matplotlib-devel Mailing List for matplotlib

Hello Russell,
thanks for getting back to me

On Mon, Jan 5, 2009 at 20:29, Russell E. Owen <rowen@u.washington.edu> wrote:
> In article
> <8b2...@ma...>,
>  "Sandro Tosi" <mo...@de...> wrote:
>> - what are you using matplotlib for?
>
> Plotting data from a networked Tkinter application.

May I ask you to expand a bit what "networked" is? something like:
read data from a remote server and plot on the client? Just to have an
idea :)

>> - what are the (basic) things that, when you were beginning to use
>> matplotlib, you wanted to see grouped up but couldn't find?
>> - what would you like to see in a book about matplotlib?
>
> I want a user's guide for the class API. So far I've figured it out by
> reading examples, trying to extrapolate from the pylab user's guide
> (which is quite good) and reading the class API reference, but I feel
> that I barely understand what I am doing.

The idea of the book is to start with simple plots, describing the
methods we call and how they work, to go into more details along the
book.

>> - what are the things you'd like to explore of matplotlib and never
>> had time to do?
>
> I'd like to know how best to handle plotting data as it arrives (e.g.
> strip charts and evolving x-y plots). I've got code that works but am
> not convinced I'm doing it in the best fashion.

I already thought about an examples of "plotting with data changing on
time" like plotting the cpu usage or so, so it might be useful to you
that too :)

> Histograms.

If there's something particular interesting for you, it would be
helpful to me to know it :)

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

Hello Andrew,
thanks for taking the time to reply.

First of all, let me clarify that I received a proposal (and not the
opposite) so some decision were already made about the book format.

On Mon, Jan 5, 2009 at 20:00, Andrew Straw <str...@as...> wrote:
> Hi Sandro,
>
> It's great news that a book may come out on MPL.
>
> Speaking as an aspiring university professor in neuroscience, I would
> like to see something that could be used as a resource for undergraduate
> students just learning Python and MPL.

The cut of the book is for already experienced Python programmers. For
sure, in the "approaching" chapter to mpl, I won't go too much into
deep of python programming, and I suppose they'll be easy to read even
for new comers.

> Due to this perspective, I think
> such a book would cover both numpy and MPL. The emphasis could clearly
> by on MPL, but basic numpy idioms and concepts should also be taught.

Mh, the focus the editor would like to see is about introducing mpl +
integrating into apps. The examples I have in mind for the pratical
part of apps integration already cointains some sort of "introduction"
to gather data and plot them (but I can't go to much on the scientific
side :) ). I will propose a chapter like "Matplotlib for the science"
and here your suggestion on what you'd like to see there is welcome.

> I
> think an example-driven approach would be very useful -- something like
> an undergraduate laboratory experiment where students measure and plot
> raw values and compute histograms and statistics (e.g. mean and std).
> More advanced sections might perform statistical comparisons of
> different treatments (e.g. using chi squared, KS and/or T tests), do
> linear least squares fitting (with np.linalg.lstsq), and possibly
> non-linear curve fitting using something like scipy.optimize.fmin.

That could be a beginning of that chapter contents: more more more ideas :)

> That's my self-serving $0.02, since you asked! :)

And they are very much welcome!!

> You may also want to speak with John Hunter and Fernando Perez about the
> possibility of collaborating -- they've already done some work towards a
> book, too.

I'm sure be happy to hear their voice on this product, but (given the
preamble) I don't know if the editor would be fine with co-authorship;
I'll ask, just to be sure.

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

Hello João,
thanks for replying

On Mon, Jan 5, 2009 at 13:40, João Luís Silva <js...@fc...> wrote:
> Sandro Tosi wrote:
>> - what are the (basic) things that, when you were beginning to use
>> matplotlib, you wanted to see grouped up but couldn't find?
>
> I don't know if you consider it basic or not, but I would have liked
> better documentation of the object oriented interface (matplotlib). The

could you be a little more specific on what you mean here?

>> - what would you like to see in a book about matplotlib?
>
> As above, at least a chapter about the object oriented interface showing
> how to embed matplotlib on a application, and outlining the structure of
> the OO interface.

Well, this is part of the purpose of the book: show how to embed mpl
in applications.

>> - what are some those advanced feature that made you yell "WOW!!" ?
>
> I haven't really used matplotlib's advanced features. There are some
> that I like, such as automatic legend placement and mathtext support.

mathtext and latex support will be in the advanced features section

> The number of supported backends is impressive just by itself, making
> matplotlib much more useful. There are some little things such as the
> search order for the matplotlibrc file that make it possible to specify
>  different settings for a given directory.

There will be a part even on configuration (of course :) ).

>> - what are the things you'd like to explore of matplotlib and never
>> had time to do?
>
> I never had the time to try the masked arrays although I think they will
> be useful for me. I should also explore how to create custom color maps.

