Hi all,
Thanks for all your help over the last couple of days. One more question:
- Can I plot particles on a volume rendered image?
I have stars and I want to show where they are!
Thanks,
Libby
--
Elizabeth Harper-Clark MA MSci
PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT
Sciences and Engineering Coordinator, Teaching Assistants' Training Program,
UofT
www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark>
h-clark(a)cita.utoronto.ca
Astronomy office phone: +1-416-978-5759
Hi, Everybody!
Does anyone out there have a technique for getting the variance out of
a profile object? A profile object is good at getting <X> vs. B, I'd
then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the
possibility some time ago, but I was wondering if anyone out there had
successfully done it.
Thanks,
d.
--
Sent from my computer.
Hello everyone.
I was wondering if anyone has had experience with producing a profile plot
from a 2d projection object (FRB object).
Essentially, what I am trying to do is plot the stellar surface density of
a galaxy as a function of radius.
This is achieved by doing the following from a disk YT object called
cylinder (in which the origional simulation object is called shot)
center = cylinder.get_field_parameter("center")
normal = cylinder.get_field_parameter("normal")
image_width = (100,"kpc")
three_image_width = YTArray((image_width[0], image_width[0],
image_width[0]),image_width[1])
left = center - image_width
right = center + image_width
region = shot.region(center, left, right)
proj =
yt.ProjectionPlot(cylinder.ds,"z",[("deposit","stars_density")],center=center,width=image_width,data_source=region,axes_unit="kpc")
the error arrises here
prof =
yt.create_profile(proj,bin_fields="cylindrical_r",fields=[("deposit","stars_density")],n_bins=128,weight_field=None
)
where I get the error
/gpfs/home/........./profiles.pyc in create_profile(data_source,
bin_fields, fields, n_bins, extrema, logs, units, weight_field,
accumulation, fractional)
1304 else:
1305 raise NotImplementedError
-> 1306 bin_fields = data_source._determine_fields(bin_fields)
1307 fields = data_source._determine_fields(fields)
1308 if units is not None:
AttributeError: 'FixedResolutionBuffer' object has no attribute
'_determine_fields'
Any ideas how to get around this error?
Also some other things to add as a postscript. Since how the projection
works, if I provide weights=None as a keyword argument within the
ProjectionPlot object, I get a surface density (g/cm^2). But also a
"cylindrical_r" in cm^2 as well. I *think* the way to get around this is to
do another projection where weights="ones", get the radius values out of
that profile.. and then in matplotlib, useing the surface density array
from the former profile, and the radius bin array from the latter...
Produce a plot of the surface density as a function of radius from those
two arrays (I might check by hand afterwards to see if this does the
trick). This seems kinda convoluted so I am wondering if there is an easier
way than this.
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Dear yt-users,
I am having a little problem on finding the exact center of a halo. I used
to do
"hc = HaloCatalog(data_ds=data_ds, finder_method='hop')"
to create a halo catalog. But I think the position in the catalog is a
little bit off the exact center judging from the plots I made. I need the
exact center to compute the angular momentum so the off-center result could
cause some problem. I tried to recenter at the maximum gas density by
adding this line
"hc.sphere_field_max_recenter('density')"
But I got an error, AttributeError: 'HaloCatalog' object has no attribute
'sphere_field_max_recenter'.
Can anyone tell me what is the right way to find the center as the location
of maximum gas density?
Thanks,
Jingjing
--
Jingjing Chen [ chenjj235(a)gmail.com ]
Department of Astronomy
Columbia University
550 West 120th Street
New York, New York 10027
Cell Phone: +1(347)5746709
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Hi Stuart,
On Mon, Mar 30, 2015 at 3:59 PM, Stuart Levy <salevy(a)illinois.edu> wrote:
> I'm trying to use the notebook interface to render, view image result, tweak
> parameters, etc. within a single yt session.
>
> I want to disable auto-brightness-scaling of images, so am calling
>
> ImageArray.write_png()
>
> Although write_png() takes a rescale= parameter, it effectively always
> rescales.
> It passes its array to write_bitmap(), which does rescaling unless the image
> datatype is already numpy.uint8.
You're right. It does look like write_bitmap accepts a max_val, which
will be used in lieu of computing the max, before converting to uint8.
Would that work for your purposes?
>
> But if you try to do that yourself, then write_png() crashes inside
> matplotlib, because write_bitmap "must be an rgba buffer". It's using a
> Python C-level routine to do this check, but I think the problem is that the
> array is not C-contiguous,
> since write_bitmap() has called swapaxes(0,1) on it and not copy()ied it
> afterward.
