Mailman 3 June 2012 - yt-users

Incoming: Threaded volume rendering, and changes to off-axis projections
by Matthew Turk 21 Jun '12

21 Jun '12

Hi all, SInce last December, Sam and I have been working on and off on threading the volume rendering system and providing a major step forward in its speed and quality. We've issued a pull request to finish off these efforts and move them into the main yt core. This includes a threaded volume renderer, transfer functions with a degree of opacity, and the ability to (in the future) much more explicitly control the behavior of the volume renderer on the cell-level. All of the code is now separated into very small component pieces, and it is more maintainable. The threading works in conjunction with both MPI parallelism and MPI parallelism for tiling, which means in theory the yt volume renderer now operates at three levels of parallelism. (Which is kind of neat, I think.) However, once this is accepted, the minimum requirements to build the development branch of yt will be upgraded to include Cython 0.16. This is because Cython 0.16 includes OpenMP support. The installation script has been updated to include Cython 0.16, so if you re-run that (or install Cython 0.16 manually with "pip install -U Cython") then you should be set. Otherwise you may run into problems during your next "yt update". Additionally, _amr_utils has been renamed to lib, which I don't think will cause issues but there is an outside chance it will. Finally, the off-axis-projections have changed in behavior. They no longer interpolate within a cell. The end result is that the projections are truer to the data, but this comes at the expense of a bit of smoothness. They are now also ~20x faster. This will be a core component of the yt 2.4 release, scheduled for a few weeks from now. We encourage you to test this branch and new behavior. Also, please reply if you have any questions or comments about any of this! Reference info: http://lists.spacepope.org/pipermail/yt-dev-spacepope.org/2012-June/002039.… https://bitbucket.org/yt_analysis/yt/pull-request/168/volume-rendering-refa… example "samplers": https://bitbucket.org/MatthewTurk/yt-refactor/src/ec374f56d5b6/yt/utilities… https://bitbucket.org/MatthewTurk/yt-refactor/src/ec374f56d5b6/yt/utilities… -Matt

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Fwd: [astropy-dev] ANN: Astropy v0.1
by Matthew Turk 19 Jun '12

19 Jun '12

---------- Forwarded message ---------- From: Erik Tollerud <erik.tollerud(a)gmail.com> Date: Tue, Jun 19, 2012 at 2:51 AM Subject: [astropy-dev] ANN: Astropy v0.1 To: astropy-dev(a)googlegroups.com, astropy(a)scipy.org Hello all, On behalf of the Astropy team, I'm excited to announce the first release of the Astropy core package: v0.1! The Astropy core package is intended to provide much of the common functionality and tools needed for performing astronomy and astrophysics with Python. This release should be thought of as a "developer preview" - it has much of the packaging and data handling framework in place, but the actual astronomy functionality and frameworks are still incomplete. Nevertheless, you can already make use of the existing functionality, which is fully tested. Key features include: * Standard cosmological distance calculations (astropy.cosmology) * Data Tables (astropy.table) including a wide variety of ASCII formats common in astronomy (astropy.io.ascii) * FITS File handling - formerly PyFITS (astropy.io.fits) * VOTable parser and writer (astropy.io.vo) * WCS representations - formerly pywcs (astropy.wcs) * Consistent documentation style * Utilities to ease creation of new, independent packages (affiliated packages) * A dedicated logging system The package can be downloaded from http://github.com/downloads/astropy/astropy/astropy-0.1.tar.gz . More information is available at the Astropy site ( http://astropy.org ), the package documentation ( http://docs.astropy.org ), and the github repository ( http://github.com/astropy/astropy ). We also encourage developers writing new packages to begin writing the code against this version. Packages making use of Astropy should feel free to join up as affiliated packages and begin transitioning to the affiliated package template ( https://github.com/astropy/package-template ). In the next version, we hope to implement a working affiliated package installer, so it will be worth your while! For the Astropy developers, Erik Tollerud

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clump finder crash
by Elizabeth Tasker 19 Jun '12

19 Jun '12

Hi, I'm having some problems with clump finder. Specifically, it gets to this point: yt : [INFO ] 2012-06-13 02:10:34,119 Getting field TotalEnergy from 1 yt : [INFO ] 2012-06-13 02:10:34,139 Getting field x from 1 yt : [INFO ] 2012-06-13 02:10:34,147 Getting field y from 1 yt : [INFO ] 2012-06-13 02:10:34,155 Getting field z from 1 yt : [INFO ] 2012-06-13 02:10:34,159 Adjusting clump for periodic boundaries in dim z and then stops (no error). My region actually isn't periodic and this must be a memory intensive step that isn't appropriate. Does the clump find tools/wrapper have a switch for non-periodic regions? Thanks! Elizabeth

