<div dir="ltr"><div><div>Dear Suoqing Ji:<br><br></div>Think I was able to overcome the previous error and currently running without any errors (however a few warnings do show up). <br><br>I would have to test a few cases before I can confirm on the same.<br><br></div>Thanks in advance.<br><div><div><br><br><br><br><div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 5, 2016 at 7:44 PM, <span dir="ltr"><<a href="mailto:yt-users-request@lists.spacepope.org" target="_blank">yt-users-request@lists.spacepope.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send yt-users mailing list submissions to<br>
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Today's Topics:<br>
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1. Camera/Off Axis Options (Sushilkumar)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 5 May 2016 19:44:22 -0500<br>
From: Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
Subject: [yt-users] Camera/Off Axis Options<br>
Message-ID:<br>
<CAKARaKUGCFF1L2x+AcsinaA1M2dEksTO=<a href="mailto:0_WuVjJaporyGc6sg@mail.gmail.com">0_WuVjJaporyGc6sg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Suoqing Ji:<br>
<br>
For the frb off axis I get the below error. The script (yt_frb_offaxis.py)<br>
for your reference is available on the drive link.<br>
<br>
Thanks in advance<br>
<br>
<a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a><br>
<br>
<br>
<br>
Error:<br>
<br>
Traceback (most recent call last):<br>
File "yt_frb_offaxis.py", line 63, in <module><br>
plt.colorbar()<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py",<br>
line 2237, in colorbar<br>
ret = gcf().colorbar(mappable, cax = cax, ax=ax, **kw)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/figure.py",<br>
line 1569, in colorbar<br>
cb = cbar.colorbar_factory(cax, mappable, **kw)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 1330, in colorbar_factory<br>
cb = Colorbar(cax, mappable, **kwargs)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 905, in __init__<br>
ColorbarBase.__init__(self, ax, **kw)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 323, in __init__<br>
self.draw_all()<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 348, in draw_all<br>
self._config_axes(X, Y)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 444, in _config_axes<br>
self.update_ticks()<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 373, in update_ticks<br>
ticks, ticklabels, offset_string = self._ticker()<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py",<br>
line 594, in _ticker<br>
b = np.array(locator())<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/ticker.py",<br>
line 1535, in __call__<br>
return self.tick_values(vmin, vmax)<br>
File<br>
"/state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/ticker.py",<br>
line 1553, in tick_values<br>
"Data has no positive values, and therefore can not be "<br>
ValueError: Data has no positive values, and therefore can not be<br>
log-scaled.<br>
<br>
<br>
On Thu, May 5, 2016 at 3:09 PM, <<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>><br>
wrote:<br>
<br>
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><br>
> 1. Re: Camera/Off Axis Options (Suoqing Ji)<br>
><br>
><br>
> ----------------------------------------------------------------------<br>
><br>
> Message: 1<br>
> Date: Thu, 5 May 2016 13:09:35 -0700<br>
> From: Suoqing Ji <<a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a>><br>
> To: Discussion of the yt analysis package<br>
> <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> Subject: Re: [yt-users] Camera/Off Axis Options<br>
> Message-ID: <<a href="mailto:CFD3270F-3DD0-42FB-A13C-7AF897B410DA@physics.ucsb.edu">CFD3270F-3DD0-42FB-A13C-7AF897B410DA@physics.ucsb.edu</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><br>
> Hi Sushil,<br>
><br>
> It?s a derived field and will be automatically computed by yt based on<br>
> three components of velocity field. You could replace it to any other<br>
> fields you want.<br>
><br>
> Best wishes,<br>
> --<br>
> Suoqing JI<br>
> Ph.D Candidate<br>
> Department of Physics<br>
> University of California, Santa Barbara<br>
> <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a><br>
><br>
> > On May 5, 2016, at 1:07 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>><br>
> wrote:<br>
> ><br>
> > Dear Suoqing Ji:<br>
> ><br>
> > In your draft script what field does 'velocity_magnitude' refer to? I do<br>
> not have a field that correspond to magnitude.<br>
> ><br>
> > On Mon, May 2, 2016 at 6:19 PM, <<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a><br>
> <mailto:<a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>>> wrote:<br>
