[yt-users] Error while using annotate magnetic fields

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, wrote:

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Today's Topics:

1. Re: Making averaged line plot. (Suoqing Ji)

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Message: 1 Date: Tue, 15 Mar 2016 15:23:43 -0700 From: Suoqing Ji To: Discussion of the yt analysis package Subject: Re: [yt-users] Making averaged line plot. Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109@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 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")

=================================== I'm using yt

Version = 2.6.1

Changeset = c994959ed3be

===================================

Regards,

Dai

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