yt-users August 2013

yt-users@python.org

30 participants
34 discussions

line annotations, center and zooming
by David Collins 12 Aug '13

12 Aug '13

Hi, everybody-- I'm having trouble getting plot_window coordinages and annotate_image_line coordinates to agree. I have a small region that I'm trying to annotate with lines, and zoom in on. I'm having trouble getting my coordinates working together. If I do proj = oober.pf.h.proj(ax,'Density',source=source) pw = proj.to_pw(center=proj_center,origin='domain' ) pw.zoom( 1/size) I have the object centered on the plot and zoomed appropriately. If I do proj = oober.pf.h.proj(ax,'Density',source=source) pw = proj.to_pw() pw.annotate_image_line(p1, p2, data_coords=True) the lines show up in the position I expect relative to my object. However, if I include both the re-centering in to_pw and the call to annotate_image_line, the line doesn't show up where I want relative to the object. If I skip the data_coords or origin argument it doesn't seem to help. I've dug around the docs and source but haven't sorted how to make the plot window coordinages and annotate_image_line coordinates agree. Thanks! d. -- -- Sent from a computer.

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Re: [yt-users] line annotations, center and zooming
by Mark Subbarao 12 Aug '13

12 Aug '13

I'll be away till August 19th, with semi-limited connectivity. Will respond when I can. Visit our website: http://www.adlerplanetarium.org

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In temperature plot unable to plot in normal scale
by Reju Sam John 10 Aug '13

10 Aug '13

Dear All, I am trying to plot a multi plot of temperatures at different red-shifts with following script. from yt.mods import * # set up our namespace import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 1, colorbar='vertical', bw = 4) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" list = [11,13,22] m=0 #for kk in range(20,37): for kk in list: fn_i=str(kk) fn=file1+fn_i+file2+fn_i # parameter file to load print fn pf = load(fn) # load data pc = PlotCollection(pf, center=[0.5,0.5,0.5]) # defaults to center at most dense point#dd = pf.h.all_data() p = pc.add_slice("Temperature", 1, figure = fig, axes = axes[0][m], use_colorbar=False) p.set_log_field(False) p.set_zlim(1e4,5e7) #p.set_cmap("jet")# a different colormap p.modify["contour"]("Density", ncont=9, plot_args = {'colors':'w'},clim=(5e-30,5e-25)) #p.modify["contour"]("Temperature", ncont=10, plot_args = {'colors':'k'},clim=(3e7,1e8)) pc.set_width(15, 'mpc') # change width of all plots in pc m=m+1 #pc.save("%s_p.png" % pf) # save all plots for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("Temperature_at_rd00_11,13,22" % pf) The problem is that I am getting the temperature in log scale, even-though I used p.set_log_field(False) in my script. Please suggest me how to get-rid of this problem. -- Reju Sam John

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Re: [yt-users] yt-3.0 error on update, now yt doesn't work (Kyle Stewart)
by Kyle Stewart 09 Aug '13

09 Aug '13

Ah, that was the problem. After updating all, including updating Cython, it works fine. Thanks! -Kyle -- Kyle Stewart, Ph.D. Assistant Professor of Physics Department of Natural and Mathematical Sciences California Baptist University 8432 Magnolia Avenue Riverside, CA 92504 On 8/9/13 10:55 AM, "yt-users-request(a)lists.spacepope.org" <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. yt-3.0 error on update, now yt doesn't work (Kyle Stewart) > 2. Re: yt-3.0 error on update, now yt doesn't work (Kacper Kowalik) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Fri, 9 Aug 2013 16:06:26 +0000 >From: Kyle Stewart <kstewart(a)calbaptist.edu> >To: "yt-users(a)lists.spacepope.org" <yt-users(a)lists.spacepope.org> >Subject: [yt-users] yt-3.0 error on update, now yt doesn't work >Message-ID: <CE2A61BA.2EB2%kstewart(a)calbaptist.edu> >Content-Type: text/plain; charset="us-ascii" > >After updating yt (3.0) to the latest version with a simple "yt update" >command, I got the following error in the update log: > >Error compiling Cython file: >------------------------------------------------------------ >... > cdef void *tree_root > cdef int num_root > cdef int max_root > >cdef extern from "search.h" nogil: > void *tsearch(const void *key, void **rootp, > ^ >------------------------------------------------------------ > >yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' > >error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with >Cython > > > >Now yt won't work at all. If I try to call it I get the error: >"ImportError: No module named particle_oct_container" > >Does anyone know what's going on here? >Thanks! > >-Kyle > >-- >Kyle Stewart, Ph.D. >Assistant Professor of Physics >Department of Natural and Mathematical Sciences >California Baptist University >8432 Magnolia Avenue >Riverside, CA 92504 > >

