matplotlib-devel Mailing List for matplotlib

Hi all,
as always, in threaded mode ipython creates crash reports for exceptions in 
threads. I think the one below belongs in the matplotlib court.
Cheers,
f
ps - for ipython 0.7.0 I changed things, so now exceptions in threads will get 
nicely formatted on-screen (including pdb support) instead of dumping these 
bogus crash reports.
-------- Original Message --------
Subject: IPython Crash Report
Date: Tue, 3 Jan 2006 16:55:10 -0500
From: Yoshua Bengio <be...@ir...>
To: fp...@co...
***************************************************************************
IPython post-mortem report
IPython version: 0.6.15
Platform info : os.name -> posix, sys.platform -> linux2
***************************************************************************
Current user configuration structure:
{'Version': 0,
 'alias': [],
 'args': [],
 'autocall': 1,
 'autoindent': 1,
 'automagic': 1,
 'banner': 1,
 'c': '',
 'cache_size': 1000,
 'classic': 0,
 'color_info': 1,
 'colors': 'Linux',
 'confirm_exit': 1,
 'debug': 0,
 'deep_reload': 0,
 'editor': 'emacs -nw',
 'execfile': [],
 'execute': [''],
 'gthread': 0,
 'help': 0,
 'ignore': 0,
 'import_all': [],
 'import_mod': [],
 'import_some': [[]],
 'include': [],
 'ipythondir': '/u/bengioy/.ipython',
 'log': 0,
 'logfile': '',
 'logplay': '',
 'magic_docstrings': 0,
 'messages': 1,
 'multi_line_specials': 1,
 'nosep': 0,
 'opts': Struct({'pylab': 1}),
 'pdb': 0,
 'pprint': 1,
 'profile': '',
 'prompt_in1': 'In [\\#]: ',
 'prompt_in2': ' .\\D.: ',
 'prompt_out': 'Out[\\#]: ',
 'prompts_pad_left': 1,
 'pylab': 1,
 'qthread': 0,
 'quick': 0,
 'rcfile': 'ipythonrc',
 'readline': 1,
 'readline_merge_completions': 1,
 'readline_omit__names': 0,
 'readline_parse_and_bind': ['tab: complete',
 '"\\C-l": possible-completions',
 'set show-all-if-ambiguous on',
 '"\\C-o": tab-insert',
 '"\\M-i": " "',
 '"\\M-o": "\\d\\d\\d\\d"',
 '"\\M-I": "\\d\\d\\d\\d"',
 '"\\C-r": reverse-search-history',
 '"\\C-s": forward-search-history',
 '"\\C-p": history-search-backward',
 '"\\C-n": history-search-forward',
 '"\\e[A": history-search-backward',
 '"\\e[B": history-search-forward'],
 'readline_remove_delims': '-/~',
 'screen_length': -2,
 'separate_in': '\n',
 'separate_out': '',
 'separate_out2': '',
 'system_verbose': 0,
 'tk': 0,
 'upgrade': 0,
 'wthread': 0,
 'xmode': 'Context'}
***************************************************************************
Crash traceback:
---------------------------------------------------------------------------
exceptions.TypeError Python 2.4.1: 
/usr/bin/python
 Tue Jan 3 16:55:02 2006
A problem occured executing Python code. Here is the sequence of function
calls leading up to the error, with the most recent (innermost) call last.
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/backends/backend_gtk.py 
in expose_event(self=<FigureCanvasGTKAgg object (GtkDrawingArea)>, 
widget=<FigureCanvasGTKAgg object (GtkDrawingArea)>, event=<GdkEvent>)
 262 self._renderer._set_width_height (width, height)
 263 self.figure.draw (self._renderer)
 264
 265
 266 def expose_event(self, widget, event):
 267 """Expose_event for all GTK backends
 268 Should not be overridden.
 269 """
 270 if DEBUG: print 'FigureCanvasGTK.%s' % fn_name()
 271
 272 if not GTK_WIDGET_DRAWABLE(self):
 273 return False
 274
 275 if self._draw_pixmap:
 276 width, height = self.allocation.width, self.allocation.height
--> 277 self._render_figure(width, height)
 self._render_figure = <bound method FigureCanvasGTKAgg._render_figure 
of <FigureCanvasGTKAgg object (GtkDrawingArea) at 0x2aaab2488f00>>
 width = 640
 height = 480
 278 self.window.set_back_pixmap (self._pixmap, False)
 279 self.window.clear() # draw pixmap as the gdk.Window's bg
 280 self._draw_pixmap = False
 281 else: # workaround pygtk 2.6 problem - bg not being redrawn
 282 self.window.clear_area (event.area.x, event.area.y,
 283 event.area.width, event.area.height)
 284
 285 return False # allow signal to propagate further
 286
 287
 288 def print_figure(self, filename, dpi=150, facecolor='w', 
edgecolor='w',
 289 orientation='portrait'):
 290 # TODO - use gdk print figure?
