[sage-support] Re: Problem in displaying graphs

2011-03-22 Thread Jason Grout 

On 3/22/11 9:42 PM, Jason Grout wrote:

On 3/21/11 10:13 AM, kcrisman wrote:

I think there
was a 'needs info' involved on the relevant ticket?


I think #9211 might be the ticket you are referring to? I just looked at
#9211 and it looks like it's probably ready, except for some doctests
and further stress-testing. Anyone want to give it a try?


Oops, I think you were talking about the show options getting passed 
around properly, which is indeed a different ticket.


Regardless, I think #9211 takes care of the OPs problem without 
resorting to manually changing the axes padding.  Does someone want to 
try #9211?


Jason


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[sage-support] Re: Problem in displaying graphs

2011-03-22 Thread Jason Grout 

On 3/21/11 10:13 AM, kcrisman wrote:

I think there
was a 'needs info' involved on the relevant ticket?


I think #9211 might be the ticket you are referring to?  I just looked 
at #9211 and it looks like it's probably ready, except for some doctests 
and further stress-testing.  Anyone want to give it a try?


Jason


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[sage-support] Re: Problem in displaying graphs

2011-03-22 Thread pong 
The only "fiddling" that I did was instead of putting axes_pad=0.1
within the scope of plot(), like Graph(d).plot(axes_pad=0.1),
I put it outside as an argument for \sageplot

And yes, I forgot to type } in my previous post, sorry.

On Mar 21, 8:13 am, kcrisman  wrote:
> On Mar 20, 4:14 pm, pong  wrote:
>
> > With some fiddling,
>
> > \sageplot{Graph(d).plot(), axes_pad=0.1)
>
> > works around the problem.
>
> Can you be more explicit about 'fiddling'?  Does that mean you patched
> SageTeX, or Sage?  Also, is there a } or a ) at the end of the
> command?
>
> Thanks!  It's true that the fix for this was only about show().  I
> can't remember myself whether this got fixed or not... I think there
> was a 'needs info' involved on the relevant ticket? it looks fine with
> your graph in my 4.6.2, though.
>
> - kcrisman

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[sage-support] Re: Problem in displaying graphs

2011-03-21 Thread kcrisman 


On Mar 20, 4:14 pm, pong  wrote:
> With some fiddling,
>
> \sageplot{Graph(d).plot(), axes_pad=0.1)
>
> works around the problem.

Can you be more explicit about 'fiddling'?  Does that mean you patched
SageTeX, or Sage?  Also, is there a } or a ) at the end of the
command?

Thanks!  It's true that the fix for this was only about show().  I
can't remember myself whether this got fixed or not... I think there
was a 'needs info' involved on the relevant ticket? it looks fine with
your graph in my 4.6.2, though.

- kcrisman

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[sage-support] Re: Problem in displaying graphs

2011-03-20 Thread pong 
With some fiddling,

\sageplot{Graph(d).plot(), axes_pad=0.1)

works around the problem.

On Mar 19, 6:50 pm, pong  wrote:
> Sage plots some graphs with vertices partially chopped off.
> For example:
>
> sage: d={1:[2,3,5], 2:[3], 3:[4,5], 4:[5]}
> sage: Graph(d).plot()
>
> I thought the bug was fixed, but looks like it still exists.
> There is a work around using something like G.show(axes_pad=0.1).
> However, I couldn't make it works with sagetex because axes_pad seems
> to have no effect on G.plot().
>
> Any help?
> Thanks in advance

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[sage-support] Re: problem in displaying graphs

2009-10-23 Thread Jason Grout 

William Stein wrote:

> 
> That's one of those quick hackish design decisions that comes back to
> haunt us over the years...  can one just query matplotlib for a range
> that contains all the elements in the plot?


Indeed!

Some discussion:

For tick labels and other things that extend beyond the axes, you can 
shrink the entire plot to fit inside of the figure.  I wrote some code 
to do that, but it is not finished yet.  I posted a short example to the 
matplotlib mailing list to include in their documentation (based on a 
more limited example already in their FAQ):

http://www.nabble.com/Automatically-make-room-for-tick-labels-FAQ-entry-td25251691.html

That code takes care of tick labels extending out, but could be expanded 
to look at all interesting graphical objects in a plot.  This doesn't 
address the clipping at axes boundaries, though (see below).

Another thing to deal with is not clipping the circles at the axes 
boundaries (plot a graph and do frame=True and axes_pad=0 in show to see 
what I mean, or try plotting a bunch of points with axes_pad=0).  There 
is a bug in our current version of matplotlib (fixed in matplotlib svn) 
where the clipping parameter is ignored for scatter plots (which is what 
our vertices are), so we can't turn off clipping right now.  See 
http://www.mail-archive.com/matplotlib-de...@lists.sourceforge.net/msg05486.html
 
for the relevant discussion.

