yt-users September 2020

yt-users@python.org

8 participants
7 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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comoving scale annotation?
by Salome Mtchedlidze 05 Dec '20

05 Dec '20

Hello again, I am using yt slices and projections with scale annotation. I have my plots in comoving units ("Mpccm/h") but whenever I want to use the same units for annotation: slc.annotate_scale(corner='lower_right', coeff=10, units='Mpccm/h'), yt does not recognize these units. Am I missing something or only the physical scale annotation is possible ? Thanks, Salome

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General octree data
by Paco Holguin 22 Oct '20

22 Oct '20

Hello, I've looked at the documentation and it seems that octree datasets are loadable for a few specific codes, but not in general. I have an octree that represents galaxy simulation data, but it's produced as an output of an analysis script. It would be nice to take advantage of yt's capabilities to do analysis. Is there a simple way to load an generic octree or would I have to write a front-end myself (as described in the documentation and by looking at ART, for example)? Thanks! Paco Holguin

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Re: yt-users Digest, Vol 151, Issue 6
by guido 23 Sep '20

23 Sep '20

Hi Matthew, Thanks for your reply. Then if there is no translation for the spatial coordinates what is happening to the velocities of the cells belonging to the disk? I'm asking that because what I see on my code is that the velocities and the disk that is on the negative X region show a distribution that corresponds to the middle of the computational domain and the same happens to the distribution of the velocities on the disk that is on the positive X region. However, since the coordinate system of both the cylinder and the computational domain are at rest there shouldn't be a any difference. So, I wonder what are the velocities that I get when I do something like this: disk['velocity_x'] The fact that the velocities that I'm getting correspond to another region makes me believe that there is something wrong on the disk structure code and it is always taking cells locate on the center that correspond to a center c=[0.5,0.5,0.5]. Is there any way to verify where the cylinder is located in the computational domain? Regards, El sáb., 19 sept. 2020 a las 11:02, <yt-users-request(a)python.org <mailto:yt-users-request@python.org>> escribió: Send yt-users mailing list submissions to yt-users(a)python.org <mailto:yt-users@python.org> To subscribe or unsubscribe via the World Wide Web, visit https://mail.python.org/mailman3/lists/yt-users.python.org/ or, via email, send a message with subject or body 'help' to yt-users-request(a)python.org <mailto:yt-users-request@python.org> You can reach the person managing the list at yt-users-owner(a)python.org <mailto:yt-users-owner@python.org> When replying, please edit your Subject line so it is more specific than "Re: Contents of yt-users digest..." Today's Topics: 1. yt.disk (Guido granda muñoz) 2. Re: yt.disk (Matthew Turk) ---------------------------------------------------------------------- Message: 1 Date: Fri, 18 Sep 2020 16:05:21 -0500 From: Guido granda muñoz <guidogranda(a)gmail.com <mailto:guidogranda@gmail.com>> Subject: [yt-users] yt.disk To: yt-users(a)python.org <mailto:yt-users@python.org> Message-ID: <CALOHZ_0=sr94xUKaxvBuRki99xZtKQtezhx3nEXXqDV9Ly4S1g(a)mail.gmail.com <mailto:sr94xUKaxvBuRki99xZtKQtezhx3nEXXqDV9Ly4S1g@mail.gmail.com>> Content-Type: multipart/alternative; boundary="000000000000855e3c05af9cdca7" --000000000000855e3c05af9cdca7 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello yt-users, I have a question about the disk data object. The first input it needs is center, which according to your website is the coordinates of the geometrical center of the disk on the simulation length units. So, the center of the computational domain is c=3D[0.5,0.5,0.5]. I set the center of two different cylinders in a way that they don=E2=80=99= t overlap. The axis of these cylinders are parallel to the x axis and one is on the negative X coordinate region while the other one on the positive region. But, I found that they actually have exactly the same cell centers. Did I do something wrong? On the following code the box side is 256 pc, so the center of the first disk c_1=3D[0.25,0.5,0.5] with a height of 32 pc does not overlap with the second