Re: [Matplotlib-users] open ascii grid data and plot

[Benjamin Root]

On Wednesday, March 7, 2012, questions anon 
wrote:
> Hi all,
> I am still having a problem with the same code. I am not sure if maybe
the problem is how I read the data in as numpy.genfromtxt
> Is there a step I need to take to convert the data to numpy array to then
read into matplotlib?

Sorry for the delay.

As far as I can tell, you are doing everything correctly.  The error you
are getting would seem to indicate something wrong with your EPD install,
or perhaps a conflict with another install on numpy or mpl.

I would suggest completely clearing out your python and EPD install and
reinstalling it fresh.

Ben Root
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[Matplotlib-users] Centering Text with axes_divider

[Patrick Marsh]

Greetings,

Let me begin by saying that I've fallen in love with ImageGrid. I love the
control it gives me in setting up plots, and I really like the control it
offers for setting up a colorbar. Unfortunately, like all relationships,
ImageGrid and I have hit a rough patch.

I like to manually place titles and other boxes of texts on plots that I
make using ImageGrid. However, to center things I have to know what the
axes bounds are so I can do the centering calculations. Unfortunately, when
using ImageGrid, or axes_divider, I have yet to find a way to get the axes
bounds that are actually used to do the plotting. When I try to use

ax.get_position().bounds

I get the pre-adjusted bounds, even if I use plt.draw() before requesting
the axes_positions. This means the only way I can center the text is by
guessing what the final axes bounds will be.  Is there any way of getting
the final bounds? It appears anchored text is able to do it, but I haven't
been able to...


Here's a self-contained example script that demonstrates the problem.  I
don't use ImageGrid, instead using axes_divider, however this is the same
problem that AxesGrid has. (I'm guessing this is because ImageGrid
ultimately does what I did here behind the scenes.)

https://gist.github.com/2004869


Thanks for any help!


Patrick
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Re: [Matplotlib-users] open ascii grid data and plot

[Paul Hobson]

In my GIS experience, rasters don't have prj files. That's something
that seems to be pretty specific to ESRI shapefiles. Point is, I don't
think that's going to help you.

All of the basemap examples use netcdf files. I think your path of
least resistance right now is to figure out how to convert your text
file to a numpy array (check?), and then that array to a netcdf that
is structured such that you can follow the basemap examples:
http://matplotlib.github.com/basemap/users/examples.html

Hope that helps,
-paul

On Wed, Mar 7, 2012 at 8:21 PM, questions anon  wrote:
> Hi all,
> I am still having a problem with the same code. I am not sure if maybe the
> problem is how I read the data in as numpy.genfromtxt
> Is there a step I need to take to convert the data to numpy array to then
> read into matplotlib?
> Thanks
>
>
> On Fri, Mar 2, 2012 at 11:49 AM, questions anon 
> wrote:
>>
>> python, numpy through enthought -
>> Python 2.7.2 |EPD 7.1-1 (32-bit)| (default, Jul  3 2011, 15:13:59) [MSC
>> v.1500 32 bit (Intel)] on win32
>> imports at the top of the script:
>>
>> import numpy as N
>> import matplotlib.pyplot as plt
>> from numpy import ma as MA
>> from mpl_toolkits.basemap import Basemap
>> import os
>>
>>
>>
>> On Thu, Mar 1, 2012 at 4:42 PM, Benjamin Root  wrote:
>>>
>>>
>>>
>>> On Wednesday, February 29, 2012, questions anon wrote:

 I have had some progress reading in the data but am unsure how to create
 lats and lons from the info I have (see above).
 the error I am receiving is:

 Traceback (most recent call last):
   File "d:\plotrainfall.py", line 40, in 
     CS = map.contourf(x,y, f, 15,cmap=plt.cm.jet)
   File "C:\Python27\lib\site-packages\mpl_toolkits\basemap\__init__.py",
 line 3072, in contourf

 np.logical_or(outsidemask,np.logical_or(ma.getmaskarray(data),xymask))
 AttributeError: logical_or


 from the below code:


 onefile=r"E:/test_in/r19000117.txt"

 f=N.genfromtxt(onefile, skip_header=6,  dtype=float, names=True)
 print f


 map = Basemap(projection='merc',llcrnrlat=-45,urcrnrlat=-9,

 llcrnrlon=111.975,urcrnrlon=156.525,lat_ts=0,resolution='i')
 map.drawcoastlines()
 map.drawstates()
 xi=N.linspace(111.975, 156.275, 886)
 yi=N.linspace(-44.525, -9.975, 691)
 x,y=map(*N.meshgrid(xi,yi))
 plt.title('rainfall')
 CS = map.contourf(x,y, f, 15,cmap=plt.cm.jet)
 l,b,w,h =0.1,0.1,0.8,0.8
 cax = plt.axes([l+w+0.025, b, 0.025, h])
 plt.colorbar(CS,cax=cax, drawedges=True)
 plt.savefig((os.path.join(OutputFolder, 'rainfall.png')))
 plt.show()
 plt.close()


>>>
>>> How did you install numpy?  Which version are you using?  What are your
>>> imports at the top of this script?
>>>
>>> Ben Root
>>
>>
>
>
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Re: [Matplotlib-users] imshow of scalar 2D array using a shared color scale

[Benjamin Root]

On Thursday, March 8, 2012, Wolfgang Draxinger <
wdraxinger.maill...@draxit.de> wrote:
> Hi,
>
> I've got a datasets of a pixel particle detector for a number of
> independent events. I'd like to show them in a row but have them all
> use the same value and thus color range. What's the most straigtforward
> way to do this?
>
>
> Cheers,
>
> Wolfgang Draxinger

Quick and dirty way is to set vmin and vmax for each of them using common
values.  You could also pass in a "norm" argument that does something
similar.

