[yt-users] Camera/Off Axis Options
Sushilkumar
sushil.sush19us at gmail.com
Thu May 5 17:44:22 PDT 2016
Dear Suoqing Ji:
For the frb off axis I get the below error. The script (yt_frb_offaxis.py)
for your reference is available on the drive link.
Thanks in advance
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
Error:
Traceback (most recent call last):
File "yt_frb_offaxis.py", line 63, in <module>
plt.colorbar()
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py",
line 2237, in colorbar
ret = gcf().colorbar(mappable, cax = cax, ax=ax, **kw)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/figure.py",
line 1569, in colorbar
cb = cbar.colorbar_factory(cax, mappable, **kw)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 1330, in colorbar_factory
cb = Colorbar(cax, mappable, **kwargs)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 905, in __init__
ColorbarBase.__init__(self, ax, **kw)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 323, in __init__
self.draw_all()
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 348, in draw_all
self._config_axes(X, Y)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 444, in _config_axes
self.update_ticks()
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 373, in update_ticks
ticks, ticklabels, offset_string = self._ticker()
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",
line 594, in _ticker
b = np.array(locator())
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/ticker.py",
line 1535, in __call__
return self.tick_values(vmin, vmax)
File
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/ticker.py",
line 1553, in tick_values
"Data has no positive values, and therefore can not be "
ValueError: Data has no positive values, and therefore can not be
log-scaled.
On Thu, May 5, 2016 at 3:09 PM, <yt-users-request at lists.spacepope.org>
wrote:
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> 1. Re: Camera/Off Axis Options (Suoqing Ji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 5 May 2016 13:09:35 -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: <CFD3270F-3DD0-42FB-A13C-7AF897B410DA at physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sushil,
>
> It?s a derived field and will be automatically computed by yt based on
> three components of velocity field. You could replace it to any other
> fields you want.
>
> Best wishes,
> --
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> http://web.physics.ucsb.edu/~suoqing
>
> > On May 5, 2016, at 1:07 PM, Sushilkumar <sushil.sush19us at gmail.com>
> wrote:
> >
> > 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
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
> > Send yt-users mailing list submissions to
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> > Today's Topics:
> >
> > 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 <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: <820FD28B-2CB2-4131-AD64-0A07990F5055 at physics.ucsb.edu
> <mailto: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 <
> http://web.physics.ucsb.edu/~suoqing>
> >
> > > On Apr 30, 2016, at 4:04 PM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto: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> <
> 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> <mailto:
> yt-users-request at lists.spacepope.org <mailto:
> yt-users-request at lists.spacepope.org>>> wrote:
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> > > Today's Topics:
> > >
> > > 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> <mailto: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> <mailto: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> <mailto:
> 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>>
> <
> 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> <
> 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> <mailto: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>> <
> 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 <mailto:negri.andre at gmail.com
> >>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > Subject: Re: [yt-users] load structured mesh
> > Message-ID:
> > <
> CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w at mail.gmail.com
> <mailto:CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w at mail.gmail.com
> >>
> > Content-Type: text/plain; charset=UTF-8
> >
> > 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 <mailto:
> 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
> <mailto: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
> <mailto: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
> <mailto: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 <
> https://bitbucket.org/yt_analysis/grid_data_format>
> > >>>>
> > >>>>
> > >>>> Thanks,
> > >>>> Andrea
> > >>>>
> > >>>> _______________________________________________
> > >>>> yt-users mailing list
> > >>>> yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
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> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> > >>>>
> > >>>
> > >>>
> > >>> _______________________________________________
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> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> >
> >
> > ------------------------------
> >
> > End of yt-users Digest, Vol 99, Issue 3
> > ***************************************
> >
> >
> >
> > --
> > 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."
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
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> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
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> ------------------------------
>
> End of yt-users Digest, Vol 99, Issue 15
> ****************************************
>
--
*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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