Mailman 3 February 2018 - yt-dev

GSoC
by Ashley Kelly Feb. 24, 2018

Feb. 24, 2018

Hi all, I'm currently 4rth student at Durham University (UK) studying physics (MPhys) and in October I will be undertaking a phd in the field of theoretical astrophysics (SPH simulations - likely working on improving feedback models for next gen sph codes). My phd destination is currently undecided, I'm waiting to receive all of my offers before making a final decision, but I will know before the end of March. It will probably not be surprising that I am really interested in the sph smoothing project, 'Interpolating particle data onto grids'. I actually have a reasonable amount of experience with this kind of stuff, I've worked with a variety of sph codes, and even written some toy ones myself. I'm just following the list of things to do to apply on https://github.com/yt-project/gsoc-2018 and this is number 3. I have 4 phd interviews in the next 10 days, which with travel and prep, take up a large amount of my time, as such I will probably start my application and take a look at open issues in a weeks time! Cheers, Ashley Kelly

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new paper repository
by Matthew Turk Feb. 20, 2018

Feb. 20, 2018

Hi folks, I've moved the yt-3.0-paper repository to use manubot now, which is an automated manuscript build system that integrates hypothes.is and builds to both web and PDF. https://github.com/yt-project/yt-3.0-paper There are links to the build at the top there. I drafted an authorship policy (designed to be extensive and inclusive!), which is not final, and included it in the README.md file, but because this is a draft, I've created an issue as well: https://github.com/yt-project/yt-3.0-paper/issues/1 If you are interested in contributing text, please create an issue indicating what you are interested in writing, or do so in a pull request adding your name. https://github.com/yt-project/yt-3.0-paper/issues/new Manubot was developed to support a project out of the Greene Lab at Penn; if you want to see it in action, check out their repo: https://github.com/greenelab/deep-review -Matt