Ben Root
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Re: [Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

[Benjamin Root]

On Thursday, March 8, 2012, Benjamin Root  wrote:
>
>
> On Thursday, March 8, 2012, Wolfgang Draxinger <
wdraxinger.maill...@draxit.de> wrote:
>> Hi,
>>
>> I've a problem with some errorbars not drawn correctly in (double)
>> logarithmic plots. See this PDF for an example:
>>
>> http://dl.wolfgang-draxinger.net/C6_77MeV_raddamage.pdf
>>
>> The vertical errorbar for the datapoint at x=1e3 are not drawn. Similar
>> also happens for some horizontal errorbars. Using the very same drawing
>> commands, except switching to a logarithmic scaling the errorbars draw
>> just fine.
>>
>> So what's going on there?
>>
>>
>> Wolfgang Draxinger
>
> Which version of matplotlib are you using?  Also, are you setting the log
scale before (preferred) or after (won't work) the call to hist()?
>
> Ben Root


Grrr, not hist(), but errorbar().

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Re: [Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

[Benjamin Root]

On Thursday, March 8, 2012, Wolfgang Draxinger <
wdraxinger.maill...@draxit.de> wrote:
> Hi,
>
> I've a problem with some errorbars not drawn correctly in (double)
> logarithmic plots. See this PDF for an example:
>
> http://dl.wolfgang-draxinger.net/C6_77MeV_raddamage.pdf
>
> The vertical errorbar for the datapoint at x=1e3 are not drawn. Similar
> also happens for some horizontal errorbars. Using the very same drawing
> commands, except switching to a logarithmic scaling the errorbars draw
> just fine.
>
> So what's going on there?
>
>
> Wolfgang Draxinger

Which version of matplotlib are you using?  Also, are you setting the log
scale before (preferred) or after (won't work) the call to hist()?

Ben Root
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[Matplotlib-users] Errorbars not drawn correctly in logarithmic scales

[Wolfgang Draxinger]

Hi,

I've a problem with some errorbars not drawn correctly in (double)
logarithmic plots. See this PDF for an example:

http://dl.wolfgang-draxinger.net/C6_77MeV_raddamage.pdf

The vertical errorbar for the datapoint at x=1e3 are not drawn. Similar
also happens for some horizontal errorbars. Using the very same drawing
commands, except switching to a logarithmic scaling the errorbars draw
just fine.

So what's going on there?


Wolfgang Draxinger

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[Matplotlib-users] imshow of scalar 2D array using a shared color scale

[Wolfgang Draxinger]

Hi,

I've got a datasets of a pixel particle detector for a number of
independent events. I'd like to show them in a row but have them all
use the same value and thus color range. What's the most straigtforward
way to do this?


Cheers,

Wolfgang Draxinger

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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Michael Droettboom]

There is a proposed solution to all of this here:

https://github.com/matplotlib/matplotlib/pull/746

Please test -- I don't have any nxutils-using code myself, and 
matplotlib itself has none.  We should probably convert some of the 
nxutils code in the wild into some unit tests.


Mike

On 03/08/2012 12:37 PM, Benjamin Root wrote:



On Thu, Mar 8, 2012 at 11:16 AM, Benjamin Root > wrote:




On Thu, Mar 8, 2012 at 10:47 AM, John Hunter mailto:jdh2...@gmail.com>> wrote:



On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root
mailto:ben.r...@ou.edu>> wrote:


+1 as well.  I just took another look at the Path object
and I see no such function.  The lack of this function is
a problem for me as well in my existing apps.  In order to
deprecate nxutils, this functionality needs to be added to
Path.  Otherwise, nxutils *must* be reinstated before the
next release.


Michael has already agreed to make a nxutils compatibility
layer that would have the same interface as the old nxutils.
 So we are talking about performance, not core functionality.

We should remember that Michael did the lion's share of the
work on  porting mpl to python 3
(https://github.com/matplotlib/matplotlib/pull/565/commits).
 He elected not to port all of the C++ if he could replace
some of the functionality with the core.  So those who rely on
bare metal speed the you are getting in nxutils should step up
to either :

1) help with the port of nxutils to python 3

2) help with exposing methods in _path.cpp that are almost as
fast or faster

3) live with slower speeds in the compatibility layer he has
agreed to write

4) ask (nicely) for someone to help you

I prefer option 2 because this is fairly easy and avoids code
redundancy.  It would take just a few lines of extra code to
do this with the python sequence protocol as inputs and python
lists as return values.  It would take a bit more to support
numpy arrays as input and output, and we should get input from
Michael about the desirability of making _path.cpp depend on
numpy.  I don't see the harm, but I'd like to verify.

In my opinion, a slower implementation in a
nxutils.py compatibility module is not a release stopper, even
if it is undesirable.

JDH


Don't get me wrong.  If help is needed, I can certainly provide it
since it is my itch.  I am just a little exasperated with how this
issue has been handled up to now.  The shim is a very good idea
and it should have been done back when the py3k merge happened.  I
didn't press the issue then because I was traveling and didn't
have time to examine the issue closely, and having _nxutils.so
still in my build hide the problem from me (my own fault).

