[Matplotlib-users] Artifacts when saving as PDF

[Steven B. <bo...@ph...>]

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 University
bo...@ph...