yt-users May 2015

yt-users@python.org

34 participants
33 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

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

8 16

local install of yt on Blue Waters
by Kenza Arraki 01 Jun '15

01 Jun '15

Hi all, I am trying to locally install yt on Blue Waters. I did a module of swap to PrgEnv-gnu and then bash install_script.sh. Has anyone run into this error before? http://paste.yt-project.org/show/5576/ Thanks, Kenza

7 9

Rendering Volume of FLASH file
by Kilian Gärtner 30 May '15

30 May '15

Hi, I want to render a Volume Plot based on data from a FLASH file, which uses HDF5 file format. I tried the tutorial at http://yt-project.org/doc/cookbook/simple_plots.html#cookbook-simple-volume… with my file, but I always get this error: yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) This is the complete log: yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter forcedplotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter nbegin overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,302 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: current_time = 1.10472907814e+17 yt : [INFO ] 2015-05-29 20:51:30,331 Parameters: domain_dimensions = [16 16 16] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_left_edge = [ -2.20000000e+25 -2.20000000e+25 -2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: domain_right_edge = [ 2.20000000e+25 2.20000000e+25 2.20000000e+25] yt : [INFO ] 2015-05-29 20:51:30,332 Parameters: cosmological_simulation = 0.0 yt : [INFO ] 2015-05-29 20:51:32,513 Loading field plugins. yt : [INFO ] 2015-05-29 20:51:32,513 Loaded angular_momentum (8 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded astro (15 new fields) yt : [INFO ] 2015-05-29 20:51:32,515 Loaded cosmology (22 new fields) yt : [WARNING ] 2015-05-29 20:51:32,515 Field ('gas', 'number_density') already exists. To override use force_override=True. yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid (63 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded fluid_vector (95 new fields) yt : [INFO ] 2015-05-29 20:51:32,516 Loaded geometric (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded local (111 new fields) yt : [INFO ] 2015-05-29 20:51:32,517 Loaded magnetic_field (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded my_plugins (119 new fields) yt : [INFO ] 2015-05-29 20:51:32,519 Loaded species (121 new fields) yt : [INFO ] 2015-05-29 20:51:42,595 Warning: no_ghost is currently True (default). This may lead to artifacts at grid boundaries. Ray casting100% ||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:01 C:\Anaconda\lib\site-packages\yt\units\yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) C:\Anaconda\lib\site-packages\yt\data_objects\image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) The image itself is created, but only black, also the rendering process is instantly finished. I've tried it with the "Enzo_64/DD0043/data0043" file as used for the tutorial, this works with errors. Then I've tried using a given FLASH dataset, the "GalaxyClusterMerger" - same result as my dataset, also the error. I'm using Win 8.1 64-bit Anaconda distribution and yt-project 3.1. Also tried the same thing on Ubuntu 14 with freshly installed yt-project, same error. Is there a solution to create a volume render with FLASH files? Thank you for your attention! Kilian

2 1

is there a limit on image size?
by Dave Semeraro 29 May '15

29 May '15

Helly yt-crowd. I am doing some volume rendering in yt and getting some errors when I try to grow the image size. I am trying to write a png image that is 1024 x 1024. I get the following errors: image_array.py:229: RuntimeWarning: invalid value encountered in multiply np.multiply(self[:, :, :3], 1.0/cmax, out[:, :, :3]) yt_array.py:764: RuntimeWarning: divide by zero encountered in divide return YTArray(super(YTArray, self).__rdiv__(lo)) The largest image I can generate is about 800x 800. It is a nice image too I tell ya. Just wish I could do a bigger one to submit for publication. Attached is the script I am using. Any help would be great. Thanks, Dave Semeraro _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 4

Temperature with Enzo
by David Collins 28 May '15

28 May '15

Hi, Everybody-- I have a dumb question about temperature in enzo. Where is it? I thought I rememberd that being a stock derived field, but I don't see it in the enzo frontends. I can go ahead and make a PR for that if there's not something obvious I'm missing. Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 3

Storing multiple calculations using yt.parallel_objects
by Joshua Wall 27 May '15

