Mailman 3 July 2017 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman Aug. 14, 2022

Aug. 14, 2022

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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Stars on volume rendering
by Elizabeth Harper-Clark Dec. 11, 2021

Dec. 11, 2021

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 April 11, 2020

April 11, 2020

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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3-D Mass power spectra
by 梁家豪 June 3, 2019

June 3, 2019

Dear yt Can current yt calculate 3-D Mass power spectra? I checked the website but I didn't find any information. I think calculating 3-D Mass power spectra is a very useful for cosmological simulations. So I guess maybe yt supports this function now....? Thanks in advance

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Can these colormaps be imported?
by Joseph Smidt July 26, 2017

July 26, 2017

Hey everyone, This repo has some perceptually uniform colormaps that are not in standard matplotlib/yt. [1] More info here[2] Anyway, it is not clear to me from his documentation how I might import these colormaps in a way I could use with YT. Does anyone have an idea how that can be done? They seem to be a set of .csv files. Thanks. [1] https://github.com/bokeh/colorcet [2] http://peterkovesi.com/projects/colourmaps/

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yt unpacking error on Pleiades
by Clayton Strawn July 25, 2017

July 25, 2017

Hello, I have a request for help. I am trying to run some analysis code remotely through ssh in yt on NASA Pleiades. I have been able to install yt and trident and am running in a virtualenv, but something is having a very deeply buried error that I don't understand and fatally kills any task I send to Pleiades. The same code works fine on my home laptop with the same input files, so I assume the problem is something to do with the yt distribution on Pleiades, but I used "pip install -U yt" so it should be up-to-date. The error code comes from the fortran_utils file, and it says "unpack requires a string argument of length 4" (myenv) cstrawn@pfe27:~/quasarlines/quasarlines> python quasar_scan.py VELA_v2_08 10MpcBox_csf512_a0.330.d "[H I,H II,O IV,O V,O VI,Si II,Si III,Si IV,C I,C II,C III,C IV,Mg II,Mg III,Mg IV]" yt : [INFO ] 2017-07-25 12:11:26,454 discovered particle_data:/home1/cstrawn/quasarlines/quasarlines/PMcrs0a0.330.DAT yt : [INFO ] 2017-07-25 12:11:26,454 discovered particle_header:/home1/cstrawn/quasarlines/quasarlines/PMcrda0.330.DAT yt : [INFO ] 2017-07-25 12:11:26,462 Using root level of 14 yt : [INFO ] 2017-07-25 12:11:26,463 Discovered 7 species of particles yt : [INFO ] 2017-07-25 12:11:26,463 Particle populations: 28016640 4263936 752640 123904 19552 2089406 85309 yt : [INFO ] 2017-07-25 12:11:26,658 Max level is 12 yt : [INFO ] 2017-07-25 12:11:26,682 Parameters: current_time = 3.350407555 Gyr yt : [INFO ] 2017-07-25 12:11:26,682 Parameters: domain_dimensions = [128 128 128] yt : [INFO ] 2017-07-25 12:11:26,683 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2017-07-25 12:11:26,683 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2017-07-25 12:11:26,683 Parameters: cosmological_simulation = True yt : [INFO ] 2017-07-25 12:11:26,683 Parameters: current_redshift = 2.02694081565 yt : [INFO ] 2017-07-25 12:11:26,683 Parameters: omega_lambda = 0.730000019073 yt : [INFO ] 2017-07-25 12:11:26,684 Parameters: omega_matter = 0.270000010729 yt : [INFO ] 2017-07-25 12:11:26,684 Parameters: hubble_constant = 0.699999988079 18426 LOSs to scan. Is this an appropriate number? (0 for no) 1 1/18426 Traceback (most recent call last): File "quasar_scan.py", line 375, in <module> q.get_coldens(save = 10) File "quasar_scan.py", line 148, in get_coldens ftype='gas') File "/u/cstrawn/myenv/lib/python2.7/site-packages/trident/ray_generator.py", line 239, in make_simple_ray particle_type = _determine_particle_type_from_ftype(ds, ftype) File "/u/cstrawn/myenv/lib/python2.7/site-packages/trident/ray_generator.py", line 590, in _determine_particle_type_from_ftype field_list_arr = np.asarray(ds.derived_field_list) File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 164, in ireq self.index File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 419, in index self, dataset_type=self.dataset_type) File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py", line 65, in __init__ super(ARTIndex, self).__init__(ds, dataset_type) File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/geometry/geometry_handler.py", line 50, in __init__ self._setup_geometry() File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/geometry/oct_geometry_handler.py", line 25, in _setup_geometry self._initialize_oct_handler() File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py", line 91, in _initialize_oct_handler self.domains] File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py", line 761, in level_count self.level_offsets File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py", line 782, in level_offsets self.ds.min_level, self.ds.max_level) File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/frontends/art/data_structures.py", line 820, in _count_art_octs ns = fpu.peek_record_size(f, endian='>') File "/u/cstrawn/myenv/lib/python2.7/site-packages/yt/utilities/fortran_utils.py", line 250, in peek_record_size s = struct.unpack('>i', f.read(struct.calcsize('>i'))) struct.error: unpack requires a string argument of length 4 Please let me know if this is a known problem or if you have any idea what I should do to avoid running into it. I don't really understand fortran enough to know what is even supposed to be happening in fortran_utils. Thanks so much, Clayton Strawn

