[matplotlib-devel] Refactoring/bugfixing of path simplification was: Re: Bug in Agg-based backends when yscale == "log"?

[Michael Droettboom]

I just completed some open-heart surgery on the path simplification code 
to resolve this and other issues.  Though the integer overflow bug is on 
the maintenance branch, the proper solution was large enough and risky 
enough that I have only committed it to the development trunk.

Before, the path simplification code jumbled a number of discrete steps 
together in the code:

   1. Nan (nonfinite) handling
   2. Clipping
   3. Quantization
   4. Simplification


This has been rewritten (see path_converters.h) so each step is handled 
by a separate iterator class that can be independently switched on-and-off.

This refactoring made it much easier to rewrite the clipping algorithm 
to actually bisect line segments at the figure boundary, rather than (as 
before) simply removing vertices after crossing outside the boundary.

Additionally, nan-value-handling was formerly handled in both Python and 
C++, which was both double the maintenance and slower in Python.  Now, 
the C++ version of the entire pipeline has been exposed to Python, so we 
have a single (and faster) code path to debug.  (Note that whereas it 
behaves as an iterator in C++, it actually writes to a new array in the 
Python-wrapped version to avoid lots of tiny Python function calls).  
All backends now use this pipeline (through the use of 
Path.iter_segments). 

A side effect of this is that whereas before Python backends were forced 
to get clipping and simplification together, they now have independent 
control.  This fixes two long-standing bugs in non-Agg backends:

   1.   large values would cause integer overflow (causes the lines to
  appear to go in the wrong direction)
   2.   clipping should be turned off for filled regions, but that
  wasn't previously possible without also losing simplification


Lastly, the threshold of angular similarity below which simplification 
will start removing vertices has been exposed to the user as an rcParam 
(path.simplify_threshold).  It can also be set on an individual basis to 
any Path object.

The one remaining major piece is to get the native Cocoa backend to 
support this infrastructure.  Right now, it reimplements its own 
nan-handling and doesn't perform any of the other steps.  This will 
probably require some code compiled in C++ but exported as C to make it 
accessible to Objective-C.  The general roadmap is in "cleanup_path" in 
_path.cpp.  I'm happy to help with this, but without a Mac, it will be 
hard to compile and test these changes.

I've looked through all the backend_driver images, and everything seems 
ok, but let me know if you see any strangely drawn paths etc.

Cheers,
Mike



Michael Droettboom wrote:
> Okay -- I think I've at least narrowed it down to a cause.  Agg uses 
> fixed-point arithmetic to render at the low-level -- by default it uses 
> 24.8 (i.e. 24 integer bits and 8 fractional bits).  Therefore, it can 
> only handle pixel coordinates in the range -2^23 to 2^23.  Both of the 
> provided examples, after the data has been scaled, draw outside of this 
> range, which results in integer overflow, hence things going in the 
> wrong direction etc.
>
> We could change the fixed point in agg_basics.h, but I hesitate to do 
> so, as it's at the expense of fine detail.  We could possibly move to 
> 64-bits, but I'm not sure how easy that would be, or what the impact 
> might be on 32-bit platforms.
>
> 
> //poly_subpixel_scale_e
> // These constants determine the subpixel accuracy, to be more precise,
> // the number of bits of the fractional part of the coordinates.
> // The possible coordinate capacity in bits can be calculated by 
> formula:
> // sizeof(int) * 8 - poly_subpixel_shift, i.e, for 32-bit integers and
> // 8-bits fractional part the capacity is 24 bits.
> enum poly_subpixel_scale_e
> {
> poly_subpixel_shift = 8,  
> //poly_subpixel_shift
> poly_subpixel_scale = 1< //poly_subpixel_scale
> poly_subpixel_mask  = poly_subpixel_scale-1,  
> //poly_subpixel_mask
> };
>
>
> One thing I will look into is whether the line simplification algorithm 
> can be extended to actually clip the lines when they go outside of the 
> image range.  At the moment, it does some work to reduce the number of 
> points outside of the image, but it always draws at least one point 
> outside at its original location.  It looks like Agg has some of the 
> pieces necessary to do this -- whether it's feasible to integrate that 
> into our existing line simplification algorithm remains to be seen.
>
> Mike
>
>
> Michael Droettboom wrote:
>   
>> Thanks for this.
>>
>> I believe both of these examples illustrate a shortcoming in Agg when 
>> the distance between two points on either end of a line is too great.
>>
>> I'll do some digging around and see what may be causing this and if any 
>> limits can be adjusted -- I may not get to this t

Re: [matplotlib-devel] Updated units.ConversionInterface

[James Evans]

Okay. Done.

