[yt-users] Camera/Off Axis Options
Sushilkumar
sushil.sush19us at gmail.com
Mon May 9 09:23:55 PDT 2016
Dear Suoqing Ji:
I was able to include the off axis using frb options (script
yt_frb_offaxis.py on drive link)
But it gives me a plot with its edges chopped. For example L(1,0,0)
N(0,1,1).png and L(1,0,1) N(0,1,1).png have empty cells on the edges. I
should not have empty cells as all of the cells are filled like L(1,0,0)
N(0,0,1).png. Since only the viewing angle is changed it should still fill
all the cells.
I tried it for different angles as well but there are always some empty
cells present for every off axis slices.
Can you suggest wherein these edges are not empty and have quiver vectors?
Thanks in advance.
https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc
On Thu, May 5, 2016 at 8:22 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 18:19:51 -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: <CF41248A-0BEA-4CF7-A2FE-DA7ECA15B0AE at physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Great! You could switch to linear or symlog normalization for non-positive
> values.
>
> 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 6:02 PM, Sushilkumar <sushil.sush19us at gmail.com>
> wrote:
> >
> > Dear Suoqing Ji:
> >
> > Think I was able to overcome the previous error and currently running
> without any errors (however a few warnings do show up).
> >
> > I would have to test a few cases before I can confirm on the same.
> >
> > Thanks in advance.
> >
> >
> >
> >
> >
> > On Thu, May 5, 2016 at 7:44 PM, <yt-users-request at lists.spacepope.org
> <mailto:yt-users-request at lists.spacepope.org>> wrote:
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> > Today's Topics:
> >
> > 1. Camera/Off Axis Options (Sushilkumar)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Thu, 5 May 2016 19:44:22 -0500
> > From: Sushilkumar <sushil.sush19us at gmail.com <mailto:
> sushil.sush19us at gmail.com>>
> > To: Discussion of the yt analysis package
> > <yt-users at lists.spacepope.org <mailto:
> yt-users at lists.spacepope.org>>
> > Subject: [yt-users] Camera/Off Axis Options
> > Message-ID:
> > <CAKARaKUGCFF1L2x+AcsinaA1M2dEksTO=
> 0_WuVjJaporyGc6sg at mail.gmail.com <mailto:0_WuVjJaporyGc6sg at mail.gmail.com
> >>
> > Content-Type: text/plain; charset="utf-8"
> >
> > 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 <
> 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
> <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: Thu, 5 May 2016 13:09:35 -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: <CFD3270F-3DD0-42FB-A13C-7AF897B410DA at physics.ucsb.edu
> <mailto: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 <
> http://web.physics.ucsb.edu/~suoqing>
> > >
> > > > On May 5, 2016, at 1:07 PM, Sushilkumar <sushil.sush19us at gmail.com
> <mailto: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>
> > > <mailto: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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> > > >
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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> <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: <820FD28B-2CB2-4131-AD64-0A07990F5055 at physics.ucsb.edu
> <mailto:820FD28B-2CB2-4131-AD64-0A07990F5055 at physics.ucsb.edu>
> > > <mailto: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> <
> > > 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>
> > > <mailto: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>> <
> > > 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:
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> > > 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>> <mailto:
> 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>>
> <mailto: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>> <mailto:
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> 9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78 at physics.ucsb.edu> <mailto:
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> 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
> >>>
> > > <
> > >
> 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>> <
> > > 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>>
> <mailto: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>>> <
> > > 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>>>>
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > > -------------- next part --------------
> > > > > An HTML attachment was scrubbed...
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> > >
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> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> >
> > > <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> >>
> > > <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> >
> > > <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160429/cf49a1ce/attachment.html
> >
> > > >>>
> > > > >
> > > > > ------------------------------
> > > > >
> > > > > Subject: Digest Footer
> > > > >
> > > > > _______________________________________________
> > > > > yt-users mailing list
> > > > > 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
> >>
> > > <mailto: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>
> > > >>
> > > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-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 98, Issue 43
> > > > > ****************************************
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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 <mailto:yt-users at lists.spacepope.org>
> <mailto: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> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
> > > >
> > > > -------------- next part --------------
> > > > An HTML attachment was scrubbed...
> > > > URL: <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160502/953460d9/attachment-0001.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160502/953460d9/attachment-0001.htm
> >
> > > <
> > >
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160502/953460d9/attachment-0001.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160502/953460d9/attachment-0001.htm
> >
> > > >>
> > > >
> > > > ------------------------------
> > > >
> > > > 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> <mailto: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> <mailto:
> > > 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
> >
> > > <mailto:
> 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> <mailto:
> > > 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>
> > > <mailto: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>
> > > <mailto: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>
> > > <mailto: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> <
> > > 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> <mailto: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> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
> > > > >>>>
> > > > >>>
> > > > >>>
> > > > >>> _______________________________________________
> > > > >>> yt-users mailing list
> > > > >>> 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>>
> > > > >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
> > > > >>>
> > > > >> _______________________________________________
> > > > >> yt-users mailing list
> > > > >> 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
> >>
> > > > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>
> > > > >
> > > > > _______________________________________________
> > > > > yt-users mailing list
> > > > > 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
> >>
> > > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> <
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <
> 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>
> <mailto: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> <
> > > 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 <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>
> > >
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
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> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160505/c4b4677e/attachment.htm
> >
> > > >
> > >
> > > ------------------------------
> > >
> > > 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 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.**"*
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160505/ef6bf628/attachment.htm
> <
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160505/ef6bf628/attachment.htm
> >>
> >
> > ------------------------------
> >
> > 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 16
> > ****************************************
> >
> >
> >
> > --
> > 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
>
> -------------- next part --------------
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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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