Mailman 3 September 2013 - yt-users

After updating YT an error occurs
by Seyit Hocuk 12 Sep '13

12 Sep '13

Hi, After I update my YT, I get this error when using my script. Probably some paths are wrong? I included the updater.log. ./ytmaps.py Traceback (most recent call last): File "./ytmaps.py", line 5, in <module> from yt.mods import * File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/mods.py", line 60, in <module> from yt.data_objects.api import \ File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 31, in <module> from grid_patch import \ File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/data_objects/grid_patch.py", line 35, in <module> from yt.data_objects.data_containers import YTFieldData File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 45, in <module> from yt.data_objects.derived_quantities import GridChildMaskWrapper File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 36, in <module> from yt.utilities.parallel_tools.parallel_analysis_interface import \ File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 39, in <module> from yt.utilities.lib import \ File "/net/ulubey/data/users/seyit/programmas/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/__init__.py", line 42, in <module> from .write_array import * ImportError: No module named write_array I use the activate.csh and I don't know which version I was using before. It wasn't that old though. -- With kind regards, Seyit S. Hocuk Postdoctoral Researcher Kapteyn Astronomical Institute P.O. box 800 9700AV Groningen, the Netherlands

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Re: [yt-users] yt-users Digest, Vol 67, Issue 18
by Seyit Hocuk 11 Sep '13

11 Sep '13

Hi Matt, Sorry, I'm new to the mailing list and I didn't notice your email before. I was set on Digest mode, which I find quite chaotic. I now switched to regular mode. Thank you for your reply. I already found a workaround actually, but it's ugly. I will try your suggestion the next time I need it. Thanks for the swift reply. Kind regards, Seyit On 09/10/2013 07:37 PM, yt-users-request(a)lists.spacepope.org wrote: > ------------------------------ > > Message: 4 > Date: Tue, 10 Sep 2013 09:03:19 -0400 > From: Matthew Turk<matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Annotate_contour > Message-ID: > <CALO3=5GvDOjx854OXCGsSdKxWq4JzH9FmaCHeokHocp7+WCNgA(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Seyit, > > As you note, right now what the contours do is essentially take the > underlying data source, query the field to be contoured, and then > perform an interpolation on that field. This means if you have a > weighted projection, because queries will also have the same weight, > the result will be weighted. > > I've issued a pull request to enable the behavior you describe: > > https://bitbucket.org/yt_analysis/yt/pull-request/595/adding-alternate-data… > > You can test this by pulling from my repo: > > cd $YT_DEST/src/yt-hg/ > hg pull -r 0b52b74 > hg up -r 0b52b74 > python2.7 setup.py build_ext -i > > Now when you call annotate_contours, you can specify data_source as an > option. You can specify a projection you have created by hand, or a > slice, or whatever is most appropriate. > > The repository is in a bit of a state at the moment and we're waiting > on bitbucket support, so there may be a holdup on accepting the pull > request, but let us know if this accomplishes what you're looking for. > > -Matt > > On Tue, Sep 10, 2013 at 5:13 AM, Seyit Hocuk<seyit(a)astro.rug.nl> wrote: >> >Dear all, >> > >> >I don't know if this is a simple question or not, but is it possible to >> >annotate_contours independent of the conditions of the main plot? >> > >> >For example, I'm doing a projection plot "prj = ProjectionPlot(pf, "z", >> >"Velocitydispersion",center=cent,width=wide,weight_field='volinv')" and my >> >contour callback is >> >"prj.annotate_contour("T_{gas}",clim=(1.0e0,2.8e1),ncont=ncont)". My problem >> >is that the contours are also weighted by the chosen weight_field, which I >> >do not want. >> > >> >Is there a workaround? >> > >> >Kind regards, >> >Seyit >> > >> >-- >> >With kind regards, >> >Seyit >> > >> > >> >S. Hocuk >> >Postdoctoral Researcher >> >Kapteyn Astronomical Institute >> >P.O. box 800 >> >9700AV Groningen, the Netherlands >> > >> >_______________________________________________ >> >yt-users mailing list >> >yt-users(a)lists.spacepope.org >> >http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > ------------- -- With kind regards, Seyit S. Hocuk Postdoctoral Researcher Kapteyn Astronomical Institute P.O. box 800 9700AV Groningen, the Netherlands

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yt-3.0 vs/and yt-2.5 for ramses simulation
by Junhwan Choi (최준환) 10 Sep '13

