Mailman 3 April 2016 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

3 2

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

6 8

Problem when run yt dev in parallel on Blue Waters
by Pengfei Chen 23 Aug '16

23 Aug '16

Hi all, I have trouble running yt in parallel on Blue Waters. I installed yt using miniconda, the version of yt is ~/miniconda/lib $yt version yt module located at: /u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg The current version and changeset for the code is: --- Version = 3.3-dev Changeset = 90f900be7a36+ yt Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried to make the following simple output in parallel, I get: import yt yt.enable_parallelism() from yt.utilities.parallel_tools.parallel_analysis_interface import\ parallel_objects, communication_system comm = communication_system.communicators[-1] print comm.rank, comm.size 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 ... When I run a similar code but with yt-2.x also on Blue Waters, I get what I expect: 7 16 15 16 6 16 9 16 11 16 8 16 0 16 4 16 ... I'm confused about it. Could anyone give me some suggestions please? Thanks, Pengfei

3 11

FLASH particle trajectories
by Ariadna Murguia 03 May '16

03 May '16

Dear yt-users, I'm trying to plot some particle trajectories taken from a FLASH simulation that has particle files. The number of particle files is greater than the checkpoint files. I was wondering if I could use a similar recipe to the yt documentation for particle trajectories but loading data from the particle files instead of using the checkpoints so I have more trajectory points. Thank you very much! Ariadna

4 7

Camera/Off Axis Options
by Sushilkumar 02 May '16

02 May '16

Dear Suoqing Ji: Thanks. In the meanwhile can you suggest any alternate function/method in yt that I can use for my vector plots? I also have a 3d (streamlines_t000.png) and 2d streamline plot (UniformGridData_Slice_y_field_x_t000.png), which needs to treated in the same way. Can you suggest any approach for these plots? Drive link: https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc Thanks in advance On Sat, Apr 30, 2016 at 12:56 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: Camera/Off Axis Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 29 Apr 2016 12:35:04 -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] Camera/Off Axis Options > Message-ID: <9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78(a)physics.ucsb.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Sushil, > > I was able to reproduce your error and created an issue here: > https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-a… > < > https://bitbucket.org/yt_analysis/yt/issues/1214/vector-annotation-of-off-a… > > > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Apr 28, 2016, at 7:17 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji: > > > > With a combination of center [0,0,0] and adjusting the width w, I was > able to eliminate all the warnings mentioned earlier. But the off axis > slice plots still wont give me a desired result. > > > > Plot available on the drive below below. > > > > The two plots L(010),N(0,0,1).png and L(101),N(001).png are plotted for > x-z plane and viewing angle of 45 degrees but both are drastically > different from each other. In fact the off axis slice plots > (L(101),N(001).png) is not in the x-z plane either. > > > > I am aiming for a plot similar to vector_rotate.png which is same as > vector_original.png but rotated/viewed at an angle. > > > > The vector_rotate.png was created using the python image library. I was > hoping if yt has any similar options with off axis which would tilt the > vector plots and fill all the vector grids (which cannot be done using PIL). > > > > The script (yt_velocity_fields.py) and sample data file > (Expl_Bt101.mtx.tar.gz) is available on drive link for your reference. > > > > Thanks in advance and my sincere apologies for repeated queries. But > this is extremely critical in reproducing my result and putting it for > publication. > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > > > > > > > > > > > -------------- 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 98, Issue 43 > **************************************** > -- *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.**"*

2 1

Camera/Off Axis Options
by Sushilkumar 29 Apr '16

29 Apr '16

Dear Suoqing Ji: With a combination of center [0,0,0] and adjusting the width w, I was able to eliminate all the warnings mentioned earlier. But the off axis slice plots still wont give me a desired result. Plot available on the drive below below. The two plots L(010),N(0,0,1).png and L(101),N(001).png are plotted for x-z plane and viewing angle of 45 degrees but both are drastically different from each other. In fact the off axis slice plots (L(101),N(001).png) is not in the x-z plane either. I am aiming for a plot similar to vector_rotate.png which is same as vector_original.png but rotated/viewed at an angle. The vector_rotate.png was created using the python image library. I was hoping if yt has any similar options with off axis which would tilt the vector plots and fill all the vector grids (which cannot be done using PIL). The script (yt_velocity_fields.py) and sample data file (Expl_Bt101.mtx.tar.gz) is available on drive link for your reference. Thanks in advance and my sincere apologies for repeated queries. But this is extremely critical in reproducing my result and putting it for publication. https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc On Wed, Apr 27, 2016 at 11:54 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: Camera/Off Axis Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Apr 2016 21:54:41 -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] Camera/Off Axis Options > Message-ID: <63F3D1C4-9EEB-4FC8-8C6E-8A46A781F3A9(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushil, > > Your code looks good to me at the first glance ? maybe you could try to > add the argument such as ?center=[0, 0, 0]" in SlicePlot call, to make sure > the slice will cut through the region you want to inspect? With a random > field data, I can not reproduce this on my laptop. > > Also, Kacper has fixed the issue of B field annotation ( > https://bitbucket.org/yt_analysis/yt/pull-requests/2146/create-vector-field…), > and you could use it as soon as this pull request gets merged. > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Apr 27, 2016, at 5:09 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji: > > > > I was able to implement the off axis using velocity field (drive link > below). My script yt_velocity_fields.py plots for a normal vector (L=0,1,0) > in the x-z plane (figure L010.png) which is correct. > > > > But for an azimuth angle of say 45 degrees (L=1,0,1) it gives me a plot > L101.png which is not what I am looking for. > > > > I would like to view the same plot L010.png but at an azimuth of 45 > degrees (in the x-z plane). > > > > Could you let me know if there is any error in my script or any > suggestion for the same? > > > > PS: While running the script I do get a runtime warning which is below > > > > Thanks in advance > > > > > > Drive link: > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > > > > > > > Runtime Warning:- > > > > yt : [WARNING ] 2016-04-27 18:42:52,889 Plot image for field ('gas', > 'velocity_y') has both positive and negative values. Min = -0.016403, Max = > 0.016403. > > yt : [WARNING ] 2016-04-27 18:42:52,890 Switching to symlog colorbar > scaling unless linear scaling is specified later > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1115: > RuntimeWarning: invalid value encountered in greater > > masked = np.abs(a) > self.linthresh > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1127: > RuntimeWarning: invalid value encountered in greater > > masked = np.abs(a) > (self.linthresh * self._linscale_adj) > > > /state/partition1/anaconda/lib/python2.7/site-packages/numpy/ma/core.py:809: > RuntimeWarning: invalid value encountered in greater_equal > > return umath.absolute(a) * self.tolerance >= umath.absolute(b) > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: > RuntimeWarning: invalid value encountered in less_equal > > b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: > RuntimeWarning: invalid value encountered in greater_equal > > b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] > > yt : [WARNING ] 2016-04-27 18:42:53,336 Plot image for field ('gas', > 'velocity_z') has both positive and negative values. Min = -0.071274, Max = > 0.012600. > > yt : [WARNING ] 2016-04-27 18:42:53,336 Switching to symlog colorbar > scaling unless linear scaling is specified later > > yt : [WARNING ] 2016-04-27 18:42:53,896 Plot image for field ('gas', > 'velocity_x') has both positive and negative values. Min = -0.000971, Max = > 0.047361. > > yt : [WARNING ] 2016-04-27 18:42:53,896 Switching to symlog colorbar > scaling unless linear scaling is specified later > > yt : [INFO ] 2016-04-27 18:42:54,742 Saving plot > UniformGridData_OffAxisSlice_velocity_y.png > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:581: > RuntimeWarning: invalid value encountered in less > > cbook._putmask(xa, xa < 0.0, -1) > > yt : [INFO ] 2016-04-27 18:42:55,407 Saving plot > UniformGridData_OffAxisSlice_velocity_z.png > > yt : [INFO ] 2016-04-27 18:42:56,004 Saving plot > UniformGridData_OffAxisSlice_velocity_x.png > > > > > > > > > > > > > > On Tue, Apr 26, 2016 at 2:32 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: Camera/Off axis Options (Suoqing Ji) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 26 Apr 2016 12:32:46 -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] Camera/Off axis Options > > Message-ID: <9C1BAC66-15F1-4488-BC94-DCB9CBF0E5D8(a)physics.ucsb.edu > <mailto:9C1BAC66-15F1-4488-BC94-DCB9CBF0E5D8@physics.ucsb.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Sushil, > > > > Thanks for reporting this! I?ve filed an issue here: > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa…> > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > >> > > > > In the meanwhile, you could temporarily circumvent this problem by > loading your dataset as velocity field and use ?annotate_velocity?... > > > > 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 Apr 26, 2016, at 6:31 AM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > > > > > > Dear Suoqing Ji: > > > > > > I was able to implement the off axis in my script (drive link below, > file is yt_magnetic_fields.py). But there seems to be a problem. For any > off axis value like (1,1,0) I get an error which is given below. > > > > > > I am trying to get a z-x plane and view it at an angle of 15,45,60 > degrees respectively. It works for along the axis normal vector like > (1,0,0) and so on but for off axis value it gives me the error. > > > > > > Could you let me know if there is any error in the script or ways to > overcome it? > > > > > > Thanks in advance > > > > > > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> > > > > > > > > > > > > Error: > > > > > > Traceback (most recent call last): > > > File "yt_magnetic_fields.py", line 39, 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 837, in __call__ > > > 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', > 'cutting_plane_bx')' in UniformGridData > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:46 PM, <yt-users-request(a)lists.spacepope.org > <mailto:yt-users-request@lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> wrote: > > > Send yt-users mailing list submissions to > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: Camera Options (Suoqing Ji) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Thu, 21 Apr 2016 13:45:53 -0700 > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > > > Subject: Re: [yt-users] Camera Options > > > Message-ID: <AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu > <mailto:AAE382DD-ADD2-4D85-BB1E-150B49CFBA40@physics.ucsb.edu> <mailto: > AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu <mailto: > AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu>>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Sushi, > > > > > > What you need to do this to make use of off-axis slice plot instead of > camera; for example, in your code: > > > > > > L = [1, 0, 0] # View along x axis > > > north_vector = [0, 0, 1] > > > slc = yt.SlicePlot(pf, L, ?magnetic_field_x", width=(100,'km?), > north_vector=north_vector) > > > slc.annotate_magnetic_field(factor=40, normalize=True) > > > > > > which gives you the view along x axis. And if you want to rotate the > viewing angle by, say 45 degree, you could change the normal vector L to be > L = [1, 1, 0], and redo the plotting. > > > > > > Also, when you load the data, you probably need to change the name > ?field_x? to be ?magnetic_field_x? and so on, so the > annotate_magnetic_field function will recognize these names. > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > > > > > > On Apr 21, 2016, at 1:28 PM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com> <mailto:sushil.sush19us@gmail.com > <mailto:sushil.sush19us@gmail.com>>> wrote: > > > > > > > > Dear Suoqing Ji: > > > > > > > > The fields Bx,By and Bz are already calculated taking into account > the rotation. So I am not sure if I need to calculate it again. > > > > > > > > What I would like is only change the camera view to a desired angle > after I do a slice plot and that is where I am having trouble with? > > > > > > > > Thanks in advance. > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:20 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> wrote: > > > > Send yt-users mailing list submissions to > > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Camera Options (Suoqing Ji) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Thu, 21 Apr 2016 13:20:32 -0700 > > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > > > Subject: Re: [yt-users] Camera Options > > > > Message-ID: <FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu > <mailto:FB001F5B-2521-4705-8D31-3166451BCA58@physics.ucsb.edu> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu>> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu>>>> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > I see ? that?s a smart way of doing this! > > > > > > > > Best wishes, > > > > Suoqing > > > > > > > > > On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum < > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>>> wrote: > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>>> wrote: > > > > > Hi Nathan, > > > > > > > > > > I do not have a 3D MHD data at hand, but I?ve tried one with > slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following > error: > > > > > > > > > > File "off_axis.py", line 49, in <module> > > > > > slc.save(pf.basename) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 76, in newfunc > > > > > args[0].run_callbacks() > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1029, in run_callbacks > > > > > sys.exc_info()[2]) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1025, in run_callbacks > > > > > callback(cbw) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 352, in __call__ > > > > > (xi, yi) = (ds.coordinates.x_axis[ax], > > > > > yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver > callback failed with the following error: 4 > > > > > > > > > > > > > > > Right, I bet it will work if you do `annotate_velocity()` though. > > > > > > > > > > You should take a look at the definition of the VelocityCallback > to see how it handles off-axis slices. > > > > > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>>> > > > > >> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum < > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>>>> wrote: > > > > >> > > > > >> > > > > >> > > > > >> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>>> wrote: > > > > >> Hi Sushi, > > > > >> > > > > >> The quiver/streamline option you?ve used works for 2d plotting > but not for volume rendering, so I might suggest to use off-axis slice > plot: http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/p > lots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>> > > > > >> > > > > >> Unfortunately, quiver/streamline does not work (and/or does not > work correctly) for off axis slice plot now, but your goal is still > achievable via the following steps: > > > > >> > > > > >> Are you sure about that? There's a `CuttingQuiverCallback` for > off-axis slices. If you do `annotate_magnetic_fields`, it will > automatically choose the `CuttingQuiverCallback` for off-axis slices. > > > > >> > > > > >> > > > > >> 1. Use fixed resolution buffer to get the off-axis sliced field > values including Bx, By and Bz (see this as an example, and replace > SlicePlot with OffAxisSlicePlot: > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > <http://yt-project.org/docs/dev/cookbook/complex_plots.html?hig > hlight=fixedresolutionbuffer#multi-plot-slice-and-projections < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>> > <http://yt-project.org/docs/dev/cookbook/complex_plots.html?highl < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highl> > > ight=fixedresolutionbuffer#multi-plot-slice-and-projections < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>>>), > then you get a 2D array for each field; > > > > >> > > > > >> 2. Compute the magnetic field vectors projected onto the rotated > viewing plane (perpendicular to your normal vector), based on field values > of Bx, By and Bz; now you have two 2D arrays for each components of B field > vectors after rotation; > > > > >> > > > > >> 3. Use quiver function in matplotlib and plot the B field vectors > after rotation, see: > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver > _demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>>>> > > > > >> > > > > >> Hope this helps! Perhaps there?s an easier way that I do not > know... > > > > >> > > > > >> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>>> > > > > >>> On Apr 21, 2016, at 10:31 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>>> wrote: > > > > >>> > > > > >>> Dear yt: > > > > >>> > > > > >>> I am having trouble with the camera option on yt. > > > > >>> > > > > >>> The google drive link is > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc > <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>>> > > > > >>> > > > > >>> I want to change the view of the camera at an angle after the > Slice (x-z plane) and Quiver option. > > > > >>> > > > > >>> My script is yt_cam_rot.py. Without the camera options I get the > desired plot (UniformGridData_Slice.png) but when I use the camera I get a > empty screen. I am not sure where I am going wrong. > > > > >>> > > > > >>> I am using these links for my reference > > > > >>> > > > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > <http > :// > yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-ca…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>>> > > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>>> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>> > <http://yt-project.org/doc/visualiz > ing/volume_rendering.html#volume-rendering < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > >>>> > > > > >>> > > > > >>> Thanks in advance > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>>> wrote: > > > > >>> Dear Suoqing JI: > > > > >>> > > > > >>> Thank you > > > > >>> > > > > >>> On Fri, Apr 15, 2016 at 12:59 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>>> wrote: > > > > >>> Send yt-users mailing list submissions to > > > > >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <h > ttp://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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Camera Options (Suoqing Ji) > > > > >>> > > > > >>> > > > > >>> > ---------------------------------------------------------------------- > > > > >>> > > > > >>> Message: 1 > > > > >>> Date: Fri, 15 Apr 2016 10:59:22 -0700 > > > > >>> From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>>> > > > > >>> Subject: Re: [yt-users] Camera Options > > > > >>> Message-ID: < > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D > 8FCEAA1366(a)physics.ucsb.edu>>>>> > > > > >>> Content-Type: text/plain; charset="utf-8" > > > > >>> > > > > >>> Hi Sushi, > > > > >>> > > > > >>> I think the off-axis slice/projection plot will meet your > requirement best, where the camera orientation is determined by the normal > vector: > > > > >>> > > > > >>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices > <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.h > tml#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.htm < > http://yt-project.org/doc/visualizing/plots.htm > > > > l#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>>> > > > > >>> > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > <http://yt-project.org/doc/visualizing/plots.html#off-axis- > projection-plots < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>> > <http://yt-project.org/doc/visualizing/plots.html#off-axis-pr < > http://yt-project.org/doc/visualizing/plots.html#off-axis-pr> > > ojection-plots < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > >>>>> > > > > >>> > > > > >>> And of course, if you?re interested in the features provided by > volume rendering, it?s also worth a try. This cookbook gives an example of > moving a camera; specifically you might want to use the camera.rotation: > > > > >>> > > > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > <http > :// > yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-ca…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > <http:/ > > / > yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-ca… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>>>> > > > > >>> > > > > >>> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>>> > > > > >>> > > > > >>> > On Apr 15, 2016, at 8:38 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>>> wrote: > > > > >>> > > > > > >>> > Dear yt: > > > > >>> > > > > > >>> > I would like to change/customize/rotate my camera angle for my > slice plots without rotating the axis. > > > > >>> > > > > > >>> > What options do I have using yt if I want to move my camera > angle by say 45 degrees? > > > > >>> > > > > > >>> > Can I use the following link or can you suggest me something > else > > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_renderi > ng.html>>>> <http://yt-project.org/doc/visualizing/volume_rendering.html > <http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering < > http://yt-project.org/doc/visualizing/volume_rendering> > > .html>>>> > > > > >>> > > > > > >>> > Thanks in advance > > > > > > > -------------- 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 98, Issue 35 > > **************************************** > > > > > > > > -- > > 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 98, Issue 38 > **************************************** > -- *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.**"*

2 1

creating a max_density and max_temperature sweep line plot
by tazkera haque 28 Apr '16

28 Apr '16

Hi, I am trying to create a max_dens and max_temp sweep plot in yt. I am using the following code for n in range (0,118): fn = flashFolder+'super3d_hdf5_plt_cnt_%04d' % n pf = yt.load(fn) # load data #print pf.current_time c = pf.h.find_max('temp')[1] ax = 0 # take a line cut along the x axis # cutting through the y0,z0 such that we hit the max density #ray = ds.h.ortho_ray(ax, (c[1], c[2])) # ray with start and end point ray = pf.h.ray([0.,0.,0.],c) # Sort the ray values by 'x' so there are no discontinuities # in the line plot srt = np.argsort(ray['x']) plt.subplot(211) plt.semilogy(np.array(ray['x'][srt]), np.array(ray['dens'][srt])) plt.ylabel('dens') plt.subplot(212) plt.semilogy(np.array(ray['x'][srt]), np.array(ray['temp'][srt])) plt.xlabel('x') plt.ylabel('temp') plt.savefig("test_plots/den_temp_xsweep.png") and getting the the following error: IOError: [Errno 2] No such file or directory: 'test_plots/den_temp_xsweep.png' Any suggestion on how to fix this error is highly appreciated. THanks

2 1

Installing yt on TACC / Stampede : getaddrinfo() / ipv6 error
by Amit Kashi 28 Apr '16

28 Apr '16

Hi, I have installed yt once with no problems, but now I'm trying to install it on TACC/Stampede, and I'm getting an error message during the Python 2 installation stage: Fatal: You must get working getaddrinfo() function. or you can specify "--disable-ipv6" I don't know what is getaddrinfo() and where I can get it. I know what ipv6 is, but I don't know where I should specify "--disable-ipv6" (and whether it is a good thing to do or I better get working getaddrinfo() function). If anyone got this error message and knows what to do please help. Thanks, Amit

