Mailman 3 March 2016 - yt-users

Inclined rotator
by Sushilkumar March 28, 2016

March 28, 2016

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 Thanks in advance On Sun, Mar 27, 2016 at 1:07 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: Plotting mesh cells (cell edges) (Matthew Turk) > 2. Re: Plotting mesh cells (cell edges) (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 27 Mar 2016 09:42:44 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Plotting mesh cells (cell edges) > Message-ID: > <CALO3= > 5Hpndt85jra405LCQ4KP1ugYyX_GkAv-6dWXn865u2HPw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Xinsheng, > > Right now this isn't possible -- it tends not to be something that comes up > too often. But, I think it should be relatively straightforward. I've > added an issue for it, and I'm going to try to take a look at it tomorrow. > > > https://bitbucket.org/yt_analysis/yt/issues/1198/add-ability-to-plot-cell-e… > > I've marked it a blocker for our next release. > > -Matt > > On Sun, Mar 27, 2016 at 1:00 AM, Shawn Qin <xsqin(a)uw.edu> wrote: > > > Hello, > > > > Does anybody know if yt can plot mesh cells (cell edges) besides edges of > > patches in a 2D slice plot (with AMR grid data), like the one below (only > > cell edges in some patches were plotted)? I was able to plot edges of > > different AMR grid patches with the *annotate_grids* method of > > *OffAxisSlicePlot* object. I checked all annotate_* methods but didn't > > find any method that seems to do this job? > > > > > > I am using yt 3.2.3. > > > > Any suggestions and discussion will be appreciated. > > > > Thank you! > > > > Best, > > > > -- > > ~~~~~~~~~~~~~~~~~ > > > > Xinsheng Qin > > Ph.D. candidate > > Department of Civil and Environmental Engineering > > University of Washingtonxsqin(a)uw.edu > > > > > > _______________________________________________ > > 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… > > > > ------------------------------ > > Message: 2 > Date: Sun, 27 Mar 2016 10:36:52 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Plotting mesh cells (cell edges) > Message-ID: > <CALO3=5HO7gQEF=71Y+6ObG= > uCwd2KzjnDivLdO6QpbLi4ALAQw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I've found a few minutes and issued a pull request: > > > https://bitbucket.org/yt_analysis/yt/pull-requests/2088/adding-annotate_cel… > > > On Sun, Mar 27, 2016 at 9:42 AM, Matthew Turk <matthewturk(a)gmail.com> > wrote: > > > Hi Xinsheng, > > > > Right now this isn't possible -- it tends not to be something that comes > > up too often. But, I think it should be relatively straightforward. > I've > > added an issue for it, and I'm going to try to take a look at it > tomorrow. > > > > > > > https://bitbucket.org/yt_analysis/yt/issues/1198/add-ability-to-plot-cell-e… > > > > I've marked it a blocker for our next release. > > > > -Matt > > > > On Sun, Mar 27, 2016 at 1:00 AM, Shawn Qin <xsqin(a)uw.edu> wrote: > > > >> Hello, > >> > >> Does anybody know if yt can plot mesh cells (cell edges) besides edges > of > >> patches in a 2D slice plot (with AMR grid data), like the one below > (only > >> cell edges in some patches were plotted)? I was able to plot edges of > >> different AMR grid patches with the *annotate_grids* method of > >> *OffAxisSlicePlot* object. I checked all annotate_* methods but didn't > >> find any method that seems to do this job? > >> > >> > >> I am using yt 3.2.3. > >> > >> Any suggestions and discussion will be appreciated. > >> > >> Thank you! > >> > >> Best, > >> > >> -- > >> ~~~~~~~~~~~~~~~~~ > >> > >> Xinsheng Qin > >> Ph.D. candidate > >> Department of Civil and Environmental Engineering > >> University of Washingtonxsqin(a)uw.edu > >> > >> > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > >> > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 97, Issue 32 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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Plotting mesh cells (cell edges)
by Shawn Qin March 27, 2016

March 27, 2016

Hello, Does anybody know if yt can plot mesh cells (cell edges) besides edges of patches in a 2D slice plot (with AMR grid data), like the one below (only cell edges in some patches were plotted)? I was able to plot edges of different AMR grid patches with the *annotate_grids* method of *OffAxisSlicePlot* object. I checked all annotate_* methods but didn't find any method that seems to do this job? I am using yt 3.2.3. Any suggestions and discussion will be appreciated. Thank you! Best, -- ~~~~~~~~~~~~~~~~~ Xinsheng Qin Ph.D. candidate Department of Civil and Environmental Engineering University of Washington xsqin(a)uw.edu �PNG

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non-uniform Cartesian grid volume rendering
by Samuel Jones March 24, 2016

