - [ here:
>> *http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml*
>> <http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml>*]*
>>
>> The following line is causing a *Segmentation fault* error even when
>> adding an 8GB swap memory to the process:
>>
>> cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)
>>
>> I also tryed to execute other, similar samples that use pcolormesh, but
>> receiving the same error. Is this a known issue or might it be be related
>> to the memory environment ? Any hints how to debug this error?
>>
>> Regards,
>>
>> *Claude Falbriard*
>> Certified IT Specialist L2 - Middleware
>> --
>> *Phone:*55-13-99662-5703 | *Mobile:*55-13-98117-3316
>> *E-mail:* *clau...@br.ibm.com* <clau...@br.ibm.com>
>>
>>
>>
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Re: [Matplotlib-users] Matplotlib 1.5.1 - Function pcolormesh throws Segmentation Fault

[Benjamin Root]

Could you try using faulthandler and post the traceback please? That'll
help us isolate the problem better.

Ben Root

On Wed, Feb 24, 2016 at 3:04 PM, Claude Falbriard 
wrote:

> Dear colleagues,
>
>  I've done a build from source of latest *Matplotlib* package and
> deployed it at our IBM z13 machine (s390x). It uses the current release
> 1.5.1.
> During the unit tests I found an issue with a test case from NOAA which
> uses a* pcolormesh* draw function with *basemap*.
>
> Example 2: Plot data from an NWW3 GRiB2 file - [ here:
> *http://polar.ncep.noaa.gov/waves/examples/usingpython.shtml*
> *]*
>
> The following line is causing a *Segmentation fault* error even when
> adding an 8GB swap memory to the process:
>
> cs = m.pcolormesh(x,y,data,shading='flat',cmap=plt.cm.jet)
>
> I also tryed to execute other, similar samples that use pcolormesh, but
> receiving the same error. Is this a known issue or might it be be related
> to the memory environment ? Any hints how to debug this error?
>
> Regards,
>
> *Claude Falbriard*
> Certified IT Specialist L2 - Middleware
> --
> *Phone:*55-13-99662-5703 | *Mobile:*55-13-98117-3316
> *E-mail:* *clau...@br.ibm.com* 
>
>
>
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Re: [Matplotlib-users] pyplot.hexbin

[Benjamin Root]

Hmm, you are right, there is no way to get back the information that hexbin
computed. The hexbin function is massive (in lib/matplotlib/axes/_axes.py)
and is a bit tangled up with the artist-handling code, too. I think it
would make sense to factor out the hexbinning component into its own
hexbin.py that others might be able to use separately.

Ben Root


On Fri, Jan 29, 2016 at 5:15 PM, Sebastian  wrote:

> Is there a simple way to hexbin using "pyplot.hexbin" and to return the
> ids of the set of
> points in each hexbin? That is to output an array of n elements
> (one for each hexbin), and each element itself an array with the point
> ids? The sum
> of the number of inner elements would be equal the sum of all points (x,y).
>
> Is hexbin missing this simple feature?
>
> Or perhaps specifying C=N.arange(len(x)) then some specific
> "reduced_C_function"
> to return those elements. But I don't know if there is a
> "reduced_C_function" available,
> or perhaps one could be added?
>
> many thanks in advance...
>
> link:
> http://stackoverflow
> .com/questions/18886461/how-can-i-print-a-list-of-the-outputs-from-the-
> hexbin-reduce-c-function/35088073#35088073
>
>
>
>
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Re: [Matplotlib-users] applying an image's colormap to another image

[Benjamin Root]

You might have better luck asking the scikit-image people, or the Pillow
people. ImageMagick might also have what you are looking for.

Cheers!
Ben Root


On Wed, Jan 27, 2016 at 11:23 PM, Matteo Niccoli  wrote:

> Can something like this (which by the way I can't get to work):
>
> http://stackoverflow.com/questions/3114925/pil-convert-rgb-image-to-a-specific-8-bit-palette
>
> What I would like to do is this:
> 1) Import an RGB image, which would have its own colormap - say this one
> for example:
>
> https://upload.wikimedia.org/wikipedia/commons/b/b3/Jupiter_new_hubble_view_above_pole.png
>
> 2) convert it to intensity, display the intensity color-mapped to the same
> colours the original RGB had.
>
> Any tips, or even better code or pseudocode would be greatly appreciated.
>
> Thanks
> Matteo
>
>
>
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Re: [Matplotlib-users] Looking for feedback on figures using matplotlib and jupyter notebook

[Benjamin Root]

In mpl, our figure objects get numbers assigned to them by default, but
they can also be strings. These labels are used in the figure window title
bar. Perhaps that existing data could be hijacked? Admittedly, most people
use the string name to give nice short names to their figures, so maybe
those names could be the "tag" name in latex? So, all we would need is some
way to supply the actual caption string.

Ben Root


On Thu, Jan 28, 2016 at 10:17 PM, Fernando Perez 
wrote:

> On Thu, Jan 28, 2016 at 3:23 PM, Andreas Mueller  wrote:
>
>> Hi all.
>>
>> This is about a joint jupyter-notebook / matplotlib problem I've been
>> thinking about.
>> So I'm writing a book using jupyter-notebook, and all my figures are
>> generated using matplotlib.
>>
>> In books, there is usually a figure caption with a running number and
>> some description.
>>  From what I read, the best way to add captions is just using plt.text.
>> However, the caption should probably be in the markup,
>> not in a rendered PNG. I'm not sure if changing the backend might help,
>> but that probably doesn't make the notebook happy?
>>
>> The other problem is that I want to have running numbers that I can
>> refer to by a tag (as you would in latex).
>> That is more of a notebook problem, though.
>>
>> Any feedback would be very welcome
>>
>
> I've been wanting to do something about this problem for a while, but
> haven't had the cycles to work on it...  Here's my current idea, perhaps I
> can goad you into implementing it :)
>
> I think that IPython.display should provide a Figure object, capable of
> wrapping any input image (with nice code to automatically swallow a
> matplotlib figure without asking the user to convert it to an image first),
> and taking an optional caption.
>
> Figure() would then produce as output the displayed image but with a bit
> of nice CSS to center it on the page, along with the caption.
>
> The trick is to send the entire data bundle correctly structured so that,
> at the other end, nbconvert could recognize these figures as such, and not
> only produce nice HTML, but more importantly, push them into the LaTeX
> output with the correct call to \figure, including \caption as well as size
> and placement specifiers.
>
> The signature of Figure() might be something like
>
> def Figure(fig, caption=None, width=None, height=None,
>latex_placement=None):
>
>
> I would try implementing this first as a standalone tool, and once it's
> been tested enough in real-world usage with both HTML and LaTeX output from
> nbconvert, it could be merged in.  I suspect it's going to take a few
> iterations to get it right.
>
> But it's not particularly hard, and someone working on a book would be the
> perfect candidate to have enough test cases to be able to iterate until
> happy ;)
>
> If you think you want to take a stab at this, don't hesitate to ping us on
> the jupyter list. We can help with some of the more obscure parts of
> getting this to work on nbconvert (and there may be things I've overlooked
> in the sketch above).
>
> Cheers,
>
> f
>
> --
> Fernando Perez (@fperez_org; http://fperez.org)
> fperez.net-at-gmail: mailing lists only (I ignore this when swamped!)
> fernando.perez-at-berkeley: contact me here for any direct mail
>
>
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Re: [Matplotlib-users] MultiCursor messes with xlim and ylim autoscaling

[Benjamin Root]

Add "blit=False" in the instantiation for multicursor to get around the
copy_from_bbox issue.

I wonder if the use of fig.axes might be a problem?
On Jan 20, 2016 2:27 PM, "Bilheux, Jean-Christophe" 
wrote:

> HI all,
>
> I wanted to help (for a change) but running the script on mac (with the
> multi cursor code commented out), I got the following error. If anyone can
> figure out why !
>
> File
> "/Users/j35/anaconda/lib/python3.4/site-packages/matplotlib/widgets.py",
> line 1046, in clear
> self.canvas.copy_from_bbox(self.canvas.figure.bbox))
> AttributeError: 'FigureCanvasMac' object has no attribute ‘copy_from_bbox'
>
> I’m using python 3.4 and matplotlib 1.4.3
>
> Thanks
>
> Jean
>
>
>
> > On Jan 20, 2016, at 1:26 PM, Michael Kaufman  wrote:
> >
> > Hi Gurus:
> >
> > I'm having a serious problem with MultiCursor and autoscaling...
> >
> > If I do the code below with both MultiCursor instantiations commented
> out, then all plots are xscaled to [50,55] and yscaled to each plot's
> appropriate ylimits.
> >
> > If I uncomment the top MultiCursor instantiation, then both the xlimits
> and ylimits are screwed up: xlim=[0,60] and ylim is all over the place,
> certainly not autoscaled tight.
> >
> > If I uncomment the bottom MultiCursor instantiation, then the xlimit
> appears to be scaled correctly, [50,55], but two of the four plots (lower
> left and upper right) are not autoscaled in y.
> >
> > How to I instantiate MultiCursor to get the normal and expected
> autoscaling behavior?
> >
> > Not that it should matter, but I'm using here Tk and Python3 with MPL
> 1.5dev1 (91ca2a3724ae91d28d97)
> >
> > Thanks for any help,
> >
> > M
> >
> > =
> >
> > from matplotlib import pyplot as pl
> > from matplotlib.widgets import MultiCursor
> > from matplotlib import gridspec
> > import numpy as np
> >
> > if __name__ == "__main__":
> >
> >  fig = pl.gcf()
> >  gs = gridspec.GridSpec(2,2)
> >
> >  ax = None
> >  for g in gs:
> >ax = pl.subplot(g, sharex=ax)
> >
> >  #multi = MultiCursor(fig.canvas, tuple(fig.axes),
> >  #useblit=True, horizOn=True, color='k', lw=1)
> >
> >  x = np.arange(50,55,0.01)
> >  y1 = np.sin(x)
> >  y2 = np.cos(x) + 4
> >  y3 = 0.2*np.cos(x) - 4
> >  y4 = np.cos(2*x) - 1
> >
> >  for ax,y in zip(fig.axes, [y1,y2,y3,y4]):
> >ax.plot(x,y)
> >
> >  for ax in fig.axes:
> >ax.grid()
> >
> >  #multi = MultiCursor(fig.canvas, tuple(fig.axes),
> >  #useblit=True, horizOn=True, color='k', lw=1)
> >
> >  pl.draw()
> >  pl.show()
> >
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Re: [Matplotlib-users] How do I make a Mercator map larger

[Benjamin Root]

Without seeing the code, it would be hard to tell what is wrong. Setting
the figure size should work. I do this all the time myself.

As for converting map coordinates to inches, are you talking about inches
of the display? or inches of the map (as opposed to km or miles)?

Ben Root

On Sun, Jan 3, 2016 at 5:20 PM, Martin McGlensey 
wrote:

> Hello,
>
>
>
> I’m a new user to both python and basemap. I’ve got my map working OK, but
> would like to make it larger on the display. I’ve tried the height and
> width parameters in the map definition (m=basemap(…) and
> plt.figure(figuresize=(x,y)). Neither appear to have any effect on the size
> of the map.
>
>
>
> Is there an easy way to convert map coordinates to inches?
>
>
>
> Thanks,
>
> Marty
>
>
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Re: [Matplotlib-users] Set matplotlibrc color cycle to custom colors using axes.prop_cycle (v1.5)

[Benjamin Root]

You can't use the hash symbol when doing colors as a hex in an rcfile. The
rcfile parser is so simple that it treats it as a comment. Don't drop the
quotes.

Ben Root

On Mon, Dec 21, 2015 at 12:51 AM, Thomas Caswell  wrote:

> Not at a computer to test, but try dropping the quotes.
>
> On Sun, Dec 20, 2015, 20:56 Julian Irwin  wrote:
>
>> Hi,
>>
>> I'm trying to set my default color cycle in my matplotlibrc using
>> axes.prop_cycle. The documentation (as far as I could find...) only gives
>> examples like
>>
>> axes.prop_cycle: cycler('color', 'bgrcmyk')
>>
>>
>> And then the comment below says, cryptically:
>>
>> # as list of string colorspecs:
>> # single letter, long name, or
>> # web-style hex
>>
>> But I have tried all sorts of variatns on:
>>
>> axes.prop_cycle: cycler('color', ['#e41a1c', '#377eb8', '#4daf4a', 
>> '#ff7f00', '#a65628', '#f781bf', '#99', '#984ea3', '#33'])
>>
>> But I always get an error upon importing matplotlib. Is there any doc on
>> how to do this properly? Is this even supported?
>>
>> Thanks,
>> Julian
>>
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Re: [Matplotlib-users] SpanSelector span_stays does not work for me

[Benjamin Root]

Have you tried setting "useblit=False"? If that works, I wonder if we
accidentally broke something in the recent widget interactivity work...


Ben Root

On Fri, Dec 11, 2015 at 7:48 PM, Edward Richards 
wrote:

> I am selecting a region of a color plot with span selector, and I would
> like the selected region to stay highlighted. I found the span_stays flag,
> but the selection rectangle still disappears after I release the mouse.
>
> Any help is appreciated.
> Thanks,
> Ned
>
> My backend is 'TkAgg'
>
> I am running the script from python3.4 at the command line, my version is:
>
> Python 3.4.3 (default, Jun 19 2015, 05:46:30)
> [GCC 4.8.3 20140911 (Red Hat 4.8.3-9)] on linux
> Type "help", "copyright", "credits" or "license" for more information.
>
> >>> print(matplotlib.__version__)
> 1.5.0
>
> code example:
>
> import numpy as np
> import matplotlib.pyplot as plt
> from matplotlib.widgets import SpanSelector
>
> test_data = np.random.randn(1000, 1000)
> fig, ax = plt.subplots()
> ax.imshow(test_data)
>
> def selection(x1, x2):
>  """This function isn't the point"""
>  pass
>
> span = SpanSelector(ax, selection, 'horizontal', useblit=True,
>  rectprops=dict(alpha=0.5, facecolor='red'),
> span_stays=True)
> plt.show()
>
>
>
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Re: [Matplotlib-users] Legend frame edgecolor and linewidth

[Benjamin Root]

Indeed, it looks like there isn't a very good way to control all of the
properties of the frame portion of a legend. This could certainly use some
improvements, partly in allowing a dictionary of property values to be
passed in `plt.legend()` (there is already a dictionary of font
properties), but also to have some rcParams that could be made available,
too. Such improvements are always welcome!

Cheers!
Ben Root

On Fri, Nov 13, 2015 at 7:57 AM, Daniele Nicolodi 
wrote:

> Hello,
>
> there is a way to control the edgecolor and the linewidth of the frame
> drawn around the legend?  I set the axes linewidth to 0.5 but the legend
> frame linewidth is set to 1.0 and it does not look nice. Also, most of
> the time I don't want the frame edge to be drawn at all.
>
> Always doing:
>
>   l = plt.legend()
>   l.get_frame().set_edgecolor('none')
>
> is boring.
>
> If the setting are not there, would a patch adding a setting to style
> the legend frame be considered? Additionally, would it make sense to
> default the legend frame linewidth to the axes linewidth?
>
> Cheers,
> Daniele
>
>
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Re: [Matplotlib-users] Inset plot with a previously draw plot

[Benjamin Root]

An axes can only belong to one figure at a time. And I also don't think I
have ever seen anyone try and transfer an axes from one figure to another.

You *might* have luck with inset locators from axes_grid:
http://matplotlib.org/examples/axes_grid/inset_locator_demo.html

Cheers!
Ben Root

On Thu, Oct 29, 2015 at 12:07 PM, Alejandro Weinstein <
alejandro.weinst...@gmail.com> wrote:

> Hi,
>
> I have a previously draw plot that I want to place as an inset in
> another figure. I've tried with passing the previously drawn axes as
> the `axes` parameter to the `add_axes` method of the figure, and also
> tried using the `set_axes` method of the new axes, without success: I
> get the new inset axes, but without the previously drawn plot, in both
> cases.
>
> The following code shows both approaches:
>
> # Passing the inset axes as a parameter to add_axes
> fig_in, ax_in = plt.subplots()
> ax_in.plot([1,2,3])
> fig, ax = plt.subplots()
> ax.plot([1,2,1])
> fig.add_axes([0.72, 0.72, 0.16, 0.16], axes=ax_in)
>
> # Using set_axes
> fig_in, ax_in = plt.subplots()
> ax_in.plot([1,2,3])
> fig, ax = plt.subplots()
> ax.plot([1,2,1])
> ax_new = fig.add_axes([0.72, 0.72, 0.16, 0.16])
> ax_new.set_axes(ax_in)
>
> Any help with this will be appreciated.
>
> Regards,
> Alejandro
>
>
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Re: [Matplotlib-users] basemap: how to plot "toothed" curves

[Benjamin Root]

Hmmm, this is actually an interesting problem. I am also a meteorologist,
so this is interesting to me.

I haven't figured it out yet, but here are my thoughts:

1) There are the "^" triangle markers as well as "2" tri_up markers:
http://nbviewer.ipython.org/github/WeatherGod/AnatomyOfMatplotlib/blob/master/AnatomyOfMatplotlib-Part3-HowToSpeakMPL.ipynb#Markers
2) The markevery property should be set to a float value to have the
markers spaced out evenly along the line regardless of aspect ratios and
zooming (note, this assumes that the line is defined with many vertices to
give a smooth appearance).

Problem:
Using markers and markevery in a Line2D object has an inherent limitation:
all of the markers will be drawn in the same orientation. So, we can't
orient the markers along the normal of the line.
Also, there is no pre-defined marker for half-circles, so this approach
wouldn't work well for warm-fronts/dry-lines/etc.

I'll have to see if a PolygonCollection + Line2D might be the right
approach here...

Ben Root




On Fri, Oct 16, 2015 at 7:22 AM, Phil Cummins 
wrote:

> Hi,
>
> I would like to plot "toothed" curves using basemap. These are curves with
> triangles on one side, that are used to plot pressure fronts in meteorology
> or thrust faults in geology. You need to be able to say which side of the
> curve the triangles should appear on. Does anyone know whether such curves
> can be plotted using mtplotlib/basemap?
>
> Thanks,
>
> - Phil
>
> Australian National University
>
>
>
>
> --
>
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Re: [Matplotlib-users] basemap: how to plot "toothed" curves

[Benjamin Root]

Looks like someone else figured out a creative solution using quiver:
http://stackoverflow.com/questions/19918502/sawtooth-line-style-in-matplotlib

Here it is (slightly cleaned up):

import matplotlib.pyplot as pltimport numpy as np

x = np.linspace(0, 2*np.pi, 100)
y = np.sin(x)

dx = np.diff(x)
dy = np.diff(y)

x2 = np.linspace(0, 2*np.pi, 10)
y2 = np.sin(x2)

dx = np.zeros_like(x2) + 1e-12
dy = np.sin(x2 + dx) - y2

length = np.hypot(dx, dy)
dx /= length
dy /= length

fig, ax = plt.subplots()
ax.set_aspect("equal")
ax.plot(x, y, lw=4)

size = 20
ax.quiver(x2, y2, -dy, dx, headaxislength=size, headlength=size,
headwidth=size, color="blue")
plt.margins(0.2)


I don't know yet how to get rounded heads, though. Now I am looking to see
how the text box styles of "sawtooth" and "roundtooth" are handled in the
code to see if that could be exploited, instead.

Cheers!
Ben Root



On Fri, Oct 16, 2015 at 10:24 AM, Benjamin Root <ben.v.r...@gmail.com>
wrote:

> Hmmm, this is actually an interesting problem. I am also a meteorologist,
> so this is interesting to me.
>
> I haven't figured it out yet, but here are my thoughts:
>
> 1) There are the "^" triangle markers as well as "2" tri_up markers:
> http://nbviewer.ipython.org/github/WeatherGod/AnatomyOfMatplotlib/blob/master/AnatomyOfMatplotlib-Part3-HowToSpeakMPL.ipynb#Markers
> 2) The markevery property should be set to a float value to have the
> markers spaced out evenly along the line regardless of aspect ratios and
> zooming (note, this assumes that the line is defined with many vertices to
> give a smooth appearance).
>
> Problem:
> Using markers and markevery in a Line2D object has an inherent limitation:
> all of the markers will be drawn in the same orientation. So, we can't
> orient the markers along the normal of the line.
> Also, there is no pre-defined marker for half-circles, so this approach
> wouldn't work well for warm-fronts/dry-lines/etc.
>
> I'll have to see if a PolygonCollection + Line2D might be the right
> approach here...
>
> Ben Root
>
>
>
>
> On Fri, Oct 16, 2015 at 7:22 AM, Phil Cummins <phil.cumm...@anu.edu.au>
> wrote:
>
>> Hi,
>>
>> I would like to plot "toothed" curves using basemap. These are curves
>> with triangles on one side, that are used to plot pressure fronts in
>> meteorology or thrust faults in geology. You need to be able to say which
>> side of the curve the triangles should appear on. Does anyone know whether
>> such curves can be plotted using mtplotlib/basemap?
>>
>> Thanks,
>>
>> - Phil
>>
>> Australian National University
>>
>>
>>
>>
>> --
>>
>> ___
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>>
>>
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Re: [Matplotlib-users] TypeError: can't multiply sequence by non-int of type 'float'

[Benjamin Root]

You have some logic issues here. First off, I wouldn't be updating the plot
in the same function that is updating the data values. Assuming that
"loop_start()" is asynchronous, the update frequency for it is likely to be
entirely different from the Animation update frequency. So, just have that
function do updates. You should also declare x, y, and z as globals in that
function so that the reassignment of those arrays persist properly.


Your list comprehension prior to concatenating uses a variable "x", which
is likely causing the current error that you see. Change that name to
something else.

Lastly, I implore you to use "set_data()" like in the original example,
rather than calling plot() repeatedly.

Cheers!
Ben Root


On Tue, Sep 29, 2015 at 2:05 PM, Shakthi Kannan 
wrote:

> Hi,
>
> I was able to get past the error, and I am now trying to add a
> callback to receive values from a queue, add it to the existing poly
> line, and render the same using matplotlib. The code snippet is shown
> below:
>
> === BEGIN ===
>
> import matplotlib as mpl
> from mpl_toolkits.mplot3d import Axes3D
> import numpy as np
> import matplotlib.pyplot as plt
> import matplotlib.animation as animation
> import sys
> import paho.mqtt.client as mqtt
>
> def update_line(num, x, y, z, l):
> print x, y, z
> l, = ax.plot(x, y, z, label='Line')
> return l,
>
> def on_connect(client, userdata, flags, rc):
> print("Connected with result code "+str(rc))
> client.subscribe("hello/world")
>
> def on_message(client, userdata, msg):
> data = msg.payload
> print(msg.topic+" "+str(msg.payload))
> point = np.asarray([float(x) for x in data.split()])
> print point
> x=np.concatenate((x,[point[0]]))
> y=np.concatenate((y,[point[1]]))
> z=np.concatenate((z,[point[2]]))
> l, = ax.plot(x, y, z, label='Line')
> return l,
>
> fig = plt.figure()
> ax = fig.gca(projection='3d')
> ax.set_xlabel('X')
> ax.set_ylabel('Y')
> ax.set_zlabel('Z')
>
> x = np.array([1.0, 2.0, 3.0])
> print type(x)
> y = np.array([4.0, 7.0, 8.0])
> z = np.array([6.0, 9.0, 5.0])
>
> l, = ax.plot(x, y, z, label='Line')
> ax.legend()
>
> client = mqtt.Client()
> client.on_connect = on_connect
> client.on_message = on_message
> client.connect_async("localhost", 1883, 60)
> client.loop_start()
>
> line_ani = animation.FuncAnimation(fig, update_line, 25, fargs=(x, y,
> z, l), interval=2000, blit=True)
>
> plt.show()
>
> === END ===
>
> I now hit the following error:
>
> === ERROR ===
>
>  $ python mat-3.py
> 
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
>  Connected with result code 0
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
> hello/world 34.56 15.912 0.72
> [ 34.56   15.912   0.72 ]
> Exception in thread Thread-1:
> Traceback (most recent call last):
>   File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
> self.run()
>   File "/usr/lib/python2.7/threading.py", line 763, in run
> self.__target(*self.__args, **self.__kwargs)
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 2287, in _thread_main
> self.loop_forever()
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 1261, in loop_forever
> rc = self.loop(timeout, max_packets)
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 811, in loop
> rc = self.loop_read(max_packets)
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 1073, in loop_read
> rc = self._packet_read()
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 1475, in _packet_read
> rc = self._packet_handle()
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 1943, in _packet_handle
> return self._handle_publish()
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 2118, in _handle_publish
> self._handle_on_message(message)
>   File "/usr/local/lib/python2.7/dist-packages/paho/mqtt/client.py",
> line 2274, in _handle_on_message
> self.on_message(self, self._userdata, message)
>   File "mat-3.py", line 23, in on_message
> x=np.concatenate((x,[point[0]]))
> ValueError: zero-dimensional arrays cannot be concatenated
>
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
> [ 1.  2.  3.] [ 4.  7.  8.] [ 6.  9.  5.]
>
> ...
>
> === END ===
>
> Is there a better way to re-render the plot after receiving data?
>
> Thanks!
>
> SK
>
> --
> Shakthi Kannan
> http://www.shakthimaan.com
>
>
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Re: [Matplotlib-users] TypeError: can't multiply sequence by non-int of type 'float'

[Benjamin Root]

Jerzy,

On Mon, Sep 28, 2015 at 4:25 PM, Jerzy Karczmarczuk <
jerzy.karczmarc...@unicaen.fr> wrote:

>
> Le 28/09/2015 21:03, Benjamin Root a écrit :
>
>> Where does he multiply a list by a float? The traceback shows the
>> multiplication happening much further down in the draw stack.
>>
>
> Look, Benjamin Root, I don't know, and I will not "investigate" where this
> operation happens.


