[yt-users] Camera/Off Axis Options

Sushilkumar sushil.sush19us at gmail.com
Thu May 5 13:07:20 PDT 2016 

Dear Suoqing Ji:

In your draft script what field does 'velocity_magnitude' refer to? I do
not have a field that correspond to magnitude.

On Mon, May 2, 2016 at 6:19 PM, <yt-users-request at lists.spacepope.org>
wrote:

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>    1. Re: Camera/Off Axis Options (Suoqing Ji)
>    2. Re: load structured mesh (Andrea Negri)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 2 May 2016 13:42:32 -0700
> From: Suoqing Ji <suoqing at physics.ucsb.edu>
> To: Discussion of the yt analysis package
>         <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Camera/Off Axis Options
> Message-ID: <820FD28B-2CB2-4131-AD64-0A07990F5055 at physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sushil,
>
> What you can do currently is to get the data from fixed resolution buffer
> and make the plot with quiver callback in matplotlib. The following is a
> basic draft for this:
>
> L = [1, -1, 0]
> north_vector = [0, 0, 1]
> slc = yt.OffAxisSlicePlot(ds, L, 'cutting_plane_velocity_x',
> center=[0,0,0], width=(180,'km'), north_vector=north_vector)
>
> # Now get the fixed resolution buffer
> vel = slc._frb['velocity_magnitude?]
> U = slc._frb['cutting_plane_velocity_x']
> V = slc._frb['cutting_plane_velocity_y']
>
> extentx = [slc.xlim[i].in_units('km') for i in (0, 1)]
> extenty = [slc.ylim[i].in_units('km') for i in (0, 1)]
> extent = extentx + extenty
>
> x = np.linspace(extentx[0], extentx[1], vel.shape[0])
> y = np.linspace(extenty[1], extenty[0], vel.shape[1])
>
> X, Y = np.meshgrid(x, y)
>
> normalize = True
> if normalize is True:
>         N = np.sqrt(U**2+V**2)
>         U /= N
>         V /= N
>
> norm = matplotlib.colors.LogNorm(vmin=vel.min(), vmax=vel.max())
> factor = 40
>
> plt.quiver(X[::factor, ::factor], Y[::factor, ::factor], U[::factor,
> ::factor], V[::factor, ::factor])
> plt.imshow(vel.d, extent=extent, norm=norm)
> plt.colorbar()
> plt.savefig('quiver_plot.png')
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On Apr 30, 2016, at 4:04 PM, Sushilkumar <sushil.sush19us at gmail.com>
> wrote:
> >
> > Dear Suoqing Ji:
> >
> > Thanks. In the meanwhile can you suggest any alternate function/method
> in yt that  I can use for my vector plots?
> >
> > I also have a 3d (streamlines_t000.png) and 2d streamline plot
> (UniformGridData_Slice_y_field_x_t000.png), which needs to treated in the
> same way. Can you suggest any approach for these plots?
> >
> > Drive link:
> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>
> >
> >
> > Thanks in advance
> >
> >
> >
> > On Sat, Apr 30, 2016 at 12:56 PM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
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> > Today's Topics:
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> >    1. Re: Camera/Off Axis Options (Suoqing Ji)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 29 Apr 2016 12:35:04 -0700
> > From: Suoqing Ji <suoqing at physics.ucsb.edu <mailto:
> suoqing at physics.ucsb.edu>>
> > To: Discussion of the yt analysis package
> >         <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > Subject: Re: [yt-users] Camera/Off Axis Options
> > Message-ID: <9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78 at physics.ucsb.edu
> <mailto:9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78 at physics.ucsb.edu>>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hi Sushil,
> >
> > I was able to reproduce your error and created an issue here:
> https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot
> <
> https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot>
> <
> https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot
> <
> https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot
> >>
> >
> > Best wishes,
> > --
> > Suoqing JI
> > Ph.D Candidate
> > Department of Physics
> > University of California, Santa Barbara
> > http://web.physics.ucsb.edu/~suoqing <
> http://web.physics.ucsb.edu/~suoqing>
> >
> > > On Apr 28, 2016, at 7:17 PM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto:sushil.sush19us at gmail.com>> wrote:
> > >
> > > Dear Suoqing Ji:
> > >
> > > With a combination of center [0,0,0] and adjusting the width w, I was
> able to eliminate all the warnings mentioned earlier. But the off axis
> slice plots still wont give me a desired result.
> > >
> > > Plot available on the drive below below.
> > >
> > > The two plots L(010),N(0,0,1).png and L(101),N(001).png are plotted
