Re: Newbie question: ParticlePlot(...)
Nathan, Done (I tared 4 files together): /data/gnedin/REI/TMP >tar cvf gnedin_hop.tar hop.* hop.0.h5 hop.1.h5 hop.2.h5 hop.3.h5 /data/gnedin/REI/TMP >yt upload gnedin_hop.tar Stream body handler: received 9687040 bytes http://use.yt/upload/318d837f The files are available on BlueWaters at: /mnt/c/scratch/sciteam/ngnedin/PERM/B40/A.DMO/a=1.0008/hop/hop.*.h5 Thanks a lot. Nick On 05/16/2018 09:38 AM, Nathan Goldbaum wrote:
Hi,
Is there any chance you can share the hdf5 file? I'm not able to reproduce this warning using a test dataset I have so it might have something to do with the data.
You can share a dataset with "yt upload path/to/data.h5". That will upload to a server at NCSA and then print a link out to share here once its done.
If the data cannot be shared publicly you can send me an e-mail off-list with e.g. a dropbox link.
-Nathan
On Wed, May 16, 2018 at 10:32 AM, Nick Gnedin
mailto:ngnedin@gmail.com> wrote: I am trying to make a plot of all halos found by HOP. I copied your example from http://yt-project.org/doc/cookbook/simple_plots.html http://yt-project.org/doc/cookbook/simple_plots.html
If I just plot partile positions:
--------------------- script ------------------- import yt import numpy as np
# load the dataset ds = yt.load('../B40/A.DMO/a=1.0008/hop/hop.0.h5')
# create our plot p = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y')
m = ds.all_data()[('all', 'particle_mass')] print(np.amin(m),np.amax(m))
# pick some appropriate units p.set_axes_unit('Mpc') p.set_unit('particle_mass', 'Msun')
#save result p.save() -----------------------------------------------
then everything works fine. However, if I use mass weighting:
p = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y', 'particle_mass')
I get the following error:
... yt : [INFO ] 2018-05-16 09:27:39,004 Allocating for 1.997e+05 particles (index particle type 'all') yt : [INFO ] 2018-05-16 09:27:39,381 Identified 5.972e+04 octs yt : [INFO ] 2018-05-16 09:27:40,021 xlim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,021 ylim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,023 xlim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,023 ylim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,042 Splatting (('all', 'particle_mass')) onto a 800 by 800 mesh 4.1036023233207635e+41 g 1.921697915571756e+47 g yt : [INFO ] 2018-05-16 09:27:44,084 Saving plot hop.0.h5_Particle_z_particle_mass.png /u/sciteam/ngnedin/.local/lib/python3.5/site-packages/matplotlib/colors.py:1020: RuntimeWarning: invalid value encountered in less_equal mask |= resdat <= 0
Notice, that there are no nonpositive masses in the catalog print(np.amin(m),np.amax(m)): 4.1036023233207635e+41 g 1.921697915571756e+47 g
_______________________________________________ yt-users mailing list -- yt-users@python.org mailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org mailto:yt-users-leave@python.org
So this isn't really a bug (or a problem at all) - matplotlib is just
warning that the image yt is passing to matplotlib's imshow command
contains NaN values.
This was actually done on purpose in yt, you can see what the code looks
like here:
https://github.com/yt-project/yt/blob/master/yt/visualization/fixed_resoluti...
That was added in this commit:
https://github.com/yt-project/yt/commit/6f378028f7a1eedd553f7641be719762f0c1...
And you can see a test script that explains why we did this change in this
PR:
https://bitbucket.org/yt_analysis/yt/pull-requests/2565/remove-values-in-no-...
(I can't remember why that was declined, I think it was manually merged in
right around when we we moved to GitHub)
I guess in principle we could suppress that warning on the yt side,
although that might be a case of using a cudgel when all we need is a
hammer. We could also think about ways to mask out images without relying
on NaN in matplotlib. One could also argue that passing NaN to matplotlib
as a mask is a common enough thing that matplotlib itself should be doing
special handing at the line raising the warning to avoid generating it.
It's not really a problem that matplotlib is generating the warning. You
can safely ignore it.
On Wed, May 16, 2018 at 10:49 AM, Nick Gnedin
Nathan,
Done (I tared 4 files together):
/data/gnedin/REI/TMP >tar cvf gnedin_hop.tar hop.* hop.0.h5 hop.1.h5 hop.2.h5 hop.3.h5 /data/gnedin/REI/TMP >yt upload gnedin_hop.tar Stream body handler: received 9687040 bytes http://use.yt/upload/318d837f
The files are available on BlueWaters at: /mnt/c/scratch/sciteam/ngnedin/PERM/B40/A.DMO/a=1.0008/hop/hop.*.h5
Thanks a lot.
Nick
On 05/16/2018 09:38 AM, Nathan Goldbaum wrote:
Hi,
Is there any chance you can share the hdf5 file? I'm not able to reproduce this warning using a test dataset I have so it might have something to do with the data.
You can share a dataset with "yt upload path/to/data.h5". That will upload to a server at NCSA and then print a link out to share here once its done.
If the data cannot be shared publicly you can send me an e-mail off-list with e.g. a dropbox link.
-Nathan
On Wed, May 16, 2018 at 10:32 AM, Nick Gnedin
> wrote: I am trying to make a plot of all halos found by HOP. I copied your example from http://yt-project.org/doc/cookbook/simple_plots.html http://yt-project.org/doc/cookbook/simple_plots.html
If I just plot partile positions:
--------------------- script ------------------- import yt import numpy as np
# load the dataset ds = yt.load('../B40/A.DMO/a=1.0008/hop/hop.0.h5')
# create our plot p = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y')
m = ds.all_data()[('all', 'particle_mass')] print(np.amin(m),np.amax(m))
# pick some appropriate units p.set_axes_unit('Mpc') p.set_unit('particle_mass', 'Msun')
#save result p.save() -----------------------------------------------
then everything works fine. However, if I use mass weighting:
p = yt.ParticlePlot(ds, 'particle_position_x', 'particle_position_y', 'particle_mass')
I get the following error:
... yt : [INFO ] 2018-05-16 09:27:39,004 Allocating for 1.997e+05 particles (index particle type 'all') yt : [INFO ] 2018-05-16 09:27:39,381 Identified 5.972e+04 octs yt : [INFO ] 2018-05-16 09:27:40,021 xlim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,021 ylim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,023 xlim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,023 ylim = 0.000000 199229564535610884216586240.000000 yt : [INFO ] 2018-05-16 09:27:40,042 Splatting (('all', 'particle_mass')) onto a 800 by 800 mesh 4.1036023233207635e+41 g 1.921697915571756e+47 g yt : [INFO ] 2018-05-16 09:27:44,084 Saving plot hop.0.h5_Particle_z_particle_mass.png /u/sciteam/ngnedin/.local/lib/python3.5/site-packages/matplo tlib/colors.py:1020: RuntimeWarning: invalid value encountered in less_equal mask |= resdat <= 0
Notice, that there are no nonpositive masses in the catalog print(np.amin(m),np.amax(m)): 4.1036023233207635e+41 g 1.921697915571756e+47 g
_______________________________________________ yt-users mailing list -- yt-users@python.org mailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org mailto:yt-users-leave@python.org
participants (2)
-
Nathan Goldbaum
-
Nick Gnedin