matplotlib-users Mailing List for matplotlib

Dear colleagues, 
Is there a artist function or routine available in matplotlib for drawing 
animated arrows following lines (like streamplot) in a 2D space, or even 
better in a 3D space? 
Thanks in advance for any hint, or sample code. 
Regards, 
Claude
Claude Falbriard 
Certified IT Specialist L2 - Middleware
AMS Hortolândia / SP - Brazil
phone: +55 13 9 9760 0453
cell: +55 13 9 8117 3316
e-mail: cl...@br...

On 2014年04月24日 11:40 PM, Tom Grydeland wrote:
> Hi all,
>
> I will explain what I’m trying to achieve first, then the approaches I’ve attempted so far, with results.
>
> I have data on a 2D grid which I want to present as an image — a la pyplot.imshow() — except that the grid is hexagonal, not rectangular. The grid can be represented in multiple ways, I use a regular 2D array with the convention that the lower left hex is (0,0), x increases to the right (crossing vertical hex boundaries) and y increases upwards slanting to the right.
>
Tom,
Have you considered adapting the code from the Axes.hexbin() method?
Ideally, the hexbin method might be split into two parts, one for the 
calculation and another for the plotting.
Eric
> Ideally, I’d also be able to have a colorbar.
>
> I’m giving my routines three input vectors: x, y and c. X and y are initially integers, then transformed to centerpoint coordinates using
> x, y = x+.5*y, y*np.cos(np.pi/6)
> while c is used to look up values in a colormap.
>
> I first tried to adapt ‘scatter_demo2.py’ to my needs. Unfortunately, the pyplot.scatter routine fails when given ‘c’ or ’s’ keywords, as has been reported elsewhere by somebody else:
> http://stackoverflow.com/questions/20524888/attributeerror-numpy-ndarray-object-has-no-attribute-get-matrix
>
> I’ve dug around in the code for a bit without finding out how this arises. It seems to me it has to do with how transforms are being handed around and at what point their representation is changed from objects to pure matrices. This backend appears to expect to see objects only, but is handed matrices instead. I’ve hacked my way around that one in backends/backend_macosx.py by changing lines around 79-80 from
> master_transform = master_transform.get_matrix()
> all_transforms = [t.get_matrix() for t in all_transforms]
> to
> try:
> master_transform = master_transform.get_matrix()
> except AttributeError: pass
> try:
> all_transforms = [t.get_matrix() for t in all_transforms]
> except AttributeError: pass
> (which is a dirty hack, but I don’t know how to do it right)
>
> Now I can run the scatter_demo2 script, and I can obviously have it produce hexes at uniform size, but the size of the hexagons are set independently of the axes. Good for symbols used to mark arbitrary coordinates, not so good when I try to cover the plane without gaps.
>
> Next, I’ve tried creating the patches one by one, essentially this:
>
> r = 1./np.sqrt(3)
> for xy, cc in zip(zip(x, y), c):
> hexp = mpl.patches.RegularPolygon(xy, 6, radius=r, facecolor=cc, edgecolor=’none')
> ax.add_patch(hexp)
> ax.autoscale_view()
> ax.figure.canvas.draw()
>
> This works as I want it to, but becomes unbearably slow when the number of hexes grows beyond a few thousand.
>
> Given that RegularPolygon can do the trick, it seems likely that RegularPolyCollection should also be able to?
>
> This is what I tried:
>
> ax = gca()
> collection = RegularPolyCollection(
> 6, # a pentagon
> rotation=(np.pi/7,),
> sizes=(.5/np.sqrt(3),),
> facecolors = cc,
> edgecolors = None,
> linewidths = (1,),
> offsets = zip(xx,yy),
> transOffset = ax.transData,
> )
> #collection.set_transform(ax.transData)
> ax.add_collection(collection, autolim=True)
>
> ax.autoscale_view()
> ax.figure.canvas.draw()
>
> This produces dots of minute sizes at the desired coordinates. I can tweak the size to make them bigger, but they don’t scale with the axes, as for the scatter_demo script used initially. Digging in the docs, I found a reference to the set_transform() method of Artists, so I tried setting that to ax.transData (the line commented out in the above snippet), and voila! I have hexagons covering the plane again. Strangely enough, they’re not in the right place anymore (and the locations change when zooming in or out), the sizes aren’t _quite_ right, the autoscaling of axes appear to believe the patches are where I wanted them to be, not where they appear on the plot, results are very different if saving to a figure instead of drawing to a figure window, etc.
>
> Is there a way I can make RegularPolyCollection patches transform with axes coordinates in the same way that RegularPolygon patches do?
>
> Am I barking up the wrong tree, is there another, blindingly obvious, way I should be doing this?
>
> The observant reader will also notice the strange rotation keyword given to RegularPolyCollection. This keyword is ignored in the macosx backend, and I have been unable to find out why.
>
> Thank you for all tips and pointers
>
> --Tom Grydeland
>
>
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Nathan,
Thanks for bringing this up. It looks like the short-term fix is to 
make the documentation match the code. Longer term, it seems to me like 
this is the sort of thing that should be deprecated; it doesn't belong 
in matplotlib any more.
Would you open an issue on Github, please? Even better: submit a pull 
request that fixes the documentation.
Eric
On 2014年04月25日 1:26 AM, Nathan Lindop wrote:
> Hello,
>
> I have been using the matplotlib.mlab.entropy function and have noticed
> that it may be incorrect. I have posted a question on stackoverflow here:
> http://stackoverflow.com/questions/23291576/matplotlib-mlab-entropy-calculation-incorrect
>
> I thought I would should it on the mailing list too. Does anyone have
> any ideas?
>
> Thanks,
> Nathan
>
>
> ------------------------------------------------------------------------------
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>
>
>
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>