--James

> -Original Message-
> From: John Hunter [mailto:jdh2...@gmail.com]
> Sent: Wednesday, January 28, 2009 11:46 AM
> To: James Evans
> Cc: Eric Firing; matplotlib development list
> Subject: Re: [matplotlib-devel] Updated units.ConversionInterface
> 
> On Wed, Jan 28, 2009 at 1:19 PM, James Evans  wrote:
> > Eric,
> >
> > I was looking at it from the perspective of most of the other API calls 
> > throughout matplotlib have
> the Axes or Axis as the first
> > argument.  Typically this is because it is what wants the work to be done 
> > or is being worked on.  I
> was just following suit.  I can
> > see where you are coming from.  I have no real strong argument for or 
> > against, so if I should swap
> them around as you had suggested,
> > then I have no problem changing it.
> 
> I tend to agree with Eric -- then people writing converters who don't
> care about the axis input can ignore it more easily.
> 
> JDH


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[matplotlib-devel] Small doc patch

[Sandro Tosi]

Hello,
while reading the doc, I've encountered some little errors I've fixed
in the attached patch; nothing extremely difficult, but still worth
fixing :)

I'm even wondering if the svnmerge section in "Coding guide" is still
valid, since I've seen some emails passing here about that, but that's
too hard for me (as of now) :) .

Cheers,
-- 
Sandro Tosi (aka morph, morpheus, matrixhasu)
My website: http://matrixhasu.altervista.org/
Me at Debian: http://wiki.debian.org/SandroTosi
Index: doc/devel/coding_guide.rst
===
--- doc/devel/coding_guide.rst	(revision 6847)
+++ doc/devel/coding_guide.rst	(working copy)
@@ -44,7 +44,7 @@
 * if your changes are non-trivial, please make an entry in the
   :file:`CHANGELOG`
 
-* if you change the API, please document it in :file:`API_CHANGES`,
+* if you change the API, please document it in :file:`doc/api/api_changes.rst`,
   and consider posting to `matplotlib-devel
   `_
 
Index: doc/devel/documenting_mpl.rst
===
--- doc/devel/documenting_mpl.rst	(revision 6847)
+++ doc/devel/documenting_mpl.rst	(working copy)
@@ -252,7 +252,7 @@
 taken, these figures can be included in the usual way::
 
.. plot:: pyplots/tex_unicode_demo.py
-  :include-source
+  :include-source:
 
 Examples
 
Index: doc/faq/howto_faq.rst
===
--- doc/faq/howto_faq.rst	(revision 6847)
+++ doc/faq/howto_faq.rst	(working copy)
@@ -137,7 +137,7 @@
 used to calculate the text size, is not known until the figure is
 drawn (:meth:`matplotlib.figure.Figure.draw`).  After the window is
 drawn and the text instance knows its renderer, you can call
-:meth:`matplotlib.text.Text.get_window_extent``.  One way to solve
+:meth:`matplotlib.text.Text.get_window_extent`.  One way to solve
 this chicken and egg problem is to wait until the figure is draw by
 connecting
 (:meth:`matplotlib.backend_bases.FigureCanvasBase.mpl_connect`) to the
@@ -374,7 +374,7 @@
 
 A frequent request is to have two scales for the left and right
 y-axis, which is possible using :func:`~matplotlib.pyplot.twinx` (more
-than two scales are not currently supported, though it is on the wishq
+than two scales are not currently supported, though it is on the wish
 list).  This works pretty well, though there are some quirks when you
 are trying to interactively pan and zoom, since both scales do not get
 the signals.
@@ -483,7 +483,7 @@
 
 This is not what show does and unfortunately, because doing blocking
 calls across user interfaces can be tricky, is currently unsupported,
-though we have made some pregress towards supporting blocking events.
+though we have made some progress towards supporting blocking events.
 
 
 .. _howto-contribute:
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Re: [matplotlib-devel] Small doc patch

[John Hunter]

On Thu, Jan 29, 2009 at 12:07 PM, Sandro Tosi  wrote:
> Hello,
> while reading the doc, I've encountered some little errors I've fixed
> in the attached patch; nothing extremely difficult, but still worth
> fixing :)
>
> I'm even wondering if the svnmerge section in "Coding guide" is still
> valid, since I've seen some emails passing here about that, but that's
> too hard for me (as of now) :) .

Thanks Sandro -- applied to the branch and trunk.  The merge docs are
up to date.