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Derivative Error
by Nathan Butcher 15 Jun '12

15 Jun '12

Hello, Using an Enzo dataset, I have written a function to find the derivative in the x-direction of a field. When I try to plot the derivative, I see lines that throughout the plot that I'm guessing are due to the edges of cells. The attached plot is a slice of the x-direction derivative of the PotentialField viewed down the x-axis, but this error appears in plots for density and pressure as well. I am new to using yt, and I am not sure what is causing this. Thank you, Nathan Butcher

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Odd array size issue
by Elizabeth Tasker 13 Jun '12

13 Jun '12

Hi, I have a smoothed covering grid object: In [2]: print scg AMRSmoothedCoveringGrid (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0001): level=3, left_edge=[ 0. 31. 0.], right_edge=[ 64. 33. 64.], ActiveDimensions=[2048 64 2048] which should have dims [2048, 64, 2048] as it claims above. Yet: In [5]: print scg["Density"].shape (256, 8, 256) Any idea why it's downsized? Oddly, this code (that creates the above) worked fine on a different machine but unfortunately, I inadvertently trashed it's OS earlier in the week. Both systems (i.e. this system that did the above and the one that is now a deadman) are linux. Any ideas? Elizabeth

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slice from fixed resolution data
by Wolfram Schmidt 12 Jun '12

12 Jun '12

Hi, is it possible to produce a slice of fixed resolution data, extracted with covering_grid? I tried the following: pf = load(file) cube = pf.h.covering_grid(0, ...) pc = PlotCollection(cube) pc.add_slice(...) But this produces again a slice from the multi-level data as if I had used pc = PlotCollection(pf). Thanks, Wolfram

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Can't locate Tcl/Tk libs and/or headers
by Alejandro Bolaños 12 Jun '12

12 Jun '12

Hello dear yt-users! I'm new to yt and am having some initial problems getting it up and running. I would be glad if you guys could help me. The installation script ran fine, but apparently some modules for python like tcl/tkinter coudn't be built. It seems to be a similar problem to that Chris Malone had, though it wasn't solved in the mailing list: http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2010-December/0… I have installed python2.7, tlc8.5 tk8.5 and the developement packages, but the installation script seems not to be able to find the tcl/tk headers. The error message in the logfile is: Python build finished, but the necessary bits to build these modules were not found: _bsddb _curses _curses_panel _tkinter bsddb185 dbm dl gdbm imageop readline sunaudiodev To find the necessary bits, look in setup.py in detect_modules() for the module's name. and several: running build_ext INFO: Can't locate Tcl/Tk libs and/or headers In setup.py I have found detect_modules() and detect_tkinter*() functions, but I am at a loss which part(s) I should edit. I am running Debian wheezy/sid. Thank you for any help! Greets, Alejandro

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scale on colourbar?
by Elizabeth Tasker 12 Jun '12

12 Jun '12

Hi, I'm creating a slice image but it's refusing to tick mark my colour bar properly: http://i.imgur.com/YQBWJ.png pc = PlotCollection(pf, center=position) p = pc.add_slice("NegEscapeVelocity", 2, field_parameters={"disk_vector":disk_vector, "disk_center":disk_center, "disk_radius":profile["DiskRadius"], "disk_potential":profile["PotentialField"]}) p.set_log_field(False) p.set_zlim(0.0, 30.0) p.set_width(8, 'kpc') Is there something simple I've done wrong? I tried rearranging the last 3 lines, but to no avail! Elizabeth

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projection results
by Geoffrey So 12 Jun '12

12 Jun '12

Hi, sorry for asking a dumb question, but when I do a projection of density field = "Density" proj = pf.h.proj(direction, field, weight_field=field) the numbers I get are ~1e-28 but when I do proj = pf.h.proj(direction, field, weight_field=None) the numbers become ~1e-4 this is a 64 cube simulation, if I were to multiply 64 * 1e-28 for a projection with no weighting, shouldn't I still get numbers on the order of 1e-26 or 1e-27? I'm guessing there's something I've misunderstood about pf.h.proj. Am I missing like a CGS conversion factor when I don't weight it by some field? From G.S.

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