As for shim implementation, I would be willing to accept a
slightly slower function now (with the promise of improvements
later), but if the implementation is too much slower, then effort
will need to be made to get it up to acceptable levels.  I know of
several users **cough**my future employer**cough** who uses
functionality such as this, and they would not be happy if their
products are dragged down by such a bottleneck.

Probably about time I dug more into CXX wrapped stuff...

Ben Root



Looking over the code, it looks like we could generalize 
point_in_path_impl() into points_in_path_impl().  The current code 
iterates through the path vertices to test a single point.  Putting 
this action inside a loop (for each point that we want to test) would 
mean that this iterator has to be processed each time, which I suspect 
would kill performance when the number of vertices is far greater than 
the number of test points.


Tinkering

Ben Root



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Re: [Matplotlib-users] histogram and a line

[Paul Hobson]

Jerzy et al,

Check out the axvline method (of pyplot or an axes object). You'll
only have to specify the x-value, and it'll won't rescale your y-axis.
-paul

On Thu, Mar 8, 2012 at 4:50 AM, Jerzy Karczmarczuk
 wrote:
> Nicolas Rougier, (to Mic, who can't see a histogram and a line
> simultaneously):
>
>> You need to specify the ylim because your height may be larger than your 
>> histogram and then you cannot see it.
> I suspect something similar. The height of matplot_hist.png is 0.040.
> The line goes from 0 to 300. The histogram reduces to the bottom line.
> There is no immediate relation between max(hist_data) and the height of
> a *normed* histogram.
>
> And, please, if you want to point out the difficulties in making your
> programs fulfil your aims, show the REAL, COMPLETE programs, perhaps
> with fake, random data, but without useless : "hist_data=[]"
>
> And don't call a mean: "median" or vice-versa...
>
> Scaling the axes is easy. "ylim" should be changed, use also the
> "extent" parameter (see doc). Drawing axes shifted, as in hist.png is a
> bit more involved, and I don't know if you really want that as well.
>
> Jerzy K.
>
>
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Re: [Matplotlib-users] Error when saving as PDF using $\alpha$ and 'text.usetex':True

[Jouni K . Seppänen]

Alejandro Weinstein  writes:

> TypeError: unicode argument expected, got 'str'
> I am using MPL verion 1.2.x (built from commit 396a6446).

That reminds me of a problem fixed in commit 680edf7, so could you
either try cherry-picking that commit or updating to a later revision?
Your test case doesn't produce an error on a recent-ish master.

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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Michael Droettboom]

On 03/08/2012 12:35 PM, Michael Droettboom wrote:
It shouldn't be a problem to build a compatibility shim -- I'd much 
rather do that than have multiple functions


Oops -- hit send too soon.  I meant to say "I'd much rather do that than 
have multiple functions that do virtually the same thing"


Mike



Mike

On 03/08/2012 12:16 PM, Benjamin Root wrote:



On Thu, Mar 8, 2012 at 10:47 AM, John Hunter > wrote:




On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root mailto:ben.r...@ou.edu>> wrote:


+1 as well.  I just took another look at the Path object and
I see no such function.  The lack of this function is a
problem for me as well in my existing apps.  In order to
deprecate nxutils, this functionality needs to be added to
Path.  Otherwise, nxutils *must* be reinstated before the
next release.


Michael has already agreed to make a nxutils compatibility layer
that would have the same interface as the old nxutils.  So we are
talking about performance, not core functionality.

We should remember that Michael did the lion's share of the work
on  porting mpl to python 3
(https://github.com/matplotlib/matplotlib/pull/565/commits).  He
elected not to port all of the C++ if he could replace some of
the functionality with the core.  So those who rely on bare metal
speed the you are getting in nxutils should step up to either :

1) help with the port of nxutils to python 3

2) help with exposing methods in _path.cpp that are almost as
fast or faster

3) live with slower speeds in the compatibility layer he has
agreed to write

4) ask (nicely) for someone to help you

I prefer option 2 because this is fairly easy and avoids code
redundancy.  It would take just a few lines of extra code to do
this with the python sequence protocol as inputs and python lists
as return values.  It would take a bit more to support numpy
arrays as input and output, and we should get input from Michael
about the desirability of making _path.cpp depend on numpy.  I
don't see the harm, but I'd like to verify.

In my opinion, a slower implementation in a
nxutils.py compatibility module is not a release stopper, even if
it is undesirable.

JDH


Don't get me wrong.  If help is needed, I can certainly provide it 
since it is my itch.  I am just a little exasperated with how this 
issue has been handled up to now.  The shim is a very good idea and 
it should have been done back when the py3k merge happened.  I didn't 
press the issue then because I was traveling and didn't have time to 
examine the issue closely, and having _nxutils.so still in my build 
hide the problem from me (my own fault).


As for shim implementation, I would be willing to accept a slightly 
slower function now (with the promise of improvements later), but if 
the implementation is too much slower, then effort will need to be 
made to get it up to acceptable levels.  I know of several users 
**cough**my future employer**cough** who uses functionality such as 
this, and they would not be happy if their products are dragged down 
by such a bottleneck.


Probably about time I dug more into CXX wrapped stuff...

