[yt-users] yt-users Digest, Vol 117, Issue 22
Matias Enrique Suazo Campos
matias.suazo at ug.uchile.cl
Wed Nov 15 04:55:36 PST 2017
Thanks Everybody!!!
There was no problem after all :P
I hope this to be useful for someone else.
Matías Suazo,
MSc student at Universidad de Chile
2017-11-14 17:42 GMT-03:00 <yt-users-request at lists.spacepope.org>:
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> Today's Topics:
>
> 1. Re: Projection (Jos? Mauricio Utreras)
> 2. Re: Projection (Nathan Goldbaum)
> 3. Re: Projection (Matthew Turk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 14 Nov 2017 15:45:23 -0300
> From: Jos? Mauricio Utreras <jutreras at ug.uchile.cl>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CANhQbF5OzXEhNzguuXR8iNRrAryy74iQ=sVg8zZg5QCzyzqvJg at mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi everyone,
>
> I got the same result using the IsolatedGalaxy dataset
>
> ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> proj=ds.proj('density',axis='z',weight_field='density',
> data_source=disk,method='integrate')
> proj['density']
> >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
>
> 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343 at gmail.com>:
> > Can I get one of you to open an issue?
> >
> > https://github.com/yt-project/yt/issues/new
> >
> > If you can, please include a script to reproduce the problem, making use
> of
> > one of the public datasets on yt-project.org/data.
> >
> > -Nathan
> >
> > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> > <aje2123 at columbia.edu
> >> wrote:
> >
> >> Hello Matias and Nathan,
> >>
> >> I was able to reproduce this error on my own Enzo data set(s) using
> >> similar code. I did a little more playing around and it looks like it
> >> only
> >> breaks when having a weight_field. weight_field = None seems to be O.K.
> .
> >> It also occurs for the "region" objects, in addition to the disk.
> >> Interestingly, as Matias pointed out, doing something like this works:
> >>
> >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> source=region,method='integrate')
> >>
> >> but this does not:
> >>
> >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> >> proj =ds.proj('density',axis='z',weight_field='density',data_
> >> source=region,method='integrate')
> >>
> >> In short, this indeed appears to be a bug, and possibly not specific to
> a
> >> single dataset.
> >>
> >>
> >>
> >>
> >> Andrew
> >>
> >>
> >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> nathan12343 at gmail.com>
> >> wrote:
> >>
> >>> This sounds like a bug. I don't think you should ever get back NaNs
> from
> >>> a projection operation.
> >>>
> >>> Is there any chance you can share the dataset that's triggering this
> >>> behavior?
> >>>
> >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> >>> matias.suazo at ug.uchile.cl> wrote:
> >>>
> >>>> Dear YT users,
> >>>>
> >>>> I'm trying to make a density projection, in the following lines I show
> >>>> you the lines that I have.
> >>>>
> >>>> #Ramses output
> >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> >>>> source=disk,method='integrate')
> >>>>
> >>>> However when I print proj["density"] I get a list of nan, however when
> >>>> I
> >>>> use the whole domain as my data_source I get reasonable numbers.
> >>>>
> >>>> Thanks,
> >>>> Mat?as Suazo
> >>>> MSc student at Universidad de Chile
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users at lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>
> >>
> >> --
> >> NSF Graduate Fellow
> >> Columbia University
> >> Department of Astronomy
> >>
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >>
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 14 Nov 2017 13:04:04 -0600
> From: Nathan Goldbaum <nathan12343 at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CAJXewOm3f91Z66L8WPYZ3ztnVx=BPaKAO9FuZ1Lq28qJZHNVZg at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Ah, so this isn't actually a bug. There's even a comment in the code
> indicating that this is the intended behavior:
>
> https://github.com/yt-project/yt/blob/master/yt/data_
> objects/construction_data_containers.py#L373
>
> So the choices about what to do here are, in my opinion:
>
> * Change this behavior to fill the array with zeros instead of NaNs
> * Improve the documentation to make this choice clearer
>
> I'm not sure offhand what is the best approach, especially given that
> changing this behavior would be a backward compatibility break.
>
> For the original question: your data aren't all NaNs I suspect. E.g. take a
> look at this example script:
>
> import yt
> import numpy as np
> ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc'))
> proj = ds.proj('density', axis='z', weight_field='density',
> data_source=disk,
> method='integrate')
> dens_proj = proj['density']
> print(dens_proj[np.isfinite(dens_proj)])
> print(np.nanmax(dens_proj))
> print(np.nanmin(dens_proj))
>
> Which prints out values in regions where the projection isn't filled with
> NaNs.
>
>
> On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras <
> jutreras at ug.uchile.cl> wrote:
>
> > Hi everyone,
> >
> > I got the same result using the IsolatedGalaxy dataset
> >
> > ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> > disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> > proj=ds.proj('density',axis='z',weight_field='density',
> > data_source=disk,method='integrate')
> > proj['density']
> > >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
> >
> > 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343 at gmail.com>:
> > > Can I get one of you to open an issue?
