yt-users February 2011

yt-users@python.org

19 participants
23 discussions

Stars on volume rendering
by Elizabeth Harper-Clark 11 Dec '21

11 Dec '21

Hi all, Thanks for all your help over the last couple of days. One more question: - Can I plot particles on a volume rendered image? I have stars and I want to show where they are! Thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

8 14

Re: [yt-users] Problem in simple volume rendering (yt-users Digest, Vol 36, Issue 18)
by Kuo-Chuan Pan 12 Mar '11

12 Mar '11

Dear Matt, Thank you very much for your quick reply. 1. The balck_center I found is back_center = [-0.28306926 -0.1132277 -0.39629696] 2. The physical size I used is from -8.2605e11 cm to 8.2605e11 cm (same for x,y,z directions) The domain is correctly printing when running my yt script yt INFO 2011-02-24 13:08:20,186 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11] yt INFO 2011-02-24 13:08:20,186 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11] 3. I set the width = 1 as used in the example code. (all value are the same as the example code, except center, c=[0.,0.,0.] and the datafile is the Flash output file) Thank you very much for your kindly assistance. Best, Kuo-Chuan I have got some warning from yt, but I think that may not relate to my problem. The whole output are listed as bellow: [kpan2@taranaki yt-scripts]$ ./ShowPlots.py yt WARNING 2011-02-24 13:21:00,791 Setting 1.0 in code units to be 1.0 cm yt WARNING 2011-02-24 13:21:00,793 No time units. Setting 1.0 = 1 second. yt INFO 2011-02-24 13:21:00,794 Parameters: current_time = 5635.73778789 yt ERROR 2011-02-24 13:21:00,794 Missing domain_dimensions in parameter file definition! yt INFO 2011-02-24 13:21:00,794 Parameters: domain_left_edge = [ -8.26050000e+11 -8.26050000e+11 -8.26050000e+11] yt INFO 2011-02-24 13:21:00,794 Parameters: domain_right_edge = [ 8.26050000e+11 8.26050000e+11 8.26050000e+11] yt INFO 2011-02-24 13:21:00,795 Parameters: cosmological_simulation = 0.0 yt WARNING 2011-02-24 13:21:00,795 Setting 1.0 in code units to be 1.0 cm yt WARNING 2011-02-24 13:21:00,795 No time units. Setting 1.0 = 1 second. Warning: invalid value encountered in sqrt Warning: invalid value encountered in sqrt Adding gaussian at -5.8560788466 with width 0.02 and colors (0.2867691866508944, 0.015686274509803921, 0.031372549019607843, 0.01) Adding gaussian at -4.32198464433 with width 0.02 and colors (0.23702881439314105, 0.20784313725490194, 0.41568627450980389, 0.025118864315095794) Adding gaussian at -2.78789044206 with width 0.02 and colors (0.40392156862745099, 0.40392156862745099, 0.80784313725490198, 0.063095734448019331) Adding gaussian at -1.25379623979 with width 0.02 and colors (0.59607843137254901, 0.59607843137254901, 0.59115561118064242, 0.15848931924611143) Adding gaussian at 0.280297962486 with width 0.02 and colors (0.792156862745098, 0.792156862745098, 0.21568627450980413, 0.39810717055349731) Adding gaussian at 1.81439216476 with width 0.02 and colors (0.98431372549019602, 0.98431372549019602, 0.94080651128375881, 1.0) THIS MANY GRIDS! 0| | ETA: --:--:-- Partitioning 100% |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time: 00:00:00 KC>>> back_center = [ 0.21693074 0.3867723 0.10370304] KC>>> bricks = [] KC>>> LE = [] Traceback (most recent call last): File "./ShowPlots.py", line 161, in <module> test.plotVR() File "./ShowPlots.py", line 126, in plotVR vp.ray_cast() File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 111, in ray_cast LE = na.array(LE) - self.back_center ValueError: shape mismatch: objects cannot be broadcast to a single shape Exception AttributeError: "'NoneType' object has no attribute 'chdir'" in <bound method ShowPlots.__del__ of <__main__.ShowPlots instance at 0x17bb3200>> ignored PS. (the lines with "KC>>>" are my debug outputs ) On Feb 24, 2011, at 1:11 PM, yt-users-request(a)lists.spacepope.org wrote: > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. Problem in simple volume rendering (Kuo-Chuan Pan) > 2. Re: Problem in simple volume rendering (Matthew Turk) > 3. Forthon and yt installation problems. (Andrew Davis) > 4. Re: Forthon and yt installation problems. (Matthew Turk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 24 Feb 2011 04:12:18 -0600 > From: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Problem in simple volume rendering > Message-ID: <7301A4B8-2601-4AFB-960D-D6CAC55F6D29(a)astro.illinois.edu> > Content-Type: text/plain; charset=us-ascii > > Dear Sir/Madam, > > I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering. > I followed the cookbook in: > > http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_renderi… > > However I got an error message: > > File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast > LE = na.array(LE) - self.back_center > ValueError: shape mismatch: objects cannot be broadcast to a single shape > > I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct. > I guess there are some problems when setting self.bricks. > > If anyone has any suggestions, I would be very happy to hear. > Thank you. > > Best regards, > Kuo-Chuan > > ------------------------------ > > Message: 2 > Date: Thu, 24 Feb 2011 07:49:45 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Cc: Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> > Subject: Re: [yt-users] Problem in simple volume rendering > Message-ID: > <AANLkTi=MeytZo=-7ENNgHs7KTeGmemtrT32CYUGYpep1(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Kuo-Chuan, > > Sorry to hear it didn't work for you! Do you think you could help us > out with a bit more information, and then we'll see if we can get it > working for you? > > * What is the exact value of back_center that you find? > * What is the physical