Mailman 3 Error while using annotate magnetic fields - yt-users

16 Mar 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.
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Today's Topics:

Error while using annotate magnetic fields (Sushilkumar)
Re: Error while using annotate magnetic fields (Suoqing Ji)

Message: 1
Date: Wed, 16 Mar 2016 14:16:37 -0500
From: Sushilkumar sushil.sush19us@gmail.com
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: [yt-users] Error while using annotate magnetic fields
Message-ID:
        <
CAKARaKWgFBsh7qZj8Px+OS0-tDUOuKcv2MrWyJh3NaGtj06-9g@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.
===============
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Today's Topics:

Re: Making averaged line plot. (Suoqing Ji)

Message: 1
Date: Tue, 15 Mar 2016 15:23:43 -0700
From: Suoqing Ji suoqing@physics.ucsb.edu
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
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%3E),
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@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

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Message: 2
Date: Wed, 16 Mar 2016 12:49:09 -0700
From: Suoqing Ji suoqing@physics.ucsb.edu
To: Discussion of the yt analysis package
        yt-users@lists.spacepope.org
Subject: Re: [yt-users] Error while using annotate magnetic fields
Message-ID: 9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA@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@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%3E 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%3E
...
===============
===============
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.
...
===============
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mailto:yt-users-request@lists.spacepope.org> wrote:
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...
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Today's Topics:

Re: Making averaged line plot. (Suoqing Ji)

Message: 1
Date: Tue, 15 Mar 2016 15:23:43 -0700
From: Suoqing Ji <suoqing@physics.ucsb.edu <mailto:
suoqing@physics.ucsb.edu>>
...
To: Discussion of the yt analysis package
        <yt-users@lists.spacepope.org <mailto:
yt-users@lists.spacepope.org>>
...
Subject: Re: [yt-users] Making averaged line plot.
Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu
mailto: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%3E <
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%3E%3E),
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%3E
...
...
On Mar 14, 2016, at 10:57 PM, Yuxiao Dai <yuxiao.dai@nyu.edu <mailto:
yuxiao.dai@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
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Einstein."
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parties; friends never return phone calls. You just don’t mess with Albert
Einstein.**"*