Re: [yt-dev] 3.1: PRs to merge
by John ZuHone
Yes, unfortunately, so I apologize for ranting about it.
> On Jan 13, 2015, at 6:41 PM, Cameron Hummels <chummels(a)gmail.com> wrote:
>
> So this is what you were referencing in IRC today. I only *just* received this, despite it being sent yesterday. Weird. Anyway, perhaps there was a problem in the mail routing, which is why people weren't responsive to it?
>
> Good luck with everything!
>
> Cameron
>
> ---------- Forwarded message ----------
> From: John ZuHone <jzuhone(a)gmail.com <mailto:jzuhone@gmail.com>>
> Date: Mon, Jan 12, 2015 at 12:44 PM
> Subject: [yt-dev] 3.1: PRs to merge
> To: yt-dev(a)lists.spacepope.org <mailto:yt-dev@lists.spacepope.org>
>
>
> Hi all,
>
> Since we’re trying to get 3.1 out soon (today if possible), we’d like some more eyeballs to go over the following PRs, which barring any other comments are ready to go:
>
> https://bitbucket.org/yt_analysis/yt/pull-request/1400/check-if-pyfits-is... <https://bitbucket.org/yt_analysis/yt/pull-request/1400/check-if-pyfits-is...>
>
> https://bitbucket.org/yt_analysis/yt/pull-request/1398/controlling-the-de... <https://bitbucket.org/yt_analysis/yt/pull-request/1398/controlling-the-de...>
>
> https://bitbucket.org/yt_analysis/yt/pull-request/1394/gadget-temperature... <https://bitbucket.org/yt_analysis/yt/pull-request/1394/gadget-temperature...>
>
> https://bitbucket.org/yt_analysis/yt/pull-request/1381/positions-and-velo... <https://bitbucket.org/yt_analysis/yt/pull-request/1381/positions-and-velo...>
>
> There was some contention over the last one in particular. Please indicate your approval on each PR, or if you think something is missing please comment.
>
> Best,
>
> John Z
>
>
>
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>
>
>
>
> --
> Cameron Hummels
> Postdoctoral Researcher
> Steward Observatory
> University of Arizona
> http://chummels.org <http://chummels.org/>
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4 years, 2 months
Issue #974: OffAxisProjectionPlots with RAMSES and
particle data (yt_analysis/yt)
by Benjamin Thompson
New issue 974: OffAxisProjectionPlots with RAMSES and particle data
https://bitbucket.org/yt_analysis/yt/issue/974/offaxisprojectionplots-wit...
Benjamin Thompson:
Hello.
I am trying to produce an off axis projection plot with RAMSES using YT. More specifically using the star (or particle) density deposit field.
It works fine for gas (although since this data object is only 10 kpc thick, there are odd "grating like" lines in the image
But when it comes to producing an off axis plot of stellar density, I get this output
```
#!python
yt : [INFO ] 2015-01-13 15:31:56,772 xlim = -0.001753 0.001753
yt : [INFO ] 2015-01-13 15:31:56,772 ylim = -0.001753 0.001753
yt : [INFO ] 2015-01-13 15:31:56,772 zlim = -0.001753 0.001753
yt : [INFO ] 2015-01-13 15:31:56,772 Making a fixed resolutuion buffer of (('deposit', 'stars_density')) 800 by 800
```
and then the terminal crashes
Any idea why this might be the case?
Ben
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4 years, 2 months
Issue #973: Sliceplot of 2D cylindrical data
(yt_analysis/yt)
by Andrea Derdzinski
New issue 973: Sliceplot of 2D cylindrical data
https://bitbucket.org/yt_analysis/yt/issue/973/sliceplot-of-2d-cylindrica...
Andrea Derdzinski:
When I try to make a sliceplot of output from a 2D cylindrical FLASH simulation,
```
#!python
from yt.mods import *
pf = load('disc_hdf5_plt_cnt_0000') #attached
slc = SlicePlot(pf, 'theta', 'dens')
```
but I get the following error:
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1842, in SlicePlot
return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1017, in __init__
window_size=window_size, aspect=aspect)
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 618, in __init__
PlotWindow.__init__(self, *args, **kwargs)
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 210, in __init__
self.data_source.center, ax)
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/geometry/coordinates/coordinate_handler.py", line 184, in sanitize_center
return self.ds.arr(center), self.convert_to_cartesian(center)
File "/Users/Shark/yt-x86_64/src/yt-hg/yt/geometry/coordinates/cylindrical_coordinates.py", line 146, in convert_to_cartesian
return cylindrical_to_cartesian(coord)
NameError: global name 'cylindrical_to_cartesian' is not defined
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4 years, 2 months
Issue #971: yt-3.0 gadget InternalEnergy field unit (yt_analysis/yt)
by Junhwan Choi
New issue 971: yt-3.0 gadget InternalEnergy field unit
https://bitbucket.org/yt_analysis/yt/issue/971/yt-30-gadget-internalenerg...