I did not ask you to investigate anything for me. You made the assertion
that the user was multiplying a list by a float, therefore, I assumed that
you were seeing something that I had not seen.


> The diagnosis is a standard Python message. Thus, I took the program of
> Shakhti Kannan, and in a few seconds I changed
>
>
> x = [1.0, 2.0, 3.0] into  x = np.array([1.0, 2.0, 3.0])
>
> and in update_line:   x.append(1.0)   into x=np.concatenate((x,[1.0]))
>
> And the program began to run without error messages. So, please, these are
> FACTS: somewhere the lists x,y,z get down in this draw stack.
>
>
I realize that, and that isn't in dispute. Nowhere did I say that
converting the lists into numpy arrays would not solve the problem.


> That shouldn't matter. ax.plot() accepts lists as valid inputs and it
>> should be converting them into numpy arrays under the hood.
>>
>
> There are two different issues, accepting any sequences/iterators is one,
> converting them into arrays - another one. This second operation visibly
> doesn't take place.
>
>
Of course the second operation isn't visible. I did say that it happens
"under the hood". His program is perfectly valid (albeit not ideal) and
demonstrated a bug in matplotlib's codebase. That is why I asked him to
file a bug report. My reading of your email is that you are upset for some
reason, but I have no clue why.

Ben Root
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Re: [Matplotlib-users] Fwd: bug report

[Benjamin Root]

What version of numpy do you have installed?

On Wed, Sep 16, 2015 at 5:35 AM, Bobby Wilkins 
wrote:

> OS: Windows 8.1 Pro
>
> matplotlib version: 1.4.3
>
> where obtained: http://www.lfd.uci.edu/~gohlke/pythonlibs/
>
> customizations: none
>
> Sample Program: attached py file; this is a Physics homework problem; I
> have the answers I need, but would like to fix the errors to be able to
> label all lines.
>
> Debug output in attached output.txt file
>
> If you uncomment line 180, the error is reported as if it came from that
> line even though there is no float64 on that line (savefig).  If commented,
> it does not report a line from my .py file...
>
> If you make line 170 read as follows, the error goes away:
>
> if (maxTerm<32):
>
> This suggests to me that the additional labels for the 32, 64, 128, and
> 154 term runs is what is triggering the bug, but I cannot figure out what
> it is.
>
> Also, separate note, just about any time I make figures, when closing the
> last figure I get a python.exe app crash and this message:
>
> alloc: invalid block: 044E7680: 0 d
>
>
> Thank you for any help,
> Bobby
>
>
>
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Re: [Matplotlib-users] Fwd: bug report

[Benjamin Root]

Btw, I can't reproduce the problem using matplotlib master, numpy master
and linux. I know it isn't at all similar to your setup, but it is a data
point.

On Wed, Sep 16, 2015 at 9:43 AM, Benjamin Root <ben.v.r...@gmail.com> wrote:

> What version of numpy do you have installed?
>
> On Wed, Sep 16, 2015 at 5:35 AM, Bobby Wilkins <bobby.wilk...@gmail.com>
> wrote:
>
>> OS: Windows 8.1 Pro
>>
>> matplotlib version: 1.4.3
>>
>> where obtained: http://www.lfd.uci.edu/~gohlke/pythonlibs/
>>
>> customizations: none
>>
>> Sample Program: attached py file; this is a Physics homework problem; I
>> have the answers I need, but would like to fix the errors to be able to
>> label all lines.
>>
>> Debug output in attached output.txt file
>>
>> If you uncomment line 180, the error is reported as if it came from that
>> line even though there is no float64 on that line (savefig).  If commented,
>> it does not report a line from my .py file...
>>
>> If you make line 170 read as follows, the error goes away:
>>
>> if (maxTerm<32):
>>
>> This suggests to me that the additional labels for the 32, 64, 128, and
>> 154 term runs is what is triggering the bug, but I cannot figure out what
>> it is.
>>
>> Also, separate note, just about any time I make figures, when closing the
>> last figure I get a python.exe app crash and this message:
>>
>> alloc: invalid block: 044E7680: 0 d
>>
>>
>> Thank you for any help,
>> Bobby
>>
>>
>>
>> --
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>>
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Re: [Matplotlib-users] Creating axes with fixed distance from figure edge

[Benjamin Root]

What might be more generally useful is to make it easier to specify which
coordinate system you wish some spec to apply to. To be frank, I can never
keep the transform names straight, and it isn't possible to specify it at
all in some places.
On Sep 9, 2015 6:04 PM, "Thomas Robitaille" 
wrote:

> I managed to write an Axes sub-class to do this:
>
> https://gist.github.com/astrofrog/8d579ea83e578a9cdb99
>
> Try running this then resize the figure and the margin between axes
> and figure edge will stay constant.
>
> Is this something that would be useful to have in Matplotlib itself? I
> could foresee something like:
>
> fig.add_axes([0.1, 0.1, 0.8, 0.8], preserve_absolute_margins=True)
>
> If this would be useful, I can open a pull request.
>
> Cheers,
> Tom
>
> On 9 September 2015 at 23:29, Thomas Robitaille
>  wrote:
> > Thanks Eric - unfortunately I need to be able to resize the figure
> > interactively and have the axes follow.
> >
> > So an alternative that would be equally useful for me would be to
> > specify axes using add_subplot or add_axes but then essentially have
> > an option to say that the distance to the edge of the figure should be
> > preserved when resizing. In other words, I'm not too concerned about
> > whether I specify the original axes position in relative units or in
> > inches, but the important thing is that the distance to the edge of
> > the figure stays constant in absolute terms.
> >
> > Is this something that would be easy to build as an Axes subclass?
> >
> > Cheers,
> > Tom
> >
> >
> >
> > On 9 September 2015 at 23:12, Eric Firing  wrote:
> >> On 2015/09/09 11:01 AM, Thomas Robitaille wrote:
> >>>
> >>> Hi everyone,
> >>>
> >>> I am interested in creating axes in an interactive figure where the
> >>> distance from the spines of the axes to the figure edge are constant
> >>> in absolute terms.
> >>>
> >>> To clarify what I mean, when using add_axes([0.1, 0.1, 0.8, 0.8]), the
> >>> spines of the axes are always located a distance from the edge of the
> >>> figure that is 10% of the size of the figure. However, in my case,
> >>> since the font size is constant, I want to be able to say that the
> >>> spines should always be e.g. 0.5" from the edge of the figure, which
> >>> would avoid wasting space when making the figure larger.
> >>>
> >>> Is there a way to do this currently?
> >>
> >>
> >> This is what I use for positioning in inches:
> >>
> >> def axes_inches(fig, rect, **kw):
> >> """
> >> Wrapper for Figure.add_axes in which *rect* is given in inches.
> >> The translation to normalized coordinates is done immediately
> >> based on the present figsize.
> >>
> >> *rect* is left, bottom, width, height in inches
> >> *kw* are passed to Figure.add_axes
> >>
> >> """
> >>
> >> fw = fig.get_figwidth()
> >> fh = fig.get_figheight()
> >> l, b, w, h = rect
> >> relrect = [l / fw, b / fh, w / fw, h / fh]
> >> ax = fig.add_axes(relrect, **kw)
> >> return ax
> >>
> >> Note, however, that this works correctly only if you don't change
> figsize
> >> after calling it, so maybe it is not what you are looking for.
> >>
> >> Eric
> >>
> >>>
> >>> (I am aware of set_tight_layout which would result in something
> >>> similar, but this is not what I am after - I would like to be able to
> >>> specify the exact absolute distance from the figure edge)
> >>>
> >>> Thanks!
> >>> Tom
> >>>
> >>>
> >>>
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> >>
>
>
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Re: [Matplotlib-users] Matplotlib Curve Overlapping with Animated plot

[Benjamin Root]

Thales,

Sorry for the delay in responding. This mailing list has actually moved to
https://mail.python.org/mailman/listinfo/matplotlib-users

Let's start up a new thread there with this information, plus also which
version of matplotlib you are using and which backend.

Cheers!
Ben Root


On Wed, Aug 26, 2015 at 6:12 PM, Thales Maia  wrote:

> Hello,
>
> I am migrating from octave to python and found matplotlib as an useful and
> powerful resource.
> I played with many animations examples and tried to build my own.
>
> The objective is to build a live plot from data coming from an arduino.
> The serial is working perfect (I can receive and plot data without
> problem).
>
> Unfortunately, when I resize my animation windows, I get curves
> overlapped.
>
> I must use blit because I have 6 subplots.
>
> Please, check the attached files:
> Python:
> -> animationR00.py (main)
> -> lib/
>  -> AnalogPlot.py
>  -> RingBuffer.py
>  -> crc8.py
>
> Arduino:
> Teste.cpp (main)
> Teste.h
> ComSerial.cpp
> ComSerial.h
> OneWire.cpp
> OneWire.h
> I appreciate any help.
> -
> Thales Alexandre Carvalho Maia
>
>
>
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Re: [Matplotlib-users] Plotting from a data file

[Benjamin Root]

All cbook.get_sample_data(..., asfileobj=False) does is returns the full
filename path to a given file stored in our package for demonstration
purposes. You can ignore that entirely. Just say fname = 'foobar.csv' and
have your own csv file called foobar.csv sitting in your current working
directory. plotfile() works by reading in a CSV file and plotting the
columns given. So, the CSV file will need in its first line those column
headers. The first one given will be for the x-axis, while the rest are for
the individual lines.

Does that help?
Ben Root


On Fri, Aug 14, 2015 at 1:05 PM, Kevin Parks k...@me.com wrote:

 Hi,

 That doesn’t work. Just having my own msft.csv file in my directory
 doesn't change anything as it is still pointing to some other msft.csv
 someplace on my computron. (what and where is this file?)

 I also have never opened a file this way. I had prevously just used
 something like:

 for l in open(filename).readlines():
l = l.strip().split()
data.append([float(l[0]), float(l[1]), float(l[2]), int(l[3])])

 values = [1,2,3,4]

 -

 I think ithis is just some example file that gets installed some place so
 that the examples work?

 What does asfileobj=False do?

 Goodness the whole world of Python has radically changed in the short time
 I have been out of the game.



  On Aug 15, 2015, at 1:50 AM, Christian Alis iana...@gmail.com wrote:
 
  The sample code reads data from msft.csv. If you enter your data into
  a text editor and save it as msft.csv in python's current working
  directory, then the following minimal code (pruned from plotfile_demo)
  should work:
 
  from pylab import plotfile, show, gca
  import matplotlib.cbook as cbook
 
  fname = cbook.get_sample_data('msft.csv', asfileobj=False)
 
  #test 5; single subplot
  plotfile(fname, ('date', 'open', 'high', 'low', 'close'), subplots=False)
 
  show()
 



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Re: [Matplotlib-users] [matplotlib-devel] IMPORTANT: Mailing lists are moving

[Benjamin Root]

nabble is also another fairly commonly used resource for viewing archived
discussions.

On Fri, Jul 31, 2015 at 2:14 PM, Jouni K. Seppänen j...@iki.fi wrote:

 Neal Becker ndbeck...@gmail.com writes:

  I read via gmane: I guess this will need to be updated?

 I attempted to send a message to gmane.discuss to request this, but it
 seems there is some problem with that mailing list - the latest message
 is from July 17 when viewed via NNTP, and usually there are at several
 messages per week. I have emailed the gmane.org administrator to ask
 about the status.

 --
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 http://www.iki.fi/jks



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Re: [Matplotlib-users] Matplotlib differences MacOSXAgg and others

[Benjamin Root]

We have been recently fixing a bunch of issues in the macosx backend (which
is default on Macs). Having the circle be dotted sounds exactly like the
sort of problem that would be caused by some of the bugs we are addressing.
I think we have some of the fixes committed to the master branch, so if you
could build and install from git, you can see if the problem is fixed yet
or not.

Ben Root


On Wed, Jul 15, 2015 at 10:29 AM, John Coppens j...@jcoppens.com wrote:

 Hello again,

 I've posted these two issues in separate mails, as I suspect they're
 actually different problems.

 This error is particular to the default version of MacOSX's matplotlib
 version 1.4.3:

 When doing a simple plot:

 import matplotlib.pyplot as plt

 def test_plot():
 x = range(11)
 y = [x0**2 for x0 in x]

 plt.plot(x, y, 'o:', fillstyle='none', label = 1, ms = 10)
 plt.legend()
 plt.show()

 def main(args):
 test_plot()
 return 0

 if __name__ == '__main__':
 import sys
 sys.exit(main(sys.argv))

 Much of the data is available on this thread on stackoverflow:


 http://stackoverflow.com/questions/31408928/how-can-i-plot-hollowed-symbols-connected-with-dotted-lines-in-one-go/31410105?noredirect=1#comment50794519_31410105

 The gist is that a dotted line ('o:') works correctly
 on my system (Linux Slackware/matplotlib 1.3.1 and 1.4.3), on C.C.Yang's
 Linux Mint, but not on his MacOSX (on which the _circle symbols_ are also
 dotted).

 It does work if he defines TkAgg or GtkAgg (even though he does not have
 Gtk installed on his Mac)

 Any suggestions to solve this?

 Is there a problem in the MacOSXAgg backend?

 John


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Re: [Matplotlib-users] Matplotlib 1.4.3 Agg problem

[Benjamin Root]

If your backend is set to Agg, then no interactive window will appear upon
call to show(). Agg is intended for headless servers. What might be
happening is that somewhere, you have Agg set as the default backend.

Ben Root

On Wed, Jul 15, 2015 at 10:16 AM, John Coppens j...@jcoppens.com wrote:

 Hello all.

 I had MatPlotLib 1.3.1 installed, and decided to upgrade to 1.4.3. I
 compiled the
 .tar.gz package, which went without a hitch (except for a number of
 warnings
 from gcc). Installation also completed without problems.

 But, on running the same simple plot I was working on, no plot was output:

 import matplotlib.pyplot as plt

 def test_plot():
 x = range(11)
 y = [x0**2 for x0 in x]

 plt.plot(x, y, 'o:', fillstyle='none', label = 1, ms = 10)
 plt.legend()
 plt.show()

 def main(args):
 test_plot()
 return 0

 if __name__ == '__main__':
 import sys
 sys.exit(main(sys.argv))

 which was somewhat annoying, as I was trying to help out someone on
 Stackoverflow. Only after experimenting somewhat, I found that
 setting the Agg to GtkAgg, the plot started working again:

 import matplotlib
 matplotlib.use('GtkAgg')

 Is this normal? I'm not actually using gtk in this project.
 TkAgg also works.

 John


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Re: [Matplotlib-users] Efficient matplotlib use on iOS and Android apps

[Benjamin Root]

why not use MathJax?

On Thu, Jul 9, 2015 at 8:03 AM, asiga asigan...@yahoo.com wrote:

 Hi,

 I need to render LaTeX math formulas on mobile apps (iOS/Android), with
 high
 quality, and as efficiently as possible.

 I'm considering matplotlib as the best candidate at the moment. Maybe it
 might be a bit overkill because I don't need plotting, just math formulas
 rendering, but it has a copycenter license (very welcome when you target
 iOS), and it seems to render LaTeX math with high quality. So I think it
 beats other options I found (MathGL: copyleft license; and MathJax: setting
 a complete Javascript engine just for rendering math does seem overkill to
 me).

 However, I still have some doubts before choosing matplotlib:

 1) Can I redirect the output of math rendering to OpenGL calls, or convert
 it into a 2D triangle mesh for example? (if the drawing commands issued by
 matplotlib when rendering math are a relatively small set, I can translate
 them to OpenGL myself, but I need to know where should I do that
 translation
 (I've zero idea about matplotlib internals, and I'm a Python newbie -I'm
 here because I need math rendering, not because I use Python).

 (note that I wish to render through OpenGL because I want to be able to
 interactively pan and zoom math very efficiently: the best approach would
 be
 to cache the matplotlib output as a -for example- 2D triangle mesh, and
 then
 just send the triangles to OpenGL, without having to call matplotlib on
 each
 screen redraw, which would kill performance)

 2) In order to get matplotlib running as efficient as possible on mobile
 devices, would you recommend that I translate matplotlib to C/C++ using any
 of the translators available? If affirmative, what translator would you
 suggest me to use?

 Thanks a lot!!





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Re: [Matplotlib-users] background color of text plots as foreground

[Benjamin Root]

Which backend are you using? It works fine for me with a recent-ish master
using Qt4Agg backend.

Ben Root

On Thu, Jul 9, 2015 at 6:52 AM, Mark Bakker mark...@gmail.com wrote:

 Hello list,

 I am trying to set the backgroundcolor of a textbox:

 from pylab import *
 plot([1, 2, 3])
 text(1, 2, 'Hello', backgroundcolor = 'red')

 This plots a nice red box but no text. It looks like the backgroundcolor
 is set as the foreground. Am I doing something wrong or is this a bug? mpl
 version 1.4.3

 Thanks, Mark



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Re: [Matplotlib-users] Plot : Too many ticks on X axe

[Benjamin Root]

Your code example is incomplete. Even if I add in the typical imports and
fig, ax = plt.subplots() and plt.show(), The x tick labels aren't
rotated, and I certainly don't have too many tick labels. Could you provide
a complete working example that demonstrate the problem?

Ben Root

On Wed, Jul 8, 2015 at 9:15 AM, manik971 nechmacle...@hotmail.fr wrote:

 code
 date_range = (735599.0, 735745.0)
 x = (735610.5, 735647.0, 735647.5, 735648.5, 735669.0, 735699.0, 735701.5,
 735702.5, 735709.5, 735725.5, 735728.5, 735735.5, 735736.0)
 y = (227891.25361545716, 205090.4880046467, 208352.59317388065,
 175462.99296699322, 98209.836461969651, 275063.37219361769,
 219456.93600708069, 230731.12613806152, 209043.19805037521,
 218297.51486296533, 208036.88967207001, 206311.71988471842,
 216036.56824433553)
 y0 = 218206.79192
 x_after = (735610.5, 735647.0, 735647.5, 735701.5, 735702.5, 735709.5,
 735725.5, 735728.5, 735735.5, 735736.0)
 y_after = (227891.25361545716, 205090.4880046467, 208352.59317388065,
 219456.93600708069, 230731.12613806152, 209043.19805037521,
 218297.51486296533, 208036.88967207001, 206311.71988471842,
 216036.56824433553)
 ax.plot_date(x, numpy.array(y) / y0, color='r', xdate=True, marker='x')
 linex = -39.1175584541
 liney = 28993493.5251

 ax.set_xlim(date_range)
 steps = list(ax.get_xlim())
 steps.append(steps[-1] + 2)
 steps = [steps[0] - 2] + steps
 ax.plot(steps, numpy.array([linex * a + liney for a in steps]) / y0,
 color='b')
 /code



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Re: [Matplotlib-users] Zorder and Clip_on issues

[Benjamin Root]

Which version of matplotlib? This is familiar I could have sworn we
fixed this.

Ben Root
On Jul 3, 2015 10:25 PM, Gael Grissonnanche gael.grissonnanc...@gmail.com
wrote:

 Hi everyone,



 I had recently experienced a frustration regarding zorder and clip_on in
 Matplotlib.



 In figure 1 attached here, I would like to put blue horizontal error bars
 above the x-axis. As you can see right now, half of it is cut by the x-axis
 (for the blue point at H = 0). I used:



 axes.errorbar(data[:,0], data[:,1], xerr=data[:,2], fmt='', ls =, c =
 ‘b’, capthick=2, elinewidth=2, clip_on = False, zorder = 10)



 But even if I change zorder = 1000, the error bar never goes above the
 axis. Is it a bug?



 Regarding the same topic, I also discovered that when using axes.twinx()
 in Figure 2 (A : axes; B : axes2 = axes.twinx()). The blue curve (A) never
 goes above the red curve (B), whatever zorder I use. I even tried
 axes2.set_axisbelow(True), but it doesn’t change anything. I really want
 “axes2” to be below the “axes”. Is it a bug? I had to change it manually
 with Illustrator and it worked, but it is of course really not convenient.



 Thank you very much for your help !






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Re: [Matplotlib-users] Removing a shapefile after it is loaded

[Benjamin Root]

You would need to save the artist object that is returned by
drawshapefile() in a list or something. Then, when you want to get rid of
it. you can call its `remove()` method or just do a `set_visible(False)` to
just hide it. This all requires having a reference to the artist object
itself.

Does that help?

Ben Root

On Wed, Jul 1, 2015 at 1:58 PM, Ronquillo, Edgar Nahum eronqui...@lanl.gov
wrote:

  Hello All,



 I am working with Basemap and loading several shapefiles using checkboxes
 in python. However, when I uncheck a checkbox I would like a shapefile to
 be removed and stay with the other shapefiles that are already loaded. I
 tried reloading and replotting the whole thing when I remove a checkbox but
 it will remove all the other shapefiles as well. In simpler words, is it
 possible to remove a shapefile from Basemap after m.readshapefile() has
 been called?



 Thanks in advance






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Re: [Matplotlib-users] TypeError: Dimensions of C (645, 536) are incompatible with X (538) and/or Y (646); see help(pcolormesh)

[Benjamin Root]

It looks like your X data is one element larger than it needs to be. I know
pcolor() accepts grids that are (N+1,M+1), and I *think* pcolormesh does
the same. It will also accept grids that are (N,M) as well, but will drop
the last row and collumn.

Given your statement that it sometimes works, I suspect you have a bug in
your code somewhere that is causing your Xs and Ys to not always be exactly
the length you'd expect them to be.

I hope that helps!
Ben Root


On Mon, Jun 29, 2015 at 2:06 PM, Ronquillo, Edgar Nahum eronqui...@lanl.gov
 wrote:

  Hello,

 I am getting this error when I try calling pcolormesh this way:



 pcolormesh(x, y, data.T, cmap=cmap, vmin=0, vmax=100)



 I am doing the transpose of data so I don’t know what could be causing
 this. By the way, it does work with some images. Any suggestions?



 Thanks in advance


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Re: [Matplotlib-users] get_3d_properties

[Benjamin Root]

Yeah, this is a long-standing design issue:
https://github.com/matplotlib/matplotlib/issues/1483

There are some changes that are happening that would make it possible for
me to refactor mplot3d in a way that would make this feasible. I could bite
the bullet and just provide a partial workaround to this problem by
providing a get_3d_data() method to each Artist3D subclass. Should be a
fairly easy task for someone at SciPy 2015.

On Tue, Jun 30, 2015 at 11:51 AM, kola k...@sprynt.com wrote:

 Hi,

 I am able to use set_3d_properties to set z data for my 3D line. However,
 if
 I want to get the zdata, I cannot find a function like get_zdata or
 get_3d_properites.

 Is there anyway to get the zdata associated with the line?

 Thanks,
 Kola



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Re: [Matplotlib-users] Multiple Projections On Same Axes

[Benjamin Root]

twinx()/twiny() I think is your best bet. It isn't a fully generic
solution, but I think it addresses most needs.

Ben Root

On Mon, Jun 29, 2015 at 6:00 PM, T J tjhn...@gmail.com wrote:

 When I read the transformations documentation:


 http://matplotlib.org/devel/add_new_projection.html#creating-a-new-projection

 it seems like each projection is tied to an Axes instance.  How might I go
 about plotting two different projections on the same axes? Let's just
 assume that the actual axes each projection draws is exactly same and all
 that differs between to the two is how data is mapped to axis coordinates.




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Re: [Matplotlib-users] Multiple Projections On Same Axes

[Benjamin Root]

Well, the way those work is essentially overlay one axes object over
another along with some extra fanagiling to link up the shared axis and put
ticks on opposing sides. If your projection is already available as an
axes, then you are good to go that way. However, it sounds what you want is
to have some things follow one transform while others follow another? That
is certainly doable, it is just a question of bookkeeping.

I would check to see if the axis_artist1 toolkit supplies what you need (or
at least some of it).

Ben Root


On Tue, Jun 30, 2015 at 1:20 PM, T J tjhn...@gmail.com wrote:

 Ok, sounds like I'll have to copy what those do, as I'm not planning on
 working with Cartesian or even curvilinear coordinates.

 On Tue, Jun 30, 2015 at 11:36 AM, Benjamin Root ben.r...@ou.edu wrote:

 twinx()/twiny() I think is your best bet. It isn't a fully generic
 solution, but I think it addresses most needs.