1 1

Re: yt-dev Digest, Vol 110, Issue 5
by Mark Richardson Feb. 20, 2018

Feb. 20, 2018

Hi Nathan, > > thanks! I won't be able to look at this in earnest until later next > week, so if you think you can look at it in the meantime, then great. I > have filed an issue. Sorry I wasn't able to get back to this last week. > > Cheers, > -Mark > > On 12 February 2018 at 19:38, <yt-dev-request(a)python.org> wrote: > >> Send yt-dev mailing list submissions to >> yt-dev(a)python.org >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mail.python.org/mm3/mailman3/lists/yt-dev.python.org/ >> or, via email, send a message with subject or body 'help' to >> yt-dev-request(a)python.org >> >> You can reach the person managing the list at >> yt-dev-owner(a)python.org >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of yt-dev digest..." >> >> Today's Topics: >> >> 1. OctTree cut_region OffAxis Projections (Mark Richardson) >> 2. Re: OctTree cut_region OffAxis Projections (Nathan Goldbaum) >> >> >> ---------------------------------------------------------------------- >> >> Date: Mon, 12 Feb 2018 17:49:21 -0500 >> From: Mark Richardson <mark.richardson.work(a)gmail.com> >> Subject: [yt-dev] OctTree cut_region OffAxis Projections >> To: yt-dev(a)python.org >> Message-ID: >> <CA+qw_EzS2jGka-B+jqg0MJBqH5em2SAwi3GNuyb1J_xGtkgP1Q@mail. >> gmail.com> >> Content-Type: multipart/alternative; >> boundary="001a1148215464247f05650bb037" >> >> --001a1148215464247f05650bb037 >> Content-Type: text/plain; charset="UTF-8" >> >> Hey, I've previously been able to make off-axis projections of ramses >> datasets with geometric data containers. However, I've recently tried to >> do >> this with a cut_region for dens gas, without success. Here is a script >> that >> should work with a ramses cosmo dataset: >> >> import yt >> import numpy as np >> >> num = 1 >> Look = [1.,1.,0] >> Up = [0.,1.,1.] >> >> >> c = np.array([0.5,0.5,0.5]) >> rad = 0.2 >> width = 2*rad >> extra = 1.05 >> left = c - rad*extra >> right = c + rad*extra >> bb = [left,right] >> >> fn = "../output_{0:05d}/info_{0:05d}.txt" >> ds = yt.load(fn.format(num),bbox=bb) >> >> region = ds.region(c,left,right) >> >> d20 = region.cut_region(['obj["density"] > 1e-20']) >> >> p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> weight_field='density',center=c,width=width,data_source=regi >> on,north_vector=Up) >> p1.save("OAProjDens_Region_{0:03d}.png".format(nout)) >> >> p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> weight_field='density',center=c,width=width,data_source=d20, >> north_vector=Up) >> p1.save("OAProjDens_D20_{0:03d}.png".format(nout)) >> >> The first OA Projection is generated correctly, but the second one crashes >> with the message: >> >> yt : [INFO ] 2018-02-12 22:20:08,915 Making a fixed resolution buffer >> of (('gas', 'density')) 800 by 800 >> yt : [INFO ] 2018-02-12 22:22:05,737 Saving plot >> OAProjDens_Region_001.png >> yt : [INFO ] 2018-02-12 22:22:06,641 xlim = -0.2 0.2 >> yt : [INFO ] 2018-02-12 22:22:06,641 ylim = -0.2 0.2 >> yt : [INFO ] 2018-02-12 22:22:06,641 zlim = -0.500000 0.500000 >> yt : [INFO ] 2018-02-12 22:23:58,431 Making a fixed resolution buffer >> of (('gas', 'density')) 800 by 800 >> Traceback (most recent call last): >> File "MakeOffAxisProjClouds.py", line 176, in <module> >> p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> weight_field='density',center=c,width=width,data_source=d20, >> north_vector=Up) >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 1727, in __init__ >> fontsize=fontsize) >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 660, in __init__ >> PlotWindow.__init__(self, *args, **kwargs) >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 219, in __init__ >> self._setup_plots() >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 748, in _setup_plots >> self._recreate_frb() >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 1733, in _recreate_frb >> super(OffAxisProjectionPlot, self)._recreate_frb() >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> line 272, in _recreate_frb >> self._frb._get_data_source_fields() >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/fixed_resolution.py", >> line 155, in _get_data_source_fields >> self[f] >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/fixed_resolution.py", >> line 543, in __getitem__ >> method=dd.method) >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/volume_rendering/off_axis_projection.py", >> line 189, in off_axis_projection >> for i, (grid, mask) in enumerate(data_source.blocks): >> File >> "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/data_ >> objects/selection_data_containers.py", >> line 836, in blocks >> with obj._field_parameter_state(self.field_parameters): >> AttributeError: 'OctreeSubsetBlockSlicePosition' object has no attribute >> '_field_parameter_state' >> >> I'm trying to find how to have d20 inherit _field_parameter_state from >> region, but thought someone might be able to point me in the right >> direction a bit faster. >> >> Thanks! >> -Mark >> >> -- >> >> Mark Richardson >> MAT Postdoctoral Fellow >> Department of Astrophysics >> American Museum of Natural History >> Mark.Richardson.Work(a)gmail.com >> My Website <https://sites.google.com/site/marklarichardson/> >> 212 496 3432 >> >> --001a1148215464247f05650bb037 >> Content-Type: text/html; charset="UTF-8" >> Content-Transfer-Encoding: quoted-printable >> >> <div dir=3D"ltr"><div><font size=3D"4">Hey, I've previously been able >> t= >> o make off-axis projections of ramses datasets with geometric data >> containe= >> rs. However, I've recently tried to do this with a cut_region for >> dens = >> gas, without success. Here is a script that should work with a ramses >> cosmo= >> dataset:<br></font><br><span style=3D"font-family:monospace >> ,monospace">imp= >> ort yt<br>import numpy as np<br><br>num =3D 1<br>Look =3D [1.,1.,0]<br>Up >> = >> =3D [0.,1.,1.]<br><br></span><br><span style=3D"font-family:monospace >> ,monos= >> pace"><span style=3D"font-family:monospace,monospace">c =3D >> np.array([0.5,0= >> .5,0.5])<br>rad =3D 0.2<br></span></span><span >> style=3D"font-family:monospa= >> ce,monospace"><span style=3D"font-family:monospace,monospace"><span >> style= >> =3D"font-family:monospace,monospace">width =3D 2*rad<br></span>extra =3D >> 1.