> > Send yt-users mailing list submissions to<br>
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> ><br>
> > When replying, please edit your Subject line so it is more specific<br>
> > than "Re: Contents of yt-users digest..."<br>
> ><br>
> ><br>
> > Today's Topics:<br>
> ><br>
> > 1. Re: Camera/Off Axis Options (Suoqing Ji)<br>
> > 2. Re: load structured mesh (Andrea Negri)<br>
> ><br>
> ><br>
> > ----------------------------------------------------------------------<br>
> ><br>
> > Message: 1<br>
> > Date: Mon, 2 May 2016 13:42:32 -0700<br>
> > From: Suoqing Ji <<a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a> <mailto:<br>
> <a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a>>><br>
> > To: Discussion of the yt analysis package<br>
> > <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>>><br>
> > Subject: Re: [yt-users] Camera/Off Axis Options<br>
> > Message-ID: <<a href="mailto:820FD28B-2CB2-4131-AD64-0A07990F5055@physics.ucsb.edu">820FD28B-2CB2-4131-AD64-0A07990F5055@physics.ucsb.edu</a><br>
> <mailto:<a href="mailto:820FD28B-2CB2-4131-AD64-0A07990F5055@physics.ucsb.edu">820FD28B-2CB2-4131-AD64-0A07990F5055@physics.ucsb.edu</a>>><br>
> > Content-Type: text/plain; charset="utf-8"<br>
> ><br>
> > Hi Sushil,<br>
> ><br>
> > What you can do currently is to get the data from fixed resolution<br>
> buffer and make the plot with quiver callback in matplotlib. The following<br>
> is a basic draft for this:<br>
> ><br>
> > L = [1, -1, 0]<br>
> > north_vector = [0, 0, 1]<br>
> > slc = yt.OffAxisSlicePlot(ds, L, 'cutting_plane_velocity_x',<br>
> center=[0,0,0], width=(180,'km'), north_vector=north_vector)<br>
> ><br>
> > # Now get the fixed resolution buffer<br>
> > vel = slc._frb['velocity_magnitude?]<br>
> > U = slc._frb['cutting_plane_velocity_x']<br>
> > V = slc._frb['cutting_plane_velocity_y']<br>
> ><br>
> > extentx = [slc.xlim[i].in_units('km') for i in (0, 1)]<br>
> > extenty = [slc.ylim[i].in_units('km') for i in (0, 1)]<br>
> > extent = extentx + extenty<br>
> ><br>
> > x = np.linspace(extentx[0], extentx[1], vel.shape[0])<br>
> > y = np.linspace(extenty[1], extenty[0], vel.shape[1])<br>
> ><br>
> > X, Y = np.meshgrid(x, y)<br>
> ><br>
> > normalize = True<br>
> > if normalize is True:<br>
> > N = np.sqrt(U**2+V**2)<br>
> > U /= N<br>
> > V /= N<br>
> ><br>
> > norm = matplotlib.colors.LogNorm(vmin=vel.min(), vmax=vel.max())<br>
> > factor = 40<br>
> ><br>
> > plt.quiver(X[::factor, ::factor], Y[::factor, ::factor], U[::factor,<br>
> ::factor], V[::factor, ::factor])<br>
> > plt.imshow(vel.d, extent=extent, norm=norm)<br>
> > plt.colorbar()<br>
> > plt.savefig('quiver_plot.png')<br>
> ><br>
> > Best wishes,<br>
> > --<br>
> > Suoqing JI<br>
> > Ph.D Candidate<br>
> > Department of Physics<br>
> > University of California, Santa Barbara<br>
> > <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a> <<br>
> <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a>><br>
> ><br>
> > > On Apr 30, 2016, at 4:04 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a><br>
> <mailto:<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>>> wrote:<br>
> > ><br>
> > > Dear Suoqing Ji:<br>
> > ><br>
> > > Thanks. In the meanwhile can you suggest any alternate function/method<br>
> in yt that I can use for my vector plots?<br>
> > ><br>
> > > I also have a 3d (streamlines_t000.png) and 2d streamline plot<br>
> (UniformGridData_Slice_y_field_x_t000.png), which needs to treated in the<br>
> same way. Can you suggest any approach for these plots?<br>
> > ><br>
> > > Drive link:<br>
> > > <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>>><br>
> > ><br>
> > ><br>
> > > Thanks in advance<br>
> > ><br>
> > ><br>
> > ><br>
> > > On Sat, Apr 30, 2016 at 12:56 PM, <<br>
> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>> <mailto:<br>
> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>>>> wrote:<br>
> > > Send yt-users mailing list submissions to<br>
> > > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
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> > > or, via email, send a message with subject or body 'help' to<br>
> > > <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users-request@lists.spacepope.org">yt-users-request@lists.spacepope.org</a>> <mailto:<br>
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> > ><br>
> > > You can reach the person managing the list at<br>
> > > <a href="mailto:yt-users-owner@lists.spacepope.org">yt-users-owner@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users-owner@lists.spacepope.org">yt-users-owner@lists.spacepope.org</a>> <mailto:<br>