 Ben Root

 On Mon, Jun 29, 2015 at 6:00 PM, T J tjhn...@gmail.com wrote:

 When I read the transformations documentation:


 http://matplotlib.org/devel/add_new_projection.html#creating-a-new-projection

 it seems like each projection is tied to an Axes instance.  How might I
 go about plotting two different projections on the same axes? Let's just
 assume that the actual axes each projection draws is exactly same and all
 that differs between to the two is how data is mapped to axis coordinates.




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Re: [Matplotlib-users] Use _cntr.so in fortran?

[Benjamin Root]

_cntr.so has been deprecated (it might take a couple of releases before we
remove it entirely). _contour.so has a newer, better interface and comes
with a python wrapper.  Don't know if that is an issue at all for you, just
noting that is the case.

I might also suggest looking at scikit-image, as I think it has some
contouring algorithms that might be easier to link to.

Ben Root

On Thu, Jun 25, 2015 at 2:28 PM, Sterling Smith smit...@fusion.gat.com
wrote:

 The contour finder in matplotlib is more robust than I currently have in a
 legacy fortran project.  I would like to link to matplotlib’s instead.  Has
 anyone done this before?  Are there any suggestions or pitfalls for
 proceeding?

 Thanks,
 Sterling

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Re: [Matplotlib-users] zorder taking an array

[Benjamin Root]

I see what you are getting at. The issue is that artists are first sorted
by the zorder and then drawn one at a time. The draw for a collection
artist is an at-once operation, it can't (currently) be split out and
interspersed with the draws from another artist. This is one of the major
limitations for mplot3d, as it would be nice to compose a 3d scene properly
so that everything is logically consistent.

I have actually been working on some changes that would allow one to sort
the draws of individual elements of a collection, but I still haven't
figured out a way to break out the elements with other collection
elements in a way that doesn't break the current design or introduce major
performance penalties. Maybe I'll figure something out during SciPy2015.

Cheers!
Ben Root


On Tue, Jun 23, 2015 at 5:44 AM, Simon Walker s.r.walker...@googlemail.com
wrote:

 When multiple datasets are plotted on the same axis, the points overlay
 each other making it hard to see the points under the most recent ones. One
 way to avoid this is to give each point a random zorder, randomising its
 position in the z axis. This way, points from the first dataset may overly
 points from the last dataset.

 This could be achieved nicely if the zorder keyword took an array so the
 random zorder values per point can be pre-computed, but currently it only
 accepts a single number for the whole dataset. Would this be a useful
 feature for others to have? How difficult would it be to implement?

 Thanks,

 Simon Walker

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Re: [Matplotlib-users] zorder taking an array

[Benjamin Root]

Right, when zorder is not explicitly specified, all the artists of the same
type get the same default zorder (I think 2, but I can't remember). We then
use a stable sort to determine the draw order, so two artists with the same
zorder are drawn in the order that they were created (the exception being
mplot3d, because it mucks about with zorders to achieve the 3d effect).

Ben Root

On Tue, Jun 23, 2015 at 1:53 PM, Jody Klymak jkly...@uvic.ca wrote:


 For my backend (nbagg), the order of the data determines the order of
 drawing.  So in the following, the third diamond covers the first two in
 the first plot, but the first diamond covers them all in the second plot.
 Perhaps not as elegant as a matrix zorder, but can achieve the effect you
 are after.

 Cheers,   Jody

 fig, ax = plt.subplots(2,1)
 x = np.arange(3)
 y = 0.*x
 ax[0].plot(x,y,'d',markersize=52)
 ax[0].set_xlim(-10.,10.)
 ax[1].plot(x[[2,1,0]],y[[2,1,0]],'d',markersize=52)
 ax[1].set_xlim(-10.,10.)


 On Jun 23, 2015, at  9:44 AM, Benjamin Root ben.r...@ou.edu wrote:

 I see what you are getting at. The issue is that artists are first sorted
 by the zorder and then drawn one at a time. The draw for a collection
 artist is an at-once operation, it can't (currently) be split out and
 interspersed with the draws from another artist. This is one of the major
 limitations for mplot3d, as it would be nice to compose a 3d scene properly
 so that everything is logically consistent.

 I have actually been working on some changes that would allow one to sort
 the draws of individual elements of a collection, but I still haven't
 figured out a way to break out the elements with other collection
 elements in a way that doesn't break the current design or introduce major
 performance penalties. Maybe I'll figure something out during SciPy2015.

 Cheers!
 Ben Root


 On Tue, Jun 23, 2015 at 5:44 AM, Simon Walker 
 s.r.walker...@googlemail.com wrote:

 When multiple datasets are plotted on the same axis, the points overlay
 each other making it hard to see the points under the most recent ones. One
 way to avoid this is to give each point a random zorder, randomising its
 position in the z axis. This way, points from the first dataset may overly
 points from the last dataset.

 This could be achieved nicely if the zorder keyword took an array so the
 random zorder values per point can be pre-computed, but currently it only
 accepts a single number for the whole dataset. Would this be a useful
 feature for others to have? How difficult would it be to implement?

 Thanks,

 Simon Walker

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Re: [Matplotlib-users] xticks not lining up with data

[Benjamin Root]

Why are you calling ax.set_xticklabels()?. Why not pass the x values to
ax.plot() along with the y values? Then you won't need to set the labels
because matplotlib will do it for you.

Ben Root

On Wed, Jun 17, 2015 at 10:13 AM, Ted To rainexpec...@theo.to wrote:

 Hi,

 I'm having a strange problem and I don't understand why this is
 happening.  I am plotting the dataframe in: http://pastebin.com/C0Pt0iYd
 but I'm getting too few tick marks.  My code for the plot is:

   fig, ax = plt.subplots()
   plt.rc('text', usetex=True)
   fig.autofmt_xdate()
   ax.plot(indices.carli,'b-',label=r'\textsf{Carli}')
   ax.plot(indices.geomean,'g-',label=r'\textsf{GeoMean}')
   ax.plot(indices.laspeyres,'c-',label=r'\textsf{Laspeyres}')
   ax.plot(indices.paasche,'m-',label=r'\textsf{Paasche}')
   ax.plot(indices.tornqvist,'y-',label=r'\textsf{T\ornqvist}')
   plt.xlabel(r'\textsf{Month}')
   plt.ylabel(r'\textsf{Index value}')
   ax.set_xticklabels(indices.index)

 Any ideas what I'm doing wrong?

 Thanks,
 Ted


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Re: [Matplotlib-users] xticks not lining up with data

[Benjamin Root]

Then convert them to date objects? Also, I am guessing that the length of
indices.index is not the same as indices.carli, which could also be the
reason for a ValueError. So you would need to use whatever pandas variable
that indices.index derived from.

Ben Root

On Wed, Jun 17, 2015 at 12:48 PM, Ted To rainexpec...@theo.to wrote:

 Unless I recall incorrectly, I think I am using set_xticklabels because
 indices.index are strings.  When I tried specifying
 ax.plot(indices.index,indices.carli) I get a ValueError.

 Ted


 On 2015-06-17 10:28 am, Benjamin Root wrote:

 Why are you calling ax.set_xticklabels()?. Why not pass the x values
 to ax.plot() along with the y values? Then you won't need to set the
 labels because matplotlib will do it for you.

 Ben Root

 On Wed, Jun 17, 2015 at 10:13 AM, Ted To rainexpec...@theo.to wrote:

  Hi,

 I'm having a strange problem and I don't understand why this is
 happening. I am plotting the dataframe in:
 http://pastebin.com/C0Pt0iYd [1]
 but I'm getting too few tick marks. My code for the plot is:

 fig, ax = plt.subplots()
 plt.rc('text', usetex=True)
 fig.autofmt_xdate()
 ax.plot(indices.carli,'b-',label=r'textsf{Carli}')
 ax.plot(indices.geomean,'g-',label=r'textsf{GeoMean}')
 ax.plot(indices.laspeyres,'c-',label=r'textsf{Laspeyres}')
 ax.plot(indices.paasche,'m-',label=r'textsf{Paasche}')
 ax.plot(indices.tornqvist,'y-',label=r'textsf{Tornqvist}')
 plt.xlabel(r'textsf{Month}')
 plt.ylabel(r'textsf{Index value}')
 ax.set_xticklabels(indices.index)

 Any ideas what I'm doing wrong?

 Thanks,
 Ted



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Re: [Matplotlib-users] Basemap Problems

[Benjamin Root]

By the way, if you want quick-n-easy plotting of shapefiles, I suggest
using GeoPandas, which makes it dead simple.

On Mon, Jun 8, 2015 at 1:49 PM, Ronquillo, Edgar Nahum eronqui...@lanl.gov
wrote:

  Hello,
 I am currently working with Basemap to plot a shapefile on the map.
 However, I am confused on how to initialize llcrnrx and llcrnry and same
 for the upper corner. I currently have both latitudes and longitudes for
 lower and upper corners in degrees. Does this mean I have to convert from
 degrees to x,y coordinates? I tried using llcrnrlon and llcrnrlat but it
 doesn't seem to like this. Please help me clarify this, any help would be
 great.

 Thank You


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Re: [Matplotlib-users] matplotlib documentation from python notebook?

[Benjamin Root]

No, there isn't an accepted way to do that AFAIK. However, it doesn't seem
like it is all that far off. Our doc-build process will create the images
from the examples automatically, so you don't need to include the image
tag. It is sort of a way to make sure the examples work and that the image
matches the code correctly.

On Mon, Jun 8, 2015 at 1:06 PM, Jody Klymak jkly...@uvic.ca wrote:


 Hi all,

 If I want to contribute *.rst files to the matplotlib documentation, I can
 see a few styles already contributed, at least one of which makes extensive
 use of ipython (http://matplotlib.org/users/image_tutorial.html).
 However, even it makes use of `.. sourcecode:: python` and `.. plot::`
 blocks.

 If I convert an ipython notebook to rst, it formats as: `.. code:: python`
 and instead of making plots it loads images:
  `.. image:: MyExample_files/MyExample_1_0.png`

 So, is there an acceptable way to directly make matplotlib documentation
 directly from a notebook?  I didn’t see anything, but wanted to check, as
 that would by far be the easiest way to make a *.rst that had structured
 text, code, and plots.

 Thanks,   Jody

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Re: [Matplotlib-users] Fwd: [matplotlib-devel] RFC: candidates for a new default colormap

[Benjamin Root]

It is funny that you mention that you prefer the warmer colors over the
cooler colors. There has been some back-n-forth about which is better. I
personally have found myself adverse to using just cool or just warm
colors, preferring a mix of cool and warm colors. Perhaps it is my
background in meteorology and viewing temperature maps?

Another place where a mix of cool and warm colors are useful is for
severity indications such as radar maps. It is no accident that radar maps
are colored greens and blues for weak precipitation, then yellow for
heavier, and then reds for heaviest (possibly severe) precipitation -- it
came from the old FAA color guides. While we all know that that colormap is
fundamentally flawed, there was a rationale behind it.

Hopefully I will have some time today to play around with the D option. I
want to see if I can shift the curve a bit to include more yellows and
orange so that it can have a mix of cool and warm colors.

Ben Root


On Fri, Jun 5, 2015 at 11:21 AM, Philipp A. flying-sh...@web.de wrote:

 I vote for A and B. Only B if i get just one vote.

 C is too washed out and i like the warm colors more than the cold ones in
 D.

 It’s funny that this comes up while I’m handling colormaps in my own work
 at the moment.

 Neal Becker ndbeck...@gmail.com schrieb am Fr., 5. Juni 2015 um
 12:58 Uhr:

 I vote for D, although I like matlab's new default even better



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Re: [Matplotlib-users] [matplotlib-devel] RFC: candidates for a new default colormap

[Benjamin Root]

Furthermore, I think there is some work being done to add functionality to
the Norm to allow specifying a middle value along with a vmin and a vmax.

Ben Root

On Fri, Jun 5, 2015 at 3:20 PM, Eric Firing efir...@hawaii.edu wrote:

 On 2015/06/05 8:17 AM, Sourish Basu wrote:
  Very often the zero of an anomaly is not at the center of the extrema,
  and requires creating a custom diverging colormap anyway (see attached
  example).

 Reminder: in matplotlib, color mapping is done with the combination of a
 colormap and a norm.  This allows one to design a norm to handle the
 mapping, including any nonlinearity or difference between the handling
 of positive and negative values.  This is more general than customizing
 a colormap; once you have a norm to suit your purpose, you can use it
 with any colormap.

 Maybe this is actually what you are already doing, but I wanted to point
 it out here in case some readers are not familiar with this
 colormap+norm strategy.

 Eric


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Re: [Matplotlib-users] Live Scrolling Matplotlib graph

[Benjamin Root]

The plot will autoscale base on the data that has been plotted to it. In
your code, you are repeatedly calling plot(), albeit with a scrolled
version of the data, but all of the previous calls to plot() are still
visible. Also, no x-coordinate information is provided to the calls to
plot(), so each new call to plot() only overlays on top of the previous
calls.

I also see that you are using the interactive mode. This isn't really
necessary. I would suggest reading through some of the animation examples
to see how to automatically update your plot:
http://matplotlib.org/examples/animation/index.html . I would particularly
point out the animate_decay example. While it isn't a scrolling example,
you can see how to update an existing plot with new data from a generator.
It would then just be a matter of updating the x-limits for each update.

I hope that helps!
Ben Root


On Wed, Jun 3, 2015 at 12:17 PM, Alejandro Ureta 
alejandro.r.ur...@gmail.com wrote:

 Hi, I am trying to get a live scrolling graph built from data send by two
 arduino sensors. Although live data is being shown in the graph  I am not
 able to get  it scrolling. The arduino and Python codes I am working with
 are included below. I would very much appreciate if you can help me getting
 the scrolling graph working.



 PYTHON CODE:

 import serial # import Serial Library

 import numpy  # Import numpy

 import matplotlib.pyplot as plt #import matplotlib library

 from drawnow import *



 tempF= []

 pressure= []



 arduinoData = serial.Serial('com6', 115200) #Creating our serial object
 named arduinoData

 plt.ion() #Tell matplotlib you want interactive mode to plot live data

 cnt=0



 def makeFig(): #Create a function that makes our desired plot

 plt.ylim(0,500) #Set y min and max
 values

 plt.title('Frequency vs Time')  #Plot the title

 plt.grid(True)  #Turn the grid on

 plt.ylabel('Frequency (pulses/sec)')#Set
 ylabels

 plt.plot(tempF, 'ro-', label='pulses/sec')   #plot the temperature

 plt.legend(loc='upper left')#plot the legend





 plt2=plt.twinx()#Create a second y axis

 plt.ylim(0,500)   #Set limits of second y
 axis- adjust to readings you are getting

 plt2.plot(pressure, 'b^-', label='Pressure (Pa)') #plot pressure data

 plt2.set_ylabel('Pressrue (Pa)')#label second y
 axis

 plt2.ticklabel_format(useOffset=False)   #Force matplotlib to
 NOT autoscale y axis

 plt2.legend(loc='upper right')  #plot the legend





 while True: # While loop that loops forever

 while (arduinoData.inWaiting()==0): #Wait here until there is data

 pass #do nothing

 arduinoString = arduinoData.readline() #read the line of text from the
 serial port

 dataArray = arduinoString.split(',')   #Split it into an array called
 dataArray

 temp = float(dataArray[0])   #Convert first element to
 floating number and put in temp

 pres = float(dataArray[1])#Convert second element to
 floating number and put in P

 tempF.append(temp) #Build our tempF array by
 appending temp readings

 pressure.append(pres)#Building our pressure
 array by appending P readings

 drawnow(makeFig)   #Call drawnow to update our
 live graph

 plt.pause(.01) #Pause Briefly. Important to
 keep drawnow from crashing

 cnt=cnt+1

 if(cnt10):#If you have 50 or more points,
 delete the first one from the array

 tempF.pop(0)   #This allows us to just see the
 last 50 data points

 pressure.pop(0)















  ARDUINO CODE:





 #include Wire.h// imports the wire library for talking over I2C

 #include Adafruit_BMP085.h  // import the Pressure Sensor Library

 Adafruit_BMP085 mySensor;  // create sensor object called mySensor



 float tempC;  // Variable for holding temp in C

 float tempF;  // Variable for holding temp in F

 float pressure; //Variable for holding pressure reading



 void setup(){

 Serial.begin(115200); //turn on serial monitor

 mySensor.begin();   //initialize mySensor

 }



 void loop() {

 tempC = mySensor.readTemperature(); //  Be sure to declare your variables

 tempF = tempC*1.8 + 32.; // Convert degrees C to F

 pressure=mySensor.readPressure(); //Read Pressure





 Serial.print(tempF);

 Serial.print( , );

 Serial.println(pressure);

 delay(250); //Pause between readings.

 }


























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Re: [Matplotlib-users] Annotate not Drawing Properly in a Gridspec - Version 1.4.3

[Benjamin Root]

I think this is a feature/bug that got reverted in the master branch.
Perhaps you could try building matplotlib from source and seeing if the
problem goes away?

Cheers!
Ben Root

On Tue, May 26, 2015 at 3:00 PM, Sean Lake odysseus9...@gmail.com wrote:

 Sterling,

 Thanks for the pointer. I've already used a workaround where I used data
 coordinates and put it at:
 0.9 * (xmax - xmin) + xmin, and similar for y.

 I'm really only reporting this so that it can be fixed if there is someone
 who does need to annotate something in a grid.

 Sean

  On May 26, 2015, at 11:54, Sterling Smith smit...@fusion.gat.com
 wrote:
 
  Sean,
 
  Do you need an `annotate`, or just a `text`?  `text` has the `transform`
 keyword, to which you can pass `ax.transAxes`.
 
  ax.text(.9,.9, r$\mathbf{ + lab +
 )}$”,transform=ax.transAxes,ha=‘right’,va=‘center’)
 
  -Sterling
 
  On May 26, 2015, at 10:06AM, Sean Lake odysseus9...@gmail.com wrote:
 
  Hello all,
 
  I'm using matplotlib 1.4.3 installed using fink with python 2.7.
 
  I'm trying to produce a grid of plots using gridspec that has
 annotations to label each plot.
 
  Here is the call to annotate the current axes:
  ax.annotate( r$\mathbf{ + lab + )}$,
 xy=(0.5*(xmin+xmax), 0.5*(ymin+ymax)),
 xytext=(0.9, 0.9),
 textcoords=axes fraction, fontsize=14 )
 
  Where ax is initialized by:
  ax = plt.subplot(gs[ coords[0], coords[1] ])
 
  and gs by:
  gs = mpgs.GridSpec( 3, 2, wspace=0.0, hspace=0.0 )
 
  The trouble comes in when abs(ymax)  abs(ymin). When that is true, the
 labels are offset upward by one row, for some reason.
 
  I've attached a script that demonstrates the problem, and an example of
 the output. I can work around this problem by using data coordinates, but
 even so this reveals a bug somewhere.
 
  Thanks,
  Sean Lake
 
 
 BugDemo.pyBugDemo.pdf--
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Re: [Matplotlib-users] matplotlib.backends.backend_gtk3cairo memory leak

[Benjamin Root]

I take it that it doesn't happen using the GTK3Agg backend? What about the
threading portion? Does it happen if you take the threading out?

Ben Root

On Tue, May 26, 2015 at 8:23 AM, David dhug...@rapiscansystems.com wrote:

 Hi, I seem to have a memory leak while generating a 'live' plot display.
 This wasn't the case for GTK2, but the example below is consuming
 ~800k/second (Matplotlib 1.4.3, PyGI aio-3.14.0_rev18, Windows 7 x64,
 python 3.4.3). I have checked the garbage collector but it doesn't show
 anything interesting (no massive incrementing count of uncollected items).
 Anyway, I would be very grateful if somebody could confirm and/or fix this
 (or tell me what I'm doing wrong). Many thanks David Code below:

 from gi.repository import Gtk, Gdk, GLib


 from matplotlib.figure import Figure
 # Tell matplotlib to use a GTK canvas for drawing
 #from matplotlib.backends.backend_gtk3agg import FigureCanvasGTK3Agg as 
 FigureCanvas
 from matplotlib.backends.backend_gtk3cairo import FigureCanvasGTK3Cairo as 
 FigureCanvas


 # Application Class
 class pyMatPlotLibTest(object):

 def update_gui(self):
 y = [self.index] * 1024

 self.index += 1
 if self.index  1024: self.index = 0

 Gdk.threads_enter()
 self.line.set_ydata(y)
 self.axes.set_title(%d % self.index)
 self.canvas.draw()
 Gdk.threads_leave()

 return True

 def __init__(self):
 self.index = 0
 self.x = range(1024)

 # Initialise the threads system and allow threads to work with GTK
 GLib.threads_init()

 # Draw scope
 self.figure = Figure(dpi=100)
 self.canvas = FigureCanvas(self.figure)  # a Gtk.DrawingArea
 #self.widget.alignment_ScopeDisplay.add(self.canvas)

 # Draw initial scope
 self.axes = self.figure.add_subplot(111)
 self.line, = self.axes.plot(self.x, [0]* 1024)
 self.axes.set_title(None)
 self.axes.set_xbound(0.0, 1024)
 self.axes.set_ybound(-16, 1040)

 self.window_main = Gtk.Window(title=pyMatPlotLibTest)
 self.window_main.connect(destroy, lambda x: Gtk.main_quit())
 self.window_main.add(self.canvas)
 self.window_main.show_all()

 # Ticker for the update of the input state monitoring
 Gdk.threads_add_timeout(priority = GLib.PRIORITY_DEFAULT_IDLE,
 interval = 10, # msec
 function = self.update_gui)
 Gtk.main()


 if __name__ == __main__:
 gui = pyMatPlotLibTest()


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 Sent from the matplotlib - users mailing list archive
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Re: [Matplotlib-users] Plotting a imshow() image in 3d in matplotlib

[Benjamin Root]

On Tue, May 26, 2015 at 12:36 PM, Raj Kumar Manna rajphysics@gmail.com
wrote:

 import matplotlib.pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 import numpy as np

 # create a 21 x 21 vertex mesh
 xx, yy = np.meshgrid(np.linspace(0,1,21), np.linspace(0,1,21))

 # create vertices for a rotated mesh (3D rotation matrix)
 X =  xx
 Y =  yy
 Z =  10*np.ones(X.shape)

 # create some dummy data (20 x 20) for the image
 data = np.cos(xx) * np.cos(xx) + np.sin(yy) * np.sin(yy)

 # create the figure
 fig = plt.figure()

 # show the reference image
 ax1 = fig.add_subplot(121)
 ax1.imshow(data, cmap=plt.cm.BrBG, interpolation='nearest',
 origin='lower', extent=[0,1,0,1])

 # show the 3D rotated projection
 ax2 = fig.add_subplot(122, projection='3d')
 ax2.plot_surface(X, Y, Z, rstride=1, cstride=1,
 facecolors=plt.cm.BrBG(data), shade=False)



The call to imshow() without vmin/vmax arguments will automatically scale
the colormap to cover the entire range of values. Meanwhile, when you did
plt.cm.BrBG(data), it assumed that the vmin/vmax is 0 and 1, respectively.
The min and max of your data is actually 0.292 and 1.708. If you normalize
your data, it should look much more correct.

Cheers!
Ben Root
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Re: [Matplotlib-users] streamplot: vectors not pointing in the right direction!

[Benjamin Root]

The documentation for streamplot:

```
*x*, *y* : 1d arrays
an *evenly spaced* grid.
*u*, *v* : 2d arrays
x and y-velocities. Number of rows should match length of y, and
the number of columns should match x.
```

Note that the rows in *u* and *v* should match *y*, and the columns should
match *x*. I think your *u* and *v* are transposed.

Cheers!
Ben Root


On Fri, May 22, 2015 at 2:50 AM, Gabriele Brambilla 
gb.gabrielebrambi...@gmail.com wrote:

 Hi,

 I have problems with streamplot

 I want to use a 3d vector field in coordinates (x,y,z) stored in a numpy
 array, and plot slices of it with streamplot.

 To test it I wanted to use a vector field with arrows pointed up in the
 z0 region and pointed down in the z0 region.


 import numpy as np

 import matplotlib.pyplot as plt

 from math import *



 max = 100

 min = -100





 X = np.linspace(min, max, num=100)

 Y = np.linspace(min, max, num=100)

 Z = np.linspace(min, max, num=100)



 N = X.size



 #single components in the 3D matrix


 Bxa = np.zeros((N, N, N))

 Bya = np.zeros((N, N, N))

 Bza = np.zeros((N, N, N))





 for i, x in enumerate(X):

 for j, y in enumerate(Y):

 for k, z in enumerate(Z):

 Bxa[ i, j, k] = 0.0 #x

 Bya[ i, j, k] = 0.0 #y

 Bza[ i, j, k] = z



 #I take a slice close to Y=0

 Bx_sec = Bxa[:,N/2,:]

 By_sec = Bya[:,N/2,:]

 Bz_sec = Bza[:,N/2,:]



 fig = plt.figure()

 ax = fig.add_subplot(111)

 ax.streamplot(X, Z, Bx_sec, Bz_sec, color='b')

 ax.set_xlim([X.min(), X.max()])

 ax.set_ylim([Z.min(), Z.max()])



 plt.show()


 But I obtain something that looks like if I have put Bza = x! I tried to
 invert the order of vectors but it is unuseful!