= >> 05<br></span></span><span style=3D"font-family:monospace,monospace"><span >> s= >> tyle=3D"font-family:monospace,monospace">left =C2=A0=3D c - >> rad*extra<br>ri= >> ght =3D c + rad*extra<br>bb =3D [left,right]<br><br></span>fn =3D >> "../= >> output_{0:05d}/info_{0:05d}.txt"<br>ds =3D >> yt.load(fn.format(num),bbox= >> =3Dbb)<br><br>region =3D ds.region(c,left,right)<br><br>d20 =3D >> region.cut_= >> region(['obj["density"] > 1e-20'])<br><br>p1 =3D >> yt.Of= >> fAxisProjectionPlot(ds,Look,"density", >> weight_field=3D'densit= >> y',center=3Dc,width=3Dwidth,data_source=3Dregion,north_ >> vector=3DUp)<br>= >> p1.save("OAProjDens_Region_{0:03d}.png".format(nout))<br><br>p1 >> = >> =3D yt.OffAxisProjectionPlot(ds,Look,"density", >> weight_field=3D&#= >> 39;density',center=3Dc,width=3Dwidth,data_source=3Dd20, >> north_vector=3DU= >> p)<br>p1.save("OAProjDens_D20_{0:03d}.png".format( >> nout))</span><b= >> r><br></div><font size=3D"4">The first OA Projection is generated >> correctly= >> , but the second one crashes with the message: </font><span >> style=3D"font-f= >> amily:monospace,monospace"><br><br>yt : [INFO =C2=A0 =C2=A0 ] 2018-02-12 >> 22= >> :20:08,915 Making a fixed resolution buffer of (('gas', >> 'densit= >> y')) 800 by 800<br>yt : [INFO =C2=A0 =C2=A0 ] 2018-02-12 22:22:05,737 >> S= >> aving plot OAProjDens_Region_001.png<br>yt : [INFO =C2=A0 =C2=A0 ] >> 2018-02-= >> 12 22:22:06,641 xlim =3D -0.2 0.2<br>yt : [INFO =C2=A0 =C2=A0 ] >> 2018-02-12 = >> 22:22:06,641 ylim =3D -0.2 0.2<br>yt : [INFO =C2=A0 =C2=A0 ] 2018-02-12 >> 22:= >> 22:06,641 zlim =3D -0.500000 0.500000<br>yt : [INFO =C2=A0 =C2=A0 ] >> 2018-02= >> -12 22:23:58,431 Making a fixed resolution buffer of (('gas', >> '= >> density')) 800 by 800<br>Traceback (most recent call last):<br>=C2=A0 >> F= >> ile "MakeOffAxisProjClouds.py", line 176, in >> <module><br>= >> =C2=A0 =C2=A0 p1 =3D yt.OffAxisProjectionPlot(ds,Look,"density", >> = >> weight_field=3D'density',center=3Dc,width=3Dwidth,da >> ta_source=3Dd20= >> ,north_vector=3DUp)<br>=C2=A0 File "/mnt/blackwhale/home/mri >> chard/soft= >> /yt/yt_cphyc/yt/visualization/plot_window.py", line 1727, in >> __init__<= >> br>=C2=A0 =C2=A0 fontsize=3Dfontsize)<br>=C2=A0 File >> "/mnt/blackwhale/= >> home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", >> line = >> 660, in __init__<br>=C2=A0 =C2=A0 PlotWindow.__init__(self, *args, >> **kwargs= >> )<br>=C2=A0 File "/mnt/blackwhale/home/mri >> chard/soft/yt/yt_cphyc/yt/vi= >> sualization/plot_window.py", line 219, in __init__<br>=C2=A0 =C2=A0 >> se= >> lf._setup_plots()<br>=C2=A0 File "/mnt/blackwhale/home/mri >> chard/soft/y= >> t/yt_cphyc/yt/visualization/plot_window.py", line 748, in >> _setup_plots= >> <br>=C2=A0 =C2=A0 self._recreate_frb()<br>=C2=A0 File >> "/mnt/blackwhale= >> /home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", >> line= >> 1733, in _recreate_frb<br>=C2=A0 =C2=A0 super(OffAxisProjectionPlot, >> self)= >> ._recreate_frb()<br>=C2=A0 File "/mnt/blackwhale/home/mri >> chard/soft/yt= >> /yt_cphyc/yt/visualization/plot_window.py", line 272, in >> _recreate_frb= >> <br>=C2=A0 =C2=A0 self._frb._get_data_source_fields()<br>=C2=A0 File >> "= >> /mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualizat >> ion/fixed_resol= >> ution.py", line 155, in _get_data_source_fields<br>=C2=A0 =C2=A0 >> self[= >> f]<br>=C2=A0 File "/mnt/blackwhale/home/mri >> chard/soft/yt/yt_cphyc/yt/v= >> isualization/fixed_resolution.py", line 543, in >> __getitem__<br>=C2=A0 = >> =C2=A0 method=3Ddd.method)<br>=C2=A0 File "/mnt/blackwhale/home/mri >> cha= >> rd/soft/yt/yt_cphyc/yt/visualization/volume_rendering/off_ >> axis_projection.p= >> y", line 189, in off_axis_projection<br>=C2=A0 =C2=A0 for i, (grid, >> ma= >> sk) in enumerate(data_source.blocks):<br>=C2=A0 File >> "/mnt/blackwhale/= >> home/mrichard/soft/yt/yt_cphyc/yt/data_objects/selection_ >> data_containers.py= >> ", line 836, in blocks<br>=C2=A0 =C2=A0 with >> obj._field_parameter_stat= >> e(self.field_parameters):<br>AttributeError: >> 'OctreeSubsetBlockSlicePos= >> ition' object has no attribute '_field_parameter_state&#3 >> 9;</span><= >> br><div><div><br></div><div><font size=3D"4">I'm trying to find how >> to = >> have d20 inherit _field_parameter_state from region, but thought someone >> mi= >> ght be able to point me in the right direction a bit faster. >> <br><br></font= >> ></div><div><font size=3D"4">Thanks!<br></font>< >> /div><div>=C2=A0=C2=A0<font= >> size=3D"4"> -Mark</font><br></div><div><br>-- <br><div >> class=3D"gmail_sign= >> ature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div dir=3D"ltr"><div >> dir=3D"= >> ltr"><div dir=3D"ltr"><div dir=3D"ltr"><div dir=3D"ltr"><br><span >> style=3D"= >> font-size:12.8px">Mark Richardson</span><br style=3D"font-size:12.8px"><di >> v= >> style=3D"font-size:small"><span style=3D"font-size:12.8px">MAT >> Postdoctora= >> l Fellow</span><div style=3D"font-size:12.8px">Department of >> Astrophysics</= >> div><div><span style=3D"font-size:12.8px">American Museum of Natural >> Histor= >> y</span><div style=3D"font-size:12.8px"><a href=3D"mailto:Mark.Richardson >> .W= >> ork(a)gmail.com" style=3D"color:rgb(17,85,204)" >> target=3D"_blank">Mark.Richar= >> dson.Work(a)gmail.com</a></div><div><a href=3D"https://sites.google.c >> om/site/= >> marklarichardson/ <https://sites.google.com/site/=marklarichardson/>" >> style=3D"color:rgb(17,85,204)" target=3D"_blank">My Webs= >> ite</a><br><div style=3D"font-size:12.8px">212 496 3432 >> <(212)%20496-3432></div></div></div></= >> div></div></div></div></div></div></div></div></div></div> >> </div></div></div> >> >> --001a1148215464247f05650bb037-- >> >> ------------------------------ >> >> Date: Mon, 12 Feb 2018 18:37:46 -0600 >> From: Nathan Goldbaum <nathan12343(a)gmail.com> >> Subject: [yt-dev] Re: OctTree cut_region OffAxis Projections >> To: yt-dev(a)python.org >> Message-ID: >> <CAJXewO=eL-F5FtrpY83ddkN=_fh+MC1=Wqadx2bR0=cQrxmvZg(a)mail.gm >> ail.com> >> Content-Type: multipart/alternative; >> boundary="94eb2c0eeff24e015605650d35ca" >> >> --94eb2c0eeff24e015605650d35ca >> Content-Type: text/plain; charset="UTF-8" >> >> Hi Mark, >> >> This is caused by the fact that OctreeSubsetBlockSlicePosition is not a >> subclass of YTSelectionContainer, which implements the appropriate API. >> >> I don't remember offhand why it's designed that way. The fix would either >> be to make OctreeSubsetBlockSlicePosition inherit from >> YTSelectionContainer >> (no idea how hard this would be or what it would break to do that) or >> simply implement the _field_parameter_state context manager for the >> OctreeSubsetBlockSlicePosition class. >> >> For reference, here's the implementation of the field_parameter_state >> context manager for the base data object class: >> >> https://github.com/yt-project/yt/blob/master/yt/data_objects >> /data_containers.py#L1084 >> >> If you want to take this on to fix the issue you're running into then >> that's great. If not then I'd be happy to take a look at this this week. >> For the latter option, it would be great if you could file an issue for >> this, along with a script that triggers this problem and makes use of one >> of the public RAMSES test datasets we have on yt-project.org/data. That >> will make it easier for me to start on the fix. >> >> -Nathan >> >> >> On Mon, Feb 12, 2018 at 4:56 PM Mark Richardson >> <mark.richardson.work@gmail. >> com> wrote: >> >> > Hey, I've previously been able to make off-axis projections of ramses >> > datasets with geometric data containers. However, I've recently tried >> to do >> > this with a cut_region for dens gas, without success. Here is a script >> that >> > should work with a ramses cosmo dataset: >> > >> > import yt >> > import numpy as np >> > >> > num = 1 >> > Look = [1.,1.,0] >> > Up = [0.,1.,1.] >> > >> > >> > c = np.array([0.5,0.5,0.5]) >> > rad = 0.2 >> > width = 2*rad >> > extra = 1.05 >> > left = c - rad*extra >> > right = c + rad*extra >> > bb = [left,right] >> > >> > fn = "../output_{0:05d}/info_{0:05d}.txt" >> > ds = yt.load(fn.format(num),bbox=bb) >> > >> > region = ds.region(c,left,right) >> > >> > d20 = region.cut_region(['obj["density"] > 1e-20']) >> > >> > p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> > weight_field='density',center=c,width=width,data_source= >> > region,north_vector=Up) >> > p1.save("OAProjDens_Region_{0:03d}.png".format(nout)) >> > >> > p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> > weight_field='density',center=c,width=width,data_source=d20, >> > north_vector=Up) >> > p1.save("OAProjDens_D20_{0:03d}.png".format(nout)) >> > >> > The first OA Projection is generated correctly, but the second one >> crashes >> > with the message: >> > >> > yt : [INFO ] 2018-02-12 22:20:08,915 Making a fixed resolution >> buffer >> > of (('gas', 'density')) 800 by 800 >> > yt : [INFO ] 2018-02-12 22:22:05,737 Saving plot >> > OAProjDens_Region_001.png >> > yt : [INFO ] 2018-02-12 22:22:06,641 xlim = -0.2 0.2 >> > yt : [INFO ] 2018-02-12 22:22:06,641 ylim = -0.2 0.2 >> > yt : [INFO ] 2018-02-12 22:22:06,641 zlim = -0.500000 0.500000 >> > yt : [INFO ] 2018-02-12 22:23:58,431 Making a fixed resolution >> buffer >> > of (('gas', 'density')) 800 by 800 >> > Traceback (most recent call last): >> > File "MakeOffAxisProjClouds.py", line 176, in <module> >> > p1 = yt.OffAxisProjectionPlot(ds,Look,"density", >> > weight_field='density',center=c,width=width,data_source=d20, >> > north_vector=Up) >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 1727, in __init__ >> > fontsize=fontsize) >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 660, in __init__ >> > PlotWindow.__init__(self, *args, **kwargs) >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 219, in __init__ >> > self._setup_plots() >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 748, in _setup_plots >> > self._recreate_frb() >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 1733, in _recreate_frb >> > super(OffAxisProjectionPlot, self)._recreate_frb() >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualiza >> tion/plot_window.py", >> > line 272, in _recreate_frb >> > self._frb._get_data_source_fields() >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/ >> > visualization/fixed_resolution.py", line 155, in >> _get_data_source_fields >> > self[f] >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/ >> > visualization/fixed_resolution.py", line 543, in __getitem__ >> > method=dd.method) >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/ >> > visualization/volume_rendering/off_axis_projection.py", line 189, in >> > off_axis_projection >> > for i, (grid, mask) in enumerate(data_source.blocks): >> > File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/ >> > data_objects/selection_data_containers.py", line 836, in blocks >> > with obj._field_parameter_state(self.field_parameters): >> > AttributeError: 'OctreeSubsetBlockSlicePosition' object has no >> attribute >> > '_field_parameter_state' >> > >> > I'm trying to find how to have d20 inherit _field_parameter_state from >> > region, but thought someone might be able to point me in the right >> > direction a bit faster. >> > >> > Thanks! >> > -Mark >> > >> > -- >> > >> > Mark Richardson >> > MAT Postdoctoral Fellow >> > Department of Astrophysics >> > American Museum of Natural History >> > Mark.Richardson.Work(a)gmail.com >> > My Website <https://sites.google.com/site/marklarichardson/> >> > 212 496 3432 <(212)%20496-3432> >> > _______________________________________________ >> > yt-dev mailing list -- yt-dev(a)python.org >> > To unsubscribe send an email to yt-dev-leave(a)python.org >> > _______________________________________________ >> > yt-dev mailing list -- yt-dev(a)python.org >> > To unsubscribe send an email to yt-dev-leave(a)python.org >> > >> >> --94eb2c0eeff24e015605650d35ca >> Content-Type: text/html; charset="UTF-8" >> Content-Transfer-Encoding: quoted-printable >> >> <div dir=3D"ltr"><div><div dir=3D"auto">Hi Mark,</div><br></div><div>This >> i= >> s caused by the fact that OctreeSubsetBlockSlicePosition is not a >> subclass = >> of YTSelectionContainer, which implements the appropriate >> API.<br><br></div= >> ><div>I don't remember offhand why it's designed that way. The >> fix = >> would either be to make OctreeSubsetBlockSlicePosition inherit from >> YTSelec= >> tionContainer (no idea how hard this would be or what it would break to >> do = >> that) or simply implement the _field_parameter_state context manager for >> th= >> e OctreeSubsetBlockSlicePosition class.<br><br></div><div>For reference, >> he= >> re's the implementation of the field_parameter_state context manager >> fo= >> r the base data object class:<br><br><a href=3D"https://github.com/yt- >> proje= >> ct/yt/blob/master/yt/data_objects/data_containers.py#L1084 >> <https://github.com/yt-proje=ct/yt/blob/master/yt/data_objects/data_containe…> >> ">https://github.= >> com/yt-project/yt/blob/master/yt/data_objects/data_container >> s.py#L1084</a><= >> br><br></div><div>If you want to take this on to fix the issue you're >> r= >> unning into then that's great. If not then I'd be happy to take a >> l= >> ook at this this week. For the latter option, it would be great if you >> coul= >> d file an issue for this, along with a script that triggers this problem >> an= >> d makes use of one of the public RAMSES test datasets we have on <a >> href=3D= >> "http://yt-project.org/data">yt-project.org/data</a>. That will make it >> eas= >> ier for me to start on the fix.<br><br></div><div>-Nathan >> <br></div><div><br= >> ></div><div><br><div class=3D"gmail_quote"><div>On Mon, Feb 12, 2018 at >> 4:5= >> 6 PM Mark Richardson <<a href=3D"mailto:mark.richardson.work@gmail.com" >> = >> target=3D"_blank">mark.richardson.work@gmail.<wbr>com</a>> >> wrote:<br></d= >> iv><blockquote class=3D"gmail_quote" style=3D"margin:0px 0px 0px >> 0.8ex;bord= >> er-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div><font >> size= >> =3D"4">Hey, I've previously been able to make off-axis projections of >> r= >> amses datasets with geometric data containers. However, I've recently >> t= >> ried to do this with a cut_region for dens gas, without success. Here is >> a = >> script that should work with a ramses cosmo dataset:<br></font><br><span >> st= >> yle=3D"font-family:monospace,monospace">import yt<br>import numpy as >> np<br>= >> <br>num =3D 1<br>Look =3D [1.,1.,0]<br>Up =3D >> [0.,1.,1.]