2 2

Camera/Off axis option
by Sushilkumar 28 Apr '16

28 Apr '16

Dear Suoqing Ji: Thank you. I will give it a try and give you an update. On Wed, Apr 27, 2016, 23:55 <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: Camera/Off Axis Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 27 Apr 2016 21:54:41 -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] Camera/Off Axis Options > Message-ID: <63F3D1C4-9EEB-4FC8-8C6E-8A46A781F3A9(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushil, > > Your code looks good to me at the first glance ? maybe you could try to > add the argument such as ?center=[0, 0, 0]" in SlicePlot call, to make sure > the slice will cut through the region you want to inspect? With a random > field data, I can not reproduce this on my laptop. > > Also, Kacper has fixed the issue of B field annotation ( > https://bitbucket.org/yt_analysis/yt/pull-requests/2146/create-vector-field…), > and you could use it as soon as this pull request gets merged. > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Apr 27, 2016, at 5:09 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji: > > > > I was able to implement the off axis using velocity field (drive link > below). My script yt_velocity_fields.py plots for a normal vector (L=0,1,0) > in the x-z plane (figure L010.png) which is correct. > > > > But for an azimuth angle of say 45 degrees (L=1,0,1) it gives me a plot > L101.png which is not what I am looking for. > > > > I would like to view the same plot L010.png but at an azimuth of 45 > degrees (in the x-z plane). > > > > Could you let me know if there is any error in my script or any > suggestion for the same? > > > > PS: While running the script I do get a runtime warning which is below > > > > Thanks in advance > > > > > > Drive link: > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > > > > > > > Runtime Warning:- > > > > yt : [WARNING ] 2016-04-27 18:42:52,889 Plot image for field ('gas', > 'velocity_y') has both positive and negative values. Min = -0.016403, Max = > 0.016403. > > yt : [WARNING ] 2016-04-27 18:42:52,890 Switching to symlog colorbar > scaling unless linear scaling is specified later > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1115: > RuntimeWarning: invalid value encountered in greater > > masked = np.abs(a) > self.linthresh > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1127: > RuntimeWarning: invalid value encountered in greater > > masked = np.abs(a) > (self.linthresh * self._linscale_adj) > > > /state/partition1/anaconda/lib/python2.7/site-packages/numpy/ma/core.py:809: > RuntimeWarning: invalid value encountered in greater_equal > > return umath.absolute(a) * self.tolerance >= umath.absolute(b) > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: > RuntimeWarning: invalid value encountered in less_equal > > b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: > RuntimeWarning: invalid value encountered in greater_equal > > b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] > > yt : [WARNING ] 2016-04-27 18:42:53,336 Plot image for field ('gas', > 'velocity_z') has both positive and negative values. Min = -0.071274, Max = > 0.012600. > > yt : [WARNING ] 2016-04-27 18:42:53,336 Switching to symlog colorbar > scaling unless linear scaling is specified later > > yt : [WARNING ] 2016-04-27 18:42:53,896 Plot image for field ('gas', > 'velocity_x') has both positive and negative values. Min = -0.000971, Max = > 0.047361. > > yt : [WARNING ] 2016-04-27 18:42:53,896 Switching to symlog colorbar > scaling unless linear scaling is specified later > > yt : [INFO ] 2016-04-27 18:42:54,742 Saving plot > UniformGridData_OffAxisSlice_velocity_y.png > > > /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:581: > RuntimeWarning: invalid value encountered in less > > cbook._putmask(xa, xa < 0.0, -1) > > yt : [INFO ] 2016-04-27 18:42:55,407 Saving plot > UniformGridData_OffAxisSlice_velocity_z.png > > yt : [INFO ] 2016-04-27 18:42:56,004 Saving plot > UniformGridData_OffAxisSlice_velocity_x.png > > > > > > > > > > > > > > On Tue, Apr 26, 2016 at 2:32 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: Camera/Off axis Options (Suoqing Ji) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 26 Apr 2016 12:32:46 -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] Camera/Off axis Options > > Message-ID: <9C1BAC66-15F1-4488-BC94-DCB9CBF0E5D8(a)physics.ucsb.edu > <mailto:9C1BAC66-15F1-4488-BC94-DCB9CBF0E5D8@physics.ucsb.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Sushil, > > > > Thanks for reporting this! I?ve filed an issue here: > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa…> > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > >> > > > > In the meanwhile, you could temporarily circumvent this problem by > loading your dataset as velocity field and use ?annotate_velocity?... > > > > 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 Apr 26, 2016, at 6:31 AM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > > > > > > Dear Suoqing Ji: > > > > > > I was able to implement the off axis in my script (drive link below, > file is yt_magnetic_fields.py). But there seems to be a problem. For any > off axis value like (1,1,0) I get an error which is given below. > > > > > > I am trying to get a z-x plane and view it at an angle of 15,45,60 > degrees respectively. It works for along the axis normal vector like > (1,0,0) and so on but for off axis value it gives me the error. > > > > > > Could you let me know if there is any error in the script or ways to > overcome it? > > > > > > Thanks in advance > > > > > > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> > > > > > > > > > > > > Error: > > > > > > Traceback (most recent call last): > > > File "yt_magnetic_fields.py", line 39, 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 837, in __call__ > > > 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', > 'cutting_plane_bx')' in UniformGridData > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:46 PM, <yt-users-request(a)lists.spacepope.org > <mailto:yt-users-request@lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> wrote: > > > Send yt-users mailing list submissions to > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: Camera Options (Suoqing Ji) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Thu, 21 Apr 2016 13:45:53 -0700 > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > > > Subject: Re: [yt-users] Camera Options > > > Message-ID: <AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu > <mailto:AAE382DD-ADD2-4D85-BB1E-150B49CFBA40@physics.ucsb.edu> <mailto: > AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu <mailto: > AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu>>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Sushi, > > > > > > What you need to do this to make use of off-axis slice plot instead of > camera; for example, in your code: > > > > > > L = [1, 0, 0] # View along x axis > > > north_vector = [0, 0, 1] > > > slc = yt.SlicePlot(pf, L, ?magnetic_field_x", width=(100,'km?), > north_vector=north_vector) > > > slc.annotate_magnetic_field(factor=40, normalize=True) > > > > > > which gives you the view along x axis. And if you want to rotate the > viewing angle by, say 45 degree, you could change the normal vector L to be > L = [1, 1, 0], and redo the plotting. > > > > > > Also, when you load the data, you probably need to change the name > ?field_x? to be ?magnetic_field_x? and so on, so the > annotate_magnetic_field function will recognize these names. > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > > > > > > On Apr 21, 2016, at 1:28 PM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com> <mailto:sushil.sush19us@gmail.com > <mailto:sushil.sush19us@gmail.com>>> wrote: > > > > > > > > Dear Suoqing Ji: > > > > > > > > The fields Bx,By and Bz are already calculated taking into account > the rotation. So I am not sure if I need to calculate it again. > > > > > > > > What I would like is only change the camera view to a desired angle > after I do a slice plot and that is where I am having trouble with? > > > > > > > > Thanks in advance. > > > > > > > > > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:20 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> wrote: > > > > Send yt-users mailing list submissions to > > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Camera Options (Suoqing Ji) > > > > > > > > > > > > > ---------------------------------------------------------------------- > > > > > > > > Message: 1 > > > > Date: Thu, 21 Apr 2016 13:20:32 -0700 > > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > > > Subject: Re: [yt-users] Camera Options > > > > Message-ID: <FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu > <mailto:FB001F5B-2521-4705-8D31-3166451BCA58@physics.ucsb.edu> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu>> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu>>>> > > > > Content-Type: text/plain; charset="utf-8" > > > > > > > > I see ? that?s a smart way of doing this! > > > > > > > > Best wishes, > > > > Suoqing > > > > > > > > > On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum < > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>>> wrote: > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>>> wrote: > > > > > Hi Nathan, > > > > > > > > > > I do not have a 3D MHD data at hand, but I?ve tried one with > slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following > error: > > > > > > > > > > File "off_axis.py", line 49, in <module> > > > > > slc.save(pf.basename) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 76, in newfunc > > > > > args[0].run_callbacks() > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1029, in run_callbacks > > > > > sys.exc_info()[2]) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1025, in run_callbacks > > > > > callback(cbw) > > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 352, in __call__ > > > > > (xi, yi) = (ds.coordinates.x_axis[ax], > > > > > yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver > callback failed with the following error: 4 > > > > > > > > > > > > > > > Right, I bet it will work if you do `annotate_velocity()` though. > > > > > > > > > > You should take a look at the definition of the VelocityCallback > to see how it handles off-axis slices. > > > > > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>>> > > > > >> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum < > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>>>> wrote: > > > > >> > > > > >> > > > > >> > > > > >> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>>> wrote: > > > > >> Hi Sushi, > > > > >> > > > > >> The quiver/streamline option you?ve used works for 2d plotting > but not for volume rendering, so I might suggest to use off-axis slice > plot: http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/p > lots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>> > > > > >> > > > > >> Unfortunately, quiver/streamline does not work (and/or does not > work correctly) for off axis slice plot now, but your goal is still > achievable via the following steps: > > > > >> > > > > >> Are you sure about that? There's a `CuttingQuiverCallback` for > off-axis slices. If you do `annotate_magnetic_fields`, it will > automatically choose the `CuttingQuiverCallback` for off-axis slices. > > > > >> > > > > >> > > > > >> 1. Use fixed resolution buffer to get the off-axis sliced field > values including Bx, By and Bz (see this as an example, and replace > SlicePlot with OffAxisSlicePlot: > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > <http://yt-project.org/docs/dev/cookbook/complex_plots.html?hig > hlight=fixedresolutionbuffer#multi-plot-slice-and-projections < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>> > <http://yt-project.org/docs/dev/cookbook/complex_plots.html?highl < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highl> > > ight=fixedresolutionbuffer#multi-plot-slice-and-projections < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>>>), > then you get a 2D array for each field; > > > > >> > > > > >> 2. Compute the magnetic field vectors projected onto the rotated > viewing plane (perpendicular to your normal vector), based on field values > of Bx, By and Bz; now you have two 2D arrays for each components of B field > vectors after rotation; > > > > >> > > > > >> 3. Use quiver function in matplotlib and plot the B field vectors > after rotation, see: > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver > _demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>>>> > > > > >> > > > > >> Hope this helps! Perhaps there?s an easier way that I do not > know... > > > > >> > > > > >> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>>> > > > > >>> On Apr 21, 2016, at 10:31 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>>> wrote: > > > > >>> > > > > >>> Dear yt: > > > > >>> > > > > >>> I am having trouble with the camera option on yt. > > > > >>> > > > > >>> The google drive link is > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc > <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>>> > > > > >>> > > > > >>> I want to change the view of the camera at an angle after the > Slice (x-z plane) and Quiver option. > > > > >>> > > > > >>> My script is yt_cam_rot.py. Without the camera options I get the > desired plot (UniformGridData_Slice.png) but when I use the camera I get a > empty screen. I am not sure where I am going wrong. > > > > >>> > > > > >>> I am using these links for my reference > > > > >>> > > > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > <http > :// > yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-ca…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>>> > > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>>> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>> > <http://yt-project.org/doc/visualiz > ing/volume_rendering.html#volume-rendering < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > >>>> > > > > >>> > > > > >>> Thanks in advance > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>>> wrote: > > > > >>> Dear Suoqing JI: > > > > >>> > > > > >>> Thank you > > > > >>> > > > > >>> On Fri, Apr 15, 2016 at 12:59 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>>> wrote: > > > > >>> Send yt-users mailing list submissions to > > > > >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org <h > ttp://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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Camera Options (Suoqing Ji) > > > > >>> > > > > >>> > > > > >>> > ---------------------------------------------------------------------- > > > > >>> > > > > >>> Message: 1 > > > > >>> Date: Fri, 15 Apr 2016 10:59:22 -0700 > > > > >>> From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>>> > > > > >>> Subject: Re: [yt-users] Camera Options > > > > >>> Message-ID: < > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D > 8FCEAA1366(a)physics.ucsb.edu>>>>> > > > > >>> Content-Type: text/plain; charset="utf-8" > > > > >>> > > > > >>> Hi Sushi, > > > > >>> > > > > >>> I think the off-axis slice/projection plot will meet your > requirement best, where the camera orientation is determined by the normal > vector: > > > > >>> > > > > >>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices > <http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.h > tml#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.htm < > http://yt-project.org/doc/visualizing/plots.htm > > > > l#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>>> > > > > >>> > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > <http://yt-project.org/doc/visualizing/plots.html#off-axis- > projection-plots < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > <http://yt-project.org/doc/visualizin > <http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>

1 0

Camera/Off Axis Options
by Sushilkumar 28 Apr '16

28 Apr '16

Dear Suoqing Ji: I was able to implement the off axis using velocity field (drive link below). My script yt_velocity_fields.py plots for a normal vector (L=0,1,0) in the x-z plane (figure L010.png) which is correct. But for an azimuth angle of say 45 degrees (L=1,0,1) it gives me a plot L101.png which is not what I am looking for. I would like to view the same plot L010.png but at an azimuth of 45 degrees (in the x-z plane). Could you let me know if there is any error in my script or any suggestion for the same? PS: While running the script I do get a runtime warning which is below Thanks in advance Drive link: https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc Runtime Warning:- yt : [WARNING ] 2016-04-27 18:42:52,889 Plot image for field ('gas', 'velocity_y') has both positive and negative values. Min = -0.016403, Max = 0.016403. yt : [WARNING ] 2016-04-27 18:42:52,890 Switching to symlog colorbar scaling unless linear scaling is specified later /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1115: RuntimeWarning: invalid value encountered in greater masked = np.abs(a) > self.linthresh /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:1127: RuntimeWarning: invalid value encountered in greater masked = np.abs(a) > (self.linthresh * self._linscale_adj) /state/partition1/anaconda/lib/python2.7/site-packages/numpy/ma/core.py:809: RuntimeWarning: invalid value encountered in greater_equal return umath.absolute(a) * self.tolerance >= umath.absolute(b) /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: RuntimeWarning: invalid value encountered in less_equal b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py:600: RuntimeWarning: invalid value encountered in greater_equal b = b[(b <= intv[1] + eps) & (b >= intv[0] - eps)] yt : [WARNING ] 2016-04-27 18:42:53,336 Plot image for field ('gas', 'velocity_z') has both positive and negative values. Min = -0.071274, Max = 0.012600. yt : [WARNING ] 2016-04-27 18:42:53,336 Switching to symlog colorbar scaling unless linear scaling is specified later yt : [WARNING ] 2016-04-27 18:42:53,896 Plot image for field ('gas', 'velocity_x') has both positive and negative values. Min = -0.000971, Max = 0.047361. yt : [WARNING ] 2016-04-27 18:42:53,896 Switching to symlog colorbar scaling unless linear scaling is specified later yt : [INFO ] 2016-04-27 18:42:54,742 Saving plot UniformGridData_OffAxisSlice_velocity_y.png /state/partition1/anaconda/lib/python2.7/site-packages/matplotlib/colors.py:581: RuntimeWarning: invalid value encountered in less cbook._putmask(xa, xa < 0.0, -1) yt : [INFO ] 2016-04-27 18:42:55,407 Saving plot UniformGridData_OffAxisSlice_velocity_z.png yt : [INFO ] 2016-04-27 18:42:56,004 Saving plot UniformGridData_OffAxisSlice_velocity_x.png On Tue, Apr 26, 2016 at 2:32 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: Camera/Off axis Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 26 Apr 2016 12:32:46 -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] Camera/Off axis Options > Message-ID: <9C1BAC66-15F1-4488-BC94-DCB9CBF0E5D8(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushil, > > Thanks for reporting this! I?ve filed an issue here: > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > < > https://bitbucket.org/yt_analysis/yt/issues/1213/annotate_magnetic_field-fa… > > > > In the meanwhile, you could temporarily circumvent this problem by loading > your dataset as velocity field and use ?annotate_velocity?... > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Apr 26, 2016, at 6:31 AM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji: > > > > I was able to implement the off axis in my script (drive link below, > file is yt_magnetic_fields.py). But there seems to be a problem. For any > off axis value like (1,1,0) I get an error which is given below. > > > > I am trying to get a z-x plane and view it at an angle of 15,45,60 > degrees respectively. It works for along the axis normal vector like > (1,0,0) and so on but for off axis value it gives me the error. > > > > Could you let me know if there is any error in the script or ways to > overcome it? > > > > Thanks in advance > > > > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > > > > > > > Error: > > > > Traceback (most recent call last): > > File "yt_magnetic_fields.py", line 39, 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 837, in __call__ > > 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', > 'cutting_plane_bx')' in UniformGridData > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:46 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: Camera Options (Suoqing Ji) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 21 Apr 2016 13:45:53 -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] Camera Options > > Message-ID: <AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu > <mailto:AAE382DD-ADD2-4D85-BB1E-150B49CFBA40@physics.ucsb.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Sushi, > > > > What you need to do this to make use of off-axis slice plot instead of > camera; for example, in your code: > > > > L = [1, 0, 0] # View along x axis > > north_vector = [0, 0, 1] > > slc = yt.SlicePlot(pf, L, ?magnetic_field_x", width=(100,'km?), > north_vector=north_vector) > > slc.annotate_magnetic_field(factor=40, normalize=True) > > > > which gives you the view along x axis. And if you want to rotate the > viewing angle by, say 45 degree, you could change the normal vector L to be > L = [1, 1, 0], and redo the plotting. > > > > Also, when you load the data, you probably need to change the name > ?field_x? to be ?magnetic_field_x? and so on, so the > annotate_magnetic_field function will recognize these names. > > > > 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 Apr 21, 2016, at 1:28 PM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > > > > > > Dear Suoqing Ji: > > > > > > The fields Bx,By and Bz are already calculated taking into account the > rotation. So I am not sure if I need to calculate it again. > > > > > > What I would like is only change the camera view to a desired angle > after I do a slice plot and that is where I am having trouble with? > > > > > > Thanks in advance. > > > > > > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:20 PM, <yt-users-request(a)lists.spacepope.org > <mailto:yt-users-request@lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> wrote: > > > Send yt-users mailing list submissions to > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: Camera Options (Suoqing Ji) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Thu, 21 Apr 2016 13:20:32 -0700 > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > > > Subject: Re: [yt-users] Camera Options > > > Message-ID: <FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu > <mailto:FB001F5B-2521-4705-8D31-3166451BCA58@physics.ucsb.edu> <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu <mailto: > FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu>>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > I see ? that?s a smart way of doing this! > > > > > > Best wishes, > > > Suoqing > > > > > > > On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum <nathan12343(a)gmail.com > <mailto:nathan12343@gmail.com> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com>>> wrote: > > > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>> wrote: > > > > Hi Nathan, > > > > > > > > I do not have a 3D MHD data at hand, but I?ve tried one with > slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following > error: > > > > > > > > File "off_axis.py", line 49, in <module> > > > > slc.save(pf.basename) > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 76, in newfunc > > > > args[0].run_callbacks() > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1029, in run_callbacks > > > > sys.exc_info()[2]) > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1025, in run_callbacks > > > > callback(cbw) > > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 352, in __call__ > > > > (xi, yi) = (ds.coordinates.x_axis[ax], > > > > yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver > callback failed with the following error: 4 > > > > > > > > > > > > Right, I bet it will work if you do `annotate_velocity()` though. > > > > > > > > You should take a look at the definition of the VelocityCallback to > see how it handles off-axis slices. > > > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>> > > > >> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum < > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com> <mailto: > nathan12343(a)gmail.com <mailto:nathan12343@gmail.com>>>> wrote: > > > >> > > > >> > > > >> > > > >> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji < > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu> <mailto: > suoqing(a)physics.ucsb.edu <mailto:suoqing@physics.ucsb.edu>>>> wrote: > > > >> Hi Sushi, > > > >> > > > >> The quiver/streamline option you?ve used works for 2d plotting but > not for volume rendering, so I might suggest to use off-axis slice plot: > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> > > > >> > > > >> Unfortunately, quiver/streamline does not work (and/or does not > work correctly) for off axis slice plot now, but your goal is still > achievable via the following steps: > > > >> > > > >> Are you sure about that? There's a `CuttingQuiverCallback` for > off-axis slices. If you do `annotate_magnetic_fields`, it will > automatically choose the `CuttingQuiverCallback` for off-axis slices. > > > >> > > > >> > > > >> 1. Use fixed resolution buffer to get the off-axis sliced field > values including Bx, By and Bz (see this as an example, and replace > SlicePlot with OffAxisSlicePlot: > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > <http://yt-project.org/docs/dev/cookbook/complex_plots.html?highl > ight=fixedresolutionbuffer#multi-plot-slice-and-projections < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>>), > then you get a 2D array for each field; > > > >> > > > >> 2. Compute the magnetic field vectors projected onto the rotated > viewing plane (perpendicular to your normal vector), based on field values > of Bx, By and Bz; now you have two 2D arrays for each components of B field > vectors after rotation; > > > >> > > > >> 3. Use quiver function in matplotlib and plot the B field vectors > after rotation, see: > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>>> > > > >> > > > >> Hope this helps! Perhaps there?s an easier way that I do not know... > > > >> > > > >> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>> > > > >>> On Apr 21, 2016, at 10:31 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>> wrote: > > > >>> > > > >>> Dear yt: > > > >>> > > > >>> I am having trouble with the camera option on yt. > > > >>> > > > >>> The google drive link is > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>> > > > >>> > > > >>> I want to change the view of the camera at an angle after the > Slice (x-z plane) and Quiver option. > > > >>> > > > >>> My script is yt_cam_rot.py. Without the camera options I get the > desired plot (UniformGridData_Slice.png) but when I use the camera I get a > empty screen. I am not sure where I am going wrong. > > > >>> > > > >>> I am using these links for my reference > > > >>> > > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>> > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering>> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > >>> > > > >>> > > > >>> Thanks in advance > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> > > > >>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>> wrote: > > > >>> Dear Suoqing JI: > > > >>> > > > >>> Thank you > > > >>> > > > >>> On Fri, Apr 15, 2016 at 12:59 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> wrote: > > > >>> Send yt-users mailing list submissions to > > > >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Camera Options (Suoqing Ji) > > > >>> > > > >>> > > > >>> > ---------------------------------------------------------------------- > > > >>> > > > >>> Message: 1 > > > >>> Date: Fri, 15 Apr 2016 10:59:22 -0700 > > > >>> From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> <mailto:suoqing@physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > > >>> Subject: Re: [yt-users] Camera Options > > > >>> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu > <mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366@physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>>>> > > > >>> Content-Type: text/plain; charset="utf-8" > > > >>> > > > >>> Hi Sushi, > > > >>> > > > >>> I think the off-axis slice/projection plot will meet your > requirement best, where the camera orientation is determined by the normal > vector: > > > >>> > > > >>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.htm > l#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>>> > > > >>> > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > <http://yt-project.org/doc/visualizing/plots.html#off-axis-pr > ojection-plots < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > >>>> > > > >>> > > > >>> And of course, if you?re interested in the features provided by > volume rendering, it?s also worth a try. This cookbook gives an example of > moving a camera; specifically you might want to use the camera.rotation: > > > >>> > > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > <http:/ > / > yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rendering-ca…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>>> > > > >>> > > > >>> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing>> > <http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >>> > > > >>> > > > >>> > On Apr 15, 2016, at 8:38 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>> wrote: > > > >>> > > > > >>> > Dear yt: > > > >>> > > > > >>> > I would like to change/customize/rotate my camera angle for my > slice plots without rotating the axis. > > > >>> > > > > >>> > What options do I have using yt if I want to move my camera > angle by say 45 degrees? > > > >>> > > > > >>> > Can I use the following link or can you suggest me something else > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering > .html>>>> > > > >>> > > > > >>> > Thanks in advance > > > > -------------- 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 98, Issue 35 > **************************************** > -- *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.**"*

