Multiple Projection Multi-panel Appearance
by Ashley Jarvis
Hi all,
I have followed one of the given examples (http://yt-project.org/doc/cookbook/complex_plots.html#mutiple-slice-multi... <http://yt-project.org/doc/cookbook/complex_plots.html#mutiple-slice-multi...>) to produce a multi-panel plot from an Enzo data output using AxesGrid in matplotlib. However, the appearance of this plot doesn’t match that of single plots made using yt.ProjectionPlot by itself. I would like the multi-panel plot (https://ibin.co/3KWlDftVLmgR.png <https://ibin.co/3KWlDftVLmgR.png>) to have a similar appearance to this standard projection plot (https://ibin.co/3KWlr0wRQrHT.png <https://ibin.co/3KWlr0wRQrHT.png>).
Is there an efficient way of invoking the style settings used by yt in matplotlib, or is it just a matter of individually changing the settings for the font style, font size, axis and tick linewidth, plot resolution, etc. in the plotting script? If the latter, are the default values for these parameters in yt listed somewhere, such that I can change the parameters to these values before plotting?
Many thanks,
Ashley
1 year, 9 months
MBH particle coords
by Marco Surace
Hi all,
I'm running an enzo simulation in which I've inserted a Massive Black Hole
(MBH) particle. I would like to know the location of it at later times
after insertion. Does anyone know how I can use yt to return this
information?
Best wishes,
Marco
1 year, 9 months
HDF5 TypeError when writing LightRay
by Joseph Tomlinson
Hi all,
I am trying to use the single dataset LightRay module but I am running into
an issue.
Whenever I use the data_filename parameter, which I believe is necessary
for use with AbsorptionSpectrum, I receive the following error.
TypeError: Object dtype dtype('O') has no native HDF5 equivalent
This error does not occur when I run the cookbook example so I am a bit
lost as to what to do.
I am running the latest stable version on anaconda and have tried both h5py
2.7 and 2.6.
The simulation is a cosmological Enzo simulation.
I have also tried using the nightly dev build which changes the error from
being on write to being on load with the following error.
AttributeError: 'str' object has no attribute 'astype'
from line 326 in _restore_light_ray_solution
self.parameters[ksp3] = self.parameters[ksp3].astype(str)
When using python 2.7 the error is the same but with 'unicode' instead of
'str'.
Any help would be greatly appreciated.
Thanks,
Joe Tomlinson
Senior Undergraduate
Department of Physics, Drexel University
1 year, 9 months
Re: [yt-users] SSLError when trying to update
by Slavin, Jonathan
Hi Nathan,
I just tried again about an hour ago and was able to successfully update.
So whatever the problem was, it seems to be fixed now.
On a different note, when I do 'conda update anaconda' it asks me if I want
to downgrade a whole slew of packages due to dependency conflicts including
astropy, matplotlib, numpy, and scipy among others. Any idea what's up
with that? I'll ask on the anaconda user's list.
Regards,
Jon
On Fri, Apr 21, 2017 at 2:05 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Date: Fri, 21 Apr 2017 11:52:56 -0500
> From: Nathan Goldbaum <nathan12343(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] SSLError when trying to update
> Message-ID:
> <CAJXewO=etF-kWGE_VS3-E8s6Dt17h6acjTXFcawF-
> gamdC3SHQ(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hey Jonathan,
>
> I asked about this in the conda-forge gitter channel and got a response
> after a few days:
>
> No worries, @ngoldbaum. So we package our certificates in a separate
> package called ca-certificates. They are just extracted from the certifi
> Python package and relocated to allow things like openssl and curl to find
> them. This differs from Continuum (or at least last time I checked), which
> has them bundled with openssl. The first thing I'd have him check is that
> package installed and can Python find them, python -c "import ssl;
> print(ssl.get_default_verify_paths())". If the answer is no, then that is
> likely a problem. If the answer is yes, then maybe it has something to do
> with how this redirection is being handled.
>
> So you should check to see if a package named ca-certificates is installed
> in your conda environment. If it is, you should also check the output of
> ssl.get_default_verify_paths(). If it turns out that your python can't
> find
> the CA certificates store, that's your issue. If it turns out that python
> is locating the CA certificates, then this might be due to a bug in how
> conda-forge or continuum have decided to handle this issue.
>
> Unfortunately kind of a headache. I hope you're able to figure this out :)
>
> -Nathan
>
--
________________________________________________________
Jonathan D. Slavin Harvard-Smithsonian CfA
jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
cell: (781) 363-0035 USA
________________________________________________________
1 year, 9 months
SSLError when trying to update
by Slavin, Jonathan
Hi,
I have a conda environment set up to use the development branch of yt.
When I just now went to update it I got:
> conda update -c http://use.yt/with_conda/ -c conda-forge yt
Fetching package metadata .............
CondaHTTPError: HTTP None None
for url <None>
An HTTP error occurred when trying to retrieve this URL.
SSLError(SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED]
certificate verify failed (_ssl.c:590)'),),)
I don't get the "None None" bit, but it looks like a problem with the SSL
certificate. Or maybe it's something else. Any help would be appreciated.
Thanks,
Jon
--
________________________________________________________
Jonathan D. Slavin Harvard-Smithsonian CfA
jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
cell: (781) 363-0035 USA
________________________________________________________
1 year, 9 months
Real-time histogram presentation based on interactive volume rendered camera properties
by E.M. Dragowsky
Greetings --
Please forgive the subject line -- it makes sense to me; hopefully after
reading the note it will make sense to me+1 or more....