disk of center c_2=3D[0.75,0.5,0.5] also with height 32 pc. http://paste.yt-project.org/show/275/ I=E2=80=99m using : --- Version =3D 3.6.dev0 And the snapshot used is here: http://use.yt/upload/c58a4c0f --=20 Guido --000000000000855e3c05af9cdca7 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr"><br clear=3D"all"><div> =09 =09 <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">Hello yt-users,</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I have a question about the disk data object. The first input it needs is center, which according to your website is the coordinates of the geometrical center of the disk on the simulation length units. So, the center of the computational domain is c=3D[0.5,0.5,0.5].<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I set the center of two different cylinders in a way that they don=E2=80=99t overlap. The axis of these cylinders are parallel to the x axis and one is on the negative X coordinate region while the other one on the positive region. But, I found that they actually have exactly the same cell centers. Did I do something wrong?<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">On the following code the box side is 256 pc, so the center of the first disk c_1=3D[0.25,0.5,0.5] with a height of 32 pc does not overlap with the second disk of center c_2=3D[0.75,0.5,0.5] also with height 32 pc.=20 </p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><a href=3D"h= ttp://paste.yt-project.org/show/275/ <http://paste.yt-project.org/show/275/>">http://paste.yt-project.org/show/275/= </a><br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I=E2=80=99m using :<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">---</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;border-top:none;border-bottom:= 1px solid rgb(0,0,0);border-left:none;border-right:none;padding:0in 0in 0.0= 3in;line-height:100%"> Version =3D 3.6.dev0</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">And the snapshot used is here:<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><a href=3D"h= ttp://use.yt/upload/c58a4c0f <http://use.yt/upload/c58a4c0f>">http://use.yt/upload/c58a4c0f</a></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><br> </p></div>-- <br><div dir=3D"ltr" class=3D"gmail_signature" data-smartmail= =3D"gmail_signature">Guido</div></div> --000000000000855e3c05af9cdca7-- ------------------------------ Message: 2 Date: Fri, 18 Sep 2020 17:13:40 -0500 From: Matthew Turk <matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>> Subject: [yt-users] Re: yt.disk To: Discussion of the yt analysis package <yt-users(a)python.org <mailto:yt-users@python.org>> Message-ID: <CALO3=5GozUpChB+gLs-F1toed22XjDM6F4zEG4j4k=9Nu1HAJw(a)mail.gmail.com <mailto:9Nu1HAJw@mail.gmail.com>> Content-Type: multipart/alternative; boundary="000000000000d95c4e05af9dd04e" --000000000000d95c4e05af9dd04e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Guido, The cell centers will indeed be the same -- there's no coordinate translation that is done when you access just the 'x' 'y' and 'z' fields. I believe that the fields you might be looking for are "cylindrical_radius" "cylindrical_z" and "cylindrical_theta". On Fri, Sep 18, 2020 at 4:06 PM Guido granda mu=C3=B1oz <guidogranda(a)gmail.= com> wrote: > > Hello yt-users, > > I have a question about the disk data object. The first input it needs is > center, which according to your website is the coordinates of the > geometrical center of the disk on the simulation length units. So, the > center of the computational domain is c=3D[0.5,0.5,0.5]. > > I set the center of two different cylinders in a way that they don=E2=80= =99t > overlap. The axis of these cylinders are parallel to the x axis and one i= s > on the negative X coordinate region while the other one on the positive > region. But, I found that they actually have exactly the same cell center= s. > Did I do something wrong? > > On the following code the box side is 256 pc, so the center of the first > disk c_1=3D[0.25,0.5,0.5] with a height of 32 pc does not overlap with th= e > second disk of center c_2=3D[0.75,0.5,0.5] also with height 32 pc. > > http://paste.yt-project.org/show/275/ > > I=E2=80=99m using : > > --- > > Version =3D 3.6.dev0 > > And the snapshot used is here: > > http://use.yt/upload/c58a4c0f > > > -- > Guido > _______________________________________________ > yt-users mailing list -- yt-users(a)python.org <mailto:yt-users@python.org> > To unsubscribe send an email to yt-users-leave(a)python.org <mailto:yt-users-leave@python.org> > https://mail.python.org/mailman3/lists/yt-users.python.org/ > Member address: matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> > --000000000000d95c4e05af9dd04e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable <div dir=3D"ltr">Hi Guido,<div><br></div><div>The cell centers will indeed = be the same -- there's no coordinate translation that is done when you = access just the 'x' 'y' and 'z' fields.