2 1

Changing font size and tick size in Profile plot
by nty＠MPA-Garching.MPG.DE 27 Apr '16

27 Apr '16

Hi all, I am trying to create a Profile plot, and the label fontsize and tick size seems to be rather small. Please let me know how this can be increased. Thanks Nitya

3 2

Re: [yt-users] problems with grid related values from an frb
by Slavin, Jonathan 27 Apr '16

27 Apr '16

Hi Matthew, Thanks for the response. None of "px", "pdx", "py", and "pdy" work for me. I perused the code a bit and it's not entirely clear why they don't. The data_source for the frb in my case is a slice, as I showed and that slice object does apparently have those fields defined -- for example doing px = slc['px'] works, though of course the result is a 1D array of values. It seems to be related to the _determine_fields method of the data_source (slice) which rather than returning a tuple, in this case returns a string. In any case, I don't really have time right now to look into it any further. Jon On Tue, Apr 26, 2016 at 1:53 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Hi Jon, > > This is expected behavior, but it probably isn't what you're looking > for. dx and dr will be the "pixelized" values of those from the > simulation, so they will reflect the cells that went into creating the > FRB, rather than the values as they would be computed in the FRB > itself. I think what you may be looking for may be accessible in the > "px" "pdx" "py" and "pdy" fields, which refer to "in the pixel plane" > and which will be with respect to the FRB. > -- ________________________________________________________ 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

