Mailman 3 March 2016 - yt-users

Error while using annotate magnetic fields
by Sushilkumar 16 Mar '16

16 Mar '16

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > 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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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. 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(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: [yt-users] Error while using annotate magnetic fields > Message-ID: > < > CAKARaKWgFBsh7qZj8Px+OS0-tDUOuKcv2MrWyJh3NaGtj06-9g(a)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(a)lists.spacepope.org> > wrote: > > > Send yt-users mailing list submissions to > > yt-users(a)lists.spacepope.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > 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(a)lists.spacepope.org > > > > You can reach the person managing the list at > > yt-users-owner(a)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(a)physics.ucsb.edu> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org> > > Subject: Re: [yt-users] Making averaged line plot. > > Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109(a)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(a)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(a)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/201… > > > > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)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.**"* > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Wed, 16 Mar 2016 12:49:09 -0700 > From: Suoqing Ji <suoqing(a)physics.ucsb.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using annotate magnetic fields > Message-ID: <9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA(a)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(a)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(a)lists.spacepope.org > <mailto:yt-users-request@lists.spacepope.org>> wrote: > > Send yt-users mailing list submissions to > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)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(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> > > > > You can reach the person managing the list at > > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)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(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> > > To: Discussion of the yt analysis package > > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org>> > > Subject: Re: [yt-users] Making averaged line plot. > > Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109(a)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> < > 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(a)nyu.edu <mailto: > yuxiao.dai(a)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(a)lists.spacepope.org <mailto:yt-users@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/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org <mailto:yt-users@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(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 97, Issue 20 > **************************************** > -- *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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Error while using annotate magnetic fields
by Sushilkumar 16 Mar '16

16 Mar '16

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(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > 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(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)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(a)physics.ucsb.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Making averaged line plot. > Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109(a)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(a)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(a)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/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)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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Making averaged line plot.
by Yuxiao Dai 15 Mar '16

15 Mar '16

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: Inline image 1] =================================== I'm using yt Version = 2.6.1 Changeset = c994959ed3be =================================== Regards, Dai

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Mirroring Cartesian data about a plane for volume rendering
by Daniel Fenn 15 Mar '16

15 Mar '16

Hi, I have a 3D Cartesian FLASH dataset that I would like to mirror about the z=0 plane for volume rendering. Is there a straightforward way to do this in yt? I was unable to find any option in the volume rendering itself. My guess is that I'd have to perhaps make a new array representing the data and do the mirroring by appropriately copying the elements. However, I'm unsure how to go about this--especially for AMR data. Does anyone know of any built-in functionality that might be useful for this? Thanks. Dan

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Can't open the IPython notebook
by Yuxiao Dai 14 Mar '16

14 Mar '16

Dear all, I tried to open an ipython notebook (yt-x86_64)[yd742@ria run5]$ *yt notebook* But got the following error. Any ideas? /home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/IPython/frontend.py:30: UserWarning: The top-level `frontend` package has been deprecated. All its subpackages have been moved to the top `IPython` level. warn("The top-level `frontend` package has been deprecated. " Traceback (most recent call last): File "/home/yd742/software/withpysci/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.6.3', 'console_scripts', 'yt')() File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1702, in run_main args.func(args) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 84, in run self(args) File "/home/yd742/software/withpysci/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1458, in __call__ from IPython.frontend.html.notebook.notebookapp import NotebookApp File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/IPython/html/notebookapp.py", line 38, in <module> from jinja2 import Environment, FileSystemLoader ImportError: No module named jinja2 =================================== I'm using yt Version = 2.6.1 Changeset = c994959ed3be ======================= I would very much appreciate it if anyone could help me on this. Regards, Dai

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Problem making line plots
by Yuxiao Dai 12 Mar '16