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pyfits error
by David Collins July 24, 2017

July 24, 2017

Hi, Everybody! I'm trying to install pyfits on stampede, and I"m running into an error: """ Setup script exited with error in setup command: Error parsing /tmp/easy_install-s4Mxa7/stsci.distutils-0.3.7/setup.cfg: TypeError: super() argument 1 must be type, not None """ Has anyone see that before, and know what to do about it? The python I'm using is the one dowloaded with yt this afternoon, 2.7.13. This happens if I use both pip and from the git repository of pyfits. Thanks, d. Installed /tmp/easy_install-s4Mxa7/stsci.distutils-0.3.7/.eggs/d2to1-0.2.12.post1-py2.7.egg Traceback (most recent call last): File "setup.py", line 14, in <module> zip_safe=False File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/distutils/core.py", line 111, in setup _setup_distribution = dist = klass(attrs) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/dist.py", line 325, in __init__ self.fetch_build_eggs(attrs['setup_requires']) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/dist.py", line 444, in fetch_build_eggs replace_conflicting=True, File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 854, in resolve dist = best[req.key] = env.best_match(req, ws, installer) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1126, in best_match return self.obtain(req, installer) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1138, in obtain return installer(requirement) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/dist.py", line 516, in fetch_build_egg return cmd.easy_install(req) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 672, in easy_install return self.install_item(spec, dist.location, tmpdir, deps) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 698, in install_item dists = self.install_eggs(spec, download, tmpdir) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 879, in install_eggs return self.build_and_install(setup_script, setup_base) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1118, in build_and_install self.run_setup(setup_script, setup_base, args) File "/home1/00369/tg456484/local-yt-2017-07-24/yt-conda/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1106, in run_setup raise DistutilsError("Setup script exited with %s" % (v.args[0],)) distutils.errors.DistutilsError: Setup script exited with error in setup command: Error parsing /tmp/easy_install-s4Mxa7/stsci.distutils-0.3.7/setup.cfg: TypeError: super() argument 1 must be type, not None -- -- Sent from a computer.

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Install failure on Stampede
by David Collins July 24, 2017

July 24, 2017

Hi, Everybody! I'm having trouble installing yt on stampede. It seems to choke on jupyter with the following message. The log doesn't contain any more useful information than whats below, so I'm really not sure what the error is. Has anyone run into this? Thanks! d. qtconsole-4.3. 100% |###############################| Time: 0:00:00 15.55 MB/s widgetsnbexten 100% |###############################| Time: 0:00:00 8.99 MB/s ipywidgets-6.0 100% |###############################| Time: 0:00:00 17.13 MB/s jupyter-1.0.0- 100% |###############################| Time: 0:00:00 1.11 MB/s dbus post-link :: /etc/machine-id not found .. dbus post-link :: .. using /proc/sys/kernel/random/boot_id ******************************************** ******************************************** Failure. Check /home1/00369/tg456484/local-yt-2017-07-24/yt-conda/yt_install.log. The last 10 lines are above. -- -- Sent from a computer.

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Issue with volume rendering saving to other figure format
by Lu, Yinghe July 21, 2017

July 21, 2017

Hi all, I seem to have trouble saving scenes from volume rendering to other image formats (pdf, eps etc.). For example if I type sc.save('test.pdf') it still gives me a file called 'test.pdf.png'. While for slice plots and projection plots works fine (so I guess I have the right backends). I am using the most updated 3.4-dev version. Thanks for help!

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Field extraction from arbitrary grids
by Carla Bernhardt July 21, 2017

July 21, 2017

Dear yt-users, I am trying to extract a unigrid data cube within a specific region and specified dimensions, thus I am using arbitrary_grid(), however, beyond the example given in the docs <http://yt-project.org/doc/analyzing/objects.html#arbitrary-grid>, my field extractions all fail. I would like to extract temperature, HI_Density and HII_Density. Here is a snippet from my code: obj = ds.arbitrary_grid(left_edge, right_edge, dims=[256, 256, 256]) print(obj["deposit", "all_density"]) print(obj["temperature"]) print(obj["HI_Density"]) The line print(obj["deposit", "all_density"]) works, but the two lines after both fail. Here is the traceback from the temperature <https://pastebin.com/BusfAeKh>, and I even tried out deposited temperature <https://pastebin.com/me9uKMHP> and deposited HI_Density <https://pastebin.com/BxPJj7B0>. Am I formatting this incorrectly, or is there a different way to extract the fields? Kind regards, Carla Bernhardt PhD Student ZAH Institut für Theoretische Astrophysik Universität Heidelberg

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