 291 root, ext = os.path.splitext(filename)
 292 ext = ext[1:]
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/backends/backend_gtkagg.py 
in _render_figure(self=<FigureCanvasGTKAgg object (GtkDrawingArea)>, 
width=640, height=480)
 76 create_pixmap = False
 77 if width > self._pixmap_width:
 78 # increase the pixmap in 10%+ (rather than 1 pixel) steps
 79 self._pixmap_width = max (int (self._pixmap_width * 
1.1), width)
 80 create_pixmap = True
 81
 82 if height > self._pixmap_height:
 83 self._pixmap_height = max (int (self._pixmap_height * 
1.1), height)
 84 create_pixmap = True
 85
 86 if create_pixmap:
 87 if DEBUG: print 'FigureCanvasGTK._render_figure new pixmap'
 88 self._pixmap = gtk.gdk.Pixmap (self.window, 
self._pixmap_width,
 89 self._pixmap_height)
 90
---> 91 FigureCanvasAgg.draw(self)
 global FigureCanvasAgg.draw = <unbound method FigureCanvasAgg.draw>
 self = <FigureCanvasGTKAgg object (GtkDrawingArea) at 0x2aaab2488f00>
 92 agg_to_gtk_drawable(self._pixmap, self.renderer._renderer)
 93
 94 def blit(self):
 95 agg_to_gtk_drawable(self._pixmap, self.renderer._renderer)
 96 self.window.set_back_pixmap (self._pixmap, False)
 97 self.window.clear() # draw pixmap as the gdk.Window's bg
 98 self._draw_pixmap = False
 99
 100 def print_figure(self, filename, dpi=150,
 101 facecolor='w', edgecolor='w',
 102 orientation='portrait'):
 103 if DEBUG: print 'FigureCanvasGTKAgg.print_figure'
 104 # delete the renderer to prevent improper blitting after print
 105
 106 root, ext = os.path.splitext(filename)
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/backends/backend_agg.py 
in draw(self=<FigureCanvasGTKAgg object (GtkDrawingArea)>)
 354 The canvas the figure renders into. Calls the draw and print fig
 355 methods, creates the renderers, etc...
 356
 357 Public attribute
 358
 359 figure - A Figure instance
 360 """
 361
 362 def draw(self):
 363 """
 364 Draw the figure using the renderer
 365 """
 366 if __debug__: verbose.report('FigureCanvasAgg.draw', 
'debug-annoying')
 367
 368 renderer = self.get_renderer()
--> 369 self.figure.draw(renderer)
 self.figure.draw = <bound method Figure.draw of 
<matplotlib.figure.Figure instance at 0x2aaab248d8c0>>
 renderer = <matplotlib.backends.backend_agg.RendererAgg instance at 
0x2aaab2661e18>
 370
 371 def get_renderer(self):
 372 l,b,w,h = self.figure.bbox.get_bounds()
 373 key = w, h, self.figure.dpi.get()
 374 try: self._lastKey, self.renderer
 375 except AttributeError: need_new_renderer = True
 376 else: need_new_renderer = (self._lastKey != key)
 377
 378 if need_new_renderer:
 379 self.renderer = RendererAgg(w, h, self.figure.dpi)
 380 self._lastKey = key
 381 return self.renderer
 382
 383 def tostring_rgb(self):
 384 if __debug__: verbose.report('FigureCanvasAgg.tostring_rgb', 
'debug-annoying')
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/figure.py in 
draw(self=<matplotlib.figure.Figure instance>, 
renderer=<matplotlib.backends.backend_agg.RendererAgg instance>)
 483 # list of (_image.Image, ox, oy)
 484 if not allequal([im.origin for im in self.images]):
 485 raise ValueError('Composite images with different 
origins not supported')
 486 else:
 487 origin = self.images[0].origin
 488
 489 ims = [(im.make_image(), im.ox, im.oy) for im in self.images]
 490 im = _image.from_images(self.bbox.height(), 
self.bbox.width(), ims)
 491 im.is_grayscale = False
 492 l, b, w, h = self.bbox.get_bounds()
 493 renderer.draw_image(0, 0, im, origin, self.bbox)
 494
 495
 496
 497 # render the axes
--> 498 for a in self.axes: a.draw(renderer)