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> <a href="mailto:yt-users-owner@lists.spacepope.org">yt-users-owner@lists.spacepope.org</a>>><br>
> > ><br>
> > > When replying, please edit your Subject line so it is more specific<br>
> > > than "Re: Contents of yt-users digest..."<br>
> > ><br>
> > ><br>
> > > Today's Topics:<br>
> > ><br>
> > > 1. Re: Camera/Off Axis Options (Suoqing Ji)<br>
> > ><br>
> > ><br>
> > > ----------------------------------------------------------------------<br>
> > ><br>
> > > Message: 1<br>
> > > Date: Fri, 29 Apr 2016 12:35:04 -0700<br>
> > > From: Suoqing Ji <<a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a> <mailto:<br>
> <a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a>> <mailto:<a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a> <mailto:<br>
> <a href="mailto:suoqing@physics.ucsb.edu">suoqing@physics.ucsb.edu</a>>>><br>
> > > To: Discussion of the yt analysis package<br>
> > > <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>>>><br>
> > > Subject: Re: [yt-users] Camera/Off Axis Options<br>
> > > Message-ID: <<a href="mailto:9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu">9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu</a><br>
> <mailto:<a href="mailto:9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu">9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu</a>> <mailto:<br>
> <a href="mailto:9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu">9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu</a> <mailto:<br>
> <a href="mailto:9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu">9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78@physics.ucsb.edu</a>>>><br>
> > > Content-Type: text/plain; charset="us-ascii"<br>
> > ><br>
> > > Hi Sushil,<br>
> > ><br>
> > > I was able to reproduce your error and created an issue here:<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a>><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a>>><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a>><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a><br>
> <<br>
> <a href="https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-axis-plot</a><br>
> >>><br>
> > ><br>
> > > Best wishes,<br>
> > > --<br>
> > > Suoqing JI<br>
> > > Ph.D Candidate<br>
> > > Department of Physics<br>
> > > University of California, Santa Barbara<br>
> > > <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a> <<br>
> <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a>> <<br>
> <a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a> <<a href="http://web.physics.ucsb.edu/~suoqing" rel="noreferrer" target="_blank">http://web.physics.ucsb.edu/~suoqing</a><br>
> >><br>
> > ><br>
> > > > On Apr 28, 2016, at 7:17 PM, Sushilkumar <<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a><br>
> <mailto:<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>> <mailto:<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a><br>
> <mailto:<a href="mailto:sushil.sush19us@gmail.com">sushil.sush19us@gmail.com</a>>>> wrote:<br>
> > > ><br>
> > > > Dear Suoqing Ji:<br>
> > > ><br>
> > > > With a combination of center [0,0,0] and adjusting the width w, I<br>
> was able to eliminate all the warnings mentioned earlier. But the off axis<br>
> slice plots still wont give me a desired result.<br>
> > > ><br>
> > > > Plot available on the drive below below.<br>
> > > ><br>
> > > > The two plots L(010),N(0,0,1).png and L(101),N(001).png are plotted<br>
> for x-z plane and viewing angle of 45 degrees but both are drastically<br>
> different from each other. In fact the off axis slice plots<br>
> (L(101),N(001).png) is not in the x-z plane either.<br>
> > > ><br>
> > > > I am aiming for a plot similar to vector_rotate.png which is same as<br>
> vector_original.png but rotated/viewed at an angle.<br>
> > > ><br>
> > > > The vector_rotate.png was created using the python image library. I<br>
> was hoping if yt has any similar options with off axis which would tilt the<br>
> vector plots and fill all the vector grids (which cannot be done using PIL).<br>
> > > ><br>
> > > > The script (yt_velocity_fields.py) and sample data file<br>
> (Expl_Bt101.mtx.tar.gz) is available on drive link for your reference.<br>
> > > ><br>
> > > > Thanks in advance and my sincere apologies for repeated queries. But<br>
> this is extremely critical in reproducing my result and putting it for<br>
> publication.<br>
> > > ><br>
> > > > <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>>> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a> <<br>
> <a href="https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc" rel="noreferrer" target="_blank">https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc</a>>>><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > > ><br>
