[yt-users] Error while using annotate magnetic fields
Sushilkumar
sushil.sush19us at gmail.com
Wed Mar 16 13:56:00 PDT 2016
Dear Suoqing Ji and yt:
Thank you for your help. It worked
In addition, does yt support 3D quiver plots?
If not what is the equivalent for visualizing 3d magnetic fields.
On Wed, Mar 16, 2016 at 2:49 PM, <yt-users-request at lists.spacepope.org>
wrote:
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> Today's Topics:
>
> 1. Error while using annotate magnetic fields (Sushilkumar)
> 2. Re: Error while using annotate magnetic fields (Suoqing Ji)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 16 Mar 2016 14:16:37 -0500
> From: Sushilkumar <sushil.sush19us at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: [yt-users] Error while using annotate magnetic fields
> Message-ID:
> <
> CAKARaKWgFBsh7qZj8Px+OS0-tDUOuKcv2MrWyJh3NaGtj06-9g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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
> 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
> ===============
>
> ===============
> 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>
> wrote:
>
> > Send yt-users mailing list submissions to
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> >
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> > or, via email, send a message with subject or body 'help' to
> > yt-users-request at lists.spacepope.org
> >
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> >
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> > 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>
> > To: Discussion of the yt analysis package
> > <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>
> > 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>),
> > 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
> >
> > > On Mar 14, 2016, at 10:57 PM, Yuxiao Dai <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
> > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.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.**"*
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> ------------------------------
>
> Message: 2
> Date: Wed, 16 Mar 2016 12:49:09 -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] Error while using annotate magnetic fields
> Message-ID: <9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA at physics.ucsb.edu>
> Content-Type: text/plain; charset="utf-8"
>
> 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>
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> >
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> >
> > _______________________________________________
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> >
> >
> > ------------------------------
> >
> > 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
>
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> Subject: Digest Footer
>
> _______________________________________________
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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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