Ben Root


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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Eric Firing]

On 03/08/2012 07:16 AM, Benjamin Root wrote:
>
>
> On Thu, Mar 8, 2012 at 10:47 AM, John Hunter  > wrote:
>
>
>
> On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root  > wrote:
>
>
> +1 as well.  I just took another look at the Path object and I
> see no such function.  The lack of this function is a problem
> for me as well in my existing apps.  In order to deprecate
> nxutils, this functionality needs to be added to Path.
> Otherwise, nxutils *must* be reinstated before the next release.
>
>
> Michael has already agreed to make a nxutils compatibility layer
> that would have the same interface as the old nxutils.  So we are
> talking about performance, not core functionality.
>
> We should remember that Michael did the lion's share of the work on
>   porting mpl to python 3
> (https://github.com/matplotlib/matplotlib/pull/565/commits).  He
> elected not to port all of the C++ if he could replace some of the
> functionality with the core.  So those who rely on bare metal speed
> the you are getting in nxutils should step up to either :
>
> 1) help with the port of nxutils to python 3
>
> 2) help with exposing methods in _path.cpp that are almost as fast
> or faster
>
> 3) live with slower speeds in the compatibility layer he has agreed
> to write
>
> 4) ask (nicely) for someone to help you
>
> I prefer option 2 because this is fairly easy and avoids code
> redundancy.  It would take just a few lines of extra code to do this
> with the python sequence protocol as inputs and python lists as
> return values.  It would take a bit more to support numpy arrays as
> input and output, and we should get input from Michael about the
> desirability of making _path.cpp depend on numpy.  I don't see the
> harm, but I'd like to verify.
>
> In my opinion, a slower implementation in a
> nxutils.py compatibility module is not a release stopper, even if it
> is undesirable.
>
> JDH
>
>
> Don't get me wrong.  If help is needed, I can certainly provide it since
> it is my itch.  I am just a little exasperated with how this issue has
> been handled up to now.  The shim is a very good idea and it should have
> been done back when the py3k merge happened.  I didn't press the issue
> then because I was traveling and didn't have time to examine the issue
> closely, and having _nxutils.so still in my build hide the problem from
> me (my own fault).
>
> As for shim implementation, I would be willing to accept a slightly
> slower function now (with the promise of improvements later), but if the
> implementation is too much slower, then effort will need to be made to
> get it up to acceptable levels.  I know of several users **cough**my
> future employer**cough** who uses functionality such as this, and they
> would not be happy if their products are dragged down by such a bottleneck.

For my own purposes I decided to simply copy the pnpoly core and write a 
cython wrapper, since nxutils did not seem to have a secure future in 
mpl.  If anyone is interested in this approach, see the files _pnpoly.c
and utility.pyx (last function therein) in the num/src subdirectory of 
my "pycurrents" repo: 
http://currents.soest.hawaii.edu/hgstage/pycurrents/shortlog/tip.  The 
wrapper is brand-new and very lightly tested; I suspect it could be 
improved considerably.  (Also, at present it has only the points_in_poly 
function.)

>
> Probably about time I dug more into CXX wrapped stuff...

mpl strategy question: stick with CXX and hand-wrapping exclusively, or 
start using cython?

Eric

>
> Ben Root
>
>
>
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Benjamin Root]

On Thu, Mar 8, 2012 at 11:16 AM, Benjamin Root  wrote:

>
>
> On Thu, Mar 8, 2012 at 10:47 AM, John Hunter  wrote:
>
>>
>>
>> On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root  wrote:
>>
>>>
>>> +1 as well.  I just took another look at the Path object and I see no
>>> such function.  The lack of this function is a problem for me as well in my
>>> existing apps.  In order to deprecate nxutils, this functionality needs to
>>> be added to Path.  Otherwise, nxutils *must* be reinstated before the next
>>> release.
>>>
>>>
>> Michael has already agreed to make a nxutils compatibility layer that
>> would have the same interface as the old nxutils.  So we are talking about
>> performance, not core functionality.
>>
>> We should remember that Michael did the lion's share of the work on
>>  porting mpl to python 3 (
>> https://github.com/matplotlib/matplotlib/pull/565/commits).  He elected
>> not to port all of the C++ if he could replace some of the functionality
>> with the core.  So those who rely on bare metal speed the you are getting
>> in nxutils should step up to either :
>>
>> 1) help with the port of nxutils to python 3
>>
>> 2) help with exposing methods in _path.cpp that are almost as fast or
>> faster
>>
>> 3) live with slower speeds in the compatibility layer he has agreed to
>> write
>>
>> 4) ask (nicely) for someone to help you
>>
>> I prefer option 2 because this is fairly easy and avoids code redundancy.
>>  It would take just a few lines of extra code to do this with the python
>> sequence protocol as inputs and python lists as return values.  It would
>> take a bit more to support numpy arrays as input and output, and we should
>> get input from Michael about the desirability of making _path.cpp depend on
>> numpy.  I don't see the harm, but I'd like to verify.
>>
>> In my opinion, a slower implementation in a
>> nxutils.py compatibility module is not a release stopper, even if it is
>> undesirable.
>>
>> JDH
>>
>
> Don't get me wrong.  If help is needed, I can certainly provide it since
> it is my itch.  I am just a little exasperated with how this issue has been
> handled up to now.  The shim is a very good idea and it should have been
> done back when the py3k merge happened.  I didn't press the issue then
> because I was traveling and didn't have time to examine the issue closely,
> and having _nxutils.so still in my build hide the problem from me (my own
> fault).
>
> As for shim implementation, I would be willing to accept a slightly slower
> function now (with the promise of improvements later), but if the
> implementation is too much slower, then effort will need to be made to get
> it up to acceptable levels.  I know of several users **cough**my future
> employer**cough** who uses functionality such as this, and they would not
> be happy if their products are dragged down by such a bottleneck.
>
> Probably about time I dug more into CXX wrapped stuff...
>
> Ben Root
>


Looking over the code, it looks like we could generalize
point_in_path_impl() into points_in_path_impl().  The current code iterates
through the path vertices to test a single point.  Putting this action
inside a loop (for each point that we want to test) would mean that this
iterator has to be processed each time, which I suspect would kill
performance when the number of vertices is far greater than the number of
test points.