I think you're mentioning something different, though---calculate a 
(tight) bounding box around the figures and resize the axes coordinates 
based on that.  It is slightly nontrivial, since the scatter plot sizes 
are specified in points, so we don't know the data coordinate sizes of 
the vertices until we actually draw them (and thus have the dpi). 
However, there is a way to have a callback adjust things as we draw the 
figure (see paragraph (1) above for an example).

Thanks,

Jason


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[sage-support] Re: problem in displaying graphs

2009-10-23 Thread William Stein 

On Fri, Oct 23, 2009 at 6:30 AM, Jason Grout
 wrote:
>
> William Stein wrote:
>
>> Thanks!  And, argh!  I stared at the output of k.plot? for 10-15
>> minutes before in response to the original email, and axes_pad isn't
>> even there.     That would have been useful many times in my class
>> last year.  That will teach me to read the source more.
>
>
> It's an option to show() (and documented there).

I see, so it has absolutely nothing at all to do a priori with
plotting graphs.  Fair enough.

> I added it in August
> when we redid the matplotlib backend with the new axes code, so I don't
> think it would have been useful last year :).  The default is .02 (so
> the picture is 4% wider and 4% taller than originally specified), so
> that we don't clip plotted points, etc.

That's one of those quick hackish design decisions that comes back to
haunt us over the years...  can one just query matplotlib for a range
that contains all the elements in the plot?

 -- William

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[sage-support] Re: problem in displaying graphs

2009-10-23 Thread Jason Grout 

William Stein wrote:

> Thanks!  And, argh!  I stared at the output of k.plot? for 10-15
> minutes before in response to the original email, and axes_pad isn't
> even there. That would have been useful many times in my class
> last year.  That will teach me to read the source more.


It's an option to show() (and documented there).  I added it in August 
when we redid the matplotlib backend with the new axes code, so I don't 
think it would have been useful last year :).  The default is .02 (so 
the picture is 4% wider and 4% taller than originally specified), so 
that we don't clip plotted points, etc.

Jason

-- 
Jason Grout


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[sage-support] Re: problem in displaying graphs

2009-10-23 Thread Jason Grout 

pong wrote:
> Hi Jason,
> 
>  Setting axes_pad=.1 does work. Thanks! However, I tried your
> codes in the previous email. The resulting graph has nodes "clump
> together". I guess the problem is with the value 1.5. When I changed
> that to a smaller value say .05 then things work just fine. Even
> though, sqrt(area/pi) is the radius...  I'm not sure what's the
> problem of your originally codes.
> 


I forgot that the area unit is points^2, so we'll need to convert 
between points and data coordinates to deal with this.  That will be a 
bit harder, as the axes padding may have to come at a slightly later stage.


Jason


-- 
Jason Grout


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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread pong 

Hi Jason,

 Setting axes_pad=.1 does work. Thanks! However, I tried your
codes in the previous email. The resulting graph has nodes "clump
together". I guess the problem is with the value 1.5. When I changed
that to a smaller value say .05 then things work just fine. Even
though, sqrt(area/pi) is the radius...  I'm not sure what's the
problem of your originally codes.


On Oct 22, 11:03 pm, Jason Grout  wrote:
> William Stein wrote:
> > On Thu, Oct 22, 2009 at 10:09 PM, pong  wrote:
> >> I am using SAGE 4.1.2 notebook on firefox on a Mac.
>
> >> k=graphs.CompleteGraph(6)
> >> show(k)
>
> >> displays K_6 but the vertices got truncated. I don't have this problem
> >> on a linux machine running SAGE 4.1.1 notebook on firefox.
>
> >> Any help?
> >> I would like to include the pic but I don't see how on using this
> >> discussion group.
>
> > That's definitely an annoying bug.  The only workaround I could easily
> > find (without just fixing the bug) is:
>
> > k=graphs.CompleteGraph(6)
> > k.plot(graph_border=1)
>
> A work-around is to pad the graphic:
>
> k=graphs.CompleteGraph(6)
> show(k,axes_pad=.1)
>
> This adds 10% of the width to both the left and right (so the figure is
> 120% its original width) and 10% of the height to the top and bottom (so
> the figure is 120% of the original height).
>
> See my other message for a better fix that uses the vertex size to
> figure out how much to pad the graphic.
>
> Thanks,
>
> Jason
>
> --
> Jason Grout
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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread William Stein 

On Thu, Oct 22, 2009 at 11:03 PM, Jason Grout
 wrote:
>
> William Stein wrote:
>> On Thu, Oct 22, 2009 at 10:09 PM, pong  wrote:
>>> I am using SAGE 4.1.2 notebook on firefox on a Mac.
>>>
>>> k=graphs.CompleteGraph(6)
>>> show(k)
>>>
>>> displays K_6 but the vertices got truncated. I don't have this problem
>>> on a linux machine running SAGE 4.1.1 notebook on firefox.
>>>
>>> Any help?
>>> I would like to include the pic but I don't see how on using this
>>> discussion group.
>>
>> That's definitely an annoying bug.  The only workaround I could easily
>> find (without just fixing the bug) is:
>>
>> k=graphs.CompleteGraph(6)
>> k.plot(graph_border=1)
>>
>
> A work-around is to pad the graphic:
>
> k=graphs.CompleteGraph(6)
> show(k,axes_pad=.1)

Thanks!  And, argh!  I stared at the output of k.plot? for 10-15
minutes before in response to the original email, and axes_pad isn't
even there. That would have been useful many times in my class
last year.  That will teach me to read the source more.