size of your domain? > * What is the width you supplied to the volume_rendering object? > > It might also be easier if you could try it with the "Camera" > interface as described here: > > http://yt.enzotools.org/doc/visualizing/volume_rendering.html#volume-render… > > That should allow for a bit more flexibility in describing the scene, > and may help us narrow down the error. > > Best wishes, > > Matt > > On Thu, Feb 24, 2011 at 5:12 AM, Kuo-Chuan Pan <kpan2(a)astro.illinois.edu> wrote: >> Dear Sir/Madam, >> >> I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering. >> I followed the cookbook in: >> >> ? ?http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_rendering.py >> >> However I got an error message: >> >> ?File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast >> ? ?LE = na.array(LE) - self.back_center >> ValueError: shape mismatch: objects cannot be broadcast to a single shape >> >> I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct. >> I guess there are some problems when setting self.bricks. >> >> If anyone has any suggestions, I would be very happy to hear. >> Thank you. >> >> Best regards, >> Kuo-Chuan >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > ------------------------------ > > Message: 3 > Date: Thu, 24 Feb 2011 11:44:37 -0500 > From: Andrew Davis <andrew.davis(a)yale.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] Forthon and yt installation problems. > Message-ID: <20110224114437.djff25pj404cc8sg(a)www.mail.yale.edu> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi folks, > > I'm updating my yt to the latest version, and so I'm just starting from scratch > in installing everything on a local cluster. I am running into errors, however > with the install script (line 479). When running the script, I get the > following output regarding Forthon: > > Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4') > Doing yt update, wiping local changes and updating to branch stable > Installing yt > install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory > Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log. > > I haven't been able to find any directory called yt/utilities, which is probably > why it can't find it. > At the end of the yt_install.log file, I see the following error, which doesn't > seem to be related to the install error at first glance: > > abort: data/doc/install_script.sh.i@908327e16660: no match found! > /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno > 2] No such file or directory > > Any thoughts? > > Thanks, > andrew > > > ************************************************************* > ** Andrew J. Davis andrew.davis(a)yale.edu ** > ** Dept. of Astronomy 203-432-5119 ** > ** Yale University www.astro.yale.edu/adavis ** > ************************************************************* > > > > > > ------------------------------ > > Message: 4 > Date: Thu, 24 Feb 2011 11:51:38 -0500 > From: Matthew Turk <matthewturk(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] Forthon and yt installation problems. > Message-ID: > <AANLkTinvoEfjmRD1n80kk4=Ppmab9M3rGWdViwY_ta3z(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Andrew, > > Sorry about the problem -- this looks like an issue with our hg > server; I don't believe it's directly with Forthon. There's something > up with the webserver, so you should be able to do this: > > cd /home/ajd53/YT_NEW/yt-x86_64/src > rm -rf yt-hg > /home/ajd53/YT_NEW/yt-x86_64/bin/hg clone --pull --uncompressed > http://hg.enzotools.org/yt ./yt-hg > > and that *should* get you the full set of yt, and then re-run the > install script with no modifications. Please let me know if that > doesn't work. > > -Matt > > PS The webserver for serving hg has been an issue for a while now, and > I'm embarrassed by the problem. I had hoped to move us to a different > host several weeks ago, but we've been trying to get the username > "yt." I think I need to give up that particular goal and settle for > something different. I'll have an update on this soon. > > On Thu, Feb 24, 2011 at 11:44 AM, Andrew Davis <andrew.davis(a)yale.edu> wrote: >> Hi folks, >> >> I'm updating my yt to the latest version, and so I'm just starting from scratch >> in installing everything on a local cluster. ?I am running into errors, however >> with the install script (line 479). ?When running the script, I get the >> following output regarding Forthon: >> >> Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4') >> Doing yt update, wiping local changes and updating to branch stable >> Installing yt >> install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory >> Failure. ?Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log. >> >> I haven't been able to find any directory called yt/utilities, which is probably >> why it can't find it. >> At the end of the yt_install.log file, I see the following error, which doesn't >> seem to be related to the install error at first glance: >> >> abort: data/doc/install_script.sh.i@908327e16660: no match found! >> /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno >> 2] No such file or directory >> >> Any thoughts? >> >> Thanks, >> andrew >> >> >> ************************************************************* >> ** ?Andrew J. Davis ? ? ? ? ? ? andrew.davis(a)yale.edu ? ? ?** >> ** ?Dept. of Astronomy ? ? ? ? ?203-432-5119 ? ? ? ? ? ? ? ** >> ** ?Yale University ? ? ? ? ? ? www.astro.yale.edu/adavis ?** >> ************************************************************* >> >> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> > > > ------------------------------ > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > End of yt-users Digest, Vol 36, Issue 18 > ****************************************