<br><br></span><br>= >> <span style=3D"font-family:monospace,monospace"><span >> style=3D"font-family:= >> monospace,monospace">c =3D np.array([0.5,0.5,0.5])<br>rad =3D >> 0.2<br></span= >> ></span><span style=3D"font-family:monospace,monospace"><span >> style=3D"font= >> -family:monospace,monospace"><span style=3D"font-family:monospace >> ,monospace= >> ">width =3D 2*rad<br></span>extra =3D 1.05<br></span></span><span >> style=3D"= >> font-family:monospace,monospace"><span style=3D"font-family:monospace >> ,monos= >> pace">left =C2=A0=3D c - rad*extra<br>right =3D c + rad*extra<br>bb =3D >> [le= >> ft,right]<br><br></span>fn =3D "../output_{0:05d}/info_{ >> 0:<wbr>05d}.tx= >> t"<br>ds =3D yt.load(fn.format(num),bbox=3D<wbr>bb)<br><br>region >> =3D = >> ds.region(c,left,right)<br><br>d20 =3D region.cut_region(['obj[&q >> uot;<w= >> br>density"] > 1e-20'])<br><br>p1 =3D >> yt.OffAxisProjectionPlot(= >> ds,<wbr>Look,"density", weight_field=3D'density&#3 >> 9;,center= >> =3D<wbr>c,width=3Dwidth,data_source=3D<wbr>region,north_vect >> or=3DUp)<br>p1.= >> save("OAProjDens_Region_{0:<wbr>03d}.png".format(n >> out))<br><br>p1= >> =3D yt.OffAxisProjectionPlot(ds,<wbr>Look,"density", >> weight_fiel= >> d=3D'density',center=3D<wbr>c,width=3Dwidth,data_sou >> rce=3Dd20,<wbr>= >> north_vector=3DUp)<br>p1.save("OAProjDens_D20_{0:<wbr>0 >> 3d}.png".f= >> ormat(nout))</span><br><br></div><font size=3D"4">The first OA >> Projection i= >> s generated correctly, but the second one crashes with the message: >> </font>= >> <span style=3D"font-family:monospace,monospace"><br><br>yt : [INFO >> =C2=A0 = >> =C2=A0 ] 2018-02-12 22:20:08,915 Making a fixed resolution buffer of >> ((&#39= >> ;gas', 'density')) 800 by 800<br>yt : [INFO =C2=A0 =C2=A0 ] >> 201= >> 8-02-12 22:22:05,737 Saving plot OAProjDens_Region_001.png<br>yt : [INFO >> = >> =C2=A0 =C2=A0 ] 2018-02-12 22:22:06,641 xlim =3D -0.2 0.2<br>yt : [INFO >> =C2= >> =A0 =C2=A0 ] 2018-02-12 22:22:06,641 ylim =3D -0.2 0.2<br>yt : [INFO >> =C2=A0= >> =C2=A0 ] 2018-02-12 22:22:06,641 zlim =3D -0.500000 0.500000<br>yt : >> [INFO= >> =C2=A0 =C2=A0 ] 2018-02-12 22:23:58,431 Making a fixed resolution buffer >> o= >> f (('gas', 'density')) 800 by 800<br>Traceback (most >> recent= >> call last):<br>=C2=A0 File "MakeOffAxisProjClouds.py", line >> 176,= >> in <module><br>=C2=A0 =C2=A0 p1 =3D yt.OffAxisProjectionPlot(ds,<w >> br= >> >Look,"density", weight_field=3D'density&#3 >> 9;,center=3D<wbr>c= >> ,width=3Dwidth,data_source=3Dd20,<wbr>north_vector=3DUp)<br>=C2=A0 File >> &qu= >> ot;/mnt/blackwhale/home/<wbr>mrichard/soft/yt/yt_cphyc/yt/<w >> br>visualizatio= >> n/plot_window.py", line 1727, in __init__<br>=C2=A0 =C2=A0 >> fontsize=3D= >> fontsize)<br>=C2=A0 File "/mnt/blackwhale/home/<wb >> r>mrichard/soft/yt/y= >> t_cphyc/yt/<wbr>visualization/plot_window.py", line 660, in >> __init__<b= >> r>=C2=A0 =C2=A0 PlotWindow.__init__(self, *args, **kwargs)<br>=C2=A0 File >> &= >> quot;/mnt/blackwhale/home/<wbr>mrichard/soft/yt/yt_cphyc/yt/ >> <wbr>visualizat= >> ion/plot_window.py", line 219, in __init__<br>=C2=A0 =C2=A0 >> self._setu= >> p_plots()<br>=C2=A0 File "/mnt/blackwhale/home/<wb >> r>mrichard/soft/yt/y= >> t_cphyc/yt/<wbr>visualization/plot_window.py", line 748, in >> _setup_plo= >> ts<br>=C2=A0 =C2=A0 self._recreate_frb()<br>=C2=A0 File >> "/mnt/blackwha= >> le/home/<wbr>mrichard/soft/yt/yt_cphyc/yt/<wbr>visualization >> /plot_window.py= >> ", line 1733, in _recreate_frb<br>=C2=A0 =C2=A0 >> super(OffAxisProjectio= >> nPlot, self)._recreate_frb()<br>=C2=A0 File >> "/mnt/blackwhale/home/<wbr= >> >mrichard/soft/yt/yt_cphyc/yt/<wbr>visualization/plot_window.py", >> line= >> 272, in _recreate_frb<br>=C2=A0 =C2=A0 self._frb._get_data_source_<wb >> r>fie= >> lds()<br>=C2=A0 File "/mnt/blackwhale/home/<wb >> r>mrichard/soft/yt/yt_cp= >> hyc/yt/<wbr>visualization/fixed_<wbr>resolution.py", line 155, in >> _get= >> _data_source_fields<br>=C2=A0 =C2=A0 self[f]<br>=C2=A0 File >> "/mnt/blac= >> kwhale/home/<wbr>mrichard/soft/yt/yt_cphyc/yt/<wbr>visualiza >> tion/fixed_<wbr= >> >resolution.py", line 543, in __getitem__<br>=C2=A0 =C2=A0 >> method=3Ddd= >> .method)<br>=C2=A0 File "/mnt/blackwhale/home/<wb >> r>mrichard/soft/yt/yt= >> _cphyc/yt/<wbr>visualization/volume_<wbr>rendering/off_axis_ >> projection.<wbr= >> >py", line 189, in off_axis_projection<br>=C2=A0 =C2=A0 for i, >> (grid, = >> mask) in enumerate(data_source.blocks):<br>=C2=A0 File >> "/mnt/blackwhal= >> e/home/<wbr>mrichard/soft/yt/yt_cphyc/yt/<wbr>data_objects/s >> election_data_<= >> wbr>containers.py", line 836, in blocks<br>=C2=A0 =C2=A0 with >> obj._fie= >> ld_parameter_state(<wbr>self.field_parameters):<br>AttributeError: >> '<wb= >> r>OctreeSubsetBlockSlicePosition<wbr>' object has no attribute >> '_fi= >> eld_parameter_state'</span><br><div><div><br></div><div><font >> size=3D"4= >> ">I'm trying to find how to have d20 inherit _field_parameter_state >> fro= >> m region, but thought someone might be able to point me in the right >> direct= >> ion a bit faster. <br><br></font></div><div><font >> size=3D"4">Thanks!<br></f= >> ont></div><div>=C2=A0=C2=A0<font size=3D"4"> >> -Mark</font><br></div><div><br= >> >-- <br><div class=3D"gmail-m_5724714285761475125m_-6614609091351070164gm >> ai= >> l_signature"><div><div><div><div><div><div><div><div><br><span >> style=3D"fon= >> t-size:12.8px">Mark Richardson</span><br style=3D"font-size:12.8px"><div >> st= >> yle=3D"font-size:small"><span style=3D"font-size:12.8px">MAT Postdoctoral >> F= >> ellow</span><div style=3D"font-size:12.8px">Department of >> Astrophysics</div= >> ><div><span style=3D"font-size:12.8px">American Museum of Natural >> History</= >> span><div style=3D"font-size:12.8px"><a href=3D"mailto:Mark.Richardson >> .Work= >> @gmail.com" style=3D"color:rgb(17,85,204)" target=3D"_blank">Mark.Richard >> so= >> n.Work(a)gmail.com</a></div><div><a href=3D"https://sites.google.c >> om/site/mar= >> klarichardson/ <https://sites.google.com/site/mar=klarichardson/>" >> style=3D"color:rgb(17,85,204)" target=3D"_blank">My Website= >> </a><br><div style=3D"font-size:12.8px"><a href=3D"tel:(212)%20496-3432" >> va= >> lue=3D"+12124963432 <(212)%20496-3432>" target=3D"_blank">212 496 3432 >> <(212)%20496-3432></a></div></div></div></= >> div></div></div></div></div></div></div></div></div></div> >> </div></div></div> >> ______________________________<wbr>_________________<br> >> yt-dev mailing list -- <a href=3D"mailto:yt-dev@python.org" >> target=3D"_blan= >> k">yt-dev(a)python.org</a><br> >> To unsubscribe send an email to <a href=3D"mailto:yt-dev-leave@python.org" >> = >> target=3D"_blank">yt-dev-leave(a)python.org</a><br> >> ______________________________<wbr>_________________<br> >> yt-dev mailing list -- <a href=3D"mailto:yt-dev@python.org" >> target=3D"_blan= >> k">yt-dev(a)python.org</a><br> >> To unsubscribe send an email to <a href=3D"mailto:yt-dev-leave@python.org" >> = >> target=3D"_blank">yt-dev-leave(a)python.org</a><br> >> </blockquote></div></div></div> >> >> --94eb2c0eeff24e015605650d35ca-- >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> yt-dev mailing list -- yt-dev(a)python.org >> To unsubscribe send an email to yt-dev-leave(a)python.org >> >> >> ------------------------------ >> >> End of yt-dev Digest, Vol 110, Issue 5 >> ************************************** >> >> -- >> >> Mark Richardson >> MAT Postdoctoral Fellow >> Department of Astrophysics >> American Museum of Natural History >> Mark.Richardson.Work(a)gmail.com >> My Website <https://sites.google.com/site/marklarichardson/> >> 212 496 3432 >> >