March 24, 2016

Dear yt-users, I have had generally a very smooth ride in the past using yt for volume rendering of data on a uniform Cartesian grid. Now, however, I am trying to do similar things with data on a non-uniform Cartesian grid, having loaded it in with load_hexahedral_mesh. I managed to get embree, pyembree built together with yt version 3.3-dev. I can create the hexahedral dataset with no problem (at least no errors), but when I try to create a scene in which to do some volume rendering I get the error copied below. I think I must doing something wrong but I don't know what! Thanks and Best Wishes, Sam --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-11-e24c1c1430d9> in <module>() ----> 1 sc = yt.create_scene(ds,'lset') /home/swj/softs/yt/yt/visualization/volume_rendering/volume_rendering.pyc in create_scene(data_source, field, lens_type) 72 73 if hasattr(data_source.ds.index, "meshes"): ---> 74 source = MeshSource(data_source, field=field) 75 else: 76 source = VolumeSource(data_source, field=field) /home/swj/softs/yt/yt/visualization/volume_rendering/render_source.pyc in __init__(self, data_source, field) 369 370 self.scene = mesh_traversal.YTEmbreeScene() --> 371 self.build_mesh() 372 373 def cmap(): /home/swj/softs/yt/yt/visualization/volume_rendering/render_source.pyc in build_mesh(self) 421 """ 422 ftype, fname = self.field --> 423 mesh_id = int(ftype[-1]) - 1 424 index = self.data_source.ds.index 425 offset = index.meshes[mesh_id]._index_offset ValueError: invalid literal for int() with base 10: 'm' ***************************************** some debug: > /home/swj/softs/yt/yt/visualization/volume_rendering/render_source.py(423)build_mesh() 422 ftype, fname = self.field --> 423 mesh_id = int(ftype[-1]) - 1 424 index = self.data_source.ds.index ipdb> print ftype stream ipdb> self.field ('stream', 'lset') ipdb> exit -- Samuel Jones Physik stellarer Objekte | Physics of Stellar Objects Heidelberger Institut für Theoretische Studien | Heidelberg Institute for Theoretical Studies samuel.jones(a)h-its.org

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Improve streamline plot
by Sushilkumar March 24, 2016