Just last week I became aware of yt, and so this is a question about
capabilities:
I'm working on a project to aid a researcher with visualizing derived data
products (a set of ~5000 histograms) along with volume rendering of
simulations performed with Flash (flash.uchicago.edu). This would involve
manipulation of the rendered volume data (e.g. temp, density data fields)
and coordinated presentation in an inset or separate window from the set of
histograms. The active camera view angles from the rendered volume display
would be used to select from the histogram set (in this case indexed by 51
polar angle bins and 101 azimuthal angle bins). The key is for the
histogram selection to take place as the rendered display is being updated
through user interaction -- so as the view is rotated, the histogram
updates without having to stop the user actions.
Right now, these histograms are created at the end of the simulation. One
could imagine a more general case in which the histogram were derived from
the volumetric data in real time.
Is this a task suited to the current state of yt development?
Best regards,
~ Em
--
----------------------------------
E.M. Dragowsky, Ph.D.
Research Computing -- UTech
Case Western Reserve University
(216) 368-0082
1 year, 9 months
Creating a projection for a derived particle field
by José Mauricio Utreras
Hi yt users!
Does anybody know how to create a projection for particles using another
field rather than "particle_mass"?
I was using this:
proj = ds.proj('density', 2,data_source=disk_dd,method='sum')
frb = proj.to_frb(width, res, center=[0.5,0.5,0.5])
M_star=frb[('deposit', 'young_stars_mass')].in_units('Msun')
But now I would like to do this with a particle mass field that depends on
the characteristic timescales of the particles rather than the default
field.
Cheers!
José Utreras
1 year, 9 months
Re: [yt-users] SSLError when trying to update
by Slavin, Jonathan
Yeah, just after I sent that message I tried other conda updates in my
other main environment and got the same problem. So it seems to be a we
hosting issue as you said.
Jon
On Tue, Apr 18, 2017 at 3:49 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
> Date: Tue, 18 Apr 2017 14:49:19 -0500
> From: Matthew Turk <matthewturk(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] SSLError when trying to update
> Message-ID:
> <CALO3=5Gb_MSy9CEzNihTcN6pp=+61RkHMqsBPHE8zdzcrP0Xzw@mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Jon,
>
> I think this happens when there are web hosting issues with conda. I think
> if you give it a little bit of time it should return to normal.
>
> -Matt
>
> On Tue, Apr 18, 2017 at 2:46 PM, Slavin, Jonathan <jslavin(a)cfa.harvard.edu
> >
> wrote:
>
> > Hi,
> >
> > I have a conda environment set up to use the development branch of yt.
> > When I just now went to update it I got:
> > > conda update -c http://use.yt/with_conda/ -c conda-forge yt
> > Fetching package metadata .............
> >
> > CondaHTTPError: HTTP None None
> > for url <None>
> >
> > An HTTP error occurred when trying to retrieve this URL.
> > SSLError(SSLError(SSLError(1, u'[SSL: CERTIFICATE_VERIFY_FAILED]
> > certificate verify failed (_ssl.c:590)'),),)
> >
> > ?I don't get the "None None" bit, but it looks like a problem with the
> SSL
> > certificate. Or maybe it's something else. Any help would be
> appreciated.
> >
> > Thanks,
> > Jon?
>
--
________________________________________________________
Jonathan D. Slavin Harvard-Smithsonian CfA
jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83
phone: (617) 496-7981 Cambridge, MA 02138-1516
cell: (781) 363-0035 USA
________________________________________________________
1 year, 9 months
Some query regarding YT rays
by Arpan Das
Hello,
I am using YT to cast rays within some galaxies simulated using ENZO. I am
using YTray for the purpose. But I am not sure if there is any way to save
the array of cell width through which the rays are passing. I know there
are some quantities like ('index', 'radius'), ('index',
'spherical_radius'), ('index', 'virial_radius_fraction'). But I am not sure
exactly which one of them is the width of the cell. Any help would be
appreciated. Thanking you in advance,
*Arpan Das*
1 year, 9 months
Inverting Plot Axes
by Greta Zhong
Hi everyone!
I’m trying to invert the horizontal axis on some simple projection plots. I’m trying to get a projection along the x axis, with y as the vertical and z as the horizontal axis where the horizontal/z axis is inverted, with the horizontal/z axis decreasing from left to right. Here’s the relevant code:
ds.coordinates.x_axis[0] = 2
ds.coordinates.x_axis['x'] = 2
ds.coordinates.y_axis[0] = 1
ds.coordinates.y_axis['x'] = 1
This is just assigning the z axis (2) to the horizontal axis and the y axis (1) to the vertical axis.
plot1 = yt.ProjectionPlot(ds,"x","velocity_x",weight_field='density')
#plot1.plots["velocity_x"].axes.invert_xaxis()
plot1.save()
plot12 = yt.ProjectionPlot(ds,"x","density")
#plot12.plots["density"].axes.invert_xaxis()
plot12.save()
And then I just use ProjectionPlot to make the plots. As you can see, I commented out a sort of matplotlib-y attempt to invert the horizontal axis, to no effect.
I’ve attached two files: the first is what I’m getting with the above code (‘Projection_x_density_actual'), and the second illustrates the orientation I’d like (‘Projection_x_density_rotated'). Unfortunately, I got to the desired orientation by swapping my vertical/horizontal axes like this:
ds.coordinates.x_axis[0] = 1
ds.coordinates.x_axis['x'] = 1
ds.coordinates.y_axis[0] = 2
ds.coordinates.y_axis['x'] = 2
and then just rotating the png in preview.
I can’t find anything in the documentation about this besides the fact that we can use matplotlib objects to customize plots. I’d really appreciate any help on this!
Thanks,
Greta
1 year, 9 months