=C2=A0 I bel= ieve that the fields you might be looking for are "cylindrical_radius&= quot; "cylindrical_z" and "cylindrical_theta".</div></d= iv><br><div class=3D"gmail_quote"><div dir=3D"ltr" class=3D"gmail_attr">On = Fri, Sep 18, 2020 at 4:06 PM Guido granda mu=C3=B1oz <<a href=3D"mailto:= guidogranda(a)gmail.com <mailto:guidogranda@gmail.com>">guidogranda(a)gmail.com <mailto:guidogranda@gmail.com></a>> wrote:<br></div><block= quote class=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1= px solid rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr"><br clear=3D"a= ll"><div> =09 =09 <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">Hello yt-users,</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I have a question about the disk data object. The first input it needs is center, which according to your website is the coordinates of the geometrical center of the disk on the simulation length units. So, the center of the computational domain is c=3D[0.5,0.5,0.5].<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I set the center of two different cylinders in a way that they don=E2=80=99t overlap. The axis of these cylinders are parallel to the x axis and one is on the negative X coordinate region while the other one on the positive region. But, I found that they actually have exactly the same cell centers. Did I do something wrong?<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">On the following code the box side is 256 pc, so the center of the first disk c_1=3D[0.25,0.5,0.5] with a height of 32 pc does not overlap with the second disk of center c_2=3D[0.75,0.5,0.5] also with height 32 pc.=20 </p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><a href=3D"h= ttp://paste.yt-project.org/show/275/ <http://paste.yt-project.org/show/275/>" target=3D"_blank">http://paste.yt-pro= ject.org/show/275/ <http://ject.org/show/275/></a><br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">I=E2=80=99m using :<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">---</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;border-top:none;border-bottom:= 1px solid rgb(0,0,0);border-left:none;border-right:none;padding:0in 0in 0.0= 3in;line-height:100%"> Version =3D 3.6.dev0</p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%">And the snapshot used is here:<br></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><a href=3D"h= ttp://use.yt/upload/c58a4c0f <http://use.yt/upload/c58a4c0f>" target=3D"_blank">http://use.yt/upload/c58a4c= 0f <http://use.yt/upload/c58a4c=0f></a></p> <p lang=3D"en-US" style=3D"margin-bottom:0in;line-height:100%"><br> </p></div>-- <br><div dir=3D"ltr">Guido</div></div> _______________________________________________<br> yt-users mailing list -- <a href=3D"mailto:yt-users@python.org <mailto:yt-users@python.org>" target=3D"_= blank">yt-users(a)python.org <mailto:yt-users@python.org></a><br> To unsubscribe send an email to <a href=3D"mailto:yt-users-leave@python.org <mailto:yt-users-leave@python.org>= " target=3D"_blank">yt-users-leave(a)python.org <mailto:yt-users-leave@python.org></a><br> <a href=3D"https://mail.python.org/mailman3/lists/yt-users.python.org/" rel= =3D"noreferrer" target=3D"_blank">https://mail.python.org/mailman3/lists/yt= -users.python.org/ <https://mail.python.org/mailman3/lists/yt=-users.python.org/></a><br> Member address: <a href=3D"mailto:matthewturk@gmail.com <mailto:matthewturk@gmail.com>" target=3D"_blank">= matthewturk(a)gmail.com <mailto:matthewturk@gmail.com></a><br> </blockquote></div> --000000000000d95c4e05af9dd04e-- ------------------------------ Subject: Digest Footer _______________________________________________ yt-users mailing list -- yt-users(a)python.org <mailto:yt-users@python.org> To unsubscribe send an email to yt-users-leave(a)python.org <mailto:yt-users-leave@python.org> https://mail.python.org/mailman3/lists/yt-users.python.org/ ------------------------------ End of yt-users Digest, Vol 151, Issue 6 **************************************** -- Guido

