yt-users December 2014

yt-users@python.org

30 participants
37 discussions

install failure on os x 10.9.5
by Desika Narayanan 04 Dec '14

04 Dec '14

Hi All, I'm getting an installation failure that I haven't seen before - I'm trying to install on 10.9.5 OSX, and have xcode and command line tools installed. The failure I get right off the bat is appended below. I haven't edited the install script to allow for root install (because I'm not sure that should be necessary?). But, at the same time, nothing seemed weird about the Xcode or command line tools installation. Has anyone seen an error like this before? Thanks, -d ******************************************** ******************************************** jam:~ desika$ cat yt-x86_64/yt_install.log cloudy_emissivity.h5: OK apec_emissivity.h5: OK hdf5-1.8.11.tar.gz: OK zlib-1.2.8.tar.gz: OK bzip2-1.0.6.tar.gz: OK libpng-1.6.3.tar.gz: OK freetype-2.4.12.tar.gz: OK sqlite-autoconf-3071700.tar.gz: OK zeromq-4.0.4.tar.gz: OK pyzmq-14.3.1.tar.gz: OK tornado-4.0.1.tar.gz: OK Python-2.7.8.tgz: OK numpy-1.8.2.tar.gz: OK matplotlib-1.4.0.tar.gz: OK mercurial-3.1.tar.gz: OK ipython-2.2.0.tar.gz: OK h5py-2.3.1.tar.gz: OK Cython-0.20.2.tar.gz: OK reason-js-20120623.zip: OK nose-1.3.4.tar.gz: OK python-hglib-1.0.tar.gz: OK sympy-0.7.5.tar.gz: OK Agreeing to the Xcode/iOS license requires admin privileges, please re-run as root via sudo.

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using show() in ipython/python
by Johanna Malinen 04 Dec '14

04 Dec '14

Hi, I just installed the yt development version http://hg.yt-project.org/yt/raw/yt/doc/install_script.sh Version = 3.1-dev Changeset = dc2ade033502 (yt) tip into ubuntu 14.04 with INST_ZLIB=0 INST_FTYPE=0 yt seemed to install properly and it works otherwise, but it doesn't open any windows when I'm trying to show an image, e.g., when running the script http://yt-project.org/doc/quickstart/3)_Simple_Visualization.py line by line in ipython: p = yt.ProjectionPlot(ds, "y", "density") p.show() #doesn't open a window In [35]: p.show() <yt.visualization.plot_window.ProjectionPlot at 0x7fe1897941d0> However, saving the image works: p.save() When I run that script directly with python, I get the following error: Traceback (most recent call last): File "3)_Simple_Visualization_short.py", line 28, in <module> p.show() File "/home/.../yt/yt-x86_64/src/yt-hg/yt/visualization/plot_container.py", line 622, in show raise YTNotInsideNotebook yt.utilities.exceptions.YTNotInsideNotebook: This function only works from within an IPython Notebook. I'm using ipython --matplotlib from pylab import * and e.g. plot() and figure() open a window normally. Is there a way to open a window with yt's show() and other functions using ipython and python, or does that really require IPython Notebook? Cheers, Johanna

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Monochrome & transparent isosurfaces
by Adam Ginsburg 04 Dec '14

