Hi all,
is there any option when performing a density plot with
OffAxisProjectionPlot to specify whether the axes in the resulting image
are labelled "x/y (pc)" or "image x/y (pc)"? I would like to output
images with the latter formatting enabled.
Many thanks,
Sam Patrick
Dear yt users,
I have a common envelope simulation where two stars orbit each other. The
cores of the stars are approximated by point-masses.
I would like to move my coordinate system on the core of one of them with
the x axis aligned with the semi-major axis of the orbit, so as to be able
to analyse the data in a co-rotating coordinate system.
Is there any pre-built function in yt that allows moving the coordinates
system to a specific point of the box and rotate them? Or I have to do it
manually?
Thanks,
Roberto
Hello yt friends!
yt 3.6.1 is now out!
It includes one backport: matplotlib 3.3.x support. See PR 2754
<https://github.com/yt-project/yt/pull/2754> and the initial bug report at
2752 <https://github.com/yt-project/yt/issues/2752> .
For release notes, see
https://yt-project.org/doc/reference/changelog.html#version-3-6-1.
Binaries for yt 3.6.1 are available via pip and conda. If you installed via
the install script or use conda to manage your python installation, you can
update yt via:
$ conda update -c conda-forge yt
And via pip if you manage your python installation with pip:
$ pip install -U yt
As always, if you have any questions, concerns, or run into any trouble
updating please don’t hesitate to send a message to the mailing list or
stop by our Slack workspace.
Thanks for being in the community!
- the yt development team
Calling any and all yt-users!
I am pleased to send out the 2nd announcement for *RHytHM:* *R*esearc*H*
using *yt* *H*ighlights *M*eeting! *It is taking place Dec 9-11 for a few
hours each day, and if you sign up early enough (Nov 16) we will try to
account for your time zone when settling on the exact hours!*
The goal of the meeting is for yt users to share how yt helps them with
their research. Sharing how yt helps *your *workflow may inspire the rest
of us to use yt in a way we had never even considered! We are so excited
to see what everyone is up to, and to make life easy, when you sign up for
a talk, *you can choose* if it is a longer, more detailed talk (25+5), a
shorter talk (15+5), or a lightning-style quick look at something for which
you use yt (5 mins).
This is meant to be a fun, informal meeting, so sign up to talk about *any*
aspect of yt *you* use!
As a yt user, let me share some talk ideas I hope *YOU* sign up to give:
*--*Share why phaseplots are the best plots *(I could look at
**phaseplots** for
a whole conference, honestly)*
--Share a new colormap that beats kamae *(a low bar, possibly? ...or
impossibly high?)*
*--*Show how phaseplots let you compare simulations to observations! *(to
figure out if the simulation in which we live is flawed)*
--Show how slices are way better than projections for your work *(I'll
believe it when I see it)*
--Explain a neat way you select data *(is cut_region your friend, too?)*
--Walk me through your yt extension! *(so many cool things use
yt: https://yt-project.org/extensions.html
<https://yt-project.org/extensions.html>, is yours on the list?)*
*-*-Show how phaseplots can sometimes be basically a projection, but
BETTER. *(phaseplots are so useful, amiright?)*
--Two words: volume. rendering. (*more words: is it scientifically
helpful or just gorgeous?)*
--A plot you can't quite make using yt that you feel like *should just
work*! *(lines on phaseplots, anyone?)*
*--*Surprise me with a phaseplot I haven't thought of! *(other things than
phaseplots are acceptable)*
*Please take a look and register (by Nov 16) if interested! Share with
your networks! *https://indico.flatironinstitute.org/event/722/
We look forward to seeing many of you (on zoom) in December!
Best,
The SOC
Stephanie Tonnesen
Matt Turk
Madicken Munk
John Zuhone
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY
stonnes(a)gmail.com
All,
I am testing a script on both windows and linux, but the latest version of
yt seems to have a conflict with matplotlib:
python yt_plots.py
/home/siegfried/anaconda3/envs/science/lib/python3.8/_collections_abc.py:666:
MatplotlibDeprecationWarning: The global colormaps dictionary is no longer
considered public API.
self[key]
Traceback (most recent call last):
File "yt_plots.py", line 3, in <module>
import yt
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/__init__.py",
line 63, in <module>
from yt.fields.api import \
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/fields/api.py",
line 19, in <module>
from . import angular_momentum
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/fields/angular_momentum.py",
line 26, in <module>
from .vector_operations import \
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/fields/vector_operations.py",
line 32, in <module>
from yt.geometry.geometry_handler import \
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/geometry/geometry_handler.py",
line 29, in <module>
from yt.utilities.parallel_tools.parallel_analysis_interface import \
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 30, in <module>
from yt.data_objects.image_array import ImageArray
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/data_objects/image_array.py",
line 18, in <module>
from yt.visualization.image_writer import write_bitmap, write_image
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/visualization/image_writer.py",
line 29, in <module>
import yt.utilities.png_writer as pw
File
"/home/siegfried/anaconda3/envs/science/lib/python3.8/site-packages/yt/utilities/png_writer.py",
line 13, in <module>
import matplotlib._png as _png
ModuleNotFoundError: No module named 'matplotlib._png'
It tries to import a package that doesn't exist. Any idea how this mistake
came about ?