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yt-3.0 error on update, now yt doesn't work
by Kyle Stewart 09 Aug '13

09 Aug '13

After updating yt (3.0) to the latest version with a simple "yt update" command, I got the following error in the update log: Error compiling Cython file: ------------------------------------------------------------ ... cdef void *tree_root cdef int num_root cdef int max_root cdef extern from "search.h" nogil: void *tsearch(const void *key, void **rootp, ^ ------------------------------------------------------------ yt/geometry/oct_container.pxd:81:29: Expected ')', found '*' error: 2 errors while compiling 'yt/geometry/oct_container.pyx' with Cython Now yt won't work at all. If I try to call it I get the error: "ImportError: No module named particle_oct_container" Does anyone know what's going on here? Thanks! -Kyle -- Kyle Stewart, Ph.D. Assistant Professor of Physics Department of Natural and Mathematical Sciences California Baptist University 8432 Magnolia Avenue Riverside, CA 92504

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Problem with multi plot
by Reju Sam John 07 Aug '13

07 Aug '13

Dear all, I am trying to create a muti plot of density's at different red-shift with the following code. from yt.mods import * import matplotlib.colorbar as cb fig, axes, colorbars = get_multi_plot( 3, 3, colorbar='vertical', bw = 3) file1="/app/run/csarkar/surajit/simulation_shock/simulation5/RD00" file2="/RedshiftOutput00" L = [11,15,18,20,22,25,30,35,40] #for i in range (0, 8): for kk in L: fn_i=str(kk) fn=file1+fn_i+file2+fn_i print fn pf = load(fn) pc = PlotCollection(pf, center=[0.5, 0.5, 0.5]) for i in range (0,3): for j in range (0, 3): p = pc.add_slice("Density", 2, axes = axes[i][j],figure = fig, use_colorbar=False) p.set_log_field(True) p.set_zlim(1e-31,5e-26) p.set_cmap("jet") p.modify["contour"]("Density", ncont=10, plot_args = {'colors':'w'},clim=(2e-28,2e-26)) p.modify["contour"]("Temperature", ncont=10, plot_args = {'colors':'k'},clim=(3e7,1e8)) #pc.set_width(3.0, 'mpc') #break # i = i+1 for p, cax in zip(pc.plots, colorbars): cbar = cb.Colorbar(cax, p.image, orientation='vertical') p.colorbar = cbar p._autoset_label() fig.savefig("multi_plot_3_3" % pf) But I am getting a wrong result. It is printing same figure in all panels. I think my logic(algorithm) is wrong. We have to reverse first two for loop. But that also making problem. Please help me. And also if I include the following line in the code. (in my code I commented it out) pc.set_width(3.0, 'mpc') it is showing following error. *Traceback (most recent call last):* * File "multi_plot_loop.py", line 24, in <module>* * pc.set_width(3.0, 'mpc') * * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 292, in set_width* * plot.set_width(width, unit)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 458, in set_width* * self._refresh_display_width()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 476, in _refresh_display_width* * self._redraw_image()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 423, in _redraw_image* * self._run_callbacks()* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 263, in _run_callbacks* * cb(self)* * File "/data1/pdf/csurajit/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 312, in __call__* * self.ncont = np.linspace(self.clim[0], self.clim[1], self.ncont)* * File "/data1/pdf/csurajit/yt-x86_64/lib/python2.7/site-packages/numpy/core/function_base.py", line 74, in linspace* * num = int(num)* *TypeError: only length-1 arrays can be converted to Python scalars* Please suggest me the most efficient way to achieve my goal (create a muti plot of density's at different red-shift). -- Reju Sam John

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problem with covering_grid for Nyx data sets
by Wolfram Schmidt 06 Aug '13

06 Aug '13

Hi, I have got problem that concerns Nyx users and/or yt developers. I want to read the root-grid level from AMR data sets with the following piece of code: num_ghost_zones=2 left=na.amin(pf.h.grid_left_edge,axis=0) right=na.amax(pf.h.grid_right_edge,axis=0) resolution = (right-left)/pf.h.grids[0]['dx']+2*num_ghost_zones cg = pf.h.covering_grid(0,left,resolution,num_ghost_zones=num_ghost_zones) This works for Enzo data sets, but it fails for Nyx data sets. The error message is Traceback (most recent call last): File "/home/h/nipiagws/scripts/spect_sb.py", line 52, in <module> cg = pf.h.covering_grid(0,left,resolution,num_ghost_zones=num_ghost_zones) File "/home/h/nipschul/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 3727, in __init__ self.dds = self.pf.domain_width/rdx.astype("float64") AttributeError: 'list' object has no attribute 'astype' The script used to work also for Nyx data sets, with an older version of yt (about a year ago). How can this be fixed? Thanks a lot, Wolfram