12 Mar '16

Dear all, I tried to inspect the magnetic field profile in one snap of my enzo output with the code: ############################################# from yt.mods import * # set up our namespace import numpy as np import pylab as P def _BMag(field, data): return np.sqrt(data["Bx"] * data["Bx"] + data["By"] * data["By"] + data["Bz"] * data["Bz"]) add_field("BMag", function=_BMag) c = pf.h.find_max('BMag')[1] ax = 0 ray = pf.h.ortho_ray(ax, (c[1], c[2])) P.subplot(212) P.semilogy(ray['x'], ray['BMag']) P.xlabel('x') P.ylabel('BMag') print "works" P.savefig("BMag_lineplot.png") ############################################# But keep getting this error message. ############################################# (yt-x86_64)[yd742@ria run5]$ python ytplots_BMag_lineplot_dai.py yt : [INFO ] 2016-03-12 19:19:31,279 Parameters: current_time = 0 yt : [INFO ] 2016-03-12 19:19:31,279 Parameters: domain_dimensions = [128 64 64] yt : [INFO ] 2016-03-12 19:19:31,279 Parameters: domain_left_edge = [-6000. -3000. -3000.] yt : [INFO ] 2016-03-12 19:19:31,280 Parameters: domain_right_edge = [ 6000. 3000. 3000.] yt : [INFO ] 2016-03-12 19:19:31,280 Parameters: cosmological_simulation = 0.0 Parsing Hierarchy 100% ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 yt : [INFO ] 2016-03-12 19:19:31,285 Gathering a field list (this may take a moment.) yt : [INFO ] 2016-03-12 19:19:31,290 Adding unknown field Phi to list of fields yt : [INFO ] 2016-03-12 19:19:31,290 Adding unknown field B_Vorticity2 to list of fields yt : [INFO ] 2016-03-12 19:19:31,290 Adding unknown field B_Vorticity3 to list of fields yt : [INFO ] 2016-03-12 19:19:31,290 Adding unknown field B_Vorticity1 to list of fields yt : [INFO ] 2016-03-12 19:19:31,290 Adding unknown field B_Div to list of fields yt : [INFO ] 2016-03-12 19:19:32,705 Max Value is 8.56382e-05 at -2501.9531250000000000 29.2968750000000000 228.5156250000000000 in grid EnzoGrid_0005 at level 3 (16, 16, 15) yt : [INFO ] 2016-03-12 19:19:32,705 Getting field x from 4 Traceback (most recent call last): File "ytplots_BMag_lineplot_dai.py", line 45, in <module> P.subplot(212) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 896, in subplot fig = gcf() File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 450, in gcf return figure() File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 423, in figure **kwargs) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 79, in new_figure_manager return new_figure_manager_given_figure(num, figure) File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/backends/backend_tkagg.py", line 87, in new_figure_manager_given_figure window = Tk.Tk() File "/home/yd742/software/withpysci/yt-x86_64/lib/python2.7/lib-tk/Tkinter.py", line 1745, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable ############################################# I'm using yt Version = 2.6.1 Changeset = c994959ed3be ======================= I would very much appreciate it if anyone could help me on this. Thank you so much. Regards, Dai

2 2

Loading and writing clumps
by David Collins 09 Mar '16

09 Mar '16

Hi, Everybody-- In yt3, is there a serialization method for clumps? I've tried pickling, and that seems to fail due to the lack of a countours_<long hash> field. Thanks! d. -- -- Sent from a computer.

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Re: [yt-users] yt-users Digest, Vol 97, Issue 12
by Slavin, Jonathan 08 Mar '16

08 Mar '16

Hi Matt, Yeah, I think I'll take you up on your offer to issue the PR. Thanks, Jon On Tue, Mar 8, 2016 at 3:45 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Tue, 8 Mar 2016 14:41:42 -0600 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] found the problem with non-square frb > Message-ID: > <CALO3=5G0vR-=7G+KaQZo= > Z5-7VoHngFZJvmbduensONdMcHbpQ(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Jon, > > That would be an awesome pull request, but I understand your > reluctance. I'm happy to issue it for you and credit you in the PR. > :) > > -Matt > > On Tue, Mar 8, 2016 at 2:39 PM, Slavin, Jonathan > <jslavin(a)cfa.harvard.edu> wrote: > > Hi all, > > > > I just located the problem referred to in my earlier message. There's a > > very small bug in data_objects/data_containers.py > > On lines 957 - 959 there is: > > elif iterable(height): > > h, u = height > > height = self.ds.quan(w, input_units = u) > > Note the w in self.ds_quan(w, input_units = u). Just replace that w > with an > > h and it works. Should I file a pull request? Seems a bit much for > such a > > minor bug, but I'm willing to do it. > > > > Jon > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

1 0

found the problem with non-square frb
by Slavin, Jonathan 08 Mar '16

08 Mar '16

Hi all, I just located the problem referred to in my earlier message. There's a very small bug in data_objects/data_containers.py On lines 957 - 959 there is: elif iterable(height): h, u = height height = self.ds.quan(w, input_units = u) Note the w in self.ds_quan(w, input_units = u). Just replace that w with an h and it works. Should I file a pull request? Seems a bit much for such a minor bug, but I'm willing to do it. Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

2 1

creating non-square frb
by Slavin, Jonathan 08 Mar '16

08 Mar '16

Hi all, I've been creating square fixed resolution buffer objects to use for plotting using matplotlib and it's been working fine. Now I did a calculation that has rectangular output, i.e. 2D cylindrical going from r = 0 - 30 pc and z = -30 - +30 pc and for some reason I can't seem to create an frb to cover the whole computational domain: ds = yt.load(file) slc = ds.slice(2,0.) frb = slc.to_frb((width=(30, 'pc'), height=(60,'pc'),resolution=(512,1024)) In [91]: frb.limits['r'] Out[91]: (-1.63714434867e+14 code_length, 9.25701637144e+19 code_length) In [92]: frb.limits['z'] Out[92]: (-4.62851637144e+19 code_length, 4.62851637144e+19 code_length) So the frb is centered correctly, but only includes half the domain in the z direction. In [94]: ds.domain_left_edge Out[94]: YTArray([ 0.00000000e+00, -9.25700000e+19, 0.00000000e+00]) code_length In [96]: ds.domain_right_edge Out[96]: YTArray([ 9.25700000e+19, 9.25700000e+19, 6.28318531e+00]) code_length Can anyone tell me a way around this? Thanks, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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