Mailman 3 July 2017 - yt-users

Re: [yt-users] customizing colorbar
by sacielo July 10, 2017

July 10, 2017

Many thanks Nathan for the brilliant reply and solution. I could edit it easily with plot._font_properties. Only, when the colorbar is horizontal one should use new_ax.xaxis instead of new_ax.yaxis (took me a bit to spot it), but it is true that like this one can have complete control over the colorbar. Best, On Sat, Jul 8, 2017 at 8:34 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. customizing colorbar (sacielo) > 2. Re: customizing colorbar (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 8 Jul 2017 10:48:20 +0200 > From: sacielo <sacielo(a)gmail.com> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] customizing colorbar > Message-ID: > <CALAgqdL+fOwJoB+8---Yh3YYHbLwimDS+DrbO0GpbV3iXCeSPQ(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I was trying to change the looks of the colorbar of slice plots; first I > found out I could create a new colorbar in a new position. I obtained > something I like very much like this (for some dataset ds): > > ?myvar = 'density' > sl = yt.SlicePlot(ds, 'x', myvar, center='c', width=(3,'kpc')) > sl.hide_colorbar() > sl.hide_axes() > plot = sl.plots[myvar] > fig = plot.figure > new_ax = fig.add_axes((0.025,0.94,0.75,0.025)) > ?? > cb = plot.figure.colorbar(plot.image, new_ax, extend='both', > orientation='horizontal', format='%.0E'?)? > sl._setup_plots() > > ?The only problem now is I cannot change the font properties of this new > colorbar. Even trying?, e.g.: > > sl.set_font({'family': 'sans-serif', 'style': 'normal', 'weight': 'normal', > 'size': 36}) > > ?will change all fonts, including the default colorbar, all text and > annotations, but not this new colorbar. > I think plot.figure.colorbar does not accept any argument to edit the font. > > Do you know how I could change this? Or maybe have I gone down the wrong > path? > ?I wouldn't like to do all manually with matplotlib, as I plan to add many > more yt annotations to this plot, which all work very well. > > ?Thank you!? > > ?Best,? > > -- > Salvatore > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://lists.spacepope.org/pipermail/yt-users-spacepope. > org/attachments/20170708/ad1d41c4/attachment.html> > > ------------------------------ > > Message: 2 > Date: Sat, 8 Jul 2017 08:29:28 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] customizing colorbar > Message-ID: > <CAJXewOns=aZfkkYoxaP+2HuBLahkrsU4zyMzp__yoiKSW- > FcoA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Sat, Jul 8, 2017 at 3:48 AM, sacielo <sacielo(a)gmail.com> wrote: > > > Hello, > > > > I was trying to change the looks of the colorbar of slice plots; first I > > found out I could create a new colorbar in a new position. I obtained > > something I like very much like this (for some dataset ds): > > > > ?myvar = 'density' > > sl = yt.SlicePlot(ds, 'x', myvar, center='c', width=(3,'kpc')) > > sl.hide_colorbar() > > sl.hide_axes() > > plot = sl.plots[myvar] > > fig = plot.figure > > > > Rather than creating a new colorbar, you can get access to the original > colorbar via plot.cb and the original colorbar axes via plot.cax. > > However, I don't think there's an easy way to make a colorbar horizontal > after its already been created. > > Right now yt's plots don't have a mode to create a horizontal colorbar. > They aren't really designed for total customization, they're optimized for > quick plotting and as such make many assumptions about how the plots look. > So you're running into a mismatch between assumptions the plotting system > needs to make about how the plots should look to avoid making people > manually create plots every time, and the inflexibility that implies if you > really *do* want to manually plot something. > > If you want fully manual control over the plot looks and don't want to use > the axes and colorbar yt is creating, then you may want to manually > construct the plots using an image buffer. Here are some examples in the > docs on how to do that: > > http://yt-project.org/docs/dev/visualizing/manual_plotting.html > http://yt-project.org/docs/dev/cookbook/complex_plots. > html?highlight=manual#multi-plot-slice-and-projections > > Of course that doesn't let you use the yt plot annotations, so I don't > think that's what you're looking for either. > > > > new_ax = fig.add_axes((0.025,0.94,0.75,0.025)) > > ?? > > cb = plot.figure.colorbar(plot.image, new_ax, extend='both', > > orientation='horizontal', format='%.0E'?)? > > sl._setup_plots() > > > > ?The only problem now is I cannot change the font properties of this new > > colorbar. Even trying?, e.g.: > > > > sl.set_font({'family': 'sans-serif', 'style': 'normal', 'weight': > > 'normal', 'size': 36}) > > > > Another way to do this using your current approach would be to customize > the colorbar you're creating using the plot's new FontProperties instance. > After calling this function you can get access to the FontProperties > instance used via plot._font_properties. > > Next, you'd need to apply the new FontProperties to the tick marks and > labels on the colorbar you've created: > > fp = plot._font_properties > labels = new_ax.yaxis.get_ticklabels() > labels += [new_ax.yaxis.label, new_ax.yaxis.get_offset_text()] > for label in labels: > label.set_fontproperties(fp) > > Here's a worked out example: > > https://gist.github.com/anonymous/9a80cd6f0148d1df362a2c9cfb6d10da > > > > > > ?will change all fonts, including the default colorbar, all text and > > annotations, but not this new colorbar. > > I think plot.figure.colorbar does not accept any argument to edit the > font. > > > > Do you know how I could change this? Or maybe have I gone down the wrong > > path? > > ?I wouldn't like to do all manually with matplotlib, as I plan to add > many > > more yt annotations to this plot, which all work very well. > > > > ?Thank you!? > > > > ?Best,? > > > > -- > > Salvatore > > > > _______________________________________________ > > 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/20170708/39ec6e27/attachment-0001.htm> > > ------------------------------ > > 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 113, Issue 11 > ***************************************** > -- Salvatore