You might have more luck reading in that data (dates with mixed format)
with pandas than numpy.
On Fri, Apr 25, 2014 at 2:37 AM, Mark Bakker <ma...@gm...> wrote:
> Thanks, Andreas, but it doesn't quite work.
>
> This works for me (I manually changed all dates to 'day-month-year' for
> testing):
>
> a = loadtxt('test.csv',converters={2:strpdate2num('%d-%m-%Y')})
>
> But when I define the same function in a separate function, as you
> suggested:
>
> def conv_date(s):
> return strpdate2num('%d-%m-%Y')
>
> and do
>
> a = loadtxt('test.csv',converters={2:conv_date})
>
> I get the non-descript error:
>
> loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols,
> unpack, ndmin)
> 847 fh.close()
> 848
> --> 849 X = np.array(X, dtype)
> 850 # Multicolumn data are returned with shape (1, N, M), i.e.
> 851 # (1, 1, M) for a single row - remove the singleton dimension
> there
>
> SystemError: error return without exception set
>
> Any suggestions?
>
> Thanks, Mark
>
>
>
>
> On Fri, Apr 25, 2014 at 11:17 AM, Andreas Hilboll <li...@hi...>wrote:
>
>> On 25.04.2014 11:02, Mark Bakker wrote:
>> > OK, I figured out I can use:
>> > converters={0:strpdate2num('%d-%m-%y')}
>> >
>> > What now if part of my dates are given as 'day-month-year' and part as
>> > 'day/month/year' in the same file (I know, who does that, an I could do
>> > a replace first and then read it in). Can I specify both formats for the
>> > converter? I guess not....
>>
>> Try this:
>>
>> def _conv_date(s):
>> try:
>> return strpdate2num('%d-%m-%y')
>> except Exception: # figure out which exception class to use
>> return strpdate2num('%d/%m/%y')
>>
>> converters={0:_conv_date}
>>
>> Cheers, Andreas.
>>
>>
>> >
>> > Thanks,
>> >
>> > Mark
>> >
>> >
>> >
>> > On Fri, Apr 25, 2014 at 10:46 AM, Mark Bakker <ma...@gm...
>> > <mailto:ma...@gm...>> wrote:
>> >
>> > Hello List,
>> >
>> > datestr2num works great when dates are stored as month/day/year (as
>> > American like).
>> >
>> > Europeans store them as day/month/year.
>> >
>> > Any quick function to convert a day/month/year string do a date? Is
>> > there an eu version: datestr2numeu?
>> >
>> > Thanks,
>> >
>> > Mark
>> >
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Start Your Social Network Today - Download eXo Platform
>> > Build your Enterprise Intranet with eXo Platform Software
>> > Java Based Open Source Intranet - Social, Extensible, Cloud Ready
>> > Get Started Now And Turn Your Intranet Into A Collaboration Platform
>> > http://p.sf.net/sfu/ExoPlatform
>> >
>> >
>> >
>> > _______________________________________________
>> > Matplotlib-users mailing list
>> > Mat...@li...
>> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>> >
>>
>>
>> --
>> -- Andreas.
>>
>
>
>
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
>
>

