[yt-users] Error while using annotate magnetic fields

Suoqing Ji suoqing at physics.ucsb.edu
Wed Mar 16 12:49:09 PDT 2016


Hi Sushil,

I think what you need to do is to assign the correct field name when loading the data. In your script, you have:

data = dict(field1 = field1,
            field2 = field2,
            field3 = field3)

which could be, say,

data = dict(magnetic_field_x = field1,
            magnetic_field_y = field2,
            magnetic_field_z = field3)

since annotate_magnetic_field will directly refer to these field names (in fact it's a specialized version of annotate_quiver).

Best wishes,
--
Suoqing JI
Ph.D Candidate
Department of Physics
University of California, Santa Barbara
http://web.physics.ucsb.edu/~suoqing

> On Mar 16, 2016, at 12:16 PM, Sushilkumar <sushil.sush19us at gmail.com> wrote:
> 
> Dear yt:
> 
> I am trying to plot magnetic field lines using the annotate magnetic field call back from the link http://yt-project.org/doc/visualizing/callbacks.html <http://yt-project.org/doc/visualizing/callbacks.html> link.
> 
> However, after running the script it gives the error below. A google drive link to my script (yt_numpy_load_B.py) is also given below. When I use quiver annotate it works fine but issue comes when I am using slc.annotate_magnetic_field(). 
> Quiver plots are also available on the drive link.
> 
> Thanks in advance
> 
> ===============
> Google drive link
> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>
> ===============
> 
> ===============
> Error while running the script
> 
>   File "yt_numpy_load_B.py", line 47, in <module>
>     slc.save()
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_container.py", line 77, in newfunc
>     args[0]._setup_plots()
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 980, in _setup_plots
>     self.run_callbacks()
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1033, in run_callbacks
>     sys.exc_info()[2])
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", line 1029, in run_callbacks
>     callback(cbw)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 316, in __call__
>     return qcb(plot)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", line 357, in __call__
>     fv_x = plot.data[self.field_x]
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 246, in __getitem__
>     f = self._determine_fields([key])[0]
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", line 518, in _determine_fields
>     finfo = self.ds._get_field_info("unknown", fname)
>   File "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.py", line 543, in _get_field_info
>     raise YTFieldNotFound((ftype, fname), self)
> yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field callback failed with the following error: Could not find field '('all', 'magnetic_field_x')' in UniformGridData.
> ===============
> 
> 
> 
> 
> On Wed, Mar 16, 2016 at 12:52 PM, <yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>> wrote:
> Send yt-users mailing list submissions to
>         yt-users at lists.spacepope.org <mailto:yt-users at lists.spacepope.org>
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>
> or, via email, send a message with subject or body 'help' to
>         yt-users-request at lists.spacepope.org <mailto:yt-users-request at lists.spacepope.org>
> 
> You can reach the person managing the list at
>         yt-users-owner at lists.spacepope.org <mailto:yt-users-owner at lists.spacepope.org>
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of yt-users digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Making averaged line plot. (Suoqing Ji)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 15 Mar 2016 15:23:43 -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] Making averaged line plot.
> Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109 at physics.ucsb.edu <mailto:70E5BA6C-7798-45F2-AE83-21233252E109 at physics.ucsb.edu>>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Yuxiao,
> 
> If you would like to start from your current code, the most straightforward way is to write a loop to smooth over a certain distance by each step, which also works for AMR data:
> 
> smooth_len = 100 # smoothing length of 100 kpc
> SmoothedBMag = np.copy(ray[?ScaledBMag?]) # store the smoothed array
> bin_num = np.ceiling((ray[?x?].max() - ray[?x?].min()) / smooth_len) # make bins every 100 kpc
> 
> for step in range(bin_num):
>     mask1 = (ray[?x?] >= ray[?x?].min() + step * smooth_len)
>     mask2 = (ray[?x?] < ray[?x?].min() + (step + 1) * smooth_len)
>     mask = np.logical_and(mask1, mask2) # mask the cells within a certain length of 100 kpc
>     SmoothedBMag[mask] = np.mean(ray[?ScaledBMag?][mask]) # take the average and save
> 
> After that the array ?SmoothedBMag? is the smoothed one.
> 
> However, an easier way is to use the the 1D ProfilePlot function (http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots> <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>>), and in this case you could do something like:
> 
> plot = ProfilePlot(pf.h.all_data(), ?x?, [?ScaledBMag?], n_bins=bin_num)
> 
> Note that this will do the average over entire y-z plane for each x bins, which is different from averaging only an array of a ray object (so maybe it?s not what you want). If you really want the data within a thin slit only, you could define a region object pf.h.region() and do ProfilePlot. I think it?s also doable to use the function ?load_uniform_grid? to create a 1D dataset from the arrays in ray object and pass it to ProfilePlot.
> 
> 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 Mar 14, 2016, at 10:57 PM, Yuxiao Dai <yuxiao.dai at nyu.edu <mailto:yuxiao.dai at nyu.edu>> wrote:
> >
> > Dear all,
> >
> > I have a line plot of some parameter along an axis as a function of distance. Now I would like to get another line plot of the same parameter but averaged over a certain distance (say 100 kpc, the plot below is supposed to be flat after this). I've been searching the document for some time but haven't found a method. Is there a simple way to do this?
> >
> > I would very much appreciate it if anyone could help me on this.
> >
> >
> > ===================================
> > import ...
> >
> > def _ScaledBMag(field, data):
> >
> >     return ...
> >
> >
> >
> > ....
> >
> > pf = load(filename)
> >
> >     add_field("ScaledBMag", function=_ScaledBMag)
> >
> >
> >
> >     c = pf.h.find_max('ScaledBMag')[1]
> >
> >     ax = 0
> >
> >     ray = pf.h.ortho_ray(ax, (c[1], c[2]))
> >
> >
> >     P.subplot(211)
> >
> >     P.semilogy(ray['x'], ray['ScaledBMag'])
> >
> >     P.xlabel('x')
> >
> >     P.ylabel('ScaledBMag')
> >
> >     print "works"
> >
> >     P.savefig("ScaledBMag_lineplot.png")
> >
> >
> > <image.png>
> >
> > ===================================
> > I'm using yt
> >
> > Version = 2.6.1
> >
> >
> > Changeset = c994959ed3be
> >
> > ===================================
> >
> >
> >
> >
> >
> > Regards,
> >
> > Dai
> >
> > _______________________________________________
> > 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...
> URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160315/8afc239c/attachment.html <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160315/8afc239c/attachment.html>>
> 
> ------------------------------
> 
> 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 97, Issue 19
> ****************************************
> 
> 
> 
> -- 
> 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 --------------
An HTML attachment was scrubbed...
URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/20160316/76eb7890/attachment.html>


More information about the yt-users mailing list