Camera/Off axis Options
by Sushilkumar 26 Apr '16

26 Apr '16

Dear Suoqing Ji: I was able to implement the off axis in my script (drive link below, file is yt_magnetic_fields.py). But there seems to be a problem. For any off axis value like (1,1,0) I get an error which is given below. I am trying to get a z-x plane and view it at an angle of 15,45,60 degrees respectively. It works for along the axis normal vector like (1,0,0) and so on but for off axis value it gives me the error. Could you let me know if there is any error in the script or ways to overcome it? Thanks in advance https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc Error: Traceback (most recent call last): File "yt_magnetic_fields.py", line 39, 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 837, in __call__ 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', 'cutting_plane_bx')' in UniformGridData On Thu, Apr 21, 2016 at 3:46 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: Camera Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Apr 2016 13:45:53 -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] Camera Options > Message-ID: <AAE382DD-ADD2-4D85-BB1E-150B49CFBA40(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushi, > > What you need to do this to make use of off-axis slice plot instead of > camera; for example, in your code: > > L = [1, 0, 0] # View along x axis > north_vector = [0, 0, 1] > slc = yt.SlicePlot(pf, L, ?magnetic_field_x", width=(100,'km?), > north_vector=north_vector) > slc.annotate_magnetic_field(factor=40, normalize=True) > > which gives you the view along x axis. And if you want to rotate the > viewing angle by, say 45 degree, you could change the normal vector L to be > L = [1, 1, 0], and redo the plotting. > > Also, when you load the data, you probably need to change the name > ?field_x? to be ?magnetic_field_x? and so on, so the > annotate_magnetic_field function will recognize these names. > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Apr 21, 2016, at 1:28 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji: > > > > The fields Bx,By and Bz are already calculated taking into account the > rotation. So I am not sure if I need to calculate it again. > > > > What I would like is only change the camera view to a desired angle > after I do a slice plot and that is where I am having trouble with? > > > > Thanks in advance. > > > > > > > > > > > > > > On Thu, Apr 21, 2016 at 3:20 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: Camera Options (Suoqing Ji) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 21 Apr 2016 13:20:32 -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] Camera Options > > Message-ID: <FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu > <mailto:FB001F5B-2521-4705-8D31-3166451BCA58@physics.ucsb.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > I see ? that?s a smart way of doing this! > > > > Best wishes, > > Suoqing > > > > > On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum <nathan12343(a)gmail.com > <mailto:nathan12343@gmail.com>> wrote: > > > > > > > > > > > > On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji <suoqing(a)physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu>>> wrote: > > > Hi Nathan, > > > > > > I do not have a 3D MHD data at hand, but I?ve tried one with > slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following > error: > > > > > > File "off_axis.py", line 49, in <module> > > > slc.save(pf.basename) > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 76, in newfunc > > > args[0].run_callbacks() > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1029, in run_callbacks > > > sys.exc_info()[2]) > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1025, in run_callbacks > > > callback(cbw) > > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 352, in __call__ > > > (xi, yi) = (ds.coordinates.x_axis[ax], > > > yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver callback > failed with the following error: 4 > > > > > > > > > Right, I bet it will work if you do `annotate_velocity()` though. > > > > > > You should take a look at the definition of the VelocityCallback to > see how it handles off-axis slices. > > > > > > 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > >> On Apr 21, 2016, at 12:35 PM, Nathan Goldbaum <nathan12343(a)gmail.com > <mailto:nathan12343@gmail.com> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com>>> wrote: > > >> > > >> > > >> > > >> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji <suoqing(a)physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu> <mailto:suoqing@physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu>>> wrote: > > >> Hi Sushi, > > >> > > >> The quiver/streamline option you?ve used works for 2d plotting but > not for volume rendering, so I might suggest to use off-axis slice plot: > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> > > >> > > >> Unfortunately, quiver/streamline does not work (and/or does not work > correctly) for off axis slice plot now, but your goal is still achievable > via the following steps: > > >> > > >> Are you sure about that? There's a `CuttingQuiverCallback` for > off-axis slices. If you do `annotate_magnetic_fields`, it will > automatically choose the `CuttingQuiverCallback` for off-axis slices. > > >> > > >> > > >> 1. Use fixed resolution buffer to get the off-axis sliced field > values including Bx, By and Bz (see this as an example, and replace > SlicePlot with OffAxisSlicePlot: > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…> > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>>), > then you get a 2D array for each field; > > >> > > >> 2. Compute the magnetic field vectors projected onto the rotated > viewing plane (perpendicular to your normal vector), based on field values > of Bx, By and Bz; now you have two 2D arrays for each components of B field > vectors after rotation; > > >> > > >> 3. Use quiver function in matplotlib and plot the B field vectors > after rotation, see: > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html>> > > >> > > >> Hope this helps! Perhaps there?s an easier way that I do not know... > > >> > > >> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > >>> On Apr 21, 2016, at 10:31 AM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com> <mailto:sushil.sush19us@gmail.com > <mailto:sushil.sush19us@gmail.com>>> wrote: > > >>> > > >>> Dear yt: > > >>> > > >>> I am having trouble with the camera option on yt. > > >>> > > >>> The google drive link is > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> > > >>> > > >>> I want to change the view of the camera at an angle after the Slice > (x-z plane) and Quiver option. > > >>> > > >>> My script is yt_cam_rot.py. Without the camera options I get the > desired plot (UniformGridData_Slice.png) but when I use the camera I get a > empty screen. I am not sure where I am going wrong. > > >>> > > >>> I am using these links for my reference > > >>> > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >> > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering> > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > >> > > >>> > > >>> Thanks in advance > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> > > >>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> wrote: > > >>> Dear Suoqing JI: > > >>> > > >>> Thank you > > >>> > > >>> On Fri, Apr 15, 2016 at 12:59 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> wrote: > > >>> Send yt-users mailing list submissions to > > >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: Camera Options (Suoqing Ji) > > >>> > > >>> > > >>> > ---------------------------------------------------------------------- > > >>> > > >>> Message: 1 > > >>> Date: Fri, 15 Apr 2016 10:59:22 -0700 > > >>> From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <mailto:suoqing@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> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > > >>> Subject: Re: [yt-users] Camera Options > > >>> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu > <mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366@physics.ucsb.edu> <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu <mailto: > B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu>>> > > >>> Content-Type: text/plain; charset="utf-8" > > >>> > > >>> Hi Sushi, > > >>> > > >>> I think the off-axis slice/projection plot will meet your > requirement best, where the camera orientation is determined by the normal > vector: > > >>> > > >>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>>> > > >>> > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots>> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > >>> > > >>> > > >>> And of course, if you?re interested in the features provided by > volume rendering, it?s also worth a try. This cookbook gives an example of > moving a camera; specifically you might want to use the camera.rotation: > > >>> > > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…>> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >>> > > >>> > > >>> 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> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > >>> > > >>> > On Apr 15, 2016, at 8:38 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> wrote: > > >>> > > > >>> > Dear yt: > > >>> > > > >>> > I would like to change/customize/rotate my camera angle for my > slice plots without rotating the axis. > > >>> > > > >>> > What options do I have using yt if I want to move my camera angle > by say 45 degrees? > > >>> > > > >>> > Can I use the following link or can you suggest me something else > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>>> > > >>> > > > >>> > Thanks in advance > > >>> > > > >>> > > > >>> > > > >>> > On Thu, Mar 31, 2016 at 10:11 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> wrote: > > >>> > Send yt-users mailing list submissions to > > >>> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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. Inclination problem (Sushilkumar) > > >>> > > > >>> > > > >>> > > ---------------------------------------------------------------------- > > >>> > > > >>> > Message: 1 > > >>> > Date: Thu, 31 Mar 2016 22:11:09 -0500 > > >>> > From: Sushilkumar <sushil.sush19us(a)gmail.com <mailto: > sushil.sush19us(a)gmail.com> <mailto:sushil.sush19us@gmail.com <mailto: > sushil.sush19us(a)gmail.com>> <mailto:sushil.sush19us@gmail.com <mailto: > sushil.sush19us(a)gmail.com> <mailto:sushil.sush19us@gmail.com <mailto: > sushil.sush19us(a)gmail.com>>>> > > >>> > To: Discussion of the yt analysis package > > >>> > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > Subject: [yt-users] Inclination problem > > >>> > Message-ID: > > >>> > < > CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com> > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > >><mailto: > CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com> > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > >>>> > > >>> > Content-Type: text/plain; charset="utf-8" > > >>> > > > >>> > Dear Nathan: > > >>> > > > >>> > Thank you very much, implementing now > > >>> > > > >>> > > > >>> > On Thu, Mar 31, 2016 at 9:50 AM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> > > >>> > wrote: > > >>> > > > >>> > > Send yt-users mailing list submissions to > > >>> > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: Inclination problem (Nathan Goldbaum) > > >>> > > > > >>> > > > > >>> > > > ---------------------------------------------------------------------- > > >>> > > > > >>> > > Message: 1 > > >>> > > Date: Thu, 31 Mar 2016 09:50:31 -0500 > > >>> > > From: Nathan Goldbaum <nathan12343(a)gmail.com <mailto: > nathan12343(a)gmail.com> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com>> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com>>>> > > >>> > > To: Discussion of the yt analysis package > > >>> > > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > Subject: Re: [yt-users] Inclination problem > > >>> > > Message-ID: > > >>> > > <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu= > > >>> > > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com> <mailto: > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com>> <mailto: > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com> <mailto: > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com>>>> > > >>> > > Content-Type: text/plain; charset="utf-8" > > >>> > > > > >>> > > Hi SK, > > >>> > > > > >>> > > I'm going to reference this example: > > >>> > > > > >>> > > > > >>> > > > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines> > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines>> > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines> > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > >>> > > >>> > > > > >>> > > specifically this snippet: > > >>> > > > > >>> > > for stream in streamlines.streamlines: > > >>> > > stream = stream[np.all(stream != 0.0, axis=1)] > > >>> > > ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1) > > >>> > > > > >>> > > Here, the 'stream' object is just a Nx3 numpy array, where N is > the number > > >>> > > of points sampled along the streamline. So each row of the numpy > array is > > >>> > > just the coordinates of the streamline along one direction. > > >>> > > > > >>> > > To answer your question, no, there's nothing in yt that will > rotate the > > >>> > > streamlines into a new coordinate system. Fortunately you should > be able to > > >>> > > do it yourself using e.g. an Euler angle rotation matrix. You > will need to > > >>> > > identify the new coordinate system you would like to transform > to, > > >>> > > calculate a 3D rotation matrix, then apply it using matrix > multiplication > > >>> > > (e.g. np.dot, which supports broadcasting) to each coordinate > along the > > >>> > > streamline. > > >>> > > > > >>> > > Hope that helps, > > >>> > > > > >>> > > Nathan > > >>> > > > > >>> > > On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>>> > > >>> > > wrote: > > >>> > > > > >>> > > > Dear Matt: > > >>> > > > > > >>> > > > Pleas correct me if I am wrong but "off axis slices" takes > slices of the > > >>> > > > plot that is already plotted. > > >>> > > > > > >>> > > > However, I would like to plot my data in a new coordinate frame > > >>> > > (x`,y`,z`) > > >>> > > > which is inclined at an angle of say alpha from the default > (x,y,z) > > >>> > > frame. > > >>> > > > > > >>> > > > Or I would like to plot my data in a rotated frame (x`,y`,z`), > which is > > >>> > > > rotated at an angle of alpha from (x,y,z). > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > On Wed, Mar 30, 2016 at 5:01 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>>> > > >>> > > > wrote: > > >>> > > > > > >>> > > >> Send yt-users mailing list submissions to > > >>> > > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: load spherical polar coordinate data with mesh > refinement > > >>> > > >> in HDF5 (Jiang, Yanfei) > > >>> > > >> 2. Re: load spherical polar coordinate data with mesh > refinement > > >>> > > >> in HDF5 (Matthew Turk) > > >>> > > >> 3. Re: Inclination problem (Matthew Turk) > > >>> > > >> 4. Re: load spherical polar coordinate data with mesh > refinement > > >>> > > >> in HDF5 (Jonah Miller) > > >>> > > >> > > >>> > > >> > > >>> > > >> > ---------------------------------------------------------------------- > > >>> > > >> > > >>> > > >> Message: 1 > > >>> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400 > > >>> > > >> From: "Jiang, Yanfei" <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu > >>>> > > >>> > > >> To: Discussion of the yt analysis package > > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > > >>> > > >> refinement in HDF5 > > >>> > > >> Message-ID: > > >>> > > >> < > > >>> > > >> > CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com> > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com>> > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com> > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%25252B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > >>>> > > >>> > > >> Content-Type: text/plain; charset="utf-8" > > >>> > > >> > > >>> > > >> Hi Jonah, > > >>> > > >> > > >>> > > >> I am able to load the data to yt now using > load_amr_grids(). I notice > > >>> > > >> that it can also set geometry to spherical. This is great. > But to make > > >>> > > >> life > > >>> > > >> more complicate. Is it possible to let yt know that the grid > is > > >>> > > >> logarithmic? Currently, load_amr_grids() just take left and > right edges > > >>> > > of > > >>> > > >> each block. I guess yt assumes the grid is uniform between > left and > > >>> > > right > > >>> > > >> edges. Is it possible to provide arrays of coordinate values > for each > > >>> > > cell > > >>> > > >> in each block? > > >>> > > >> > > >>> > > >> Thanks. > > >>> > > >> > > >>> > > >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller < > > >>> > > >> jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>> <mailto: > jonah.maxwell.miller(a)gmail.com <mailto:jonah.maxwell.miller@gmail.com> > <mailto:jonah.maxwell.miller@gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com>>>> wrote: > > >>> > > >> > > >>> > > >> > Hi Yan-Feng, > > >>> > > >> > > > >>> > > >> > I haven't tried it, but I think there is functionality for > this. You > > >>> > > can > > >>> > > >> > use the load_amr_grids() function which can load amr data in > > >>> > > Cartesian, > > >>> > > >> > spherical, or polar coordinates. Here's the documentation: > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…>> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >>> > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…>> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > <http://yt-project.org/doc/re > ference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >>> > > >>> > > >> > > > >>> > > >> > Best, > > >>> > > >> > Jonah > > >>> > > >> > > > >>> > > >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu > >>>> > > >>> > > >> > wrote: > > >>> > > >> > > > >>> > > >> >> Hi, > > >>> > > >> >> I have some data from a new version of Athena > simulations. > > >>> > > It > > >>> > > >> is > > >>> > > >> >> in spherical polar coordinate with mesh refinement written > in HDF5. > > >>> > > The > > >>> > > >> >> data structure is similar to flash data but not the same. > Does anyone > > >>> > > >> have > > >>> > > >> >> suggestions to load such data to yt directly? > > >>> > > >> >> > > >>> > > >> >> Thank you. > > >>> > > >> >> -- > > >>> > > >> >> Yan-Fei Jiang > > >>> > > >> >> > > >>> > > >> >> Einstein Fellow > > >>> > > >> >> Harvard-Smithsonian Center for Astrophysics > > >>> > > >> >> 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> >> _______________________________________________ > > >>> > > >> >> yt-users mailing list > > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > >>> > > >> > > > >>> > > >> > _______________________________________________ > > >>> > > >> > yt-users mailing list > > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > >>> > > >> > > >>> > > >> -- > > >>> > > >> Yan-Fei Jiang > > >>> > > >> > > >>> > > >> Einstein Fellow > > >>> > > >> Harvard-Smithsonian Center for Astrophysics > > >>> > > >> 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> -------------- 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…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>> > > >>> > > >> > > > >>> > > >> > > >>> > > >> ------------------------------ > > >>> > > >> > > >>> > > >> Message: 2 > > >>> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500 > > >>> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>>> > > >>> > > >> To: Discussion of the yt analysis package > > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > > >>> > > >> refinement in HDF5 > > >>> > > >> Message-ID: > > >>> > > >> <CALO3= > > >>> > > >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA(a)mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com> > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com>> > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com> > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com>>>> > > >>> > > >> Content-Type: text/plain; charset=UTF-8 > > >>> > > >> > > >>> > > >> Hi Yanfei, > > >>> > > >> > > >>> > > >> This is possible -- but it will also slow some things down. > You can > > >>> > > >> use the load_hexahedral_mesh function, and there're examples > of this. > > >>> > > >> This takes away some of the optimizations that regular grids > can do, > > >>> > > >> but we're hoping to add them back in shortly. Like the other > > >>> > > >> functions it too takes a geometry argument. > > >>> > > >> > > >>> > > >> -Matt > > >>> > > >> > > >>> > > >> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei > > >>> > > >> <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu>>>> > wrote: > > >>> > > >> > Hi Jonah, > > >>> > > >> > > > >>> > > >> > I am able to load the data to yt now using > load_amr_grids(). I > > >>> > > notice > > >>> > > >> > that it can also set geometry to spherical. This is great. > But to make > > >>> > > >> life > > >>> > > >> > more complicate. Is it possible to let yt know that the > grid is > > >>> > > >> logarithmic? > > >>> > > >> > Currently, load_amr_grids() just take left and right edges > of each > > >>> > > >> block. I > > >>> > > >> > guess yt assumes the grid is uniform between left and right > edges. Is > > >>> > > it > > >>> > > >> > possible to provide arrays of coordinate values for each > cell in each > > >>> > > >> block? > > >>> > > >> > > > >>> > > >> > Thanks. > > >>> > > >> > > > >>> > > >> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > > >>> > > >> > <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>> <mailto: > jonah.maxwell.miller(a)gmail.com <mailto:jonah.maxwell.miller@gmail.com> > <mailto:jonah.maxwell.miller@gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com>>>> wrote: > > >>> > > >> >> > > >>> > > >> >> Hi Yan-Feng, > > >>> > > >> >> > > >>> > > >> >> I haven't tried it, but I think there is functionality for > this. You > > >>> > > >> can > > >>> > > >> >> use the load_amr_grids() function which can load amr data > in > > >>> > > Cartesian, > > >>> > > >> >> spherical, or polar coordinates. Here's the documentation: > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…>> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >>> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…>> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > <http://yt-project.org/doc/re > ference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >>> > > >>> > > >> >> > > >>> > > >> >> Best, > > >>> > > >> >> Jonah > > >>> > > >> >> > > >>> > > >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu > >>>> > > >>> > > >> >> wrote: > > >>> > > >> >>> > > >>> > > >> >>> Hi, > > >>> > > >> >>> I have some data from a new version of Athena > simulations. > > >>> > > >> It is > > >>> > > >> >>> in spherical polar coordinate with mesh refinement > written in HDF5. > > >>> > > >> The data > > >>> > > >> >>> structure is similar to flash data but not the same. Does > anyone > > >>> > > have > > >>> > > >> >>> suggestions to load such data to yt directly? > > >>> > > >> >>> > > >>> > > >> >>> Thank you. > > >>> > > >> >>> -- > > >>> > > >> >>> Yan-Fei Jiang > > >>> > > >> >>> > > >>> > > >> >>> Einstein Fellow > > >>> > > >> >>> Harvard-Smithsonian Center for Astrophysics > > >>> > > >> >>> 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> >>> _______________________________________________ > > >>> > > >> >>> yt-users mailing list > > >>> > > >> >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> _______________________________________________ > > >>> > > >> >> yt-users mailing list > > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > -- > > >>> > > >> > Yan-Fei Jiang > > >>> > > >> > > > >>> > > >> > Einstein Fellow > > >>> > > >> > Harvard-Smithsonian Center for Astrophysics > > >>> > > >> > 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> > > > >>> > > >> > _______________________________________________ > > >>> > > >> > yt-users mailing list > > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> > > > >>> > > >> > > >>> > > >> > > >>> > > >> ------------------------------ > > >>> > > >> > > >>> > > >> Message: 3 > > >>> > > >> Date: Wed, 30 Mar 2016 16:16:22 -0500 > > >>> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>>> > > >>> > > >> To: Discussion of the yt analysis package > > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > >> Subject: Re: [yt-users] Inclination problem > > >>> > > >> Message-ID: > > >>> > > >> <CALO3=5HMB= > > >>> > > >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com > <mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com> > <mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com <mailto: > joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com>><mailto: > joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com <mailto: > joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com> <mailto: > joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com <mailto: > joejr6BBh%25252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com>>>> > > >>> > > >> Content-Type: text/plain; charset=UTF-8 > > >>> > > >> > > >>> > > >> Hi SK, > > >>> > > >> > > >>> > > >> I'm not sure I totally understand, but if you have an > inclination > > >>> > > >> angle you can use this directly in yt in the off axis slices > and so > > >>> > > >> on. They typically take a vector, but you should be able to > convert > > >>> > > >> one to the other. > > >>> > > >> > > >>> > > >> -Matt > > >>> > > >> > > >>> > > >> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>><mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> > > >>> > > > > > >>> > > >> wrote: > > >>> > > >> > Dear yt: > > >>> > > >> > > > >>> > > >> > I am trying to numerically solve the region around a > pulsar. Now since > > >>> > > >> > pulsar is an inclined rotator with inclination angle > between rotation > > >>> > > >> axis > > >>> > > >> > and dipole axis I would like to include in my yt script. > > >>> > > >> > > > >>> > > >> > My original code written in FORTRAN incorporated this > inclination but > > >>> > > >> how > > >>> > > >> > would I incorporate it into my visualization using yt > without changing > > >>> > > >> my > > >>> > > >> > data. > > >>> > > >> > > > >>> > > >> > Could you suggest ways for the same? > > >>> > > >> > > > >>> > > >> > The google drive link to my script (streamline.py) and > streamline plot > > >>> > > >> > (streamline_t000.png) is included > > >>> > > >> > > > >>> > > >> > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>>> > > >>> > > >> > > > >>> > > >> > Thanks in advance > > >>> > > >> > > > >>> > > >> > On Tue, Mar 29, 2016 at 12:54 PM, < > > >>> > > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> > > >>> > > >> > > > >>> > > >> > wrote: > > >>> > > >> >> > > >>> > > >> >> Send yt-users mailing list submissions to > > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > 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> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > 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> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org>> <mailto: > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> <mailto: > 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: gadget onto unigrid (Carla Bernhardt) > > >>> > > >> >> 2. Re: gadget onto unigrid (Matthew Turk) > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > > ---------------------------------------------------------------------- > > >>> > > >> >> > > >>> > > >> >> Message: 1 > > >>> > > >> >> Date: Tue, 29 Mar 2016 15:55:27 +0200 > > >>> > > >> >> From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com > <mailto:carla.j.bernhardt@gmail.com> <mailto:carla.j.bernhardt@gmail.com > <mailto:carla.j.bernhardt@gmail.com>> <mailto:carla.j.bernhardt@gmail.com > <mailto:carla.j.bernhardt@gmail.com> <mailto:carla.j.bernhardt@gmail.com > <mailto:carla.j.bernhardt@gmail.com>>>> > > >>> > > >> >> To: Discussion of the yt analysis package > > >>> > > >> >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid > > >>> > > >> >> Message-ID: > > >>> > > >> >> > > >>> > > >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF= > UhyGS_beuiUMbw7Ag(a)mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com> > <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com <mailto: > UhyGS_beuiUMbw7Ag(a)mail.gmail.com>><mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com > <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com> <mailto: > UhyGS_beuiUMbw7Ag(a)mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com > >>>> > > >>> > > >> >> Content-Type: text/plain; charset="utf-8" > > >>> > > >> >> > > >>> > > >> >> Hi All, > > >>> > > >> >> > > >>> > > >> >> A follow-up question: In using arbitrary_grid (but with > enzo data), > > >>> > > how > > >>> > > >> >> does one then extract a field of an arbitrary_grid? I tried > > >>> > > >> >> arbgrid["density"] as I have done with a > smoothed_covering_grid > > >>> > > object, > > >>> > > >> >> but > > >>> > > >> >> it does not work (here is the traceback < > > >>> > > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0> < > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>> < > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0> < > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>>>> > > >>> > > >> I > > >>> > > >> >> got). > > >>> > > >> >> > > >>> > > >> >> Thanks, > > >>> > > >> >> Carla > > >>> > > >> >> > > >>> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk < > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>>>>: > > >>> > > >> >> > > >>> > > >> >> > Hi Desika, > > >>> > > >> >> > > > >>> > > >> >> > Yup, this can be done reasonably easily using either the > > >>> > > >> >> > .arbitrary_grid object (which was designed for this) or > the > > >>> > > interface > > >>> > > >> >> > to the arbitrary grid that's in the development version, > which is > > >>> > > >> >> > ds.r[ ... ] where the ... is some combination of bounds > and steps. > > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>>> > > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > >> > > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…>> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > >>> > > >>> > > >> >> > > > >>> > > >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan > > >>> > > >> >> > <desika.narayanan(a)gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>>>> wrote: > > >>> > > >> >> > > Hi All, > > >>> > > >> >> > > > > >>> > > >> >> > > Is it possible to deposit the particles from a gadget > data set > > >>> > > >> onto a > > >>> > > >> >> > > uniform grid in yt? Or, could it be possible to trick > the octree > > >>> > > >> >> > deposition > > >>> > > >> >> > > into doing it by forcing no refinements, but some sort > of native > > >>> > > >> grid > > >>> > > >> >> > > resolution? > > >>> > > >> >> > > > > >>> > > >> >> > > thanks, > > >>> > > >> >> > > desika > > >>> > > >> >> > > > > >>> > > >> >> > > > > >>> > > >> >> > > _______________________________________________ > > >>> > > >> >> > > yt-users mailing list > > >>> > > >> >> > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > > > >>> > > >> >> > _______________________________________________ > > >>> > > >> >> > yt-users mailing list > > >>> > > >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>> > > >>> > > >> > > > >>> > > >> >> > > >>> > > >> >> ------------------------------ > > >>> > > >> >> > > >>> > > >> >> Message: 2 > > >>> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500 > > >>> > > >> >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>>> > > >>> > > >> >> To: Discussion of the yt analysis package > > >>> > > >> >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>>> > > >>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid > > >>> > > >> >> Message-ID: > > >>> > > >> >> > > >>> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR= > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com> <mailto: > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com>><mailto: > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com> <mailto: > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com>>>> > > >>> > > >> >> Content-Type: text/plain; charset=UTF-8 > > >>> > > >> >> > > >>> > > >> >> Hi Carla, > > >>> > > >> >> > > >>> > > >> >> This functionality was recently implemented and is in the > development > > >>> > > >> >> version, but not yet in the stable. We're hoping for a > release very > > >>> > > >> >> shortly, but you can also try the dev version if you'd > like! > > >>> > > >> >> > > >>> > > >> >> -Matt > > >>> > > >> >> > > >>> > > >> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt > > >>> > > >> >> <carla.j.bernhardt(a)gmail.com <mailto: > carla.j.bernhardt(a)gmail.com> <mailto:carla.j.bernhardt@gmail.com <mailto: > carla.j.bernhardt(a)gmail.com>> <mailto:carla.j.bernhardt@gmail.com <mailto: > carla.j.bernhardt(a)gmail.com> <mailto:carla.j.bernhardt@gmail.com <mailto: > carla.j.bernhardt(a)gmail.com>>>> wrote: > > >>> > > >> >> > Hi All, > > >>> > > >> >> > > > >>> > > >> >> > A follow-up question: In using arbitrary_grid (but with > enzo data), > > >>> > > >> how > > >>> > > >> >> > does > > >>> > > >> >> > one then extract a field of an arbitrary_grid? I tried > > >>> > > >> >> > arbgrid["density"] as > > >>> > > >> >> > I have done with a smoothed_covering_grid object, but it > does not > > >>> > > >> work > > >>> > > >> >> > (here > > >>> > > >> >> > is the traceback I got). > > >>> > > >> >> > > > >>> > > >> >> > Thanks, > > >>> > > >> >> > Carla > > >>> > > >> >> > > > >>> > > >> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk < > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>>>>: > > >>> > > >> >> >> > > >>> > > >> >> >> Hi Desika, > > >>> > > >> >> >> > > >>> > > >> >> >> Yup, this can be done reasonably easily using either the > > >>> > > >> >> >> .arbitrary_grid object (which was designed for this) or > the > > >>> > > >> interface > > >>> > > >> >> >> to the arbitrary grid that's in the development > version, which is > > >>> > > >> >> >> ds.r[ ... ] where the ... is some combination of bounds > and steps. > > >>> > > >> >> >> > > >>> > > >> >> >> > > >>> > > >> > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>>> > > >>> > > >> >> >> > > >>> > > >> >> >> > > >>> > > >> >> >> > > >>> > > >> > > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…>> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > >>> > > >>> > > >> >> >> > > >>> > > >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan > > >>> > > >> >> >> <desika.narayanan(a)gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>>>> wrote: > > >>> > > >> >> >> > Hi All, > > >>> > > >> >> >> > > > >>> > > >> >> >> > Is it possible to deposit the particles from a gadget > data set > > >>> > > >> onto a > > >>> > > >> >> >> > uniform grid in yt? Or, could it be possible to > trick the > > >>> > > octree > > >>> > > >> >> >> > deposition > > >>> > > >> >> >> > into doing it by forcing no refinements, but some > sort of native > > >>> > > >> grid > > >>> > > >> >> >> > resolution? > > >>> > > >> >> >> > > > >>> > > >> >> >> > thanks, > > >>> > > >> >> >> > desika > > >>> > > >> >> >> > > > >>> > > >> >> >> > > > >>> > > >> >> >> > _______________________________________________ > > >>> > > >> >> >> > yt-users mailing list > > >>> > > >> >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> >> > > > >>> > > >> >> >> _______________________________________________ > > >>> > > >> >> >> yt-users mailing list > > >>> > > >> >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > >> >> > _______________________________________________ > > >>> > > >> >> > yt-users mailing list > > >>> > > >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> ------------------------------ > > >>> > > >> >> > > >>> > > >> >> Subject: Digest Footer > > >>> > > >> >> > > >>> > > >> >> _______________________________________________ > > >>> > > >> >> yt-users mailing list > > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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 34 > > >>> > > >> >> **************************************** > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > > > >>> > > >> > -- > > >>> > > >> > 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 <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> > > > >>> > > >> > > >>> > > >> > > >>> > > >> ------------------------------ > > >>> > > >> > > >>> > > >> Message: 4 > > >>> > > >> Date: Wed, 30 Mar 2016 18:01:04 -0400 > > >>> > > >> From: Jonah Miller <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>> <mailto: > jonah.maxwell.miller(a)gmail.com <mailto:jonah.maxwell.miller@gmail.com> > <mailto:jonah.maxwell.miller@gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com>>>> > > >>> > > >> To: yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org > >>> > > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > > >>> > > >> refinement in HDF5 > > >>> > > >> Message-ID: <56FC4CA0.4030403(a)gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com> <mailto:56FC4CA0.4030403@gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com>> <mailto:56FC4CA0.4030403@gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com> <mailto:56FC4CA0.4030403@gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com>>>> > > >>> > > >> Content-Type: text/plain; charset=windows-1252; format=flowed > > >>> > > >> > > >>> > > >> Hi Yanfei, > > >>> > > >> > > >>> > > >> To add to Matt's comment. Here is the documentation for using > > >>> > > >> load_hexahedral_mesh. > > >>> > > >> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-…> > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-…>> > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-…> > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > >>> > > >>> > > >> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >>< > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >>> > > >>> > > >> > > >>> > > >> Best, > > >>> > > >> Jonah > > >>> > > >> > > >>> > > >> On 16-03-30 05:15 PM, Matthew Turk wrote: > > >>> > > >> > Hi Yanfei, > > >>> > > >> > > > >>> > > >> > This is possible -- but it will also slow some things > down. You can > > >>> > > >> > use the load_hexahedral_mesh function, and there're > examples of this. > > >>> > > >> > This takes away some of the optimizations that regular > grids can do, > > >>> > > >> > but we're hoping to add them back in shortly. Like the > other > > >>> > > >> > functions it too takes a geometry argument. > > >>> > > >> > > > >>> > > >> > -Matt > > >>> > > >> > > > >>> > > >> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei > > >>> > > >> > <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu>>>> > wrote: > > >>> > > >> >> Hi Jonah, > > >>> > > >> >> > > >>> > > >> >> I am able to load the data to yt now using > load_amr_grids(). I > > >>> > > >> notice > > >>> > > >> >> that it can also set geometry to spherical. This is great. > But to > > >>> > > make > > >>> > > >> life > > >>> > > >> >> more complicate. Is it possible to let yt know that the > grid is > > >>> > > >> logarithmic? > > >>> > > >> >> Currently, load_amr_grids() just take left and right edges > of each > > >>> > > >> block. I > > >>> > > >> >> guess yt assumes the grid is uniform between left and > right edges. Is > > >>> > > >> it > > >>> > > >> >> possible to provide arrays of coordinate values for each > cell in each > > >>> > > >> block? > > >>> > > >> >> > > >>> > > >> >> Thanks. > > >>> > > >> >> > > >>> > > >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > > >>> > > >> >> <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>> <mailto: > jonah.maxwell.miller(a)gmail.com <mailto:jonah.maxwell.miller@gmail.com> > <mailto:jonah.maxwell.miller@gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com>>>> wrote: > > >>> > > >> >>> Hi Yan-Feng, > > >>> > > >> >>> > > >>> > > >> >>> I haven't tried it, but I think there is functionality > for this. You > > >>> > > >> can > > >>> > > >> >>> use the load_amr_grids() function which can load amr data > in > > >>> > > >> Cartesian, > > >>> > > >> >>> spherical, or polar coordinates. Here's the documentation: > > >>> > > >> >>> > > >>> > > >> >>> > > >>> > > >> >>> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…>> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >>> > > >>> > > >> >>> > > >>> > > >> >>> > > >>> > > >> >>> > > >>> > > >> > > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…>> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > <http://yt-project.org/doc/re > ference/api/generated/yt.frontends.stream.data_structures.load_amr_grids.html#yt.frontends.stream.data_structures.load_amr_grids > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >>> > > >>> > > >> >>> > > >>> > > >> >>> Best, > > >>> > > >> >>> Jonah > > >>> > > >> >>> > > >>> > > >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>> <mailto: > yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu> > <mailto:yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu > >>>> > > >>> > > >> >>> wrote: > > >>> > > >> >>>> Hi, > > >>> > > >> >>>> I have some data from a new version of Athena > > >>> > > simulations. > > >>> > > >> It is > > >>> > > >> >>>> in spherical polar coordinate with mesh refinement > written in HDF5. > > >>> > > >> The data > > >>> > > >> >>>> structure is similar to flash data but not the same. > Does anyone > > >>> > > have > > >>> > > >> >>>> suggestions to load such data to yt directly? > > >>> > > >> >>>> > > >>> > > >> >>>> Thank you. > > >>> > > >> >>>> -- > > >>> > > >> >>>> Yan-Fei Jiang > > >>> > > >> >>>> > > >>> > > >> >>>> Einstein Fellow > > >>> > > >> >>>> Harvard-Smithsonian Center for Astrophysics > > >>> > > >> >>>> 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> >>>> _______________________________________________ > > >>> > > >> >>>> yt-users mailing list > > >>> > > >> >>>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >>> > > >>> > > >> >>> _______________________________________________ > > >>> > > >> >>> yt-users mailing list > > >>> > > >> >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >>> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> -- > > >>> > > >> >> Yan-Fei Jiang > > >>> > > >> >> > > >>> > > >> >> Einstein Fellow > > >>> > > >> >> Harvard-Smithsonian Center for Astrophysics > > >>> > > >> >> 60 Garden Street, Cambridge MA USA 02138 > > >>> > > >> >> > > >>> > > >> >> _______________________________________________ > > >>> > > >> >> yt-users mailing list > > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> >> > > >>> > > >> > _______________________________________________ > > >>> > > >> > yt-users mailing list > > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>>> > > >>> > > >> > > >>> > > >> > > >>> > > >> > > >>> > > >> ------------------------------ > > >>> > > >> > > >>> > > >> Subject: Digest Footer > > >>> > > >> > > >>> > > >> _______________________________________________ > > >>> > > >> yt-users mailing list > > >>> > > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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 37 > > >>> > > >> **************************************** > > >>> > > >> > > >>> > > > > > >>> > > > > > >>> > > > > > >>> > > > -- > > >>> > > > *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 <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > < > 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(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> <mailto: > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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 39 > > >>> > > **************************************** > > >>> > > > > >>> > > > >>> > > > >>> > > > >>> > -- > > >>> > *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… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >>< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201…> > < > 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> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org>> > <mailto:yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-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 41 > > >>> > **************************************** > > >>> > > > >>> > > > >>> > > > >>> > -- > > >>> > 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 <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > 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…> > < > 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> > <mailto:yt-users@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> < > 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 98, Issue 14 > > >>> **************************************** > > >>> > > >>> > > >>> > > >>> -- > > >>> 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." > > >>> > > >>> > > >>> > > >>> > > >>> -- > > >>> 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 <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > > >> > > >> > > >> _______________________________________________ > > >> yt-users mailing list > > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > > >> > > >> > > >> _______________________________________________ > > >> yt-users mailing list > > >> yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > > > > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > > > > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <mailto:yt-users@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> < > 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 98, Issue 27 > > **************************************** > > > > > > > > -- > > 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 98, Issue 29 > **************************************** > -- *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.**"*

