[Matplotlib-users] Artifacts when saving as PDF
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 AM University bo...@physics.tamu.edu -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Artifacts when saving as PDF
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 AM universitybo...@physics.tamu.edu
--
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exercises
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[Matplotlib-users] I need to force the rounding of x axis limits
INTRO
=
please consider the following code (I'm trying to draw a timeline)
1 from matplotlib import pyplot, patches
2 fig = pyplot.figure()
3 ax = fig.add_subplot('111')
4 ax.add_patch(patches.Rectangle((1933,0.25), 73, 0.5))
5 pyplot.show()
that gives me a plot with the x axis that goes from 0.0 to 1.0,
now consider
...
5 ax.set_xlim((1933,1933+73))
6 pyplot.show()
this gives me an x axis that goes _exactly_ from 1933 to 2006,
eventually drawing a line superposed to the lower spine
...
5 ax.plot((1933,1933+73),(0,0))
6 pyplot.show()
gives me what I really want, that is an x axis running from 1930 to
2010, with the limits automatically rounded by matplotlib...
(I noted that the extra line forces a rounding also for the y axis
limits, but that's not a problem...)
QUESTION
I want matplotlib to round the limits of the x axis automatically,
when given explicitly the lower and upper limits of the data, how to?
Thank you in advance
--
We have met the enemy and he is us.
--- Pogo.
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