[yt-users] Phase plot pixel has white outline

Nathan Goldbaum nathan12343 at gmail.com
Wed Apr 2 14:27:51 PDT 2014


Or use the mpl_kwargs keyword argument:

phase_plot.save('plot.eps', mpl_kwargs={'rasterized' : True})


On Wed, Apr 2, 2014 at 2:25 PM, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Geoffrey,
>
> On Wed, Apr 2, 2014 at 5:21 PM, Geoffrey So <gsiisg at gmail.com> wrote:
> > Hi Matt,
> >
> > I tried different ways of getting the rasterized kwarg in PhasePlot but
> > failed.  I went back to using BinnedProfile2D and got what I wanted,
> except
> > for a minor bug.
> >
> > When I'm using the following script, the bottom bin fits right into the
> > plotting window nicely, but the top of the plotting area always has one
> > extra bin of white space compared to PhasePlot's results.  Is there a
> bug so
> > the data and the plotting window doesn't align correctly at the top?
>
> Yes -- if you look at what you're calling, it's "imshow", which
> displays it like a bitmap.  What yt will do is use pcolormesh, which
> actually requires bin edges, so that will give you a better looking
> image in that case.
>
> I think you will be able to get rasterized in as a keyword argument if
> you *manually* save your PhasePlot, similar to how the cookbook
> examples plot things by grabbing the axes/figure objects on plots.
>
> -Matt
>
> >
> > If there's a way to make PhasePlot without the white lines between pixel
> or
> > make this script create perfectly binned bins like PhasePlot then
> everything
> > will be perfect for me.
> >
> > From
> > G.S.
> >
> > #----------------
> > from yt.mods import *
> > from matplotlib import *
> >
> > i=1200
> > file='HD%04i' % i
> > pf=load(file+'/'+file)
> > dd=pf.h.all_data()
> >
> > z = pf["CosmologyCurrentRedshift"]
> > res = pf["TopGridDimensions"][0]
> >
> > def _HIFraction(field, data):
> >    return data["HI_Density"]/(data["HI_Density"]+data["HII_Density"])
> >
> > add_field("HIFraction", function=_HIFraction, \
> >           units=r"\rho_\mathrm{HI}/\rho_\mathrm{H}")
> >
> > nbins=128
> > fieldx='Density'
> > fieldy='HIFraction'
> > fieldc='CellVolumeCode'
> > xmin,xmax = dd.quantities['Extrema'](fieldx, non_zero=True)[0]
> > ymin,ymax = dd.quantities['Extrema'](fieldy, non_zero=True)[0]
> >
> > pro = BinnedProfile2D(data_source=dd,
> >     x_n_bins=nbins, x_bin_field=fieldx,
> >     x_lower_bound=xmin, x_upper_bound=xmax, x_log=True,
> >     y_n_bins=nbins, y_bin_field=fieldy,
> >     y_lower_bound=ymin, y_upper_bound=ymax, y_log=True,
> >     lazy_reader=True, end_collect=True)
> >
> > pro.add_fields(fieldc, weight=None)
> > extent = ([pro[fieldx][0], pro[fieldx][-1],pro[fieldy][0],
> pro[fieldy][-1]])
> > M=(pro[fieldc].transpose())
> > pylab.imshow(M, extent=extent, interpolation='nearest',
> >              origin='lower',aspect='auto',norm=colors.LogNorm())
> > pylab.yscale('log')
> > pylab.xscale('log')
> > pylab.ylabel(fieldy +
> >              " [$"+pf.field_info[fieldy].get_units()+"$]")
> > pylab.xlabel(fieldx +
> >              " [$"+pf.field_info[fieldx].get_units()+"$] (z=%2.2f)"
> >              % z, labelpad=0)
> >
> > cb=pylab.colorbar()
> > cb.set_label(fieldc +
> >              " [$"+pf.field_info[fieldc].get_units()+"$]")
> > pylab.savefig('frames/'+file+fieldx+fieldy+fieldc+'.eps')
> > #-------------------
> >
> >
> > On Tue, Apr 1, 2014 at 11:27 AM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> >>
> >> Hi Geoffrey,
> >>
> >> I think the solution is in the rasterize=True argument to saving out
> >> the figure, which needs to be fed in at the matplotlib level.
> >>
> >> -Matt
> >>
> >> On Tue, Apr 1, 2014 at 2:24 PM, Geoffrey So <gsiisg at gmail.com> wrote:
> >> > Hi all,
> >> >
> >> > Is it possible when saving phase plots in EPS format to get rid of the
> >> > white
> >> > outline of each pixel?  When shrinking the diagram the white makes the
> >> > colors look faded.
> >> >
> >> > From
> >> > G.S.
> >> >
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