2 1

problems with grid related values from an frb
by Slavin, Jonathan 26 Apr '16

26 Apr '16

Hi, I have been doing calculations in cylindrical symmetry using FLASH and using yt to read in the results. To do analysis, I create a fixed resolution buffer at the highest resolution of the AMR grid. Dynamical variables, density, temperature, etc. show expected behavior but things like dr, and dz don't work as I expect. ds = yt.load(...) slc = ds.slice(2,0) frb = slc.to_frb(...) dr = frb['dr'] dz = frb['dz'] (where I've left out the arguments to the to_frb method for brevity). Both dr and dz are not at all uniform in the way I expect them to be. Is this a bug or am I misunderstanding something? 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

Camera/Off axis Options
by Sushilkumar 26 Apr '16

26 Apr '16

Dear Suoqing Ji: I was able to implement the off axis in my script (drive link below, file is yt_magnetic_fields.py). But there seems to be a problem. For any off axis value like (1,1,0) I get an error which is given below. I am trying to get a z-x plane and view it at an angle of 15,45,60 degrees respectively. It works for along the axis normal vector like (1,0,0) and so on but for off axis value it gives me the error. Could you let me know if there is any error in the script or ways to overcome it? Thanks in advance https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc Error: Traceback (most recent call last): File "yt_magnetic_fields.py", line 39, 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 837, in __call__ 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', 'cutting_plane_bx')' in UniformGridData -- *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.**"*

1 0

Issue installing yt from script.
by Navarro Boullosa, Atalia 24 Apr '16

24 Apr '16

Hello, I've been trying to install yt from the script many times and I continue having the same issue, checking if unsupported combinations of configure options are allowed... no checking if Fortran interface enabled... no checking if Fortran 2003 interface enabled... yes checking whether we are using the GNU C++ compiler... no checking whether g++ accepts -g... no checking dependency style of g++... none checking how to run the C++ preprocessor... /lib/cpp configure: error: in `/home/boullosa/yt-x86_64/src/hdf5-1.8.14': configure: error: C++ preprocessor "/lib/cpp" fails sanity check See `config.log' for more details ******************************************** ******************************************** Failure. Check /home/boullosa/yt-x86_64/yt_install.log. The last 10 lines are above. I hope you can help me. Best, Atalia Navarro Boullosa. Bachelor Student in Physics. División de Ciencias e Ingenierías. Universidad de Guanajuato.

2 1

ProfilePlot(), How to write the plotted values to a file?
by Reju Sam John 23 Apr '16

23 Apr '16

Hi, I would like to know, how to write the plotted values of a 'ProfilePlot()' to a file? For example, I made a histogram with the following line. plot = ProfilePlot(sphere_200, "ProtonMomentum", ["NoOfProton"], weight_field="CellMass") But how can I write the values of "ProtonMomentum" and "NoOfProton" to a file? Thankyou. -- Reju Sam John

3 4

Issue loading large RAMSES dataset
by Søren Frimann 22 Apr '16

22 Apr '16

Dear yt users, I have an issue when I'm trying to load a RAMSES snapshot, which I think comes about because the snapshot is too large (51GB, code below). I have been able to successfully load several smaller simulation with yt. Is there any way to circumvent this issue, for example by just loading a small part of the simulation into yt? I have tried to use some data objects to pick out regions of interest (ds.sphere, ds.box) but to no avail. I have also considered just reading out the raw data from a region of interest like I usually do, and then read it into yt as a generic mesh, but it appears that you cannot do this in yt for an oct-tree AMR, only layered AMR. If anyone have any insight as to how I might process I would be very grateful. I use yt ver 3.2.3 Best, Søren ##################################################### ##################################################### ##################################################### import yt ds = yt.load('./output_00400/info_00400.txt') yt : [INFO ] 2016-04-15 16:18:45,575 Parameters: current_time = 403509140194502.0 yt : [INFO ] 2016-04-15 16:18:45,575 Parameters: domain_dimensions = [512 512 512] yt : [INFO ] 2016-04-15 16:18:45,576 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2016-04-15 16:18:45,577 Parameters: domain_right_edge = [ 1. 1. 1.] yt : [INFO ] 2016-04-15 16:18:45,577 Parameters: cosmological_simulation = 0 ds.index --------------------------------------------------------------------------- error Traceback (most recent call last) <ipython-input-3-2b95fa135b88> in <module>() ----> 1 ds.index /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/data_objects/static_output.py in index(self) 319 raise RuntimeError("You should not instantiate Dataset.") 320 self._instantiated_index = self._index_class( --> 321 self, dataset_type=self.dataset_type) 322 # Now we do things that we need an instantiated index for 323 # ...first off, we create our field_info now. /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/frontends/ramses/data_structures.py in __init__(self, ds, dataset_type) 349 350 self.float_type = np.float64 --> 351 super(RAMSESIndex, self).__init__(ds, dataset_type) 352 353 def _initialize_oct_handler(self): /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/geometry/geometry_handler.py in __init__(self, ds, dataset_type) 55 56 mylog.debug("Setting up domain geometry.") ---> 57 self._setup_geometry() 58 59 mylog.debug("Initializing data grid data IO") /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/geometry/oct_geometry_handler.py in _setup_geometry(self) 41 def _setup_geometry(self): 42 mylog.debug("Initializing Octree Geometry Handler.") ---> 43 self._initialize_oct_handler() 44 45 def get_smallest_dx(self): /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/frontends/ramses/data_structures.py in _initialize_oct_handler(self) 353 def _initialize_oct_handler(self): 354 self.domains = [RAMSESDomainFile(self.dataset, i + 1) --> 355 for i in range(self.dataset['ncpu'])] 356 total_octs = sum(dom.local_oct_count #+ dom.ngridbound.sum() 357 for dom in self.domains) /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/frontends/ramses/data_structures.py in <listcomp>(.0) 353 def _initialize_oct_handler(self): 354 self.domains = [RAMSESDomainFile(self.dataset, i + 1) --> 355 for i in range(self.dataset['ncpu'])] 356 total_octs = sum(dom.local_oct_count #+ dom.ngridbound.sum() 357 for dom in self.domains) /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/frontends/ramses/data_structures.py in __init__(self, ds, domain_id) 62 for t in ['grav', 'hydro', 'part', 'amr']: 63 setattr(self, "%s_fn" % t, basename % t) ---> 64 self._read_amr_header() 65 self._read_hydro_header() 66 self._read_particle_header() /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/frontends/ramses/data_structures.py in _read_amr_header(self) 183 f = open(self.amr_fn, "rb") 184 for header in ramses_header(hvals): --> 185 hvals.update(fpu.read_attrs(f, header)) 186 # That's the header, now we skip a few. 187 hvals['numbl'] = np.array(hvals['numbl']).reshape( /astro/sfrimann/miniconda3/lib/python3.5/site-packages/yt/utilities/fortran_utils.py in read_attrs(f, attrs, endian) 72 net_format += "".join(["I"] + ([t] * n) + ["I"]) 73 size = struct.calcsize(net_format) ---> 74 vals = list(struct.unpack(net_format, f.read(size))) 75 vv = {} 76 for a, n, t in attrs: error: unpack requires a bytes object of length 61253615840 ##################################################### ##################################################### #####################################################