04 Dec '14

Hi folks, I'm trying to use the isosurface tools (export_sketchfab & export_obj; http://yt-project.org/doc/visualizing/sketchfab.html) to make renderings of multiple line species from ALMA data cubes. I'm doing this using both the yt-fits interface and spectral-cube (spectral-cube.rtfd.org). I've had some success in getting multicolored and transparent contours to show up (e.g., https://sketchfab.com/models/8cddb94df8024c28ab3e4e5a43c2b069), but I still don't have complete control over the colors. To make that model, I created pure red/green/blue colormaps and added them to the colormap registry, e.g.: blue = mpl.colors.LinearSegmentedColormap('blue', {'red':[(0,0,0),(1,1,1)], 'green':[(0,0,0),(1,1,1)], 'blue':[(0,1,1),(1,1,1)]}) from yt.visualization._colormap_data import color_map_luts color_map_luts['blue'] = blue(np.linspace(0,1,256)).T but that was fairly awkward, and the contours are still showing up white-ish. I think this is because I have set the color_field to the flux_field (I only have one field to work with!): surf = dataset.surface(dataset.all_data(), dataset.field_list[0], level) surf.export_obj(filename, transparency=transparency, color_field=dataset.field_list[0], color_map='blue', plot_index=jj) but I can't figure out an alternative way to specify color, except perhaps to define a dummy field that is all 1 - which I also don't know how to do, but I'm sure I could figure it out. Is there a better way, though? Also, when I try importing my meshes into MeshLab, I get the error: Error details: Some materials definitions were not found, a default white material is used where no material was available and then the contours all show up as gray and opaque, even if I change "render->color" to "per face" as suggested in the docs. But, I've never used MeshLab before, so I might just be misusing the program. Thanks, -- Adam Ginsburg Fellow, European Southern Observatory http://www.adamgginsburg.com/

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domain-decomposition for volume rendering huge brick?
by Stuart Levy 02 Dec '14

02 Dec '14

Hello all, We're hoping to use yt parallel volume rendering on a very large generic brick - it's a simple rectangular unigrid slab, but containing something like 1.5e11 points, so much too large for load_uniform_grid() to load into memory in a single machine. I imagine it wouldn't be hard to do the domain decomposition by hand, loading a different chunk of grid into each MPI process. But then what? What would it take to invoke the volume renderer on each piece and composite them together? Would it help if the chunks were stored in a KDTree? Is there some example (one of the existing data loaders?) which I could follow?

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Reading athena output
by almog yalin 02 Dec '14

02 Dec '14

Hi. I ran a 2D simulation with Athena and exported the data to vtk files. I was even able to load the file with yt and inspect some of its elements. What I would like to do is to compare the density from the simulation to an analytic solution (which I can evaluate at the grid points). The problem is I cannot figure out how to extract the relevant information from the yt.frontends.athena.data_structures.AthenaDataset object. What I expect are 2d arrays of the x coordinate, y coordinate and density. Thanks in Advance, Almog

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Performance when using derived fields
by Daniel Fenn 02 Dec '14

02 Dec '14

Hi everyone. Is it normal for slices to take substantially longer to be created if they're made from a derived field rather than an intrinsic one? Specifically, I'm having an issue creating an axis-aligned slice using the divergence of the velocity field. It's taking around 6.5 minutes just to make the slice, whereas if I use temperature or density, it takes around 10 seconds or so for the same dataset. I also notice that the amount of time it takes is not dependent on the number of processors I'm using. I've used 1, 12, and 24 processors, with identical results, even though I'm calling enable_parallelism(), and I can see that all the processes are running. I read in the docs that slice operations aren't generally done in parallel, but in this case it seems that maybe it would be beneficial. A similar operation in VisIt completes much faster, so I'm wondering if I've misconfigured something, or if there is something I can do to speed things up. I'd appreciate any thoughts anyone has on the subject. Thanks, Dan

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Volume Rendering and Field lines
by Dionysopoulou K. 01 Dec '14

01 Dec '14

Dear all, I would like to ask if there has been any progress on the volume rendering refactoring since late October. In particular, I would like to know if volume rendering and the new camera implementation allows for plotting field lines together with the rendering. If so, are there any examples on the web? Unfortunately, matplotlib contour plots with field lines are not good enough for me. Thanks in advance, Kiki Kyriaki Dionysopoulou ======================================================= Mathematical Sciences University of Southampton Southampton, SO17 1BJ, UK K.Dionysopoulou(a)soton.ac.uk<mailto:K.Dionysopoulou@soton.ac.uk>

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yt-users December 2014