 a = <matplotlib.axes.Subplot instance at 0x2aaab248dab8>
 self.axes = [<matplotlib.axes.Subplot instance at 0x2aaab248dab8>]
 a.draw = <bound method Subplot.draw of <matplotlib.axes.Subplot 
instance at 0x2aaab248dab8>>
 renderer = <matplotlib.backends.backend_agg.RendererAgg instance at 
0x2aaab2661e18>
 499
 500 # render the figure text
 501 for t in self.texts: t.draw(renderer)
 502
 503 for legend in self.legends:
 504 legend.draw(renderer)
 505
 506 self.transFigure.thaw() # release the lazy objects
 507 renderer.close_group('figure')
 508
 509 def get_axes(self):
 510 return self.axes
 511
 512 def legend(self, handles, labels, loc, **kwargs):
 513 """
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/axes.py in 
draw(self=<matplotlib.axes.Subplot instance>, 
renderer=<matplotlib.backends.backend_agg.RendererAgg instance>)
 1363
 1364
 1365
 1366 artists = []
 1367 artists.extend(self.collections)
 1368 artists.extend(self.patches)
 1369 artists.extend(self.lines)
 1370 artists.extend(self.texts)
 1371
 1372 # keep track of i to guarantee stable sort for python 2.2
 1373 dsu = [ (a.zorder, i, a) for i, a in enumerate(artists)
 1374 if a not in self.animated]
 1375 dsu.sort()
 1376
 1377 for zorder, i, a in dsu:
-> 1378 a.draw(renderer)
 a.draw = <bound method Text.draw of <matplotlib.text.Text instance at 
0x2aaab2496200>>
 renderer = <matplotlib.backends.backend_agg.RendererAgg instance at 
0x2aaab2661e18>
 1379
 1380 self.title.draw(renderer)
 1381 if 0: bbox_artist(self.title, renderer)
 1382 # optional artists
 1383 for a in self.artists:
 1384 a.draw(renderer)
 1385
 1386
 1387 if self.legend_ is not None:
 1388 self.legend_.draw(renderer)
 1389
 1390
 1391 for table in self.tables:
 1392 table.draw(renderer)
 1393
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/text.py in 
draw(self=<matplotlib.text.Text instance>, 
renderer=<matplotlib.backends.backend_agg.RendererAgg instance>)
 319 w, h = renderer.get_text_width_height(
 320 s, self._fontproperties, ismath)
 321
 322 renderx, rendery = thisx, thisy
 323 if renderer.flipy():
 324 canvasw, canvash = renderer.get_canvas_width_height()
 325 rendery = canvash-rendery
 326
 327 renderer.draw_text(gc, renderx, rendery, s,
 328 self._fontproperties, angle,
 329 ismath)
 330 thisx += w
 331
 332
 333 return
--> 334 bbox, info = self._get_layout(renderer)
 bbox = undefined
 info = undefined
 self._get_layout = <bound method Text._get_layout of 
<matplotlib.text.Text instance at 0x2aaab2496200>>
 renderer = <matplotlib.backends.backend_agg.RendererAgg instance at 
0x2aaab2661e18>
 335
 336 if ismath=='TeX':
 337 canvasw, canvash = renderer.get_canvas_width_height()
 338 for line, wh, x, y in info:
 339 x, y = self._transform.xy_tup((x, y))
 340 if renderer.flipy():
 341 y = canvash-y
 342 renderer.draw_tex(gc, x, y, line,
 343 self._fontproperties, angle)
 344 return
 345
 346 for line, wh, x, y in info:
 347 x, y = self._transform.xy_tup((x, y))
 348 #renderer.draw_arc(gc, (1,0,0),
 349 # x, y, 2, 2, 0.0, 360.0)
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/text.py in 
_get_layout(self=<matplotlib.text.Text instance>, 
renderer=<matplotlib.backends.backend_agg.RendererAgg instance>)
 147 'Copy properties from t to self'
 148 Artist.update_from(self, other)
 149 self._color = other._color
 150 self._multialignment = other._multialignment
 151 self._verticalalignment = other._verticalalignment
 152 self._horizontalalignment = other._horizontalalignment
 153 self._fontproperties = other._fontproperties.copy()
