yt-users September 2011

yt-users@python.org

33 participants
24 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

trouble with callback on phase plot
by Christine Simpson 03 Oct '11

03 Oct '11

Hi all, I'm having trouble adding text through a callback onto a phase plot. I tried this code: pc.add_phase_sphere(r200[j],'kpc',["Density","Temperature","CellMassMsun"],weight = None) pc.set_zlim(1.0e-2,1.0e5) pc.set_xlim(1.0e-30,5.0e-19) pc.set_ylim(10.0,1.0e7) pc.plots[-1].modify["text"]([0.92,0.92],redshift_string) pc.save("output_%(file_num)s_branch_%yt-users(a)lists.spacepope.org(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) And I get this error: Traceback (most recent call last): File "test_phase_plots.py", line 41, in <module> pc.save("output_%(file_num)s_branch_%(br)i" % {"file_num":fn,"axis":ax,"br":branch_index[j]}) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_collection.py", line 157, in save override=override, force_save=force_save)) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 108, in save_image self._redraw_image() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 903, in _redraw_image self._run_callbacks() File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_types.py", line 800, in _run_callbacks cb(self) File "/share/home/01112/tg803911/yt_17May2011/yt-x86_64/src/yt-hg/yt/visualization/plot_modifications.py", line 910, in __call__ y = plot.image._A.shape[1] * self.pos[1] IndexError: tuple index out of range The error arises in the save command, but the problem only happens when I add the modify["text"] command. Any ideas? Christine

2 5

log-linear phase plot
by Wolfram Schmidt 01 Oct '11

01 Oct '11

Hi everyone, I defined two fields, say, FieldOne and FieldTwo, to make 2D phase plot. FieldOne is logarithmic by default, FieldTwo is linear (i.e., I set take_log=False in add_field). I want to produce a phase plot with logarithmic bins for FieldOne and linear bins for FieldTwo, where the range of FieldTwo is [-10,10] I thought that pc.add_phase_object(dd, ["FieldOne", "FieldTwo", "CellMass"], weight=None, x_bins=100,y_bins=100, \ x_bounds=[1e0,1e10], y_bounds=[-10,10]) might do the job, but yt returns the error message: Warning: invalid value encountered in log10 yt : [ERROR ] 2011-09-30 16:55:05,610 Your min/max values for x, y have given me a nan. yt : [ERROR ] 2011-09-30 16:55:05,610 Usually this means you are asking for log, with a zero bound. Traceback (most recent call last): File "stability.py", line 352, in <module> x_bounds=[1e0,1e10], y_bounds=[-10,10]) File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/visualization/plot_collection.py", line 1149, in add_phase_object lazy_reader) File "/nics/e/sw/analysis/yt/2.1/sles11.1_gnu4.3.4/src/yt-hg/yt/data_objects/profiles.py", line 408, in __init__ raise ValueError ValueError It appears that add_phase_object treats FieldTwo logarithmically, although it is linear. So how can I do a log-linear phase plot? Best, Wolfram

3 2

who is interested in a yt workshop?
by Britton Smith 30 Sep '11

30 Sep '11

Hi everyone, There has been some discussion on the developers list about holding a yt workshop within roughly the next six months. Ideally, this workshop would have two parts. The first part would focus on education for users, from basic intro to advanced usage, and perhaps spending time helping users craft specific analysis routines. The second part would focus on development, where we discuss new features we would like the code to have as well as existing parts that are in need of some work, and then we actually get down to working on these thing and coding. Since one of the main goals of yt is to blur the lines between user and developer, we would try to aim the end of the users portion at understanding yt internals and how best to work on the code. The goal here would be to make a natural transition between the two parts to maximize the number of people willing to stick around for the development section. As it's not yet clear what kind of external funding we can get, we would like to make this as accessible as possible. This probably means choosing a city that is a major airport hub, like Chicago, Detroit, etc. The timing would be sometime early next year, currently anywhere between late January and say March. Before any of this can move forward, we really would like to know how many people are actually interested in such a thing. If you are at all interested in participating in a yt users/developers workshop, please respond to this email in at least the following way: I am [am not] interested in coming to a users workshop. I am [am not] interested in coming to a developers workshop. Any and all other comments are also welcome, as to timing, location, content, etc. Personally, I think this could really be a great thing, but let's here what you think. Britton

