yt-users February 2014

yt-users@python.org

34 participants
42 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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Notebook server question
by Andrew Myers 19 Apr '14

19 Apr '14

Hello yt users, I have a (perhaps naive) ssh question related to the yt notebook. I would like to run a yt notebook server on machine A. However, machine A cannot be directly accessed via ssh from the wider internet. Instead, I must first ssh into machine B, and then ssh from B to A. Machine B cannot run the notebook server itself. Does anyone know how I can configure things - perhaps by using a more complicated ssh tunnel command - so I that access a notebook server running on machine A through machine B? Thanks, Andrew

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change size of phase plot
by Stephanie Tonnesen 15 Apr '14

15 Apr '14

Hi all, I am trying to make my phase plots smaller so they can fit more nicely into a paper. Alternatively, I would be fine with upping the font size so when I shrink them you can read the axes. I found advise on how to do this for slices, but not for phase_objects. pc = PlotCollection(pf) tracerp25 = alld.cut_region(["grid['specific_scalar[0]'] > 0.5", "grid['z'] < 0.192","grid['z'] > -0.192","grid['cyl_RCode'] < 1.2"]) pc.add_phase_object(tracerp25,["Density","z-velocity","CellMassSolar"],weight=None,x_bins=50,y_bins=50,y_bounds = [-4e7,8e7],x_bounds=[5e-28,5e-23],x_log=True,y_log=False) Any help is much appreciated! Thanks, Stephanie

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GADGET visualization
by Andrew Weis 08 Mar '14

08 Mar '14

Hello, I am an astronomy graduate student at Columbia University, and am trying to use YT to create a 3D visualization of GADGET simulations. Matt Turk suggested I send an email to this list while he is traveling. I have seen that the source code for visualizing GADGET data is in yt/frontends/sph/data_structures.py, but am not sure how to access/use this? I have looked at: http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/e209c55b6aaa4a… and http://yt-project.org/doc/visualizing/volume_rendering.html#generating-a-ho… but remain unsure of where to find the relevant source code/what I do with it after I find it. Matt explained that yt/frontends/sph/data_structures.py is "where the data frontend is. The broader yt codebase uses that to index and manage the data but it uses generic interfaces on top," and encouraged me to email the list for more information. Where is the relevant code? Also, where does the generic vs. frontend interface distinction appear? Best, Andrew Weis

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Fitting an absorption spectrum
by Pengfei Chen 06 Mar '14

06 Mar '14

Hi all, I've used the yt.analysis_modules.absorption_spectrum.absorption_spectrum_fit script to fit an Lya absorption spectrum generated by yt. But there are some abnormal peaks when I did statistics of line width b and column density N. Two figures are attached. I've tried with different redshifts and all of them had peaks in b-distribution at init_b (which is 40km/s here) and maxb(which is 300km/s here). For the N-distribution I got peaks around 10^12 cm^-2 at every redshift. The parameters I used were: HI_parameters = {'name':'HI', 'f': [.4164], 'Gamma':[6.265E8], 'wavelength':[1215.67], 'numLines':1, 'maxN': 1E22, 'minN':1E11, 'maxb': 300, 'minb':1, 'maxz': 5, 'minz':0, 'init_b':40, 'init_N':1E14} Could someone please tell me how to solve this? All the analysis were done with the latest development version of yt and I made no changes to the source code. Please tell me if you need any datasets. Thank you! Pengfei

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FLASH polar coordinates support
by Miguel de Val-Borro 03 Mar '14

03 Mar '14

Hello, I have tried to plot the results of 2D FLASH simulation using the SlicePlot function and got the attached images using the development versions of yt-2.7 and yt-3.0. It looks like the range in the radial coordinate and the labels are not correct. Also I would like to transform to a Cartesian coordinate system, is this possible for FLASH 2D polar data? Thanks, Miguel

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Light Cone Projection
by Pengfei Chen 02 Mar '14

02 Mar '14

Hi all, I downloaded the example script of light cone projectoin( http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-pr…) to my laptop and changed the Enzo simulation parameter file and redshifts. But when I ran it the following error occurred: File "light_cone_projection.py", line 19, in <module> find_outputs=False) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py", line 158, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 44, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line 131, in simulation find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 81, in __init__ find_outputs=find_outputs) File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py", line 343, in __init__ self._parse_parameter_file() File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py", line 273, in _parse_parameter_file param, vals = (i.strip() for i in line.split("=")) ValueError: need more than 1 value to unpack Does the parameters "near_redshift" and "far_redshift" in LightCone need to be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in enzo parameter file? Does anyone know how to solve this? Thank you all! Pengfei

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fixed coordinates when pan_rel is used.
by Juan Camilo Ibanez Mejia 28 Feb '14

28 Feb '14

Hi all, is there is a way to maintain fixed the coordinates in a slice plot when moving the camera around. Every time I use the slc.pan_rel(*args, **kwargs), the coordinates are rested with (0.0 , 0.0) in the center of the plot. Thanks, Juan _____________________________ Juan Camilo Ibañez Mejia Department of Astrophysics American Museum of Natural History +1-212-313-7435 jibanezmejia(a)amnh.org<mailto:jibanezmejia@amnh.org> _____________________________

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seg fault in Quadtree
by Britton Smith 28 Feb '14

28 Feb '14

Hi all, I'm trying to make projections of a rather large Enzo dataset and getting a segfault somewhere in Quadtree.so. This dataset is ~230 GB in size with 27 levels of AMR. As far as I can tell, the only hard coded limit I could find in QuadTree.pyx is for 80 levels, which I am clearly below. Does anyone familiar with this part of the code have any idea if there are any other hard-coded limits in here that I might be exceeding? If not, does anyone have any advice for how I might debug this? I'm seeing this behavior in both yt-2.x and yt-3.0, so it does seem to be something intrinsic to the quadtree code. Thanks! Britton

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yt-users February 2014