 154 self._rotation = other._rotation
 155
 156
 157 def _get_layout(self, renderer):
 158
 159 # layout the xylocs in display coords as if angle = zero and
 160 # then rotate them around self._x, self._y
 161
--> 162 key = self.get_prop_tup()
 key = undefined
 self.get_prop_tup = <bound method Text.get_prop_tup of 
<matplotlib.text.Text instance at 0x2aaab2496200>>
 163 if self.cached.has_key(key): return self.cached[key]
 164
 165 horizLayout = []
 166 pad =2
 167 thisx, thisy = self._transform.xy_tup( (self._x, self._y) )
 168 width = 0
 169 height = 0
 170
 171 xmin, ymin = thisx, thisy
 172 if self.is_math_text():
 173 lines = [self._text]
 174 else:
 175 lines = self._text.split('\n')
 176
 177 whs = []
/u/lisa/local/linux-x86_64/lib/python2.3/site-packages/matplotlib/text.py in 
get_prop_tup(self=<matplotlib.text.Text instance>)
 406 return self._horizontalalignment
 407
 408 def get_position(self):
 409 "Return x, y as tuple"
 410 return self._x, self._y
 411
 412 def get_prop_tup(self):
 413 """
 414 Return a hashable tuple of properties
 415
 416 Not intended to be human readable, but useful for backends who
 417 want to cache derived information about text (eg layouts) and
 418 need to know if the text has changed
 419 """
 420
--> 421 x, y = self._transform.xy_tup((self._x, self._y))
 x = undefined
 y = undefined
 self._transform.xy_tup = <built-in method xy_tup of tuple object at 
0x2aaab24c0a28>
 self._x = 1
 self._y = [2, 3]
 422 return (x, y, self._text, self._color,
 423 self._verticalalignment, self._horizontalalignment,
 424 hash(self._fontproperties), self._rotation)
 425
 426 def get_text(self):
 427 "Get the text as string"
 428 return self._text
 429
 430 def get_va(self):
 431 'alias for getverticalalignment'
 432 return self.get_verticalalignment()
 433
 434 def get_verticalalignment(self):
 435 "Return the vertical alignment as string"
 436 return self._verticalalignment
TypeError: float() argument must be a string or a number
***************************************************************************
History of session input:
from plot_representation import *
from plot_representation import *
embeddings = [[1,2],[2,3],[1,4]]
names = ['ab','cde','fgh']
classes = [0,1,2]
plot_representation(embeddings,names,classes)
*** Last line of input (may not be in above history):

Hi Chris,
On Tuesday 03 January 2006 10:48, Chris Walker wrote:
> This was originally on Matplotlib-users, but -devel seems more appropriate.
[...]
> Darren Dale <dd...@co...> writes:
> > However, mpl uses a latex package called PSFrag to
> >render the text in an intermediate postscript file, which is not
> > compatible with pdflatex. Unfortunately, if you embed that intermediate
> > postscript file in a new document, the text will frequently be upside
> > down, because PSFrag uses some commands that are illegal in embedded
> > documents. So by default, mpl uses ghostscript to "distill" the
> > intermediate postscript file, converting the fonts to outlines and
> > circumventing the problem.
>
> I attach a patch against matplotlib 0.85 that uses a picture
> environment to position text instead of using psfrag.
>
> It isn't complete, and therefore probably shouldn't be applied just yet,
> but may be a useful starting point. In particular, I haven't taken out
> the distill code, but suspect that it could be replaced by using the
> right options to dvips.
>
> If I had the right dvips command instead of the ghostscript distilling
> process, would this result in a legal eps file? Ie is this worth pursuing?