27 31

IsBound and mpi4py
by Eve Lee 28 Sep '11

28 Sep '11

Hello, I'm doing a simple analysis of looking for a gravitationally bound sphere centred at the most dense point in each level of clumps by iteratively increasing the radius from 0.5pc to 4pc until the derived quantity "IsBound" is True. I'm trying to use mpi4py as this iteration takes a very long time on serial but I'm getting an error very similar to the error I received when I tried mpi4py with clump finding routine: Traceback (most recent call last): bound = sp_cand.quantities["IsBound"](truncate=True, include_thermal_energy=False) File "/home/elee/accretion/analysis/codes/clump_excise_sph.py", line 71, in <module> File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 86, in __call__ self.func(e, *args, **kwargs) self.func(e, *args, **kwargs) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound self.func(e, *args, **kwargs) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound bound = sp_cand.quantities["IsBound"](truncate=True, include_thermal_energy=False) File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 86, in __call__ bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' self.func(e, *args, **kwargs) AttributeError: 'FieldDetector' object has no attribute 'quantities' File "/home/jchong/ytdev/yt-x86_64/src/yt-hg/yt/data_objects/derived_quantities.py", line 351, in _IsBound bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' bv_x,bv_y,bv_z = data.quantities["BulkVelocity"]() AttributeError: 'FieldDetector' object has no attribute 'quantities' It seems like parallelization loses the attribute "quantities" associated with data, which, if I understand correctly, should be the sphere object. Does this mean it somehow loses the sphere object that was passed in as an argument? Or is this somehow related to the parallel contouring algorithm that Britton has mentioned before? Thanks. Best Regards, Eve

4 6

change resolution of a slice
by Jean-Claude Passy 27 Sep '11

27 Sep '11

Hi all, I have a pretty dumb question. I have data from which I would like to take a slice with a resolution of one cell per pixel. How can I do that ? Thanks a lot, JC

3 3

Kraken YT/SQLite3 Issues
by Brian Crosby 23 Sep '11

23 Sep '11

Hi everyone, I was trying to use the YT installation on Kraken to create a merger tree and seem to have run into a problem with it being unable to import SQLite3. The error appears to stem from the following: P190 yt : [ERROR ] 2011-09-20 00:02:03,730 sqlite3 not imported! Digging around the YT installs, it appears that SQLite3 isn't there. Oddly, when I installed and built it in my home directory I still got the same error, so perhaps this is an issue with YT or Kraken rather than with the community install. Do anyone have an idea what might be going on? The output file is attached. Thanks, Brian

2 1

Yt version 2.2 on Nautilus and Kraken
by Harinarayan Krishnan 23 Sep '11

23 Sep '11

Hi all, Nautilus and Kraken now have yt-2.2 installed. Please let me know if there are any issues. The yt module on Kraken is still using h5py 1.2.0. I will try to update it to 1.3.1 as soon as I can. Kraken: module swap PrgEnv-pgi PrgEnv-gnu module load yt/2.2 Nautilus: module load yt/2.2 If no major issues come up, I will make them "default." That is, "module load yt" will load version 2.2 Thanks, Hari

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Re: [yt-users] pc.save with old Enzo
by Elizabeth Tasker 22 Sep '11

