yt-users March 2014

yt-users@python.org

36 participants
35 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

8 14

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.

6 8

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

4 5

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

4 17

PhasePlot give inconsistent results with different core count and fieldc
by Geoffrey So 31 Mar '14

31 Mar '14

The following script gives me different results in the 2d phase plot when I use multiple cores and switch the fieldc parameter. The results are consistent if I only use a single core. Some of the plots produced seems like it is missing data points or under-sampled, so I'm guessing maybe not all the data from all the cores were collected at the end. From G.S. #----------------------------------------------------------------------------------- from yt.mods import * i=2 file = "RD%04i" % i fn = file+"/"+file pf=load(fn) dd=pf.h.all_data() fieldx='Density' fieldy='Temperature' fieldc='CellVolumeCode' #fieldc='CellVolume' #fieldc='CellMassMsun' #fieldc='CellMass' #fieldc='Ones' pplot = PhasePlot(dd, fieldx, fieldy, [fieldc],weight_field=None) pplot.save('example/'+file) #---------------------------------------------------------------------------------------

3 6

volume rendering
by Renyue Cen 29 Mar '14

29 Mar '14

Hi folks, Some time ago John Wise kindly gave me a yt script that uses AMRKDTree to speed up "camera" 3-d rendering, it worked very well and fast (takes like a few minutes to do a rendering of a galaxy with 2048x2048 pixel). It looks like volume = AMRKDTree(pf, le=le, re=re, fields=["Density"], no_ghost=False) then used in cam = pf.h.camera(c, L, W, (N,N), tf, volume=volume, no_ghost=False, north_vector=Ldm,steady_north=True) It appears that yt has evolved and the "volume ..." statement no longer works. Is there a solution to that in the newer version? Alternatively, is there another speedy way to do 3-d rendering? Thanks very much, Renyue

4 4

updated examples for 3.0 volume rendering
by Michael Zingale 29 Mar '14

29 Mar '14

Is there any updated examples for using the yt 3.0 volume rendering? For instance, looking at this: http://yt-project.org/docs/dev/cookbook/simple_plots.html#simple-volume-ren… The field name is no longer simply "Density", but now, for my data, I need to use a tuple like: field = ('boxlib', 'magvel') And then when I look at the extrema, I no longer take the [0] index, as that just gives the min, but instead if I look at: dd.quantities["Extrema"](field) I get: (124.858613718 dimensionless, 18061918.0546 dimensionless) (not sure why they are dimensionless, but that's a different problem). Finally, if I try to make a transfer function, like: tf = ColorTransferFunction((mi, ma)) I get: NameError: name 'ColorTransferFunction' is not defined I just synced up with the development version today. Mike -- Michael Zingale Associate Professor Dept. of Physics & Astronomy * Stony Brook University * Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale(a)stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale

3 9

Combining a large number of disjoint shells
by Thomas Hansen 28 Mar '14

28 Mar '14

Hi everybody, I'm a bit of a yt-newb, and I was wondering what the best way to handle a problem I'm working on it. Basically, I have a (large) list of locations (centers of galaxies), and I want to make a profile plot using the data from all of the shells a distance r > 10kpc, r < 100 kpsc from each of these centers. I tried using a loop with the expression x = pf.h.boolean([x, "AND", newShell]) to just build the data up over many iterations before finally using create_profile after the end of the loop, but this approach ran out of memory. Is there a better way to get the sum of a large data set? Thanks in advance for any help, Thomas

1 0

Website font rendering issue
by Nathan Goldbaum 26 Mar '14

26 Mar '14

Hi all, If over the past month or so you've noticed some font rendering issues on yt-project.org when using the Google Chrome web browser, that should be fixed now. Unfortunately it was due to an as yet unpatched bug in the browser. We have implemented a workaround that should fix it. Sorry for any trouble this has caused. Cheers, Nathan Goldbaum

1 0

pyx install error
by Junhwan Choi (최준환) 26 Mar '14

26 Mar '14

Hi yt users, I try to install pyx onto my existing yt package (including yt, python, numpy ....). Buit I get following error message: ====== Downloading/unpacking pyx Could not find any downloads that satisfy the requirement pyx Some externally hosted files were ignored (use --allow-external pyx to allow). Cleaning up... No distributions at all found for pyx Storing debug log for failure in /home52/jhchoi/.pip/pip.log ==== The pip.log file says ------------------------------------------------------------ /home/jhchoi/common/bin/pip run on Wed Mar 26 10:05:31 2014 Downloading/unpacking pyx Getting page https://pypi.python.org/simple/pyx/ URLs to search for versions for pyx: * https://pypi.python.org/simple/pyx/ Analyzing links from page https://pypi.python.org/simple/PyX/ Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.12.1/PyX-0.12.1.tar.gz#… (from https://pypi.python.org/simple/PyX/) because it is externally hosted. Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.13/PyX-0.13.tar.gz#md5=… (from https://pypi.python.org/simple/PyX/) because it is externally hosted. Could not find any downloads that satisfy the requirement pyx Some externally hosted files were ignored (use --allow-external pyx to allow). Cleaning up... Removing temporary dir /tmp/pip_build_jhchoi... No distributions at all found for pyx Exception information: Traceback (most recent call last): File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/basecommand.py", line 122, in main status = self.run(options, args) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/commands/install.py", line 278, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py", line 1177, in prepare_files url = finder.find_requirement(req_to_install, upgrade=self.upgrade) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/index.py", line 277, in find_requirement raise DistributionNotFound('No distributions at all found for %s' % req) DistributionNotFound: No distributions at all found for pyx What does this error mean? And could anyone inform me how to resolve this problem? Thank you in advance, Junhwan Choi

2 2

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users March 2014