Mailman 3 March 2014 - yt-users

pyx install error
by Junhwan Choi (최준환) March 26, 2014

March 26, 2014

Hi yt users, I try to install pyx onto my existing yt package (including yt, python, numpy ....). Buit I get following error message: ====== Downloading/unpacking pyx Could not find any downloads that satisfy the requirement pyx Some externally hosted files were ignored (use --allow-external pyx to allow). Cleaning up... No distributions at all found for pyx Storing debug log for failure in /home52/jhchoi/.pip/pip.log ==== The pip.log file says ------------------------------------------------------------ /home/jhchoi/common/bin/pip run on Wed Mar 26 10:05:31 2014 Downloading/unpacking pyx Getting page https://pypi.python.org/simple/pyx/ URLs to search for versions for pyx: * https://pypi.python.org/simple/pyx/ Analyzing links from page https://pypi.python.org/simple/PyX/ Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.12.1/PyX-0.12.1.tar.gz#… (from https://pypi.python.org/simple/PyX/) because it is externally hosted. Skipping https://downloads.sourceforge.net/project/pyx/pyx/0.13/PyX-0.13.tar.gz#md5=… (from https://pypi.python.org/simple/PyX/) because it is externally hosted. Could not find any downloads that satisfy the requirement pyx Some externally hosted files were ignored (use --allow-external pyx to allow). Cleaning up... Removing temporary dir /tmp/pip_build_jhchoi... No distributions at all found for pyx Exception information: Traceback (most recent call last): File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/basecommand.py", line 122, in main status = self.run(options, args) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/commands/install.py", line 278, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py", line 1177, in prepare_files url = finder.find_requirement(req_to_install, upgrade=self.upgrade) File "/home/jhchoi/common/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/index.py", line 277, in find_requirement raise DistributionNotFound('No distributions at all found for %s' % req) DistributionNotFound: No distributions at all found for pyx What does this error mean? And could anyone inform me how to resolve this problem? Thank you in advance, Junhwan Choi

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IPython Widgets for Slice/Projection Plots
by Sam Skillman March 25, 2014

March 25, 2014

Hi all, Just posting an example of how folks might like to use IPython notebook interactive widgets to explore plots in yt (you'll need to download/run locally to enjoy the fun): http://nbviewer.ipython.org/url/hub.yt-project.org/notebooks/af2da7e70e534a… I think there is interest in developing a fully-fledged widget interaction, so hopefully this can be used a bit in terms of tossing around ideas. Cheers, Sam

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Code Units to CGS for PLUTO.
by Varadarajan Parthasarathy March 25, 2014

March 25, 2014

Hi There, There is a PlutoGrid.convert(datatype) for converting the data sets like 'prs', 'rho' etc to CGS from code units. Have any one used it ? In case can you let me know of how you loaded the dataset ? Cheers, Varadarajan

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ucsc workshop march23-25
by Tonathiu Redrovan March 23, 2014

March 23, 2014

hello,i would like to attend this workshop i talk to my my professor (joel primack) and he said we will keep in touch with me as of what time will it be today, i know is in room 102 usb. he also told me is not open for the public hence i contact directly to you. best Tonathiu

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Fwd: [astropy-dev] OT: job opening at STScI
by Matthew Turk March 20, 2014

March 20, 2014

---------- Forwarded message ---------- From: "Perry Greenfield" <stsci.perry(a)gmail.com> Date: Mar 20, 2014 1:33 PM Subject: [astropy-dev] OT: job opening at STScI To: <astropy-dev(a)googlegroups.com>, "Discussion of Numerical Python" < numpy-discussion(a)scipy.org>, "SciPy Developers List" <scipy-dev(a)scipy.org> Cc: The Science Software Branch at the Space Telescope Science Institute is seeking a developer that enjoys and is good at digging into and understanding the details of Python internals and its libraries--particularly those related to scientific computing--in order to support of our development of software tools for Python and the astronomical community, particularly for the Hubble Space Telescope and the next telescope under construction (JWST). Details on the position and how to apply can be found at this link: https://rn11.ultipro.com/SPA1004/JobBoard/JobDetails.aspx?__ID=*5ECC2DFF670… (applications are still being taken despite the date given...) Perry Greenfield -- You received this message because you are subscribed to the Google Groups "astropy-dev" group. To unsubscribe from this group and stop receiving emails from it, send an email to astropy-dev+unsubscribe(a)googlegroups.com. For more options, visit https://groups.google.com/d/optout.