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Parallel Projection Plot Question
by Jared Coughlin July 8, 2017

July 8, 2017

Hello! I have a gadget snapshot with a modified block structure (namely, it's dark matter only and I've calculated densities and smoothing lengths for the dark matter particles). I wrote a simple script to make a projection plot, which works just fine in serial, but when I run it in parallel (on two processors, just for testing), I get the following error: https://pastebin.com/yjqR4Zw5 Basically, the error seems to be that task 1 is not recognizing the field ('deposit', 'Halo_density') but root does. This is my script: https://pastebin.com/0qhKDWhU I was just wondering how to fix this? Thanks! -Jared

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customizing colorbar
by sacielo July 8, 2017

July 8, 2017

Hello, I was trying to change the looks of the colorbar of slice plots; first I found out I could create a new colorbar in a new position. I obtained something I like very much like this (for some dataset ds): myvar = 'density' sl = yt.SlicePlot(ds, 'x', myvar, center='c', width=(3,'kpc')) sl.hide_colorbar() sl.hide_axes() plot = sl.plots[myvar] fig = plot.figure new_ax = fig.add_axes((0.025,0.94,0.75,0.025)) cb = plot.figure.colorbar(plot.image, new_ax, extend='both', orientation='horizontal', format='%.0E') sl._setup_plots() The only problem now is I cannot change the font properties of this new colorbar. Even trying, e.g.: sl.set_font({'family': 'sans-serif', 'style': 'normal', 'weight': 'normal', 'size': 36}) will change all fonts, including the default colorbar, all text and annotations, but not this new colorbar. I think plot.figure.colorbar does not accept any argument to edit the font. Do you know how I could change this? Or maybe have I gone down the wrong path? I wouldn't like to do all manually with matplotlib, as I plan to add many more yt annotations to this plot, which all work very well. Thank you! Best, -- Salvatore