> > ><br>
> > > -------------- next part --------------<br>
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> >>><br>
> > ><br>
> > > ------------------------------<br>
> > ><br>
> > > Subject: Digest Footer<br>
> > ><br>
> > > _______________________________________________<br>
> > > yt-users mailing list<br>
> > > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
> >><br>
> > > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> > ><br>
> > ><br>
> > > ------------------------------<br>
> > ><br>
> > > End of yt-users Digest, Vol 98, Issue 43<br>
> > > ****************************************<br>
> > ><br>
> > ><br>
> > ><br>
> > > --<br>
> > > SK2<br>
> > ><br>
> > > "Claiming that something can move faster than light is a good<br>
> conversation-stopper in physics. People edge away from you in cocktail<br>
> parties; friends never return phone calls. You just don?t mess with Albert<br>
> Einstein."<br>
> > ><br>
> > > _______________________________________________<br>
> > > yt-users mailing list<br>
> > > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> ><br>
> > -------------- next part --------------<br>
> > An HTML attachment was scrubbed...<br>
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> <<br>
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> >><br>
> ><br>
> > ------------------------------<br>
> ><br>
> > Message: 2<br>
> > Date: Tue, 3 May 2016 01:18:38 +0200<br>
> > From: Andrea Negri <<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a> <mailto:<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a><br>
> >><br>
> > To: Discussion of the yt analysis package<br>
> > <<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<br>
> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>>><br>
> > Subject: Re: [yt-users] load structured mesh<br>
> > Message-ID:<br>
> > <<br>
> <a href="mailto:CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w@mail.gmail.com">CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w@mail.gmail.com</a><br>
> <mailto:<a href="mailto:CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w@mail.gmail.com">CAPUxaiR17QnvGze88Y61scioy20NwDx7Qfir2-cUqEwFZeOB7w@mail.gmail.com</a><br>
> >><br>
> > Content-Type: text/plain; charset=UTF-8<br>
> ><br>
> > Dear John,<br>
> ><br>
> > thanks for the suggestions. Do you know if the grid data format is<br>
> > compatible with a non uniform mesh? I was thinking of porting my<br>
> > outputs in this format.<br>
> ><br>
> ><br>
> > Cheers,<br>
> > Andrea<br>
> ><br>
> > On 2 May 2016 at 18:52, John Zuhone <<a href="mailto:jzuhone@gmail.com">jzuhone@gmail.com</a> <mailto:<br>
> <a href="mailto:jzuhone@gmail.com">jzuhone@gmail.com</a>>> wrote:<br>
> > > Hi Andrea,<br>
> > ><br>
> > > yt has some support for axisymmetric grids in 2D, so you won?t need to<br>
> convert to a 3D array.<br>
> > ><br>
> > > The bigger issue is the logarithmic grid spacing. This is currently<br>
> being worked on, but is in a very early state. Currently what it does is<br>
> use ?logr? as the coordinate instead of r, which may not be very ideal for<br>
> every situation. A lot of yt functionality is probably not compatible with<br>
> this way of doing things.<br>
> > ><br>
> > > Nevertheless, if you would like to explore it further, let us know.<br>
> > ><br>
> > > Best,<br>
> > ><br>
> > > John Z<br>
> > ><br>
> > >> On May 2, 2016, at 10:53 AM, Andrea Negri <<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a><br>
> <mailto:<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a>>> wrote:<br>
> > >><br>
> > >> Of course. I have a 2.5D simulation in spherical coordinates. It is<br>
> > >> axial symmetric, so the actual grid is 2D, r and theta. The grid is<br>
> > >> structured, the grid spacing in theta is constant, while the spacing<br>
> > >> in r follows a geometrical progression, i.e. dr[i+1] = dr[i] * factor,<br>
> > >> where factor is a constant.<br>
> > >><br>
> > >> I don't know if yt supports axisymmetric grids, but I can bypass this<br>
> > >> issue by duplicating the 2D array into a 3D one. Sure, it is not<br>
> > >> efficient...<br>
> > >><br>
> > >> My ultimate goal is to produce projections, off axis projections and<br>
> > >> mock X-ray observations.<br>
> > >><br>
> > >><br>
> > >> Thanks,<br>
> > >> Andrea<br>
> > >><br>
> > >> On 2 May 2016 at 16:43, Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a><br>
> <mailto:<a href="mailto:nathan12343@gmail.com">nathan12343@gmail.com</a>>> wrote:<br>
> > >>> Can you share a little bit more detail about your grid structure? I<br>
> know<br>
