yt-users April 2015

yt-users@python.org

29 participants
31 discussions

Porting .ply files to Blender with colors?
by Jill P. Naiman 14 Aug '22

14 Aug '22

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 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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create and save multiple plot at the same time
by Clementel Nicola 29 Apr '15

29 Apr '15

Dear yt users, I’m trying to write a script to create different multi-grid figures with in each the slice plot of one quantity from different snapshots (e.g. density slice for the snapshot from 1 to 4, see example below). density_snapshot_1 | density_snapshot_2 ________________ |_________________ | density_snapshot_3 | density_snapshot_4 I’m able to do it looping first over the quantities and for each open the snapshots, but in they way I’m reopening the snapshots several times (i.e. the number of quantities I want to plot). I think that the smart way of doing it is to have the for loops as below. My problem is that I need to create and save the figures at the "same time" and not one after the other. I tried several option using the ‘field’ index, but I end up saving only the last ‘field’ figure. Any suggestion? Thanks, Nicola Clementel snapshots = ['./snapshot_001','./snapshot_002','./snapshot_003','./snapshot_004’] fields = [‘density’, ‘velocity’, ’temperature’] for i, snapshot in enumerate(snapshots): ds = yt.GadgetDataset(fn, unit_base=unit_base, bounding_box=bbox) # load data for j, field in enumerate(fields): p = yt.SlicePlot(ds, 'z', field, center="center", width=2) p.set_cmap(field, "gist_rainbow") # This forces the SlicePlot to redraw itself on the AxesGrid axes. # need to differentiate between figures using j index here plot = p.plots[field] plot.figure = plt.figure() plot.axes = grid[i].axes plot.cax = grid.cbar_axes[i] # Finally, this actually redraws the plot. p._setup_plots() for j, field in enumerate(fields): #need to call the different figures with j index here plt.savefig(field +’_evolution.png') _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Particles in FLASH output
by Jason Galyardt 28 Apr '15

28 Apr '15

Hi all, I'm sure I've just overlooked some bit of documentation, but I'm having trouble plotting particles generated by FLASH on top of the gas density. I've been able to load a plot file with the associated particle file via ds = yt.load(plotfileName, particle_filename=partfileName) However, when I try to create a projection and annotate the particles with p = yt.ProjectionPlot(ds, "y", "density") p.annotate_particles(1.0) # ValueError! # p.annotate_particles((4.0, 'kpc')) # ValueError! I get a ValueError from h5py indicating that zero-length selections are not allowed. I have also tried passing the full width of the simulation domain to the annotation function without success. I suspect that this is a user error stemming from differences between the way that Enzo and FLASH store particle data. However, I can't find much in the way of documentation or examples for the FLASH particle data format. Of course, it would also be handy to be able to write my own analysis scripts using both gas and particles, but for now, I'll settle for any help I can get on simple plotting functionality. Thanks, Jason Galyardt Department of Physics and Astronomy University of Georgia _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Plot 2D magnetic field lines
by Dominik Derigs 28 Apr '15

28 Apr '15

Hi together, I want to use yt for plotting magnetic field lines in FLASH simulations from 2D simulations and slices from 3D simulations. An example of what it could look like can be seen here: http://aprg.mae.ufl.edu/wp-content/uploads/2014/07/tang_51.png I tried to use yt's streamline function, but this does not work for me: http://yt-project.org/doc/visualizing/streamlines.html The error shown is: ValueError: operands could not be broadcast together with shapes (9,9,2) (9,9,95) (9,9,2) The used FLASH file is attached. Thanks a lot Dominik -- Dominik Derigs I. Physikalisches Institut Universität zu Köln Zülpicher Straße 77 50937 Köln GERMANY Tel. (+49|0) 221 470-8352 Fax. (+49|0) 221 470-5162 Diese Email ist vertraulich und nur für den angegebenen Empfänger bestimmt. Zugang, Freigabe, die Kopie, die Verteilung oder Weiterleitung durch jemand anderen außer dem Empfänger selbst ist verboten und kann eine kriminelle Handlung sein. Bitte löschen Sie die Email, wenn Sie sie durch einen Fehler erhalten haben und informieren Sie den Absender. This email and any files transmitted with it may contain confidential and/or privileged material and is intended only for the person or entity to which it is addressed. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you have received this email in error, please notify the sender immediately and delete this material from all known records. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Making density and velocity field
by Junhwan Choi (최준환) 24 Apr '15

24 Apr '15

Hi yt users, I have a few questions regarding to density and velocity field. I try to make the 3-dimension dark matter and baryon density and velocity fields from enzo simulation. In order to use SPH/CIC smoothing, I tried to use ('deposit', 'Dark_Matter_cic') for enzo dark matter, and it does not work. What is particletype for Dark Matter density and velocity in enzo? After making the density field, I would like to deposit the density for fixed grid cube. I knew the FixedResolutionBuffer, that does a similar thing for 2D, but I can not find 3D version of the similar object. Is there any such object (uni-grid Buffer) for 3D? Lastly, I try to use the dark matter velocity arrow with annotate_velocity(), but it looks to me that the annotation only works for gas, because it does not have any argument distinct field type. How can I plot the dark matter (or particle in general) velocity arrow in yt? Thank you in advance, Junhwan _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Error using install script: <urlopen error unknown url type: https>
by Ricarda Beckmann 24 Apr '15

24 Apr '15

Hello everbody, I forked and cloned the repo on bitbucket and am now trying to install yt using the install script. Unfortunately I keep running into trouble: The installation runs fine until: Installing PNG Installing FreeType2 Installing SQLite3 Installing Python. This may take a while, but don't worry. yt loves you. Installing mercurial-3.1 Setting YT_DIR=/home/beckmann/soft/yt Installing distribute at which point it exits with ******************************************** FAILURE REPORT: ******************************************** return self.parent.open(new, timeout=req.timeout) File "/home/beckmann/soft/yt/yt-x86_64/lib/python2.7/urllib2.py", line 404, in open response = self._open(req, data) File "/home/beckmann/soft/yt/yt-x86_64/lib/python2.7/urllib2.py", line 427, in _open 'unknown_open', req) File "/home/beckmann/soft/yt/yt-x86_64/lib/python2.7/urllib2.py", line 382, in _call_chain result = func(*args) File "/home/beckmann/soft/yt/yt-x86_64/lib/python2.7/urllib2.py", line 1247, in unknown_open raise URLError('unknown url type: %s' % type) urllib2.URLError: <urlopen error unknown url type: https> ******************************************** ******************************************** I have tried installing distribute manually but I immediately run into the same error with the next package so that is not a solution. This website suggests that the issue is that SSL is not supported: http://www.xinotes.net/notes/note/628/ <http://www.xinotes.net/notes/note/628/> and I need to recompile python with SSL? How do I do that in this context? Is there another solution? I do not have root access on this machine. Thank you, Ricarda _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Rodeo IDE
by Nathan Goldbaum 23 Apr '15

23 Apr '15

Hi all, If you like how the IPython notebook lives in your browser but you miss writing code in an IDE, this might be perfect for you. http://blog.yhathq.com/posts/introducing-rodeo.html Hope it's useful for someone, Nathan _______________________________________________ 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 April 2015