Tinkering

Ben Root
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Michael Droettboom]

_path.cpp already has a  number of methods that use Numpy arrays (John 
is mistaken that it doesn't depend on Numpy), so adding another is no 
problem.


It was my understanding that nxutils was an internal usage module and 
not part of the public API, and therefore could be removed as long as 
all of the internal references were updated.  It doesn't have a '_' 
prefix, so of course it being private wasn't explicit, but there are 
number of things in matplotlib that fall into that category.  
Apparently, I was mistaken and there are a lot of users using it from 
outside.  It shouldn't be a problem to build a compatibility shim -- I'd 
much rather do that than have multiple functions -- and adding a 
points_in_poly to _path.cpp should be pretty straightforward.


Mike

On 03/08/2012 12:16 PM, Benjamin Root wrote:



On Thu, Mar 8, 2012 at 10:47 AM, John Hunter > wrote:




On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root mailto:ben.r...@ou.edu>> wrote:


+1 as well.  I just took another look at the Path object and I
see no such function.  The lack of this function is a problem
for me as well in my existing apps.  In order to deprecate
nxutils, this functionality needs to be added to Path. 
Otherwise, nxutils *must* be reinstated before the next release.



Michael has already agreed to make a nxutils compatibility layer
that would have the same interface as the old nxutils.  So we are
talking about performance, not core functionality.

We should remember that Michael did the lion's share of the work
on  porting mpl to python 3
(https://github.com/matplotlib/matplotlib/pull/565/commits).  He
elected not to port all of the C++ if he could replace some of the
functionality with the core.  So those who rely on bare metal
speed the you are getting in nxutils should step up to either :

1) help with the port of nxutils to python 3

2) help with exposing methods in _path.cpp that are almost as fast
or faster

3) live with slower speeds in the compatibility layer he has
agreed to write

4) ask (nicely) for someone to help you

I prefer option 2 because this is fairly easy and avoids code
redundancy.  It would take just a few lines of extra code to do
this with the python sequence protocol as inputs and python lists
as return values.  It would take a bit more to support numpy
arrays as input and output, and we should get input from Michael
about the desirability of making _path.cpp depend on numpy.  I
don't see the harm, but I'd like to verify.

In my opinion, a slower implementation in a
nxutils.py compatibility module is not a release stopper, even if
it is undesirable.

JDH


Don't get me wrong.  If help is needed, I can certainly provide it 
since it is my itch.  I am just a little exasperated with how this 
issue has been handled up to now.  The shim is a very good idea and it 
should have been done back when the py3k merge happened.  I didn't 
press the issue then because I was traveling and didn't have time to 
examine the issue closely, and having _nxutils.so still in my build 
hide the problem from me (my own fault).


As for shim implementation, I would be willing to accept a slightly 
slower function now (with the promise of improvements later), but if 
the implementation is too much slower, then effort will need to be 
made to get it up to acceptable levels.  I know of several users 
**cough**my future employer**cough** who uses functionality such as 
this, and they would not be happy if their products are dragged down 
by such a bottleneck.


Probably about time I dug more into CXX wrapped stuff...

Ben Root


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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Benjamin Root]

On Thu, Mar 8, 2012 at 10:47 AM, John Hunter  wrote:

>
>
> On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root  wrote:
>
>>
>> +1 as well.  I just took another look at the Path object and I see no
>> such function.  The lack of this function is a problem for me as well in my
>> existing apps.  In order to deprecate nxutils, this functionality needs to
>> be added to Path.  Otherwise, nxutils *must* be reinstated before the next
>> release.
>>
>>
> Michael has already agreed to make a nxutils compatibility layer that
> would have the same interface as the old nxutils.  So we are talking about
> performance, not core functionality.
>
> We should remember that Michael did the lion's share of the work on
>  porting mpl to python 3 (
> https://github.com/matplotlib/matplotlib/pull/565/commits).  He elected
> not to port all of the C++ if he could replace some of the functionality
> with the core.  So those who rely on bare metal speed the you are getting
> in nxutils should step up to either :
>
> 1) help with the port of nxutils to python 3
>
> 2) help with exposing methods in _path.cpp that are almost as fast or
> faster
>
> 3) live with slower speeds in the compatibility layer he has agreed to
> write
>
> 4) ask (nicely) for someone to help you
>
> I prefer option 2 because this is fairly easy and avoids code redundancy.
>  It would take just a few lines of extra code to do this with the python
> sequence protocol as inputs and python lists as return values.  It would
> take a bit more to support numpy arrays as input and output, and we should
> get input from Michael about the desirability of making _path.cpp depend on
> numpy.  I don't see the harm, but I'd like to verify.
>
> In my opinion, a slower implementation in a
> nxutils.py compatibility module is not a release stopper, even if it is
> undesirable.
>
> JDH
>

Don't get me wrong.  If help is needed, I can certainly provide it since it
is my itch.  I am just a little exasperated with how this issue has been
handled up to now.  The shim is a very good idea and it should have been
done back when the py3k merge happened.  I didn't press the issue then
because I was traveling and didn't have time to examine the issue closely,
and having _nxutils.so still in my build hide the problem from me (my own
fault).

