Mailman 3 April 2010 - yt-users

2d radial profiles
by david collins April 17, 2010

April 17, 2010

Hi, all-- Is it possible to make a 2d radial profile from a projection with the existing profile tool? I think a better question is how do I make an extraction from a projection that I can then hand to BinnedProfile1d? Thanks, d. -- Sent from my Stone Tablet and carried by my Pterodactyl.

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If statement for particles existing?
by Elizabeth Harper-Clark April 16, 2010

April 16, 2010

Hi guys, I sometimes have particles in my sims and when i do I want to plot them. At the moment I have: if sp["ParticleMassMsun"].size > 0: p.modify["particles"](1.0, p_size=10.0, col='k') but if there are no particles I get this error message: yt INFO 2010-04-16 11:58:29,408 Getting ParticleMassMsun using ParticleIO Traceback (most recent call last): File "Density_movie.py", line 29, in <module> if sp["ParticleMassMsun"].size > 0: File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-2.0dev-py2.5-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 249, in __getitem__ self.get_data(key) File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-2.0dev-py2.5-linux-x86_64.egg/yt/lagos/BaseDataTypes.py", line 1636, in get_data self[field] = self.particles[field] File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-2.0dev-py2.5-linux-x86_64.egg/yt/lagos/ParticleIO.py", line 45, in __getitem__ return self.get_data(key) File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-2.0dev-py2.5-linux-x86_64.egg/yt/lagos/ParticleIO.py", line 91, in get_data conv_factors) File "/scratch/YT-x86_64/lib/python2.5/site-packages/yt-2.0dev-py2.5-linux-x86_64.egg/yt/lagos/DataReadingFuncs.py", line 206, in _read_particles filenames, ids, conv_factors = zip(*sorted(zip(filenames, ids, conv_factors))) ValueError: need more than 0 values to unpack Can anyone think of a better if statement to check if i have particles that doesn't crash YT if there isn't? Many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Astrophysics, UofT www.astro.utoronto.ca/~h-clark h-clark(a)cita.utoronto.ca AIM: edphc1 MSN: edphc1(a)hotmail.com Skype: eharperclark Office phone: 416-978-5759

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solution to wxPython installation problem
by Michael Kuhlen April 15, 2010

April 15, 2010

I just installed yt 1.6 (stable branch) for the first time. I ran into some trouble with the wxPython installation. I realize that it's an optional component, but since I found a solution to my problem, I thought I'd share it here. I'm installing yt on an x86_64 machine running Ubuntu 9.04, 2.6.28-18. The error I got during the wxPython installation was: src/gtk/_gdi_wrap.cpp:31407: error: ‘class wxGraphicsRenderer’ has no member named ‘CreateBitmap’ Some googling revealed this: http://groups.google.com/group/wxPython-users/browse_thread/thread/129ba27e… Applying the patch discussed at the end of that thread allowed the compilation of wxPython to complete successfully. To be more specific, you need to add this one line wxGraphicsBitmap CreateBitmap( const wxBitmap &bitmap ) const { return wxNullGraphicsBitmap; } after line 4197 in the file $YT_DIR/src/wxPython-src-2.8.10.1/wxPython/src/gtk/_gdi_wrap.cpp. Might be worth including this patch in the version of wxPython that is downloaded from yt.enzotools.org. Mike -- ********************************************************************* * * * Dr. Michael Kuhlen Theoretical Astrophysics Center * * email: mqk(a)astro.berkeley.edu UC Berkeley * * cell phone: (831) 588-1468 601 Campbell Hall * * skype username: mikekuhlen Berkeley, CA 94720 * * * *********************************************************************

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projection depth
by Luigi Iapichino April 13, 2010

April 13, 2010

Dear all, by comparing volume renderings and projections in my simulation I realised that I don't have control on the projection depth, in the latter case. This is the relevant part of my script: ... L = 0.1 # projection width pf = load(data_dir+fn) # load data reg = pf.h.region([0.5, 0.5, 0.5],[0.45,0.45,0.45],[0.55,0.55,0.55]) # a small region #reg = pf.h.region([0.5, 0.5, 0.5],[0,0,0],[1,1,1]) # the whole box pc = PlotCollection(reg, center=[0.5,0.5,0.5]) p = pc.add_projection("Density", 0, weight_field="Density",fig_size=(7.5,6)) p.modify["contour"]("Density", ncont=5,take_log=True) pc.set_width(L, '1') pc.save("%s_test-proj" % pf,override=True) If I set L = 0.2, I don't see in the central region of the projection more structures than with L=0.1 (only the plot width is, of course, larger). Moreover, the result do not depend on the region that I select (either third or fourth line). It seems to me that, in all cases, the projection is actually performed along the whole simulation box, and not on the region that I select. In other words, I can control the plot width, but not the projection depth. In the volume rendering, on the other hand, the plot width sets the depth, too. Is anything wrong or missing in my script? If needed, I can send you a few explanatory plots and the whole sample script for reproducing my issue. Looking forward to your suggestions, Luigi -- --------------------------------------------------------------- Luigi Iapichino Zentrum fuer Astronomie der Universitaet Heidelberg Institut fuer Theoretische Astrophysik Albert-Ueberle-Str. 2, D-69120 Heidelberg, Germany Tel: +49 6221 548983, Fax: +49 6221 544221 e-mail: luigi(a)ita.uni-heidelberg.de URL: http://www.ita.uni-heidelberg.de/~luigi/

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Error: cannot convert float infinity to integer
by Jean-Claude Passy April 7, 2010