27 May '15

Dear users, This there a simple way to store multiple values at each step using parallel_objects? I'm doing: ######################################################## yt.enable_parallelism() num_procs = 4 plot = glob.glob(./plot*) my_storage = {} for sto, p in yt.parallel_objects(plots, num_procs, my_storage): sto.result_id = 'energy' + p sto.resutl = dd["total_energy"] sto.result_id = 'Px' + p sto.result = dd["total_mom_x"] ###################################################### which is just overwriting my energy with the momentum. I also tried to just set to different dictionaries without passing it to yt.parallel_objects as storage, but of course each proc as only a local copy then. Cordially, Josh _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 6

code units
by David Collins 26 May '15

26 May '15

Hi, Everyone-- I'm trying to get code units from enzo for a cosmology run, but in_units('code_density') seems to do nothing. 'code_mass/code_length**3' seems to work. Is this a bug, or a feature? >>> ad['density'].in_units('code_mass/code_length**3') YTArray([ 0.9970247 , 0.99774731, 0.99854185, ..., 0.99993769, 0.99914176, 0.99841755]) code_mass/code_length**3 >>> ad['density'].in_units('code_density') YTArray([ 1.87321000e-29, 1.87456764e-29, 1.87606042e-29, ..., 1.87868293e-29, 1.87718755e-29, 1.87582689e-29]) code_density Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

3 4

Re: [yt-users] How to use yt.load_hexahedral_mesh?
by Matthew Turk 25 May '15

25 May '15

Hi Jonah, That's right -- the volume rendering won't work, but slices will. The VR should be working relatively soon, though. -Matt On Sun, May 24, 2015 at 8:47 PM, Jonah Miller <jonah.maxwell.miller(a)gmail.com> wrote: > Oh, I should add that I don't think 3D visualization is possible with > hexahedral meshes at the moment. The pixelizer doesn't support them yet... > At least that's my understanding. If you really need a 3D visualization, you > might want to try transforming your data into a regularly spaced grid (using > another tool) and then loading uniformly spaced data as in this example: > http://yt-project.org/docs/dev/examining/spherical_data.html > > Best, > Jonah > > > On 15-05-24 09:41 PM, Jonah Miller wrote: > > Hi Katharina, Andrew, > > There is a convenience function to create the coordinates and connectivity > arguments: hexahedral_connectivity. This function takes three 1D arrays, > which are the projections of your grid points onto your coordinate axes, > here called x,y, and z. The function then returns the connectivity and > coordinates arrays. > > Here's an example: > http://yt-project.org/docs/dev/examining/loading_data.html#semi-structured-… > > Best, > Jonah > > On 15-05-24 09:35 PM, Andrew Myers wrote: > > Hi Katharina, > > I don't have an example handy, but the "coordinates" and "connectivity" > arguments are arrays you construct that describe the vertices and zones of > the hexahedral mesh you want. The "coordinates" argument is supposed to be a > (N_vertices, 3) - shaped array of floats that has the x, y, and z positions > of all the vertices in the hexahedral mesh. The "connectivity" argument is a > (N_zone, 8) - shaped array of ints that gives, for each zone, the indices of > the 8 vertices that surround it. So for example, if connectivity[0][2] is > '12', then coordinates[12] would give the position coordinate of the third > vertex surrounding the first zone, if that makes sense. > > Once you've constructed those arrays from the information in your dataset > and fed them into "load_hexadral_mesh", yt shouldn't care whether the data > came from an HDF5 file or not. > > -Andrew > > On Sun, May 24, 2015 at 11:46 AM, Katharina Wollenberg > <kwollenberg89(a)gmail.com> wrote: >> >> Hello together, >> >> for visualising a 3D disk from ZEUS-MP HDF5 data in yt, I need to load a >> single spherical polar coordinate grid where x1,x2,x3 are R,T,P and R has >> ratioed zones. For that I want to use the command >> yt.load_hexahedral_mesh(data, connectivity, coordinates, length_unit=None, >> ...) . However, since I am new to yt, I am a little bit stuck right now… >> I am not quite sure what is meant in detail by the arguments connectivity >> and coordinates and how to formulate them in the load_hexahedral_mesh >> command. >> >> Furthermore, do I need to pay particular attention on some commands >> because of using HDF5 data? >> >> If anyone has an example for me, that’d be very helpful! >> >> Thanks a lot! >> >> Katharina Wollenberg >> >> >> >> _______________________________________________ >> 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 > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

1 0

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

yt-users May 2015