1 0

Re: GSoC'18 participation with yt
by Abhishek Singh Feb. 17, 2018

Feb. 17, 2018

Thank you Nathan for the details on the project. I will get back to you shortly once I familiarize myself with the concepts/background. Best, Abhishek On Sat, Feb 17, 2018 at 1:57 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > > > On Sat, Feb 17, 2018 at 12:42 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > >> >> >> On Sat, Feb 17, 2018 at 10:09 AM, <abhisheksing(a)umass.edu> wrote: >> >>> Hi everyone, >>> >>> I am a Masters student at the University of Massachusetts, Amherst >>> studying Computer Science. I did my undergraduate from BITS Pilani (India) >>> in Computer Science and Masters in Mathematics. I have two and a half years >>> of software development experience at Citi (full-time), Software Robotics >>> Corp (full-time) and Amazon(internship). >>> >>> >> Welcome! And thanks also for the pull request you sent in. >> >> >>> I would like to work on yt projects as part of GSoC'18. Could you help >>> me know more about the project "Interpolating particle data onto grids" and >>> point me to the related materials. >>> >> >> Sure, besides the idea description itself I'd take a look at the >> following background material related to "the demeshening" (our codename >> for the overall project the GSOC project is a piece of): >> >> * YTEP-0032: http://ytep.readthedocs.io/en/latest/YTEPs/YTEP-0032.html >> * The talk Meagan Lang and I gave at SciPy 2017: >> https://www.youtube.com/watch?v=pkZgQIGac6I >> >> The project you are interested in will require an understanding of >> methods for interpolating data from an N-body simulation onto various grid >> types. To understand the motivation and the algorithms you'll be using, it >> would be good to get some background on smoothed particle hydrodynamics, >> KDTrees and the k-nearest neighbors problem. Some materials that might be >> helpful: >> >> * The paper describing the SPLASH visualization software ( >> http://users.monash.edu.au/~dprice/splash/): >> https://doi.org/10.1071/AS07022 >> * "Smoothed Particle Hydrodynamics and Magnetohydroynamics" by Dan Price: >> https://arxiv.org/abs/1012.1885 (in particular Sections 1, 2, and 4) >> * cykdtree, the cython KDTree library by Meagan Lang we've been using for >> this project: https://github.com/cykdtree/cykdtree >> * If your university library has it, the discussion in "Computer >> Simulation using Particles" by Hockney and Eastwood about particle >> deposition methods >> >> SPLASH is a piece of Fortran SPH visualization software. We don't make >> use of SPLASH ourselves much, but the paper describing it has some >> excellent discussion on how to visualize SPH data in practice. >> >> I hope that's not too much background info! >> > > Although I should also mention that the code itself for this project > currently lives on the "sph-viz" branch on my fork of yt: > > https://github.com/ngoldbaum/yt/tree/sph-viz > > Hopefully in the next few weeks we'll move the code to a branch in the > main repository to ease the contribution process. > > If you want to install this branch of yt, Cameron Hummels set up some > instructions for users of the Trident package, which has preliminary > support for the demeshening: > > https://nbviewer.jupyter.org/url/trident-project.org/ > notebooks/trident_demesh_install.ipynb > > >> >> Please let me know if you want to discuss this more or have questions >> about the project itself and how it fits in with this background info. >> >> Best, >> >> Nathan >> >> >>> Also, I would love to be added to the yt Slack, my email address is >>> abhisheksing(a)umass.edu. >>> >>> Thank you, >>> Abhishek Singh >>> _______________________________________________ >>> yt-dev mailing list -- yt-dev(a)python.org >>> To unsubscribe send an email to yt-dev-leave(a)python.org >>> _______________________________________________ >>> yt-dev mailing list -- yt-dev(a)python.org >>> To unsubscribe send an email to yt-dev-leave(a)python.org >>> >> >> > > _______________________________________________ > yt-dev mailing list -- yt-dev(a)python.org > To unsubscribe send an email to yt-dev-leave(a)python.org > > _______________________________________________ > yt-dev mailing list -- yt-dev(a)python.org > To unsubscribe send an email to yt-dev-leave(a)python.org > >

1 0

GSoC'18 participation with yt
by abhisheksing＠umass.edu Feb. 17, 2018

Feb. 17, 2018

Hi everyone, I am a Masters student at the University of Massachusetts, Amherst studying Computer Science. I did my undergraduate from BITS Pilani (India) in Computer Science and Masters in Mathematics. I have two and a half years of software development experience at Citi (full-time), Software Robotics Corp (full-time) and Amazon(internship). I would like to work on yt projects as part of GSoC'18. Could you help me know more about the project "Interpolating particle data onto grids" and point me to the related materials. Also, I would love to be added to the yt Slack, my email address is abhisheksing(a)umass.edu. Thank you, Abhishek Singh

2 2

Regarding GSOC 2018 in yt-project
by aayush tiwari Feb. 17, 2018

Feb. 17, 2018

Hello , I am an undergraduate student at IIIT-Hyderabad, I have decent experience with python,C,C++ and I was interested in contributing to yt-project. Can you please guide me as to where should I start with. Thanks, Aayush Tiwari