10 Sep '13

Dear yt user, I have a new project that needs to deal with ramses simulation. Since I have used the yt, I would like to keep using yt for my ramses project. I find that the yt-3.0 supports ramses much better than yt-2.5.x version. Since yt-3.0 is still developed stage, I would like to use both of them together. Is it possible to have yt-2.5 version and yt-3.0? In this case, how can I install both yt? (Or you can recommend that simply move on yt-3.0). Is there yt-3.0 version of instal_script.sh? In addition, is there any document or site that explain how to use ramses output in yt? Thank you, Junhwan

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error while installing yt
by mohammad safarzadeh 10 Sep '13

10 Sep '13

Hi, I get this error and I like to know what I should do about it. Installing BZLIB Installing ZLIB Installing PNG Installing FreeType2 Installing HDF5 Installing SQLite3 Installing Python. This may take a while, but don't worry. yt loves you. Setting YT_DIR=/home/safarzadeh/yt-x86_64/src/yt-hg/ Installing distribute ******************************************** FAILURE REPORT: ******************************************** return self.parent.open(new, timeout=req.timeout) File "/home/safarzadeh/yt-x86_64/lib/python2.7/urllib2.py", line 404, in open response = self._open(req, data) File "/home/safarzadeh/yt-x86_64/lib/python2.7/urllib2.py", line 427, in _open 'unknown_open', req) File "/home/safarzadeh/yt-x86_64/lib/python2.7/urllib2.py", line 382, in _call_chain result = func(*args) File "/home/safarzadeh/yt-x86_64/lib/python2.7/urllib2.py", line 1247, in unknown_open raise URLError('unknown url type: %s' % type) urllib2.URLError: <urlopen error unknown url type: https> ******************************************** ******************************************** Failure. Check /home/safarzadeh/yt-x86_64/yt_install.log. The last 10 lines are above. Thanks! -Mohammad

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Annotate_contour
by Seyit Hocuk 10 Sep '13

10 Sep '13

Dear all, I don't know if this is a simple question or not, but is it possible to annotate_contours independent of the conditions of the main plot? For example, I'm doing a projection plot "prj = ProjectionPlot(pf, "z", "Velocitydispersion",center=cent,width=wide,weight_field='volinv')" and my contour callback is "prj.annotate_contour("T_{gas}",clim=(1.0e0,2.8e1),ncont=ncont)". My problem is that the contours are also weighted by the chosen weight_field, which I do not want. Is there a workaround? Kind regards, Seyit -- With kind regards, Seyit S. Hocuk Postdoctoral Researcher Kapteyn Astronomical Institute P.O. box 800 9700AV Groningen, the Netherlands

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Colormaps
by Matthew Turk 06 Sep '13

06 Sep '13

Hi all, Just a quick note -- thanks to some awesome work mostly by Cameron, but with assists from Kacper and Nathan, we now have a diagram of colormaps in yt: http://yt.readthedocs.org/en/latest/visualizing/colormaps/index.html It covers the native matplotlib colormaps, as well as the ones yt includes in addition. (Such as little-known gems like kamae, cubehelix and our very own algae.) This will be on the main yt docs site once we release 2.6. On the main site, there'll even be a demonstration of a projection in different colormaps. Thanks, Cameron! -Matt

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output file option in yt stats command
by Semyeong Oh 05 Sep '13

05 Sep '13

Hello, I get this error when using -o option for yt stats command. $ yt stats -o test.txt parameter_file ….(print out yt stats results) ... Width: 2.180e+20 cmh Width: 3.114e+20 cm Width: 3.531e+20 cmhcm Width: 5.045e+20 cmcm Traceback (most recent call last): File "/home/semyeong/soft/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.5', 'console_scripts', 'yt')() File "/home/semyeong/soft/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1696, in run_main args.func(args) File "/home/semyeong/soft/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 97, in run self(args) File "/home/semyeong/soft/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1602, in __call__ "%s (%0.5e years): %0.5e at %s\n" % (pf, t, v, c)) UnboundLocalError: local variable 'v' referenced before assignment Here is my yt instinfo: yt module located at: /home/semyeong/soft/yt-x86_64/src/yt-hg The supplemental repositories are located at: /home/semyeong/soft/yt-x86_64/src/yt-supplemental The current version of the code is: --- b118390aa42c --- Is the option working properly? Thanks for your help. Semyeong

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install script crash in older version of Mac OS X
by Junhwan Choi (최준환) 05 Sep '13