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log scale issues when zero.....
by Elizabeth Harper-Clark 28 Feb '11

28 Feb '11

Hi guys, one more thing. I want to calculate the radiation pressure force, and when there is some then plot it with a log scale. However if I set: def _ConvertAccel(data): return data.convert("Length") / (data.convert("Time"))**2.0 def _RadiationAccelerationMagnitude(field, data): return ( (data["RadAccel1"])**2.0 + \ (data["RadAccel2"])**2.0 + \ (data["RadAccel3"])**2.0 )**(1.0/2.0) add_field("RadiationAccelerationMagnitude", function=_RadiationAccelerationMagnitude, *take_log=True*,convert_function=_ConvertAccel, units=r"\rm{cm}/\rm{s}^{2}") def _RadiationForceMagnitude(field, data): return ( data["RadiationAccelerationMagnitude"] * data["Density"] * data["CellVolume"]) add_field("RadiationForceMagnitude", function=_RadiationForceMagnitude, * take_log=True*, units=r"\rm{dynes}") before the stars switch on when the radiation acceleration baryon fields are all 0.0 everywhere I get the following error: Traceback (most recent call last): File "MultiPlotProj.py", line 65, in <module> s = pc.add_projection("RadiationForceMagnitude", ax, weight_field="Density", figure=fig, axes=axes[0][3], use_colorbar=False) File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_collection.py", line 742, in add_projection size=fig_size, periodic=periodic)) File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line 310, in __init__ self.__init_temp_image(use_colorbar) File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line 347, in __init_temp_image self.set_width(1,'unitary') File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line 436, in set_width self._refresh_display_width() File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line 454, in _refresh_display_width self._redraw_image() File "/home/h-clark/YT/src/yt-hg/yt/visualization/plot_types.py", line 384, in _redraw_image newmin = na.nanmin(buff[bI]) File "/home/h-clark/YT/lib/python2.6/site-packages/numpy/lib/function_base.py", line 1494, in nanmin return _nanop(np.min, np.inf, a, axis) File "/home/h-clark/YT/lib/python2.6/site-packages/numpy/lib/function_base.py", line 1355, in _nanop res = op(y, axis=axis) File "/home/h-clark/YT/lib/python2.6/site-packages/numpy/core/fromnumeric.py", line 1829, in amin return amin(axis, out) ValueError: zero-size array to ufunc.reduce without identity Is there a way to set it so I get a log scale when plotting projections that does not break when the fields are all zero? Many thanks, Libby -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