> for x-z plane and viewing angle of 45 degrees but both are drastically
> different from each other. In fact the off axis slice plots
> (L(101),N(001).png) is not in the x-z plane either.
> > >
> > > I am aiming for a plot similar to vector_rotate.png which is same as
> vector_original.png but rotated/viewed at an angle.
> > >
> > > The vector_rotate.png was created using the python image library. I
> was hoping if yt has any similar options with off axis which would tilt the
> vector plots and fill all the vector grids (which cannot be done using PIL).
> > >
> > > The script (yt_velocity_fields.py) and sample data file
> (Expl_Bt101.mtx.tar.gz) is available on drive link for your reference.
> > >
> > > Thanks in advance and my sincere apologies for repeated queries. But
> this is extremely critical in reproducing my result and putting it for
> publication.
> > >
> > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> <
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>
> > >
> > >
> > >
> > >
> > >
> >
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> > --
> > SK2
> >
> > "Claiming that something can move faster than light is a good
> conversation-stopper in physics. People edge away from you in cocktail
> parties; friends never return phone calls. You just don?t mess with Albert
> Einstein."
> >
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> Message: 2
> Date: Tue, 3 May 2016 01:18:38 +0200
> From: Andrea Negri <negri.andre at gmail.com>
> To: Discussion of the yt analysis package
>         <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] load structured mesh
> Message-ID:
>         <
> CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w at mail.gmail.com>
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> Dear John,
>
> thanks for the suggestions. Do you know if the grid data format is
> compatible with a non uniform mesh? I was thinking of porting my
> outputs in this format.
>
>
> Cheers,
> Andrea
>
> On 2 May 2016 at 18:52, John Zuhone <jzuhone at gmail.com> wrote:
> > Hi Andrea,
> >
> > yt has some support for axisymmetric grids in 2D, so you won?t need to
> convert to a 3D array.
> >
> > The bigger issue is the logarithmic grid spacing. This is currently
> being worked on, but is in a very early state. Currently what it does is
> use ?logr? as the coordinate instead of r, which may not be very ideal for
> every situation. A lot of yt functionality is probably not compatible with
> this way of doing things.
> >
> > Nevertheless, if you would like to explore it further, let us know.
> >
> > Best,
> >
> > John Z
> >
> >> On May 2, 2016, at 10:53 AM, Andrea Negri <negri.andre at gmail.com>
> wrote:
> >>
> >> Of course. I have a 2.5D simulation in spherical coordinates. It is
> >> axial symmetric, so the actual grid is 2D, r and theta. The grid is
> >> structured, the grid spacing in theta is constant, while the spacing
> >> in r follows a geometrical progression, i.e. dr[i+1] = dr[i] * factor,
> >> where factor is a constant.
> >>
> >> I don't know if yt supports axisymmetric grids, but I can bypass this
> >> issue by duplicating the 2D array into a 3D one. Sure, it is not
> >> efficient...
> >>
> >> My ultimate goal is to produce projections, off axis projections and
> >> mock X-ray observations.
> >>
> >>
> >> Thanks,
> >> Andrea
> >>
> >> On 2 May 2016 at 16:43, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> >>> Can you share a little bit more detail about your grid structure? I
> know
> >>> that support for log-radial bins is being worked on right now, for
> example.
> >>>
> >>> On Mon, May 2, 2016 at 3:18 AM, Andrea Negri <negri.andre at gmail.com>
> wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> I'm trying to read ZEUS-MP 2 data, and I'm building my programs step
> >>>> by step. I was able to load data regularly spaced in spherical
> >>>> coordinates. However, I actually have a non-uniform radial grid.
> >>>>
> >>>> I tried with the script in attachment, but I have got odd errors...
> >>>>
> >>>> Also, I have found this page, is it relevant for my case (just because
> >>>> my code is mentioned, the answer would be yes :) )?
> >>>> https://bitbucket.org/yt_analysis/grid_data_format
> >>>>
> >>>>
> >>>> Thanks,
> >>>> Andrea
> >>>>
> >>>> _______________________________________________
> >>>> yt-users mailing list
> >>>> yt-users at lists.spacepope.org
> >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>>
> >>>
> >>>
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-- 
*SK2*

*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*
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