[yt-users] Clumps, contours, n_contours

[Matthew Turk]

Hi Dave,

I think the way contours works is that it sets N contours.  What might
work better, since we're contouring images, would be to explicitly
specify the contours.  Can you test if something like range(N+1) works
better, rather than len(contours)?

-Matt

On Mon, May 20, 2013 at 7:04 PM, David Collins <dcollins4096 at gmail.com> wrote:
> Hi, Nathan--
>
> I thought about the colorbar thing, so I made the image grayscale and it
> still doesnt' show up.  I also set the zlim so that the data was either all
> white or black, and it shows up in neither.
>
> I've attached two representative images.  By construction all of these
> contours are disjoint.  The missing clump is pretty obvious, as it takes up
> most of the image where it exists.
>
> The two attached plots are two tweaks to
> plot_modifications.py/ClumpContourCallback, at line ~700
> the "plus_3" plot uses
> self.rv = plot._axes.contour(buff,  len(self.clumps)+3,
>                                      extent=extent,**self.plot_args)
> the "plus_5" plot uses
>
> self.rv = plot._axes.contour(buff,  len(self.clumps)+5,
>                                      extent=extent,**self.plot_args)
>
> The code to reproduce the plot is pretty benign, and is below for
> generality.  the list clumps_to_use comes from a set of pickled clumps for
> this dataset.  I'll see if I can reproduce it with something more
> universally accessible.  I'm quite sure that it doesn't have anything to do
> with the clump itself, as I've seen this behavior with other calls to
> 'contour'.  I'm working on a simpler thing that demonstrates this-- I've
> seen it with code that uses no piece of yt, so I'm 97.2% sure that it's
> contour and not yt.  (Might be something else dumb I'm doing, that's pretty
> common, but I haven't been able to sort out what it is.)
>
> <code>
>     field='Density'
>     center = [0.5]*3
>     proj = pf.h.proj(ax,field,center=center)
>     plot = proj.to_pw(origin='domain')
>     plot.set_cmap('Density','gray')
>     subset = 'black_map_fixed'
>     plot.set_zlim('Density',1e6,1e7)
>     if clumps_to_use is not None:
>         plot.annotate_clumps(clumps_to_use)
>     print plot.save('%s_n%04d_%s'%(name,frame,subset))
> </code>
>
>
>
>
> On Mon, May 20, 2013 at 4:21 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>>
>> Hi Dave,
>>
>> I haven't seen this.  Could this be due to the colorbar?  I believe it
>> picks the contour colors based on a colorbar.  If the colors it picks are
>> invisible on your plot, you won't see the contours.
>>
>> It would help to figure out what's going on if you could come up with a
>> sample script that illustrates the issue.  Bonus points if you use one of
>> the datasets on yt-project.org/data.
>>
>> -Nathan
>>
>>
>> On Mon, May 20, 2013 at 3:17 PM, david collins <dcollins4096 at gmail.com>
>> wrote:
>>>
>>> Hi, all--
>>>
>>> I'm seeing a glitch in the matplotlib countor function, as employed by
>>> annotate_clumps.  As is, I'm seeing some clumps that are not plotted by the
>>> countour plotter unless I bump the number of contours-- I get all the plots
>>> if I change the contour line to:
>>>
>>> self.rv = plot._axes.contour(buff, len(self.clumps)+5,
>>>                                      extent=extent,**self.plot_args)
>>>
>>> instead of
>>>
>>> self.rv = plot._axes.contour(buff, len(self.clumps)+1,
>>>                                      extent=extent,**self.plot_args)
>>>
>>>
>>> Is this a glitch that anyone is aware of?  Is there a more general fix?
>>> The clump contour is not the only time I've run into this glitch. It seems
>>> to happen on large contours, for what that's worth.
>>>
>>> Thanks!
>>> d.
>>>
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>>
>>
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