 I attach the picture. Do you understand why? (the code I posted should run)

 Gabriele


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Re: [Matplotlib-users] How to plot a 2d streamline in 3d view in matplotlib

[Benjamin Root]

Well, there is the new 3D quiver feature:
http://matplotlib.org/examples/mplot3d/quiver3d_demo.html. Not quite
streamlines, but it might do in a pinch.

Another approach:
There is the 2d streamplot() function that returns a specialized object.
From the docstring:
```
Returns:

*stream_container* : StreamplotSet
Container object with attributes

- lines: `matplotlib.collections.LineCollection` of
streamlines

- arrows: collection of `matplotlib.patches.FancyArrowPatch`
  objects representing arrows half-way along stream
  lines.
```

You might be able to get away with using the lines object and feeding it
through art3d.line_collection_2d_to_3d(), kind of like how it is done for
pathpatch objects here:
http://matplotlib.org/examples/mplot3d/pathpatch3d_demo.html. You might
also be able to pass the individual objects in the arrows list through
art3d.patch_2d_to_3d(), but I have no clue if that would actually work or
not.

I hope that helps!
Ben Root


On Thu, May 21, 2015 at 7:45 AM, Raj Kumar Manna rajphysics@gmail.com
wrote:

 Hi,

 I need to plot a 2d streamline in 3d view like this
 http://stackoverflow.com/questions/14963004/continuous-shades-on-matplotlib-3d-surface.
 As suggested by the post
 http://stackoverflow.com/questions/16252231/symmetric-streamplot-with-matplotlib/16373060#16373060,
 I need to extract streamlines and arrows from a 2d plot and then transform
 it to 3d data. How to transform this 2d streamline data to 3d data and plot
 using mplot3d?

 Thanks in advance.

 Raj


 --
 ##
 Raj Kumar Manna
 Complex Fluid  Biological Physics Lab
 IIT Madras

 Ph. No. 8144637401

 alternate email: r...@physics.iitm.ac.in rajphysics@gmail.com
 


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Re: [Matplotlib-users] Fixing axes for imshow plot on top of a figure

[Benjamin Root]

I think you want figimage():
http://matplotlib.org/examples/pylab_examples/figimage_demo.html

I use it all the time for adding the company's logo to graphs. Keep in mind
that it will plot the unsampled version of the image, so the final result
depends on the figure size and resolution.

I hope that helps!
Ben Root


On Wed, May 20, 2015 at 7:43 AM, aradand arada...@gmail.com wrote:

 I'm trying to plot an image on top of a Figure, but imshow seems to always
 distort the size of the axes. What I want is that the lower part of the top
 image stay always in the same position, for any image height

 This minimal example shows my issue

 import matplotlib.pyplot as plt
 import numpy as np

 fig = plt.figure()
 ax = fig.add_axes([0.1, 0, 1, 1])

 # Top figure aligned with the bottom figure
 # keeping the same width (?)
 ax2 = fig.add_axes([0.1, 1, 1, 1])
 ax2.set_xticks([])

 # Depending on the number of rows or columns
 # the top image will be moved further to the top
 # or will be stretched if rows  columns
 # I dont know how to control this to stay always
 # with the same separation with respect
 # to the bottom figure and keeping the same width
 # (so the frame is the same width than the bottom figure)
 im = np.random.rand(10, 30)
 ax2.imshow(im)
 plt.plot()

 If it is possible to

 I would prefer to avoid using subplots or grid, since I have already
 specified a lot of things using the add_axes method.



 --
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Re: [Matplotlib-users] How to plot a 2d streamline in 3d view in matplotlib

[Benjamin Root]

Sorry, it is line_collection_2d_to_3d().

On Thu, May 21, 2015 at 12:02 PM, Raj Kumar Manna rajphysics@gmail.com
wrote:

 Its giving a error,

 art3d.linecollection_2d_to_3d(stream.lines)
 AttributeError: 'module' object has no attribute 'linecollection_2d_to_3d'



 Here is my script,


 import matplotlib.pyplot as plt
 from matplotlib.patches import Circle, PathPatch
 from mpl_toolkits.mplot3d import Axes3D
 import mpl_toolkits.mplot3d.art3d as art3d
 import numpy as np
 from pylab import *
 from matplotlib.collections import LineCollection



 fig = plt.figure()
 ax=fig.gca(projection='3d')


 f=np.loadtxt('flow-velocity343.dat')
 dx,dz=1.0,1.0

 xmin,zmin,xmax,zmax=min(f[:,0]),min(f[:,2]),max(f[:,0]),max(f[:,2])
 nbinx,nbinz=int((xmax-xmin)/dx)+1,int((zmax-zmin)/dz)+1
 Ux=np.zeros([nbinz,nbinx],'d')
 Uy=np.zeros([nbinz,nbinx],'d')
 Uz=np.zeros([nbinz,nbinx],'d')
 speed=np.zeros([nbinz,nbinx],'d')
 logv=np.zeros([nbinz,nbinx],'d')



 for f1 in f:
 binx,binz=int((f1[0]-xmin)/dx),int((f1[2]-zmin)/dz)
 Ux[binz][binx]=f1[3]
 Uy[binz][binx]=f1[4]
 Uz[binz][binx]=f1[5]
 speed[binz][binx] = np.sqrt( Ux[binz][binx]*Ux[binz][binx] +
 Uz[binz][binx]*Uz[binz][binx] + Uy[binz][binx]*Uy[binz][binx] )
 logv[binz][binx] = log(speed[binz][binx])
 x,z=np.arange(xmin,xmax+dx,dx),np.arange(zmin,zmax+dz,dz)
 y=np.arange(0,71,1)
 X,Z=np.meshgrid(x,z)

 stream = ax.streamplot(X, Z, Ux, Uz, color='black', linewidth=2)
 #lines = stream.lines.get_paths()

 art3d.linecollection_2d_to_3d(stream.lines)
 for p in stream.arrows:
 art3d.patch_2d_to_3d(p)



 plt.show()





 Thanks
 Raj


 On Thu, May 21, 2015 at 9:19 PM, Benjamin Root ben.r...@ou.edu wrote:

 (keeping the discussion on the mailing list)

 The object you get back have two attributes: lines and arrows. This
 is just psuedo-code, but it would look something like this:

 ```
 stream = ax.streamplot(..)
 art3d.linecollection_2d_to_3d(stream.lines, )
 for p in stream.arrows:
 art3d.patch_2d_to_3d(p, ...)
 ```
 Again, I have no clue if this actually would work. I haven't tried doing
 this myself.

 Ben Root

 On Thu, May 21, 2015 at 11:39 AM, Raj Kumar Manna 
 rajphysics@gmail.com wrote:

 Thanks for your quick reply.

 I have plotted the streamplot in 2d . I am not able to extract lines or
 arrow from streamplot. I am new user of matplotlib, can you please tell me
 the syntax to extract lines and arrows from streamplot().

 Thanks for you help.
 Raj

 On Thu, May 21, 2015 at 8:30 PM, Benjamin Root ben.r...@ou.edu wrote:

 Well, there is the new 3D quiver feature:
 http://matplotlib.org/examples/mplot3d/quiver3d_demo.html. Not quite
 streamlines, but it might do in a pinch.

 Another approach:
 There is the 2d streamplot() function that returns a specialized
 object. From the docstring:
 ```
 Returns:

 *stream_container* : StreamplotSet
 Container object with attributes

 - lines: `matplotlib.collections.LineCollection` of
 streamlines

 - arrows: collection of
 `matplotlib.patches.FancyArrowPatch`
   objects representing arrows half-way along stream
   lines.
 ```

 You might be able to get away with using the lines object and feeding
 it through art3d.line_collection_2d_to_3d(), kind of like how it is done
 for pathpatch objects here:
 http://matplotlib.org/examples/mplot3d/pathpatch3d_demo.html. You
 might also be able to pass the individual objects in the arrows list
 through art3d.patch_2d_to_3d(), but I have no clue if that would actually
 work or not.

 I hope that helps!
 Ben Root


 On Thu, May 21, 2015 at 7:45 AM, Raj Kumar Manna 
 rajphysics@gmail.com wrote:

 Hi,

 I need to plot a 2d streamline in 3d view like this
 http://stackoverflow.com/questions/14963004/continuous-shades-on-matplotlib-3d-surface.
 As suggested by the post
 http://stackoverflow.com/questions/16252231/symmetric-streamplot-with-matplotlib/16373060#16373060,
 I need to extract streamlines and arrows from a 2d plot and then transform
 it to 3d data. How to transform this 2d streamline data to 3d data and 
 plot
 using mplot3d?

 Thanks in advance.

 Raj


 --
 ##
 Raj Kumar Manna
 Complex Fluid  Biological Physics Lab
 IIT Madras

 Ph. No. 8144637401

 alternate email: r...@physics.iitm.ac.in rajphysics@gmail.com
 


 --
 One dashboard for servers and applications across
 Physical-Virtual-Cloud
 Widest out-of-the-box monitoring support with 50+ applications
 Performance metrics, stats and reports that give you Actionable
 Insights
 Deep dive visibility with transaction tracing using APM Insight.
 http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
 ___
 Matplotlib-users

Re: [Matplotlib-users] How to plot a 2d streamline in 3d view in matplotlib

[Benjamin Root]

(keeping the discussion on the mailing list)

The object you get back have two attributes: lines and arrows. This is
just psuedo-code, but it would look something like this:

```
stream = ax.streamplot(..)
art3d.linecollection_2d_to_3d(stream.lines, )
for p in stream.arrows:
art3d.patch_2d_to_3d(p, ...)
```
Again, I have no clue if this actually would work. I haven't tried doing
this myself.

Ben Root

On Thu, May 21, 2015 at 11:39 AM, Raj Kumar Manna rajphysics@gmail.com
wrote:

 Thanks for your quick reply.

 I have plotted the streamplot in 2d . I am not able to extract lines or
 arrow from streamplot. I am new user of matplotlib, can you please tell me
 the syntax to extract lines and arrows from streamplot().

 Thanks for you help.
 Raj

 On Thu, May 21, 2015 at 8:30 PM, Benjamin Root ben.r...@ou.edu wrote:

 Well, there is the new 3D quiver feature:
 http://matplotlib.org/examples/mplot3d/quiver3d_demo.html. Not quite
 streamlines, but it might do in a pinch.

 Another approach:
 There is the 2d streamplot() function that returns a specialized object.
 From the docstring:
 ```
 Returns:

 *stream_container* : StreamplotSet
 Container object with attributes

 - lines: `matplotlib.collections.LineCollection` of
 streamlines

 - arrows: collection of
 `matplotlib.patches.FancyArrowPatch`
   objects representing arrows half-way along stream
   lines.
 ```

 You might be able to get away with using the lines object and feeding
 it through art3d.line_collection_2d_to_3d(), kind of like how it is done
 for pathpatch objects here:
 http://matplotlib.org/examples/mplot3d/pathpatch3d_demo.html. You might
 also be able to pass the individual objects in the arrows list through
 art3d.patch_2d_to_3d(), but I have no clue if that would actually work or
 not.

 I hope that helps!
 Ben Root


 On Thu, May 21, 2015 at 7:45 AM, Raj Kumar Manna 
 rajphysics@gmail.com wrote:

 Hi,

 I need to plot a 2d streamline in 3d view like this
 http://stackoverflow.com/questions/14963004/continuous-shades-on-matplotlib-3d-surface.
 As suggested by the post
 http://stackoverflow.com/questions/16252231/symmetric-streamplot-with-matplotlib/16373060#16373060,
 I need to extract streamlines and arrows from a 2d plot and then transform
 it to 3d data. How to transform this 2d streamline data to 3d data and plot
 using mplot3d?

 Thanks in advance.

 Raj


 --
 ##
 Raj Kumar Manna
 Complex Fluid  Biological Physics Lab
 IIT Madras

 Ph. No. 8144637401

 alternate email: r...@physics.iitm.ac.in rajphysics@gmail.com
 


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 --
 ##
 Raj Kumar Manna
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 IIT Madras

 Ph. No. 8144637401

 alternate email: r...@physics.iitm.ac.in rajphysics@gmail.com
 

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Re: [Matplotlib-users] plot problem

[Benjamin Root]

I noticed in your output that another figure seems to have been created
(you see its output as matplotlib.figure.Figure at 0x1354cb70). It
would be useful to add some print statements to figure out exactly which
line is emitting that. Second, you are calling plt.savefig() in the
for-loop for the same filename. I suspect that isn't what you want. I am
going to assume that you want to save a final figure after the for-loop is
complete, right?

Also, it would be more clear to use fig.savefig() instead of the more
magical plt.savefig() as the latter would automatically create a figure
if one didn't exist for some reason.

Ben Root


On Sat, May 16, 2015 at 11:57 AM, Thomas Caswell tcasw...@gmail.com wrote:

 This is coming out of the pandas plotting tools, you might get better
 answers on their mailing list.

 Tom

 On Sat, May 16, 2015 at 11:51 AM Juan Wu wujua...@gmail.com wrote:

 Hi, List experts,

 I have a matplotlib problem when I tried to use a tool called HDDM. As
 HDDM is another issue, I here just post my problem with Matplotlib. In
 short, the error alarm appeard when I input fig = plt.figure(). I am a
 beginner with those stuff.

 I would appreciate if anyone can give me any good pointers.

 Thanks so much,
 Juan

 ==

 In [8]: fig = plt.figure()
 matplotlib.figure.Figure at 0x13293890

 In [9]: ax = fig.add_subplot(111, xlabel='RT', ylabel='count',
 title='RT distributions')

 In [10]: for i, subj_data in data.groupby('subj_idx'):
 ...: subj_data.rt.hist(bins=20, histtype='step', ax=ax)
 ...: plt.savefig('hddm_demo_fig_00.pdf')

 matplotlib.figure.Figure at 0x1354cb70
 Traceback (most recent call last):

   File ipython-input-15-3b0b3c83094c, line 2, in module
 subj_data.rt.hist(bins=20, histtype='step', ax=ax)

   File C:\Anaconda\lib\site-packages\pandas\tools\plotting.py, line
 2830, in hist_series
 raise AssertionError('passed axis not bound to passed figure')

 AssertionError: passed axis not bound to passed figure

 (relevant link:
 https://groups.google.com/forum/#!topic/hddm-users/yBeIRJaHGwo
 there very few experts view and reply questions)


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Re: [Matplotlib-users] Good line plot color cycle for colorblind readers?

[Benjamin Root]

I am a huge fan of cycling line styles in conjunction with cycling colors
in general. There is a cycler PR that achieves that goal fairly nicely:
https://github.com/matplotlib/matplotlib/pull/4258

On Fri, May 15, 2015 at 5:59 PM, Eric Firing efir...@hawaii.edu wrote:

 On 2015/05/15 11:41 AM, Nathan Goldbaum wrote:
  Hi all,
 
  This is a bit of a case of lazy mailing list, but I'm hoping there might
  be some experts here who can point me in the right direction.
 
  Does anyone know of a good resource to pull a color cycle for line plots
  that are good for color-blind readers?  I'm currently writing a paper
  that includes a number of plots that include multiple line plots in the
  same axes, and it would be nice if I'm not alienating a significant
  fraction of my readers with a poor color choice.

 You might want to cycle line types and/or thicknesses along with colors.
   You could also check out the seaborn line color palettes.

 http://stanford.edu/~mwaskom/software/seaborn/

 Eric

 
  Thanks very much for your help!
 
  -Nathan
 
 
 
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Re: [Matplotlib-users] Basemap - UTM Support

[Benjamin Root]

Nick,

Just to be clear, cartopy is intended to supersede basemap, but there are
still many advantages at the moment to basemap over cartopy. The codebase
is much more mature, and it is much easier to install than cartopy. I still
regularly use basemap because I don't need the more advanced features of
cartopy (yet).

This isn't to discourage you from cartopy, just simply to help put the
utility of the projects in the right context.

Cheers!
Ben Root


On Wed, May 13, 2015 at 6:20 PM, Nick Eubank nickeub...@gmail.com wrote:

 Thanks Don. The consensus seems to be that I need to move to Cartopy,
 which apparently supersedes Basemap.

 (Just realized the helpful responses I received weren't cc'd to the list,
 so responding here for the record).

 On Wed, May 13, 2015 at 1:47 PM Don Morton don.mor...@borealscicomp.com
 wrote:

 Hi,

 I only partially know what I'm talking about, but what the heck.  Have
 you considered pyproj (which Basemap is apparently built on)?  Pyproj seems
 to support any kind of projection you could even imagine, and a quick
 ggogle suggests UTM would be included.

 I had to learn all about this to some depth in order to teach it last
 summer to a group in Vienna, and I have slides at


 https://sites.google.com/a/borealscicomp.com/zamg-scientific-python-aug-sep-2014/home

 and if you go to course slides, 06-PlottingMetData, starting at about
 Slide 60, I have some examples which lead up to Basemap.  My intent was to
 try to get students to understand the how and why of plotting grids in
 projections, then moving on to Basemap.  This way they might have a better
 idea of how to deal with Basemap when things go wrong.  I think I just
 confused them, though :)

 At any rate, I haven't tried it, but I think it would be fairly simple to
 do what you want, IF you understand some of the low-level aspects.  But,
 maybe UTM is harder than I am imagining.

 All the best,

 Don Morton



 ---
 Don Morton, Owner/Manager
 Boreal Scientific Computing LLC
 Fairbanks, Alaska USA
 http://www.borealscicomp.com/
 http://www.borealscicomp.com/Miscellaneous/MortonBio/

 On Mon, May 11, 2015 at 4:45 PM, Nick Eubank nickeub...@gmail.com
 wrote:

 Hi All,

 Trying to move from ArcGIS into pure python GIS, but am a little
 surprised to find that UTM is not (directly) supported as a projection.
 Going through the machinations in the utmtest.py file
 https://github.com/matplotlib/basemap/blob/ee6a2f7f95b7a5eff022fcbb2800d7c50b8c97b5/examples/utmtest.py
 every time I want to plot a map in UTM seems a little unwieldy.

 Please excuse my ignorance, but is there a reason it is so hard to
 support / any plans to integrate in the future / any other easier paths to
 plotting UTMs I don't know about?

 Thanks,

 Nick


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Re: [Matplotlib-users] Cartopy install problem: this correct forum?

[Benjamin Root]

No, it isn't this list. I think it is the Iris list instead:
https://groups.google.com/forum/#!forum/scitools-iris

On Wed, May 13, 2015 at 1:06 PM, Nick Eubank nickeub...@gmail.com wrote:

 Not sure if this is the right forum; also posting to Stack Overflow (
 http://stackoverflow.com/questions/30221047/cartopy-conda-install-error-osx-library-not-loaded-rpath-libproj-0-dylib
 ). Will re-post any answers from here to SO.

 Did conda install:

 conda install -c scitools cartopy

 Seemed to go find, but now I'm getting the following error:

 import cartopy.crs as ccrs
 Traceback (most recent call last):

   File ipython-input-1-762e43a32730, line 1, in module
 import cartopy.crs as ccrs

   File 
 /Users/Nick/anaconda/lib/python2.7/site-packages/cartopy/__init__.py, line 
 110, in module
 import cartopy.crs

   File /Users/Nick/anaconda/lib/python2.7/site-packages/cartopy/crs.py, 
 line 37, in module
 from cartopy._crs import CRS, Geocentric, Geodetic, Globe, PROJ4_RELEASE
 ImportError: 
 dlopen(/Users/Nick/anaconda/lib/python2.7/site-packages/cartopy/_crs.so, 2): 
 Library not loaded: @rpath/libproj.0.dylib
   Referenced from: 
 /Users/Nick/anaconda/lib/python2.7/site-packages/cartopy/_crs.so
   Reason: image not found

 Any suggestions?

 I also tried building from source and got the same problem.

 I had a prior install of GDAL Complete, if that matters.
 Thanks!


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Re: [Matplotlib-users] getting equation from a surface-fit model

[Benjamin Root]

This question would be much more suited for the scipy mailing list.

On Fri, May 8, 2015 at 2:19 AM, diffracteD abhisek.m...@gmail.com wrote:

 Hi.
   I have a data set like following:
 x = [2.06, 2.07, 2.14, 2.09, 2.2, 2.05, 1.92, 2.06, 2.11, 2.07]
 y = [171.82, 170.8, 159.59, 164.28, 169.98, 162.23, 167.37, 173.81,166.66,
 155.13]
 z = [-1.41, -1.26, -1.07, -1.07, -1.46, -0.95, -0.08, -1.28, -1.2, -0.86]

 Using matplotlib, scipy.linalg.lstsq function I've got a surface-fit model.
 But is it possible to print the equation of the surface ??
 Found no clue in documentation page.

 Please help !
 thank you.



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Re: [Matplotlib-users] bug in zorder example

[Benjamin Root]

you can always change the zorder of the frame using set_zorder(). Are you
talking about the frame of the legend or the plotting area?

On Mon, Apr 6, 2015 at 11:23 AM, plotter plot...@trash-mail.com wrote:

 The second example on
 http://matplotlib.org/examples/pylab_examples/zorder_demo.html seems to
 expose a bug, which is clearly visible in the vector version:

 The blue curve with zorder=2 is plotted below the frame and all others with
 zorder = 3 are plotted above the frame. This is because the frame zorder
 is
 hardcoded to be 2.5. This behaviour is certainly unexpected by most users.
 How can one modify the mutual zorder of lines without conflicting with
 standard axis elements?



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Re: [Matplotlib-users] How to draw circles in logscale plots

[Benjamin Root]

A quick-n-dirty way would be to use markers via the scatter() function.
Just set the facecolor to 'none', and some very large markersize value.

Ben Root

On Wed, Apr 8, 2015 at 12:49 PM, LowDepth hagbar...@gmx.de wrote:

 Hello,

 how can I plot circles or other shapes in plots which have logarithmic
 axis?
 I have a grid of 3 plots and want to plot some kind of sketches in the
 lower
 right corner of
 each subplot. How should I do that?

 import numpy as np
 from matplotlib import pyplot as plt
 from matplotlib import gridspec

 fig = plt.figure(figsize=(6, 10))
 gs = gridspec.GridSpec(3, 1, height_ratios=[1.5, 1, 1])#, height_ratios=[2,
 1, 1])
 ax0 = plt.subplot(gs[0])
 ax1 = plt.subplot(gs[1])
 ax2 = plt.subplot(gs[2])
 plt.setp(ax_new.get_yticklabels(), visible=False)
 plt.setp(ax_new.get_xticklabels(), visible=False)
 ax_new = fig.add_axes([0,0,1,1], frameon=False,aspect=equal)
 ax_new.axes.get_yaxis().set_visible(False)
 ax_new.axes.get_xaxis().set_visible(False)
 circle1=plt.Circle((0.2,0.0),0.05, color=0.8)
 circle2=plt.Circle((0.4,0.0),0.05, color=0.8)
 ax_new.add_artist(circle1)
 ax_new.add_artist(circle2)

 ax0.semilogx(x,x**2, k-, linewidth=2)
 ax1.semilogx(x,x**3, k--, linewidth=2)
 ax2.semilogx(x,np.exp(-x)+x**4, k-., linewidth=2)
 plt.tight_layout()
 plt.show()



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Re: [Matplotlib-users] Axes3d.mouse_init(), facing problems when embedding matplotlib 3d-projection into PyQt5 App

[Benjamin Root]

.

 At last I have a good advice for you: Go and switch to using Qt Designer
 and PyQt5, it really helps having good gui's for the uninitiated.

 cheers,
 Christian

 Ps: I'll get back to you, when I'm done reading your book completely.
 --
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   On Wednesday, April 29, 2015 1:46 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 Here is a proof of concept (yes, it uses qt4... my work computer doesn't
 have qt5, but that should be a straight-forward modification to make). Note
 the complete lack of any call to mouse_init() and the complete lack of any
 use of pyplot (in fact, I commented it out to make the point that you
 shouldn't use pyplot *at all* when doing this sort of embedding).

 ```
 import numpy as np
 #import matplotlib.pyplot as plt
 import sys
 from matplotlib.backends.qt4_compat import QtGui, QtCore
 from matplotlib.figure import Figure
 from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
 FigureCanvas

 from mpl_toolkits.mplot3d import Axes3D


 if __name__ == '__main__':
 # Must come before any Qt widgets are made
 app = QtGui.QApplication(sys.argv)
 win = QtGui.QMainWindow()
 fig = Figure()
 canvas = FigureCanvas(fig)
 ax = fig.add_subplot(1, 1, 1, projection='3d')

 xs = np.random.rand(25)
 ys = np.random.rand(25)
 zs = np.random.rand(25)
 ax.scatter(xs, ys, zs)

 win.resize(int(fig.bbox.width), int(fig.bbox.height))
 win.setWindowTitle(Embedding with Qt)
 # Needed for keyboard events
 canvas.setFocusPolicy(QtCore.Qt.StrongFocus)
 canvas.setFocus()
 win.setCentralWidget(canvas)
 win.show()
 sys.exit(app.exec_())
 ```

 I hope this helps!
 Ben Root


 On Wed, Apr 29, 2015 at 5:38 AM, Christian Ambros ambr...@ymail.com
 wrote:

 Ok, back from revision...