3 2

ANN: yt 3.4.1 releaed
by Nathan Goldbaum Feb. 16, 2018

Feb. 16, 2018

yt 3.4.1 release notes The yt community is proud to announce the release of yt 3.4.1. This is a patch release and includes a number of improvements and bugfixes. Note that one of the bugs fixed in this release silently produced invalid results for the values of certain yt fields. See the release notes below for more details. yt (https://yt-project.org) is an open source, community developed toolkit for the analysis and visualization of volumetric data. Development is hosted on GitHub (https://github.com/yt-project/yt). This release includes contributions from 20 contributors, five of whom contributed for the first time: - *Christoph Behrens* - *Josh Borrow* - Corentin Cadiou - Yi-Hao Chen - Bili Dong - Nathan Goldbaum - Philipp Grete - *Stephanie Ho* - Cameron Hummels - Suoqing Ji - Max Katz - Kacper Kowalik - Andrew Myers - Hugo Pfister - Justin Schive - Britton Smith - *Josh Soref* - Matthew Turk - *Daniel Wilcox* - John ZuHone The bolded names indicate first-time contributors. We extend our sincere gratitude to everyone who has contributed! See the changelog below for a summary of new features, changes, and bugfixes. For more information, including installation instructions, links to community resources, and information on contributing to yt’s development, please see the yt homepage at http://yt-project.org and the documentation for yt 3.4.1 at http://yt-project.org/docs/3.4.1. Binaries for yt 3.4.1 are available via pip and conda. If you installed via the install script or use conda to manage your python installation, you can update yt via: $ conda update -c conda-forge yt And via pip if you manage your python installation with pip: $ pip install -U yt As always, if you have any questions, concerns, or run into any trouble updating please don’t hesitate to send a message to the mailing list or stop by our Slack or IRC channel. yt is the product of a large community of developers and users and we are extraordinarily grateful for and proud of their contributions. Please forward this announcement on to any interested parties. Best, The yt development team <https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?both…>Critical Bugfixes - The data returned by fields corresponding to the theta or phi component of a vector field in spherical coordinates or the theta component in cylindrical coordinates, including velocity_spherical_theta, velocity_spherical_phi, and velocity_cylindrical_theta as well as the corresponding magnetic field components have been silently returning incorrect results. If you are doing analysis using those fields we strongly encourage you to update to this latest release to get fixed versions of these fields. See PR 1687 <https://github.com/yt-project/yt/pull/1687>. - Define the code_specific_energy unit and ds.specific_energy_unit attribute. This allows user control over the value of the specific energy unit independent of the velocity unit and fixes an inconsistency in the units of the Gadget internal energy and temperature fields. See PR 1611 <https://github.com/yt-project/yt/pull/1611> and PR 1675 <https://github.com/yt-project/yt/pull/1675>. - Numpy 1.14.0 introduced changes to array printing which caused recursion errors when printing a YTArray instance. This will be fixed upstream in 1.14.1 but we have also restored support for NumPy 1.14.0 in yt by avoiding triggering the error. See PR 1661 <https://github.com/yt-project/yt/pull/1661>. <https://hackmd.io/CYMwhgjGYBzAtAUwGwQEbwCwFYQbIgMabwAMYAnMmoYQOywgDMQA?both…>Minor Improvements and Bugfixes - Halo finders can now run in parallel on Python 3. See PR 1538 <https://github.com/yt-project/yt/pull/1538> and pPR 1690]( https://github.com/yt-project/yt/pull/1690). - The QT5 backend can now be used to display yt plots interactively. See PR 1540 <https://github.com/yt-project/yt/pull/1540>. - A number of misspellings across the codebase and documentation have been corrected. See PR 1542 <https://github.com/yt-project/yt/pull/1542> and PR 1575 <https://github.com/yt-project/yt/pull/1575>. - An off-by-one error in the particle_filter_sfr.py cookbook recipe has been fixed. See PR 1547 <https://github.com/yt-project/yt/pull/1547>. - The tipsy frontend will ignore invalid auxiliary files instead of raising an exception. See PR 1549 <https://github.com/yt-project/yt/pull/1549>. - Fixed a typo in the Gadget header specification. See PR 1550 <https://github.com/yt-project/yt/pull/1550>. - Parse units more gracefully in the FITS frontend. See PR 1553 <https://github.com/yt-project/yt/pull/1553>. - Handle units more gracefully when calculating quantities in the halo catalog. See PR 1558 <https://github.com/yt-project/yt/pull/1558>. - Ensure the PPVCube functionality works when a temperature field is not present. See PR 1562 <https://github.com/yt-project/yt/pull/1562>. - Avoid an error when saving spatial fields for a clump data object. See PR 1567 <https://github.com/yt-project/yt/pull/1567>. - ProfilePlot.set_unit and PhasePlot.set_unit will now handle tuple field names correctly. See PR 1568 <https://github.com/yt-project/yt/pull/1568>. - Properly set attributes when reloading ytdata datasets generated from an arbitrary_grid data object. See PR 1569 <https://github.com/yt-project/yt/pull/1569>. - Fix units in light cone projection. See PR 1574 <https://github.com/yt-project/yt/pull/1574>. - Allow loading Gadget datasets when some cosmology parameters are not present in the header. See PR 1578 <https://github.com/yt-project/yt/pull/1578>. - Correct typo in WarpX field definitions. See PR 1583 <https://github.com/yt-project/yt/pull/1583>. - Fix corner case in parsing Enzo parameter files. See PR 1586 <https://github.com/yt-project/yt/pull/1586>. - Ensure clump parents ids are updated correctly when child clumps are pruned. See PR 1587 <https://github.com/yt-project/yt/pull/1587>. - Ensure the bulk_magnetic_field field parameter is always set to a null default value if it is not otherwise explicitly set. See PR 1588 <https://github.com/yt-project/yt/pull/1588>. - Prevent NaNs from polluting profile calculations when the profile weight field has values equal to zero. See PR 1590 <https://github.com/yt-project/yt/pull/1590>. - Ensure _switch_ds() works with ParticleProjectionPlot. See PR 1594 <https://github.com/yt-project/yt/pull/1594>. - Fix the colors of the axes triad generated by the volume rendering annotate_axes helper function. See PR 1596 <https://github.com/yt-project/yt/pull/1596>. - Fix zooming of slices and projections of data with a 2D cylindrical geometry. See PR 1597 <https://github.com/yt-project/yt/pull/1597>. - Ensure field accesses on 2D grid data objects return data with a dummy dimension. See PR 1603 <https://github.com/yt-project/yt/pull/1603>. - Fix broken links in the documentation. See PR 1615 <https://github.com/yt-project/yt/pull/1615> and PR 1627 <https://github.com/yt-project/yt/pull/1627>. - Avoid errors when parsing boolean parameters in the Boxlib frontend. See PR 1619 <https://github.com/yt-project/yt/pull/1619>. - Populate the _particle_type_counts dictionary for AMReX datasets. This means that ds.particle_type_counts will function correctly. See PR 1621 <https://github.com/yt-project/yt/pull/1621>. - Ensure the "rad" (an alias to the "radian" unit defined for compatibility with Astropy) has the correct dimensions of angle instead of solid angle. See PR 1628 <https://github.com/yt-project/yt/pull/1628>. - Fix unit conversion issue in the annotate_quiver plot callback. See PR 1633 <https://github.com/yt-project/yt/pull/1633>. - Fix unit conversion error in deposited particle velocity and age fields. See PR 1638 <https://github.com/yt-project/yt/pull/1638>. - Added deprecation warnings for the LightRay and AbsorptionSpectrum functionality. Development of this functionality has moved to the Trident package. See PR 1644 <https://github.com/yt-project/yt/pull/1644>. - Support new AMReX particle data files with 5 digit IDs. See PR 1653 <https://github.com/yt-project/yt/pull/1653>. - Handle reloading pickle files with very early YTArray data. See PR 1656 <https://github.com/yt-project/yt/pull/1656>. - Fix initializing species charge and mass fields in the AMReX frontend. See PR 1658 <https://github.com/yt-project/yt/pull/1658>. - Keep units for domain edges when saving ytdata datasets from a FixedResolutionBuffer object. See PR 1659 <https://github.com/yt-project/yt/pull/1659>. - Use the correct matplotlib keyword argument name when specifying contour colors. See PR 1664 <https://github.com/yt-project/yt/pull/1664>. - Support Enzo active particle fields that map to arrays. See PR 1665 <https://github.com/yt-project/yt/pull/1665>. - Use a smarter algorithm for clipping particle positions to the domain boundaries in the rockstar halo finder. See PR 1679 <https://github.com/yt-project/yt/pull/1679>. - Make the annotate_clumps plot callback work correctly with reloaded ytdata clump datasets. See PR 1683 <https://github.com/yt-project/yt/pull/1683>. - Calculate velocity vector components without using the velocity_magnitude field. This avoids inconsistencies when the bulk_velocity field parameter is set to a nonzero value. See PR 1688 <https://github.com/yt-project/yt/pull/1688>. - Avoid truncating Gadget particle IDs by casting from uint32 to float32. See PR 1692 <https://github.com/yt-project/yt/pull/1692>.