As for shim implementation, I would be willing to accept a slightly slower
function now (with the promise of improvements later), but if the
implementation is too much slower, then effort will need to be made to get
it up to acceptable levels.  I know of several users **cough**my future
employer**cough** who uses functionality such as this, and they would not
be happy if their products are dragged down by such a bottleneck.

Probably about time I dug more into CXX wrapped stuff...

Ben Root
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Ryan May]

On Thu, Mar 8, 2012 at 10:47 AM, John Hunter  wrote:
> I prefer option 2 because this is fairly easy and avoids code redundancy.
>  It would take just a few lines of extra code to do this with the python
> sequence protocol as inputs and python lists as return values.  It would
> take a bit more to support numpy arrays as input and output, and we should
> get input from Michael about the desirability of making _path.cpp depend on
> numpy.  I don't see the harm, but I'd like to verify.
>
> In my opinion, a slower implementation in a nxutils.py compatibility module
> is not a release stopper, even if it is undesirable.

 +1
Python 3 support is more important and, quite frankly,
overdue--especially given how long it's been sitting in the tree.

Ryan

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School of Meteorology
University of Oklahoma

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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[John Hunter]

On Thu, Mar 8, 2012 at 10:32 AM, Benjamin Root  wrote:

>
> +1 as well.  I just took another look at the Path object and I see no such
> function.  The lack of this function is a problem for me as well in my
> existing apps.  In order to deprecate nxutils, this functionality needs to
> be added to Path.  Otherwise, nxutils *must* be reinstated before the next
> release.
>
>
Michael has already agreed to make a nxutils compatibility layer that would
have the same interface as the old nxutils.  So we are talking about
performance, not core functionality.

We should remember that Michael did the lion's share of the work on
 porting mpl to python 3 (
https://github.com/matplotlib/matplotlib/pull/565/commits).  He elected not
to port all of the C++ if he could replace some of the functionality with
the core.  So those who rely on bare metal speed the you are getting in
nxutils should step up to either :

1) help with the port of nxutils to python 3

2) help with exposing methods in _path.cpp that are almost as fast or faster

3) live with slower speeds in the compatibility layer he has agreed to write

4) ask (nicely) for someone to help you

I prefer option 2 because this is fairly easy and avoids code redundancy.
 It would take just a few lines of extra code to do this with the python
sequence protocol as inputs and python lists as return values.  It would
take a bit more to support numpy arrays as input and output, and we should
get input from Michael about the desirability of making _path.cpp depend on
numpy.  I don't see the harm, but I'd like to verify.

In my opinion, a slower implementation in a nxutils.py compatibility module
is not a release stopper, even if it is undesirable.

JDH
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Re: [Matplotlib-users] Changing a single marker on a line

[Jerzy Karczmarczuk]

federico vaggi:
  I am drawing a line with n points, using a particle marker - 
something like:


x = np.linspace(1,10,11) ** 2
y = np.linspace(1,10,11)
ZZZ=plot(x,y,'ro')

Is there any way to change the 7th dot (7, 49) to be a blue star 
instead of a red circle?


I was considering using the scatter function to scatter points 1:6 and 
8:10 separately with 'ro' and then scatter 7 with the right 
properties... is that the easiest way?
I might be silly, but I believe that this IS the easiest way. In the 
program above ZZZ (which I put myself) is a list containing just ONE 
Line2D object, with a common set of properties, such as 
set_markerfacecolor() or set_marker_size(), and if you use them, all 
markers change. The data attached to the plot have no information about 
markers. So, if a way exists at all, to change just one marker, it would 
be quite involved, and a second plot seems easier than anything else.

But a true specialist might know The Real Magic...


Jerzy Karczmarczuk

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Re: [Matplotlib-users] Changing a single marker on a line

[Benjamin Root]

On Thu, Mar 8, 2012 at 10:18 AM, federico vaggi wrote:

> Hi,
>
> I have a very simple request - I am drawing a line with n points, using a
> particle marker - something like:
>
> x = np.linspace(1,10,11) ** 2
> y = np.linspace(1,10,11)
> plot(x,y,'ro')
>
> Is there any way to change the 7th dot (7, 49) to be a blue star instead
> of a red circle?
>
> I was considering using the scatter function to scatter points 1:6 and
> 8:10 separately with 'ro' and then scatter 7 with the right properties...
> is that the easiest way?
> Thanks a lot,
>
> Federico
>
>
Pretty much.  Although, you could possibly just do the first plot normally
and then have the scatter function simply plot the red star over the blue
circle (maybe make the star size bigger to fully cover the blue circle?).