March 24, 2016

Dear yt: How do I adjust the line width and color for streamline plots? Drive link to streamline plot (streamlines_t000.png) and the script (yt_streamline.py) is below. I also checked the yt link below but it does not seem to have options for line width and line color. Thanks in advance https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc http://yt-project.org/doc/reference/api/generated/yt.visualization.streamli… On Wed, Mar 23, 2016 at 12:52 PM, <yt-users-request(a)lists.spacepope.org> wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Re: yt3.3dev MPI puzzle (Stuart Levy) > 2. smoothed particle velocities onto unigrid (Desika Narayanan) > 3. covering_grid with RAMSES dataset (Enrico Garaldi) > 4. Re: covering_grid with RAMSES dataset (Nathan Goldbaum) > 5. Re: covering_grid with RAMSES dataset (Enrico Garaldi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Mar 2016 12:54:49 -0500 > From: Stuart Levy <salevy(a)illinois.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] yt3.3dev MPI puzzle > Message-ID: <56F186E9.2010506(a)illinois.edu> > Content-Type: text/plain; charset="windows-1252" > > Ooh, slick! Thank you again! > > On 3/22/16 12:44 PM, Kacper Kowalik wrote: > > cd $HOME > > hg clone https://bitbucket.org/MatthewTurk/hgbb > > > > create or edit your $HOME/.hgrc to contain: > > > > [extensions] > > hgbb = $HOME/hgbb/hgbb.py > > > > Then you'll be able to do the following in your local clone of yt repo: > > > > hg bbpr # will give you list of PRs > > hg bbpr -p 2066 # would download incoming changes and suggest rev > > # to update to > > > > Cheers, > > Kacper > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: signature.asc > Type: application/pgp-signature > Size: 842 bytes > Desc: OpenPGP digital signature > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Wed, 23 Mar 2016 11:04:28 -0400 > From: Desika Narayanan <desika.narayanan(a)gmail.com> > To: yt-users <yt-users(a)lists.spacepope.org> > Subject: [yt-users] smoothed particle velocities onto unigrid > Message-ID: > < > CAMMxB+MCMtJgT_YLg0iwQQHZC2E5Bhg-vBr9D7u7uKDuWjBZMQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hey All, > > I'm having some trouble smoothing particle velocities onto a uniform > (arbitrary_grid) grid. The basic idea is that I create an arbitrary grid, > then want to access the particle quantities smoothed onto that grid. Some > are relatively easy, like: > > mass = obj[('deposit','PartType0_mass')].in_units('Msun') > > > and for others, where deposited fields don't already exist, I can create > those fields and it all works well: > > ds.add_deposited_particle_field(('PartType0', 'Temperature'),'sum') > temp = obj[('deposit', 'PartType0_sum_Temperature')] > > but when either trying to access a deposited particle field, or creating > one with the velocities, errors are abound. I'm sure I'm just doing > something foolish, but could use a little nudge in the right direction. I > created a self-contained script using the gadget zoom data set on the yt > datsets to show the problem, with two different error messages pastebinned > (links in the script) here: > > http://paste.yt-project.org/show/6352/ > > any help would be greatly appreciated! > > thanks, > desika > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Wed, 23 Mar 2016 17:36:34 +0100 > From: "Enrico Garaldi" <egaraldi(a)uni-bonn.de> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] covering_grid with RAMSES dataset > Message-ID: <ximss-98622(a)be4.uni-bonn.de> > Content-Type: text/plain; charset="utf-8"; format="flowed" > > Hi, > I am having troubles using the smoothed_covering_grid and covering_grid > with > RAMSES dataset. > I have yt-project version 3.2.3 and I am using the "output_00080" dataset > from the yt sample datasets. > > smoothed_covering_grid fails (raising a RuntimeError because tot != 0, line > 880 of construction_data_containers.pyc), while covering_grid seems to > leave > unfilled the refined regions. What I mean is that if a cell is refined > beyond the maximum allowed level for the grid, it is left unfilled > (contrary > to what happens with ENZO datasets). > > I am using this code: > > import yt > import matplotlib.pyplot as plt > > ds = yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt') > > cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge, > dims=ds.domain_dimensions) > > density_field = cgrid["density"] > > print (density_field == 0.0).any() #should be False but it is True > > plt.imshow(density_field[:,:,48].v, interpolation='none') > plt.show() ? #holes with zero-density corresponding to refined regions > > Am I doing something wrong? > > Thanks in advance, > Enrico > > ------------------------------------- > Enrico Garaldi - Ph.D. student > Argelander-Institut f?r Astronomie > Address: Auf dem H?gel 71, 53121 Bonn, Germany > Room: 1.024 > Phone: +49 (0) 228 73 3433 > egaraldi[at]uni-bonn[dot]de > > > ------------------------------ > > Message: 4 > Date: Wed, 23 Mar 2016 09:47:16 -0700 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] covering_grid with RAMSES dataset > Message-ID: > < > CAJXewOn3N_fJWBNQpXNVUtGg2s8tN_71wjmS3aL9yzqpNXVZ4A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Enrico, > > I don't think you're doing anything wrong - this is a bug, likely a generic > issue with the way covering grids get filled out for octree data. > > This issue with smoothed_covering_grid is likely another, different but > related bug. > > Can you create an issue to track this? > > https://bitbucket.org/yt_analysis/yt/issues/new > > -Nathan > > On Wed, Mar 23, 2016 at 9:36 AM, Enrico Garaldi <egaraldi(a)uni-bonn.de> > wrote: > > > Hi, > > I am having troubles using the smoothed_covering_grid and covering_grid > > with RAMSES dataset. > > I have yt-project version 3.2.3 and I am using the "output_00080" dataset > > from the yt sample datasets. > > > > smoothed_covering_grid fails (raising a RuntimeError because tot != 0, > > line 880 of construction_data_containers.pyc), while covering_grid seems > to > > leave unfilled the refined regions. What I mean is that if a cell is > > refined beyond the maximum allowed level for the grid, it is left > unfilled > > (contrary to what happens with ENZO datasets). > > > > I am using this code: > > > > import yt > > import matplotlib.pyplot as plt > > > > ds = yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt') > > > > cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge, > > dims=ds.domain_dimensions) > > > > density_field = cgrid["density"] > > > > print (density_field == 0.0).any() #should be False but it is True > > > > plt.imshow(density_field[:,:,48].v, interpolation='none') > > plt.show() #holes with zero-density corresponding to refined regions > > > > Am I doing something wrong? > > > > Thanks in advance, > > Enrico > > > > ------------------------------------- > > Enrico Garaldi - Ph.D. student > > Argelander-Institut f?r Astronomie > > Address: Auf dem H?gel 71, 53121 Bonn, Germany > > Room: 1.024 > > Phone: +49 (0) 228 73 3433 > > egaraldi[at]uni-bonn[dot]de > > _______________________________________________ > > 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… > > > > ------------------------------ > > Message: 5 > Date: Wed, 23 Mar 2016 18:24:07 +0100 > From: "Enrico Garaldi" <egaraldi(a)uni-bonn.de> > To: "Discussion of the yt analysis package" > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] covering_grid with RAMSES dataset > Message-ID: <ximss-99088(a)be4.uni-bonn.de> > Content-Type: text/plain; charset="utf-8"; format="flowed" > > Hi Nathan, > thanks for the feedback. I will create the issue right away. > > Enrico > > On Wed, 23 Mar 2016 09:47:16 -0700 > Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > > Hi Enrico, > > > > I don't think you're doing anything wrong - this is a > >bug, likely a generic > > issue with the way covering grids get filled out for > >octree data. > > > > This issue with smoothed_covering_grid is likely > >another, different but > > related bug. > > > > Can you create an issue to track this? > > > > https://bitbucket.org/yt_analysis/yt/issues/new > > > > -Nathan > > > > On Wed, Mar 23, 2016 at 9:36 AM, Enrico Garaldi > ><egaraldi(a)uni-bonn.de> > > wrote: > > > >> Hi, > >> I am having troubles using the smoothed_covering_grid > >>and covering_grid > >> with RAMSES dataset. > >> I have yt-project version 3.2.3 and I am using the > >>"output_00080" dataset > >> from the yt sample datasets. > >> > >> smoothed_covering_grid fails (raising a RuntimeError > >>because tot != 0, > >> line 880 of construction_data_containers.pyc), while > >>covering_grid seems to > >> leave unfilled the refined regions. What I mean is that > >>if a cell is > >> refined beyond the maximum allowed level for the grid, > >>it is left unfilled > >> (contrary to what happens with ENZO datasets). > >> > >> I am using this code: > >> > >> import yt > >> import matplotlib.pyplot as plt > >> > >> ds = > >>yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt') > >> > >> cgrid = ds.covering_grid(0, > >>left_edge=ds.domain_left_edge, > >> dims=ds.domain_dimensions) > >> > >> density_field = cgrid["density"] > >> > >> print (density_field == 0.0).any() #should be False but > >>it is True > >> > >> plt.imshow(density_field[:,:,48].v, > >>interpolation='none') > >> plt.show() #holes with zero-density corresponding to > >>refined regions > >> > >> Am I doing something wrong? > >> > >> Thanks in advance, > >> Enrico > >> > >> ------------------------------------- > >> Enrico Garaldi - Ph.D. student > >> Argelander-Institut f?r Astronomie > >> Address: Auf dem H?gel 71, 53121 Bonn, Germany > >> Room: 1.024 > >> Phone: +49 (0) 228 73 3433 > >> egaraldi[at]uni-bonn[dot]de > >> _______________________________________________ > >> yt-users mailing list > >> yt-users(a)lists.spacepope.org > >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > >> > > ------------------------------------- > Enrico Garaldi - Ph.D. student > Argelander-Institut f?r Astronomie > Address: Auf dem H?gel 71, 53121 Bonn, Germany > Room: 1.024 > Phone: +49 (0) 228 73 3433 > egaraldi[at]uni-bonn[dot]de > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 97, Issue 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.**"*

