yt-users February 2017

yt-users@python.org

12 participants
18 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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Surface extraction in FLASH
by C.S. Howard 27 Feb '17

27 Feb '17

Hi all, I'm trying to calculate the total amount of photons crossing a spherical surface using FLASH simulation data. I noticed yt has a surface extraction method, and I used this to extract the spherical surface. I only have the flux of photons in each cell and therefore need to mulitply by the cross-sectional area of each cell to get what I need. I have a couple questions about this surface extraction method: - What exactly does it return? - Can I get the cross sectional area of each cell on the surface (as seen from the center of the simulation volume) - If not, is there a better way to do this using yt? Cheers and thanks for the help, Corey

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Failure in annotate_particles
by Andrew James Emerick 24 Feb '17

24 Feb '17

HI all, I'm getting a weird failure in the annotate particles callback that I'm having trouble reproducing on another machine. Here is the error message output I'm getting: http://paste.yt-project.org/show/7048/ . I'm just doing a simple: $ sp = yt.SlicePlot(ds, 'z', 'density') $ sp.annotate_particles(0.9) $ sp.save() This error occurs only on a machine where I have yt installed from source (version 3.3.4, changeset 6e21d8723012 of the stable branch.. this also occured on changeset 7f76a9ccfcca). I could not reproduce the error on a local machine where I've installed yt using anaconda (yt version 3.3.4). It fails on a ProjectionPlot as well. Any thoughts on what could be causing this? Thanks, Andrew -- NSF Graduate Fellow Columbia University Department of Astronomy

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Halo catalog error.
by Reju Sam John 23 Feb '17

23 Feb '17

Dear All, I am trying to create a HaloCatalog with the following code. import yt from yt.analysis_modules.halo_analysis.api import HaloCatalog data_ds = yt.load('../RD0057/RedshiftOutput0057') hc = HaloCatalog(data_ds=data_ds, finder_method='hop', finder_kwargs={"threshold": 500.0, "dm_only": False, "ptype": "all", "padding": 0.02}) hc.add_filter("quantity_value", "particle_mass", ">", 5e12, "Msun") hc.create() With this, I am able to create the catalog. But when we are trying to load it, I am unable to get almost all fields. Here i am copying the error message. File "tra_flux_on_earth.py", line 161, in <module> hc = HaloCatalog(halos_ds=halos) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/analysis_modules/halo_analysis/halo_catalog.py", line 126, in __init__ halos_ds.index File "/home/john/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 424, in index self.create_field_info() File "/home/john/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 481, in create_field_info self.field_info.load_all_plugins() File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_info_container.py", line 279, in load_all_plugins self.find_dependencies(loaded) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_info_container.py", line 292, in find_dependencies deps, unavailable = self.check_derived_fields(loaded) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_info_container.py", line 362, in check_derived_fields fd = fi.get_dependencies(ds = self.ds) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 178, in get_dependencies e[self.name] File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_detector.py", line 99, in __missing__ vv = finfo(self) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 204, in __call__ dd = self._function(self, data) File "tra_flux_on_earth.py", line 72, in _fact tempo = Obs_freq/(1.6e6*data["MagField"]/for_mag) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_detector.py", line 99, in __missing__ vv = finfo(self) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/derived_field.py", line 204, in __call__ dd = self._function(self, data) File "tra_flux_on_earth.py", line 36, in _magfeed mag = (0.05*4.0*pie*data["density"]*(data["TurbVel"]**2))**0.5 File "/home/john/anaconda3/lib/python3.6/site-packages/yt/fields/field_detector.py", line 89, in __missing__ finfo = self.ds._get_field_info(*field) File "/home/john/anaconda3/lib/python3.6/site-packages/yt/data_objects/static_output.py", line 666, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'density')' in catalog.0.h5. What could be the problem? -- Reju Sam John

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Calculating center of mass of a halo in yt 3.3.3
by Reju Sam John 22 Feb '17

22 Feb '17

Dear All, I am very new in YT 3.3's HaloCatalog functionality. With the following piece of code, I am able to get paerical mass and virial radius. import yt from yt.analysis_modules.halo_analysis.api import HaloCatalog data_ds = yt.load('/run/media/john/Seagate_Expansion_Drive/cosmo-sim_20/RD0057/RedshiftOutput0057') hc = HaloCatalog(data_ds=data_ds, finder_method='hop') hc.create() ad = hc.halos_ds.all_data() pm = ad['particle_mass'][:] vr = ad['virial_radius'][:] I would like to calculate the center of mass of the halo. I tried with the following line com = ad['center_of_mass'][:] since like virial_radius(), center_of_mass() was available in YT2.6. But this is not working. Could you please suggest me how to calculate the center of mass of a halo in yt 3.3.3 ? -- Reju Sam John