 The is no mix-up for the show command. The only explicit show() command is
 commented out in line 41. It can be deleted. But I haven't done that, yet.
 There are several bits of code which are remains of the design process
 since this is work in progress. Code cleaning will be done when the main
 functionality is in place.

 Back to addmpl where I embedded gui elements into the canvas. Taking out
 the matplotlib taskbar doesn't change a thing as I wrote earlier, but to
 make sure it doesn't bother the mainloop, it should be commented out. I may
 not put it back in, because I don't see the point in needing it. It was
 just to see if it's possible.

 But option 2 relinquishes that control to the developer's GUI app. You
 *cannot* use pyplot for option 2, which is what you are doing.

 Is that so? In line 116 I create the canvas, which is derived from
 matplotlib's backend's FigureCanvasQTAgg and given to the QWidget at line
 119. That's the only part where both interact with each other. the rest is
 handle by matplotlib.

 The error message says that Axes3D.figure.canvas is 'None' and that's why
 mouse rotation is disabled.
 It's None because there is no content at that point, when it's passed to
 the QWidget. It's filled with content in line 38. So if matplotlib disables
 the mouse rotation by default, when the canvas is empty how do I prevent
 this disabling by default?
 If I can't, at what point do I have to pass the filled canvas to the
 QWidget? How does that impact the GUI itself?
 If I can't enable the mouse rotation by hand and I just can pass filled
 canvas around, do I have to build a work around with initialize it with an
 empty 2D canvas and replace it later with the filled 3D canvas? How's the
 mouse rotation activated then?

 In general, I wouldn't have to enable the rotation if it wouldn't be
 switch off for an empty canvas.

 I'm going to consult your book, now, for different ways of coping with
 such things...

 cheers,
 Christian

 --
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   On Tuesday, April 28, 2015 8:28 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 One thing I see off the bat is your addmpl() method:

 ```
 def addmpl(self, fig):
 #FigureCanvas.__init__(self, fig)
 self.canvas = FigureCanvas(fig)

 Axes3D.mouse_init(self, rotate_btn=1, zoom_btn=2)
 self.mplvl.addWidget(self.canvas)
 self.canvas.draw()
 self.toolbar = NavigationToolbar(self.canvas, self.mplwindow,
 coordinates=True)
 self.mplvl.addWidget(self.toolbar)
 ```

 You are calling Axes3D.mouse_init() on the Main object (that is `self`).
 That is completely wrong. It can only be called for the 3d axes objects.

 Also, what I see happening here is some mixing up of how to do embedding.
 There are two approaches to embedding. 1) you can embedded GUI elements
 into your canvas widget, or 2) you can embed your canvas widget into your
 GUI app. The important distinction between the two is who controls the
 mainloop

Re: [Matplotlib-users] Axes3d.mouse_init(), facing problems when embedding matplotlib 3d-projection into PyQt5 App

[Benjamin Root]

Here is a proof of concept (yes, it uses qt4... my work computer doesn't
have qt5, but that should be a straight-forward modification to make). Note
the complete lack of any call to mouse_init() and the complete lack of any
use of pyplot (in fact, I commented it out to make the point that you
shouldn't use pyplot *at all* when doing this sort of embedding).

```
import numpy as np
#import matplotlib.pyplot as plt
import sys
from matplotlib.backends.qt4_compat import QtGui, QtCore
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as
FigureCanvas

from mpl_toolkits.mplot3d import Axes3D


if __name__ == '__main__':
# Must come before any Qt widgets are made
app = QtGui.QApplication(sys.argv)
win = QtGui.QMainWindow()
fig = Figure()
canvas = FigureCanvas(fig)
ax = fig.add_subplot(1, 1, 1, projection='3d')

xs = np.random.rand(25)
ys = np.random.rand(25)
zs = np.random.rand(25)
ax.scatter(xs, ys, zs)

win.resize(int(fig.bbox.width), int(fig.bbox.height))
win.setWindowTitle(Embedding with Qt)
# Needed for keyboard events
canvas.setFocusPolicy(QtCore.Qt.StrongFocus)
canvas.setFocus()
win.setCentralWidget(canvas)
win.show()
sys.exit(app.exec_())
```

I hope this helps!
Ben Root


On Wed, Apr 29, 2015 at 5:38 AM, Christian Ambros ambr...@ymail.com wrote:

 Ok, back from revision...

 The is no mix-up for the show command. The only explicit show() command is
 commented out in line 41. It can be deleted. But I haven't done that, yet.
 There are several bits of code which are remains of the design process
 since this is work in progress. Code cleaning will be done when the main
 functionality is in place.

 Back to addmpl where I embedded gui elements into the canvas. Taking out
 the matplotlib taskbar doesn't change a thing as I wrote earlier, but to
 make sure it doesn't bother the mainloop, it should be commented out. I may
 not put it back in, because I don't see the point in needing it. It was
 just to see if it's possible.

 But option 2 relinquishes that control to the developer's GUI app. You
 *cannot* use pyplot for option 2, which is what you are doing.

 Is that so? In line 116 I create the canvas, which is derived from
 matplotlib's backend's FigureCanvasQTAgg and given to the QWidget at line
 119. That's the only part where both interact with each other. the rest is
 handle by matplotlib.

 The error message says that Axes3D.figure.canvas is 'None' and that's why
 mouse rotation is disabled.
 It's None because there is no content at that point, when it's passed to
 the QWidget. It's filled with content in line 38. So if matplotlib disables
 the mouse rotation by default, when the canvas is empty how do I prevent
 this disabling by default?
 If I can't, at what point do I have to pass the filled canvas to the
 QWidget? How does that impact the GUI itself?
 If I can't enable the mouse rotation by hand and I just can pass filled
 canvas around, do I have to build a work around with initialize it with an
 empty 2D canvas and replace it later with the filled 3D canvas? How's the
 mouse rotation activated then?

 In general, I wouldn't have to enable the rotation if it wouldn't be
 switch off for an empty canvas.

 I'm going to consult your book, now, for different ways of coping with
 such things...

 cheers,
 Christian

 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Tuesday, April 28, 2015 8:28 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 One thing I see off the bat is your addmpl() method:

 ```
 def addmpl(self, fig):
 #FigureCanvas.__init__(self, fig)
 self.canvas = FigureCanvas(fig)

 Axes3D.mouse_init(self, rotate_btn=1, zoom_btn=2)
 self.mplvl.addWidget(self.canvas)
 self.canvas.draw()
 self.toolbar = NavigationToolbar(self.canvas, self.mplwindow,
 coordinates=True)
 self.mplvl.addWidget(self.toolbar)
 ```

 You are calling Axes3D.mouse_init() on the Main object (that is `self`).
 That is completely wrong. It can only be called for the 3d axes objects.

 Also, what I see happening here is some mixing up of how to do embedding.
 There are two approaches to embedding. 1) you can embedded GUI elements
 into your canvas widget, or 2) you can embed your canvas widget into your
 GUI app. The important distinction between the two is who controls the
 mainloop. In option 1 (and in matplotlib in general), pyplot will create
 the GUI app for you automatically (it is completely transparent to you) and
 kicks it off upon call to show(). But option 2 relinquishes that control to
 the developer's GUI app. You *cannot* use pyplot for option 2, which is
 what you are doing. Rip out all of the pyplot stuff, and instantiate the
 Qt5 Figure object directly, and then obtain the axes objects from the
 figure object via calls to add_subplot(). You

Re: [Matplotlib-users] Axes3d.mouse_init(), facing problems when embedding matplotlib 3d-projection into PyQt5 App

[Benjamin Root]

One thing I see off the bat is your addmpl() method:

```
def addmpl(self, fig):
#FigureCanvas.__init__(self, fig)
self.canvas = FigureCanvas(fig)

Axes3D.mouse_init(self, rotate_btn=1, zoom_btn=2)
self.mplvl.addWidget(self.canvas)
self.canvas.draw()
self.toolbar = NavigationToolbar(self.canvas, self.mplwindow,
coordinates=True)
self.mplvl.addWidget(self.toolbar)
```

You are calling Axes3D.mouse_init() on the Main object (that is `self`).
That is completely wrong. It can only be called for the 3d axes objects.

Also, what I see happening here is some mixing up of how to do embedding.
There are two approaches to embedding. 1) you can embedded GUI elements
into your canvas widget, or 2) you can embed your canvas widget into your
GUI app. The important distinction between the two is who controls the
mainloop. In option 1 (and in matplotlib in general), pyplot will create
the GUI app for you automatically (it is completely transparent to you) and
kicks it off upon call to show(). But option 2 relinquishes that control to
the developer's GUI app. You *cannot* use pyplot for option 2, which is
what you are doing. Rip out all of the pyplot stuff, and instantiate the
Qt5 Figure object directly, and then obtain the axes objects from the
figure object via calls to add_subplot(). You shouldn't even need to do the
whole mouse_init() stuff.

I now think this has nothing to do with Qt Designer. While I don't
specifically cover qt5 in my book, I do make all of these distinctions very
clear in chapter 5 of my book Interactive Applications using Matplotlib.

Cheers!
Ben Root


On Tue, Apr 28, 2015 at 4:03 PM, Christian Ambros ambr...@ymail.com wrote:

 Hi Benjamin,

 I would do that if my task were my private stuff, but in this case it's
 work-related and my boss wants me to use the designer and he already set a
 deadline, which, I already knew, is set to tight. I told him before, that
 it would be just a try but he sold it to his boss after some pressure. You
 know how the bosses' bosses are, they don't get the idea that innovation
 can't be dictated. They don't understand the concept that software is
 written and doesn't come into existence out of nothing.

 Without PyQt5 it's working fine. I got the plots and they are gorgeous,
 but that doesn't help when presenting to the bosses. If I just would know
 how to activate the 3d-draw's mouse action again, by hand, than it has to
 last just some moments for the presentation, afterwards I have the time to
 examine and find a more robust solution.

 Thanks for the effort.
 cheers,
 Christian

 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Tuesday, April 28, 2015 7:30 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 I think there is something wrong with the embedding code rather than there
 being an actual bug. I have embedded mplot3d stuff before (admittedly, not
 in qt5) with no problems. I haven't had the time yet to examine your code
 to see what the potential issue is, though. I have also never used Qt
 designer, so I have no clue if there is something that it is doing that
 might be making things difficult.

 I already know that the code you originally posted has errors in it. I
 would suggest first making a prototype without Qt Designer as a
 proof-of-concept, perhaps starting with one of our examples in the gallery?

 Ben Root


 On Tue, Apr 28, 2015 at 2:12 PM, Christian Ambros ambr...@ymail.com
 wrote:

  Since there seems to be no progress with this issue, may I assume there
 isn't any interest in it?
 I took a further look around in the internet but couldn't any solution.
 It leads to an other question: How many users of matplotlib are using
 3d-plots anyway? It we are just a few and there won't be anyone who wants
 to embed it in PyQt5, than I can understand that this issue doesn't concern
 no-one and I have to look somewhere else to find a 3d-plotting lib which is
 embedable.

 cheers,
 Christain
 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Tuesday, April 21, 2015 1:44 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 The addmpl() method isn't right. You created a canvas object, assigned it
 to self.canvas, but then tried to call FigureCanvas.__init__(), passing it
 whatever object self is. What class is addmpl() a part of? What does it
 subclass?

 On Tue, Apr 21, 2015 at 7:24 AM, Christian Ambros ambr...@ymail.com
 wrote:

 Hi,

 I embedded Ryan's examble for PyQt5-matplotlib use into my App but I get
 the following error:

 /usr/local/lib/python3.4/dist-packages/mpl_toolkits/mplot3d/axes3d.py:1009:
 UserWarning: Axes3D.figure.canvas is 'None', mouse rotation disabled.  Set
 canvas then call Axes3D.mouse_init().
   warnings.warn('Axes3D.figure.canvas is \'None\', mouse rotation
 disabled.  Set canvas then call

Re: [Matplotlib-users] Axes3d.mouse_init(), facing problems when embedding matplotlib 3d-projection into PyQt5 App

[Benjamin Root]

I think there is something wrong with the embedding code rather than there
being an actual bug. I have embedded mplot3d stuff before (admittedly, not
in qt5) with no problems. I haven't had the time yet to examine your code
to see what the potential issue is, though. I have also never used Qt
designer, so I have no clue if there is something that it is doing that
might be making things difficult.

I already know that the code you originally posted has errors in it. I
would suggest first making a prototype without Qt Designer as a
proof-of-concept, perhaps starting with one of our examples in the gallery?

Ben Root


On Tue, Apr 28, 2015 at 2:12 PM, Christian Ambros ambr...@ymail.com wrote:

  Since there seems to be no progress with this issue, may I assume there
 isn't any interest in it?
 I took a further look around in the internet but couldn't any solution.
 It leads to an other question: How many users of matplotlib are using
 3d-plots anyway? It we are just a few and there won't be anyone who wants
 to embed it in PyQt5, than I can understand that this issue doesn't concern
 no-one and I have to look somewhere else to find a 3d-plotting lib which is
 embedable.

 cheers,
 Christain
 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Tuesday, April 21, 2015 1:44 PM, Benjamin Root ben.r...@ou.edu
 wrote:


 The addmpl() method isn't right. You created a canvas object, assigned it
 to self.canvas, but then tried to call FigureCanvas.__init__(), passing it
 whatever object self is. What class is addmpl() a part of? What does it
 subclass?

 On Tue, Apr 21, 2015 at 7:24 AM, Christian Ambros ambr...@ymail.com
 wrote:

 Hi,

 I embedded Ryan's examble for PyQt5-matplotlib use into my App but I get
 the following error:

 /usr/local/lib/python3.4/dist-packages/mpl_toolkits/mplot3d/axes3d.py:1009:
 UserWarning: Axes3D.figure.canvas is 'None', mouse rotation disabled.  Set
 canvas then call Axes3D.mouse_init().
   warnings.warn('Axes3D.figure.canvas is \'None\', mouse rotation
 disabled.  Set canvas then call Axes3D.mouse_init().')

 From Stackoverflow, which host to question about this, I know that mouse
 actions are disabled when the canvas is re-initialized by whatever.

 The only position I do such an operation is in here:







 *def addmpl(self, fig):self.canvas = FigureCanvas(fig)
 #FigureCanvas.__init__(self, fig)#Axes3D.mouse_init(self)
 self.mplvl.addWidget(self.canvas)self.canvas.draw()
 self.toolbar = NavigationToolbar(self.canvas, self.mplwindow,
 coordinates=True)self.mplvl.addWidget(self.toolbar)*

 On of the Stackoverflow suggestion says, that re initializing FigureCanvas
 should do the trick but I'll get:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 145, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 116, in addmpl
 FigureCanvas.__init__(self, fig)
   File
 /usr/local/lib/python3.4/dist-packages/matplotlib/backends/backend_qt5agg.py,
 line 181, in __init__
 FigureCanvasQT.__init__(self, figure)
   File
 /usr/local/lib/python3.4/dist-packages/matplotlib/backends/backend_qt5.py,
 line 237, in __init__
 super(FigureCanvasQT, self).__init__(figure=figure)
 TypeError: super(type, obj): obj must be an instance or subtype of type

 as follow-up error message.

 just using *Axes3D.mouse_init()* , as suggested by matplotlib itself,
 leads to:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 146, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 118, in addmpl
 Axes3D.mouse_init()
 TypeError: mouse_init() missing 1 required positional argument: 'self'

 adding self leads to:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 146, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 118, in addmpl
 Axes3D.mouse_init(self)
   File
 /usr/local/lib/python3.4/dist-packages/mpl_toolkits/mplot3d/axes3d.py,
 line 1002, in mouse_init
 canv = self.figure.canvas
 AttributeError: 'Main' object has no attribute 'figure'
 ./ex_0.1.py 

 Maybe I'm adding those lines at the wrong place, but I could fined
 anything useful in the matplotlib documantation, that would help me out,
 either.

 Any thougts that might help?

 Cheers,
 Christian

 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!


 --
 BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
 Develop your own process in accordance with the BPMN 2 standard
 Learn Process modeling best practices with Bonita BPM through live
 exercises
 http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual

Re: [Matplotlib-users] animation.FuncAnimation example --- how does it work?

[Benjamin Root]

The documentation should say the number, not a number. This particular
argument expects either a generator, an iterable, or an integer. If none is
given, it will try and figure out something for itself. The integer is used
to create a number generator, and so you effectively have an iterable that
supplies the first argument to the animation function.

Often times, the first argument to this function is just a frame index. It
is quite possible that you don't need it at all, but it is a part of the
defined API that the FuncAnimation assumes to be able to call the
user-supplied function.

Does that help?

Ben Root

shameless_plug
P.S. - My new book Interactive Applications using Matplotlib has an
entire chapter devoted to animations
/shameless_plug


On Thu, Apr 23, 2015 at 12:05 PM, Virgil Stokes v...@it.uu.se wrote:

  Thanks for your reply to my post, Jerzy.

 On 23-Apr-2015 13:18, Jerzy Karczmarczuk wrote:



 Le 23/04/2015 12:22, Virgil Stokes a écrit :

 The following interesting example (random_data.py) is posted at:

 http://matplotlib.org/1.4.2/examples/animation/random_data.html


 import matplotlib.pyplot as plt
 import matplotlib.animation as animation

 import numpy as np

 Yes, I forgot to include this


 fig, ax = plt.subplots()
 line, = ax.plot(np.random.rand(10))
 ax.set_ylim(0, 1)

 def update(data):
 line.set_ydata(data)
 return line,

 def data_gen():
 while True: yield np.random.rand(10)

 ani = animation.FuncAnimation(fig, update, data_gen, interval=100)
 plt.show()

 This codes works; but, I am very confused by it. For example:

 1. There are 3 positional arguments given for animation.FuncAnimation;
 but, in the
 API documentation for this class (
 http://matplotlib.org/api/animation_api.html), only
 two positional arguments are shown.

 The third one is the third one,
 *frames* can be a generator, an iterable, or a number of frames.

 This makes very little sense to me --- what does or a number of frames
 mean?

 The name data_gen could suggest its meaning (after having read the doc).

 I am not sure what you are referencing as the doc; but I did read the
 documentation several times and English is my native language.

 Note please that the keyword parameters are specified extra.

 I am aware of this.  Perhaps, I am a Python dummy --- when I see something
 like value = None in a Python API argument, I interpret this as a keyword
 argument and not a generator.


  2. data, the argument to the update function seems to be undefined.

 FuncAnimation usually passes the frame number: 0, 1, 2, ... as the first
 parameter of the update function, when frames is None, or the number of
 frames. If - as here - the third parameter is a generator, it passes the
 yielded data to update.
  It may be used or not.

 Ok, I understand that better now. But, you say or *the number* of
 frames but the documentation reads or *a number* of frames --- what
 does this mean?

 And I still do not understand how to use the first argument of the
 function to be called for the animation. In another animation example (
 histogram.py), the animation function is defined by:

 def animate(i):
 # simulate new data coming in
 data = np.random.randn(1000
 n, bins = np.histogram(data, 100)
 top = bottom + n
 verts[1::5,1] = top
 verts[2::5,1] = top

 This works of course; but, why is the i required? There is no other
 reference to it in the entire script. If I remove it; i.e. use def
 animate(): I get the following error:

 TypeError: animate() takes no arguments (1 given)

 I do not understand how this explains the fact that the function no longer
 has any arguments. Please explain the meaning of this error message?


 Please, in such cases test your programs by adding some simple tracing
 contraptions, say, print(data) inside update.

 I did this and more before posting my email. I would not have posted this
 unless I thought it was necessary. And I thought one purpose of this user
 group was to help people --- even if they ask a question which may be
 annoying or stupid in some subscribers opinion. I try to remember what a
 very wise teacher once said --- there is no such thing as a stupid
 question.


 --
 BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
 Develop your own process in accordance with the BPMN 2 standard
 Learn Process modeling best practices with Bonita BPM through live
 exercises
 http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
 event?utm_
 source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF
 ___
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Develop your own process in accordance 

Re: [Matplotlib-users] animation.FuncAnimation example --- how does it work?

[Benjamin Root]

Brendan, good catch, I didn't notice Virgil's confusion earlier. I think
that is a good explanation. I remember getting very confused by all of that
stuff back when I started in Python. I think mostly because I don't know of
any other language that does argument handling like how Python does it. I
learned it all by school-of-hard-knocks. Does anybody recommend a really
good online reference that explains the ins-and-outs of positional and
keyword arguments for newbies?

Cheers!
Ben Root


On Thu, Apr 23, 2015 at 1:00 PM, Brendan Barnwell brenb...@brenbarn.net
wrote:

 On 2015-04-23 03:22, Virgil Stokes wrote:
 
  1. There are 3 positional arguments given for animation.FuncAnimation;
  but, in the
  API documentation for this class
  (http://matplotlib.org/api/animation_api.html), only
  two positional arguments are shown.

 One thing I think may be misleading you is that you seem to be
 misunderstanding how positional and keyword arguments work in Python.
 Specifying a default value for an argument in a function definition
 doesn't mean that you can *only* pass it by keyword when you call it.
 Any named argument can always be passed positionally or by keyword (in
 Python 2).  For instance, if I define a function like this:

 def foo(a, b=2):
  print a+b

 I can still call it like this:

 foo(8, 10)

 I can even call it like this (passing both arguments as keywords out of
 order)

 foo(b=10, a=8)

 Writing b=2 in the function definition doesn't so much make b a
 keyword argument as just specify a default value for b.  So in the
 FuncAnimation documentation you mentioned, frames is not required to
 be a keyword argument, and can still be passed positionally.  (In Python
 3 there are keyword-only arguments, and even in Python 2 the variadic
 **kwargs syntax collects only keyword arguments, but those aren't
 involved as far as the frame argument here is concerned.)

 --
 Brendan Barnwell
 Do not follow where the path may lead.  Go, instead, where there is no
 path, and leave a trail.
 --author unknown


 --
 BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
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 Matplotlib-users@lists.sourceforge.net
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Re: [Matplotlib-users] animation.FuncAnimation example --- how does it work?

[Benjamin Root]

... keeping conversation on-list ...

The reason why you get that error is because you took out the argument from
the call signature. But, FuncAnimation assumes that it can send in at least
one argument. That argument is not optional, even if you aren't using it.
So, animate() was called with an argument by FuncAnimation internally, but
since animate() as defined by you did not have that argument, it fails.

Cheers!
Ben Root


On Thu, Apr 23, 2015 at 12:32 PM, Virgil Stokes v...@it.uu.se wrote:

  On 23-Apr-2015 18:25, Benjamin Root wrote:

   The documentation should say the number, not a number. This
 particular argument expects either a generator, an iterable, or an integer.
 If none is given, it will try and figure out something for itself. The
 integer is used to create a number generator, and so you effectively have
 an iterable that supplies the first argument to the animation function.

 Ok Benjamin :-)   --- thanks for the clarification.


  Often times, the first argument to this function is just a frame index.
 It is quite possible that you don't need it at all, but it is a part of the
 defined API that the FuncAnimation assumes to be able to call the
 user-supplied function.

  Does that help?

 Yes, this does indeed help. But I am still puzzled by the error message
 given when I remove the argument to the animate function.


  Ben Root

  shameless_plug
  P.S. - My new book Interactive Applications using Matplotlib has an
 entire chapter devoted to animations
  /shameless_plug


 On Thu, Apr 23, 2015 at 12:05 PM, Virgil Stokes v...@it.uu.se wrote:

  Thanks for your reply to my post, Jerzy.

 On 23-Apr-2015 13:18, Jerzy Karczmarczuk wrote:



 Le 23/04/2015 12:22, Virgil Stokes a écrit :

 The following interesting example (random_data.py) is posted at:

 http://matplotlib.org/1.4.2/examples/animation/random_data.html


 import matplotlib.pyplot as plt
 import matplotlib.animation as animation

 import numpy as np

  Yes, I forgot to include this


 fig, ax = plt.subplots()
 line, = ax.plot(np.random.rand(10))
 ax.set_ylim(0, 1)

 def update(data):
 line.set_ydata(data)
 return line,

 def data_gen():
 while True: yield np.random.rand(10)

 ani = animation.FuncAnimation(fig, update, data_gen, interval=100)
 plt.show()

 This codes works; but, I am very confused by it. For example:

 1. There are 3 positional arguments given for animation.FuncAnimation;
 but, in the
 API documentation for this class (
 http://matplotlib.org/api/animation_api.html
 http://matplotlib.org/api/animation_api.html), only
 two positional arguments are shown.

 The third one is the third one,
 *frames* can be a generator, an iterable, or a number of frames.

  This makes very little sense to me --- what does or a number of frames
 mean?

 The name data_gen could suggest its meaning (after having read the
 doc).

  I am not sure what you are referencing as the doc; but I did read the
 documentation several times and English is my native language.

 Note please that the keyword parameters are specified extra.

  I am aware of this.  Perhaps, I am a Python dummy --- when I see
 something like value = None in a Python API argument, I interpret this as a
 keyword argument and not a generator.


  2. data, the argument to the update function seems to be undefined.

 FuncAnimation usually passes the frame number: 0, 1, 2, ... as the first
 parameter of the update function, when frames is None, or the number of
 frames. If - as here - the third parameter is a generator, it passes the
 yielded data to update.
  It may be used or not.