> > >
> > > https://github.com/yt-project/yt/issues/new
> > >
> > > If you can, please include a script to reproduce the problem, making
> use
> > of
> > > one of the public datasets on yt-project.org/data.
> > >
> > > -Nathan
> > >
> > > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> > > <aje2123 at columbia.edu
> > >> wrote:
> > >
> > >> Hello Matias and Nathan,
> > >>
> > >> I was able to reproduce this error on my own Enzo data set(s) using
> > >> similar code. I did a little more playing around and it looks like it
> > >> only
> > >> breaks when having a weight_field. weight_field = None seems to be
> O.K.
> > .
> > >> It also occurs for the "region" objects, in addition to the disk.
> > >> Interestingly, as Matias pointed out, doing something like this works:
> > >>
> > >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> > >> proj=ds.proj('density',axis='z',weight_field='density',data_
> > >> source=region,method='integrate')
> > >>
> > >> but this does not:
> > >>
> > >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> > >> proj =ds.proj('density',axis='z',weight_field='density',data_
> > >> source=region,method='integrate')
> > >>
> > >> In short, this indeed appears to be a bug, and possibly not specific
> to
> > a
> > >> single dataset.
> > >>
> > >>
> > >>
> > >>
> > >> Andrew
> > >>
> > >>
> > >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> > nathan12343 at gmail.com>
> > >> wrote:
> > >>
> > >>> This sounds like a bug. I don't think you should ever get back NaNs
> > from
> > >>> a projection operation.
> > >>>
> > >>> Is there any chance you can share the dataset that's triggering this
> > >>> behavior?
> > >>>
> > >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> > >>> matias.suazo at ug.uchile.cl> wrote:
> > >>>
> > >>>> Dear YT users,
> > >>>>
> > >>>> I'm trying to make a density projection, in the following lines I
> show
> > >>>> you the lines that I have.
> > >>>>
> > >>>> #Ramses output
> > >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> > >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> > >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> > >>>> source=disk,method='integrate')
> > >>>>
> > >>>> However when I print proj["density"] I get a list of nan, however
> when
> > >>>> I
> > >>>> use the whole domain as my data_source I get reasonable numbers.
> > >>>>
> > >>>> Thanks,
> > >>>> Mat?as Suazo
> > >>>> MSc student at Universidad de Chile
> > >>>>
> > >>>> _______________________________________________
> > >>>> yt-users mailing list
> > >>>> yt-users at lists.spacepope.org
> > >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>>>
> > >>>>
> > >>>
> > >>> _______________________________________________
> > >>> yt-users mailing list
> > >>> yt-users at lists.spacepope.org
> > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>>
> > >>>
> > >>
> > >>
> > >> --
> > >> NSF Graduate Fellow
> > >> Columbia University
> > >> Department of Astronomy
> > >>
> > >> _______________________________________________
> > >> yt-users mailing list
> > >> yt-users at lists.spacepope.org
> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> > >>
> > >>
> > >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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> ------------------------------
>
> Message: 3
> Date: Tue, 14 Nov 2017 14:42:01 -0600
> From: Matthew Turk <matthewturk at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Projection
> Message-ID:
> <CALO3=5GimZpK9u2i40ZWfECXx3btj1GFT1jLO+6OhVn6_DqQGg at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Tue, Nov 14, 2017 at 1:04 PM, Nathan Goldbaum <nathan12343 at gmail.com>
> wrote:
>
> > Ah, so this isn't actually a bug. There's even a comment in the code
> > indicating that this is the intended behavior:
> >
> > https://github.com/yt-project/yt/blob/master/yt/data_
> > objects/construction_data_containers.py#L373
> >
> > So the choices about what to do here are, in my opinion:
> >
> > * Change this behavior to fill the array with zeros instead of NaNs
> >
>
> I think this would give the wrong impression, especially for things like
> weighted average velocity fields.
>
>
> > * Improve the documentation to make this choice clearer
> >
>
> Probably a good thing.
>
> I think I would suggest another option, which would be to filter it based
> on which values are non-NaN. In the cases identified in the emails, I
> would *suspect* that what's happening is that there are elements in the
> quad tree that are initialized from the tree initialization step (which
> just looks at the mesh from the container, not the selected elements in the
> mesh) and left at zero following initialization. We could either have a
> "touched" flag on all of the mesh elements (i.e., "has this been touched by
> data, or is it left at initialized value) and filter in the conversion of
> the quad tree to the flat arrays, or we could filter in the python code
> based on NaNs. My preference would be to filter it in the creation of the
> flat arrays, as then it will be uniformly applied even without weight
> fields.
>
>
> >
> > I'm not sure offhand what is the best approach, especially given that
> > changing this behavior would be a backward compatibility break.
> >
>
> I think filtering NaNs is not a big change in compatibility. I think we'd
> just need to make sure that the cmap normalization has the same behavior
> for missing values as for NaN values, which I think it does.
