This is probaly due to issues with not all of the vector backends
supporting alpha gracefully.
This can be reproduced more simply by
x, y = np.ogrid[-5:5:.1, -5:5:.1]
dd = np.exp(-(x**2 + y**2))
dd[dd < .1] = np.nan
fig, ax = plt.subplots()
ax.imshow(dd, interpolation='none', cmap='gray_r')
plt.savefig('test.pdf')
@steven In the future it is best to report bugs with minimal copy-paste
able examples.
On Mon, Apr 6, 2015 at 5:41 PM Steven Boada <bo...@physics.tamu.edu> wrote:
> Getting some strange artifacts when I save a figure as a PDF in
> matplotlib. Here are some screen shots. PDF <http://imgur.com/oQDXkWn>
> and PNG <http://imgur.com/bCw3Fn4>. Any idea why that is happening?
>
> Here is (most of) the source code that makes the plot. I stripped out the
> data generation, because it is long and involved, and doesn't really
> matter. Basically what the script is supposed to do is make a scatter plot
> where the density is below some threshold, and a 2d histogram when it is
> above that threshold. The code seems to work fine, but when I save the
> figure (using savefig in Ipython) it shows up funny.
>
> Thanks.
>
> import pylab as pyl
>
> bins = [50,50]
> thresh = 3
>
> xdat = #generate or load some data
> ydat = #generate or load some data
>
> hh, locx, locy = pyl.histogram2d(xdat, ydat, range=[[-1,4],[-26,-10]],
> bins=bins)
> posx = pyl.digitize(xdat, locx)
> posy = pyl.digitize(ydat, locy)
>
> # finds the bins which contain points. posx = 0 for points outside
> "range"
> ind = (posx > 0) & (posx <= bins[0]) & (posy > 0) & (posy <= bins[1])
> # values of histogram with points in the bins.
> hhsub = hh[posx[ind] - 1, posy[ind] - 1]
>
> xdat1 = xdat[ind][hhsub < thresh] # low density points
> ydat1 = ydat[ind][hhsub < thresh]
> hh[hh < thresh] = pyl.nan # fill the areas with low density by NaNs
>
> pyl.scatter(xdat1, ydat1, s=20, c='0.8')
> pyl.imshow(pyl.log10(hh.T), cmap='gray_r',
> extent=pyl.array([[-1,4],[-26,-10]]).flatten(),
> interpolation='none')
>
> pyl.show()
>
> --
>
> Steven Boada
>
> Doctoral Student
> Dept of Physics and Astronomy
> Texas A&M universitybo...@physics.tamu.edu
>
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