Mailman 3 April 2011 - yt-dev

Request for review of "minimal image" structure
by Matthew Turk 03 May '11

03 May '11

Hi all, I've been thinking about the best way to construct minimal image representations, which feed into the Reason / plotting refactor ideas. I started sketching out a minimally-reproducible phase plot in yt/visualization/profile_plotter.py, in the objects AxisSpec ColorbarSpec ImagePlotContainer I think that as it stands it encompasses how to save and then recreate a (simply) visualization, but I was wondering if some other people could look that over, and help me come up with ideas for what would be necessary to also make sure it faithfully represents image plots, 1D line plots, and so on. IT doesn't need to cover all possibilities, just the basic ones. Anyway, ideas would be greatly appreciated! Thanks! -Matt

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linear tickers
by j s oishi 27 Apr '11

27 Apr '11

hi Guys, I just put linear tickers into the Reason plot widget, copying from matplotlib like Matt did for the log tickers. However, it doesn't seem to want to print negative tick labels. The negative sign is there, but no number. I think this might be on the js side, and a cursory glance didn't reveal anything. Any ideas? thanks, j

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SciAm article
by Stephen Skory 25 Apr '11

25 Apr '11

Hi All, I wonder if any of you saw this: http://www.scientificamerican.com/article.cfm?id=the-lost-galaxies It's about baryonic inflows and outflows from galaxies, and discusses both observations and simulations. There are a few images shown made from their simulations that use streamlines to show the path of gas in and out of galaxies. The neat thing is I think that yt isn't too far from being able to do this, we just have to make the streamlines work over time-ordered datasets. I just thought you all might find it interesting, and hopefully all of your various .edu institutions have a subscription so you can see the full article online. -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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install script error?
by gso＠physics.ucsd.edu 23 Apr '11

23 Apr '11

I'm having trouble writing a plot png to disk, and it seems that my dev installation script might be the culprit, it's giving me the error: File "/nics/b/home/gsiisg/NautilusYT/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 180, in get_text_width_height_descent font = self._get_agg_font(prop) File "/nics/b/home/gsiisg/NautilusYT/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 221, in _get_agg_font font = FT2Font(str(fname)) RuntimeError: Could not open facefile /nics/b/home/gsiisg/NautilusYT/lib/python2.6/site-packages/matplotlib/mpl-data/fonts/ttf/Vera.ttf; Cannot_Open_Resource In the installation script on line 578 there's: if [ -e $HOME/.matplotlib/fontList.cache ] && \ ( grep -q python2.6 $HOME/.matplotlib/fontList.cache ) looking for the 2.6 stuff, even though it installed 2.7, could this be the cause of my problem? Will changing the 2.6 to 2.7 fix it? From G.S.

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Debugging Reason and next steps
by Matthew Turk 22 Apr '11

22 Apr '11

Hi all, I added some debugging statements to Reason that get turned on with the -d flag. These will output whenever a payload is added, whenever a heartbeat is felt, whenever payloads are delivered, and with the input/output of cell contents and executed code. This should do it: yt serve -d (There are also the -f and -o options.) Also, I discovered that I added a Python 2.7-only feature without thinking, so Reason currently won't work with < 2.7. http://docs.python.org/library/threading.html#threading.Event.wait This gets used in extdirect_repl.py on line 162 -- if somebody has a better idea how to handle this, it'd be great if we could simply replace it. Otherwise, we'll just mandate 2.7. As it stands there are a couple big fish that need to be landed before this can be public: debugging and lots of use (although I am now using it all the time, almost exclusively, for analyzing my data), volume rendering widget (maybe something that looks like a less busy version of the widget I made with Traits in 2009? http://www.flickr.com/photos/matthewturk/4189749374/ ), phase plot / histogram of currently visible rectangular prism in the plot window widget, colorbar for plot window, and a few other things that are slipping my mind. Anyway, because it's still in flux and a bit finicky in places, it's probably better not to publicize it too much. Once it's working better we can have a go at asking for beta testers and whatnot. -Matt

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halo profiler recentering bug-thing
by Stephen Skory 20 Apr '11