JDH

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[matplotlib-devel] python make.py html

[Nils Wagner]

Hi all,

I tried to build the HTML documentation.
Here are some failures


matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py
Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig
 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))
   File "axes_divider.py", line 168
  rs, as = s.get_size(renderer)
   ^
  SyntaxError: invalid syntax

   warnings.warn(s)
examples/pylab_examples/axes_grid 
/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py:190: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_grid.py
Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig
 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))
   File "axes_grid.py", line 5, in 
   File 
"/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py", 
line 168
  rs, as = s.get_size(renderer)
   ^
  SyntaxError: invalid syntax

   warnings.warn(s)
  Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig
 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))
   File "geo_demo.py", line 9, in 
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
line 636, in subplot
 a = fig.add_subplot(*args, **kwargs)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
line 690, in add_subplot
 a = subplot_class_factory(projection_class)(self, 
*args, **kwargs)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
line 7460, in __init__
 self._axes_class.__init__(self, fig, self.figbox, 
**kwargs)
   File "custom_projection_example.py", line 35, in 
__init__
TypeError: expected string or Unicode object, NoneType 
found
oc/sphinxext/plot_directive.py:190: UserWarning: Exception 
running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/loadrec.py
Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig
 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))
   File "loadrec.py", line 14, in 
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/exceltools.py", 
line 31, in 
 raise ImportError('You must install xlwt or 
pyExcelterator to use the exceltools')
ImportError: You must install xlwt or pyExcelterator to 
use the exceltools

Nils

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[matplotlib-devel] matplotlib Mac binary aborts with 3rd party Tcl/Tk

[Russell E. Owen]

The current matplotlib Mac binary installer unfortunately reintroduces 
an old problem: it does not work if the user has a 3rd party Tcl/Tk 
installed (as anyone who uses Tkinter seriously would have).

The solution is simple: if one is building a matplotlib Mac binary 
installer then please, please install ActiveState Tcl/Tk first 
(preferably the latest version of 8.4 -- which is 8.4.19 last I 
checked). The resulting binary will work with the built-in Tcl/Tk as 
well as any user's 3rd party Tcl/Tk.

Without this "fix", the resulting binary will abort with any attempt to 
produce a graph using TkAgg and a 3rd party Tcl/Tk.

ISo...could I request a new Mac binary with this fix in place? Or at 
least that future Mac binaries will be built this way?

-- Russell

P.S. the situation could get "interesting" with a future version of 
MacOS X during the transition from Tcl/Tk 8.4 to 8.5. But for now just 
sticking with 8.4 is safe since it is the recommended version for Python 
2.5 and is also what comes with MacOS X.

P.P.S. I suspect (but have not confirmed) that Mac Python 2.5.4 has this 
same problem. Mac Python 2.5.2 is definitely OK.


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Re: [matplotlib-devel] python make.py html

[Michael Droettboom]

Comments below.

Nils Wagner wrote:
> Hi all,
>
> I tried to build the HTML documentation.
> Here are some failures
>
>
> matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py
> Traceback (most recent call last):
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 187, in makefig
>  runfile(fullpath)
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 128, in runfile
>  module = imp.load_module("__main__", fd, fname, 
> ('py', 'r', imp.PY_SOURCE))
>File "axes_divider.py", line 168
>   rs, as = s.get_size(renderer)
>^
>   SyntaxError: invalid syntax
>
>warnings.warn(s)
> examples/pylab_examples/axes_grid 
> /home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py:190: 
> UserWarning: Exception running plot 
> /home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_grid.py
> Traceback (most recent call last):
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 187, in makefig
>  runfile(fullpath)
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 128, in runfile
>  module = imp.load_module("__main__", fd, fname, 
> ('py', 'r', imp.PY_SOURCE))
>File "axes_grid.py", line 5, in 
>File 
> "/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py",
>  
> line 168
>   rs, as = s.get_size(renderer)
>^
>   SyntaxError: invalid syntax
>   
I can't reproduce this here.  What version of matplotlib are you running?
>warnings.warn(s)
>   Traceback (most recent call last):
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 187, in makefig
>  runfile(fullpath)
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 128, in runfile
>  module = imp.load_module("__main__", fd, fname, 
> ('py', 'r', imp.PY_SOURCE))
>File "geo_demo.py", line 9, in 
>File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
> line 636, in subplot
>  a = fig.add_subplot(*args, **kwargs)
>File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
> line 690, in add_subplot
>  a = subplot_class_factory(projection_class)(self, 
> *args, **kwargs)
>File 
> "/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
> line 7460, in __init__
>  self._axes_class.__init__(self, fig, self.figbox, 
> **kwargs)
>File "custom_projection_example.py", line 35, in 
> __init__
> TypeError: expected string or Unicode object, NoneType 
> found
> oc/sphinxext/plot_directive.py:190: UserWarning: Exception 
> running plot 
> /home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/loadrec.py
> Traceback (most recent call last):
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 187, in makefig
>  runfile(fullpath)
>File 
> "/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
> line 128, in runfile
>  module = imp.load_module("__main__", fd, fname, 
> ('py', 'r', imp.PY_SOURCE))
>File "loadrec.py", line 14, in 
>File 
> "/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/exceltools.py",
>  
> line 31, in 
>  raise ImportError('You must install xlwt or 
> pyExcelterator to use the exceltools')
> ImportError: You must install xlwt or pyExcelterator to 
> use the exceltools
>   
This is exactly as it says:

"You must install xlwt or pyExcelterator to 
use the exceltools"

Since that particular example uses the exceltools, and you haven't installed 
it's requirements, it can't generate the example.  Worst case, however, it 
should continue to generate the rest of the docs without it.