4 3

Multiplot - 2x2 and 4 different color bars
by Elizabeth Harper-Clark 28 Feb '11

28 Feb '11

Hi guys, I want a 2x2 multiplot showing 4 different things (density, temperature, HII fraction and radiation force). How do i get 4 different colorbars on a 2x2 image? currently it will only give me two. Thanks, Libby my scripts as it stands: from yt.mods import * # set up our namespace import matplotlib.colorbar as cb import os orient = 'horizontal' frame_template = "aaSN/%s/Multiplotproj_%02ipc_%01i_%04i.eps" ss = float(sys.argv[2]) rho_min = 1.e-25 rho_max = 1.e-20 temp_min = 1 temp_max = 10000 HII_min = 1.e-5 HII_max = 1.0 rp_min = 1e24 rp_max = 1e26 name = sys.argv[1] firststar = 0 def _ConvertAccel(data): return data.convert("Length") / (data.convert("Time"))**2.0 def _RadiationAccelerationMagnitude(field, data): return ( (data["RadAccel1"])**2.0 + \ (data["RadAccel2"])**2.0 + \ (data["RadAccel3"])**2.0 )**(1.0/2.0) add_field("RadiationAccelerationMagnitude", function=_RadiationAccelerationMagnitude, take_log=False,convert_function=_ConvertAccel, units=r"\rm{cm}/\rm{s}^{2}") def _RadiationForceMagnitude(field, data): return ( data["RadiationAccelerationMagnitude"] * data["Density"] * data["CellVolume"]) add_field("RadiationForceMagnitude", function=_RadiationForceMagnitude, take_log=False, units=r"\rm{dynes}") for n in range(50,100,10): pf = load("SciNet/%s/DD%04i/data%04i" % (name,n, n)) # load data if pf is None: continue for ax in range (0,1): if os.path.exists(frame_template % (name,ss,ax,n)) is True: print "file exists" continue xc = 0.5 yc = 0.5 zc = 0.5 print "Dump:", n, "axis:", ax fig, axes, colorbars = get_multi_plot( 2, 2, colorbar=orient, bw = 6) pc = PlotCollection(pf, center=(xc, yc, zc)) p = pc.add_projection("Density", ax, weight_field="Density", figure = fig, axes = axes[0][0], use_colorbar=False) p.set_cmap("bds_highcontrast") p.set_zlim(rho_min, rho_max) q = pc.add_projection("Temperature", ax, weight_field="Density", figure=fig, axes=axes[0][1], use_colorbar=False) q.set_cmap("hot") q.set_zlim(temp_min, temp_max) r = pc.add_projection("HII_Fraction", ax, weight_field="Density", figure=fig, axes=axes[1][0], use_colorbar=False) r.set_cmap("jet") r.set_zlim(HII_min, HII_max) s = pc.add_projection("RadiationForceMagnitude", ax, weight_field="Density", figure=fig, axes=axes[1][1], use_colorbar=False) s.set_cmap("Greys") s.set_zlim(rp_min, rp_max) pc.set_width(ss, 'pc') sp = pf.h.all_data() if na.any(pf.h.grid_particle_count): p.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass= 6.e0) q.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass= 6.e0) r.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass= 6.e0) s.modify["particles"](2.0, p_size=1.0, col='k', minimum_mass= 6.e0) print " XXXXX Particles present XXXXX" Timemyr = pf["InitialTime"]*pf["years"]/1.e6 - firststar*.1 p.modify["text"]((0.051,0.949),"Time = %5.1f Myr" % (Timemyr), text_args = {'color':'k'}) p.modify["text"]((0.05,0.95),"Time = %5.1f Myr" % (Timemyr), text_args = {'color':'w'}) for p, cax in zip(pc.plots, colorbars): p._redraw_image() cbar = cb.Colorbar(cax, p.image, orientation=orient) p.colorbar = cbar p._autoset_label() fig.savefig(frame_template % (name,ss,ax,n), format="eps") -- Elizabeth Harper-Clark MA MSci PhD Candidate, Canadian Institute for Theoretical Astrophysics, UofT Sciences and Engineering Coordinator, Teaching Assistants' Training Program, UofT www.astro.utoronto.ca/~h-clark <http://www.astro.utoronto.ca/%7Eh-clark> h-clark(a)cita.utoronto.ca Astronomy office phone: +1-416-978-5759