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Problems reading GADGET 2 Binary datafile using yt
by Alankar Dutta 22 Feb '17

22 Feb '17

Hello YT-community, I have been trying to use yt for analysis of the output from a GADGET 2 simulation stored as an Unformatted Fortran Binary. It consists of files named as snapshot_068 which is divided into 1024 subfiles named as snapshot_068.0, snapshot_068.1 and so on. Whenever I am loading this with yt I am getting the following error message and I have got no idea as to how to fix this. I have also tried reading only one subfile of this multi part snapshot but with no success. I am relying on the community to help me in this regard. My code: fname = 'snapdir_068/snapshot_068' ds = yt.load(fname) Error displayed: yt : [ERROR ] 2017-02-22 21:55:34,587 None of the arguments provided to load() is a valid file yt : [ERROR ] 2017-02-22 21:55:34,587 Please check that you have used a correct path Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/alankar/anaconda3/lib/python3.5/site-packages/yt/convenience.py", line 76, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('snapshot_068',) {}, but could not load! #Trying to read only one of the multi part file My code: fname = 'snapdir_068/snapshot_068.0' ds = yt.load(fname) Error displayed: yt : [ERROR ] 2017-02-22 21:57:17,625 Couldn't figure out output type for /media/alankar/Seagate Expansion Drive/mb2/snapshots/snapdir_068/snapshot_068.0 Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/alankar/anaconda3/lib/python3.5/site-packages/yt/convenience.py", line 98, in load raise YTOutputNotIdentified(args, kwargs) yt.utilities.exceptions.YTOutputNotIdentified: Supplied ('snapshot_068.0',) {}, but could not load! Cheers, Alankar

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loading eagle data using yt
by Charlotte Brand 20 Feb '17

20 Feb '17

Hi yt users! For my master research, I'm working on virtual observations from the EAGLE (gadget based) simulations. Currently I'm trying out pyXSIM for this, which uses yt to load the data, but I'm having some problems. First, yt only loads the non-smoothed element abundances, as fields "PartType0, (element)", while the eagle data has 2 fields: PartType0/SmoothedElementAbundance/(element) and PartType0/ElementAbundance/(element). Does anyone have any idea on how to get the smoothed abundances out? Also, I'm wondering: I have a script that selects the subhalos you want from the eagle data, and then saves the particle data you need (temperature, density, etc.) of only the particles in those subhalos to a hdf5 file. However, when I try to load this data with yt, it recognises it as gadget data, and then expects more than one file to be present, I guess because usually there is more than one snapshot file. E.g. if my file is called partialdata.0.hdf5 yt starts to look for partialdata.1.hdf5 (if i just call it partialdata.hdf5 it still looks for partialdata.0.hdf5). However, in gadget, the number of output files can be chosen freely, so you could also choose to save your entire snapshot in one hdf5 file. So it seems that in yt there should be a way to specify the number of files you're dealing with... Does anyone know how to solve this problem? I think that yt recognises the eagle files as owls data (they are very similar), it may have something to do with that. The reason I want to select my subhalos before loading the data is that when I load the entire dataset (a 100Mpc box, 1504^3 particles) and then select e.g. a slice, when creating a derived field, I think that yt allocates memory (or something like that) for it for the entire dataset, and not just for the slice I have selected. Is this true? Cheers and thanks in advance, Charlotte Brand

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Re: [yt-users] Profile data
by Jason Galyardt 20 Feb '17