  Ok, I understand that better now. But, you say or *the number* of
 frames but the documentation reads or *a number* of frames --- what
 does this mean?

 And I still do not understand how to use the first argument of the
 function to be called for the animation. In another animation example (
 histogram.py), the animation function is defined by:

 def animate(i):
 # simulate new data coming in
 data = np.random.randn(1000
 n, bins = np.histogram(data, 100)
 top = bottom + n
 verts[1::5,1] = top
 verts[2::5,1] = top

 This works of course; but, why is the i required? There is no other
 reference to it in the entire script. If I remove it; i.e. use def
 animate(): I get the following error:

 TypeError: animate() takes no arguments (1 given)

 I do not understand how this explains the fact that the function no
 longer has any arguments. Please explain the meaning of this error message?


 Please, in such cases test your programs by adding some simple tracing
 contraptions, say, print(data) inside update.

  I did this and more before posting my email. I would not have posted
 this unless I thought it was necessary. And I thought one purpose of this
 user group was to help people --- even if they ask a question which may be
 annoying or stupid in some subscribers opinion. I try to remember what a
 very wise teacher once said --- there is no such thing

Re: [Matplotlib-users] Axes3d.mouse_init(), facing problems when embedding matplotlib 3d-projection into PyQt5 App

[Benjamin Root]

The addmpl() method isn't right. You created a canvas object, assigned it
to self.canvas, but then tried to call FigureCanvas.__init__(), passing it
whatever object self is. What class is addmpl() a part of? What does it
subclass?

On Tue, Apr 21, 2015 at 7:24 AM, Christian Ambros ambr...@ymail.com wrote:

 Hi,

 I embedded Ryan's examble for PyQt5-matplotlib use into my App but I get
 the following error:

 /usr/local/lib/python3.4/dist-packages/mpl_toolkits/mplot3d/axes3d.py:1009:
 UserWarning: Axes3D.figure.canvas is 'None', mouse rotation disabled.  Set
 canvas then call Axes3D.mouse_init().
   warnings.warn('Axes3D.figure.canvas is \'None\', mouse rotation
 disabled.  Set canvas then call Axes3D.mouse_init().')

 From Stackoverflow, which host to question about this, I know that mouse
 actions are disabled when the canvas is re-initialized by whatever.

 The only position I do such an operation is in here:







 *def addmpl(self, fig):self.canvas = FigureCanvas(fig)
 #FigureCanvas.__init__(self, fig)#Axes3D.mouse_init(self)
 self.mplvl.addWidget(self.canvas)self.canvas.draw()
 self.toolbar = NavigationToolbar(self.canvas, self.mplwindow,
 coordinates=True)self.mplvl.addWidget(self.toolbar)*

 On of the Stackoverflow suggestion says, that re initializing FigureCanvas
 should do the trick but I'll get:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 145, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 116, in addmpl
 FigureCanvas.__init__(self, fig)
   File
 /usr/local/lib/python3.4/dist-packages/matplotlib/backends/backend_qt5agg.py,
 line 181, in __init__
 FigureCanvasQT.__init__(self, figure)
   File
 /usr/local/lib/python3.4/dist-packages/matplotlib/backends/backend_qt5.py,
 line 237, in __init__
 super(FigureCanvasQT, self).__init__(figure=figure)
 TypeError: super(type, obj): obj must be an instance or subtype of type

 as follow-up error message.

 just using *Axes3D.mouse_init()* , as suggested by matplotlib itself,
 leads to:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 146, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 118, in addmpl
 Axes3D.mouse_init()
 TypeError: mouse_init() missing 1 required positional argument: 'self'

 adding self leads to:

 Traceback (most recent call last):
   File ./ex_0.1.py, line 146, in module
 main(sys.argv)
   File ./ex_0.1.py, line 53, in main
 mainwindow.addmpl(fig1)
   File ./ex_0.1.py, line 118, in addmpl
 Axes3D.mouse_init(self)
   File
 /usr/local/lib/python3.4/dist-packages/mpl_toolkits/mplot3d/axes3d.py,
 line 1002, in mouse_init
 canv = self.figure.canvas
 AttributeError: 'Main' object has no attribute 'figure'
 ./ex_0.1.py 

 Maybe I'm adding those lines at the wrong place, but I could fined
 anything useful in the matplotlib documantation, that would help me out,
 either.

 Any thougts that might help?

 Cheers,
 Christian

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Re: [Matplotlib-users] Some questions regarding pcolor(mesh)/nbagg/FuncAnimate

[Benjamin Root]

I just noticed your use of animated=True. I have had trouble using that
in the past with the animation module. It is a leftover from the days
before the animation module and isn't actually used by it, IIRC. Try not
supplying that argument.

On Thu, Apr 16, 2015 at 8:18 AM, Ryan Nelson rnelsonc...@gmail.com wrote:

 Tom,

 Thanks for the code. As it was given, I had to change `blit=True` in the
 `FuncAnimation` call in order to get this to work in a regular Qt backend.
 It did not work with the nbagg backend; however, if I used this code it
 works fine:
 
 %matplotlib nbagg

 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.animation as animate

 class Testing(object):
 def __init__(self, ):
 self.fig = plt.figure()
 array = np.random.rand(4,5)
 array = np.zeros((4,5))
 self.pc = plt.pcolor(array, edgecolor='k', linewidth=1.)#,
 animated=True)
 self.pc.set_clim([0, 1])
 self.points = [plt.scatter(np.random.rand(), np.random.rand())]#,
 animated=True)]

 def update(self, iter_num):
 array = np.random.rand(4*5)
 self.pc.set_array(array)
 for point in self.points:
 point.set_offsets([np.random.rand(), np.random.rand()])
 #return (self.pc, ) + tuple(self.points)


 test = Testing()
 ani = animate.FuncAnimation(test.fig, test.update, interval=250,
 blit=False, frames=50)
 plt.show()
 
 Also this code solves the problem I was having with several scatter points
 being displayed upon multiple runs of the same code cell.

 I wasn't familiar with the animated keyword, and it is not well
 documented yet. Can you give me a quick explanation of what it is doing?

 Ben: thanks for the hint about the _stop() method. I might look into that
 for my example.

 Thank you all for your assistance. Things are working pretty much as I
 need now!

 Ryan

 On Sun, Apr 12, 2015 at 9:24 AM, Thomas Caswell tcasw...@gmail.com
 wrote:

 You can


 ```

 #import matplotlib

 #matplotlib.use('nbagg')

 #%matplotlib nbagg

 import numpy as np

 import matplotlib.pyplot as plt

 import matplotlib.animation as animate


 class Testing(object):

 def __init__(self, ):

 self.fig = plt.figure()

 array = np.random.rand(4,5)

 array = np.zeros((4,5))

 self.pc = plt.pcolor(array, edgecolor='k', linewidth=1.,
 animated=True)

 self.pc.set_clim([0, 1])

 self.points = [plt.scatter(np.random.rand(), np.random.rand(),
 animated=True)]


 def update(self, iter_num):

 array = np.random.rand(4*5)

 self.pc.set_array(array)

 for point in self.points:

 point.set_offsets([np.random.rand(), np.random.rand()])


 return (self.pc, ) + tuple(self.points)



 test = Testing()

 ani = animate.FuncAnimation(test.fig, test.update, interval=10,
 blit=False, frames=50)

 plt.show()

 ```

 note the addition of the `set_clim` line in the `__init__` method.


 You can also update the scatter artist in-place.  The other changes will
 make it a bit for performant if you use bliting (which does not work with
 nbagg currently)

 Sorry I missed that part of the question first time through.

 Tom

 On Sun, Apr 12, 2015, 08:31 Ryan Nelson rnelsonc...@gmail.com wrote:

 Tom,

 Thanks for the links. It does seem like fragments of my problem are
 addressed in each of those comments, so I guess I'll have to wait for a bit
 until those things get resolved. For now, I can just tell my students to
 restart the IPython kernel each time they run the animation, which isn't
 that hard. It's too bad that there isn't a 'stop' method now, but it's good
 to hear that it isn't a completely terrible idea.

 I do still need help with Question #3 from my original email, though,
 because it affects both the Qt and nbagg backends, and it is a bit of a
 show stopper. I can't quite understand why initializing a pcolor(mesh) with
 random numbers makes it possible to update the array in an animation, but
 if you use all zeros or ones, it seems to be immutable.

 Ryan

 On Sat, Apr 11, 2015 at 8:35 PM, Thomas Caswell tcasw...@gmail.com
 wrote:

 Ryan,

 I have not looked at your exact issue yet, but there seems to be some
 underlying issues with animation and nbagg which we have not tracked down
 yet. See:

 https://github.com/matplotlib/matplotlib/pull/4290
 https://github.com/matplotlib/matplotlib/issues/4287
 https://github.com/matplotlib/matplotlib/issues/4288

 Running until a given condition is an interesting idea, but I think
 that means the animation objects needs to have a public 'stop' method 
 first!

 Tom

 On Fri, Apr 10, 2015 at 3:00 PM Ryan Nelson rnelsonc...@gmail.com
 wrote:

 Good afternoon, all!

 I'm really digging the nbagg backend, and I'm trying to use it to make
 an animation. As the subject suggests, though, I'm having some issues with
 these features. I'm using Python 3.4, Matplotlib 1.4.3, and IPython 3.1.
 Below is a small code sample that 

Re: [Matplotlib-users] Qt4 Designer Example

[Benjamin Root]

That will be up to him. The only reason why I know about the work is
because our publisher wanted to make sure that our two books didn't cover
the same material. He isn't a regular on the mailing list, so I don't know
if he even would see this message. I'll let him know that there is interest.

Ben Root

On Wed, Apr 15, 2015 at 9:16 PM, Chris O'Halloran cmo...@gmail.com wrote:

 On 16 April 2015 at 09:51, Benjamin Root ben.r...@ou.edu wrote:

 A little birdie has told me that someone else is writing a new
 comprehensive matplotlib book (I think it would replace Sandros' book).
 Last I heard from the birdie, he was most of the way done with the
 manuscript. Based on my experience with the edit/review process, I would
 guess 2-3 more months to see it finished and published.


 Oh cool. I'll look out for this. Will it be advertised on this list?


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Re: [Matplotlib-users] Qt4 Designer Example

[Benjamin Root]

A little birdie has told me that someone else is writing a new
comprehensive matplotlib book (I think it would replace Sandros' book).
Last I heard from the birdie, he was most of the way done with the
manuscript. Based on my experience with the edit/review process, I would
guess 2-3 more months to see it finished and published.

Cheers!
Ben Root

On Wed, Apr 15, 2015 at 5:43 PM, Chris O'Halloran cmo...@gmail.com wrote:

 That's cool. I just found the book provided the right level of detail for
 me to start using QtDesigner with my projects.  I can't speak for PyQt5 but
 I don't see the concepts have changed much over the past 5 or so years.
 Agreed though, if you're brand new to python and are only familiar with
 python3 then typing in the code verbatim (python2 style) may cause you
 problems that frustrate the learning process.



 On 15 April 2015 at 19:49, Christian Ambros ambr...@ymail.com wrote:

 No offense, but it really is outdated. Consider that it'll take two years
 to do the writing and the lecture work the research material is form 2007
 to 2008. We now are in 2015. As you can tell from other books which have
 been published between 2013 and a really helpy book from March, 24th 2015
 (yes, Benjamin Root wrote it), even they don't cover latest enhancements up
 to six month before print, (which might be seen a reasonable since changing
 is easy in a digitized world like ours).
 A good tutorial for the once, who do not have much experience in this
 field (I count myself in with the just one and a half year of experience in
 gui programming) is two things, actual up to six month to a year and
 straight forward, meaning It tells you what to do and doesn't bother you
 with design thoughts, API explanations nor tries to teach you programming.
 I have that book in my possession, but it didn't turn out to be helpful
 if you do not have the time do read it in whole. If you have the time to
 spin freely, you still will have conquered 80% by yourself and because it
 is still outdated for pyhton3 and matplotlib 1.4.3 the use is questionable.

 cheers,
 Christian

 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Wednesday, April 15, 2015 3:44 AM, Chris O'Halloran 
 cmo...@gmail.com wrote:


 Can I recommend this book.  It was very helpful to me in figuring much of
 this out.


 https://www.packtpub.com/application-development/matplotlib-python-developers

 On 14 April 2015 at 18:14, Christian Ambros ambr...@ymail.com wrote:

 Hi Ryan,

 wow! This tutorial is one of the best I ever encountered. Nothing is
 missing, nothing is cryptic or unclear. What I like best is, that it get's
 along without using Qt Designer plugins or something similar strange. It's
 a good basis to start. Maybe you should write a book, covering all the
 untold things one needs to solve problems like that. I browsed through
 plenty of books the last weeks and what really is missing, is a cookbook
 about Qt Designer, Glade and wxWidgets and how to fill it with python3 and
 it's lib's like matplotlib, pyqtgraph, numpy, sympy etc.

 I would buy it right away!
 cheers,
 Christian

 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Friday, April 10, 2015 7:14 PM, Ryan Nelson rnelsonc...@gmail.com
 wrote:


 Christian,

 As it turns out, I wrote a blog post (for my terrible blog) about using
 Designer to create a MPL based GUI (
 http://blog.rcnelson.com/building-a-matplotlib-gui-with-qt-designer-part-1/).
 I was going to write this up for the MPL docs... But it got really long (3
 parts), so I just used my personal site. It got so long because this was
 the second time I needed to figure this out, and I wanted to make a very
 detailed outline for my own future reference. Unfortunately, I don't have
 any experience with Qt5, but I imagine things are similar. I think they
 just rearranged the locations of some of the widgets, but I'd be curious to
 hear your experience. I gave up on PyQtdesignerplugins. I think it makes
 more sense to just use a generic widget as the MPL container.

 I would be very happy if you had comments for my Qt designer posts.

 Ryan

 On Wed, Apr 8, 2015 at 5:47 AM, Christian Ambros ambr...@ymail.com
 wrote:

 Hi Ryan,

 could you write down, as a tutorial, how you built the example with the
 qt designer?
 In the last hours I read all most everything what can be found on the
 issue of getting matplotlib running with pyqt5 and the designer but as you
 realized yourself, there is little to be found handy.

 I'm stuck at a project, which has to use python3, and pyqt5 and am not
 allowed by my boss to fall back to pyqt4 or qt_compat. He wants to make
 sure that we use the latest revisions.

 So I#m very pleased to read that someone already set food on this
 terrain.
 Qt5.4.1 is running and I installed PyQtdesingerplugins, in mind

Re: [Matplotlib-users] Some questions regarding pcolor(mesh)/nbagg/FuncAnimate

[Benjamin Root]

animation objects have a private _stop() method. That might have to be a
workaround.

On Sun, Apr 12, 2015 at 9:24 AM, Thomas Caswell tcasw...@gmail.com wrote:

 You can


 ```

 #import matplotlib

 #matplotlib.use('nbagg')

 #%matplotlib nbagg

 import numpy as np

 import matplotlib.pyplot as plt

 import matplotlib.animation as animate


 class Testing(object):

 def __init__(self, ):

 self.fig = plt.figure()

 array = np.random.rand(4,5)

 array = np.zeros((4,5))

 self.pc = plt.pcolor(array, edgecolor='k', linewidth=1.,
 animated=True)

 self.pc.set_clim([0, 1])

 self.points = [plt.scatter(np.random.rand(), np.random.rand(),
 animated=True)]


 def update(self, iter_num):

 array = np.random.rand(4*5)

 self.pc.set_array(array)

 for point in self.points:

 point.set_offsets([np.random.rand(), np.random.rand()])


 return (self.pc, ) + tuple(self.points)



 test = Testing()

 ani = animate.FuncAnimation(test.fig, test.update, interval=10,
 blit=False, frames=50)

 plt.show()

 ```

 note the addition of the `set_clim` line in the `__init__` method.


 You can also update the scatter artist in-place.  The other changes will
 make it a bit for performant if you use bliting (which does not work with
 nbagg currently)

 Sorry I missed that part of the question first time through.

 Tom

 On Sun, Apr 12, 2015, 08:31 Ryan Nelson rnelsonc...@gmail.com wrote:

 Tom,

 Thanks for the links. It does seem like fragments of my problem are
 addressed in each of those comments, so I guess I'll have to wait for a bit
 until those things get resolved. For now, I can just tell my students to
 restart the IPython kernel each time they run the animation, which isn't
 that hard. It's too bad that there isn't a 'stop' method now, but it's good
 to hear that it isn't a completely terrible idea.

 I do still need help with Question #3 from my original email, though,
 because it affects both the Qt and nbagg backends, and it is a bit of a
 show stopper. I can't quite understand why initializing a pcolor(mesh) with
 random numbers makes it possible to update the array in an animation, but
 if you use all zeros or ones, it seems to be immutable.

 Ryan

 On Sat, Apr 11, 2015 at 8:35 PM, Thomas Caswell tcasw...@gmail.com
 wrote:

 Ryan,

 I have not looked at your exact issue yet, but there seems to be some
 underlying issues with animation and nbagg which we have not tracked down
 yet. See:

 https://github.com/matplotlib/matplotlib/pull/4290
 https://github.com/matplotlib/matplotlib/issues/4287
 https://github.com/matplotlib/matplotlib/issues/4288

 Running until a given condition is an interesting idea, but I think that
 means the animation objects needs to have a public 'stop' method first!

 Tom

 On Fri, Apr 10, 2015 at 3:00 PM Ryan Nelson rnelsonc...@gmail.com
 wrote:

 Good afternoon, all!

 I'm really digging the nbagg backend, and I'm trying to use it to make
 an animation. As the subject suggests, though, I'm having some issues with
 these features. I'm using Python 3.4, Matplotlib 1.4.3, and IPython 3.1.
 Below is a small code sample that emulates my system. The pcolor call can
 be substituted for pcolormesh, and I see the same behavior. (Sorry this is
 a bit long. I tried to break it up as best as possible.)

 #
 #import matplotlib
 #matplotlib.use('nbagg')
 #%matplotlib nbagg
 import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.animation as animate

 class Testing(object):
 def __init__(self, ):
 self.fig = plt.figure()
 array = np.random.rand(4,5)
 #array = np.zeros((4,5))
 self.pc = plt.pcolor(array, edgecolor='k', linewidth=1.)
 self.points = [plt.scatter(np.random.rand(), np.random.rand())]

 def update(self, iter_num):
 array = np.random.rand(4*5)
 self.pc.set_array(array)
 for point in self.points:
 point.remove()
 self.points = [plt.scatter(np.random.rand(), np.random.rand())]

 test = Testing()
 animate.FuncAnimation(test.fig, test.update, interval=1000, blit=False)
 plt.show()
 ###

 1. As is, this code runs fine with a Qt backend. It also runs fine as a
 first call in a notebook if the `show` call is commented out and the
 `%matplotlib` line is uncommented. However, if the `show` call is left in
 and the `matplotlib.use` call is uncommented, then the pcolor array
 changes, but the scatterpoint only shows on the first update and then
 disappears forever. What is the difference between these two invocations?

 2. With the `%matplotlib` magic uncommented and `show` removed, the
 first invocation of this as a cell works fine. Closing the figure (with the
 red X) and running the cell again shows two scatter plot points. Running it
 a third time shows three scatter plot points. If you call `plt.clf` in the
 next cell, I get a series of errors as follows:
 _
 

Re: [Matplotlib-users] Color Bar Limits

[Benjamin Root]

No, that's not what he is asking for. John wants the norm to go from -1 to
4, but he wants the colorbar to display only the 0 to 4 portion. Your
approach (setting vmin=0) would change the normalization and change the
colors.

The axes limits do not appear to be scaled by the values. They are set to
(0, 1). So, the kludgy way would seem to be to set the xlimits to be (0.2,
1) (taking out a fifth of the colorbar, but the frame is still there...

Ben Root

On Thu, Apr 2, 2015 at 12:32 PM, Jody Klymak jkly...@uvic.ca wrote:

 Hi John,

 I got this off stack exchange, apologies to the original contributor...

 Cheers,   Jody


 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.colors import LinearSegmentedColormap

 x = np.arange(100)
 y = np.random.rand(100)
 z = 4 * np.random.rand(100)

 cmap = plt.get_cmap('rainbow_r’)
 start=0.2
 stop = 1.
 colors = cmap(np.linspace(start, stop, cmap.N))
 # Create a new colormap from those colors
 color_map = LinearSegmentedColormap.from_list('Upper Half', colors)

 fig = plt.figure(figsize=(12,9))
 ax1 = plt.subplot(111)
 sc = ax1.scatter(x, y, c=z, s=50, cmap=color_map, vmin=0, vmax=4)

 position=fig.add_axes([0.37, 0.16, 0.5, 0.02])
 cb = fig.colorbar(sc, cax=position, orientation='horizontal',
 drawedges=False)
 cb.set_label('Z-Colors', fontsize=14)

 # I tried this after talking with Ben Root, but it
 # results in some odd behavior
 # cb.ax.set_xlim(0,4)

 plt.show()



 On 2 Apr 2015, at  5:47 AM, John Leeman kd5...@gmail.com wrote:

 Hi all,

 I’m plotting some scatter points colored by a third variable, but want to
 use a limited subset of a colormap. In the example below, the color axis
 data ranges from 0-4, but I want to not use the red portion of the bar.
 Doing the first part is just accomplished by setting the vmin/vmax. But
 when I plot a color bar I don’t want to show the colors and values for
 anything below zero. Other than just white-boxing that part of the bar I’m
 not sure how to do it. I tried a suggestion of setting the limit properties
 of the bar axis attribute, but that results in the bar getting shrunk and
 shifted (a very weird behavior). Any ideas?

 Thank you,

 John Leeman

 import numpy as np
 import matplotlib.pyplot as plt

 x = np.arange(100)
 y = np.random.rand(100)
 z = 4 * np.random.rand(100)

 color_map = plt.get_cmap('rainbow_r')

 fig = plt.figure(figsize=(12,9))
 ax1 = plt.subplot(111)
 sc = ax1.scatter(x, y, c=z, s=50, cmap=color_map, vmin=-1, vmax=4)

 position=fig.add_axes([0.37, 0.16, 0.5, 0.02])
 cb = fig.colorbar(sc, cax=position, orientation='horizontal',
 drawedges=False)
 cb.set_label('Z-Colors’, fontsize=14)

 # I tried this after talking with Ben Root, but it
 # results in some odd behavior
 # cb.ax.set_xlim(0,4)

 plt.show()
 Color_Bar.png

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 http://web.uvic.ca/~jklymak/







 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
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 news, videos, case studies, tutorials and more. Take a look and join the
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 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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Re: [Matplotlib-users] Color Bar Limits

[Benjamin Root]

::Looks again::

Ok, I see what you did here:

cmap = plt.get_cmap('rainbow_r’)
start=0.2
stop = 1.
colors = cmap(np.linspace(start, stop, cmap.N))
# Create a new colormap from those colors
color_map = LinearSegmentedColormap.from_list('Upper Half', colors)

I missed this part the first time through, noticing only the change to the
vmin. Yeah, I think that would work just fine. Sorry for the confusion.

Cheers!
Ben Root


On Thu, Apr 2, 2015 at 12:56 PM, Jody Klymak jkly...@uvic.ca wrote:



 On 2 Apr 2015, at  9:50 AM, Benjamin Root ben.r...@ou.edu wrote:

 No, that's not what he is asking for. John wants the norm to go from -1 to
 4, but he wants the colorbar to display only the 0 to 4 portion. Your
 approach (setting vmin=0) would change the normalization and change the
 colors.


 Hmm, well his values go from 0 to 4, and he wants his colorbar to go from
 0 to 4, but just over the last 4/5ths of the colormap.  I think I gave him
 what he wants.  But I guess he can decide!

 Cheers,   Jody

 The axes limits do not appear to be scaled by the values. They are set to
 (0, 1). So, the kludgy way would seem to be to set the xlimits to be (0.2,
 1) (taking out a fifth of the colorbar, but the frame is still there...

 Ben Root

 On Thu, Apr 2, 2015 at 12:32 PM, Jody Klymak jkly...@uvic.ca wrote:

 Hi John,

 I got this off stack exchange, apologies to the original contributor...

 Cheers,   Jody


 import numpy as np
 import matplotlib.pyplot as plt
 from matplotlib.colors import LinearSegmentedColormap

 x = np.arange(100)
 y = np.random.rand(100)
 z = 4 * np.random.rand(100)

 cmap = plt.get_cmap('rainbow_r’)
 start=0.2
 stop = 1.
 colors = cmap(np.linspace(start, stop, cmap.N))
 # Create a new colormap from those colors
 color_map = LinearSegmentedColormap.from_list('Upper Half', colors)

 fig = plt.figure(figsize=(12,9))
 ax1 = plt.subplot(111)
 sc = ax1.scatter(x, y, c=z, s=50, cmap=color_map, vmin=0, vmax=4)

 position=fig.add_axes([0.37, 0.16, 0.5, 0.02])
 cb = fig.colorbar(sc, cax=position, orientation='horizontal',
 drawedges=False)
 cb.set_label('Z-Colors', fontsize=14)

 # I tried this after talking with Ben Root, but it
 # results in some odd behavior
 # cb.ax.set_xlim(0,4)

 plt.show()



 On 2 Apr 2015, at  5:47 AM, John Leeman kd5...@gmail.com wrote:

 Hi all,

 I’m plotting some scatter points colored by a third variable, but want to
 use a limited subset of a colormap. In the example below, the color axis
 data ranges from 0-4, but I want to not use the red portion of the bar.
 Doing the first part is just accomplished by setting the vmin/vmax. But
 when I plot a color bar I don’t want to show the colors and values for
 anything below zero. Other than just white-boxing that part of the bar I’m
 not sure how to do it. I tried a suggestion of setting the limit properties
 of the bar axis attribute, but that results in the bar getting shrunk and
 shifted (a very weird behavior). Any ideas?

