Mailman 3 January 2018 - yt-users

Re: [yt-users] yt-users Digest, Vol 119, Issue 4
by Kezman Saboi 17 Jan '18

17 Jan '18

Hi Suoqing and all, I tried following the examples for projection generation that are shown in the yt manual but my plots are still not coming out as desired. The first three plots I have plotted are indicated below. Plots for checkpoints 1 and 2 are fine but checkpoint 3 and others that follow are coming out as either extreme zoomed in or distorted. Any ideas how I might correct this? Thank you, Kezman 1st checkpoint 2nd checkpoint 3rd checkpoint [image: Inline image 4] [image: Inline image 2] [image: Inline image 1] Kezman Saboi Barrett Honors College|Arizona State University Astrophysics Phone|480-819-5031 On Thu, Jan 4, 2018 at 12:39 AM, <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: Tracking a blob (Suoqing Ji) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Jan 2018 13:49:45 -0800 > 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] Tracking a blob > Message-ID: <4D51786E-22B3-4F62-938E-A6CE8B2387F9(a)physics.ucsb.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Kezman, > > ?origin? specifies the axis and your plot domain, and what you?re looking > for is the ?center? parameter, and provide the coordinates of the blob to > the parameter ?center?. You can find some similar SlicePlot examples with a > specified plot center here: http://yt-project.org/docs/ > dev/visualizing/plots.html#slice-plots <http://yt-project.org/docs/ > dev/visualizing/plots.html#slice-plots> > > Best wishes, > ? > Suoqing JI > Ph.D Candidate > Department of Physics > University of California, Santa Barbara > http://physics.ucsb.edu/~suoqing > > > On Jan 3, 2018, at 12:30 PM, Kezman Saboi <ksaboi(a)asu.edu> wrote: > > > > Hi, > > > > I am trying to create projections of a blob (a gas cloud) that is in > motion but I keep on having problems with plotting it such that it is at > the center of the plot. I have tried using origin = 'native' but it does > not seem to be helping. Could anyone please offer guidance? > > > > > > Thank you, > > > > > > Kezman Saboi > > Barrett Honors College|Arizona State University > > Astrophysics > > Phone|480-819-5031 > > _______________________________________________ > > 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/20180103/eab58eea/attachment-0001.html> > > ------------------------------ > > 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 119, Issue 4 > **************************************** >

2 1

Reading Array Data
by John Regan 11 Jan '18

11 Jan '18

Hi All, I'm trying to get YT to read a vector which is stored as part of particle structure in Enzo (a vector in the active particle structure). The data looks OK when I view the raw HDF5 data using hdfview. I find that in some snapshots YT can read the data but not in others. If there is more than one particle things get worse for sure. It could be that when writing to the HDF5 file I haven't put the data in a format that is compatible with YT. I've attached a simple script that will fall over when trying to read the data and a link to the enzo output (size = 12 GBs). The active particles are in files DD0120.cpu0022 (Grid 3072), DD0120.cpu0023 (Grid 3076) and DD0014 (Grid 3080). YT falls over in the io_handler but it's not obvious to me whether I need to modify that code or the format that I write the data to the HDF5 file in. Any help/pointers would be much appreciated. Cheers, John Link to dataset: https://www.dropbox.com/sh/o6acuvia1sqyp7y/AAC0lEI5lZ6bGa0tP2-G1jLea?dl=0

2 9

RecursionError when using SlicePlot
by Nicholas Wimer 10 Jan '18

10 Jan '18

Hello, I previously have not had any issues using yt, but today was forced to do a clean install of yt using the install script (same as I had done two months ago). However, this time I get a RecursionError when trying to use SlicePlot. The installer installed Python 3.6.4 and yt version 3.4.0. Perhaps of note is an additional FutureWarning message that I previously had not seen saying that the “Conversion of the second argument of issubdtype from ‘float’ to ‘np.floating’ is deprecated. In the future, it will be treated as ‘np.float64 == np.dtype(float).type’.” This warning originated from “yt-conda/lib/python3.6/site-packages/h5py/__init__.py:36” I would greatly appreciate any assistance in fixing this issue with SlicePlot. Thank you very much, Nick

3 3

Tracking a blob
by Kezman Saboi 03 Jan '18

03 Jan '18

Hi, I am trying to create projections of a blob (a gas cloud) that is in motion but I keep on having problems with plotting it such that it is at the center of the plot. I have tried using origin = 'native' but it does not seem to be helping. Could anyone please offer guidance? Thank you, Kezman Saboi Barrett Honors College|Arizona State University Astrophysics Phone|480-819-5031

2 1

Interactive Volume Rendering Screenshot
by Nicole DyAnn Melso 03 Jan '18

03 Jan '18

Hello, I am attempting to create a series of volume rendered images of my simulation at different time steps so that I can compile them into a movie. I want to use the maximum intensity fragment shader, which I believe is only available in the yt interactive volume rendering with OpenGL (I've looked into simply using a maximum intensity projection, but this is only available on-axis). I would like to be able to take a screenshot of the OpenGL window created when I run the yt interactive volume rendering, but I'm having difficulty adding this feature to the volume rendering source code in my local yt directory. Below is the modification I’ve made to the code as well as a screenshot of the problem. I have no prior experience with OpenGL. */yt/visualization/volume_rendering/interactive_vr.py* 846 def _retrieve_framebuffer(self): 847 ox, oy, width, height = GL. glGetIntegery(GL.GL_VIEWPORT) 848 + my_buffer = GL.glReadBuffer(GL.GL_FRONT) 849 - debug_buffer = GL.glReadPixels(0, 0, width, height, GL.GL_RGB, GL.GL_UNSIGNED_BYTE) 849 + debug_buffer = GL.glReadPixels(0, 0, width, height, GL.GL_RGB, GL.GL_UNSIGNED_BYTE, my_buffer) 850 arr = np.fromstring(debug_buffer, “unit8”, count, width*height*3) 851 return arr.reshape((width, height, 3)) */yt/visualization/volume_rendering/interactive_loop.py* 187 def __call__(self, scene, camera, callbacks): 188 while not glfw.WindowShouldClose(self.window) or self.should_quit: 189 callbacks(self.window) 190 if callbacks.draw: 191 camera.compute_matrices() 192 scene.set_camera(cameara) 193 scene.render() 194 glfw.SwapBuffers(self.window) 195 callbacks.draw = False 196 + arr = scene._retrieve_framebuffer() 197 + write_bitmap(arr, “test.png”) 198 glfw.PollEvents() 199 yield self 200 glfw.Terminate() The simulation is a single rectangular box, but the screenshot I get with the above code is multiple boxes that look like they should be overlaid? Maybe there is a simpler method of accomplishing this? I'd appreciate any suggestions. Thanks, Nicole Melso -- Nicole Melso NSF Graduate Research Fellow Columbia Astronomy Department

3 3