warmest regards,
Siegfried Vanaverbeke
Hello All,
I have a question regarding how yt finds the cell_mass of a sphere in ART simulations. I am currently doing an analysis of the mass profiles within the virial radius of a galaxy, finding the masses using these commands:
sp_new_rvir = ds.sphere(center, (float(new_rvir.in_units('kpc')), 'kpc'))
sp_new_rvir_010 = ds.sphere(center, (float(new_rvir.in_units('kpc'))*.1, 'kpc'))
sp_new_rvir_015 = ds.sphere(center, (float(new_rvir.in_units('kpc'))*.15, 'kpc'))
sp_new_rvir_020 = ds.sphere(center, (float(new_rvir.in_units('kpc'))*.2, 'kpc'))
stellar_mass_rvir, darkmatter_mass_rvir, gas_mass_rvir = sp_new_rvir.quantities.total_quantity([('stars', 'particle_mass'),\
('darkmatter', 'particle_mass'),\
('gas', 'cell_mass')])
stellar_mass_010, gas_mass_010 = sp_new_rvir_010.quantities.total_quantity([('stars', 'particle_mass'),\
('gas', 'cell_mass')])
stellar_mass_015, gas_mass_015 = sp_new_rvir_015.quantities.total_quantity([('stars', 'particle_mass'),\
('gas', 'cell_mass')])
stellar_mass_020, gas_mass_020 = sp_new_rvir_020.quantities.total_quantity([('stars', 'particle_mass'),\
('gas', 'cell_mass')])
These work just fine, and return results, but when I compare these values to ones collected by a collaborator, I disagree on the total masses within each sphere by a small amount. I imagine that there might be a difference in how yt calculates these quantities compared to the other methodology, which I would like to understand, as both are probably acceptable methods, but understanding the difference seems important. I have a gut feeling that gas mass is probably the cause of this difference, as I dont see how a difference in the particle fields could arise. I was looking through the yt fields list page (https://yt-project.org/doc/reference/field_list.html) to see how the cell_mass paramater was defined to compare to this other method, and saw that it is multiplying the density and cell volume field. On that page, it lists the method for the density field as follows:
def _TranslationFunc(field, data):
# We do a bunch of in-place modifications, so we will copy this.
return data[field_name].copy()
I am not sure where to look to see where the method for the density field calculation is stored. I looked a bit around the ART frontend here https://github.com/yt-project/yt/tree/master/yt/frontends/art but could not find anything. I was wondering if anyone could point me to where this is?
Hello,
I am working with pyxsim and have had no issues for the past year or so, however recently after switching to the YT development build on the server I use, and then back to my own install of the stable build I am getting an issue in importing YT into my script. I get the error that the fnv_hash module doesn't exist.
When looking in the directory it is attempting to find fnv_hash I find fav_hash.pyx.
I was hoping anyone may have some insight into how this error may have arisen and how I might be able to fix it.
Cheers
Dylan
Hello,
I've looked at the documentation and it seems that octree datasets are
loadable for a few specific codes, but not in general. I have an
octree that represents galaxy simulation data, but it's produced as an
output of an analysis script. It would be nice to take advantage of yt's
capabilities to do analysis.
Is there a simple way to load an generic octree or would I have to write a
front-end myself (as described in the documentation and by looking at ART,
for example)?
Thanks!
Paco Holguin
Hi everyone!
I am so excited to announce a virtual meeting on Dec 9-11 called *RHytHM*:
*R*esearc*H *using *yt* *H*ighlights *M*eeting! It will be the first (that
I know of) meeting where we all just share how we use yt (and hopefully
cool images). The summary is:
Answering scientific questions using large datasets rich with information
is often a matter of examining data in a new and informative way. The
ability to analyze and visualize data in physically-meaningful ways is one
of the most powerful uses of yt and has allowed for its use across many
scientific domains. In this meeting, we aim to share the ways in which yt
has been used to enhance research.
We plan to have a series of talks in which people introduce their
scientific problem to a diverse group of scientists (domain amateurs) and
highlight how yt was used in their research. We look forward to hearing
about how yt slices, phaseplots, and volume-rendering have been used,
interesting ways to select data or an extension based on yt. We also hope
to hear about yt uses we have not yet considered!
*Please take a look and register (by Nov 9) if interested! Share with your
networks! *https://indico.flatironinstitute.org/event/722/
*Note: We do not yet have times set for the meeting. We are asking
participants for their timezones so we can try and strike a good balance.
Looking forward to zooming with you in December!
Best,
Stephanie (for the SOC)
--
Dr. Stephanie Tonnesen
Associate Research Scientist
CCA, Flatiron Institute
New York, NY
stonnes(a)gmail.com
Dear YT-Users,
I'm a beginner with YT, and trying to analyze the GIZMO output with it. I
can understand that the default 'YT derived fields' creates a mesh and
outputs the averaged particle values (either simple neighboring particle
averaging or kernel averaging, etc), but I'm not sure which particular
method has been used to create the GIZMO output data-mesh. Is it kernel
smoothing like GADGET data or finding neighbors and simply averaging over
the number of NGB particles? Where to find the detailed mesh creating
routines in YT other than this place
<https://yt-project.org/doc/analyzing/fields.html#general-particle-fields>?
Any help is appreciated!
Thanks,
Arpita
--
Dr. Arpita Roy,
Postdoctoral Fellow,
Research School of Astronomy & Astrophysics,
Mount Stromlo Observatory,
Australian National University,
Cotter Road, Weston Creek,
Canberra, ACT 2611, Australia.
https://www.researchgate.net/profile/Arpita_Roy12