20 Feb '17

Hi Nathan, For a single profile plot, it's straightforward to save it as a yt dataset and reload it later: #### Begin #### ds = yt.load('GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150') ad = ds.all_data() prof = yt.create_profile(ad,["z"],fields=["velocity_z"], n_bins=100, logs={"z":False}) fn = prof.save_as_dataset() # restore... prof_ds = yt.load(fn) prof_ds_plot = yt.ProfilePlot.from_profiles([prof_ds.profile], y_log= {"velocity_z":False}) #### End #### The above workflow breaks down when one has several different profiles to generate from a time series. One can manage it via the filenames, but this seems prone to error and inefficient. Here's a sketch of what I'd like to do, with the time series processing removed for clarity: #### Begin #### import yt import gzip import cPickle ds = yt.load('GasSloshing/sloshing_nomag2_hdf5_plt_cnt_0150') ad = ds.all_data() prof = yt.create_profile(ad,["z"],fields=["velocity_z"], n_bins=100, logs={"z":False}) fname = 'test_pkl.gz' ## Here's where things break down ## # The following does NOT work because prof is a function object with gzip.open(fname,'wb') as f: cPickle.dump(prof, f) f.close() # TypeError: can't pickle function objects # Resuming... # From here, I'd like to load the profile object from the pickle file. If the profile # prof were a regular object, I would be able to do the following: with gzip.open(fname, 'rb') as f: prof_pkl = cPickle.load(f) f.close() # With the time series processing, there would be several profiles available # for plotting on the same set of axes, but for the purposes of this example, # I'm only including the one profile loaded above: prof_plot = yt.ProfilePlot.from_profiles([prof_pkl], y_log={"velocity_z":False}, labels=['aa']) #### End #### As a stop gap, I'll just save all the critical bits of the profile function object (e.g. prof.field_data, prof.x, prof.x_bins, etc.) to a dictionary, then pickle the dictionary. Is there a better way? Thanks, Jason On Sat, Feb 18, 2017 at 2:05 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > Today's Topics: > > 1. Profile data (Jason Galyardt) > 2. Re: Profile data (Nathan Goldbaum) > > > ---------- Forwarded message ---------- > From: Jason Galyardt <jason.galyardt(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Fri, 17 Feb 2017 15:58:27 -0500 > Subject: [yt-users] Profile data > Dear yt Users, > > Does anyone know of a way to export the data of a profile object to a byte > stream? Specifically, I'd like to be able to store several byte streams > from several different simulation files into a single dictionary object > (for example), and then pickle the dictionary. I'd like to then unpickle > the dictionary object at a later time for plotting, etc. > > I have figured out a way to do this, but it involves saving each profile > to a temporary file, reading the temp file into a byte stream, and then > pickling the byte stream; then to reload, I would have to unpickle the byte > stream, write it to a temporary file, then use yt.load() to get the profile > object back. This works, but boy, it's inefficient. Dealing with a whole > bunch of separate files generated by profile.save_as_dataset() is > inefficient in different way. Any ideas on streamlining this workflow? > > Thanks, > Jason > > ------ > Jason Galyardt > University of Georgia > > > > ---------- Forwarded message ---------- > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package <yt-users(a)lists.spacepope.org> > Cc: > Date: Fri, 17 Feb 2017 15:01:21 -0600 > Subject: Re: [yt-users] Profile data > > > On Fri, Feb 17, 2017 at 2:58 PM, Jason Galyardt <jason.galyardt(a)gmail.com> > wrote: > >> Dear yt Users, >> >> Does anyone know of a way to export the data of a profile object to a >> byte stream? Specifically, I'd like to be able to store several byte >> streams from several different simulation files into a single dictionary >> object (for example), and then pickle the dictionary. I'd like to then >> unpickle the dictionary object at a later time for plotting, etc. >> >> I have figured out a way to do this, but it involves saving each profile >> to a temporary file, reading the temp file into a byte stream, and then >> pickling the byte stream; then to reload, I would have to unpickle the byte >> stream, write it to a temporary file, then use yt.load() to get the profile >> object back. This works, but boy, it's inefficient. Dealing with a whole >> bunch of separate files generated by profile.save_as_dataset() is >> inefficient in different way. Any ideas on streamlining this workflow? >> > > I'm not sure I fully understand what you're trying to do. A code example > or an outline if a code example with the part you're confused about left to > be filled in would help. > > Why not just save the raw profile data for the fields you're interested > in, e.g. profile[field], which will be a numpy array. Do you need other > data that's defined on the profile object? > > >> Thanks, >> Jason >> >> ------ >> Jason Galyardt >> University of Georgia >> >> >> _______________________________________________ >> 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 > >

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Profile data
by Jason Galyardt 17 Feb '17

17 Feb '17

Dear yt Users, Does anyone know of a way to export the data of a profile object to a byte stream? Specifically, I'd like to be able to store several byte streams from several different simulation files into a single dictionary object (for example), and then pickle the dictionary. I'd like to then unpickle the dictionary object at a later time for plotting, etc. I have figured out a way to do this, but it involves saving each profile to a temporary file, reading the temp file into a byte stream, and then pickling the byte stream; then to reload, I would have to unpickle the byte stream, write it to a temporary file, then use yt.load() to get the profile object back. This works, but boy, it's inefficient. Dealing with a whole bunch of separate files generated by profile.save_as_dataset() is inefficient in different way. Any ideas on streamlining this workflow? Thanks, Jason ------ Jason Galyardt University of Georgia

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yt-users February 2017