> This adds 10% of the width to both the left and right (so the figure is
> 120% its original width) and 10% of the height to the top and bottom (so
> the figure is 120% of the original height).
>
> See my other message for a better fix that uses the vertex size to
> figure out how much to pad the graphic.
>
> Thanks,
>
> Jason
>
> --
> Jason Grout
>
>
> >
>



-- 
William Stein
Associate Professor of Mathematics
University of Washington
http://wstein.org

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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread Jason Grout 

William Stein wrote:
> On Thu, Oct 22, 2009 at 10:09 PM, pong  wrote:
>> I am using SAGE 4.1.2 notebook on firefox on a Mac.
>>
>> k=graphs.CompleteGraph(6)
>> show(k)
>>
>> displays K_6 but the vertices got truncated. I don't have this problem
>> on a linux machine running SAGE 4.1.1 notebook on firefox.
>>
>> Any help?
>> I would like to include the pic but I don't see how on using this
>> discussion group.
> 
> That's definitely an annoying bug.  The only workaround I could easily
> find (without just fixing the bug) is:
> 
> k=graphs.CompleteGraph(6)
> k.plot(graph_border=1)
> 

A work-around is to pad the graphic:

k=graphs.CompleteGraph(6)
show(k,axes_pad=.1)

This adds 10% of the width to both the left and right (so the figure is 
120% its original width) and 10% of the height to the top and bottom (so 
the figure is 120% of the original height).

See my other message for a better fix that uses the vertex size to 
figure out how much to pad the graphic.

Thanks,

Jason

-- 
Jason Grout


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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread Jason Grout 

pong wrote:
> I am using SAGE 4.1.2 notebook on firefox on a Mac.
> 
> k=graphs.CompleteGraph(6)
> show(k)
> 
> displays K_6 but the vertices got truncated. I don't have this problem
> on a linux machine running SAGE 4.1.1 notebook on firefox.
> 
> Any help?
> I would like to include the pic but I don't see how on using this
> discussion group.

I think this is because the graph plotting code sets the min/max x/y 
positions to the coordinates of the vertices, without allowing for the 
radii of the circles representing the vertices.  If the graph_border 
option is given, then a border is added to the picture and the 
xmin/xmax, ymin/ymax parameters are expanded.

To fix this, try replacing the line:

 G.set_axes_range(self.xmin, self.xmax, self.ymin, self.ymax)

(line 767 in graphs/graph_plot.py)

with the following two lines:

 v_radius = sqrt(self._options['vertex_size']/pi)*1.5 # 
vertex_size is the area of the vertex circle, then pad a bit
 G.set_axes_range(self.xmin-v_radius, self.xmax+v_radius, 
self.ymin-v_radius, self.ymax+v_radius)

to allow space for the radii of the vertices.  I can't test this right 
now because of problems with my Sage installation.

Thanks,

Jason


-- 
Jason Grout


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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread pong 

Thanks for the reply.

Is it a bug of SAGE 4.1.2 or just the Mac distribution? I guess my
question is if I upgrade SAGE to the latest version on my linux
machine, will I get the same problem?


On Oct 22, 10:22 pm, William Stein  wrote:
> On Thu, Oct 22, 2009 at 10:09 PM, pong  wrote:
>
> > I am using SAGE 4.1.2 notebook on firefox on a Mac.
>
> > k=graphs.CompleteGraph(6)
> > show(k)
>
> > displays K_6 but the vertices got truncated. I don't have this problem
> > on a linux machine running SAGE 4.1.1 notebook on firefox.
>
> > Any help?
> > I would like to include the pic but I don't see how on using this
> > discussion group.
>
> That's definitely an annoying bug.  The only workaround I could easily
> find (without just fixing the bug) is:
>
> k=graphs.CompleteGraph(6)
> k.plot(graph_border=1)
>
> William
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[sage-support] Re: problem in displaying graphs

2009-10-22 Thread William Stein 

On Thu, Oct 22, 2009 at 10:09 PM, pong  wrote:
>
> I am using SAGE 4.1.2 notebook on firefox on a Mac.
>
> k=graphs.CompleteGraph(6)
> show(k)
>
> displays K_6 but the vertices got truncated. I don't have this problem
> on a linux machine running SAGE 4.1.1 notebook on firefox.
>
> Any help?
> I would like to include the pic but I don't see how on using this
> discussion group.

That's definitely an annoying bug.  The only workaround I could easily
find (without just fixing the bug) is:

k=graphs.CompleteGraph(6)
k.plot(graph_border=1)

William

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