1 0

psf convolution
by Charles Hansen 25 Feb '11

25 Feb '11

Does anyone know a way to convolve a yt image (preferably pc.add_projection) with a telescope psf? This would be useful for simulated observations. At the moment, the best I can do is make an image in yt and then convolve that image in pixel space, but this ends up blurring out things I do not want blurred (like particle markers, or velocity arrows). The psf does not need to be fancy, I just want a 2D gaussian with an adjustable width. Ideally, there would be a call pc.add_projection("Density", 0, psf_width = 1.5e13) #create a projection with a psf width of 1 AU at the observed distance Charles

3 4

Re: [yt-users] error in creating plot collection
by Stephen Skory 25 Feb '11

25 Feb '11

Christine, > /share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in > _parse_binary_hierarchy(self) > 288 except h5py.h5.H5Error: > 289 return False > --> 290 self.grid_dimensions[:] = f["/ActiveDimensions"][:] > 291 self.grid_left_edge[:] = f["/LeftEdges"][:] > 292 self.grid_right_edge[:] = f["/RightEdges"][:] > > ValueError: shape mismatch: objects cannot be broadcast to a single > shape This error appears to be coming from the binary hierarchy in that particular data dump. The file may be corrupted. You can try deleting the "*.harrays" file, and yt should rebuild it. Good luck! Stephen Skory stephenskory(a)yahoo.com http://stephenskory.com/ 510.621.3687 (google voice)

2 1

error in creating plot collection
by Christine Simpson 25 Feb '11

25 Feb '11

Hi all, I'm getting an error in trying to do some very simple analysis on one output of an enzo simulation I have. I don't have this issue with any other output of the simulation. Basically I can load the data and that's it; every other routine I try on it crashes. I have a feeling this may be an issue with my data, not yt, but I was wondering if you yt folks could give some insight as to what is crashing yt. Any help would be appreciated. Here is a sample error where I try to create a plot collection: In [12]: pf = load("DD0008/output_0008") yt INFO 2011-02-25 17:03:41,236 Parameters: current_time = 40.8164738158 yt INFO 2011-02-25 17:03:41,236 Parameters: domain_dimensions = [128, 128, 128] yt INFO 2011-02-25 17:03:41,236 Parameters: domain_left_edge = [ 0. 0. 0.] yt INFO 2011-02-25 17:03:41,237 Parameters: domain_right_edge = [ 1. 1. 1.] yt INFO 2011-02-25 17:03:41,238 Parameters: cosmological_simulation = 1 yt INFO 2011-02-25 17:03:41,238 Parameters: current_redshift = 6.36375016055 yt INFO 2011-02-25 17:03:41,238 Parameters: omega_lambda = 0.726 yt INFO 2011-02-25 17:03:41,238 Parameters: omega_matter = 0.274 yt INFO 2011-02-25 17:03:41,238 Parameters: hubble_constant = 0.705 In [13]: pc = PlotCollectionInteractive(pf) yt INFO 2011-02-25 17:03:44,967 Getting the binary hierarchy ERROR: An unexpected error occurred while tokenizing input The following traceback may be corrupted or invalid The error message is: ('EOF in multi-line statement', (92, 0)) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /share/home/01112/tg803911/yt_new/yt/scripts/iyt in <module>() ----> 1 2 3 4 5 /share/home/01112/tg803911/yt_new/yt/yt/visualization/plot_collection.pyc in __init__(self, *args, **kwargs) 1602 import pylab 1603 self.pylab = pylab -> 1604 super(PlotCollectionInteractive, self).__init__(*args, **kwargs) 1605 1606 def redraw(self): /share/home/01112/tg803911/yt_new/yt/yt/visualization/plot_collection.pyc in __init__(self, pf, center) 101 self.pf = pf 102 if center == None: --> 103 v,self.c = pf.h.find_max("Density") # @todo: ensure no caching 104 elif center == "center" or center == "c": 105 self.c = (pf.domain_right_edge + pf.domain_left_edge)/2.0 /share/home/01112/tg803911/yt_new/yt/yt/data_objects/static_output.pyc in _get_hierarchy(self) 157 if self._hierarchy_class == None: 158 raise RuntimeError("You should not instantiate StaticOutput.") --> 159 self.__hierarchy = self._hierarchy_class(self, data_style=self.data_style) 160 return self.__hierarchy 161 /share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in __init__(self, pf, data_style) 155 self.float_type = 'float64' 156 --> 157 AMRHierarchy.__init__(self, pf, data_style) 158 # sync it back 159 self.parameter_file.data_style = self.data_style /share/home/01112/tg803911/yt_new/yt/yt/data_objects/hierarchy.pyc in __init__(self, pf, data_style) 68 69 mylog.debug("Parsing hierarchy.") ---> 70 self._parse_hierarchy() 71 72 mylog.debug("Constructing grid objects.") /share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in _parse_hierarchy(self) 217 return line.split()[2:] 218 if os.path.exists(self.hierarchy_filename[:-9] + "harrays"): --> 219 if self._parse_binary_hierarchy(): return 220 t1 = time.time() 221 pattern = r"Pointer: Grid\[(\d*)\]->NextGrid(Next| This)Level = (\d*)\s+$" /share/home/01112/tg803911/yt_new/yt/yt/frontends/enzo/data_structures.pyc in _parse_binary_hierarchy(self) 288 except h5py.h5.H5Error: 289 return False --> 290 self.grid_dimensions[:] = f["/ActiveDimensions"][:] 291 self.grid_left_edge[:] = f["/LeftEdges"][:] 292 self.grid_right_edge[:] = f["/RightEdges"][:] ValueError: shape mismatch: objects cannot be broadcast to a single shape