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Making slices of Athena SMR data
by Eve Lee 06 Aug '13

06 Aug '13

Hello, I'm trying to make a slice plot of Athena MPI SMR data using TimeSeriesData, and I find that the code only make slices out of the base level and blanks out deeper level regions. Following is how I read in the Athena vtk files: ts = TimeSeriesData.from_filenames('id0/kh*.vtk', parallel=True) my_storage={} for sto,pf in ts.piter(storage=my_storage): slc = SlicePlot(pf, 'z', 'Density') slc.set_zlim('Density', 0.0, 3.0) num = (pf.h.hierarchy_filename).split('.')[1] slc.save('./slice/'+num) all my vtk files are in id0, ..., idn where n=number of processors I used, and I'm only using 1 more level of refinement. Thanks in advance! Best Regards, Eve

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Problem with Rockstar in yt
by Brian O'Shea 05 Aug '13

05 Aug '13

Dear yt-users, I'm trying to use the Rockstar halo finder within yt, and am encountering some odd problems. I'm using the main development tree ( https://bitbucket.org/yt_analysis/yt) with changeset f936432ed45d, and attempting to use Rockstar to find halos on a small server running Ubuntu 12.04. When I call this script: ---- file test_rockstar.py ---- from yt.mods import * from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder pf = load("DD0057/data0057") rh = RockstarHaloFinder(pf) --- using the command line sequence "mpirun -np 2 python ./test_rockstar.py --parallel", I seem to be getting a seg fault (as can be seen at http://paste.yt-project.org/show/3745/). However, if I use a single processor (with "mpirun -np 1 python ./test_rockstar.py --parallel"), I get a very different error: Traceback (most recent call last): File "./test_rockstar.py", line 6, in <module> rh = RockstarHaloFinder(pf) File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 230, in __init__ self.pool, self.workgroup = self.runner.setup_pool() File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 112, in setup_pool (self.num_writers, "writers") ] File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 335, in from_sizes pool.add_workgroup(size, name = name) File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 303, in add_workgroup group = self.comm.comm.Get_group().Incl(ranks) AttributeError: 'NoneType' object has no attribute 'Get_group' I'm puzzled about the error, since I can use other parallel yt scripts without any problems (a 4-processor script making projections works just fine). This machine doesn't have infiniband (as warned about at http://yt-project.org/doc/analysis_modules/running_halofinder.html#rockstar…), and both FOF and Hop find several hundred halos with my dataset. I'd just use another halo finder, but I'm trying to do something that requires Rockstar to be run inline with Enzo, so I'm stuck with it... Does anybody have any idea what might be going on? Thanks! Brian

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MultiVariate volume rendering difficulties
by Noel Scudder 05 Aug '13

05 Aug '13

Hi all, I'm attempting to visualize multiple variables in the same volume rendering. For instance, I'd like to show some density surfaces of a star and then get temperature overlayed to show hotspots. I found the MultiVariateTransferFunction, but it is unfortunately not particularly well documented yet, and I'm being repeatedly thwarted. I'm not sure if I've set it up correctly, or how to go from the transfer function to an image. Here's my current script, using just one variable for now: #---------------------------------- from yt.mods import * pf = load('plt00100') #<some constants> pf.h pf.field_info['density'].take_log=True mv = MultiVariateTransferFunction() tf = TransferFunction((mi-1, ma+1), nbins=1.0e6) tf.add_gaussian(np.log10(9.0e5), 0.01, 1.0) mv.add_field_table(tf, 0) mv.link_channels(0, [0,1,2,3]) c = [5.0e9, 5.0e9, 5.0e9] L = [0.15, 1.0, 0.40] W = wi*0.7 Nvec = 1024 cam = pf.h.camera(c, L, W, (Nvec,Nvec), transfer_function = mv, fields=['density'], pf=pf, no_ghost=True) im = cam.snapshot(num_threads=4) im.write_png('plt00100.png' ) #---------------------------------- I checked to make sure density is indeed my 0-index field. I get the following error after ray casting: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "multivol.py", line 153, in <module> im = cam.snapshot(num_threads=4) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 742, in snapshot image, sampler), File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 632, in _render image = self.finalize_image(image) File "/home/noel/shocks/yt-x86_64/src/yt-hg/yt/visualization/volume_rendering/camera.py", line 611, in finalize_image if self.transfer_function.grey_opacity is False: AttributeError: 'MultiVariateTransferFunction' object has no attribute 'grey_opacity' Can I not use snapshot in this case, or is something else the matter entirely? Thanks, Noel Scudder

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yt-users August 2013