>
>
> >
> > For the original question: your data aren't all NaNs I suspect. E.g. take
> > a look at this example script:
> >
> > import yt
> > import numpy as np
> > ds = yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> > disk = ds.disk('c', [0, 0, 1], (1000, 'pc'), (100, 'pc'))
> > proj = ds.proj('density', axis='z', weight_field='density',
> > data_source=disk,
> > method='integrate')
> > dens_proj = proj['density']
> > print(dens_proj[np.isfinite(dens_proj)])
> > print(np.nanmax(dens_proj))
> > print(np.nanmin(dens_proj))
> >
> > Which prints out values in regions where the projection isn't filled with
> > NaNs.
> >
> >
> > On Tue, Nov 14, 2017 at 12:45 PM, Jos? Mauricio Utreras <
> > jutreras at ug.uchile.cl> wrote:
> >
> >> Hi everyone,
> >>
> >> I got the same result using the IsolatedGalaxy dataset
> >>
> >> ds=yt.load('IsolatedGalaxy/galaxy0030/galaxy0030')
> >> disk = ds.disk('c',[0,0,1],(1000,'pc'),(100,'pc'))
> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> source=disk,method='integrate')
> >> proj['density']
> >> >>> YTArray([ nan, nan, nan, ..., nan, nan, nan]) g/cm**3
> >>
> >> 2017-11-14 15:38 GMT-03:00, Nathan Goldbaum <nathan12343 at gmail.com>:
> >> > Can I get one of you to open an issue?
> >> >
> >> > https://github.com/yt-project/yt/issues/new
> >> >
> >> > If you can, please include a script to reproduce the problem, making
> >> use of
> >> > one of the public datasets on yt-project.org/data.
> >> >
> >> > -Nathan
> >> >
> >> > On Tue, Nov 14, 2017 at 12:34 PM, Andrew James Emerick
> >> > <aje2123 at columbia.edu
> >> >> wrote:
> >> >
> >> >> Hello Matias and Nathan,
> >> >>
> >> >> I was able to reproduce this error on my own Enzo data set(s) using
> >> >> similar code. I did a little more playing around and it looks like it
> >> >> only
> >> >> breaks when having a weight_field. weight_field = None seems to be
> >> O.K. .
> >> >> It also occurs for the "region" objects, in addition to the disk.
> >> >> Interestingly, as Matias pointed out, doing something like this
> works:
> >> >>
> >> >> region = ds.region([0.5,0.5,0.5], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0])
> >> >> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> >> source=region,method='integrate')
> >> >>
> >> >> but this does not:
> >> >>
> >> >> region = ds.region([0.5,0.5,0.5], [0.1,0.1,0.1], [0.9,0.9,0.9] )
> >> >> proj =ds.proj('density',axis='z',weight_field='density',data_
> >> >> source=region,method='integrate')
> >> >>
> >> >> In short, this indeed appears to be a bug, and possibly not specific
> >> to a
> >> >> single dataset.
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> Andrew
> >> >>
> >> >>
> >> >> On Tue, Nov 14, 2017 at 12:40 PM, Nathan Goldbaum <
> >> nathan12343 at gmail.com>
> >> >> wrote:
> >> >>
> >> >>> This sounds like a bug. I don't think you should ever get back NaNs
> >> from
> >> >>> a projection operation.
> >> >>>
> >> >>> Is there any chance you can share the dataset that's triggering this
> >> >>> behavior?
> >> >>>
> >> >>> On Tue, Nov 14, 2017 at 11:34 AM, Matias Enrique Suazo Campos <
> >> >>> matias.suazo at ug.uchile.cl> wrote:
> >> >>>
> >> >>>> Dear YT users,
> >> >>>>
> >> >>>> I'm trying to make a density projection, in the following lines I
> >> show
> >> >>>> you the lines that I have.
> >> >>>>
> >> >>>> #Ramses output
> >> >>>> ds = yt.load(path+"output_%05d"%snap+"/info_%05d.txt" %snap)
> >> >>>> disk = ds.disk('max',[0,0,1],(20,'pc'),(5,'pc'))
> >> >>>> proj=ds.proj('density',axis='z',weight_field='density',data_
> >> >>>> source=disk,method='integrate')
> >> >>>>
> >> >>>> However when I print proj["density"] I get a list of nan, however
> >> when
> >> >>>> I
> >> >>>> use the whole domain as my data_source I get reasonable numbers.
> >> >>>>
> >> >>>> Thanks,
> >> >>>> Mat?as Suazo
> >> >>>> MSc student at Universidad de Chile
> >> >>>>
> >> >>>> _______________________________________________
> >> >>>> yt-users mailing list
> >> >>>> yt-users at lists.spacepope.org
> >> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>>
> >> >>>>
> >> >>>
> >> >>> _______________________________________________
> >> >>> yt-users mailing list
> >> >>> yt-users at lists.spacepope.org
> >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>>
> >> >>>
> >> >>
> >> >>
> >> >> --
> >> >> NSF Graduate Fellow
> >> >> Columbia University
> >> >> Department of Astronomy
> >> >>
> >> >> _______________________________________________
> >> >> yt-users mailing list
> >> >> yt-users at lists.spacepope.org
> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >> >>
> >> >>
> >> >
> >> _______________________________________________
> >> yt-users mailing list
> >> yt-users at lists.spacepope.org
> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>
> >
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
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