2 1

Camera Options
by Sushilkumar 21 Apr '16

21 Apr '16

Dear Suoqing Ji: The fields Bx,By and Bz are already calculated taking into account the rotation. So I am not sure if I need to calculate it again. What I would like is only change the camera view to a desired angle after I do a slice plot and that is where I am having trouble with? Thanks in advance. On Thu, Apr 21, 2016 at 3:20 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: Camera Options (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 21 Apr 2016 13:20:32 -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] Camera Options > Message-ID: <FB001F5B-2521-4705-8D31-3166451BCA58(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > I see ? that?s a smart way of doing this! > > Best wishes, > Suoqing > > > On Apr 21, 2016, at 12:44 PM, Nathan Goldbaum <nathan12343(a)gmail.com> > wrote: > > > > > > > > On Thu, Apr 21, 2016 at 2:41 PM, Suoqing Ji <suoqing(a)physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu>> wrote: > > Hi Nathan, > > > > I do not have a 3D MHD data at hand, but I?ve tried one with > slc.annotate_quiver('velocity_x', 'velocity_y'), which gives the following > error: > > > > File "off_axis.py", line 49, in <module> > > slc.save(pf.basename) > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", > line 76, in newfunc > > args[0].run_callbacks() > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1029, in run_callbacks > > sys.exc_info()[2]) > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line > 1025, in run_callbacks > > callback(cbw) > > File > "/usr/local/yt3/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", > line 352, in __call__ > > (xi, yi) = (ds.coordinates.x_axis[ax], > > yt.utilities.exceptions.YTPlotCallbackError: annotate_quiver callback > failed with the following error: 4 > > > > > > Right, I bet it will work if you do `annotate_velocity()` though. > > > > You should take a look at the definition of the VelocityCallback to see > how it handles off-axis slices. > > > > 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 Apr 21, 2016, at 12:35 PM, Nathan Goldbaum <nathan12343(a)gmail.com > <mailto:nathan12343@gmail.com>> wrote: > >> > >> > >> > >> On Thu, Apr 21, 2016 at 2:30 PM, Suoqing Ji <suoqing(a)physics.ucsb.edu > <mailto:suoqing@physics.ucsb.edu>> wrote: > >> Hi Sushi, > >> > >> The quiver/streamline option you?ve used works for 2d plotting but not > for volume rendering, so I might suggest to use off-axis slice plot: > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> > >> > >> Unfortunately, quiver/streamline does not work (and/or does not work > correctly) for off axis slice plot now, but your goal is still achievable > via the following steps: > >> > >> Are you sure about that? There's a `CuttingQuiverCallback` for off-axis > slices. If you do `annotate_magnetic_fields`, it will automatically choose > the `CuttingQuiverCallback` for off-axis slices. > >> > >> > >> 1. Use fixed resolution buffer to get the off-axis sliced field values > including Bx, By and Bz (see this as an example, and replace SlicePlot with > OffAxisSlicePlot: > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html?highlight=fixedr…>), > then you get a 2D array for each field; > >> > >> 2. Compute the magnetic field vectors projected onto the rotated > viewing plane (perpendicular to your normal vector), based on field values > of Bx, By and Bz; now you have two 2D arrays for each components of B field > vectors after rotation; > >> > >> 3. Use quiver function in matplotlib and plot the B field vectors after > rotation, see: > http://matplotlib.org/examples/pylab_examples/quiver_demo.html < > http://matplotlib.org/examples/pylab_examples/quiver_demo.html> > >> > >> Hope this helps! Perhaps there?s an easier way that I do not know... > >> > >> 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 Apr 21, 2016, at 10:31 AM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > >>> > >>> Dear yt: > >>> > >>> I am having trouble with the camera option on yt. > >>> > >>> The google drive link is > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > >>> > >>> I want to change the view of the camera at an angle after the Slice > (x-z plane) and Quiver option. > >>> > >>> My script is yt_cam_rot.py. Without the camera options I get the > desired plot (UniformGridData_Slice.png) but when I use the camera I get a > empty screen. I am not sure where I am going wrong. > >>> > >>> I am using these links for my reference > >>> > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > > > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > < > http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering > > > >>> > >>> Thanks in advance > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> wrote: > >>> Dear Suoqing JI: > >>> > >>> Thank you > >>> > >>> On Fri, Apr 15, 2016 at 12:59 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)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: Camera Options (Suoqing Ji) > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Fri, 15 Apr 2016 10:59:22 -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] Camera Options > >>> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu > <mailto:B885F215-5F0A-49D5-9712-2D8FCEAA1366@physics.ucsb.edu>> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Hi Sushi, > >>> > >>> I think the off-axis slice/projection plot will meet your requirement > best, where the camera orientation is determined by the normal vector: > >>> > >>> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < > http://yt-project.org/doc/visualizing/plots.html#off-axis-slices>> > >>> > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots> > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > < > http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots > >> > >>> > >>> And of course, if you?re interested in the features provided by volume > rendering, it?s also worth a try. This cookbook gives an example of moving > a camera; specifically you might want to use the camera.rotation: > >>> > >>> > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende…> > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > < > http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… > >> > >>> > >>> 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 Apr 15, 2016, at 8:38 AM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > >>> > > >>> > Dear yt: > >>> > > >>> > I would like to change/customize/rotate my camera angle for my slice > plots without rotating the axis. > >>> > > >>> > What options do I have using yt if I want to move my camera angle by > say 45 degrees? > >>> > > >>> > Can I use the following link or can you suggest me something else > >>> > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html> < > http://yt-project.org/doc/visualizing/volume_rendering.html < > http://yt-project.org/doc/visualizing/volume_rendering.html>> > >>> > > >>> > Thanks in advance > >>> > > >>> > > >>> > > >>> > On Thu, Mar 31, 2016 at 10:11 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> wrote: > >>> > Send yt-users mailing list submissions to > >>> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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. Inclination problem (Sushilkumar) > >>> > > >>> > > >>> > > ---------------------------------------------------------------------- > >>> > > >>> > Message: 1 > >>> > Date: Thu, 31 Mar 2016 22:11:09 -0500 > >>> > From: Sushilkumar <sushil.sush19us(a)gmail.com <mailto: > sushil.sush19us(a)gmail.com> <mailto:sushil.sush19us@gmail.com <mailto: > sushil.sush19us(a)gmail.com>>> > >>> > To: Discussion of the yt analysis package > >>> > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > Subject: [yt-users] Inclination problem > >>> > Message-ID: > >>> > < > CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > ><mailto: > CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com > <mailto:CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg@mail.gmail.com > >>> > >>> > Content-Type: text/plain; charset="utf-8" > >>> > > >>> > Dear Nathan: > >>> > > >>> > Thank you very much, implementing now > >>> > > >>> > > >>> > On Thu, Mar 31, 2016 at 9:50 AM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> > >>> > wrote: > >>> > > >>> > > Send yt-users mailing list submissions to > >>> > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: Inclination problem (Nathan Goldbaum) > >>> > > > >>> > > > >>> > > > ---------------------------------------------------------------------- > >>> > > > >>> > > Message: 1 > >>> > > Date: Thu, 31 Mar 2016 09:50:31 -0500 > >>> > > From: Nathan Goldbaum <nathan12343(a)gmail.com <mailto: > nathan12343(a)gmail.com> <mailto:nathan12343@gmail.com <mailto: > nathan12343(a)gmail.com>>> > >>> > > To: Discussion of the yt analysis package > >>> > > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > Subject: Re: [yt-users] Inclination problem > >>> > > Message-ID: > >>> > > <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu= > >>> > > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com> <mailto: > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com>>> > >>> > > Content-Type: text/plain; charset="utf-8" > >>> > > > >>> > > Hi SK, > >>> > > > >>> > > I'm going to reference this example: > >>> > > > >>> > > > >>> > > > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines> > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > < > http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines > >> > >>> > > > >>> > > specifically this snippet: > >>> > > > >>> > > for stream in streamlines.streamlines: > >>> > > stream = stream[np.all(stream != 0.0, axis=1)] > >>> > > ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1) > >>> > > > >>> > > Here, the 'stream' object is just a Nx3 numpy array, where N is > the number > >>> > > of points sampled along the streamline. So each row of the numpy > array is > >>> > > just the coordinates of the streamline along one direction. > >>> > > > >>> > > To answer your question, no, there's nothing in yt that will > rotate the > >>> > > streamlines into a new coordinate system. Fortunately you should > be able to > >>> > > do it yourself using e.g. an Euler angle rotation matrix. You will > need to > >>> > > identify the new coordinate system you would like to transform to, > >>> > > calculate a 3D rotation matrix, then apply it using matrix > multiplication > >>> > > (e.g. np.dot, which supports broadcasting) to each coordinate > along the > >>> > > streamline. > >>> > > > >>> > > Hope that helps, > >>> > > > >>> > > Nathan > >>> > > > >>> > > On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> <mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>>> > >>> > > wrote: > >>> > > > >>> > > > Dear Matt: > >>> > > > > >>> > > > Pleas correct me if I am wrong but "off axis slices" takes > slices of the > >>> > > > plot that is already plotted. > >>> > > > > >>> > > > However, I would like to plot my data in a new coordinate frame > >>> > > (x`,y`,z`) > >>> > > > which is inclined at an angle of say alpha from the default > (x,y,z) > >>> > > frame. > >>> > > > > >>> > > > Or I would like to plot my data in a rotated frame (x`,y`,z`), > which is > >>> > > > rotated at an angle of alpha from (x,y,z). > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > On Wed, Mar 30, 2016 at 5:01 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>>> > >>> > > > wrote: > >>> > > > > >>> > > >> Send yt-users mailing list submissions to > >>> > > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: load spherical polar coordinate data with mesh > refinement > >>> > > >> in HDF5 (Jiang, Yanfei) > >>> > > >> 2. Re: load spherical polar coordinate data with mesh > refinement > >>> > > >> in HDF5 (Matthew Turk) > >>> > > >> 3. Re: Inclination problem (Matthew Turk) > >>> > > >> 4. Re: load spherical polar coordinate data with mesh > refinement > >>> > > >> in HDF5 (Jonah Miller) > >>> > > >> > >>> > > >> > >>> > > >> > ---------------------------------------------------------------------- > >>> > > >> > >>> > > >> Message: 1 > >>> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400 > >>> > > >> From: "Jiang, Yanfei" <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> > >>> > > >> To: Discussion of the yt analysis package > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > >>> > > >> refinement in HDF5 > >>> > > >> Message-ID: > >>> > > >> < > >>> > > >> > CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com> > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com > <mailto: > CANixPav-VmbXfhNvmA5wb5gj19mF%252B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com>>> > >>> > > >> Content-Type: text/plain; charset="utf-8" > >>> > > >> > >>> > > >> Hi Jonah, > >>> > > >> > >>> > > >> I am able to load the data to yt now using load_amr_grids(). > I notice > >>> > > >> that it can also set geometry to spherical. This is great. But > to make > >>> > > >> life > >>> > > >> more complicate. Is it possible to let yt know that the grid is > >>> > > >> logarithmic? Currently, load_amr_grids() just take left and > right edges > >>> > > of > >>> > > >> each block. I guess yt assumes the grid is uniform between left > and > >>> > > right > >>> > > >> edges. Is it possible to provide arrays of coordinate values > for each > >>> > > cell > >>> > > >> in each block? > >>> > > >> > >>> > > >> Thanks. > >>> > > >> > >>> > > >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller < > >>> > > >> jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>>> wrote: > >>> > > >> > >>> > > >> > Hi Yan-Feng, > >>> > > >> > > >>> > > >> > I haven't tried it, but I think there is functionality for > this. You > >>> > > can > >>> > > >> > use the load_amr_grids() function which can load amr data in > >>> > > Cartesian, > >>> > > >> > spherical, or polar coordinates. Here's the documentation: > >>> > > >> > > >>> > > >> > > >>> > > >> > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >> > >>> > > >> > > >>> > > >> > > >>> > > >> > > >>> > > >> > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >> > >>> > > >> > > >>> > > >> > Best, > >>> > > >> > Jonah > >>> > > >> > > >>> > > >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> > >>> > > >> > wrote: > >>> > > >> > > >>> > > >> >> Hi, > >>> > > >> >> I have some data from a new version of Athena > simulations. > >>> > > It > >>> > > >> is > >>> > > >> >> in spherical polar coordinate with mesh refinement written > in HDF5. > >>> > > The > >>> > > >> >> data structure is similar to flash data but not the same. > Does anyone > >>> > > >> have > >>> > > >> >> suggestions to load such data to yt directly? > >>> > > >> >> > >>> > > >> >> Thank you. > >>> > > >> >> -- > >>> > > >> >> Yan-Fei Jiang > >>> > > >> >> > >>> > > >> >> Einstein Fellow > >>> > > >> >> Harvard-Smithsonian Center for Astrophysics > >>> > > >> >> 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> >> _______________________________________________ > >>> > > >> >> yt-users mailing list > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > >>> > > >> > > >>> > > >> > _______________________________________________ > >>> > > >> > yt-users mailing list > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> > > >>> > > >> > > >>> > > >> > >>> > > >> > >>> > > >> -- > >>> > > >> Yan-Fei Jiang > >>> > > >> > >>> > > >> Einstein Fellow > >>> > > >> Harvard-Smithsonian Center for Astrophysics > >>> > > >> 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> -------------- 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… > >< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > >>> > > >> > > >>> > > >> > >>> > > >> ------------------------------ > >>> > > >> > >>> > > >> Message: 2 > >>> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500 > >>> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>> > >>> > > >> To: Discussion of the yt analysis package > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > >>> > > >> refinement in HDF5 > >>> > > >> Message-ID: > >>> > > >> <CALO3= > >>> > > >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA(a)mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com> > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com > <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com>>> > >>> > > >> Content-Type: text/plain; charset=UTF-8 > >>> > > >> > >>> > > >> Hi Yanfei, > >>> > > >> > >>> > > >> This is possible -- but it will also slow some things down. > You can > >>> > > >> use the load_hexahedral_mesh function, and there're examples of > this. > >>> > > >> This takes away some of the optimizations that regular grids > can do, > >>> > > >> but we're hoping to add them back in shortly. Like the other > >>> > > >> functions it too takes a geometry argument. > >>> > > >> > >>> > > >> -Matt > >>> > > >> > >>> > > >> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei > >>> > > >> <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> wrote: > >>> > > >> > Hi Jonah, > >>> > > >> > > >>> > > >> > I am able to load the data to yt now using > load_amr_grids(). I > >>> > > notice > >>> > > >> > that it can also set geometry to spherical. This is great. > But to make > >>> > > >> life > >>> > > >> > more complicate. Is it possible to let yt know that the grid > is > >>> > > >> logarithmic? > >>> > > >> > Currently, load_amr_grids() just take left and right edges of > each > >>> > > >> block. I > >>> > > >> > guess yt assumes the grid is uniform between left and right > edges. Is > >>> > > it > >>> > > >> > possible to provide arrays of coordinate values for each cell > in each > >>> > > >> block? > >>> > > >> > > >>> > > >> > Thanks. > >>> > > >> > > >>> > > >> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > >>> > > >> > <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>>> wrote: > >>> > > >> >> > >>> > > >> >> Hi Yan-Feng, > >>> > > >> >> > >>> > > >> >> I haven't tried it, but I think there is functionality for > this. You > >>> > > >> can > >>> > > >> >> use the load_amr_grids() function which can load amr data in > >>> > > Cartesian, > >>> > > >> >> spherical, or polar coordinates. Here's the documentation: > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > >> > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >> > >>> > > >> >> > >>> > > >> >> Best, > >>> > > >> >> Jonah > >>> > > >> >> > >>> > > >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> > >>> > > >> >> wrote: > >>> > > >> >>> > >>> > > >> >>> Hi, > >>> > > >> >>> I have some data from a new version of Athena > simulations. > >>> > > >> It is > >>> > > >> >>> in spherical polar coordinate with mesh refinement written > in HDF5. > >>> > > >> The data > >>> > > >> >>> structure is similar to flash data but not the same. Does > anyone > >>> > > have > >>> > > >> >>> suggestions to load such data to yt directly? > >>> > > >> >>> > >>> > > >> >>> Thank you. > >>> > > >> >>> -- > >>> > > >> >>> Yan-Fei Jiang > >>> > > >> >>> > >>> > > >> >>> Einstein Fellow > >>> > > >> >>> Harvard-Smithsonian Center for Astrophysics > >>> > > >> >>> 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> >>> _______________________________________________ > >>> > > >> >>> yt-users mailing list > >>> > > >> >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> _______________________________________________ > >>> > > >> >> yt-users mailing list > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > >>> > > >> > > >>> > > >> > > >>> > > >> > > >>> > > >> > -- > >>> > > >> > Yan-Fei Jiang > >>> > > >> > > >>> > > >> > Einstein Fellow > >>> > > >> > Harvard-Smithsonian Center for Astrophysics > >>> > > >> > 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> > > >>> > > >> > _______________________________________________ > >>> > > >> > yt-users mailing list > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> > > >>> > > >> > >>> > > >> > >>> > > >> ------------------------------ > >>> > > >> > >>> > > >> Message: 3 > >>> > > >> Date: Wed, 30 Mar 2016 16:16:22 -0500 > >>> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>> > >>> > > >> To: Discussion of the yt analysis package > >>> > > >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > >> Subject: Re: [yt-users] Inclination problem > >>> > > >> Message-ID: > >>> > > >> <CALO3=5HMB= > >>> > > >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com > <mailto:joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ@mail.gmail.com><mailto: > joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com <mailto: > joejr6BBh%252BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com>>> > >>> > > >> Content-Type: text/plain; charset=UTF-8 > >>> > > >> > >>> > > >> Hi SK, > >>> > > >> > >>> > > >> I'm not sure I totally understand, but if you have an > inclination > >>> > > >> angle you can use this directly in yt in the off axis slices > and so > >>> > > >> on. They typically take a vector, but you should be able to > convert > >>> > > >> one to the other. > >>> > > >> > >>> > > >> -Matt > >>> > > >> > >>> > > >> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar < > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com><mailto: > sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> > >>> > > > > >>> > > >> wrote: > >>> > > >> > Dear yt: > >>> > > >> > > >>> > > >> > I am trying to numerically solve the region around a pulsar. > Now since > >>> > > >> > pulsar is an inclined rotator with inclination angle between > rotation > >>> > > >> axis > >>> > > >> > and dipole axis I would like to include in my yt script. > >>> > > >> > > >>> > > >> > My original code written in FORTRAN incorporated this > inclination but > >>> > > >> how > >>> > > >> > would I incorporate it into my visualization using yt without > changing > >>> > > >> my > >>> > > >> > data. > >>> > > >> > > >>> > > >> > Could you suggest ways for the same? > >>> > > >> > > >>> > > >> > The google drive link to my script (streamline.py) and > streamline plot > >>> > > >> > (streamline_t000.png) is included > >>> > > >> > > >>> > > >> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc > <https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> > >>> > > >> > > >>> > > >> > Thanks in advance > >>> > > >> > > >>> > > >> > On Tue, Mar 29, 2016 at 12:54 PM, < > >>> > > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> <mailto: > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org>> > >>> > > >> > > >>> > > >> > wrote: > >>> > > >> >> > >>> > > >> >> Send yt-users mailing list submissions to > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@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> < > 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> <mailto: > 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> <mailto: > 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: gadget onto unigrid (Carla Bernhardt) > >>> > > >> >> 2. Re: gadget onto unigrid (Matthew Turk) > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> > >>> > > > ---------------------------------------------------------------------- > >>> > > >> >> > >>> > > >> >> Message: 1 > >>> > > >> >> Date: Tue, 29 Mar 2016 15:55:27 +0200 > >>> > > >> >> From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com <mailto: > carla.j.bernhardt(a)gmail.com> <mailto:carla.j.bernhardt@gmail.com <mailto: > carla.j.bernhardt(a)gmail.com>>> > >>> > > >> >> To: Discussion of the yt analysis package > >>> > > >> >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid > >>> > > >> >> Message-ID: > >>> > > >> >> > >>> > > >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF= > UhyGS_beuiUMbw7Ag(a)mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com > ><mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com <mailto: > UhyGS_beuiUMbw7Ag(a)mail.gmail.com>>> > >>> > > >> >> Content-Type: text/plain; charset="utf-8" > >>> > > >> >> > >>> > > >> >> Hi All, > >>> > > >> >> > >>> > > >> >> A follow-up question: In using arbitrary_grid (but with enzo > data), > >>> > > how > >>> > > >> >> does one then extract a field of an arbitrary_grid? I tried > >>> > > >> >> arbgrid["density"] as I have done with a > smoothed_covering_grid > >>> > > object, > >>> > > >> >> but > >>> > > >> >> it does not work (here is the traceback < > >>> > > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0> < > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>>> > >>> > > >> I > >>> > > >> >> got). > >>> > > >> >> > >>> > > >> >> Thanks, > >>> > > >> >> Carla > >>> > > >> >> > >>> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk < > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>>>: > >>> > > >> >> > >>> > > >> >> > Hi Desika, > >>> > > >> >> > > >>> > > >> >> > Yup, this can be done reasonably easily using either the > >>> > > >> >> > .arbitrary_grid object (which was designed for this) or the > >>> > > interface > >>> > > >> >> > to the arbitrary grid that's in the development version, > which is > >>> > > >> >> > ds.r[ ... ] where the ... is some combination of bounds > and steps. > >>> > > >> >> > > >>> > > >> >> > > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>> > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > >> > >>> > > >> >> > > >>> > > >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan > >>> > > >> >> > <desika.narayanan(a)gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>>> wrote: > >>> > > >> >> > > Hi All, > >>> > > >> >> > > > >>> > > >> >> > > Is it possible to deposit the particles from a gadget > data set > >>> > > >> onto a > >>> > > >> >> > > uniform grid in yt? Or, could it be possible to trick > the octree > >>> > > >> >> > deposition > >>> > > >> >> > > into doing it by forcing no refinements, but some sort > of native > >>> > > >> grid > >>> > > >> >> > > resolution? > >>> > > >> >> > > > >>> > > >> >> > > thanks, > >>> > > >> >> > > desika > >>> > > >> >> > > > >>> > > >> >> > > > >>> > > >> >> > > _______________________________________________ > >>> > > >> >> > > yt-users mailing list > >>> > > >> >> > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > > > >>> > > >> >> > _______________________________________________ > >>> > > >> >> > yt-users mailing list > >>> > > >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > 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… > >< > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >> > >>> > > >> > > >>> > > >> >> > >>> > > >> >> ------------------------------ > >>> > > >> >> > >>> > > >> >> Message: 2 > >>> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500 > >>> > > >> >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: > matthewturk(a)gmail.com> <mailto:matthewturk@gmail.com <mailto: > matthewturk(a)gmail.com>>> > >>> > > >> >> To: Discussion of the yt analysis package > >>> > > >> >> <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>>> > >>> > > >> >> Subject: Re: [yt-users] gadget onto unigrid > >>> > > >> >> Message-ID: > >>> > > >> >> > >>> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR= > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com><mailto: > P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com>>> > >>> > > >> >> Content-Type: text/plain; charset=UTF-8 > >>> > > >> >> > >>> > > >> >> Hi Carla, > >>> > > >> >> > >>> > > >> >> This functionality was recently implemented and is in the > development > >>> > > >> >> version, but not yet in the stable. We're hoping for a > release very > >>> > > >> >> shortly, but you can also try the dev version if you'd like! > >>> > > >> >> > >>> > > >> >> -Matt > >>> > > >> >> > >>> > > >> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt > >>> > > >> >> <carla.j.bernhardt(a)gmail.com <mailto: > carla.j.bernhardt(a)gmail.com> <mailto:carla.j.bernhardt@gmail.com <mailto: > carla.j.bernhardt(a)gmail.com>>> wrote: > >>> > > >> >> > Hi All, > >>> > > >> >> > > >>> > > >> >> > A follow-up question: In using arbitrary_grid (but with > enzo data), > >>> > > >> how > >>> > > >> >> > does > >>> > > >> >> > one then extract a field of an arbitrary_grid? I tried > >>> > > >> >> > arbgrid["density"] as > >>> > > >> >> > I have done with a smoothed_covering_grid object, but it > does not > >>> > > >> work > >>> > > >> >> > (here > >>> > > >> >> > is the traceback I got). > >>> > > >> >> > > >>> > > >> >> > Thanks, > >>> > > >> >> > Carla > >>> > > >> >> > > >>> > > >> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk < > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com> <mailto: > matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>>>: > >>> > > >> >> >> > >>> > > >> >> >> Hi Desika, > >>> > > >> >> >> > >>> > > >> >> >> Yup, this can be done reasonably easily using either the > >>> > > >> >> >> .arbitrary_grid object (which was designed for this) or > the > >>> > > >> interface > >>> > > >> >> >> to the arbitrary grid that's in the development version, > which is > >>> > > >> >> >> ds.r[ ... ] where the ... is some combination of bounds > and steps. > >>> > > >> >> >> > >>> > > >> >> >> > >>> > > >> > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid>> > >>> > > >> >> >> > >>> > > >> >> >> > >>> > > >> >> >> > >>> > > >> > >>> > > > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se…> > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > < > http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… > >> > >>> > > >> >> >> > >>> > > >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan > >>> > > >> >> >> <desika.narayanan(a)gmail.com <mailto: > desika.narayanan(a)gmail.com> <mailto:desika.narayanan@gmail.com <mailto: > desika.narayanan(a)gmail.com>>> wrote: > >>> > > >> >> >> > Hi All, > >>> > > >> >> >> > > >>> > > >> >> >> > Is it possible to deposit the particles from a gadget > data set > >>> > > >> onto a > >>> > > >> >> >> > uniform grid in yt? Or, could it be possible to trick > the > >>> > > octree > >>> > > >> >> >> > deposition > >>> > > >> >> >> > into doing it by forcing no refinements, but some sort > of native > >>> > > >> grid > >>> > > >> >> >> > resolution? > >>> > > >> >> >> > > >>> > > >> >> >> > thanks, > >>> > > >> >> >> > desika > >>> > > >> >> >> > > >>> > > >> >> >> > > >>> > > >> >> >> > _______________________________________________ > >>> > > >> >> >> > yt-users mailing list > >>> > > >> >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> >> > > >>> > > >> >> >> _______________________________________________ > >>> > > >> >> >> yt-users mailing list > >>> > > >> >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > > >>> > > >> >> > _______________________________________________ > >>> > > >> >> > yt-users mailing list > >>> > > >> >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> ------------------------------ > >>> > > >> >> > >>> > > >> >> Subject: Digest Footer > >>> > > >> >> > >>> > > >> >> _______________________________________________ > >>> > > >> >> yt-users mailing list > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > 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 34 > >>> > > >> >> **************************************** > >>> > > >> > > >>> > > >> > > >>> > > >> > > >>> > > >> > > >>> > > >> > -- > >>> > > >> > 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 <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> > > >>> > > >> > >>> > > >> > >>> > > >> ------------------------------ > >>> > > >> > >>> > > >> Message: 4 > >>> > > >> Date: Wed, 30 Mar 2016 18:01:04 -0400 > >>> > > >> From: Jonah Miller <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>>> > >>> > > >> To: yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@lists.spacepope.org > <mailto:yt-users@lists.spacepope.org>> > >>> > > >> Subject: Re: [yt-users] load spherical polar coordinate data > with mesh > >>> > > >> refinement in HDF5 > >>> > > >> Message-ID: <56FC4CA0.4030403(a)gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com> <mailto:56FC4CA0.4030403@gmail.com <mailto: > 56FC4CA0.4030403(a)gmail.com>>> > >>> > > >> Content-Type: text/plain; charset=windows-1252; format=flowed > >>> > > >> > >>> > > >> Hi Yanfei, > >>> > > >> > >>> > > >> To add to Matt's comment. Here is the documentation for using > >>> > > >> load_hexahedral_mesh. > >>> > > >> > >>> > > >> > >>> > > > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-…> > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > < > http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… > >> > >>> > > >> > >>> > > >> > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >< > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >> > >>> > > >> > >>> > > >> Best, > >>> > > >> Jonah > >>> > > >> > >>> > > >> On 16-03-30 05:15 PM, Matthew Turk wrote: > >>> > > >> > Hi Yanfei, > >>> > > >> > > >>> > > >> > This is possible -- but it will also slow some things down. > You can > >>> > > >> > use the load_hexahedral_mesh function, and there're examples > of this. > >>> > > >> > This takes away some of the optimizations that regular grids > can do, > >>> > > >> > but we're hoping to add them back in shortly. Like the other > >>> > > >> > functions it too takes a geometry argument. > >>> > > >> > > >>> > > >> > -Matt > >>> > > >> > > >>> > > >> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei > >>> > > >> > <yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> wrote: > >>> > > >> >> Hi Jonah, > >>> > > >> >> > >>> > > >> >> I am able to load the data to yt now using > load_amr_grids(). I > >>> > > >> notice > >>> > > >> >> that it can also set geometry to spherical. This is great. > But to > >>> > > make > >>> > > >> life > >>> > > >> >> more complicate. Is it possible to let yt know that the grid > is > >>> > > >> logarithmic? > >>> > > >> >> Currently, load_amr_grids() just take left and right edges > of each > >>> > > >> block. I > >>> > > >> >> guess yt assumes the grid is uniform between left and right > edges. Is > >>> > > >> it > >>> > > >> >> possible to provide arrays of coordinate values for each > cell in each > >>> > > >> block? > >>> > > >> >> > >>> > > >> >> Thanks. > >>> > > >> >> > >>> > > >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > >>> > > >> >> <jonah.maxwell.miller(a)gmail.com <mailto: > jonah.maxwell.miller(a)gmail.com> <mailto:jonah.maxwell.miller@gmail.com > <mailto:jonah.maxwell.miller@gmail.com>>> wrote: > >>> > > >> >>> Hi Yan-Feng, > >>> > > >> >>> > >>> > > >> >>> I haven't tried it, but I think there is functionality for > this. You > >>> > > >> can > >>> > > >> >>> use the load_amr_grids() function which can load amr data in > >>> > > >> Cartesian, > >>> > > >> >>> spherical, or polar coordinates. Here's the documentation: > >>> > > >> >>> > >>> > > >> >>> > >>> > > >> >>> > >>> > > >> > >>> > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a…> > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > < > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… > >> > >>> > > >> >>> > >>> > > >> >>> > >>> > > >> >>> > >>> > > >> > >>> > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_…> > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > < > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… > >> > >>> > > >> >>> > >>> > > >> >>> Best, > >>> > > >> >>> Jonah > >>> > > >> >>> > >>> > > >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < > >>> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto: > yanfei.jiang(a)cfa.harvard.edu> <mailto:yanfei.jiang@cfa.harvard.edu > <mailto:yanfei.jiang@cfa.harvard.edu>>> > >>> > > >> >>> wrote: > >>> > > >> >>>> Hi, > >>> > > >> >>>> I have some data from a new version of Athena > >>> > > simulations. > >>> > > >> It is > >>> > > >> >>>> in spherical polar coordinate with mesh refinement written > in HDF5. > >>> > > >> The data > >>> > > >> >>>> structure is similar to flash data but not the same. Does > anyone > >>> > > have > >>> > > >> >>>> suggestions to load such data to yt directly? > >>> > > >> >>>> > >>> > > >> >>>> Thank you. > >>> > > >> >>>> -- > >>> > > >> >>>> Yan-Fei Jiang > >>> > > >> >>>> > >>> > > >> >>>> Einstein Fellow > >>> > > >> >>>> Harvard-Smithsonian Center for Astrophysics > >>> > > >> >>>> 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> >>>> _______________________________________________ > >>> > > >> >>>> yt-users mailing list > >>> > > >> >>>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >>> > >>> > > >> >>> _______________________________________________ > >>> > > >> >>> yt-users mailing list > >>> > > >> >>> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >>> > >>> > > >> >> > >>> > > >> >> > >>> > > >> >> -- > >>> > > >> >> Yan-Fei Jiang > >>> > > >> >> > >>> > > >> >> Einstein Fellow > >>> > > >> >> Harvard-Smithsonian Center for Astrophysics > >>> > > >> >> 60 Garden Street, Cambridge MA USA 02138 > >>> > > >> >> > >>> > > >> >> _______________________________________________ > >>> > > >> >> yt-users mailing list > >>> > > >> >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> >> > >>> > > >> > _______________________________________________ > >>> > > >> > yt-users mailing list > >>> > > >> > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org>> > >>> > > >> > >>> > > >> > >>> > > >> > >>> > > >> ------------------------------ > >>> > > >> > >>> > > >> Subject: Digest Footer > >>> > > >> > >>> > > >> _______________________________________________ > >>> > > >> yt-users mailing list > >>> > > >> yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > 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 37 > >>> > > >> **************************************** > >>> > > >> > >>> > > > > >>> > > > > >>> > > > > >>> > > > -- > >>> > > > *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 <mailto: > yt-users(a)lists.spacepope.org> <mailto:yt-users@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> < > 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… > >< > 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> > <mailto:yt-users@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> < > 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 39 > >>> > > **************************************** > >>> > > > >>> > > >>> > > >>> > > >>> > -- > >>> > *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… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > >< > 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> > <mailto:yt-users@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> < > 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 41 > >>> > **************************************** > >>> > > >>> > > >>> > > >>> > -- > >>> > 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 <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 98, Issue 14 > >>> **************************************** > >>> > >>> > >>> > >>> -- > >>> 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." > >>> > >>> > >>> > >>> > >>> -- > >>> 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 <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> > >> > >> > >> _______________________________________________ > >> 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> > >> > >> > >> _______________________________________________ > >> 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> > > > > > > _______________________________________________ > > 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> > > > > > > _______________________________________________ > > 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… > > > > ------------------------------ > > 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 98, Issue 27 > **************************************** > -- *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.**"*

