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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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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Hi Suoqing,
Thanks, that worked.
Sandy
On Tue, Mar 24, 2015 at 4:10 PM, <yt-users-request(a)lists.spacepope.org>
wrote:
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>
> Today's Topics:
>
> 1. Re: Line-of-sight velocity dispersion? (Suoqing JI)
> 2. Periodic enzo volume? (Kalina Borkiewicz)
> 3. Re: Particle Size in Projection Plots (Yuan Li)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 24 Mar 2015 12:30:32 -0700
> From: Suoqing JI <suoqing(a)physics.ucsb.edu>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Line-of-sight velocity dispersion?
> Message-ID: <67698C33-B4FE-4E93-B9FD-01ABB2D755CC(a)physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sandy,
>
> The easiest way occurring to me is, since the standard deviation can be
> expressed as:
>
> sqrt( E(X^2) - E(X)^2 )
>
> so you could defined the ?z-velocity squared? as a new field, and
> calculate its average for each column (that is E(X^2) ). Then you have both
> E(X)^2 and E(X^2), thus the standard deviation can be computed.
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Student
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On Mar 24, 2015, at 12:04 PM, Sandy Yuan <sihany(a)princeton.edu> wrote:
> >
> > Hi all,
> > I have created a box object containing the data field "z-velocity".
> Right now, I can project "z-velocity" along the z axis to get the average
> "z-velocity" for each column, but is there a way to calculate the standard
> deviation of "z-velocity" along each column as well? What is the best way
> to do this in yt 2.6? Any suggestion would be greatly appreciated.
> > Best,
> > --
> > Sandy
> > _______________________________________________
> > yt-users mailing list
> > yt-users(a)lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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> ------------------------------
>
> Message: 2
> Date: Tue, 24 Mar 2015 14:56:02 -0500
> From: Kalina Borkiewicz <kalina(a)illinois.edu>
> To: <yt-users(a)lists.spacepope.org>
> Subject: [yt-users] Periodic enzo volume?
> Message-ID: <5511C152.3070205(a)illinois.edu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi! Yt newbie here, sorry if my question is stupid or simple or both.
> I'm trying to render a periodic enzo volume. I figured I could just set
> ds.periodicity = (True, True True) , but that didn't seem to do anything.
> Searching the docs for "periodicity" doesn't have any results relating
> to EnzoDataset, so I'm wondering, can I make this periodic? How?
>
> Thanks,
> Kalina
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> ------------------------------
>
> Message: 3
> Date: Tue, 24 Mar 2015 16:10:05 -0400
> From: Yuan Li <bear0980(a)gmail.com>
> To: Discussion of the yt analysis package
> <yt-users(a)lists.spacepope.org>
> Subject: Re: [yt-users] Particle Size in Projection Plots
> Message-ID:
> <CANx7jWiGbzZ=
> P9euh9HGa-pw-H4hzosp00N3HfeWgubtzf8icw(a)mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Cameron,
>
> I tired that, and this is the error message I get:
>
> *** YTDataSelectorNotImplemented: Data selector 'arbitrary_grid' not
> implemented.
>
>
> I looks like I will have to do it with matplotlib as Britton suggested
> after all :).
>
>
> By the way, in the examples given on Filtering Particle Fields here
> http://yt-project.org/doc/analyzing/filtering.html, sometimes "Stars" is
> used
> and sometimes it is the lowercase "stars". Is that a typo?
>
>
> Yuan
>
>
> On Tue, Mar 24, 2015 at 12:26 PM, Cameron Hummels <chummels(a)gmail.com>
> wrote:
>
> > I think you may be able to do the ProjectionPlot() by specifying the
> > keyword "data_source=obj":
> >
> >
> >
> http://yt-project.org/docs/dev/reference/api/generated/yt.visualization.plo…
> >
> > On Tue, Mar 24, 2015 at 9:03 AM, Yuan Li <bear0980(a)gmail.com> wrote:
> >
> >> Hi all,
> >>
> >> I was thinking about doing what Britton suggested or making a 2d
> >> histogram in matplotlib, but Cameron's suggestion sounds like what I was
> >> looking for. How do I project this obj after it is created? When I
> tried to
> >> do yt.ProjectionPlot(obj.....) I got the error message saying this
> object
> >> has no attribute 'coordinates'.
> >>
> >> Yuan
> >>
> >> On Tue, Mar 24, 2015 at 11:03 AM, Britton Smith <brittonsmith(a)gmail.com
> >
> >> wrote:
> >>
> >>> In this situation, you might just want to plot the particles themselves
> >>> using a scatter plot in matplotlib. The matplotlib.scatter function
> allows
> >>> you to specify both the color and/or size of the points with arrays, so
> >>> those properties can vary for the individual particles.
> >>>
> >>> Britton
> >>>
> >>> On Tue, Mar 24, 2015 at 2:58 PM, Cameron Hummels <chummels(a)gmail.com>
> >>> wrote:
> >>>
> >>>> Hi Yuan,
> >>>>
> >>>> I think the issue here is that you're taking a particle
> >>>> quantity--stellar ages--and trying to deposit that quantity on to the
> grid,
> >>>> which is primarily defined in enzo by the distribution of gas. Thus,
> young
> >>>> stars tend to occur in locations of star formation, which is to say,
> where
> >>>> there is cold dense gas, the grid is more refined there (assuming
> you're
> >>>> using density-based AMR). This means that you'll tend to get smaller
> >>>> "pixels" for young stars than for old stars where the stars may have
> >>>> drifted into regions of coarser spatial resolution and get larger
> "pixels".
> >>>>
> >>>> One solution for this would be to define your own underlying grid on
> to
> >>>> which you should deposit your particle quantities. That way you can
> make a
> >>>> fixed resolution grid (so all the pixels are the same size) and
> deposit
> >>>> your particle quantities like Stellar Age, and it should solve your
> >>>> problem. To find out more about doing this, check out this section
> of the
> >>>> docs:
> >>>>
> >>>>
> >>>>
> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grids-objec…
> >>>>
> >>>> Good luck, and let us know how it goes!
> >>>>
> >>>> Cameron
> >>>>
> >>>> On Sun, Mar 22, 2015 at 9:40 PM, Yuan Li <yuan(a)astro.columbia.edu>
> >>>> wrote:
> >>>>
> >>>>> Hi all,
> >>>>>
> >>>>> I have a basic question related to the sizes of particles in a
> >>>>> projection plot (in yt2). I am trying to make a plot that shows the
> average
> >>>>> line of sight star particle ages.
> >>>>>
> >>>>> Right now I am plotting the stellar-density-weighted star ages, and a
> >>>>> lot of the young stars look very small (see figure attached). I
> would like
> >>>>> to show that the stars far away from the center are younger. Is
> there a way
> >>>>> to make the small dots bigger? Other suggestions are also welcome!
> >>>>>
> >>>>>
> >>>>> Thank you!
> >>>>> Yuan
> >>>>> [image: Inline image 1]
> >>>>>
> >>>>> _______________________________________________
> >>>>> yt-users mailing list
> >>>>> yt-users(a)lists.spacepope.org
> >>>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>> --
> >>>> Cameron Hummels
> >>>> Postdoctoral Researcher
> >>>> Steward Observatory
> >>>> University of Arizona
> >>>> http://chummels.org
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users(a)lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users(a)lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users(a)lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >
> >
> > --
> > Cameron Hummels
> > Postdoctoral Researcher
> > Steward Observatory
> > University of Arizona
> > http://chummels.org
> >
> > _______________________________________________
> > yt-users mailing list
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