 Thank you,

 John Leeman

 import numpy as np
 import matplotlib.pyplot as plt

 x = np.arange(100)
 y = np.random.rand(100)
 z = 4 * np.random.rand(100)

 color_map = plt.get_cmap('rainbow_r')

 fig = plt.figure(figsize=(12,9))
 ax1 = plt.subplot(111)
 sc = ax1.scatter(x, y, c=z, s=50, cmap=color_map, vmin=-1, vmax=4)

 position=fig.add_axes([0.37, 0.16, 0.5, 0.02])
 cb = fig.colorbar(sc, cax=position, orientation='horizontal',
 drawedges=False)
 cb.set_label('Z-Colors’, fontsize=14)

 # I tried this after talking with Ben Root, but it
 # results in some odd behavior
 # cb.ax.set_xlim(0,4)

 plt.show()
 Color_Bar.png

 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
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 for all
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 news, videos, case studies, tutorials and more. Take a look and join the
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 Matplotlib-users mailing list
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 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


 --
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 http://web.uvic.ca/~jklymak/







 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub
 for all
 things parallel software development, from weekly thought leadership
 blogs to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
 ___
 Matplotlib-users mailing list
 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users



 --
 Jody Klymak
 http://web.uvic.ca/~jklymak

Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

Actually, look at the traceback... it is using distutils' version.py.
That's weird. Is that a result of setuptools monkey-patching?

On Wed, Apr 1, 2015 at 9:25 AM, Jens Nielsen jenshniel...@gmail.com wrote:

 I think we have seen this issue before and it seems to be caused by an out
 of date version of setuptools. I tried reproducing it on fresh ubuntu 14.04
 machine but was not able to reproduce the issue. Do you know which version
 of setuptools you are using?

 Jens

 ons. 1. apr. 2015 kl. 14.19 skrev Thomas Caswell tcasw...@gmail.com:

 Make sure you have `freetype-dev` installed at the system level.

 Tom

 On Wed, Apr 1, 2015 at 8:02 AM Christian Ambros ambr...@ymail.com
 wrote:

 Hi,

 I'm facing the same trouble with installing matplotlib 1.4.3 and
 1.5.dev1. running

 python3 setup.py build

 in the unarchived directory gives this:

 
 Edit setup.cfg to change the build options

 BUILDING MATPLOTLIB
 matplotlib: yes [1.5.dev1]
 python: yes [3.4.0 (default, Apr 11 2014, 13:05:11)  [GCC
 4.8.2]]
   platform: yes [linux]

 REQUIRED DEPENDENCIES AND EXTENSIONS
  numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
   dateutil: yes [using dateutil version 2.0]
   pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
  pyparsing: yes [using pyparsing version 2.0.1]
 libagg: yes [Requires patches that have not been merged
 upstream. Using local copy.]
 Traceback (most recent call last):
   File setup.py, line 153, in module
 result = package.check()
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 900, in check
 min_version='2.3', version=version)
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 446, in _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 173, in is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 I'm running Linux Mint 17 Quina which is based on Ubuntu's trusty
 packges.

 pip3 is up to date. Running
 print(setuptools.__file__)

 gives: /usr/local/lib/python3.4/dist-packages/setuptools/__init__.py
 which is as expected.

 Using pip3 install matplotlib --upgrade #even to 1.4.3
 get's me this:


 Collecting matplotlib from
 https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.3.tar.gz#md5=86af2e3e3c61849ac7576a6f5ca44267
   Downloading matplotlib-1.4.3.tar.gz (50.4MB)
 100% || 50.4MB 8.0kB/s
 Traceback (most recent call last):
   File string, line 20, in module
   File /tmp/pip-build-sezmzam8/matplotlib/setup.py, line 155, in
 module
 result = package.check()
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 961,
 in check
 min_version='2.3', version=version)
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 445,
 in _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 173,
 in is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 
 Edit setup.cfg to change the build options
 BUILDING MATPLOTLIB
 matplotlib: yes [1.4.3]
 python: yes [3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC
 4.8.2]]
   platform: yes [linux]
 REQUIRED DEPENDENCIES AND EXTENSIONS
  numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
   dateutil: yes [using dateutil version 2.0]
   pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
  pyparsing: yes [using pyparsing version 2.0.1]
  pycxx: yes [Official versions of PyCXX are not
 compatible
 with matplotlib on Python 3.x, since they
 lack
 support for the buffer object.  Using local
 copy]
 libagg: yes [Requires patches that have not been
 merged
 upstream. Using local copy.]
 

Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

Good point. At least put up a decent message to help users understand what
is wrong.

On Wed, Apr 1, 2015 at 9:57 AM, Thomas Caswell tcasw...@gmail.com wrote:

 Independent of what exactly is going wrong, the issue is that it _isn't_
 finding the right version of freetype and iirc LooseVersion is handling the
 'not found' return code badly.  This is coming up often enough we probably
 do need to special case this check with a try/except.

 On Wed, Apr 1, 2015 at 9:50 AM Benjamin Root ben.r...@ou.edu wrote:

 Actually, look at the traceback... it is using distutils' version.py.
 That's weird. Is that a result of setuptools monkey-patching?

 On Wed, Apr 1, 2015 at 9:25 AM, Jens Nielsen jenshniel...@gmail.com
 wrote:

 I think we have seen this issue before and it seems to be caused by an
 out of date version of setuptools. I tried reproducing it on fresh ubuntu
 14.04 machine but was not able to reproduce the issue. Do you know which
 version of setuptools you are using?

 Jens

 ons. 1. apr. 2015 kl. 14.19 skrev Thomas Caswell tcasw...@gmail.com:

 Make sure you have `freetype-dev` installed at the system level.

 Tom

 On Wed, Apr 1, 2015 at 8:02 AM Christian Ambros ambr...@ymail.com
 wrote:

 Hi,

 I'm facing the same trouble with installing matplotlib 1.4.3 and
 1.5.dev1. running

 python3 setup.py build

 in the unarchived directory gives this:

 
 Edit setup.cfg to change the build options

 BUILDING MATPLOTLIB
 matplotlib: yes [1.5.dev1]
 python: yes [3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC
 4.8.2]]
   platform: yes [linux]

 REQUIRED DEPENDENCIES AND EXTENSIONS
  numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
   dateutil: yes [using dateutil version 2.0]
   pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
  pyparsing: yes [using pyparsing version 2.0.1]
 libagg: yes [Requires patches that have not been merged
 upstream. Using local copy.]
 Traceback (most recent call last):
   File setup.py, line 153, in module
 result = package.check()
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 900, in check
 min_version='2.3', version=version)
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 446, in _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line
 173, in is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 I'm running Linux Mint 17 Quina which is based on Ubuntu's trusty
 packges.

 pip3 is up to date. Running
 print(setuptools.__file__)

 gives: /usr/local/lib/python3.4/dist-packages/setuptools/__init__.py
 which is as expected.

 Using pip3 install matplotlib --upgrade #even to 1.4.3
 get's me this:


 Collecting matplotlib from
 https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.3.tar.gz#md5=86af2e3e3c61849ac7576a6f5ca44267
   Downloading matplotlib-1.4.3.tar.gz (50.4MB)
 100% || 50.4MB 8.0kB/s
 Traceback (most recent call last):
   File string, line 20, in module
   File /tmp/pip-build-sezmzam8/matplotlib/setup.py, line 155, in
 module
 result = package.check()
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 961,
 in check
 min_version='2.3', version=version)
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 445,
 in _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 173,
 in is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in
 __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 
 Edit setup.cfg to change the build options
 BUILDING MATPLOTLIB
 matplotlib: yes [1.4.3]
 python: yes [3.4.0 (default, Apr 11 2014,
 13:05:11)  [GCC
 4.8.2]]
   platform: yes [linux]
 REQUIRED DEPENDENCIES AND EXTENSIONS
  numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
   dateutil: yes [using dateutil version 2.0]
   pytz: yes [using

Re: [Matplotlib-users] unsuscribe

[Benjamin Root]

You would need to go this link to unsubscribe:
https://lists.sourceforge.net/lists/listinfo/matplotlib-users
I don't think sourceforge does automated unsubscribes.

On Wed, Apr 1, 2015 at 11:44 AM, AdolfoE Aguirre aguirreadolf...@gmail.com
wrote:

 unsuscribe


 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
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 all
 things parallel software development, from weekly thought leadership blogs
 to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
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 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

Didn't we fix that in trunk recently?

On Wed, Apr 1, 2015 at 12:51 PM, Jens Nielsen jenshniel...@gmail.com
wrote:

 Looking more closely at this I think it is a bug on our side. When
 freetype is not found it returns version as 'Failed to identify version.' 
 which
 it tries to compare to a version number. The version number is correctly
 converted from string to numbers using loosversion but this string just
 makes it through. The workaround at the moment is to install the freetype
 dev as Tom said.


 Jens

 ons. 1. apr. 2015 kl. 17.45 skrev Christian Ambros ambr...@ymail.com:

 Hi,

 as you can see: 14.3.1 which is the latest, because before I started
 upgrading, I read about possible issues here and upgraded the setuptools as
 conclusion.

 Python 3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC 4.8.2] on linux
 Type help, copyright, credits or license for more information.
  import setuptools
  print(setuptools.__version__)
 14.3.1
  exit()

 cheers,
 Christian
 --
 A little learning never caused anyone's head to explode!


 Ein wenig Lernen hat noch niemandens Kopf zum Explodieren gebracht!



   On Wednesday, April 1, 2015 1:25 PM, Jens Nielsen 
 jenshniel...@gmail.com wrote:


 I think we have seen this issue before and it seems to be caused by an
 out of date version of setuptools. I tried reproducing it on fresh ubuntu
 14.04 machine but was not able to reproduce the issue. Do you know which
 version of setuptools you are using?

 Jens

 ons. 1. apr. 2015 kl. 14.19 skrev Thomas Caswell tcasw...@gmail.com:

 Make sure you have `freetype-dev` installed at the system level.

 Tom

 On Wed, Apr 1, 2015 at 8:02 AM Christian Ambros ambr...@ymail.com
 wrote:

 Hi,

 I'm facing the same trouble with installing matplotlib 1.4.3 and
 1.5.dev1. running

 python3 setup.py build

 in the unarchived directory gives this:

 
 Edit setup.cfg to change the build options

 BUILDING MATPLOTLIB
 matplotlib: yes [1.5.dev1]
 python: yes [3.4.0 (default, Apr 11 2014, 13:05:11)  [GCC
 4.8.2]]
   platform: yes [linux]

 REQUIRED DEPENDENCIES AND EXTENSIONS
  numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
   dateutil: yes [using dateutil version 2.0]
   pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
  pyparsing: yes [using pyparsing version 2.0.1]
 libagg: yes [Requires patches that have not been merged
 upstream. Using local copy.]
 Traceback (most recent call last):
   File setup.py, line 153, in module
 result = package.check()
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line 900,
 in check
 min_version='2.3', version=version)
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line 446,
 in _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /home/ambrosc/Downloads/matplotlib-master/setupext.py, line 173,
 in is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 I'm running Linux Mint 17 Quina which is based on Ubuntu's trusty
 packges.

 pip3 is up to date. Running
 print(setuptools.__file__)

 gives: /usr/local/lib/python3.4/dist-packages/setuptools/__init__.py
 which is as expected.

 Using pip3 install matplotlib --upgrade #even to 1.4.3
 get's me this:


 Collecting matplotlib from
 https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.4.3.tar.gz#md5=86af2e3e3c61849ac7576a6f5ca44267
   Downloading matplotlib-1.4.3.tar.gz (50.4MB)
 100% || 50.4MB 8.0kB/s
 Traceback (most recent call last):
   File string, line 20, in module
   File /tmp/pip-build-sezmzam8/matplotlib/setup.py, line 155, in
 module
 result = package.check()
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 961, in
 check
 min_version='2.3', version=version)
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 445, in
 _check_for_pkg_config
 if (not is_min_version(version, min_version)):
   File /tmp/pip-build-sezmzam8/matplotlib/setupext.py, line 173, in
 is_min_version
 return found_version = expected_version
   File /usr/lib/python3.4/distutils/version.py, line 76, in __ge__
 c = self._cmp(other)
   File /usr/lib/python3.4/distutils/version.py, line 343, in _cmp
 if self.version  other.version:
 TypeError: unorderable types: str()  int()

 
 Edit setup.cfg to change the build options
 

[Matplotlib-users] Interactive Applications using Matplotlib

[Benjamin Root]

The book I have been working on has now been published! It is about how to
use most of the interactive features that comes with matplotlib in order to
create your own GUI applications. The concepts are taught by building up a
single application piece-by-piece, feature-by-feature. The final chapter
then shows how to bring in tools from other GUIs, and also how to embed
your figure into an existing GUI application (demonstrated for gtk,
tkinter, wx and qt4).

I really hope that the book is useful to the community, and that it is as
enjoyable to read as it was for me to write!

Cheers!
Ben Root

Order it on Amazon
http://www.amazon.com/Interactive-Applications-using-Matplotlib-Benjamin/dp/1783988843/

Or directly from Packt
https://www.packtpub.com/application-development/interactive-applications-using-matplotlib
--
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/___
Matplotlib-users mailing list
Matplotlib-users@lists.sourceforge.net
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Re: [Matplotlib-users] Best way to display image from URL in Python3

[Benjamin Root]

According to the PR you reference, the fix for this was merged back in Jan
2013, so that means that this fix is in version 1.2.x and up. Are you
saying that you still can't do imread(urllib.request.urlopen(url))?

On Thu, Mar 19, 2015 at 8:54 PM, Ryan Nelson rnelsonc...@gmail.com wrote:

 Hello all,

 I'm porting over some code that used Py2.7 urllib2.urlopen(url) to grab
 some image data from the net and load with pyplot.imread. It doesn't work
 quite right in Py3.4. I found a couple of refs:

 https://github.com/matplotlib/matplotlib/pull/1650

 http://stackoverflow.com/questions/15183170/python-crash-when-downloading-image-as-numpy-array

 They suggest io.BytesIO(urllib.request.urlopen(url).read()) as a
 replacement for Py3. Is this the best practice? Does anyone know a simpler
 way to do this?

 Ryan


 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub for
 all
 things parallel software development, from weekly thought leadership blogs
 to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
 ___
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 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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news, videos, case studies, tutorials and more. Take a look and join the 
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Re: [Matplotlib-users] segmentation fault when saving images

[Benjamin Root]

The warnings probably have nothing to do with the issue at hand. Try this.
Install the package faulthandler and add the appropriate lines to your
Bdipoly.py script and run it again. That way, we can get a traceback and
find out where it is segfaulting from.

http://faulthandler.readthedocs.org/en/latest/

Ben Root

As a side-note: faulthandler is part of the standard library as of 3.3!
Neat!


On Thu, Mar 19, 2015 at 1:13 PM, Gabriele Brambilla 
gb.gabrielebrambi...@gmail.com wrote:

 Hi guys,

 I don't understand why now, after I save an image when it is prompted out,
 the image is not saved and it closes automatically and on the terminal
 appears segmentation fault.

 this is what my terminal shows:

 [gs66-stumbras:~/Desktop] gbrambil% python Bdipole.py

 Bdipole.py:52: RuntimeWarning: divide by zero encountered in divide

   lwb = 5/(np.log10(modB.max()/modB))

 Bdipole.py:55: RuntimeWarning: divide by zero encountered in divide

   lwe = 5/(np.log10(modE.max()/modE))

 Segmentation fault


 Thanks


 Gabriele





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 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub for
 all
 things parallel software development, from weekly thought leadership blogs
 to
 news, videos, case studies, tutorials and more. Take a look and join the
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 Matplotlib-users mailing list
 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users


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by Intel and developed in partnership with Slashdot Media, is your hub for all
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Re: [Matplotlib-users] segmentation fault when saving images

[Benjamin Root]

well, that still doesn't explain the segfaults. NaNs shouldn't cause
matplotlib to crash upon saving. I would still be interested in a
stacktrace.

Ben

On Thu, Mar 19, 2015 at 1:27 PM, Gabriele Brambilla 
gb.gabrielebrambi...@gmail.com wrote:

 Actually Paul Hobson was right.

 Now it works.

 Thanks

 Gabriele

 On Thu, Mar 19, 2015 at 1:19 PM, Benjamin Root ben.r...@ou.edu wrote:

 The warnings probably have nothing to do with the issue at hand. Try
 this. Install the package faulthandler and add the appropriate lines to
 your Bdipoly.py script and run it again. That way, we can get a traceback
 and find out where it is segfaulting from.

 http://faulthandler.readthedocs.org/en/latest/

 Ben Root

 As a side-note: faulthandler is part of the standard library as of 3.3!
 Neat!


 On Thu, Mar 19, 2015 at 1:13 PM, Gabriele Brambilla 
 gb.gabrielebrambi...@gmail.com wrote:

 Hi guys,

 I don't understand why now, after I save an image when it is prompted
 out, the image is not saved and it closes automatically and on the terminal
 appears segmentation fault.

 this is what my terminal shows:

 [gs66-stumbras:~/Desktop] gbrambil% python Bdipole.py

 Bdipole.py:52: RuntimeWarning: divide by zero encountered in divide

   lwb = 5/(np.log10(modB.max()/modB))

 Bdipole.py:55: RuntimeWarning: divide by zero encountered in divide

   lwe = 5/(np.log10(modE.max()/modE))

 Segmentation fault


 Thanks


 Gabriele





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 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub
 for all
 things parallel software development, from weekly thought leadership
 blogs to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
 ___
 Matplotlib-users mailing list
 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users




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Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

One thing I just noticed is that python3.4 and the distutils libraries are
installed at /usr/lib/python3.4/distutils/, but the setuptools is located
at /usr/local/lib/python3.4/dist-packages/. One of the oddities of
setuptools is that it monkey-patches distutils, if I understand it
correctly, so perhaps it isn't doing it correctly for some reason? I
haven't a clue, really.

This oddity in directory structures was actually one thing I noticed in
Ubuntu last summer/fall for py2.7 that broke a lot of things for me. I was
in a rush at the time, so I just switched to anaconda, nuked everything
python in my .local and moved on. That is always an option here, but it
would be nice to get to the bottom of this as well.

Ben Root

On Wed, Mar 18, 2015 at 1:03 PM, keith.bri...@bt.com wrote:

 Ben: thanks for your help - it's very much appreciated!
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 python3
 Python 3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC 4.8.2] on linux
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)

 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.4.egg/setuptools/__init__.py
 


 kbriggs:~/Downloads/matplotlib-1.4.3 python
 Python 2.7.6 (default, Mar 22 2014, 22:59:56)
 [GCC 4.8.2] on linux2
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/lib/python2.7/dist-packages/setuptools/__init__.pyc
 


 
 From: ben.v.r...@gmail.com [ben.v.r...@gmail.com] On Behalf Of Benjamin
 Root [ben.r...@ou.edu]
 Sent: 18 March 2015 16:58
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 Keith,

 Back to the issue at hand. could you do the following?

 import setuptools
 print(setuptools.__file__)

 It would be interesting to see if that path differs from the path of the
 egg you just listed.
 Ben

 On Wed, Mar 18, 2015 at 11:39 AM, keith.bri...@bt.commailto:
 keith.bri...@bt.com wrote:
 pip still thinks I have the latest.   I think it's a question of how to
 force the matplotlib setup.py to use actually it.
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 sudo pip3  install setuptools
 --upgrade
 Requirement already up-to-date: setuptools in
 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.4.egg
 Cleaning up...

 
 From: ben.v.r...@gmail.commailto:ben.v.r...@gmail.com [
 ben.v.r...@gmail.commailto:ben.v.r...@gmail.com] On Behalf Of Benjamin
 Root [ben.r...@ou.edumailto:ben.r...@ou.edu]
 Sent: 18 March 2015 15:33
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 I would just use pip. Ubuntu/Debian has really messed up the python
 environment in more ways than one.

 On Wed, Mar 18, 2015 at 11:08 AM, keithbriggs keith.bri...@bt.commailto:
 keith.bri...@bt.commailto:keith.bri...@bt.commailto:keith.bri...@bt.com
 wrote:
 The Ubuntu package manager tells me it is up to date.
 If I download setuptools-14.3 and install, it goes into /usr/local/lib/ and
 doesn't get used.
 How do I force it to be used?
 Or am I supposed to override the Ubuntu package manager?
 Keith






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 sponsored
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 all
 things parallel software development, from weekly thought leadership blogs
 to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
 ___
 Matplotlib-devel mailing list
 matplotlib-de...@lists.sourceforge.netmailto:
 matplotlib-de...@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-devel


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https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

please don't do that

Yes, I will make sure that any antagonizing I do in the future, it will be
completely clear that I am the one doing it.  ;-)

On Wed, Mar 18, 2015 at 2:04 PM, Thomas Caswell tcasw...@gmail.com wrote:

 Hmm, I can't read and miss-attributed who was antagonizing Sandro, please
 don't do that.

 On Wed, Mar 18, 2015 at 2:01 PM Benjamin Root ben.r...@ou.edu wrote:

 For my part, I didn't take Keith's comment as antagonizing. If anything,
 I should apologize to Sandro. It was not necessary for me to drag Debian
 into this, because all I know is that I was having issues on Ubuntu.

 Ben Root

 On Wed, Mar 18, 2015 at 1:51 PM, Thomas Caswell tcasw...@gmail.com
 wrote:

 We do support ubuntu, travis.ci (which we use for continuous
 integration testing) is ubuntu based and my main development box is ubuntu
 (but I mostly work inside conda environments rather than virtualenvs these
 days). Even though it is the worst thing for a dev to say, 'it works on my
 machine'.

 Part of the problem here is that it looks like you are doing system-wide
 installations from source so you have almost certainly driven your system
 into an inconsistent state.  Unless you know enough sys-admin magic to
 ensure you won't step on the toes of the system packages, I strongly
 suggest _never_ using sudo to install python packages.  Either use
 venv/conda or install into a directory in your home directory and modify
 $PYTHONPATH as needed.

  I know it is frustrating, but there isn't a whole lot we can do to help
 you with you knowing exactly what you have done to your system.

 In any case antagonizing the developers and the debian packager is _not_
 the most effective course of action.  I assure you all of us are making a
 good faith effort to make sure mpl works everywhere.  Starting from that
 assumption will make all of these conversations go much more smoothly.
 Also remember everyone responding to you on this list is a volunteer,
 please be respectful of our time and energy.

 Tom

 On Wed, Mar 18, 2015 at 1:27 PM Benjamin Root ben.r...@ou.edu wrote:

 We would too. This is the first time I have seen updating setuptools
 not work. That was the fix... I have no clue why it is broken on your
 system.

 On Wed, Mar 18, 2015 at 1:20 PM, keith.bri...@bt.com wrote:

 Ok, I will check out anaconda anyway.



 I would think that the matplotlib maintainers would want to make sure
 they support the very popular Ubuntu platform, even if a workaround for a
 bug elsewhere is needed.



 K





 *From:* ben.v.r...@gmail.com [mailto:ben.v.r...@gmail.com] *On Behalf
 Of *Benjamin Root
 *Sent:* 18 March 2015 17:17
 *To:* Briggs,KM,Keith,TUB2 R; Matplotlib Users


 *Subject:* Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14
 with python3



 One thing I just noticed is that python3.4 and the distutils libraries
 are installed at /usr/lib/python3.4/distutils/, but the setuptools is
 located at /usr/local/lib/python3.4/dist-packages/. One of the
 oddities of setuptools is that it monkey-patches distutils, if I 
 understand
 it correctly, so perhaps it isn't doing it correctly for some reason? I
 haven't a clue, really.

 This oddity in directory structures was actually one thing I noticed
 in Ubuntu last summer/fall for py2.7 that broke a lot of things for me. I
 was in a rush at the time, so I just switched to anaconda, nuked 
 everything
 python in my .local and moved on. That is always an option here, but it
 would be nice to get to the bottom of this as well.