Mike

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


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[matplotlib-devel] Fwd: python make.py html

[Nils Wagner]

 


  --- the forwarded message follows ---
--- Begin Message ---

On Thu, 29 Jan 2009 16:11:35 -0500
 Michael Droettboom  wrote:

Comments below.

Nils Wagner wrote:

Hi all,

I tried to build the HTML documentation.
Here are some failures


matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py
Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig

 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))

   File "axes_divider.py", line 168
  rs, as = s.get_size(renderer)
   ^
  SyntaxError: invalid syntax

   warnings.warn(s)
examples/pylab_examples/axes_grid 
/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py:190: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_grid.py

Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig

 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))

   File "axes_grid.py", line 5, in 
   File 
"/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/axes_divider.py", 
line 168

  rs, as = s.get_size(renderer)
   ^
  SyntaxError: invalid syntax
  
I can't reproduce this here.  What version of matplotlib 
are you running?

   warnings.warn(s)
  Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig

 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))

   File "geo_demo.py", line 9, in 
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/pyplot.py", 
line 636, in subplot

 a = fig.add_subplot(*args, **kwargs)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/figure.py", 
line 690, in add_subplot
 a = subplot_class_factory(projection_class)(self, 
*args, **kwargs)
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/axes.py", 
line 7460, in __init__
 self._axes_class.__init__(self, fig, self.figbox, 
**kwargs)
   File "custom_projection_example.py", line 35, in 
__init__
TypeError: expected string or Unicode object, NoneType 
found
oc/sphinxext/plot_directive.py:190: UserWarning: 
Exception 
running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/pylab_examples/loadrec.py

Traceback (most recent call last):
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig

 runfile(fullpath)
   File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
 module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))

   File "loadrec.py", line 14, in 
   File 
"/home/nwagner/local/lib64/python2.6/site-packages/mpl_toolkits/exceltools.py", 
line 31, in 
 raise ImportError('You must install xlwt or 
pyExcelterator to use the exceltools')
ImportError: You must install xlwt or pyExcelterator to 
use the exceltools
  

This is exactly as it says:

"You must install xlwt or pyExcelterator to use the 
exceltools"


Since that particular example uses the exceltools, and 
you haven't installed it's requirements, it can't 
generate the example.  Worst case, however, it should 
continue to generate the rest of the docs without it.


Mike


Hi Mike,

I installed xlwt.

I am using python2.6 on opensuse11.1  and


matplotlib.__version__

'0.98.6svn'

"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 128, in runfile
module = imp.load_module("__main__", fd, fname, 
('py', 'r', imp.PY_SOURCE))

  File "artist_tests.py", line 30, in 
  File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/collections.py", 
line 917, in __init__

self.set_segments(segments)
  File 
"/home/nwagner/local/lib64/python2.6/site-packages/matplotlib/collections.py", 
line 927, in set_segments

seg = np.asarray(seg, np.float_)
  File 
"/home/nwagner/local/lib64/python2.6/site-packages/numpy/core/numeric.py", 
line 230, in asarray

return array(a, dtype, copy=False, order=order)
ValueError: setting an array element with a sequence.

  warnings.warn(s)
examples/units/bar_demo2 ...examples/units/bar_unit_demo 
/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py:190: 
UserWarning: Exception running plot 
/home/nwagner/svn/matplotlib/doc/mpl_examples/units/bar_unit_demo.py

Traceback (most recent call last):
  File 
"/home/nwagner/svn/matplotlib/doc/sphinxext/plot_directive.py", 
line 187, in makefig

runfile(fullpath)
  File 
"/home/nwagner/svn/matplotlib/d

[matplotlib-devel] Axis.get_label question

[Evans, James R]

Is there a reason why Axis.get_label returns the label as a Text instance, or 
should there really be set_label/get_label methods that takes a string and set 
the text value of the Text instance and returns the string value of the Text 
instance?

Everywhere it is used in the code it is used in a two-step process to really 
just get and set the string value of the Text instance.

--James Evans

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