1 0

yt's moving!
by Matthew Turk 25 Feb '11

25 Feb '11

Hi all, I'm writing to let you know that we have outgrown our homegrown mercurial serving (as some of you may have noticed with the installation errors) and we have moved the yt source code to BitBucket. Here are the three takeaways: * You should not have to make any changes for "yt instinfo -u" to continue working. * This should fix all outstanding issues with the install script timing out when downloading yt. * You can now much more easily contribute changes! The new source code location is the same as the old source code location: http://hg.enzotools.org/ . The username on BitBucket is "yt_analysis". The DNS might take a few hours to get circulated around, so if it doesn't work just now, it will by tonight or tomorrow. To contribute changes you can go here: http://hg.enzotools.org/yt/fork to get your own version of the yt repository, where you can make changes and commit, and even notify the main repo when your changes are ready to push back upstream. We're very excited that this will enable much greater participation, and I hope that this will lower the barrier to entry for developing yt! I'm rewriting the developer guide now, but the short answer to how to make changes has gotten a lot shorter: just fork the repository and issue a "pull request" when you're ready to contribute back upstream. Let us know if this causes any unforeseen problems, and please feel encouraged to fork and contribute! Best, Matt

1 0

Forthon and yt installation problems.
by Andrew Davis 24 Feb '11

24 Feb '11

Hi folks, I'm updating my yt to the latest version, and so I'm just starting from scratch in installing everything on a local cluster. I am running into errors, however with the install script (line 479). When running the script, I get the following output regarding Forthon: Installing Forthon-0.8.4 (arguments: 'Forthon-0.8.4') Doing yt update, wiping local changes and updating to branch stable Installing yt install_script.sh: line 479: cd: yt/utilities/kdtree: No such file or directory Failure. Check /home/ajd53/YT_NEW/yt-x86_64/yt_install.log. I haven't been able to find any directory called yt/utilities, which is probably why it can't find it. At the end of the yt_install.log file, I see the following error, which doesn't seem to be related to the install error at first glance: abort: data/doc/install_script.sh.i@908327e16660: no match found! /home/ajd53/YT_NEW/yt-x86_64/bin/python2.6: can't open file 'setup.py': [Errno 2] No such file or directory Any thoughts? Thanks, andrew ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

2 1

Problem in simple volume rendering
by Kuo-Chuan Pan 24 Feb '11

24 Feb '11

Dear Sir/Madam, I am new in yt and trying to visualize my FLASH simulation data (3D) with volume rendering. I followed the cookbook in: http://hg.enzotools.org/cookbook/raw-file/tip/recipes/simple_volume_renderi… However I got an error message: File "/home/kpan2/softwares/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/software_sampler.py", line 110, in ray_cast LE = na.array(LE) - self.back_center ValueError: shape mismatch: objects cannot be broadcast to a single shape I looked the software_sampler.py file and found all LE, RE, self.bricks are empty lists ( = []), but self.back_center is not and correct. I guess there are some problems when setting self.bricks. If anyone has any suggestions, I would be very happy to hear. Thank you. Best regards, Kuo-Chuan

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yt-users February 2011