[yt-users] saving a plot from a plotcollection object
Matthew Turk
matthewturk at gmail.com
Mon Jul 8 05:50:32 PDT 2013
Hi Mohammad,
This looks like a bug in the definition of particle_density which was
fixed on April 18 of this year; if you run "yt update" you should get
the updated fix.
-Matt
On Sun, Jul 7, 2013 at 6:23 PM, mohammad safarzadeh
<mtsafarzadeh at gmail.com> wrote:
> Hi,
> When I want to save a plot collection object. I get this error and I would
> like to know how to resolve this.
> In [3]: pc=pc=PlotCollection(pf,[ 0.5808,0.5398, 0.4504 ])
> yt : [INFO ] 2013-07-07 18:02:49,267 Created plot collection with
> default plot-center = [0.58079999999999998, 0.53979999999999995,
> 0.45040000000000002]
>
> In [4]: pc.add_thin_projection("particle_density",0,0.1)
> yt : [INFO ] 2013-07-07 18:03:19,026 Getting the binary hierarchy
> yt : [INFO ] 2013-07-07 18:03:19,032 Finished with binary hierarchy
> reading
> yt : [INFO ] 2013-07-07 18:03:38,125 Projection completed
> Out[4]: <yt.visualization.plot_types.PCProjectionPlot at 0x3876550>
> In [20]: pc.save()
> ---------------------------------------------------------------------------
> ParseFatalException Traceback (most recent call last)
> <ipython-input-20-aabd56408a20> in <module>()
> ----> 1 pc.save()
>
> /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.pyc in
> save(self, basename, format, override, force_save)
> 181 for plot in self.plots:
> 182 fn.append(plot.save_image(basename, format=format,
> --> 183 override=override, force_save=force_save))
> 184 mylog.info("Saved %s", fn[-1])
> 185 if ytcfg.getboolean("yt", "__withinreason"):
>
> /home/safarzadeh/yt-x86_64/src/yt-hg/yt/visualization/plot_types.pyc in
> save_image(self, prefix, format, override, force_save, figure_canvas)
> 120 canvas.print_figure(fn)
> 121 else:
> --> 122 only_on_root(canvas.print_figure, fn)
> 123 self["Type"] = self._type_name
> 124 self["GeneratedAt"] = self.data.pf.unique_identifier
>
> /home/safarzadeh/yt-x86_64/src/yt-hg/yt/funcs.pyc in only_on_root(func,
> *args, **kwargs)
> 366 cfg_option = "__topcomm_parallel_rank"
> 367 if not ytcfg.getboolean("yt","__parallel"):
> --> 368 return func(*args,**kwargs)
> 369 if ytcfg.getint("yt", cfg_option) > 0: return
> 370 return func(*args, **kwargs)
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backend_bases.pyc
> in print_figure(self, filename, dpi, facecolor, edgecolor, orientation,
> format, **kwargs)
> 2015 orientation=orientation,
> 2016 bbox_inches_restore=_bbox_inches_restore,
> -> 2017 **kwargs)
> 2018 finally:
> 2019 if bbox_inches and restore_bbox:
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc
> in print_png(self, filename_or_obj, *args, **kwargs)
> 443
> 444 def print_png(self, filename_or_obj, *args, **kwargs):
> --> 445 FigureCanvasAgg.draw(self)
> 446 renderer = self.get_renderer()
> 447 original_dpi = renderer.dpi
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc
> in draw(self)
> 399
> 400 self.renderer = self.get_renderer()
> --> 401 self.figure.draw(self.renderer)
> 402
> 403 def get_renderer(self):
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
> 53 def draw_wrapper(artist, renderer, *args, **kwargs):
> 54 before(artist, renderer)
> ---> 55 draw(artist, renderer, *args, **kwargs)
> 56 after(artist, renderer)
> 57
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/figure.pyc
> in draw(self, renderer)
> 882 dsu.sort(key=itemgetter(0))
> 883 for zorder, func, args in dsu:
> --> 884 func(*args)
> 885
> 886 renderer.close_group('figure')
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
> 53 def draw_wrapper(artist, renderer, *args, **kwargs):
> 54 before(artist, renderer)
> ---> 55 draw(artist, renderer, *args, **kwargs)
> 56 after(artist, renderer)
> 57
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/axes.pyc
> in draw(self, renderer, inframe)
> 1981
> 1982 for zorder, a in dsu:
> -> 1983 a.draw(renderer)
> 1984
> 1985 renderer.close_group('axes')
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
> 53 def draw_wrapper(artist, renderer, *args, **kwargs):
> 54 before(artist, renderer)
> ---> 55 draw(artist, renderer, *args, **kwargs)
> 56 after(artist, renderer)
> 57
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/axis.pyc
> in draw(self, renderer, *args, **kwargs)
> 1047 self._update_label_position(ticklabelBoxes, ticklabelBoxes2)
> 1048
> -> 1049 self.label.draw(renderer)
> 1050
> 1051 self._update_offset_text_position(ticklabelBoxes,
> ticklabelBoxes2)
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
> 53 def draw_wrapper(artist, renderer, *args, **kwargs):
> 54 before(artist, renderer)
> ---> 55 draw(artist, renderer, *args, **kwargs)
> 56 after(artist, renderer)
> 57
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/text.pyc
> in draw(self, renderer)
> 524 renderer.open_group('text', self.get_gid())
> 525
> --> 526 bbox, info = self._get_layout(renderer)
> 527 trans = self.get_transform()
> 528
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/text.pyc
> in _get_layout(self, renderer)
> 307 w, h, d = get_text_width_height_descent(clean_line,
> 308
> self._fontproperties,
> --> 309
> ismath=ismath)
> 310 else:
> 311 w, h, d = 0, 0, 0