2 points added to the adv featues list (in part because something was
already there, in a different form).

>> Your suggestions are really appreciated :) And wish me good luck!
>
> I was going to! Good luck, I hope you manage to take this project to
> completion.

Eheh, thanks! I really hope I'll be able to handle even this task :)

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

In article 
<8b2...@ma...>,
 "Sandro Tosi" <mo...@de...> wrote:

> Hello and Happy 2009!
> 
> I received the interesting proposal to author a book on Matplotlib,
> the powerful 2D plotting library for Python.
> 
> While preparing the arguments list, I'd like to hear even your
> opinion, because different points-of-view will lead to a better
> product.
> 
> Some basic question I'd like to ask are:
> 
> - what are you using matplotlib for?

Plotting data from a networked Tkinter application.

> - what are the (basic) things that, when you were beginning to use
> matplotlib, you wanted to see grouped up but couldn't find?
> - what would you like to see in a book about matplotlib?

I want a user's guide for the class API. So far I've figured it out by 
reading examples, trying to extrapolate from the pylab user's guide 
(which is quite good) and reading the class API reference, but I feel 
that I barely understand what I am doing.

> - what are the things you'd like to explore of matplotlib and never
> had time to do?

I'd like to know how best to handle plotting data as it arrives (e.g. 
strip charts and evolving x-y plots). I've got code that works but am 
not convinced I'm doing it in the best fashion.

Histograms.

-- Russell

On Mon, Jan 5, 2009 at 9:06 AM, Michael Droettboom <md...@st...> wrote:
> Also, it seems like the text alignment in the PS output is too low by a
> small constant factor.

I'm not quite sure why this is happening. My guess is that it has
something to with the usage of psfrag in the ps backend, e.g., the
different descent values between the original text and the substituted
text. I personally think  it is better (for the ps backend) to use the
dviread module (as in the pdf backend) instead of using the psfrag.

Regards,

-JJ

Hi Sandro,

It's great news that a book may come out on MPL.

Speaking as an aspiring university professor in neuroscience, I would
like to see something that could be used as a resource for undergraduate
students just learning Python and MPL. Due to this perspective, I think
such a book would cover both numpy and MPL. The emphasis could clearly
by on MPL, but basic numpy idioms and concepts should also be taught. I
think an example-driven approach would be very useful -- something like
an undergraduate laboratory experiment where students measure and plot
raw values and compute histograms and statistics (e.g. mean and std).
More advanced sections might perform statistical comparisons of
different treatments (e.g. using chi squared, KS and/or T tests), do
linear least squares fitting (with np.linalg.lstsq), and possibly
non-linear curve fitting using something like scipy.optimize.fmin.

That's my self-serving $0.02, since you asked! :)

You may also want to speak with John Hunter and Fernando Perez about the
possibility of collaborating -- they've already done some work towards a
book, too.

Andrew

Sandro Tosi wrote:
> Hello and Happy 2009!
> 
> I received the interesting proposal to author a book on Matplotlib,
> the powerful 2D plotting library for Python.
> 
> While preparing the arguments list, I'd like to hear even your
> opinion, because different points-of-view will lead to a better
> product.
> 
> Some basic question I'd like to ask are:
> 
> - what are you using matplotlib for?
> - what are the things you like the most of matplotlib, that you want
> to give emphasis to? And why?
> - what are the (basic) things that, when you were beginning to use
> matplotlib, you wanted to see grouped up but couldn't find?
> - what would you like to see in a book about matplotlib?
> - what are some those advanced feature that made you yell "WOW!!" ?
> - what are the things you'd like to explore of matplotlib and never
> had time to do?
> 
> Your suggestions are really appreciated :) And wish me good luck!
> 
> Cheers,

Thanks for the explanation.  The TeX install I have is the stock one 
with RHEL4, which is fairly old at this point.  I've had a number of 
other problems with it as well (such as it not being compatible with 
Sphinx). 

It's nice to know that matplotlib is at least handling this situation 
without crashing.  I think this solution (to warn) is adequate, 
especially given that most newer TeX distributions shouldn't have this 
issue.

Mike

Jouni K. Seppänen wrote:
> Michael Droettboom <md...@st...> writes:
>
>   
>> The output of "python usetex_texteffects.py --verbose-debug" is attached.
>>     
>
> Thanks! The problem seems to be that your TeX configuration (pdftex.map)
> specifies using Helvetica without embedding it into the pdf file. This
> is deprecated in the PDF standard (PDF viewer applications have
> different replacements for the core 14 fonts, and many publishers insist
> that you embed all fonts you use) but I added support for it in 6737,
> with a warning displayed to the user.
>
> Could you see if it works for you now?
>
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Michael Droettboom <md...@st...> writes:

> The output of "python usetex_texteffects.py --verbose-debug" is attached.