Junhwan Choi:
Hi yt developers,
I would like to file a bug related with gadget(spy) field.
I (and Nathan Goldbaum) found that the InternalEnergy field in yt/frontends/sph/fields.py is read as dimensionless.
Indeed, the unit of the gadget InternalEnergy is Velocity_unit**2.
For example, if the unit is defined as follow:
unit_base = {'UnitLength_in_cm' : 3.08568e+21,
'UnitMass_in_g' : 1.989e+43,
'UnitVelocity_in_cm_per_s' : 100000}
The Internal Energy unit is (km/s)**2
If it is possible that I would like to ask to set up the temperature field for gadget dataset.
Indeed, the gadget output only generates the InternalEnergy and temperature need to be estimated from the InternalEnergy and chemical abundance (if there are).
Although it is possible to generate the derived temperature field, the temperature is very basic quantity and it may need to computed for both particle and cell.
Thank you,
Junhwan
4 years, 2 months
Field naming proposal
by Nathan Goldbaum
Hi all,
I've just issued a pull request that bears some developer discussion.
Right now yt is a bit of a wild west in terms of the field naming
convention for fields that reference a coordinate system. See for example,
see issue 947:
https://bitbucket.org/yt_analysis/yt/issue/947/consistent-field-naming-fo...
I'd like to propose a naming convention for fields that reference a
coordinate system. Gas and particle fields should be of the form:
(field_type, "<particle?>_<vector_field_name>_<coordinate>")
while index fields for coordinates should be of the form:
("index", "<coordinate>")
This fits within our existing field naming convention for cartesian
coordinates, e.g.:
("gas", "velocity_x")
(ptype, "particle_velocity_y")
as well as our convention for index coordinate fields, e.g.:
("index", "x")
("index", "spherical_theta")
This means that index fields do not need to explicitly reference themselves
as positions. So we *won't* have field names like:
("index", "position_x")
I don't like the above construction because it's a bit redundant ("index"
implies that we are talking about a position or something similar).
Some existing field names will need to be changed to fit this. In
particular, some of the index fields will need to be renamed to be more
verbose ("index", "spherical_r") becomes ("index", "spherical_radius") and
(ptype, "particle_spherical_position_radius") becomes (ptype,
"particle_position_spherical_radius").
Wherever an existing field name needs to change, I propose we mark the
existing field name for deprecation, stub it out, and make it an alias for
the field with the new field name. In a future release, we can then remove
the deprecated fields.
I've implemented this for the particle fields (for the most part) in PR
1378:
https://bitbucket.org/yt_analysis/yt/pull-request/1378
I'm happy to update the field naming YTEP if this proposed field naming
scheme gets approval in this thread.
What do you all think? Question, concerns?
-Nathan
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4 years, 2 months
Issue #970: bug in PPVcube viewing angle to FITS (yt_analysis/yt)
by Roger Deane
New issue 970: bug in PPVcube viewing angle to FITS
https://bitbucket.org/yt_analysis/yt/issue/970/bug-in-ppvcube-viewing-ang...
Roger Deane:
Hi
Firstly, thank you for this excellent piece of software.
I am using the PPVcube class to write to FITS images and cubes (essentially, what is being done in this example: http://yt-project.org/doc/analyzing/analysis_modules/ppv_cubes.html)
I have come across what seems to be a bug in changing the viewing angle of the rotating disk (parameter "L" in the above tutorial).
An aside: I think L should be L = [0.0,np.sin(i),np.cos(i)]; not what is currently set in the tutorial: L = [0.0,np.sin(i),np.sin(i)]
I've attached a script which is simply the original PPVCube.py script from the above webpage with an additional for loop to write out FITS images at inclination angles of 0,10,20,...,90 degrees. All that is changed is the "L" parameter. One key difference is that I write out a FITS cube with 1 velocity plane, as one would do if you would like to make a "total intensity or moment 0" map of CO or HI emission.
If you run the script, you'll produce 10 FITS images with the above inclinations. If you compare the FITS images you'll notice two strange things:
1) the inclination = 0 FITS image should be rotationally symmetric about the origin, but it is not. The effect of this is also seen in the higher inclination FITS images.
2) There is a 90 degree rotation of this asymmetry between the 20 and 30 degree inclination FITS images (more specifically between 26 and 27 degrees).
I suspect the issue is possibly caused by the fact that I am writing out to a single velocity channel. I hope I have missed anything obvious that is causing this. I am running the developer version of yt 3.0.2 and have updated.
I am under time pressure and need to decide whether to use yt or reluctantly switch to a much older, less flexible package. So I would greatly appreciate a confirmation of this perceived bug and a possible workaround or fix.
Many thanks
Roger
4 years, 2 months