 Ben Root



 On Wed, Mar 18, 2015 at 1:03 PM, keith.bri...@bt.com wrote:

 Ben: thanks for your help - it's very much appreciated!
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 python3
 Python 3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC 4.8.2] on linux
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.
 4.egg/setuptools/__init__.py
 


 kbriggs:~/Downloads/matplotlib-1.4.3 python
 Python 2.7.6 (default, Mar 22 2014, 22:59:56)
 [GCC 4.8.2] on linux2
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/lib/python2.7/dist-packages/setuptools/__init__.pyc
 


 
 From: ben.v.r...@gmail.com [ben.v.r...@gmail.com] On Behalf Of
 Benjamin Root [ben.r...@ou.edu]
 Sent: 18 March 2015 16:58
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 Keith,

 Back to the issue at hand. could you do the following?

 import setuptools
 print(setuptools.__file__)

 It would be interesting to see if that path differs from the path of
 the egg you just listed.
 Ben

 On Wed, Mar 18, 2015 at 11:39 AM, keith.bri...@bt.commailto:ke
 ith.bri...@bt.com wrote:
 pip still thinks I have the latest.   I think it's a question of how
 to force the matplotlib setup.py to use

Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

For my part, I didn't take Keith's comment as antagonizing. If anything, I
should apologize to Sandro. It was not necessary for me to drag Debian into
this, because all I know is that I was having issues on Ubuntu.

Ben Root

On Wed, Mar 18, 2015 at 1:51 PM, Thomas Caswell tcasw...@gmail.com wrote:

 We do support ubuntu, travis.ci (which we use for continuous integration
 testing) is ubuntu based and my main development box is ubuntu (but I
 mostly work inside conda environments rather than virtualenvs these days).
 Even though it is the worst thing for a dev to say, 'it works on my
 machine'.

 Part of the problem here is that it looks like you are doing system-wide
 installations from source so you have almost certainly driven your system
 into an inconsistent state.  Unless you know enough sys-admin magic to
 ensure you won't step on the toes of the system packages, I strongly
 suggest _never_ using sudo to install python packages.  Either use
 venv/conda or install into a directory in your home directory and modify
 $PYTHONPATH as needed.

  I know it is frustrating, but there isn't a whole lot we can do to help
 you with you knowing exactly what you have done to your system.

 In any case antagonizing the developers and the debian packager is _not_
 the most effective course of action.  I assure you all of us are making a
 good faith effort to make sure mpl works everywhere.  Starting from that
 assumption will make all of these conversations go much more smoothly.
 Also remember everyone responding to you on this list is a volunteer,
 please be respectful of our time and energy.

 Tom

 On Wed, Mar 18, 2015 at 1:27 PM Benjamin Root ben.r...@ou.edu wrote:

 We would too. This is the first time I have seen updating setuptools not
 work. That was the fix... I have no clue why it is broken on your system.

 On Wed, Mar 18, 2015 at 1:20 PM, keith.bri...@bt.com wrote:

 Ok, I will check out anaconda anyway.



 I would think that the matplotlib maintainers would want to make sure
 they support the very popular Ubuntu platform, even if a workaround for a
 bug elsewhere is needed.



 K





 *From:* ben.v.r...@gmail.com [mailto:ben.v.r...@gmail.com] *On Behalf
 Of *Benjamin Root
 *Sent:* 18 March 2015 17:17
 *To:* Briggs,KM,Keith,TUB2 R; Matplotlib Users


 *Subject:* Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14
 with python3



 One thing I just noticed is that python3.4 and the distutils libraries
 are installed at /usr/lib/python3.4/distutils/, but the setuptools is
 located at /usr/local/lib/python3.4/dist-packages/. One of the oddities
 of setuptools is that it monkey-patches distutils, if I understand it
 correctly, so perhaps it isn't doing it correctly for some reason? I
 haven't a clue, really.

 This oddity in directory structures was actually one thing I noticed in
 Ubuntu last summer/fall for py2.7 that broke a lot of things for me. I was
 in a rush at the time, so I just switched to anaconda, nuked everything
 python in my .local and moved on. That is always an option here, but it
 would be nice to get to the bottom of this as well.

 Ben Root



 On Wed, Mar 18, 2015 at 1:03 PM, keith.bri...@bt.com wrote:

 Ben: thanks for your help - it's very much appreciated!
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 python3
 Python 3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC 4.8.2] on linux
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.
 4.egg/setuptools/__init__.py
 


 kbriggs:~/Downloads/matplotlib-1.4.3 python
 Python 2.7.6 (default, Mar 22 2014, 22:59:56)
 [GCC 4.8.2] on linux2
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/lib/python2.7/dist-packages/setuptools/__init__.pyc
 


 
 From: ben.v.r...@gmail.com [ben.v.r...@gmail.com] On Behalf Of Benjamin
 Root [ben.r...@ou.edu]
 Sent: 18 March 2015 16:58
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 Keith,

 Back to the issue at hand. could you do the following?

 import setuptools
 print(setuptools.__file__)

 It would be interesting to see if that path differs from the path of the
 egg you just listed.
 Ben

 On Wed, Mar 18, 2015 at 11:39 AM, keith.bri...@bt.commailto:ke
 ith.bri...@bt.com wrote:
 pip still thinks I have the latest.   I think it's a question of how to
 force the matplotlib setup.py to use actually it.
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 sudo pip3  install setuptools
 --upgrade
 Requirement already up-to-date: setuptools in
 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.4.egg
 Cleaning up...

 
 From: ben.v.r...@gmail.commailto:ben.v.r...@gmail.com [
 ben.v.r...@gmail.commailto:ben.v.r...@gmail.com] On Behalf

Re: [Matplotlib-users] ImportError: No module named six

[Benjamin Root]

An important question that I should have asked before. Exactly where did
you get the installer from? That might help us figure out what happened
here.

As for a workaround, if you want to get savy with the command-line, you
could run pip install six on the command-line. That should install it for
you, and then you can try installing matplotlib through the executable.

On Tue, Mar 17, 2015 at 6:11 PM, garyr ga...@fidalgo.net wrote:

 I did as you suggest and got the No module named matplot lib message. I
 installed version 1.4.3 and got the no module named six message. I then
 deleted all the matplotlib files once again and installed version 1.3.1
 and now
 my matplotlib program runs. Is there something else could try?


 - Original Message -
 From: Benjamin Root ben.r...@ou.edu
 To: garyr ga...@fidalgo.net
 Cc: Matplotlib Users Matplotlib-users@lists.sourceforge.net
 Sent: Tuesday, March 17, 2015 10:34 AM
 Subject: Re: [Matplotlib-users] ImportError: No module named six


  Chances are, there is some sort of mixup in your installs (as evidenced
 by
  the failure to go back to the previous version). I would try uninstalling
  all matplotlib installs, then checking to see if python still sees
  matplotlib anywhere (by running the script). It *should* say No module
  named matplotlib or some such. Once all of that is removed, install
  matplotlib again.
 
  Ben Root
 
  On Tue, Mar 17, 2015 at 1:12 PM, garyr ga...@fidalgo.net wrote:
 
  I downloaded version 1.4.3 and installed it (i.e., executed
  matplotlib-1.4.3.win32-py2.6.exe). Now when I
  attempt to run a program I get the following:
 
  python rainfallYears.py
  Traceback (most recent call last):
File rainfallYears.py, line 4, in module
  import matplotlib.pyplot as plt
File C:\Python26\lib\site-packages\matplotlib\__init__.py, line
 105, in
  module
  import six
  ImportError: No module named six
  Exit code: 1
 
  So then I went back to 1.3.1 and get the same error...
  Help!
 
 
 
 
 
 --
  Dive into the World of Parallel Programming The Go Parallel Website,
  sponsored
  by Intel and developed in partnership with Slashdot Media, is your hub
 for
  all
  things parallel software development, from weekly thought leadership
 blogs
  to
  news, videos, case studies, tutorials and more. Take a look and join the
  conversation now. http://goparallel.sourceforge.net/
  ___
  Matplotlib-users mailing list
  Matplotlib-users@lists.sourceforge.net
  https://lists.sourceforge.net/lists/listinfo/matplotlib-users
 
 




 --
 Dive into the World of Parallel Programming The Go Parallel Website,
 sponsored
 by Intel and developed in partnership with Slashdot Media, is your hub for
 all
 things parallel software development, from weekly thought leadership blogs
 to
 news, videos, case studies, tutorials and more. Take a look and join the
 conversation now. http://goparallel.sourceforge.net/
 ___
 Matplotlib-users mailing list
 Matplotlib-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/matplotlib-users

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by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/___
Matplotlib-users mailing list
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https://lists.sourceforge.net/lists/listinfo/matplotlib-users

Re: [Matplotlib-users] [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with python3

[Benjamin Root]

We would too. This is the first time I have seen updating setuptools not
work. That was the fix... I have no clue why it is broken on your system.

On Wed, Mar 18, 2015 at 1:20 PM, keith.bri...@bt.com wrote:

 Ok, I will check out anaconda anyway.



 I would think that the matplotlib maintainers would want to make sure they
 support the very popular Ubuntu platform, even if a workaround for a bug
 elsewhere is needed.



 K





 *From:* ben.v.r...@gmail.com [mailto:ben.v.r...@gmail.com] *On Behalf Of 
 *Benjamin
 Root
 *Sent:* 18 March 2015 17:17
 *To:* Briggs,KM,Keith,TUB2 R; Matplotlib Users

 *Subject:* Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3



 One thing I just noticed is that python3.4 and the distutils libraries are
 installed at /usr/lib/python3.4/distutils/, but the setuptools is located
 at /usr/local/lib/python3.4/dist-packages/. One of the oddities of
 setuptools is that it monkey-patches distutils, if I understand it
 correctly, so perhaps it isn't doing it correctly for some reason? I
 haven't a clue, really.

 This oddity in directory structures was actually one thing I noticed in
 Ubuntu last summer/fall for py2.7 that broke a lot of things for me. I was
 in a rush at the time, so I just switched to anaconda, nuked everything
 python in my .local and moved on. That is always an option here, but it
 would be nice to get to the bottom of this as well.

 Ben Root



 On Wed, Mar 18, 2015 at 1:03 PM, keith.bri...@bt.com wrote:

 Ben: thanks for your help - it's very much appreciated!
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 python3
 Python 3.4.0 (default, Apr 11 2014, 13:05:11)
 [GCC 4.8.2] on linux
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)

 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.4.egg/setuptools/__init__.py
 


 kbriggs:~/Downloads/matplotlib-1.4.3 python
 Python 2.7.6 (default, Mar 22 2014, 22:59:56)
 [GCC 4.8.2] on linux2
 Type help, copyright, credits or license for more information.
 
  import setuptools
  print(setuptools.__file__)
 /usr/lib/python2.7/dist-packages/setuptools/__init__.pyc
 


 
 From: ben.v.r...@gmail.com [ben.v.r...@gmail.com] On Behalf Of Benjamin
 Root [ben.r...@ou.edu]
 Sent: 18 March 2015 16:58
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 Keith,

 Back to the issue at hand. could you do the following?

 import setuptools
 print(setuptools.__file__)

 It would be interesting to see if that path differs from the path of the
 egg you just listed.
 Ben

 On Wed, Mar 18, 2015 at 11:39 AM, keith.bri...@bt.commailto:
 keith.bri...@bt.com wrote:
 pip still thinks I have the latest.   I think it's a question of how to
 force the matplotlib setup.py to use actually it.
 Keith

 kbriggs:~/Downloads/matplotlib-1.4.3 sudo pip3  install setuptools
 --upgrade
 Requirement already up-to-date: setuptools in
 /usr/local/lib/python3.4/dist-packages/setuptools-14.3-py3.4.egg
 Cleaning up...

 
 From: ben.v.r...@gmail.commailto:ben.v.r...@gmail.com [
 ben.v.r...@gmail.commailto:ben.v.r...@gmail.com] On Behalf Of Benjamin
 Root [ben.r...@ou.edumailto:ben.r...@ou.edu]
 Sent: 18 March 2015 15:33
 To: Briggs,KM,Keith,TUB2 R
 Cc: matplotlib development list
 Subject: Re: [matplotlib-devel] 1.4.3 does not build on Ubuntu 14 with
 python3

 I would just use pip. Ubuntu/Debian has really messed up the python
 environment in more ways than one.

 On Wed, Mar 18, 2015 at 11:08 AM, keithbriggs keith.bri...@bt.commailto:
 keith.bri...@bt.commailto:keith.bri...@bt.commailto:keith.bri...@bt.com
 wrote:
 The Ubuntu package manager tells me it is up to date.
 If I download setuptools-14.3 and install, it goes into /usr/local/lib/ and
 doesn't get used.
 How do I force it to be used?
 Or am I supposed to override the Ubuntu package manager?
 Keith






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Re: [Matplotlib-users] ImportError: No module named six

[Benjamin Root]

Chances are, there is some sort of mixup in your installs (as evidenced by
the failure to go back to the previous version). I would try uninstalling
all matplotlib installs, then checking to see if python still sees
matplotlib anywhere (by running the script). It *should* say No module
named matplotlib or some such. Once all of that is removed, install
matplotlib again.

Ben Root

On Tue, Mar 17, 2015 at 1:12 PM, garyr ga...@fidalgo.net wrote:

 I downloaded version 1.4.3 and installed it (i.e., executed
 matplotlib-1.4.3.win32-py2.6.exe). Now when I
 attempt to run a program I get the following:

 python rainfallYears.py
 Traceback (most recent call last):
   File rainfallYears.py, line 4, in module
 import matplotlib.pyplot as plt
   File C:\Python26\lib\site-packages\matplotlib\__init__.py, line 105, in
 module
 import six
 ImportError: No module named six
 Exit code: 1

 So then I went back to 1.3.1 and get the same error...
 Help!




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Re: [Matplotlib-users] Draggable is not working on multiple legends of plots which are generated with twinx()

[Benjamin Root]

Thomas described the work-around and provided a link. Put both of the
legends on the second axes. It is a kludge, for sure, but it is all you can
do.

On Wed, Mar 11, 2015 at 10:58 AM, liu lily politoeso...@gmail.com wrote:

 thanks,
 then are there any workaround on my case?
 or are there any other libaries which I CAN use to plot and manipulate the
 GUI?

 On Wed, Mar 11, 2015 at 3:54 PM, Benjamin Root ben.r...@ou.edu wrote:

 By top he means whichever axes was added most recently. When twining,
 the new axes is added on top of the original axes.

 I hope that clears it up.

 Ben Root

 On Wed, Mar 11, 2015 at 10:05 AM, liu lily politoeso...@gmail.com
 wrote:

 I dont understand
 you say it is the first axe
 but why in my case, only the second legend is draggable? it is in the
 second axe

 besides, since I have to use both y-axis on the left and on the right,
 it seems I have to have two axes,
 are there any workarounds? thanks!

 On Wed, Mar 11, 2015 at 2:22 PM, Thomas Caswell tcasw...@gmail.com
 wrote:

 The mouse events only propagate to the top axes.  You will have to add
 both legends to the same (top) axes.

 See http://matplotlib.org/users/legend_guide.html#multiple-legend


 Tom
 On Wed, Mar 11, 2015, 08:57 liu lily politoeso...@gmail.com wrote:

 Hi, all:

 I have two legends, as below, I find that I can't drag the first
 legend, what is the problem? how to deal with it? thanks!

 import matplotlib.pyplot as plt

 fig1, ax1 = plt.subplots()
 ax2 = ax1.twinx()

 ax1.plot([1,2,3],[0.1,0.82,0.3],'y*', label=one)
 ax2.plot([1,2,3],[5,6,7],'ro', label=two)

 leg1 = ax1.legend()
 leg2 = ax2.legend()

 leg1.draggable(state=True)
 leg2.draggable(state=True)
 plt.show()

 
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Re: [Matplotlib-users] Draggable is not working on multiple legends of plots which are generated with twinx()

[Benjamin Root]

By top he means whichever axes was added most recently. When twining,
the new axes is added on top of the original axes.

I hope that clears it up.

Ben Root

On Wed, Mar 11, 2015 at 10:05 AM, liu lily politoeso...@gmail.com wrote:

 I dont understand
 you say it is the first axe
 but why in my case, only the second legend is draggable? it is in the
 second axe

 besides, since I have to use both y-axis on the left and on the right, it
 seems I have to have two axes,
 are there any workarounds? thanks!

 On Wed, Mar 11, 2015 at 2:22 PM, Thomas Caswell tcasw...@gmail.com
 wrote:

 The mouse events only propagate to the top axes.  You will have to add
 both legends to the same (top) axes.

 See http://matplotlib.org/users/legend_guide.html#multiple-legend


 Tom
 On Wed, Mar 11, 2015, 08:57 liu lily politoeso...@gmail.com wrote:

 Hi, all:

 I have two legends, as below, I find that I can't drag the first legend,
 what is the problem? how to deal with it? thanks!

 import matplotlib.pyplot as plt

 fig1, ax1 = plt.subplots()
 ax2 = ax1.twinx()

 ax1.plot([1,2,3],[0.1,0.82,0.3],'y*', label=one)
 ax2.plot([1,2,3],[5,6,7],'ro', label=two)

 leg1 = ax1.legend()
 leg2 = ax2.legend()

 leg1.draggable(state=True)
 leg2.draggable(state=True)
 plt.show()

 
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Re: [Matplotlib-users] Lorenz -- another Q

[Benjamin Root]

What 3D array? There shouldn't be any 3D arrays. I suspect that x_t is only
accidentally 3d by having a shape like (N, M, 1) or (1, N, M).

Ben Root

On Wed, Mar 11, 2015 at 5:05 PM, Prahas David Nafissian 
prahas.mu...@gmail.com wrote:

 Hello,

 Solved the write issue.

 I tried numpy savetxt but it chokes on 3D arrays.

 So I'm doing this:

 x_t.tofile('test3.txt',sep= ,format=%f)

 Only issue -- no end-of-lines. But I can write a quick
 Pascal program to fix this...

 Once again, thanks!


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Re: [Matplotlib-users] Lorenz - solution

[Benjamin Root]

+1000!!

Great job! Would you mind if I clean it up a bit and add it to the
mplot3d/animation gallery? Full credit, of course.


On Tue, Mar 10, 2015 at 11:30 AM, Prahas David Nafissian 
prahas.mu...@gmail.com wrote:

 Friends,

 I thought you'd like to see the solution.

 Many thanks to Jake Vanderplas for his code and teachings:


 https://jakevdp.github.io/blog/2013/02/16/animating-the-lorentz-system-in-3d/

 If you start a new IP Notebook session, run as your first entry:

 %pylab

 and then copy and paste the text below and run it, you should be good to go
 (on a Mac, at least).

 There are several parameters I've changed from his original, and I've
 commented as I've changed.  The original code is at the link above.

 There is one error in his code -- I've documented it below.

 Again, thanks to the community, Jake, and Ben Root.

 --Prahas

 **

 import numpy as np
 from scipy import integrate

 from matplotlib import pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 from matplotlib.colors import cnames
 from matplotlib import animation

 # orig value of N_traj was 20 -- very cool this way.

 N_trajectories = 1

 def lorentz_deriv((x, y, z), t0, sigma=10., beta=8./3, rho=28.0):
 Compute the time-derivative of a Lorentz system.
 return [sigma * (y - x), x * (rho - z) - y, x * y - beta * z]

 # Choose random starting points, uniformly distributed from -15 to 15

 np.random.seed(1)

 # changing from -15,30 to 10,5 below starts the drawing in the middle,
 # rather than getting the long line from below
 # if using N_Traj  1, return to orig values.

 # x0 = -15 + 30 * np.random.random((N_trajectories, 3))

 x0 = 10 + 5 * np.random.random((N_trajectories, 3))


 # Solve for the trajectories

 # orig values:  0,4,1000
 # 3rd value -- lower it, it gets choppier.
 # 2nd value -- increase it -- more points, but speedier.

 # change middle num from 4 to 15 -- this adds points

 t = np.linspace(0, 40, 3000)
 x_t = np.asarray([integrate.odeint(lorentz_deriv, x0i, t)
   for x0i in x0])

 # Set up figure  3D axis for animation
 fig = plt.figure()
 ax = fig.add_axes([0, 0, 1, 1], projection='3d')

 # changing off to on below adds axises.  slows it down but you
 # can fix that with interval value in the animation call

 ax.axis('on')

 # choose a different color for each trajectory
 colors = plt.cm.jet(np.linspace(0, 1, N_trajectories))

 # set up lines and points -- this is a correction from
 # the orig jake code.  the next four lines...

 lines = [ax.plot([], [], [], '-', c=c)[0]
 for c in colors]
 pts = [ax.plot([], [], [], 'o', c=c)[0]
 for c in colors]

 # prepare the axes limits
 ax.set_xlim((-25, 25))
 ax.set_ylim((-35, 35))
 ax.set_zlim((5, 55))

 # set point-of-view: specified by (altitude degrees, azimuth degrees)
 ax.view_init(30, 0)

 # initialization function: plot the background of each frame
 def init():
 for line, pt in zip(lines, pts):
 line.set_data([], [])
 line.set_3d_properties([])

 pt.set_data([], [])
 pt.set_3d_properties([])
 return lines + pts

 # animation function.  This will be called sequentially with the frame
 number
 def animate(i):
 # we'll step two time-steps per frame.  This leads to nice results.

 i = (2 * i) % x_t.shape[1]

 for line, pt, xi in zip(lines, pts, x_t):
 x, y, z = xi[:i].T
 line.set_data(x, y)
 line.set_3d_properties(z)

 pt.set_data(x[-1:], y[-1:])
 pt.set_3d_properties(z[-1:])

 # changed 0.3 to 0.05 below -- this slows the rotation of the view.
 # changed 30 to 20 below
 # changing 20 to (20 + (.1 * i)) rotates on the Z axis.  trippy.

 ax.view_init(10, 0.1 * i)
 # ax.view_init(10, 100)
 fig.canvas.draw()
 return lines + pts

 # instantiate the animator.  I've deleted the blit switch (for Mac)
 # enlarging frames=500 works now -- it failed before because I didn't give
 it
 # enough data -- by changing the t=np.linspace line above I generate
 more points.
 # interval larger slows it down
 # changed inteval from 30 to 200, frames from 500 to 3000

 anim = animation.FuncAnimation(fig, animate, init_func=init,
frames=3000, interval=200)

 # Save as mp4. This requires mplayer or ffmpeg to be installed.
 COMPLEX!
 # Instead, use a screen record program:  Quicktime on the Mac; MS
 Expression Encoder on PC.
 # anim.save('PDNlorentz_attractor.mp4', fps=15, extra_args=['-vcodec',
 'libx264'])

 plt.show()

 


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Re: [Matplotlib-users] plt scale x-axis by constant factor f

[Benjamin Root]

Or just do this:

formatter = FuncFormatter(lambda x, pos: %d % x/10)
fig, ax = 
plt.subplots()ax.yaxis.set_major_formatter(formatter)plt.plot(D.dtrajs[0])
plt.ylabel('O2-Fe distance')
plt.xlabel('Frame')
plt.show()



On Mon, Mar 9, 2015 at 2:11 PM, Sterling Smith smit...@fusion.gat.com
wrote:

 Christian,

 To define your x coordinate, try
 x = range(len(array))
 x = x/10.
 plot(x,array)

 -Sterling

 On Mar 9, 2015, at 10:57AM, Christian Jorgensen chrisj...@gmail.com
 wrote:

 
  My array does not have an explicit x-coordinate
  representation. The x-coordinate is simply the index.
 
  print(array)
  [ 0  0 20 ...,  8  8  8]
 
 
  Thus what I would like is to adjoin the element
  index as another row, how is this possible?
 
 
  I cannot format x because it is not explicitly defined.
 
 
 
  On Mon, Mar 9, 2015 at 5:52 PM, Benjamin Rootben.r...@ou.edu wrote:
  Ok, this really should be simple (and I am sure it is), but I cannot,
 for the life of me, find the appropriate documentation for it. We need
 better documentation about how to utilize the offset-text feature of
 tickers. It can be either a multiple offset or an additive offset.
 
  In any case, I know there is a better way to do this, but here is a
 quick-n-dirty example that can get you where you want. Just modify the
 formatter used by the tickers to report the value as divided by 10.
  http://matplotlib.org/examples/pylab_examples/custom_ticker1.html
 
  Cheers!
  Ben Root
 
 
  On Mon, Mar 9, 2015 at 1:38 PM, Christian Jorgensenchrisj...@gmail.com
 wrote:
  How can I scale my x-axis [0,3000] for the data to now correspond/show up
  as [0, 300]?
 
 
  In xmgrace, this is done with a linear transformation, but I cannot seem
  to find the command to do this with matplotlib.
 
  Best
 
 
 
 
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Re: [Matplotlib-users] plt scale x-axis by constant factor f

[Benjamin Root]

Ok, this really should be simple (and I am sure it is), but I cannot, for
the life of me, find the appropriate documentation for it. We need better
documentation about how to utilize the offset-text feature of tickers. It
can be either a multiple offset or an additive offset.

In any case, I know there is a better way to do this, but here is a
quick-n-dirty example that can get you where you want. Just modify the
formatter used by the tickers to report the value as divided by 10.
http://matplotlib.org/examples/pylab_examples/custom_ticker1.html

Cheers!
Ben Root


On Mon, Mar 9, 2015 at 1:38 PM, Christian Jorgensen chrisj...@gmail.com
wrote:

 How can I scale my x-axis [0,3000] for the data to now correspond/show up
 as [0, 300]?


 In xmgrace, this is done with a linear transformation, but I cannot seem
 to find the command to do this with matplotlib.

 Best




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