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/backends/backend_agg.pyc
> in get_text_width_height_descent(self, s, prop, ismath)
> 177 if ismath:
> 178 ox, oy, width, height, descent, fonts, used_characters =
> \
> --> 179 self.mathtext_parser.parse(s, self.dpi, prop)
> 180 return width, height, descent
> 181
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc
> in parse(self, s, dpi, prop)
> 2972 self.__class__._parser = Parser()
> 2973
> -> 2974 box = self._parser.parse(s, font_output, fontsize, dpi)
> 2975 font_output.set_canvas_size(box.width, box.height,
> box.depth)
> 2976 result = font_output.get_results(box)
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc
> in parse(self, s, fonts_object, fontsize, dpi)
> 2350 self._state_stack = [self.State(fonts_object, 'default',
> 'rm', fontsize, dpi)]
> 2351 try:
> -> 2352 self._expression.parseString(s)
> 2353 except ParseException, err:
> 2354 raise ValueError("\n".join([
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseString(self, instring, parseAll)
> 1046 if not self.keepTabs:
> 1047 instring = instring.expandtabs()
> -> 1048 loc, tokens = self._parse( instring, 0 )
> 1049 if parseAll:
> 1050 StringEnd()._parse( instring, loc )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 922 if self.mayIndexError or loc >= len(instring):
> 923 try:
> --> 924 loc,tokens = self.parseImpl( instring, preloc,
> doActions )
> 925 except IndexError:
> 926 raise ParseException( instring, len(instring),
> self.errmsg, self )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseImpl(self, instring, loc, doActions)
> 2557 def parseImpl( self, instring, loc, doActions=True ):
> 2558 if self.expr is not None:
> -> 2559 return self.expr._parse( instring, loc, doActions,
> callPreParse=False )
> 2560 else:
> 2561 raise ParseException("",loc,self.errmsg,self)
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 922 if self.mayIndexError or loc >= len(instring):
> 923 try:
> --> 924 loc,tokens = self.parseImpl( instring, preloc,
> doActions )
> 925 except IndexError:
> 926 raise ParseException( instring, len(instring),
> self.errmsg, self )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseImpl(self, instring, loc, doActions)
> 2305 raise ParseSyntaxException(
> ParseException(instring, len(instring), self.errmsg, self) )
> 2306 else:
> -> 2307 loc, exprtokens = e._parse( instring, loc, doActions
> )
> 2308 if exprtokens or exprtokens.keys():
> 2309 resultlist += exprtokens
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 922 if self.mayIndexError or loc >= len(instring):
> 923 try:
> --> 924 loc,tokens = self.parseImpl( instring, preloc,
> doActions )
> 925 except IndexError:
> 926 raise ParseException( instring, len(instring),
> self.errmsg, self )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseImpl(self, instring, loc, doActions)
> 2670 tokens = []
> 2671 try:
> -> 2672 loc, tokens = self.expr._parse( instring, loc,
> doActions, callPreParse=False )
> 2673 hasIgnoreExprs = ( len(self.ignoreExprs) > 0 )
> 2674 while 1:
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 922 if self.mayIndexError or loc >= len(instring):
> 923 try:
> --> 924 loc,tokens = self.parseImpl( instring, preloc,
> doActions )
> 925 except IndexError:
> 926 raise ParseException( instring, len(instring),
> self.errmsg, self )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseImpl(self, instring, loc, doActions)
> 2305 raise ParseSyntaxException(
> ParseException(instring, len(instring), self.errmsg, self) )
> 2306 else:
> -> 2307 loc, exprtokens = e._parse( instring, loc, doActions
> )
> 2308 if exprtokens or exprtokens.keys():
> 2309 resultlist += exprtokens
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 922 if self.mayIndexError or loc >= len(instring):
> 923 try:
> --> 924 loc,tokens = self.parseImpl( instring, preloc,
> doActions )
> 925 except IndexError:
> 926 raise ParseException( instring, len(instring),
> self.errmsg, self )
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in parseImpl(self, instring, loc, doActions)
> 2414 for e in self.exprs:
> 2415 try:
> -> 2416 ret = e._parse( instring, loc, doActions )
> 2417 return ret
> 2418 except ParseException, err:
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseCache(self, instring, loc, doActions, callPreParse)
> 979 else:
> 980 try:
> --> 981 value = self._parseNoCache( instring, loc,
> doActions, callPreParse )
> 982 ParserElement._exprArgCache[ lookup ] =
> (value[0],value[1].copy())
> 983 return value
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/pyparsing.pyc
> in _parseNoCache(self, instring, loc, doActions, callPreParse)
> 948 else:
> 949 for fn in self.parseAction:
> --> 950 tokens = fn( instring, tokensStart, retTokens )
> 951 if tokens is not None:
> 952 retTokens = ParseResults( tokens,
>
> /home/safarzadeh/yt-x86_64/lib/python2.7/site-packages/matplotlib/mathtext.pyc
> in raise_error(s, loc, toks)
> 2047 """
> 2048 def raise_error(s, loc, toks):
> -> 2049 raise ParseFatalException(msg + "\n" + s)
> 2050
> 2051 empty = Empty()
>
> ParseFatalException: Expected end of math '$'
> $\rm{$\mathrm{Particle}\/\mathrm{Density}$}$ (at char 0), (line:1, col:1)
>
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