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yt.disk
by Guido granda muñoz 18 Sep '20

18 Sep '20

Hello yt-users, I have a question about the disk data object. The first input it needs is center, which according to your website is the coordinates of the geometrical center of the disk on the simulation length units. So, the center of the computational domain is c=[0.5,0.5,0.5]. I set the center of two different cylinders in a way that they don’t overlap. The axis of these cylinders are parallel to the x axis and one is on the negative X coordinate region while the other one on the positive region. But, I found that they actually have exactly the same cell centers. Did I do something wrong? On the following code the box side is 256 pc, so the center of the first disk c_1=[0.25,0.5,0.5] with a height of 32 pc does not overlap with the second disk of center c_2=[0.75,0.5,0.5] also with height 32 pc. http://paste.yt-project.org/show/275/ I’m using : --- Version = 3.6.dev0 And the snapshot used is here: http://use.yt/upload/c58a4c0f -- Guido

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Error performing volume render in Enzo
by Sam Patrick 16 Sep '20

16 Sep '20

Hi all, I'm trying to do a volume render of the temperature field inside a sphere with the following code: val, loc = ds.find_max('density') sp = ds.sphere(loc, SP_DIST) source = VolumeSource(sp, 'temperature') scene = Scene() scene.add_source(source) # v is calculated based on angular momentum camera = scene.add_camera(sp, lens_type= 'perspective') cam_position = loc + v * CAM_DIST camera.set_position(cam_position) camera.set_focus(loc) source.set_field('temperature') source.set_log(True) bounds = (UPPER, LOWER) tf = yt.ColorTransferFunction(np.log10(bounds)) tf.add_layers(12, colormap='jet') source.tfh.tf = tf source.tfh.bounds = bounds source.tfh.plot('transfer_function.png', profile_field='temperature') scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1) Upon saving though I encounter the error: Traceback (most recent call last): File "plot_3d.py", line 51, in <module> scene.save("render_t={:.3f}".format(times[i]), sigma_clip= 1) #last sigma = 2 File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/visualization/volume_rendering/scene.py", line 310, in save yt : [INFO ] 2020-09-15 10:34:02,783 Saving render render_t=0.000.png self._last_render.write_png(fname, sigma_clip=sigma_clip) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py", line 289, in write_png scaled = self.rescale(inline=False) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/data_objects/image_array.py", line 242, in rescale np.clip(out, 0.0, 1.0, out) File "<__array_function__ internals>", line 6, in clip File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 2084, in clip return _wrapfunc(a, 'clip', a_min, a_max, out=out, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc return bound(*args, **kwds) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py", line 132, in _clip um.clip, a, min, max, out=out, casting=casting, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/numpy/core/_methods.py", line 85, in _clip_dep_invoke_with_casting return ufunc(*args, out=out, **kwargs) File "/opt/apps/pkgs/cpython/3.7.1/intel64/intel_2019.2/lib/python3.7/site-packages/yt/units/yt_array.py", line 1401, in __array_ufunc__ "added to YTArray." % (str(ufunc), len(inputs))) RuntimeError: Support for the <ufunc 'clip'> ufunc with 3 inputs has not beenadded to YTArray. I would also like to eventually add a colorbar to the side of the created image which represents the transfer function and annotate text as well. Does the render functionality allow me to do this? Any help on these topics would be much appreciated. Many thanks, Sam Patrick

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data_source in SlicePlot does not work
by fujitaa＠shinshu-u.ac.jp 04 Sep '20

04 Sep '20

Hello, data_source in SlicePlot does not work (data_source in ProjectionPlot works). Would you explain how to enable it or fix the problem? ds= yt.load("../DD2000/jf2000") ad = ds.all_data() dense_ad = ad.cut_region(["obj['Density'] >= 0"]) p = yt.SlicePlot(ds, 'x',"density",center=[6.5536/2, 6.5536/2,(15.5/2+2.5)],origin=["lower", "center", "domain"] ,data_source=dense_ad ) I chose 0 so that it will pick up all the gas but it does not. There is no error message. It just does not show anything much in the figure. How can I attach figures here?

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yt-users September 2020