05 Sep '13

Hi yt user, I happen to install yt into somewhat old Mac (OS X 10.5.8). When I start run install script by "bash install_script.sh", I get following message: ---------------------------------- .... Awesome! Here we go. Using wget I am unable to locate any shasum-like utility. ALL FILE INTEGRITY IS NOT VERIFIABLE. THIS IS PROBABLY A BIG DEAL. (I'll hang out for a minute for you to consider this.) Downloading xray_emissivity.h5 from yt-project.org Downloading zlib-1.2.8.tar.gz from yt-project.org 2013-09-05 08:57:04 URL:http://yt-project.org/dependencies/zlib-1.2.8.tar.gz[571091/571091] -> "zlib-1.2.8.tar.gz" [1] ******************************************** FAILURE REPORT: ******************************************** install_script.sh: line 533: -c: command not found install_script.sh: line 526: -c: command not found install_script.sh: line 534: -c: command not found install_script.sh: line 526: -c: command not found install_script.sh: line 533: -c: command not found install_script.sh: line 533: -c: command not found ******************************************** ******************************************** Failure. Check /Users/jhchoi/common/yt_install.log. The last 10 lines are above. ---------------------------------- After this message the install script is crash and yt_install.log only says: install_script.sh: line 533: -c: command not found install_script.sh: line 526: -c: command not found install_script.sh: line 534: -c: command not found install_script.sh: line 526: -c: command not found install_script.sh: line 533: -c: command not found install_script.sh: line 533: -c: command not found I do not know what is shasum-like utility. How can I resolve this crash? Thanks in advance, Junhwan Choi

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Issue with "yt serve command"
by k.grisdale＠surrey.ac.uk 05 Sep '13

05 Sep '13

Hi, I am a new user to both python and yt. I have installed yt on a MacBook Pro running os x 10.8.4. I installed yt by following the steps on yt-project.org. The install went without displaying any errors. When the install completed it gave me several instructions, first the source command and then to use the "yt serve" command. However when I type in the "yt serve" command after the source command I get the message below in the terminal and nothing else happens. I have installed python separately using home-brew and the command "$ brew install python --framework" I am using the b118390aa42c version of yt. Can anyone suggest how I can get yt serve to work. Thanks Kearn Traceback (most recent call last): File "/Applications/Code/yt/yt-x86_64/bin/yt", line 9, in <module> load_entry_point('yt==2.5.5', 'console_scripts', 'yt')() File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1696, in run_main args.func(args) File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 94, in run self(args) File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/command_line.py", line 1561, in __call__ hr = ExtDirectREPL(reasonjs_path, use_pyro=args.use_pyro) File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/gui/reason/extdirect_repl.py", line 249, in __init__ reason_pylab() File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/gui/reason/extdirect_repl.py", line 193, in reason_pylab import pylab, matplotlib File "/Applications/Code/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/pylab.py", line 1, in <module> from matplotlib.pylab import * File "/Applications/Code/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/pylab.py", line 269, in <module> from matplotlib.pyplot import * File "/Applications/Code/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/pyplot.py", line 98, in <module> _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup() File "/Applications/Code/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/backends/__init__.py", line 25, in pylab_setup globals(),locals(),[backend_name]) File "/Applications/Code/yt/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-macosx-10.4-x86_64.egg/matplotlib/backends/backend_macosx.py", line 21, in <module> from matplotlib.backends import _macosx RuntimeError: Python is not installed as a framework. The Mac OS X backend will not be able to function correctly if Python is not installed as a framework. See the Python documentation for more information on installing Python as a framework on Mac OS X. Please either reinstall Python as a framework, or try one of the other backends.

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error on volume rendering on zoom-in simulation
by mohammad safarzadeh 04 Sep '13

04 Sep '13

Hi, I am trying to do VR on a halo in my zoom-in region which is a dark matter only sim, but I get a black image when I try this: L=[1,1,1] W=1/pf["Mpc"] n [16]: mi,ma=region.quantities["Extrema"]("particle_density")[0] In [17]: mi Out[17]: 0.0 In [18]: ma Out[18]: 4.5282895435060503e-24 In [21]: np.log10(ma) Out[21]: -23.344065811694637 mi=-24 ma=np.log10(ma) tf = ColorTransferFunction((mi,ma)) cam=region.pf.h.camera(c, L, W, Npixels, tf,fields=["particle_density"],log_fields=True) ImageArray([[[ 0., 0., 0., 1.], [ 0., 0., 0., 1.], [ 0., 0., 0., 1.], ..., [ 0., 0., 0., 1.], [ 0., 0., 0., 1.], [ 0., 0., 0., 1.]], [[ 0., 0., 0., 1.], [ 0., 0., 0., 1.], [ 0., 0., 0., 1.], ..., [ 0., 0., 0., 1.], [ 0., 0., 0., 1.], [ 0., 0., 0., 1.]],…. what is the mistake that I am doing? -Regards, Mohammad

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yt-users September 2013