Ben Root
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Benjamin Root]

On Thu, Mar 8, 2012 at 10:21 AM, Dharhas Pothina <
dharhas.poth...@twdb.texas.gov> wrote:

>
>  + one on this issue. One of the big advantages of the nxutils points in
> poly is that you could pass it a large numpy array of points and get back a
> mask. We found this to be significantly faster than using looping through
> the single point in poly algorithms from packages like shapely. Echoing
> Jorge's question how would we do this using contains_point().
>
>
>  - dharhas
>
>
>
> >>> Jorge Scandaliaris  3/8/2012 3:33 AM >>>
>
> Benjamin Root  writes:
>
> 
> >
> > Essentially, you make a Path object using the vertices, and then use its
> > contains_point() method.
> > Ben Root
> >
>
> OK, but given that contains_point works with a *single* point at a time, I
> have
> to call it for all my points which is a bit more cumbersome, or am I
> missing
> something?
>
> Jorge
>
>
>
+1 as well.  I just took another look at the Path object and I see no such
function.  The lack of this function is a problem for me as well in my
existing apps.  In order to deprecate nxutils, this functionality needs to
be added to Path.  Otherwise, nxutils *must* be reinstated before the next
release.

Ben Root
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[John Hunter]

On Thu, Mar 8, 2012 at 10:21 AM, Dharhas Pothina <
dharhas.poth...@twdb.texas.gov> wrote:

>
>  + one on this issue. One of the big advantages of the nxutils points in
> poly is that you could pass it a large numpy array of points and get back a
> mask. We found this to be significantly faster than using looping through
> the single point in poly algorithms from packages like shapely. Echoing
> Jorge's question how would we do this using contains_point().
>

One could modify src/_path.cpp to expose a "points_in_path" method so the
looping would be done in C++.  The underlying work is being done
in point_in_path_impl and exposed to python as  point_in_path.  It would
not be too much work to expose a points_in_path method, but we would have
to think about what arguments to take and to return.  _path.cpp does not
currently depend on numpy, and doing things via python list would be slower
than what we currently have in nxutils which is array aware.

JDH
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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Dharhas Pothina]

+ one on this issue. One of the big advantages of the nxutils points in poly is 
that you could pass it a large numpy array of points and get back a mask. We 
found this to be significantly faster than using looping through the single 
point in poly algorithms from packages like shapely. Echoing Jorge's question 
how would we do this using contains_point(). 


- dharhas 


>>> Jorge Scandaliaris  3/8/2012 3:33 AM >>>
Benjamin Root  writes:


>
> Essentially, you make a Path object using the vertices, and then use its
> contains_point() method.
> Ben Root
>

OK, but given that contains_point works with a *single* point at a time, I have
to call it for all my points which is a bit more cumbersome, or am I missing
something?

Jorge




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[Matplotlib-users] Changing a single marker on a line

[federico vaggi]

Hi,

I have a very simple request - I am drawing a line with n points, using a
particle marker - something like:

x = np.linspace(1,10,11) ** 2
y = np.linspace(1,10,11)
plot(x,y,'ro')

Is there any way to change the 7th dot (7, 49) to be a blue star instead of
a red circle?

I was considering using the scatter function to scatter points 1:6 and 8:10
separately with 'ro' and then scatter 7 with the right properties... is
that the easiest way?
Thanks a lot,

Federico
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[Matplotlib-users] pylab TclError: out of stack space - tkinter?

[spey_skaddet]

Hi, first time I'm posting here.  I'm fairly new to using pylab, and I
recently started using tkinter and the canvas widget, and I think I really
messed something up!  

I'm running a pdsoft version Python 2.6.2 (r262:71600, Sep 24 2009,
11:47:14) on UNIX (AFS system - not by choice)! 

Some background info, might be useful:
A few weeks ago I could happily run my .py script, though knew I may have
been doing something wrong (not opening/closing a loop as needed):  Every
time I would run my script, the 'canvas' with my images would pop up, and
then when I'd edit my file and re-run the script, I'd simply close the 'old'
canvas with the mouse when the new canvas would appear.  I could not figure
out how to elegantly exit using tkinter/canvas (tried Google searches but
didn't find anything after a while). 

Here is an excerpt from the script that worked (comments deleted): 

===
from Tkinter import *
window=Tk()
window.title('Canvas Window')
evol=Canvas(window,width=500,height=1000,background='white')
evol.pack()
evol.create_oval(90,210,170,290,fill="light blue")
evol.create_oval(350,230,390,270,fill="cyan")
evol.create_text(130,250,text='He',font=('verdana',11))
evol.create_line(170,250,350,250,width=3)
evol.create_polygon(350,250,340,240,340,260,fill="black")
evol.create_text(255,230,text=' MT ',font=('verdana',11))
evol.create_text(50,240,text='t=102',font=('verdana',11))
evol.create_text(50,260,text='M1=0.96',font=('verdana',11))
evol.create_text(440,260,text='M2=6.62',font=('verdana',11))
evol.create_text(440,240,text='a=258',font=('verdana',11))
retval = evol.postscript(file="blah.eps", height=1000, width=500,
colormode="color")
===

Anyway this all seemed to be working, until last week when I ran my script
again, and now I receive the following message: 

===
TclError  Traceback (most recent call last)

/MYDIR/ in ()

/MYDIR/evolgrid.py in ()
 26
 27 ## create a window:

---> 28 window=Tk()
 29 ## change window's name to 'Canvas Window':

 30 window.title('Canvas Window')

/usr/common/pdsoft/appl/pyapps/lib/python2.6/lib-tk/Tkinter.pyc in
__init__(self, screenName, baseName, className, useTk, sync, use)
   1641 baseName = baseName + ext
   1642 interactive = 0
-> 1643 self.tk = _tkinter.create(screenName, baseName, className,
interactive, wantobjects, useTk, sync, use)
   1644 if useTk:
   1645 self._loadtk()

TclError: out of stack space (infinite loop?)
===
  
Also, since this problem, now whenever I start up with 'ipython -pylab', and
type figure() (just as a test), I get the following message:

===
TclError  Traceback (most recent call last)

/MYDIR/ in ()

/usr/common/pdsoft/appl/pyapps/lib/python2.6/site-packages/matplotlib/pyplot.pyc
in figure(num, figsize, dpi, facecolor, edgecolor, frameon, FigureClass,
**kwargs)
268  frameon=frameon,
269 
FigureClass=FigureClass,
--> 270  **kwargs)
271
272 # make this figure current on button press event


/usr/common/pdsoft/appl/pyapps/lib/python2.6/site-packages/matplotlib/backends/backend_tkagg.pyc
in new_figure_manager(num, *args, **kwargs)
 81 FigureClass = kwargs.pop('FigureClass', Figure)
 82 figure = FigureClass(*args, **kwargs)
---> 83 window = Tk.Tk()
 84 canvas = FigureCanvasTkAgg(figure, master=window)
 85 figManager = FigureManagerTkAgg(canvas, num, window)

/usr/common/pdsoft/appl/pyapps/lib/python2.6/lib-tk/Tkinter.pyc in
__init__(self, screenName, baseName, className, useTk, sync, use)
   1641 baseName = baseName + ext
   1642 interactive = 0
-> 1643 self.tk = _tkinter.create(screenName, baseName, className,
interactive, wantobjects, useTk, sync, use)
   1644 if useTk:
   1645 self._loadtk()

TclError: out of stack space (infinite loop?)
===

So, something is really messed up!  Can someone help me?  :-/
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Re: [Matplotlib-users] histogram and a line

[Jerzy Karczmarczuk]

Nicolas Rougier, (to Mic, who can't see a histogram and a line 
simultaneously):

> You need to specify the ylim because your height may be larger than your 
> histogram and then you cannot see it.
I suspect something similar. The height of matplot_hist.png is 0.040. 
The line goes from 0 to 300. The histogram reduces to the bottom line. 
There is no immediate relation between max(hist_data) and the height of 
a *normed* histogram.

And, please, if you want to point out the difficulties in making your 
programs fulfil your aims, show the REAL, COMPLETE programs, perhaps 
with fake, random data, but without useless : "hist_data=[]"

And don't call a mean: "median" or vice-versa...

Scaling the axes is easy. "ylim" should be changed, use also the 
"extent" parameter (see doc). Drawing axes shifted, as in hist.png is a 
bit more involved, and I don't know if you really want that as well.

Jerzy K.


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Re: [Matplotlib-users] Has nxutils been removed from mpl?

[Jorge Scandaliaris]

Benjamin Root  writes:


> 
> Essentially, you make a Path object using the vertices, and then use its 
> contains_point() method.
> Ben Root
> 

OK, but given that contains_point works with a *single* point at a time, I have
to call it for all my points which is a bit more cumbersome, or am I missing
something?

Jorge




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Re: [Matplotlib-users] histogram and a line

[Nicolas Rougier]

You need to specify the ylim because your height may be larger than your 
histogram and then you cannot see it.

Here is a script that reproduce your screenshot (with random data).


import numpy as np
import matplotlib.pyplot as plt

plt.rc('xtick', direction = 'out')
plt.rc('ytick', direction = 'out')

data = np.random.normal(0,1,100)

fig = plt.figure(figsize=(8,6), dpi=72, facecolor='w')
axes = plt.subplot(111)
axes.axvline(np.mean(data), 0, data.max(), linewidth=2, color='red')
axes.hist(data, bins=50, normed=True)
axes.set_ylim(0, 1)
axes.set_xlim(-3, 3)

axes.spines['right'].set_color('none')
axes.spines['top'].set_color('none')
axes.xaxis.set_ticks_position('bottom')
axes.spines['bottom'].set_position(('data', -0.05))
axes.yaxis.set_ticks_position('left')
axes.spines['left'].set_position(('data',-3.25))

plt.show()




Nicolas



On Mar 8, 2012, at 7:54 , Mic wrote:

> Hi Jerzy,
> Thank you for your answer. With the code below I get only a green line (see 
> attached line.png):
> 
> import numpy as np
> import matplotlib.pyplot as plt
> 
> hist_data = []
> 
> heigth = max(hist_data) + 10
> mean = np.mean(hist_data)
> 
> f = plt.figure()
> h = f.add_subplot(111)
> h.hist(hist_data, bins=50, normed=True)
> h.plot([mean,mean],[0,height])
> f.savefig('myhist.png')
> 
> without h.plot() I get a histogram (see attached matplot_hist.png).
> 
> How can I get the line and the histogram at the same time in the picture? 
> How is it possible to norm the vertical axis in order to get similar results 
> like in this picture (see attached hist.png)?
> 
> Thank you in advance.
> 
> On Wed, Mar 7, 2012 at 6:41 PM, Jerzy Karczmarczuk 
>  wrote:
> Mic:
>> Hello,
>> I am able to draw a histogram with the following code:
>> 
>> ...
>> h.hist(hist_data, bins=50, normed=True)
>> 
>> However, I don't know how to draw a line for median at 249 position like in 
>> attachment.
> Are your axes really matplotlib axes? (I have doubts, since the vertical is 
> not normed, although your histogram is).
> 
> In your real axes, the command plot([249,249],[0,height]) draws a vertical 
> line (there is a primitive vert. line as well), what is the problem??
> 
> Jerzy Karczmarczuk
> 
> 
> 
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