> > >>> that support for log-radial bins is being worked on right now, for<br>
> example.<br>
> > >>><br>
> > >>> On Mon, May 2, 2016 at 3:18 AM, Andrea Negri <<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a><br>
> <mailto:<a href="mailto:negri.andre@gmail.com">negri.andre@gmail.com</a>>> wrote:<br>
> > >>>><br>
> > >>>> Hi all,<br>
> > >>>><br>
> > >>>> I'm trying to read ZEUS-MP 2 data, and I'm building my programs step<br>
> > >>>> by step. I was able to load data regularly spaced in spherical<br>
> > >>>> coordinates. However, I actually have a non-uniform radial grid.<br>
> > >>>><br>
> > >>>> I tried with the script in attachment, but I have got odd errors...<br>
> > >>>><br>
> > >>>> Also, I have found this page, is it relevant for my case (just<br>
> because<br>
> > >>>> my code is mentioned, the answer would be yes :) )?<br>
> > >>>> <a href="https://bitbucket.org/yt_analysis/grid_data_format" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/grid_data_format</a> <<br>
> <a href="https://bitbucket.org/yt_analysis/grid_data_format" rel="noreferrer" target="_blank">https://bitbucket.org/yt_analysis/grid_data_format</a>><br>
> > >>>><br>
> > >>>><br>
> > >>>> Thanks,<br>
> > >>>> Andrea<br>
> > >>>><br>
> > >>>> _______________________________________________<br>
> > >>>> yt-users mailing list<br>
> > >>>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > >>>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> > >>>><br>
> > >>><br>
> > >>><br>
> > >>> _______________________________________________<br>
> > >>> yt-users mailing list<br>
> > >>> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > >>> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> > >>><br>
> > >> _______________________________________________<br>
> > >> yt-users mailing list<br>
> > >> <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > >> <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> > ><br>
> > > _______________________________________________<br>
> > > yt-users mailing list<br>
> > > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> ><br>
> ><br>
> > ------------------------------<br>
> ><br>
> > Subject: Digest Footer<br>
> ><br>
> > _______________________________________________<br>
> > yt-users mailing list<br>
> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a> <mailto:<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a>><br>
> > <a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org</a> <<br>
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> ><br>
> ><br>
> > ------------------------------<br>
> ><br>
> > End of yt-users Digest, Vol 99, Issue 3<br>
> > ***************************************<br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > SK2<br>
> ><br>
> > "Claiming that something can move faster than light is a good<br>
> conversation-stopper in physics. People edge away from you in cocktail<br>
> parties; friends never return phone calls. You just don?t mess with Albert<br>
> Einstein."<br>
> ><br>
> > _______________________________________________<br>
> > yt-users mailing list<br>
> > <a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
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> ><br>
><br>
> ------------------------------<br>
><br>
> Subject: Digest Footer<br>
><br>
> _______________________________________________<br>
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><br>
><br>
> ------------------------------<br>
><br>
> End of yt-users Digest, Vol 99, Issue 15<br>
> ****************************************<br>
><br>
<br>
<br>
<br>
--<br>
*SK2*<br>
<br>
*"**Claiming that something can move faster than light is a good<br>
conversation-stopper in physics. People edge away from you in cocktail<br>
parties; friends never return phone calls. You just don?t mess with Albert<br>
Einstein.**"*<br>
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End of yt-users Digest, Vol 99, Issue 16<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><span style="border-collapse:collapse"><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i>SK<sup>2</sup></i></b></span></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse"><b><i><sup><br></sup></i></b></span></div><div><span style="color:rgb(80,0,80);font-family:arial,sans-serif;border-collapse:collapse"><b><sup>"</sup></b></span><font face="arial, sans-serif" color="#500050"><b>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.</b></font><b style="color:rgb(80,0,80);font-family:arial,sans-serif"><sup>"</sup></b></div><div style="color:rgb(80,0,80);font-family:arial,sans-serif;font-size:13px"><br></div></span></div>
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