Hello,
I have been using the matplotlib.mlab.entropy function and have noticed that it may be incorrect. I have posted a question on stackoverflow here:
http://stackoverflow.com/questions/23291576/matplotlib-mlab-entropy-calculation-incorrect
I thought I would should it on the mailing list too. Does anyone have any ideas?
Thanks,
Nathan

Hi all,
I will explain what I’m trying to achieve first, then the approaches I’ve attempted so far, with results.
I have data on a 2D grid which I want to present as an image — a la pyplot.imshow() — except that the grid is hexagonal, not rectangular. The grid can be represented in multiple ways, I use a regular 2D array with the convention that the lower left hex is (0,0), x increases to the right (crossing vertical hex boundaries) and y increases upwards slanting to the right.
Ideally, I’d also be able to have a colorbar.
I’m giving my routines three input vectors: x, y and c. X and y are initially integers, then transformed to centerpoint coordinates using
 x, y = x+.5*y, y*np.cos(np.pi/6)
while c is used to look up values in a colormap.
I first tried to adapt ‘scatter_demo2.py’ to my needs. Unfortunately, the pyplot.scatter routine fails when given ‘c’ or ’s’ keywords, as has been reported elsewhere by somebody else:
 http://stackoverflow.com/questions/20524888/attributeerror-numpy-ndarray-object-has-no-attribute-get-matrix
I’ve dug around in the code for a bit without finding out how this arises. It seems to me it has to do with how transforms are being handed around and at what point their representation is changed from objects to pure matrices. This backend appears to expect to see objects only, but is handed matrices instead. I’ve hacked my way around that one in backends/backend_macosx.py by changing lines around 79-80 from
 master_transform = master_transform.get_matrix()
 all_transforms = [t.get_matrix() for t in all_transforms]
to
 try:
 master_transform = master_transform.get_matrix()
 except AttributeError: pass
 try:
 all_transforms = [t.get_matrix() for t in all_transforms]
 except AttributeError: pass
(which is a dirty hack, but I don’t know how to do it right)
Now I can run the scatter_demo2 script, and I can obviously have it produce hexes at uniform size, but the size of the hexagons are set independently of the axes. Good for symbols used to mark arbitrary coordinates, not so good when I try to cover the plane without gaps.
Next, I’ve tried creating the patches one by one, essentially this:
 r = 1./np.sqrt(3)
 for xy, cc in zip(zip(x, y), c):
 hexp = mpl.patches.RegularPolygon(xy, 6, radius=r, facecolor=cc, edgecolor=’none')
 ax.add_patch(hexp)
 ax.autoscale_view()
 ax.figure.canvas.draw()
This works as I want it to, but becomes unbearably slow when the number of hexes grows beyond a few thousand.
Given that RegularPolygon can do the trick, it seems likely that RegularPolyCollection should also be able to?
This is what I tried:
 ax = gca()
 collection = RegularPolyCollection(
 6, # a pentagon
 rotation=(np.pi/7,),
 sizes=(.5/np.sqrt(3),),
 facecolors = cc,
 edgecolors = None,
 linewidths = (1,),
 offsets = zip(xx,yy),
 transOffset = ax.transData,
 )
 #collection.set_transform(ax.transData)
 ax.add_collection(collection, autolim=True)
 ax.autoscale_view()
 ax.figure.canvas.draw()
This produces dots of minute sizes at the desired coordinates. I can tweak the size to make them bigger, but they don’t scale with the axes, as for the scatter_demo script used initially. Digging in the docs, I found a reference to the set_transform() method of Artists, so I tried setting that to ax.transData (the line commented out in the above snippet), and voila! I have hexagons covering the plane again. Strangely enough, they’re not in the right place anymore (and the locations change when zooming in or out), the sizes aren’t _quite_ right, the autoscaling of axes appear to believe the patches are where I wanted them to be, not where they appear on the plot, results are very different if saving to a figure instead of drawing to a figure window, etc.
Is there a way I can make RegularPolyCollection patches transform with axes coordinates in the same way that RegularPolygon patches do?
Am I barking up the wrong tree, is there another, blindingly obvious, way I should be doing this?
The observant reader will also notice the strange rotation keyword given to RegularPolyCollection. This keyword is ignored in the macosx backend, and I have been unable to find out why.
Thank you for all tips and pointers
--Tom Grydeland