Thanks! The problem seems to be that your TeX configuration (pdftex.map)
specifies using Helvetica without embedding it into the pdf file. This
is deprecated in the PDF standard (PDF viewer applications have
different replacements for the core 14 fonts, and many publishers insist
that you embed all fonts you use) but I added support for it in 6737,
with a warning displayed to the user.

Could you see if it works for you now?

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

Jouni: your latest commit resolves the issue for me.  Thanks!

Jae-Joon: Your preview.sty work seems to work great with the PDF backend 
(for me, at least).

Cheers,
Mike

Michael Droettboom wrote:
>
> Jouni K. Seppänen wrote:
>> Michael Droettboom <md...@st...> writes:
>>
>>  
>>> when running usetex_fonteffects.py [...]
>>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>> -> file = open(input, 'rb')
>>>     
>>
>> Perhaps your TeX installation doesn't have the font. If you run
>> "kpsewhich utmr8a.pfb", what do you get? If it does return something,
>> could you run the example with --verbose-debug?
>>
>>   
> > kpsewhich utmr8a.pfb
> /usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb
>
>
> The output of "python usetex_texteffects.py --verbose-debug" is attached.
>
> Mike
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Jouni K. Seppänen wrote:
> Michael Droettboom <md...@st...> writes:
>
>   
>> when running usetex_fonteffects.py [...]
>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>> -> file = open(input, 'rb')
>>     
>
> Perhaps your TeX installation doesn't have the font. If you run
> "kpsewhich utmr8a.pfb", what do you get? If it does return something,
> could you run the example with --verbose-debug?
>
>   
 > kpsewhich utmr8a.pfb
/usr/share/texmf/fonts/type1/urw/times/utmr8a.pfb


The output of "python usetex_texteffects.py --verbose-debug" is attached.

Mike

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Michael Droettboom <md...@st...> writes:

> when running usetex_fonteffects.py [...]
> TypeError: coercing to Unicode: need string or buffer, NoneType found
> -> file = open(input, 'rb')

Perhaps your TeX installation doesn't have the font. If you run
"kpsewhich utmr8a.pfb", what do you get? If it does return something,
could you run the example with --verbose-debug?

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

Sorry about the wild good chase.  I had fixed up an earlier exception 
which was simply a problem with formatting a verbose message.  That 
gives this, when running usetex_fonteffects.py (with all rcParams at 
defaults):

Traceback (most recent call last):
  File "usetex_fonteffects.py", line 22, in <module>
    pylab.savefig('usetex_fonteffects.pdf')
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/pyplot.py", line 
345, in savefig
    return fig.savefig(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 
990, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1429, in print_figure
    **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1323, in print_pdf
    return pdf.print_pdf(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 1911, in print_pdf
    file.close()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 440, in close
    self.writeFonts()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 521, in writeFonts
    fontdictObject = self.embedType1(filename, self.dviFontInfo[filename])
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 550, in embedType1
    ' and effects ' + `fontinfo.effects`,
TypeError: cannot concatenate 'str' and 'NoneType' objects
 > 
/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py(550)embedType1()
-> ' and effects ' + `fontinfo.effects`,*
*
Do an SVN update (r6736) and try again.  Then I get this:

 > python usetex_fonteffects.py
Traceback (most recent call last):
  File "usetex_fonteffects.py", line 22, in <module>
    pylab.savefig('usetex_fonteffects.pdf')
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/pyplot.py", line 
345, in savefig
    return fig.savefig(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 
990, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1429, in print_figure
    **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1323, in print_pdf
    return pdf.print_pdf(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 1911, in print_pdf
    file.close()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 440, in close
    self.writeFonts()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 521, in writeFonts
    fontdictObject = self.embedType1(filename, self.dviFontInfo[filename])
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 553, in embedType1
    t1font = type1font.Type1Font(fontinfo.fontfile)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/type1font.py", 
line 55, in __init__
    file = open(input, 'rb')
TypeError: coercing to Unicode: need string or buffer, NoneType found
 > 
/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/type1font.py(55)__init__()
-> file = open(input, 'rb')

So somehow, input is None, but I haven't had a chance to look any further.

Cheers,
Mike

Jouni K. Seppänen wrote:
> Michael Droettboom <md...@st...> writes:
>
>   
>> I'm currently getting this traceback with the PDF backend, whether 
>> "text.latex.preview" is True or False -- so it may be unrelated to your 
>> change, but I'm unable to test PDF at the moment.
>>     
>
> Based on the traceback, it looks like I have broken something recently --
> but what is the exact exception? I can't replicate the traceback myself.
>
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Michael Droettboom <md...@st...> writes:

> I'm currently getting this traceback with the PDF backend, whether 
> "text.latex.preview" is True or False -- so it may be unrelated to your 
> change, but I'm unable to test PDF at the moment.