Here is a post from way back describing the embedding issue: 
http://sourceforge.net/mailarchive/message.php?msg_id=12030448
"PSFrag was not designed to do what I am trying to do: 
 generate an eps file that can later be embedded in a document. It uses a 
 number of PostScript operators that are illegal in an eps file: setglobal, 
 statusdict and userdict. Here is the blurb from PostScript Language 
 Reference, Second Edition, Appendix I: setglobal disrupts page independence 
 and nesting of included documents. [...] Creation and modification of global 
 objects are uneffected by save-restore operators."
So, to answer your question, if you need to use a PostScript operator that is 
illegal in an eps file, it is not worth pursuing. I think your patched 
backend_ps.py still generates a .tex file that uses the PSFrag package, which 
will unavoidably end up using illegal PostScript operators. Is this correct?
Darren

This was originally on Matplotlib-users, but -devel seems more appropriate.
Darren Dale <dd...@co...> writes:
>>On Wednesday 07 December 2005 08:41, Christian Kristukat wrote:
>>
>>Darren Dale wrote:
>>
>>>On Tuesday 06 December 2005 10:03, Christian Kristukat wrote:
>>>
>>>>Darren Dale wrote:
>>>>
>>>>>On Tuesday 06 December 2005 09:10, Alex Gontmakher wrote:
>>>>>
>>>>>>Hi,
>>>>>>
>>>>>>I'm trying to use matplotlib solely for my plotting needs.
>>>>>>Problem is, the fonts are embedded in each EPS file, and
>>>>>>when I import several plots (I have tens of them...) into a
>>>>>>single Latex, the resulting file is HUGE.
>>>>>>
>>>>>>Any suggestions?
>>>>>
>>>>>There are currently two options: you can either set ps.useafm = True, or
>>>>>you can set text.usetex = True in your rc settings. Since you are
>>>>>importing figures into latex, I suggest the usetex option. That way,
>>>>>your figure fonts can be the same as your text fonts. You'll take a bit
>>>>>of a speed hit with the latter option, but in my opinion, its the only
>>>>>way to go for generating plots for publication.
>>>>
>>>>When using tex for font rendering I noticed that parts of the text are
>>>>not converted to polygons but embedded as bitmaps. That makes the files
>>>>big again. Do you now how to avoid that? E.g. using the r'$C_{12}$ will
>>>>produce two images for the numbers and a polygon for the 'C'.
>>>
>>>I made a wiki entry a while back about how to work around this problem,
>>>but it looks like someone deleted it in mid-November, and I dont have a
>>>backup copy. My solution requires ghostview and xpdf, which is why we
>>>dont include it in mpl by default.
>>
>>Thanks!
>>Has using pdflatex for tex labels been considered? Or is that too much
>>dependency? It could possibly even be faster.
>
>I'm guessing pdflatex is provided by default by every up-to-date latex 
>installation out there.
I believe that the latest version of tetex even uses the same binary for 
latex and pdflatex.
> However, mpl uses a latex package called PSFrag to 
>render the text in an intermediate postscript file, which is not compatible 
>with pdflatex. Unfortunately, if you embed that intermediate postscript file 
>in a new document, the text will frequently be upside down, because PSFrag 
>uses some commands that are illegal in embedded documents. So by default, mpl 
>uses ghostscript to "distill" the intermediate postscript file, converting 
>the fonts to outlines and circumventing the problem.
I attach a patch against matplotlib 0.85 that uses a picture 
environment to position text instead of using psfrag.
It isn't complete, and therefore probably shouldn't be applied just yet, 
but may be a useful starting point. In particular, I haven't taken out 
the distill code, but suspect that it could be replaced by using the 
right options to dvips.
If I had the right dvips command instead of the ghostscript distilling 
process, would this result in a legal eps file? Ie is this worth pursuing?
>
>The code I posted last time replaces the distilling step with a ridiculous 
>renormalization step (converting the file to pdf using ghostscript, and then 
>converting back to eps using xpdf) which generates a new eps file that can be 
>embedded in another document. This seems to be pretty robust, convoluted 
>though it is. I generated all the figures in my dissertation this way.
>
>A side note, if you intend to compile a document with pdflatex, you can 
>convert mpl's eps files with epstopdf, which is included in recent versions 
>of TeTeX.
>
My .tex file does seem to be able to be compiled with pdflatex - if you 
include a .pdf rather than .eps graphic. Whether this is useful or not, 
I'm not sure.
Chris
ps While doing this, I noticed that \paperheight is set to the paper 
width, and vice versa.