Thanks, Andreas, but it doesn't quite work.
This works for me (I manually changed all dates to 'day-month-year' for
testing):
a = loadtxt('test.csv',converters={2:strpdate2num('%d-%m-%Y')})
But when I define the same function in a separate function, as you
suggested:
def conv_date(s):
 return strpdate2num('%d-%m-%Y')
and do
a = loadtxt('test.csv',converters={2:conv_date})
I get the non-descript error:
loadtxt(fname, dtype, comments, delimiter, converters, skiprows, usecols,
unpack, ndmin)
 847 fh.close()
 848
--> 849 X = np.array(X, dtype)
 850 # Multicolumn data are returned with shape (1, N, M), i.e.
 851 # (1, 1, M) for a single row - remove the singleton dimension
there
SystemError: error return without exception set
Any suggestions?
Thanks, Mark
On Fri, Apr 25, 2014 at 11:17 AM, Andreas Hilboll <li...@hi...> wrote:
> On 25.04.2014 11:02, Mark Bakker wrote:
> > OK, I figured out I can use:
> > converters={0:strpdate2num('%d-%m-%y')}
> >
> > What now if part of my dates are given as 'day-month-year' and part as
> > 'day/month/year' in the same file (I know, who does that, an I could do
> > a replace first and then read it in). Can I specify both formats for the
> > converter? I guess not....
>
> Try this:
>
> def _conv_date(s):
> try:
> return strpdate2num('%d-%m-%y')
> except Exception: # figure out which exception class to use
> return strpdate2num('%d/%m/%y')
>
> converters={0:_conv_date}
>
> Cheers, Andreas.
>
>
> >
> > Thanks,
> >
> > Mark
> >
> >
> >
> > On Fri, Apr 25, 2014 at 10:46 AM, Mark Bakker <ma...@gm...
> > <mailto:ma...@gm...>> wrote:
> >
> > Hello List,
> >
> > datestr2num works great when dates are stored as month/day/year (as
> > American like).
> >
> > Europeans store them as day/month/year.
> >
> > Any quick function to convert a day/month/year string do a date? Is
> > there an eu version: datestr2numeu?
> >
> > Thanks,
> >
> > Mark
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Start Your Social Network Today - Download eXo Platform
> > Build your Enterprise Intranet with eXo Platform Software
> > Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> > Get Started Now And Turn Your Intranet Into A Collaboration Platform
> > http://p.sf.net/sfu/ExoPlatform
> >
> >
> >
> > _______________________________________________
> > Matplotlib-users mailing list
> > Mat...@li...
> > https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> >
>
>
> --
> -- Andreas.
>