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zlim on python notebooks
by Elizabeth Tasker March 19, 2014

March 19, 2014

Hi, Python notebooks seems to hate set_zlim (or rather demand an unreasonable number of arguments): p.set_zlim(1e-28, 1e-20) TypeError Traceback (most recent call last) <ipython-input-31-664f4ddf25f0> in <module>() ----> 1 p.set_zlim(1e-28, 1e-20) /Users/buttonmoon/yt/src/yt-hg/yt/visualization/plot_container.pyc in newfunc(*args, **kwargs) 52 @wraps(f) 53 def newfunc(*args, **kwargs): ---> 54 rv = f(*args, **kwargs) 55 args[0]._plot_valid = False 56 args[0]._setup_plots() TypeError: set_zlim() takes at least 4 arguments (3 given) Elizabeth

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Define a derived field of disk surface density
by Suoqing JI March 19, 2014

March 19, 2014

Hi, I’m working on FLASH 3D Cartesian AMR data, and would like to define a derived field of surface density, so I can use surface density field to calculate other derived fields. My current script does give desired results (slice_y: http://i.imgur.com/XigIYJc.png slice_z: http://i.imgur.com/kA2Fmlt.png, and the disk is cut from original data). However, it’s extremely inefficient, because I cast a ray through disk height for every cells located on x-y plane surface of each AMR block. So is there any clever way to define surface density as a derived field in YT, as what the figures attached show? Or some way without defining surface density as a derived field, but I can get access to surface density values when computing other derived fields? Thanks a lot! Best wishes, -- Suoqing JI Ph.D Student Department of Physics University of California, Santa Barbara CA 93106, USA

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Incorrect particle index for halo particles
by Josh Moloney March 18, 2014

March 18, 2014

Hi all, I'm working on a script to calculate star formation rates for halos in different mass bins from Enzo simulation ouput. As part of the script, I need to access the dynamical_time values for all of the star particles associated with a given halo. The halos have been previously stored to disk, so I'm loading them with LoadHaloes and then for each halo identifying the star particles with the typical stars = halo["creation_time"] > 0 mask. When I try to get the associated dynamical times with halo["dynamical_time"][stars] I get -99999. instead of the expected values. When I perform the same operation on the entire dataset instead of an individual halo I get the correct dynamical times, so the values I want do exist. I was testing out different fields with halo[field][stars] to see if I could find any patterns, and I noticed that for all the fields that are actually saved to disk for the halos (creation_time, ParticleMassMsun, particle_positions, etc.) I get values that match those in the halo hdf5 files. However, this is not true for "particle_index", where I get incorrect values. The values do correspond to particles in the halo, but they aren't the indices of the star particles. I'm not sure, but I assume this is why I'm getting incorrect values for dynamical_time which isn't saved in the halo hdf5 files. I'm not familiar enough with the code for the halo finder to know where to start looking for the source of this problem. Does anyone with more experience have an idea? My version of yt is a copy of 2.6.1 that I updated about 3 weeks ago. Thanks. - Josh

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Error when installing
by Jacob Hamer March 18, 2014

March 18, 2014

Here is the error as outputted. ____________________________________ gcc -fPIC -c blocksort.c make: gcc: No such file or directory make: *** [blocksort.o] Error 1 _____________________________________ How can I fix this? I have OSX Mavericks 10.9.1. I have Xcode and Command Line Tools installed. What am I doing wrong? Thank you!

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Profile plots don't show in notebook
by Caroline Van Borm March 18, 2014

March 18, 2014

Hi all, I'm just starting to use IPython notebooks, but I don't seem to be able to get profile plots to show. Projection plots and phase plots show up fine, though. This is the error I'm getting: NameError Traceback (most recent call last) <ipython-input-14-72f7221a8772> in<module>() 1 p= ProfilePlot(sphere, "Radiuspc", ["NumberDensity"], weight_field="CellMassMsun") ----> 2 p.show() 3 /home/uni05/cborm/YT/yt-x86_64/src/yt-hg/yt/visualization/profile_plotter.pyc inshow(self) 274 275 """ --> 276 if "__IPYTHON__" in dir(__builtin__): 277 api_version= get_ipython_api_version() 278 if api_versionin ('0.10', '0.11'): NameError: global name '__builtin__' is not defined My yt version is ec9a5117fc08. Does anyone know what is happening here? Thanks! Cheers, Caroline

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