2 1

Camera Options
by Sushilkumar 21 Apr '16

21 Apr '16

Dear yt: I am having trouble with the camera option on yt. The google drive link is https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc I want to change the view of the camera at an angle after the Slice (x-z plane) and Quiver option. My script is yt_cam_rot.py. Without the camera options I get the desired plot (UniformGridData_Slice.png) but when I use the camera I get a empty screen. I am not sure where I am going wrong. I am using these links for my reference http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… http://yt-project.org/doc/visualizing/volume_rendering.html#volume-rendering Thanks in advance On Fri, Apr 15, 2016 at 4:49 PM, Sushilkumar <sushil.sush19us(a)gmail.com> wrote: > Dear Suoqing JI: > > Thank you > > On Fri, Apr 15, 2016 at 12:59 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: Camera Options (Suoqing Ji) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Fri, 15 Apr 2016 10:59:22 -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] Camera Options >> Message-ID: <B885F215-5F0A-49D5-9712-2D8FCEAA1366(a)physics.ucsb.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Sushi, >> >> I think the off-axis slice/projection plot will meet your requirement >> best, where the camera orientation is determined by the normal vector: >> >> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices < >> http://yt-project.org/doc/visualizing/plots.html#off-axis-slices> >> http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots >> < >> http://yt-project.org/doc/visualizing/plots.html#off-axis-projection-plots >> > >> >> And of course, if you?re interested in the features provided by volume >> rendering, it?s also worth a try. This cookbook gives an example of moving >> a camera; specifically you might want to use the camera.rotation: >> >> >> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… >> < >> http://yt-project.org/doc/cookbook/complex_plots.html#moving-a-volume-rende… >> > >> >> Best wishes, >> -- >> Suoqing JI >> Ph.D Candidate >> Department of Physics >> University of California, Santa Barbara >> http://web.physics.ucsb.edu/~suoqing >> >> > On Apr 15, 2016, at 8:38 AM, Sushilkumar <sushil.sush19us(a)gmail.com> >> wrote: >> > >> > Dear yt: >> > >> > I would like to change/customize/rotate my camera angle for my slice >> plots without rotating the axis. >> > >> > What options do I have using yt if I want to move my camera angle by >> say 45 degrees? >> > >> > Can I use the following link or can you suggest me something else >> > http://yt-project.org/doc/visualizing/volume_rendering.html < >> http://yt-project.org/doc/visualizing/volume_rendering.html> >> > >> > Thanks in advance >> > >> > >> > >> > On Thu, Mar 31, 2016 at 10:11 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. Inclination problem (Sushilkumar) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Thu, 31 Mar 2016 22:11:09 -0500 >> > From: Sushilkumar <sushil.sush19us(a)gmail.com <mailto: >> sushil.sush19us(a)gmail.com>> >> > To: Discussion of the yt analysis package >> > <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > Subject: [yt-users] Inclination problem >> > Message-ID: >> > < >> CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com >> <mailto: >> CAKARaKXPyQedHNjW0PwFvrO0qyjFGY4FMU6c2O5_PZWt-OxKEg(a)mail.gmail.com>> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Dear Nathan: >> > >> > Thank you very much, implementing now >> > >> > >> > On Thu, Mar 31, 2016 at 9:50 AM, <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: Inclination problem (Nathan Goldbaum) >> > > >> > > >> > > ---------------------------------------------------------------------- >> > > >> > > Message: 1 >> > > Date: Thu, 31 Mar 2016 09:50:31 -0500 >> > > From: Nathan Goldbaum <nathan12343(a)gmail.com <mailto: >> nathan12343(a)gmail.com>> >> > > To: Discussion of the yt analysis package >> > > <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > > Subject: Re: [yt-users] Inclination problem >> > > Message-ID: >> > > <CAJXewOnvXjZ+shfKG4SPubn_TYTAbLUu8y9ZRvovzBu= >> > > DcFZtQ(a)mail.gmail.com <mailto:DcFZtQ@mail.gmail.com>> >> > > Content-Type: text/plain; charset="utf-8" >> > > >> > > Hi SK, >> > > >> > > I'm going to reference this example: >> > > >> > > >> > > >> http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines >> < >> http://yt-project.org/doc/visualizing/streamlines.html?highlight=streamlines >> > >> > > >> > > specifically this snippet: >> > > >> > > for stream in streamlines.streamlines: >> > > stream = stream[np.all(stream != 0.0, axis=1)] >> > > ax.plot3D(stream[:,0], stream[:,1], stream[:,2], alpha=0.1) >> > > >> > > Here, the 'stream' object is just a Nx3 numpy array, where N is the >> number >> > > of points sampled along the streamline. So each row of the numpy >> array is >> > > just the coordinates of the streamline along one direction. >> > > >> > > To answer your question, no, there's nothing in yt that will rotate >> the >> > > streamlines into a new coordinate system. Fortunately you should be >> able to >> > > do it yourself using e.g. an Euler angle rotation matrix. You will >> need to >> > > identify the new coordinate system you would like to transform to, >> > > calculate a 3D rotation matrix, then apply it using matrix >> multiplication >> > > (e.g. np.dot, which supports broadcasting) to each coordinate along >> the >> > > streamline. >> > > >> > > Hope that helps, >> > > >> > > Nathan >> > > >> > > On Thu, Mar 31, 2016 at 8:56 AM, Sushilkumar < >> sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com>> >> > > wrote: >> > > >> > > > Dear Matt: >> > > > >> > > > Pleas correct me if I am wrong but "off axis slices" takes slices >> of the >> > > > plot that is already plotted. >> > > > >> > > > However, I would like to plot my data in a new coordinate frame >> > > (x`,y`,z`) >> > > > which is inclined at an angle of say alpha from the default (x,y,z) >> > > frame. >> > > > >> > > > Or I would like to plot my data in a rotated frame (x`,y`,z`), >> which is >> > > > rotated at an angle of alpha from (x,y,z). >> > > > >> > > > >> > > > >> > > > >> > > > On Wed, Mar 30, 2016 at 5:01 PM, < >> yt-users-request(a)lists.spacepope.org <mailto: >> yt-users-request(a)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: load spherical polar coordinate data with mesh refinement >> > > >> in HDF5 (Jiang, Yanfei) >> > > >> 2. Re: load spherical polar coordinate data with mesh refinement >> > > >> in HDF5 (Matthew Turk) >> > > >> 3. Re: Inclination problem (Matthew Turk) >> > > >> 4. Re: load spherical polar coordinate data with mesh refinement >> > > >> in HDF5 (Jonah Miller) >> > > >> >> > > >> >> > > >> >> ---------------------------------------------------------------------- >> > > >> >> > > >> Message: 1 >> > > >> Date: Wed, 30 Mar 2016 15:49:26 -0400 >> > > >> From: "Jiang, Yanfei" <yanfei.jiang(a)cfa.harvard.edu <mailto: >> yanfei.jiang(a)cfa.harvard.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] load spherical polar coordinate data with >> mesh >> > > >> refinement in HDF5 >> > > >> Message-ID: >> > > >> < >> > > >> CANixPav-VmbXfhNvmA5wb5gj19mF+-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com >> <mailto: >> CANixPav-VmbXfhNvmA5wb5gj19mF%2B-Ryq5YD-LrYrByDe3Ne7A(a)mail.gmail.com>> >> > > >> Content-Type: text/plain; charset="utf-8" >> > > >> >> > > >> Hi Jonah, >> > > >> >> > > >> I am able to load the data to yt now using load_amr_grids(). I >> notice >> > > >> that it can also set geometry to spherical. This is great. But to >> make >> > > >> life >> > > >> more complicate. Is it possible to let yt know that the grid is >> > > >> logarithmic? Currently, load_amr_grids() just take left and right >> edges >> > > of >> > > >> each block. I guess yt assumes the grid is uniform between left and >> > > right >> > > >> edges. Is it possible to provide arrays of coordinate values for >> each >> > > cell >> > > >> in each block? >> > > >> >> > > >> Thanks. >> > > >> >> > > >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller < >> > > >> jonah.maxwell.miller(a)gmail.com <mailto: >> jonah.maxwell.miller(a)gmail.com>> wrote: >> > > >> >> > > >> > Hi Yan-Feng, >> > > >> > >> > > >> > I haven't tried it, but I think there is functionality for this. >> You >> > > can >> > > >> > use the load_amr_grids() function which can load amr data in >> > > Cartesian, >> > > >> > spherical, or polar coordinates. Here's the documentation: >> > > >> > >> > > >> > >> > > >> >> > > >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> < >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> >> > > >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> < >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> > >> > > >> > >> > > >> > Best, >> > > >> > Jonah >> > > >> > >> > > >> > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < >> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu >> >> >> > > >> > wrote: >> > > >> > >> > > >> >> Hi, >> > > >> >> I have some data from a new version of Athena >> simulations. >> > > It >> > > >> is >> > > >> >> in spherical polar coordinate with mesh refinement written in >> HDF5. >> > > The >> > > >> >> data structure is similar to flash data but not the same. Does >> anyone >> > > >> have >> > > >> >> suggestions to load such data to yt directly? >> > > >> >> >> > > >> >> Thank you. >> > > >> >> -- >> > > >> >> Yan-Fei Jiang >> > > >> >> >> > > >> >> Einstein Fellow >> > > >> >> Harvard-Smithsonian Center for Astrophysics >> > > >> >> 60 Garden Street, Cambridge MA USA 02138 >> > > >> >> _______________________________________________ >> > > >> >> yt-users mailing list >> > > >> >> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> >> > > >> > >> > > >> > _______________________________________________ >> > > >> > yt-users mailing list >> > > >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> > >> > > >> > >> > > >> >> > > >> >> > > >> -- >> > > >> Yan-Fei Jiang >> > > >> >> > > >> Einstein Fellow >> > > >> Harvard-Smithsonian Center for Astrophysics >> > > >> 60 Garden Street, Cambridge MA USA 02138 >> > > >> -------------- 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… >> > >> > > >> > >> > > >> >> > > >> ------------------------------ >> > > >> >> > > >> Message: 2 >> > > >> Date: Wed, 30 Mar 2016 16:15:30 -0500 >> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: >> matthewturk(a)gmail.com>> >> > > >> To: Discussion of the yt analysis package >> > > >> <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with >> mesh >> > > >> refinement in HDF5 >> > > >> Message-ID: >> > > >> <CALO3= >> > > >> 5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA(a)mail.gmail.com >> <mailto:5F1-_9V5XHS4vF_eXvKoPerz3Zo20X8uPtcFjQSAQS1MA@mail.gmail.com>> >> > > >> Content-Type: text/plain; charset=UTF-8 >> > > >> >> > > >> Hi Yanfei, >> > > >> >> > > >> This is possible -- but it will also slow some things down. You >> can >> > > >> use the load_hexahedral_mesh function, and there're examples of >> this. >> > > >> This takes away some of the optimizations that regular grids can >> do, >> > > >> but we're hoping to add them back in shortly. Like the other >> > > >> functions it too takes a geometry argument. >> > > >> >> > > >> -Matt >> > > >> >> > > >> On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei >> > > >> <yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu>> >> wrote: >> > > >> > Hi Jonah, >> > > >> > >> > > >> > I am able to load the data to yt now using load_amr_grids(). I >> > > notice >> > > >> > that it can also set geometry to spherical. This is great. But >> to make >> > > >> life >> > > >> > more complicate. Is it possible to let yt know that the grid is >> > > >> logarithmic? >> > > >> > Currently, load_amr_grids() just take left and right edges of >> each >> > > >> block. I >> > > >> > guess yt assumes the grid is uniform between left and right >> edges. Is >> > > it >> > > >> > possible to provide arrays of coordinate values for each cell in >> each >> > > >> block? >> > > >> > >> > > >> > Thanks. >> > > >> > >> > > >> > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller >> > > >> > <jonah.maxwell.miller(a)gmail.com <mailto: >> jonah.maxwell.miller(a)gmail.com>> wrote: >> > > >> >> >> > > >> >> Hi Yan-Feng, >> > > >> >> >> > > >> >> I haven't tried it, but I think there is functionality for >> this. You >> > > >> can >> > > >> >> use the load_amr_grids() function which can load amr data in >> > > Cartesian, >> > > >> >> spherical, or polar coordinates. Here's the documentation: >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> > > >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> < >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> > >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> > > >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> < >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> > >> > > >> >> >> > > >> >> Best, >> > > >> >> Jonah >> > > >> >> >> > > >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < >> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu >> >> >> > > >> >> wrote: >> > > >> >>> >> > > >> >>> Hi, >> > > >> >>> I have some data from a new version of Athena >> simulations. >> > > >> It is >> > > >> >>> in spherical polar coordinate with mesh refinement written in >> HDF5. >> > > >> The data >> > > >> >>> structure is similar to flash data but not the same. Does >> anyone >> > > have >> > > >> >>> suggestions to load such data to yt directly? >> > > >> >>> >> > > >> >>> Thank you. >> > > >> >>> -- >> > > >> >>> Yan-Fei Jiang >> > > >> >>> >> > > >> >>> Einstein Fellow >> > > >> >>> Harvard-Smithsonian Center for Astrophysics >> > > >> >>> 60 Garden Street, Cambridge MA USA 02138 >> > > >> >>> _______________________________________________ >> > > >> >>> yt-users mailing list >> > > >> >>> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> >> > > >> >> >> > > >> >> _______________________________________________ >> > > >> >> yt-users mailing list >> > > >> >> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> >> > > >> > >> > > >> > >> > > >> > >> > > >> > -- >> > > >> > Yan-Fei Jiang >> > > >> > >> > > >> > Einstein Fellow >> > > >> > Harvard-Smithsonian Center for Astrophysics >> > > >> > 60 Garden Street, Cambridge MA USA 02138 >> > > >> > >> > > >> > _______________________________________________ >> > > >> > yt-users mailing list >> > > >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> > >> > > >> >> > > >> >> > > >> ------------------------------ >> > > >> >> > > >> Message: 3 >> > > >> Date: Wed, 30 Mar 2016 16:16:22 -0500 >> > > >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: >> matthewturk(a)gmail.com>> >> > > >> To: Discussion of the yt analysis package >> > > >> <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > > >> Subject: Re: [yt-users] Inclination problem >> > > >> Message-ID: >> > > >> <CALO3=5HMB= >> > > >> joejr6BBh+zdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com <mailto: >> joejr6BBh%2BzdxkwGzJS2NPrkK9tvMJnbch5-7BgQ(a)mail.gmail.com>> >> > > >> Content-Type: text/plain; charset=UTF-8 >> > > >> >> > > >> Hi SK, >> > > >> >> > > >> I'm not sure I totally understand, but if you have an inclination >> > > >> angle you can use this directly in yt in the off axis slices and so >> > > >> on. They typically take a vector, but you should be able to >> convert >> > > >> one to the other. >> > > >> >> > > >> -Matt >> > > >> >> > > >> On Tue, Mar 29, 2016 at 1:37 PM, Sushilkumar < >> sushil.sush19us(a)gmail.com <mailto:sushil.sush19us@gmail.com> >> > > > >> > > >> wrote: >> > > >> > Dear yt: >> > > >> > >> > > >> > I am trying to numerically solve the region around a pulsar. Now >> since >> > > >> > pulsar is an inclined rotator with inclination angle between >> rotation >> > > >> axis >> > > >> > and dipole axis I would like to include in my yt script. >> > > >> > >> > > >> > My original code written in FORTRAN incorporated this >> inclination but >> > > >> how >> > > >> > would I incorporate it into my visualization using yt without >> changing >> > > >> my >> > > >> > data. >> > > >> > >> > > >> > Could you suggest ways for the same? >> > > >> > >> > > >> > The google drive link to my script (streamline.py) and >> streamline plot >> > > >> > (streamline_t000.png) is included >> > > >> > >> > > >> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < >> https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> >> > > >> > >> > > >> > Thanks in advance >> > > >> > >> > > >> > On Tue, Mar 29, 2016 at 12:54 PM, < >> > > yt-users-request(a)lists.spacepope.org <mailto: >> yt-users-request(a)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: gadget onto unigrid (Carla Bernhardt) >> > > >> >> 2. Re: gadget onto unigrid (Matthew Turk) >> > > >> >> >> > > >> >> >> > > >> >> >> > > ---------------------------------------------------------------------- >> > > >> >> >> > > >> >> Message: 1 >> > > >> >> Date: Tue, 29 Mar 2016 15:55:27 +0200 >> > > >> >> From: Carla Bernhardt <carla.j.bernhardt(a)gmail.com <mailto: >> carla.j.bernhardt(a)gmail.com>> >> > > >> >> To: Discussion of the yt analysis package >> > > >> >> <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > > >> >> Subject: Re: [yt-users] gadget onto unigrid >> > > >> >> Message-ID: >> > > >> >> >> > > >> >> <CAFK0O=2vH24ViqeZ5QS3DY3uido0kEaF= >> UhyGS_beuiUMbw7Ag(a)mail.gmail.com <mailto:UhyGS_beuiUMbw7Ag@mail.gmail.com >> >> >> > > >> >> Content-Type: text/plain; charset="utf-8" >> > > >> >> >> > > >> >> Hi All, >> > > >> >> >> > > >> >> A follow-up question: In using arbitrary_grid (but with enzo >> data), >> > > how >> > > >> >> does one then extract a field of an arbitrary_grid? I tried >> > > >> >> arbgrid["density"] as I have done with a smoothed_covering_grid >> > > object, >> > > >> >> but >> > > >> >> it does not work (here is the traceback < >> > > http://pastebin.com/afgcgpp0 <http://pastebin.com/afgcgpp0>> >> > > >> I >> > > >> >> got). >> > > >> >> >> > > >> >> Thanks, >> > > >> >> Carla >> > > >> >> >> > > >> >> 2016-02-23 17:21 GMT+01:00 Matthew Turk <matthewturk(a)gmail.com >> <mailto:matthewturk@gmail.com>>: >> > > >> >> >> > > >> >> > Hi Desika, >> > > >> >> > >> > > >> >> > Yup, this can be done reasonably easily using either the >> > > >> >> > .arbitrary_grid object (which was designed for this) or the >> > > interface >> > > >> >> > to the arbitrary grid that's in the development version, >> which is >> > > >> >> > ds.r[ ... ] where the ... is some combination of bounds and >> steps. >> > > >> >> > >> > > >> >> > >> > > http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid >> <http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> >> > > >> >> > >> > > >> >> > >> > > >> >> > >> > > >> >> > > >> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… >> < >> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… >> > >> > > >> >> > >> > > >> >> > On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan >> > > >> >> > <desika.narayanan(a)gmail.com <mailto: >> desika.narayanan(a)gmail.com>> wrote: >> > > >> >> > > Hi All, >> > > >> >> > > >> > > >> >> > > Is it possible to deposit the particles from a gadget data >> set >> > > >> onto a >> > > >> >> > > uniform grid in yt? Or, could it be possible to trick the >> octree >> > > >> >> > deposition >> > > >> >> > > into doing it by forcing no refinements, but some sort of >> native >> > > >> grid >> > > >> >> > > resolution? >> > > >> >> > > >> > > >> >> > > thanks, >> > > >> >> > > desika >> > > >> >> > > >> > > >> >> > > >> > > >> >> > > _______________________________________________ >> > > >> >> > > yt-users mailing list >> > > >> >> > > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> > > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> > > >> > > >> >> > _______________________________________________ >> > > >> >> > yt-users mailing list >> > > >> >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)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… >> > >> > > >> > >> > > >> >> >> > > >> >> ------------------------------ >> > > >> >> >> > > >> >> Message: 2 >> > > >> >> Date: Tue, 29 Mar 2016 08:57:08 -0500 >> > > >> >> From: Matthew Turk <matthewturk(a)gmail.com <mailto: >> matthewturk(a)gmail.com>> >> > > >> >> To: Discussion of the yt analysis package >> > > >> >> <yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org>> >> > > >> >> Subject: Re: [yt-users] gadget onto unigrid >> > > >> >> Message-ID: >> > > >> >> >> > > >> >> <CALO3=5HR=zLHujWKgLpqwei_98vBOjpYvQ4m8nnUFR= >> P098utA(a)mail.gmail.com <mailto:P098utA@mail.gmail.com>> >> > > >> >> Content-Type: text/plain; charset=UTF-8 >> > > >> >> >> > > >> >> Hi Carla, >> > > >> >> >> > > >> >> This functionality was recently implemented and is in the >> development >> > > >> >> version, but not yet in the stable. We're hoping for a release >> very >> > > >> >> shortly, but you can also try the dev version if you'd like! >> > > >> >> >> > > >> >> -Matt >> > > >> >> >> > > >> >> On Tue, Mar 29, 2016 at 8:55 AM, Carla Bernhardt >> > > >> >> <carla.j.bernhardt(a)gmail.com <mailto: >> carla.j.bernhardt(a)gmail.com>> wrote: >> > > >> >> > Hi All, >> > > >> >> > >> > > >> >> > A follow-up question: In using arbitrary_grid (but with enzo >> data), >> > > >> how >> > > >> >> > does >> > > >> >> > one then extract a field of an arbitrary_grid? I tried >> > > >> >> > arbgrid["density"] as >> > > >> >> > I have done with a smoothed_covering_grid object, but it does >> not >> > > >> work >> > > >> >> > (here >> > > >> >> > is the traceback I got). >> > > >> >> > >> > > >> >> > Thanks, >> > > >> >> > Carla >> > > >> >> > >> > > >> >> > 2016-02-23 17:21 GMT+01:00 Matthew Turk < >> matthewturk(a)gmail.com <mailto:matthewturk@gmail.com>>: >> > > >> >> >> >> > > >> >> >> Hi Desika, >> > > >> >> >> >> > > >> >> >> Yup, this can be done reasonably easily using either the >> > > >> >> >> .arbitrary_grid object (which was designed for this) or the >> > > >> interface >> > > >> >> >> to the arbitrary grid that's in the development version, >> which is >> > > >> >> >> ds.r[ ... ] where the ... is some combination of bounds and >> steps. >> > > >> >> >> >> > > >> >> >> >> > > >> >> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid < >> http://yt-project.org/docs/dev/analyzing/objects.html#arbitrary-grid> >> > > >> >> >> >> > > >> >> >> >> > > >> >> >> >> > > >> >> > > >> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… >> < >> http://yt-project.org/docs/dev/analyzing/objects.html#slicing-syntax-for-se… >> > >> > > >> >> >> >> > > >> >> >> On Tue, Feb 23, 2016 at 10:18 AM, Desika Narayanan >> > > >> >> >> <desika.narayanan(a)gmail.com <mailto: >> desika.narayanan(a)gmail.com>> wrote: >> > > >> >> >> > Hi All, >> > > >> >> >> > >> > > >> >> >> > Is it possible to deposit the particles from a gadget data >> set >> > > >> onto a >> > > >> >> >> > uniform grid in yt? Or, could it be possible to trick the >> > > octree >> > > >> >> >> > deposition >> > > >> >> >> > into doing it by forcing no refinements, but some sort of >> native >> > > >> grid >> > > >> >> >> > resolution? >> > > >> >> >> > >> > > >> >> >> > thanks, >> > > >> >> >> > desika >> > > >> >> >> > >> > > >> >> >> > >> > > >> >> >> > _______________________________________________ >> > > >> >> >> > yt-users mailing list >> > > >> >> >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> >> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> >> > >> > > >> >> >> _______________________________________________ >> > > >> >> >> yt-users mailing list >> > > >> >> >> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> > >> > > >> >> > >> > > >> >> > >> > > >> >> > _______________________________________________ >> > > >> >> > yt-users mailing list >> > > >> >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> > >> > > >> >> >> > > >> >> >> > > >> >> ------------------------------ >> > > >> >> >> > > >> >> Subject: Digest Footer >> > > >> >> >> > > >> >> _______________________________________________ >> > > >> >> yt-users mailing list >> > > >> >> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)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 34 >> > > >> >> **************************************** >> > > >> > >> > > >> > >> > > >> > >> > > >> > >> > > >> > -- >> > > >> > 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 <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> > >> > > >> >> > > >> >> > > >> ------------------------------ >> > > >> >> > > >> Message: 4 >> > > >> Date: Wed, 30 Mar 2016 18:01:04 -0400 >> > > >> From: Jonah Miller <jonah.maxwell.miller(a)gmail.com <mailto: >> jonah.maxwell.miller(a)gmail.com>> >> > > >> To: yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> Subject: Re: [yt-users] load spherical polar coordinate data with >> mesh >> > > >> refinement in HDF5 >> > > >> Message-ID: <56FC4CA0.4030403(a)gmail.com <mailto: >> 56FC4CA0.4030403(a)gmail.com>> >> > > >> Content-Type: text/plain; charset=windows-1252; format=flowed >> > > >> >> > > >> Hi Yanfei, >> > > >> >> > > >> To add to Matt's comment. Here is the documentation for using >> > > >> load_hexahedral_mesh. >> > > >> >> > > >> >> > > >> http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… >> < >> http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-… >> > >> > > >> >> > > >> >> > > >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> < >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> > >> > > >> >> > > >> Best, >> > > >> Jonah >> > > >> >> > > >> On 16-03-30 05:15 PM, Matthew Turk wrote: >> > > >> > Hi Yanfei, >> > > >> > >> > > >> > This is possible -- but it will also slow some things down. You >> can >> > > >> > use the load_hexahedral_mesh function, and there're examples of >> this. >> > > >> > This takes away some of the optimizations that regular grids can >> do, >> > > >> > but we're hoping to add them back in shortly. Like the other >> > > >> > functions it too takes a geometry argument. >> > > >> > >> > > >> > -Matt >> > > >> > >> > > >> > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei >> > > >> > <yanfei.jiang(a)cfa.harvard.edu <mailto: >> yanfei.jiang(a)cfa.harvard.edu>> wrote: >> > > >> >> Hi Jonah, >> > > >> >> >> > > >> >> I am able to load the data to yt now using >> load_amr_grids(). I >> > > >> notice >> > > >> >> that it can also set geometry to spherical. This is great. But >> to >> > > make >> > > >> life >> > > >> >> more complicate. Is it possible to let yt know that the grid is >> > > >> logarithmic? >> > > >> >> Currently, load_amr_grids() just take left and right edges of >> each >> > > >> block. I >> > > >> >> guess yt assumes the grid is uniform between left and right >> edges. Is >> > > >> it >> > > >> >> possible to provide arrays of coordinate values for each cell >> in each >> > > >> block? >> > > >> >> >> > > >> >> Thanks. >> > > >> >> >> > > >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller >> > > >> >> <jonah.maxwell.miller(a)gmail.com <mailto: >> jonah.maxwell.miller(a)gmail.com>> wrote: >> > > >> >>> Hi Yan-Feng, >> > > >> >>> >> > > >> >>> I haven't tried it, but I think there is functionality for >> this. You >> > > >> can >> > > >> >>> use the load_amr_grids() function which can load amr data in >> > > >> Cartesian, >> > > >> >>> spherical, or polar coordinates. Here's the documentation: >> > > >> >>> >> > > >> >>> >> > > >> >>> >> > > >> >> > > >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> < >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-a… >> > >> > > >> >>> >> > > >> >>> >> > > >> >>> >> > > >> >> > > >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> < >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_… >> > >> > > >> >>> >> > > >> >>> Best, >> > > >> >>> Jonah >> > > >> >>> >> > > >> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < >> > > >> yanfei.jiang(a)cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu >> >> >> > > >> >>> wrote: >> > > >> >>>> Hi, >> > > >> >>>> I have some data from a new version of Athena >> > > simulations. >> > > >> It is >> > > >> >>>> in spherical polar coordinate with mesh refinement written in >> HDF5. >> > > >> The data >> > > >> >>>> structure is similar to flash data but not the same. Does >> anyone >> > > have >> > > >> >>>> suggestions to load such data to yt directly? >> > > >> >>>> >> > > >> >>>> Thank you. >> > > >> >>>> -- >> > > >> >>>> Yan-Fei Jiang >> > > >> >>>> >> > > >> >>>> Einstein Fellow >> > > >> >>>> Harvard-Smithsonian Center for Astrophysics >> > > >> >>>> 60 Garden Street, Cambridge MA USA 02138 >> > > >> >>>> _______________________________________________ >> > > >> >>>> yt-users mailing list >> > > >> >>>> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >>>> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >>> >> > > >> >>> _______________________________________________ >> > > >> >>> yt-users mailing list >> > > >> >>> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >>> >> > > >> >> >> > > >> >> >> > > >> >> -- >> > > >> >> Yan-Fei Jiang >> > > >> >> >> > > >> >> Einstein Fellow >> > > >> >> Harvard-Smithsonian Center for Astrophysics >> > > >> >> 60 Garden Street, Cambridge MA USA 02138 >> > > >> >> >> > > >> >> _______________________________________________ >> > > >> >> yt-users mailing list >> > > >> >> yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> >> > > >> > _______________________________________________ >> > > >> > yt-users mailing list >> > > >> > yt-users(a)lists.spacepope.org <mailto: >> yt-users(a)lists.spacepope.org> >> > > >> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> >> > > >> >> > > >> >> > > >> >> > > >> ------------------------------ >> > > >> >> > > >> 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 37 >> > > >> **************************************** >> > > >> >> > > > >> > > > >> > > > >> > > > -- >> > > > *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 <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 39 >> > > **************************************** >> > > >> > >> > >> > >> > -- >> > *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… >> < >> 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 41 >> > **************************************** >> > >> > >> > >> > -- >> > 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 98, Issue 14 >> **************************************** >> > > > > -- > *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.**"* > > -- *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.**"*

3 5

yt on Blue Waters
by Jonah Miller 20 Apr '16

20 Apr '16

Hi yt users, Does anybody have experience installing the development version of yt on blue waters (as opposed to relying on the module pre-provided)? If so, do you have any tips or gotchas? I will be attempting an installation in the next few days and I'm sort of hoping it's a solved problem. Best, Jonah Miller

4 8

load and slice data in spherical coordinates
by Andrea Negri 19 Apr '16

19 Apr '16

Hi all, I would like to shape a problem and the relative (temporary) solution. I have a numerical simulation in spherical coordinates, which order is phi, theta, so I use the load_uniform_grid function with geometry=('spherical',('phi','theta','r'), and the relative bbox. However, when I try to plot a slice, I obtain an error. Long story short, now I transpose the data, and everything is OK. In attachment there is a very simple code that shows the problem, the commented lines produce a correct plot, while the uncommented lines raise an error. Cheers, Andrea

2 2

yt installation issue
by Andrea Negri 18 Apr '16

18 Apr '16

Hi all, I tried to install yt using the All-in-One Installation Script. I'm using Ubuntu 14.04, and I have installed the required packeges listed at the beginning of the script. All the installation process went fine, then I sourced the activation script in a new shell, and to check if everything was fine, I typed yt --help, and this is the output: Traceback (most recent call last): File "/home/andrea/Software/yt/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==3.2.3', 'console_scripts', 'yt')() File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 558, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2682, in load_entry_point File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2355, in load File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2361, in resolve File "/home/andrea/Software/yt/yt-x86_64/src/yt-hg/yt/__init__.py", line 146, in <module> from yt.visualization.api import \ File "/home/andrea/Software/yt/yt-x86_64/src/yt-hg/yt/visualization/api.py", line 22, in <module> from .particle_plots import \ File "/home/andrea/Software/yt/yt-x86_64/src/yt-hg/yt/visualization/particle_plots.py", line 24, in <module> from .plot_window import \ File "/home/andrea/Software/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 34, in <module> from .plot_modifications import callback_registry File "/home/andrea/Software/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 26, in <module> from mpl_toolkits.axes_grid1.anchored_artists import AnchoredSizeBar File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/mpl_toolkits/axes_grid1/__init__.py", line 9, in <module> from .axes_grid import Grid, ImageGrid, AxesGrid File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/mpl_toolkits/axes_grid1/axes_grid.py", line 8, in <module> import matplotlib.pyplot as plt File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 109, in <module> _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup() File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/backends/__init__.py", line 32, in pylab_setup globals(),locals(),[backend_name],0) File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/backends/backend_qt4agg.py", line 17, in <module> from .backend_qt5agg import NavigationToolbar2QTAgg File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/backends/backend_qt5agg.py", line 18, in <module> from .backend_qt5 import QtCore File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/backends/backend_qt5.py", line 31, in <module> from .qt_compat import QtCore, QtGui, QtWidgets, _getSaveFileName, __version__ File "/home/andrea/Software/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/backends/qt_compat.py", line 126, in <module> from PySide import QtCore, QtGui, __version__, __version_info__ ImportError: No module named PySide I tried different configurations, such as installing the stable and the yt branch, turn on/off the scipy installation flag in install_script.sh, but nothing. Please, do you have any suggestions? Thanks in advance, Andrea

3 3

Derived field "function" at runtime
by bh11e 18 Apr '16

18 Apr '16

Hi, How one gets a reference to the effective "function" of a derived field at run time? I wish to know how the derived fields I use are calculated. Thus I need the source code either as a string or a source file/line number. Thanks, --Boyan Hristov

3 3