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smoothed particle velocities onto unigrid
by Desika Narayanan March 23, 2016

March 23, 2016

Hey All, I'm having some trouble smoothing particle velocities onto a uniform (arbitrary_grid) grid. The basic idea is that I create an arbitrary grid, then want to access the particle quantities smoothed onto that grid. Some are relatively easy, like: mass = obj[('deposit','PartType0_mass')].in_units('Msun') and for others, where deposited fields don't already exist, I can create those fields and it all works well: ds.add_deposited_particle_field(('PartType0', 'Temperature'),'sum') temp = obj[('deposit', 'PartType0_sum_Temperature')] but when either trying to access a deposited particle field, or creating one with the velocities, errors are abound. I'm sure I'm just doing something foolish, but could use a little nudge in the right direction. I created a self-contained script using the gadget zoom data set on the yt datsets to show the problem, with two different error messages pastebinned (links in the script) here: http://paste.yt-project.org/show/6352/ any help would be greatly appreciated! thanks, desika

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covering_grid with RAMSES dataset
by Enrico Garaldi March 23, 2016

March 23, 2016

Hi, I am having troubles using the smoothed_covering_grid and covering_grid with RAMSES dataset. I have yt-project version 3.2.3 and I am using the "output_00080" dataset from the yt sample datasets. smoothed_covering_grid fails (raising a RuntimeError because tot != 0, line 880 of construction_data_containers.pyc), while covering_grid seems to leave unfilled the refined regions. What I mean is that if a cell is refined beyond the maximum allowed level for the grid, it is left unfilled (contrary to what happens with ENZO datasets). I am using this code: import yt import matplotlib.pyplot as plt ds = yt.load('/users/egaraldi/Documents/output_00080/info_00080.txt') cgrid = ds.covering_grid(0, left_edge=ds.domain_left_edge, dims=ds.domain_dimensions) density_field = cgrid["density"] print (density_field == 0.0).any() #should be False but it is True plt.imshow(density_field[:,:,48].v, interpolation='none') plt.show() #holes with zero-density corresponding to refined regions Am I doing something wrong? Thanks in advance, Enrico ------------------------------------- Enrico Garaldi - Ph.D. student Argelander-Institut für Astronomie Address: Auf dem Hügel 71, 53121 Bonn, Germany Room: 1.024 Phone: +49 (0) 228 73 3433 egaraldi[at]uni-bonn[dot]de

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yt3.3dev MPI puzzle
by Stuart Levy March 22, 2016