On 25.04.2014 11:02, Mark Bakker wrote:
> OK, I figured out I can use:
> converters={0:strpdate2num('%d-%m-%y')}
> 
> What now if part of my dates are given as 'day-month-year' and part as
> 'day/month/year' in the same file (I know, who does that, an I could do
> a replace first and then read it in). Can I specify both formats for the
> converter? I guess not....
Try this:
 def _conv_date(s):
 try:
 return strpdate2num('%d-%m-%y')
 except Exception: # figure out which exception class to use
 return strpdate2num('%d/%m/%y')
 converters={0:_conv_date}
Cheers, Andreas.
> 
> Thanks,
> 
> Mark
> 
> 
> 
> On Fri, Apr 25, 2014 at 10:46 AM, Mark Bakker <ma...@gm...
> <mailto:ma...@gm...>> wrote:
> 
> Hello List,
> 
> datestr2num works great when dates are stored as month/day/year (as
> American like).
> 
> Europeans store them as day/month/year.
> 
> Any quick function to convert a day/month/year string do a date? Is
> there an eu version: datestr2numeu?
> 
> Thanks,
> 
> Mark
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Start Your Social Network Today - Download eXo Platform
> Build your Enterprise Intranet with eXo Platform Software
> Java Based Open Source Intranet - Social, Extensible, Cloud Ready
> Get Started Now And Turn Your Intranet Into A Collaboration Platform
> http://p.sf.net/sfu/ExoPlatform
> 
> 
> 
> _______________________________________________
> Matplotlib-users mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-users
> 
-- 
-- Andreas.

OK, I figured out I can use:
converters={0:strpdate2num('%d-%m-%y')}
What now if part of my dates are given as 'day-month-year' and part as
'day/month/year' in the same file (I know, who does that, an I could do a
replace first and then read it in). Can I specify both formats for the
converter? I guess not....
Thanks,
Mark
On Fri, Apr 25, 2014 at 10:46 AM, Mark Bakker <ma...@gm...> wrote:
> Hello List,
>
> datestr2num works great when dates are stored as month/day/year (as
> American like).
>
> Europeans store them as day/month/year.
>
> Any quick function to convert a day/month/year string do a date? Is there
> an eu version: datestr2numeu?
>
> Thanks,
>
> Mark
>

Hello List,
datestr2num works great when dates are stored as month/day/year (as
American like).
Europeans store them as day/month/year.
Any quick function to convert a day/month/year string do a date? Is there
an eu version: datestr2numeu?
Thanks,
Mark

On 4/23/2014 2:41 PM, Eric Firing wrote:
> On 2014年04月23日 11:19 AM, Michael Mossey wrote:
>> I'm sorry, these are questions that could be found in the Axes
>> documentation, but I really don't feel like scrolling through 100 pages
>> that are irrelevant hoping I can find the relevant functions, which I
>> don't even know what they are called. Is there ever going to be a
>> concise listing of functions? Also there seem to be a lot of
> PRs for doc improvements are welcome!
>
>> undocumented functions related to bounding boxes and copying from the
>> background--I had to find Stack Overflow examples to learn about those.
> Doesn't the search box in the html docs help? Or just plain browser
> searching when you are looking at the Axes API docs?
>
> I also find that ipython is very helpful, with tab completion and the
> question mark for getting the doc string. E.g., make an axes object and
> then use tab completion to see the methods that start with auto, and
> follow with a question mark to see the docstring. Or a double question
> mark to see the code.
Thanks for the suggestions, I'll try them. I working with WinPython so I 
think I already have ipython and Spyder to help me.
Mike