yt-users March 2015

yt-users@python.org

11 participants
12 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

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

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

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.

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Profile plot of a 2d projection FRB object
by Ben Thompson 03 Jun '15

03 Jun '15

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. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Recenter Halo
by Chen Jingjing 01 Apr '15

01 Apr '15

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 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] ImageArray.write_png() always rescales ...
by Matthew Turk 31 Mar '15

31 Mar '15

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. > > > > _______________________________________________ > 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

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Tipsy Stellar Ages
by Desika Narayanan 30 Mar '15

30 Mar '15

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 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Runtime error when loading RAMSES output
by DORIS LEE 30 Mar '15

30 Mar '15

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 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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data_source SlicePlot Error
by Andrew James Emerick 28 Mar '15

28 Mar '15

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 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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cStringIO error
by Daniel Fenn 27 Mar '15

27 Mar '15

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 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Two point functions
by Stephen Skory 27 Mar '15

27 Mar '15

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/ _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt-users March 2015