March 22, 2016

Hello yt people, I'm trying to use MPI on a simple Enzo volume-rendering script, using the latest yt33 dev from bitbucket, and am getting a puzzling behavior. (MPI so as to reduce the load time.) Symptom: the datatype of the Scene.last_render field is inconsistent: it's YTImageArray when successful, but just plain YTArray when using MPI on the right (wrong) data, and so sc.save() fails. It's easy to work around and save the image another way, but makes me worried that something else is wrong, or that I'm misusing yt. It is somehow data-dependent. The error doesn't happen when I use the tiny enzo dataset in .../yt-hg/tests/DD0010/moving7_0010, nor the enzo_tiny_cosmology sample (DD0043). But it *does* happen when I use a somewhat-larger-but-not-huge simulation from John Wise - the low-resolution PopIII-star simulation he'd given us last year. A single timestep from it is ~46MB and has only a few dozen grids. I could post the data somewhere if John Wise would be OK with that - John? Demo code in: http://paste.yt-project.org/show/6343/ And its output when run under mpirun: http://paste.yt-project.org/show/6344/ The one change to the yt code from 'tip' (bed01b2c838c) is this diagnostic: diff -r bed01b2c838c yt/visualization/volume_rendering/scene.py --- a/yt/visualization/volume_rendering/scene.py Mon Mar 21 14:15:54 2016 -0700 +++ b/yt/visualization/volume_rendering/scene.py Mon Mar 21 18:01:20 2016 -0500 @@ -284,6 +284,7 @@ self.render() mylog.info("Saving render %s", fname) + print "about to write_png() - Scene.last_render", type(self.last_render), "shape",self.last_render.shape, " => ", dir(self.last_render) self.last_render.write_png(fname, sigma_clip=sigma_clip)

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editing colormap for sliceplots does not work?
by Jonah Miller March 22, 2016

March 22, 2016

Hello everyone, I am trying to create custom colorbar ticks using yt 3.2.3. I am roughly following this guide: http://yt-project.org/doc/cookbook/custom_colorbar_tickmarks.html However, this approach doesn't seem to work. I attach an example script using random input data. Is this a bug? Thanks for your help! Best, Jonah

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'FLASHDataset' object has no attribute 'field_info'
by Daniel Fenn March 18, 2016

March 18, 2016

Hi, I'm trying to calculate the center of mass of my FLASH dataset using the following: import yt ds = yt.load("path/to/file") ad = ds.all_data() print ad.quantities.center_of_mass() However, the last line throws the error: 'FLASHDataset' object has no attribute 'field_info' . As a test, I ran ds.field_info["flash", "temp"] which gives the same error. Can anyone give me any advice on what's going on and how to get past this error? Thanks, Dan

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Error while using annotate magnetic fields
by Sushilkumar March 16, 2016