Based on the traceback, it looks like I have broken something recently --
but what is the exact exception? I can't replicate the traceback myself.

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

Very nice!

I'm currently getting this traceback with the PDF backend, whether 
"text.latex.preview" is True or False -- so it may be unrelated to your 
change, but I'm unable to test PDF at the moment.

Traceback (most recent call last):
  File "usetex_baseline_test.py", line 75, in <module>
    plt.savefig("test.pdf")
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/pyplot.py", line 
345, in savefig
    return fig.savefig(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/figure.py", line 
990, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1429, in print_figure
    **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backend_bases.py", 
line 1323, in print_pdf
    return pdf.print_pdf(*args, **kwargs)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 1911, in print_pdf
    file.close()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 440, in close
    self.writeFonts()
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 521, in writeFonts
    fontdictObject = self.embedType1(filename, self.dviFontInfo[filename])
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/backends/backend_pdf.py", 
line 553, in embedType1
    t1font = type1font.Type1Font(fontinfo.fontfile)
  File 
"/home/mdroe/usr/lib/python2.5/site-packages/matplotlib/type1font.py", 
line 55, in __init__
    file = open(input, 'rb')

Also, it seems like the text alignment in the PS output is too low by a 
small constant factor.

Assuming those issues can be resolved, is there now any reason to use 
dviread, assuming preview.sty is installed?  If the preview.sty approach 
is superior, I wonder if we could:

a) Determine if preview.sty is installed, and if so, use it, otherwise 
fallback to dviread? (Then we could be a default "auto" setting for the 
rcParam).

b) Or better, include preview.sty with matplotlib and use it instead of 
a system installed copy, so that it's always available.  (This is both a 
licensing and version-compatibility question, really...)

It would be great to make this new behavior with the proper baseline 
more automatic.

Cheers,
Mike

Jae-Joon Lee wrote:
> Hello,
>
> I committed a patch to optionally use preview.sty with usetex=True.
> This is to support a baseline alignment.
>
> A summary of changes:
>
>  * added a get_text_width_height_descent() method in the TexManager
> class, and modified the agg, ps and pdf backends to utilize this
> method.
>
>  * added a new rc parameter, 'text.latex.preview'. If True,
> preview.sty is used to generate dvi files and baseline information of
> each dvi file is stored in a separate file.
> TexManager.get_text_width_height_descent() method uses this
> information.
>
>  * If text.latex.preview==False,
> TexManager.get_text_width_height_descent() method uses dviread module
> (this is what the pdf backend has been using), but the returned
> descent value of the text is sometimes incorrect.
>
>  * added an example ("usetex_baseline_test.py" ). The output is
> attached with this email.
>
> If you have a preview.sty installed, please test this (set
> "text.latex.preview=True" in you rc file) and report any problems.
> Regards,
>
> -JJ
>   
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Matplotlib-devel mailing list
> Mat...@li...
> https://lists.sourceforge.net/lists/listinfo/matplotlib-devel
>   

-- 
Michael Droettboom
Science Software Branch
Operations and Engineering Division
Space Telescope Science Institute
Operated by AURA for NASA

Hello and Happy 2009!

I received the interesting proposal to author a book on Matplotlib,
the powerful 2D plotting library for Python.

While preparing the arguments list, I'd like to hear even your
opinion, because different points-of-view will lead to a better
product.

Some basic question I'd like to ask are:

- what are you using matplotlib for?
- what are the things you like the most of matplotlib, that you want
to give emphasis to? And why?
- what are the (basic) things that, when you were beginning to use
matplotlib, you wanted to see grouped up but couldn't find?
- what would you like to see in a book about matplotlib?
- what are some those advanced feature that made you yell "WOW!!" ?
- what are the things you'd like to explore of matplotlib and never
had time to do?

Your suggestions are really appreciated :) And wish me good luck!

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

Hello,

I committed a patch to optionally use preview.sty with usetex=True.
This is to support a baseline alignment.

A summary of changes:

 * added a get_text_width_height_descent() method in the TexManager
class, and modified the agg, ps and pdf backends to utilize this
method.

 * added a new rc parameter, 'text.latex.preview'. If True,
preview.sty is used to generate dvi files and baseline information of
each dvi file is stored in a separate file.
TexManager.get_text_width_height_descent() method uses this
information.

 * If text.latex.preview==False,
TexManager.get_text_width_height_descent() method uses dviread module
(this is what the pdf backend has been using), but the returned
descent value of the text is sometimes incorrect.

 * added an example ("usetex_baseline_test.py" ). The output is
attached with this email.

If you have a preview.sty installed, please test this (set
"text.latex.preview=True" in you rc file) and report any problems.
Regards,

-JJ