20 Apr '11

Hi all, This morning and yesterday I spent some time trying to diagnose an issue with the halo profiles when using a recentering function. In summary, with a recentering fuction, a large majority of the profiles generated would have zero- and nan-valued inner-most bins for all the fields except for radius. I believe Britton saw this as well. I think I have tracked down the proximate cause, but I don't know quite what it means or the best solution. Sorry to those of you who I am going to patronize with some descriptions below. In data_objects/profiles.py, in the function _get_bins() (all of this is for 1D profiles), the radius of each cell is found in relation to the center of the sphere, and then a dict of arrays of which cells belong in which radial bin is built. This dict is then used to pull out values from fields to make the profiles. I'm finding that with recentering, for the profiles with zeroed first bins, there are no cells being put into the inner-most bin. Furthermore, I'm finding that in all* these cases there are exactly 6 cells that are within 1e-10 of the inner-most bin edge, and are being excluded from binning. If these cells were included, the inner-most bin would not be empty. It seems to me that this problem may be a numerical and geometric one, but I can't quite convince myself of this. What do all of you think? In a somewhat related question, the parameter "end_collect" controls whether or not bins that fall outside of the min/max of the profile range are included in the binning. The halo profiler currently uses the default, which turns "end_collect" off, so cells outside the min/max are thrown away. It seems to me that we may want to make including all cells inside the minimum radius default as part of the inner-most bin. This would instantly solve the problem above, but I don't know if this is correct. It may even match how observers do things with their finite beam widths. Thanks for your comments! (* "all" means I have yet to find a counter-example. The universe is very large, however.) -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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HaloProfiler vs. enzo_anyl
by Britton Smith 19 Apr '11

19 Apr '11

Hey everyone, There is a fair amount of discussion about the HaloProfiler being a replacement for enzo_anyl. I would definitely like to see this become official, since it seems to be keeping a number of people from making the switch to YT. Can somebody outline the things that enzo_anyl does that the HaloProfiler cannot? I have been under the impression that there wasn't anything, but I haven't used enzo_anyl in quite a while. Britton

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reason grid_viewer widget
by Sam Skillman 15 Apr '11

15 Apr '11

Hi all, Just wanted to update those of you who weren't following along in http://yt.enzotools.org/irc.html (which i will note led to a very fast development pace today), we've added a grid viewer widget to reason. This is a way of viewing the grid edges of your simulation, and is implemented in WebGL. You will need to grab the latest install script because this requires a package called PhiloGL. Download the new script and run it and you should be set to go. You will also have to have a browser that supports WebGL, but if you have something like the latest chrome or firefox, you _should_ be fine...no promises. There are certainly bugs to be worked out (i.e. if you are using a sim with a lot of grids they might not all show up), but you should be able to navigate with your mouse: Left-Drag: Rotate Right-Drag: Pan Scroll: Zoom Planned possible additions: Coloring grids by level "look at" button to either enter a coordinate by hand or by max density, etc. right click to focus (like an interactive "look at") Move through using arrows If you have any feedback, we'd love to hear it! Best, Sam

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Reason Sprint on Monday at 11:00 AM EDT
by Cameron Hummels 15 Apr '11

15 Apr '11

Hey peeps, The plan is to finish up our initial work on the new YT gui: Reason on Monday in a sprint. There are still a handful of outstanding issues that we should clean up before launching it to the community: -- File input dialog box -- Hotkeys for plot windows -- Relabeling plot windows to be more unique to the particular session (DD0125 Temperature Slice, etc.) -- Metadata displayed in plot windows -- Colorbar displayed in plot windows -- X, Y bounds shown on plot windows -- Center on click on plot windows -- Center on max button in plot window dialogs There may be a few more but that is all I can think of right now. After we clear these issues out, I think reason will be ready for an official launch along with the next subversion of yt: 2.2. So if you're interested in participating, let's meet on Monday at 11:00 AM EDT on the #yt irc channel. Bring the Kraftwerk! Cameron

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Proposed Halo Profiler Change
by Stephen Skory 14 Apr '11

14 Apr '11

Hi All, I am thinking of making a modification to how the halo profiler works, which I think will be an improvement. I wanted to pass this idea by you all (especially Britton) just to make surre I'm not stepping on any toes or there's some problem with this I haven't thought of. Currently, if you want to adjust the center of a halo for the purposes of making the profile, such as to the point of maximum gas density in the sphere defined by the halo, you'd call the HaloProfiler with ``use_density_center=True``. But if instead you want to use some other fields maximum point, you specify it using the ``use_field_max_center`` keyword. There is no functionality for specifying that the center should be moved to the minimum of some quantity, like the temperature for a cool-core cluster. I could easily add a parameter like that ``use_field_min_center``, but I think that this is quickly becoming unwieldy and inelegant. I propose that these two extant parameters, and any future ones like the example above, be replaced by a simple function that can be passed to the HaloProfiler object. For example, if you'd want to recenter on the maximum density point, it might look something like this: def _recenter_on_dens(sphere): ma, maxi, mx, my, mz, mg = sphere.quantities['MaxLocation']('Density') return [mx,my,mz] hp = HP.halo_profiler("DD0242/DD0242", recenter=_recenter_on_dens) The function can do whatever the user wants, unlike the limitations of the specific parameters currently in the HaloProfiler. I'd of course add some useful examples to the documentation. Let me know what you think, thanks! -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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yt-dev April 2011