March 16, 2016

Hi Suoqing Ji Thank you. On Wed, Mar 16, 2016 at 4:24 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: Error while using annotate magnetic fields (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 16 Mar 2016 14:24:00 -0700 > From: Suoqing Ji <suoqing(a)physics.ucsb.edu> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Error while using annotate magnetic fields > Message-ID: <9F981579-C3B2-44A5-840C-DB87BE75AFC6(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Sushil, > > I think so ? here is an example of 3D streamline with mplot3d: > http://yt-project.org/docs/dev/cookbook/complex_plots.html#plotting-streaml… > < > http://yt-project.org/docs/dev/cookbook/complex_plots.html#plotting-streaml…>, > and you could modify it for quiver plotting by adopting this example: > http://matplotlib.org/examples/mplot3d/quiver3d_demo.html < > http://matplotlib.org/examples/mplot3d/quiver3d_demo.html> > > Best wishes, > -- > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://web.physics.ucsb.edu/~suoqing > > > On Mar 16, 2016, at 1:56 PM, Sushilkumar <sushil.sush19us(a)gmail.com> > wrote: > > > > Dear Suoqing Ji and yt: > > > > Thank you for your help. It worked > > > > In addition, does yt support 3D quiver plots? > > > > If not what is the equivalent for visualizing 3d magnetic fields. > > > > > > On Wed, Mar 16, 2016 at 2:49 PM, <yt-users-request(a)lists.spacepope.org > <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. Error while using annotate magnetic fields (Sushilkumar) > > 2. Re: Error while using annotate magnetic fields (Suoqing Ji) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Wed, 16 Mar 2016 14:16:37 -0500 > > From: Sushilkumar <sushil.sush19us(a)gmail.com <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] Error while using annotate magnetic fields > > Message-ID: > > < > CAKARaKWgFBsh7qZj8Px+OS0-tDUOuKcv2MrWyJh3NaGtj06-9g(a)mail.gmail.com > <mailto: > CAKARaKWgFBsh7qZj8Px%2BOS0-tDUOuKcv2MrWyJh3NaGtj06-9g(a)mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > Dear yt: > > > > I am trying to plot magnetic field lines using the annotate magnetic > field > > call back from the link > http://yt-project.org/doc/visualizing/callbacks.html < > http://yt-project.org/doc/visualizing/callbacks.html> > > link. > > > > However, after running the script it gives the error below. A google > drive > > link to my script (yt_numpy_load_B.py) is also given below. When I use > > quiver annotate it works fine but issue comes when I am using > > slc.annotate_magnetic_field(). > > Quiver plots are also available on the drive link. > > > > Thanks in advance > > > > =============== > > Google drive link > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> > > =============== > > > > =============== > > Error while running the script > > > > File "yt_numpy_load_B.py", line 47, in <module> > > slc.save() > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_container.py", > > line 77, in newfunc > > args[0]._setup_plots() > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > > line 980, in _setup_plots > > self.run_callbacks() > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > > line 1033, in run_callbacks > > sys.exc_info()[2]) > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > > line 1029, in run_callbacks > > callback(cbw) > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", > > line 316, in __call__ > > return qcb(plot) > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", > > line 357, in __call__ > > fv_x = plot.data[self.field_x] > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", > > line 246, in __getitem__ > > f = self._determine_fields([key])[0] > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", > > line 518, in _determine_fields > > finfo = self.ds._get_field_info("unknown", fname) > > File > > > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.py", > > line 543, in _get_field_info > > raise YTFieldNotFound((ftype, fname), self) > > yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field > > callback failed with the following error: Could not find field '('all', > > 'magnetic_field_x')' in UniformGridData. > > =============== > > > > > > > > > > On Wed, Mar 16, 2016 at 12:52 PM, <yt-users-request(a)lists.spacepope.org > <mailto:yt-users-request@lists.spacepope.org>> > > wrote: > > > > > Send yt-users mailing list submissions to > > > yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org> > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > <http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> > > > or, via email, send a message with subject or body 'help' to > > > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(a)lists.spacepope.org> > > > > > > You can reach the person managing the list at > > > yt-users-owner(a)lists.spacepope.org <mailto: > yt-users-owner(a)lists.spacepope.org> > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of yt-users digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Re: Making averaged line plot. (Suoqing Ji) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 15 Mar 2016 15:23:43 -0700 > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu>> > > > To: Discussion of the yt analysis package > > > <yt-users(a)lists.spacepope.org <mailto: > yt-users(a)lists.spacepope.org>> > > > Subject: Re: [yt-users] Making averaged line plot. > > > Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109(a)physics.ucsb.edu > <mailto:70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Yuxiao, > > > > > > If you would like to start from your current code, the most > > > straightforward way is to write a loop to smooth over a certain > distance by > > > each step, which also works for AMR data: > > > > > > smooth_len = 100 # smoothing length of 100 kpc > > > SmoothedBMag = np.copy(ray[?ScaledBMag?]) # store the smoothed array > > > bin_num = np.ceiling((ray[?x?].max() - ray[?x?].min()) / smooth_len) # > > > make bins every 100 kpc > > > > > > for step in range(bin_num): > > > mask1 = (ray[?x?] >= ray[?x?].min() + step * smooth_len) > > > mask2 = (ray[?x?] < ray[?x?].min() + (step + 1) * smooth_len) > > > mask = np.logical_and(mask1, mask2) # mask the cells within a > certain > > > length of 100 kpc > > > SmoothedBMag[mask] = np.mean(ray[?ScaledBMag?][mask]) # take the > > > average and save > > > > > > After that the array ?SmoothedBMag? is the smoothed one. > > > > > > However, an easier way is to use the the 1D ProfilePlot function ( > > > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots > <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots> < > > > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots > <http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>>), > > > and in this case you could do something like: > > > > > > plot = ProfilePlot(pf.h.all_data(), ?x?, [?ScaledBMag?], > n_bins=bin_num) > > > > > > Note that this will do the average over entire y-z plane for each x > bins, > > > which is different from averaging only an array of a ray object (so > maybe > > > it?s not what you want). If you really want the data within a thin slit > > > only, you could define a region object pf.h.region() and do > ProfilePlot. I > > > think it?s also doable to use the function ?load_uniform_grid? to > create a > > > 1D dataset from the arrays in ray object and pass it to ProfilePlot. > > > > > > Best wishes, > > > -- > > > Suoqing JI > > > Ph.D Candidate > > > Department of Physics > > > University of California, Santa Barbara > > > http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> > > > > > > > On Mar 14, 2016, at 10:57 PM, Yuxiao Dai <yuxiao.dai(a)nyu.edu > <mailto:yuxiao.dai@nyu.edu>> wrote: > > > > > > > > Dear all, > > > > > > > > I have a line plot of some parameter along an axis as a function of > > > distance. Now I would like to get another line plot of the same > parameter > > > but averaged over a certain distance (say 100 kpc, the plot below is > > > supposed to be flat after this). I've been searching the document for > some > > > time but haven't found a method. Is there a simple way to do this? > > > > > > > > I would very much appreciate it if anyone could help me on this. > > > > > > > > > > > > =================================== > > > > import ... > > > > > > > > def _ScaledBMag(field, data): > > > > > > > > return ... > > > > > > > > > > > > > > > > .... > > > > > > > > pf = load(filename) > > > > > > > > add_field("ScaledBMag", function=_ScaledBMag) > > > > > > > > > > > > > > > > c = pf.h.find_max('ScaledBMag')[1] > > > > > > > > ax = 0 > > > > > > > > ray = pf.h.ortho_ray(ax, (c[1], c[2])) > > > > > > > > > > > > P.subplot(211) > > > > > > > > P.semilogy(ray['x'], ray['ScaledBMag']) > > > > > > > > P.xlabel('x') > > > > > > > > P.ylabel('ScaledBMag') > > > > > > > > print "works" > > > > > > > > P.savefig("ScaledBMag_lineplot.png") > > > > > > > > > > > > <image.png> > > > > > > > > =================================== > > > > I'm using yt > > > > > > > > Version = 2.6.1 > > > > > > > > > > > > Changeset = c994959ed3be > > > > > > > > =================================== > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > Dai > > > > > > > > _______________________________________________ > > > > yt-users mailing list > > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> > > > > > > -------------- next part -------------- > > > An HTML attachment was scrubbed... > > > URL: < > > > > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > > > > > > > > > ------------------------------ > > > > > > Subject: Digest Footer > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org < > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org> > > > > > > > > > ------------------------------ > > > > > > End of yt-users Digest, Vol 97, Issue 19 > > > **************************************** > > > > > > > > > > > -- > > *SK2* > > > > *"**Claiming that something can move faster than light is a good > > conversation-stopper in physics. People edge away from you in cocktail > > parties; friends never return phone calls. You just don?t mess with > Albert > > Einstein.**"* > > -------------- 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, 16 Mar 2016 12:49:09 -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] Error while using annotate magnetic fields > > Message-ID: <9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA(a)physics.ucsb.edu > <mailto:9CA99B80-FF30-44F0-B8C8-74EBC0A4E3CA@physics.ucsb.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Sushil, > > > > I think what you need to do is to assign the correct field name when > loading the data. In your script, you have: > > > > data = dict(field1 = field1, > > field2 = field2, > > field3 = field3) > > > > which could be, say, > > > > data = dict(magnetic_field_x = field1, > > magnetic_field_y = field2, > > magnetic_field_z = field3) > > > > since annotate_magnetic_field will directly refer to these field names > (in fact it's a specialized version of annotate_quiver). > > > > Best wishes, > > -- > > Suoqing JI > > Ph.D Candidate > > Department of Physics > > University of California, Santa Barbara > > http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> > > > > > On Mar 16, 2016, at 12:16 PM, Sushilkumar <sushil.sush19us(a)gmail.com > <mailto:sushil.sush19us@gmail.com>> wrote: > > > > > > Dear yt: > > > > > > I am trying to plot magnetic field lines using the annotate magnetic > field call back from the link > http://yt-project.org/doc/visualizing/callbacks.html < > http://yt-project.org/doc/visualizing/callbacks.html> < > http://yt-project.org/doc/visualizing/callbacks.html < > http://yt-project.org/doc/visualizing/callbacks.html>> link. > > > > > > However, after running the script it gives the error below. A google > drive link to my script (yt_numpy_load_B.py) is also given below. When I > use quiver annotate it works fine but issue comes when I am using > slc.annotate_magnetic_field(). > > > Quiver plots are also available on the drive link. > > > > > > Thanks in advance > > > > > > =============== > > > Google drive link > > > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc> < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc < > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc>> > > > =============== > > > > > > =============== > > > Error while running the script > > > > > > File "yt_numpy_load_B.py", line 47, in <module> > > > slc.save() > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_container.py", > line 77, in newfunc > > > args[0]._setup_plots() > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > line 980, in _setup_plots > > > self.run_callbacks() > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > line 1033, in run_callbacks > > > sys.exc_info()[2]) > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_window.py", > line 1029, in run_callbacks > > > callback(cbw) > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", > line 316, in __call__ > > > return qcb(plot) > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/visualization/plot_modifications.py", > line 357, in __call__ > > > fv_x = plot.data[self.field_x] > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", > line 246, in __getitem__ > > > f = self._determine_fields([key])[0] > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/data_containers.py", > line 518, in _determine_fields > > > finfo = self.ds._get_field_info("unknown", fname) > > > File > "/state/partition1/anaconda/lib/python2.7/site-packages/yt/data_objects/static_output.py", > line 543, in _get_field_info > > > raise YTFieldNotFound((ftype, fname), self) > > > yt.utilities.exceptions.YTPlotCallbackError: annotate_magnetic_field > callback failed with the following error: Could not find field '('all', > 'magnetic_field_x')' in UniformGridData. > > > =============== > > > > > > > > > > > > > > > On Wed, Mar 16, 2016 at 12:52 PM, < > yt-users-request(a)lists.spacepope.org <mailto: > yt-users-request(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: Making averaged line plot. (Suoqing Ji) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 15 Mar 2016 15:23:43 -0700 > > > From: Suoqing Ji <suoqing(a)physics.ucsb.edu <mailto: > suoqing(a)physics.ucsb.edu> <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] Making averaged line plot. > > > Message-ID: <70E5BA6C-7798-45F2-AE83-21233252E109(a)physics.ucsb.edu > <mailto:70E5BA6C-7798-45F2-AE83-21233252E109@physics.ucsb.edu> <mailto: > 70E5BA6C-7798-45F2-AE83-21233252E109(a)physics.ucsb.edu <mailto: > 70E5BA6C-7798-45F2-AE83-21233252E109(a)physics.ucsb.edu>>> > > > Content-Type: text/plain; charset="utf-8" > > > > > > Hi Yuxiao, > > > > > > If you would like to start from your current code, the most > straightforward way is to write a loop to smooth over a certain distance by > each step, which also works for AMR data: > > > > > > smooth_len = 100 # smoothing length of 100 kpc > > > SmoothedBMag = np.copy(ray[?ScaledBMag?]) # store the smoothed array > > > bin_num = np.ceiling((ray[?x?].max() - ray[?x?].min()) / smooth_len) # > make bins every 100 kpc > > > > > > for step in range(bin_num): > > > mask1 = (ray[?x?] >= ray[?x?].min() + step * smooth_len) > > > mask2 = (ray[?x?] < ray[?x?].min() + (step + 1) * smooth_len) > > > mask = np.logical_and(mask1, mask2) # mask the cells within a > certain length of 100 kpc > > > SmoothedBMag[mask] = np.mean(ray[?ScaledBMag?][mask]) # take the > average and save > > > > > > After that the array ?SmoothedBMag? is the smoothed one. > > > > > > However, an easier way is to use the the 1D ProfilePlot function ( > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots> < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>> < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots> < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots < > http://yt-project.org/docs/2.6/visualizing/plots.html#d-profile-plots>>>), > and in this case you could do something like: > > > > > > plot = ProfilePlot(pf.h.all_data(), ?x?, [?ScaledBMag?], > n_bins=bin_num) > > > > > > Note that this will do the average over entire y-z plane for each x > bins, which is different from averaging only an array of a ray object (so > maybe it?s not what you want). If you really want the data within a thin > slit only, you could define a region object pf.h.region() and do > ProfilePlot. I think it?s also doable to use the function > ?load_uniform_grid? to create a 1D dataset from the arrays in ray object > and pass it to ProfilePlot. > > > > > > Best wishes, > > > -- > > > Suoqing JI > > > Ph.D Candidate > > > Department of Physics > > > University of California, Santa Barbara > > > http://web.physics.ucsb.edu/~suoqing < > http://web.physics.ucsb.edu/~suoqing> < > http://web.physics.ucsb.edu/~suoqing <http://web.physics.ucsb.edu/~suoqing > >> > > > > > > > On Mar 14, 2016, at 10:57 PM, Yuxiao Dai <yuxiao.dai(a)nyu.edu > <mailto:yuxiao.dai@nyu.edu> <mailto:yuxiao.dai@nyu.edu <mailto: > yuxiao.dai(a)nyu.edu>>> wrote: > > > > > > > > Dear all, > > > > > > > > I have a line plot of some parameter along an axis as a function of > distance. Now I would like to get another line plot of the same parameter > but averaged over a certain distance (say 100 kpc, the plot below is > supposed to be flat after this). I've been searching the document for some > time but haven't found a method. Is there a simple way to do this? > > > > > > > > I would very much appreciate it if anyone could help me on this. > > > > > > > > > > > > =================================== > > > > import ... > > > > > > > > def _ScaledBMag(field, data): > > > > > > > > return ... > > > > > > > > > > > > > > > > .... > > > > > > > > pf = load(filename) > > > > > > > > add_field("ScaledBMag", function=_ScaledBMag) > > > > > > > > > > > > > > > > c = pf.h.find_max('ScaledBMag')[1] > > > > > > > > ax = 0 > > > > > > > > ray = pf.h.ortho_ray(ax, (c[1], c[2])) > > > > > > > > > > > > P.subplot(211) > > > > > > > > P.semilogy(ray['x'], ray['ScaledBMag']) > > > > > > > > P.xlabel('x') > > > > > > > > P.ylabel('ScaledBMag') > > > > > > > > print "works" > > > > > > > > P.savefig("ScaledBMag_lineplot.png") > > > > > > > > > > > > <image.png> > > > > > > > > =================================== > > > > I'm using yt > > > > > > > > Version = 2.6.1 > > > > > > > > > > > > Changeset = c994959ed3be > > > > > > > > =================================== > > > > > > > > > > > > > > > > > > > > > > > > Regards, > > > > > > > > Dai > > > > > > > > _______________________________________________ > > > > yt-users mailing list > > > > yt-users(a)lists.spacepope.org <mailto:yt-users@lists.spacepope.org> > <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 19 > > > **************************************** > > > > > > > > > > > > -- > > > SK2 > > > > > > "Claiming that something can move faster than light is a good > conversation-stopper in physics. People edge away from you in cocktail > parties; friends never return phone calls. You just don?t mess with Albert > Einstein." > > > > > > _______________________________________________ > > > yt-users mailing list > > > yt-users(a)lists.spacepope.org <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 20 > > **************************************** > > > > > > > > -- > > SK2 > > > > "Claiming that something can move faster than light is a good > conversation-stopper in physics. People edge away from you in cocktail > parties; friends never return phone calls. You just don?t mess with Albert > Einstein." > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 97, Issue 22 > **************************************** > -- *SK2* *"**Claiming that something can move faster than light is a good conversation-stopper in physics. People edge away from you in cocktail parties; friends never return phone calls. You just don’t mess with Albert Einstein.**"*

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