April 7, 2010

Dear all, I get the following error when trying to plot a radial profile of the density. Does anyone have an idea how to solve this ? Thanks a lot, Jean-Claude ##################################################################################################################### In [42]: ls CommonEnvelope0001 CommonEnvelope0001.configure CommonEnvelope0001.harrays CommonEnvelope0001.taskmap0000 CommonEnvelope0001.boundary CommonEnvelope0001.cpu0000 CommonEnvelope0001.hierarchy CommonEnvelope0001.taskmap0001 CommonEnvelope0001.boundary.hdf CommonEnvelope0001.cpu0001 CommonEnvelope0001.memorymap CommonEnvelope0001.yt In [43]: import yt.raven as R In [44]: import yt.lagos as L In [45]: filen = 'CommonEnvelope0001' In [46]: data = L.EnzoStaticOutput(filen) In [47]: plot_data = R.PlotCollection(data) yt INFO 2010-04-06 15:39:02,963 Created plot collection with default plot-center = [0.4921875, 0.4921875, 0.4921875] In [48]: plot_data.add_profile_sphere(0.5,'1',["Radius", "Density"]) yt INFO 2010-04-06 15:39:56,695 Getting field Radius from 1 yt INFO 2010-04-06 15:39:56,696 Getting field x from 1 yt INFO 2010-04-06 15:39:56,857 Getting field y from 1 yt INFO 2010-04-06 15:39:56,919 Getting field z from 1 yt INFO 2010-04-06 15:39:56,987 Getting field Density from 1 Out[48]: <yt.raven.PlotTypes.Profile1DPlot object at 0x3724d90> In [49]: plot_data.save('DensityProfile', format = 'png') --------------------------------------------------------------------------- OverflowError Traceback (most recent call last) /rpod2/jcpassy/Enzo/enzo/src/yt/scripts/iyt in <module>() ----> 1 2 3 4 5 /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotCollection.pyc in save(self, basename, format, override, force_save) 79 fn.append(plot.save_image(basename, \ 80 format=format, submit=self._run_id, ---> 81 override=override, force_save=force_save)) 82 if self.submit: 83 im = plot.im.copy() /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotTypes.pyc in save_image(self, prefix, format, submit, override, force_save) 110 *override* will force no filename generation beyond the prefix. 111 """ --> 112 self._redraw_image() 113 if not override: 114 self._generate_prefix(prefix) /rpod2/jcpassy/Enzo/enzo/src/yt/yt/raven/PlotTypes.pyc in _redraw_image(self) 711 func(self.data[self.fields[0]][indices], 712 self.data[self.fields[1]][indices], --> 713 **self.plot_options) 714 self._autoset_label(self.fields[0], self.set_x_label, 'x') 715 self._autoset_label(self.fields[1], self.set_y_label, 'y') /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in loglog(self, *args, **kwargs) 3566 b = self._hold 3567 self._hold = True # we've already processed the hold -> 3568 l = self.plot(*args, **kwargs) 3569 self._hold = b # restore the hold 3570 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in plot(self, *args, **kwargs) 3435 3436 -> 3437 self.autoscale_view(scalex=scalex, scaley=scaley) 3438 return lines 3439 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/axes.pyc in autoscale_view(self, tight, scalex, scaley) 1625 self.set_xbound(XL) 1626 if scaley and self._autoscaleYon: -> 1627 YL = self.yaxis.get_major_locator().view_limits(y0, y1) 1628 self.set_ybound(YL) 1629 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/ticker.pyc in view_limits(self, vmin, vmax) 1117 vmin = minpos 1118 -> 1119 if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base) 1120 if not is_decade(vmax,self._base): vmax = decade_up(vmax,self._base) 1121 /rpod2/jcpassy/yt-x86_64/lib/python2.6/site-packages/matplotlib/ticker.pyc in is_decade(x, base) 1028 def is_decade(x,base=10): 1029 lx = math.log(x)/math.log(base) -> 1030 return lx==int(lx) 1031 1032 class LogLocator(Locator): OverflowError: cannot convert float infinity to integer #####################################################################################################################

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problems loading yt
by Brian O'Shea April 6, 2010

April 6, 2010

Dear yt-users, I'm having a very peculiar problem, and I wonder if any of you have experienced this. I have been using my desktop machine to make tons of images of some enzo simulations - literally several thousand images at this point - and yt has mysteriously stopped working. I haven't done anything to python, attempted to upgrade yt, or anything like that... It just started throwing errors about 800 images into a script. It seems that I can get this error by simply typing 'python' and then 'from yt.mods import *'. The error message is at the end of this email. If anybody could give me some advice, I'd appreciate it - it seems like it might actually be deeper than simply a yt problem, though. Thanks! --Brian nibbler:/Users/bwoshea/Desktop/CondBubbleSims/spitzer_0_1_cool%python Python 2.5.4 (r254:67917, Dec 23 2008, 14:57:27) [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from yt.mods import * Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/mods.py", line 32, in <module> import yt.lagos as lagos File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/lagos/__init__.py", line 97, in <module> from OutputTypes import * File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/lagos/OutputTypes.py", line 37, in <module> _pf_store = ParameterFileStore() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/fido/ParameterFileStorage.py", line 73, in __init__ self._records = self.read_db() File "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/yt-2.0dev-py2.5-macosx-10.3-i386.egg/yt/fido/ParameterFileStorage.py", line 211, in read_db else: v['last_seen'] = float(v['last_seen']) ValueError: invalid literal for float(): EnzoStaticOutput >>>

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