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Inconsistency question.
by JASMIN HISON SHIN July 7, 2017

July 7, 2017

Dear yt-users, I have a vtk data file that I scp-ed onto my macbook from a supercomputer. On the supercomputer when I run this: p=yt.SlicePlot(ds,"z", "velocity_z", origin="native") p.annotate_quiver('velocity_x', 'velocity_y') on yt, I get the full picture, but when I run yt on my laptop with the same commands on the same data file, I get a fraction of the picture. Is there any reason for this? And is there anything I can do to get the same picture? Thank You, Jasmin

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writing to a file
by Stephanie Tonnesen July 7, 2017

July 7, 2017

Hi all, I am trying to write a bunch of information from a gas-only single enzo output to a file for colleagues to read. I don't think they are familiar with HDF5, so I am hoping to write to a fits file. What I want to put in the file is the x,y,z coordinates, the x,y,z velocity, and the total energy of the gas--which is a user-defined function in my case. Ideally I also only want to include gas that has a tracer fraction of some value. so basically I have something like: ds = yt.load("file") galgas = ds.cut_region(["obj['Metal_Density']/obj['density'] > 0.1"]) can I just create an array of the fields I want from galgas? Thanks, Stephanie -- Dr. Stephanie Tonnesen Alvin E. Nashman Postdoctoral Fellow Carnegie Observatories, Pasadena, CA stonnes(a)gmail.com

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Data around boundaries
by Lu, Yinghe July 4, 2017

July 4, 2017

Hi yt-ers, This may seem a stupid question but I haven't found anything in the documentation that explains it in detail. How does yt deal with accessing data outside the domain boundaries? For example, I notice that, if creating a sphere around domain left edge yt by default wraps around to the opposite edge of the domain assuming a periodic boundary condition and access data from there, while it doesn't do so for covering grids. Is there an option I can decide if I want to wrap around the domain or not based on the boundary condition that I am using? Thanks!

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Dark Sky Simulations, analysis gone wrong.
by ALEXANDROS TSOUROS July 2, 2017

July 2, 2017

Hello all! I am quite new to yt, so please bear with my ignorance! I need to perform analysis on the open data of the Dark Sky Simulation (http://darksky.slac.stanford.edu). In particular I need to create 1 dimensional profiles of the radial velocity of dark matter particles around halos. Attached, you'll find my attempt at producing such a profile. When I do this on a GADGET2 simulation I've run, I can use the 'radial_velocity' field without a problem. However, this script, where the data is that of the Dark Sky simulation, produces the following output : ' (...) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'radial_velocity')' in ds14_a_1.0000.' However, as I understand it, the field 'radial_velocity' is native to yt. How can I surpass this problem? Any help will be appreciated. Thank you very much for your time, Tsouros Alexandros

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Streamlines in FLASH
by Benny Tsang July 1, 2017

July 1, 2017

Hi yt friends, I'm trying to produce 3D streamlines using the AMR data from FLASH following the yt-project tutorial http://yt-project.org/doc/visualizing/streamlines.html. However, the execution was very slow (in particular, at the 'Streamlines' call). The code didn't complete one single streamline after an hour. Here's the excerpt of my code: ————— c = ds.domain_center streamlines = Streamlines(ds, c, 'velx', 'vely', 'velz', length=1.0*pc, get_magnitude=False) streamlines.integrate_through_volume() fig=plt.figure() ax = Axes3D(fig) 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) plt.savefig('streamlines.png') ————— I have two thoughts: 1. My FLASH file is quite large (~10GB). It may just be slow because of the large AMR grid size. Are there any ways to read only the velocities off the grid or only a subsection of the grid? 2. FLASH's octree data structure may be incompatible with the AMRKDTree construction (first step in streamlines creation). In the doc string of AMRKDTree, it says "Not applicable to particle or octree-based datasets.". If it's the case, I may have to find another way out. Thank you very much for your time! Have a great weekend! Best, Benny

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