>
> Demo program at:
>
> http://paste.yt-project.org/show/5502/
>
>
>
> and here:
>
> import yt
> from yt.data_objects.image_array import ImageArray
> import numpy
>
> # 3x4x4 array, ranging from 0 to about 0.5
> v = (numpy.arange(12)/24.) .reshape(3,4,1) * numpy.ones((1,1,4))
> # Write
> ImageArray(v).write_png('grays_rescaled.png', rescale=True)
> # Write, but asking not to rescale. It rescales anyway since
> yt.data_objects.image_array() calls write_bitmap()
> ImageArray(v).write_png('grays_unscaled.png', rescale=False)
>
> # write_bitmap rescales internally unless the image's datatype is exactly
> "numpy.uint8".
> # Let's try doing that ourselves.
> vv = (v*255).astype(numpy.uint8)
> print vv.flags
> ImageArray(vv).write_png('grays8.png', background=None, rescale=False)
>
> # Crashes! inside matplotlib/src/_png.cpp.
>
> # Why? yt/visualization/image_writer.py's write_bitmap(), if it doesn't
> rescale the image,
> # simply calls swapaxes(0,1) on it and passes the result to matplotlib.
> # But the resulting array is no longer C-contiguous (write_bitmap.flags
> shows False).
>
> # When rescaling *does* happen, write_bitmap() is constructed by
> np.concatenate() which makes a new contiguous array.
>
>
>
> _______________________________________________
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> yt-users(a)lists.spacepope.org
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>
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Hi All,
I'm trying to understand some of the stellar ages that the Tipsy example
data (the isolated galaxy) at:
http://yt-project.org/data/
When I examine the formation time with the super-simple script:
http://paste.yt-project.org/show/5501/
I get:
max star age: 100.000499852 Gyr
I thought normally the formation time was the current simulation time minus
the stellar age for Tipsy outputs - am I interpreting this wrongly?
Thanks,
desika
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Hi all,
I am just getting started with using yt and using it for analyzing output
data from RAMSES. When I loaded the info_ .txt file into yt and try to
print the field list if returns a runtime error. I also get the same run
time error if I try making projection plots. The same error shows up if I
tried loading the second output. However, if I tried loading in a 3d blast
wave example, this error does not show up and I am able to make slices and
projection plots. Is there a reason why I am seeing this runtime error for
the 2d case?
I am using yt 3.2 (Changeset d4ca808275e4 stable) The code
<http://paste.yt-project.org/show/5497/> and the error output
<http://paste.yt-project.org/show/5498/> is uploaded on the yt pastebin.
The RAMSES output that I'm working with are here
<https://www.dropbox.com/sh/jo7kxwoxio52vy1/AAASbcxNLJ2xZAP5Pry894IPa?dl=0>.
Thank you.
Doris
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Hello everyone,
I just ran into an error in using "data_source" kwarg with the SlicePlot
function (error message copied below):
slice = yt.SlicePlot(ds, axis, field, data_source=region)
File
"/home/emerick/.local/lib/python2.7/site-packages/yt-3.1dev-py2.7-linux-x86_64.egg/yt/visualization/plot_window.py",
line 1816, in SlicePlot
return AxisAlignedSlicePlot(ds, normal, fields, *args, **kwargs)
TypeError: __init__() got an unexpected keyword argument 'data_source'
I have no problem doing the above with ProjectionPlot. If anyone knows what
could be causing this I'd appreciate the help. Otherwise I can do some
digging into the code myself.
Thanks,
Andrew E.
--
Graduate Student
Columbia University
Department of Astronomy
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Hi everyone,
I've been working here and there on making the two point functions
compatible with yt 3. I've run into an issue with the file i/o that's got
me puzzled.
There's a call to write_on_root() that's failing with the error
*AttributeError: 'builtin_function_or_method' object has no attribute
'StringIO'*
Looking at the definition for write_on_root()
in parallel_analysis_interface.py, I see that the offending line is:
*return cStringIO.StringIO()*
So apparently there's no function called StringIO(), even though the
documentation for cStringIO says there should be.
I think the issue is how cStringIO is being imported:
*from yt.extern.six.moves import cStringIO*
Looking through yt/extern/six.py, it looks like it's modifying how the
modules are imported, or something like that, but I can't really figure out
what's going on in that file.
Does anyone have any thoughts on this?
Thanks,
Daniel
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Hi all,
> If you grep the source for KDTree, you should find a couple examples of its
> use. It may be a bit slower than the fortran kdtree, but it is at least
> readily available.
(Chiming in from the great beyond)
Britton makes a good suggestion, but I think that people should be
aware of two things:
- cKDTree will be much faster than KDTree. The latter is pure-python
- Looking at the source below, it looks like I never added periodicity
to KDTree operations
https://bitbucket.org/yt_analysis/yt/src/tip/yt/utilities/spatial/?at=yt
It wouldn't be difficult to add periodicity to KDTree, but I just didn't do it.
--
Stephen Skory
s(a)skory.us
http://stephenskory.com/
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