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Incorrect vector components in curvilinear coordinate systems
by Nathan Goldbaum Feb. 16, 2018

Feb. 16, 2018

Hi all, I'd like to point out a pull request I just made, which fixes a number of fields that have been returning incorrect data. In particular, the definitions of the fields `velocity_spherical_theta`, `velocity_spherical_phi`, and `velocity_cylindrical_theta` have not been correct for at least three years, possibly longer - I haven't checked to see if they were ever correct. Here's a pull request that implements a fix and adds some new tests: https://github.com/yt-project/yt/pull/1687 While it's nice that we know there's an issue now and that it's fixed, this means that if someone was making a profile of the tangential velocity around a star, or the poloidal magnetic field in a disk simulation, or a circular velocity in a galaxy simulation, yt may have silently returned incorrect results. I'm raising this issue here because it feels like it might be a big deal. Should this concern be raised more loudly to our users? I'm hesitant to do so, mostly out of sheepishness. Is this as big a deal as I'm making it out to be? Thanks, Nathan

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yt-project.github.io
by Matthew Turk Feb. 14, 2018

Feb. 14, 2018

Hi folks, as a heads up, I've created a repo on yt-project called yt-project.github.io. We *could* use this to host our website, but right now I've set it up just so that we can do subdomains using github pages. I'm using this for the yt-3.0-paper repository now, and it'll autobuild the manuscript there. -Matt

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OctTree cut_region OffAxis Projections
by Mark Richardson Feb. 13, 2018

Feb. 13, 2018

Hey, I've previously been able to make off-axis projections of ramses datasets with geometric data containers. However, I've recently tried to do this with a cut_region for dens gas, without success. Here is a script that should work with a ramses cosmo dataset: import yt import numpy as np num = 1 Look = [1.,1.,0] Up = [0.,1.,1.] c = np.array([0.5,0.5,0.5]) rad = 0.2 width = 2*rad extra = 1.05 left = c - rad*extra right = c + rad*extra bb = [left,right] fn = "../output_{0:05d}/info_{0:05d}.txt" ds = yt.load(fn.format(num),bbox=bb) region = ds.region(c,left,right) d20 = region.cut_region(['obj["density"] > 1e-20']) p1 = yt.OffAxisProjectionPlot(ds,Look,"density", weight_field='density',center=c,width=width,data_source=region,north_vector=Up) p1.save("OAProjDens_Region_{0:03d}.png".format(nout)) p1 = yt.OffAxisProjectionPlot(ds,Look,"density", weight_field='density',center=c,width=width,data_source=d20,north_vector=Up) p1.save("OAProjDens_D20_{0:03d}.png".format(nout)) The first OA Projection is generated correctly, but the second one crashes with the message: yt : [INFO ] 2018-02-12 22:20:08,915 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2018-02-12 22:22:05,737 Saving plot OAProjDens_Region_001.png yt : [INFO ] 2018-02-12 22:22:06,641 xlim = -0.2 0.2 yt : [INFO ] 2018-02-12 22:22:06,641 ylim = -0.2 0.2 yt : [INFO ] 2018-02-12 22:22:06,641 zlim = -0.500000 0.500000 yt : [INFO ] 2018-02-12 22:23:58,431 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 Traceback (most recent call last): File "MakeOffAxisProjClouds.py", line 176, in <module> p1 = yt.OffAxisProjectionPlot(ds,Look,"density", weight_field='density',center=c,width=width,data_source=d20,north_vector=Up) File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 1727, in __init__ fontsize=fontsize) File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 660, in __init__ PlotWindow.__init__(self, *args, **kwargs) File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 219, in __init__ self._setup_plots() File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 748, in _setup_plots self._recreate_frb() File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 1733, in _recreate_frb super(OffAxisProjectionPlot, self)._recreate_frb() File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/plot_window.py", line 272, in _recreate_frb self._frb._get_data_source_fields() File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/fixed_resolution.py", line 155, in _get_data_source_fields self[f] File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/fixed_resolution.py", line 543, in __getitem__ method=dd.method) File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/visualization/volume_rendering/off_axis_projection.py", line 189, in off_axis_projection for i, (grid, mask) in enumerate(data_source.blocks): File "/mnt/blackwhale/home/mrichard/soft/yt/yt_cphyc/yt/data_objects/selection_data_containers.py", line 836, in blocks with obj._field_parameter_state(self.field_parameters): AttributeError: 'OctreeSubsetBlockSlicePosition' object has no attribute '_field_parameter_state' I'm trying to find how to have d20 inherit _field_parameter_state from region, but thought someone might be able to point me in the right direction a bit faster. Thanks! -Mark -- Mark Richardson MAT Postdoctoral Fellow Department of Astrophysics American Museum of Natural History Mark.Richardson.Work(a)gmail.com My Website <https://sites.google.com/site/marklarichardson/> 212 496 3432

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