22 Sep '11

Sorry -- correction: this problem also occurs with a new data set from Enzo 2.0. It doesn't happen, however, with the older version of yt. The version it fails on is 9cb628620da6 (yt). Unfortunately, the version it works on gives an error linked with finding the mercurial libraries when I run yt instinfo, so I'm not sure which version it is. Elizabeth On Sep 22, 2011, at 6:50 PM, Elizabeth Tasker wrote: > Hi, > > I'm trying to analyse an older Enzo simulation which writes its output in hdf5 but with files that look like: > > GT_RotFrame_128AMR8_stars_0200.grid.cpu0029 > > the script runs fine until it reaches pc.save(fn), then I get: > > AttributeError Traceback (most recent call last) > > /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() > ----> 1 > 2 > 3 > 4 > 5 > > /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() > 55 > 56 > ---> 57 pc.save(fn) > 58 > 59 > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_collection.pyc in save(self, basename, format, override, force_save) > 155 for plot in self.plots: > 156 fn.append(plot.save_image(basename, format=format, > --> 157 override=override, force_save=force_save)) > 158 mylog.info("Saved %s", fn[-1]) > 159 if ytcfg.getboolean("yt", "__withinreason"): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in save_image(self, prefix, format, override, force_save, figure_canvas) > 106 prefix. > 107 """ > --> 108 self._redraw_image() > 109 if not override: > 110 self._generate_prefix(prefix) > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _redraw_image(self, *args) > 399 self.norm.autoscale(na.array((newmin,newmax), dtype='float64')) > 400 self._reset_image_parameters() > --> 401 self._run_callbacks() > 402 > 403 def _reset_image_parameters(self): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _run_callbacks(self) > 256 self._axes.texts = [] > 257 for cb in self._callbacks: > --> 258 cb(self) > 259 > 260 def set_label(self, label): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) > 83 yv = "%s-velocity" % (y_names[plot.data.axis]) > 84 qcb = QuiverCallback(xv, yv, self.factor, scale=self.scale, scale_units=self.scale_units) > ---> 85 return qcb(plot) > 86 > 87 class MagFieldCallback(PlotCallback): > > /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) > 148 X = na.mgrid[0:plot.image._A.shape[0]-1:nx*1j]# + 0.5*factor > 149 Y = na.mgrid[0:plot.image._A.shape[1]-1:ny*1j]# + 0.5*factor > --> 150 plot._axes.quiver(X,Y, pixX, pixY, scale=self.scale, scale_units=self.scale_units) > 151 plot._axes.set_xlim(xx0,xx1) > 152 plot._axes.set_ylim(yy0,yy1) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/axes.pyc in quiver(self, *args, **kw) > 5873 def quiver(self, *args, **kw): > 5874 if not self._hold: self.cla() > -> 5875 q = mquiver.Quiver(self, *args, **kw) > 5876 self.add_collection(q, False) > 5877 self.update_datalim(q.XY) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/quiver.pyc in __init__(self, ax, *args, **kw) > 392 transOffset=ax.transData, > 393 closed=False, > --> 394 **kw) > 395 self.polykw = kw > 396 self.set_UVC(U, V, C) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, verts, sizes, closed, **kwargs) > 664 %(Collection)s > 665 """ > --> 666 Collection.__init__(self,**kwargs) > 667 self._sizes = sizes > 668 self.set_verts(verts, closed) > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, edgecolors, facecolors, linewidths, linestyles, antialiaseds, offsets, transOffset, norm, cmap, pickradius, urls, **kwargs) > 106 > 107 self._pickradius = pickradius > --> 108 self.update(kwargs) > 109 > 110 > > /home/taskere/yt/lib/python2.6/site-packages/matplotlib/artist.pyc in update(self, props) > 624 func = getattr(self, 'set_'+k, None) > 625 if func is None or not callable(func): > --> 626 raise AttributeError('Unknown property %s'%k) > 627 func(v) > 628 changed = True > > AttributeError: Unknown property scale_units > > > > > > Is there an easy fix for this? If it helps, an example data set is at: > > http://www.physics.mcmaster.ca/~taskere/GT_RotFrame_128AMR8_stars_0200.tar.… > > (about 650 Mb) and the yt script: > > http://paste.yt-project.org/show/1816/ > > Elizabeth > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

2 2

pc.save with old Enzo
by Elizabeth Tasker 22 Sep '11

22 Sep '11

Hi, I'm trying to analyse an older Enzo simulation which writes its output in hdf5 but with files that look like: GT_RotFrame_128AMR8_stars_0200.grid.cpu0029 the script runs fine until it reaches pc.save(fn), then I get: AttributeError Traceback (most recent call last) /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() ----> 1 2 3 4 5 /home/taskere/yt/src/yt-hg/scripts/iyt in <module>() 55 56 ---> 57 pc.save(fn) 58 59 /home/taskere/yt/src/yt-hg/yt/visualization/plot_collection.pyc in save(self, basename, format, override, force_save) 155 for plot in self.plots: 156 fn.append(plot.save_image(basename, format=format, --> 157 override=override, force_save=force_save)) 158 mylog.info("Saved %s", fn[-1]) 159 if ytcfg.getboolean("yt", "__withinreason"): /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in save_image(self, prefix, format, override, force_save, figure_canvas) 106 prefix. 107 """ --> 108 self._redraw_image() 109 if not override: 110 self._generate_prefix(prefix) /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _redraw_image(self, *args) 399 self.norm.autoscale(na.array((newmin,newmax), dtype='float64')) 400 self._reset_image_parameters() --> 401 self._run_callbacks() 402 403 def _reset_image_parameters(self): /home/taskere/yt/src/yt-hg/yt/visualization/plot_types.pyc in _run_callbacks(self) 256 self._axes.texts = [] 257 for cb in self._callbacks: --> 258 cb(self) 259 260 def set_label(self, label): /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) 83 yv = "%s-velocity" % (y_names[plot.data.axis]) 84 qcb = QuiverCallback(xv, yv, self.factor, scale=self.scale, scale_units=self.scale_units) ---> 85 return qcb(plot) 86 87 class MagFieldCallback(PlotCallback): /home/taskere/yt/src/yt-hg/yt/visualization/plot_modifications.pyc in __call__(self, plot) 148 X = na.mgrid[0:plot.image._A.shape[0]-1:nx*1j]# + 0.5*factor 149 Y = na.mgrid[0:plot.image._A.shape[1]-1:ny*1j]# + 0.5*factor --> 150 plot._axes.quiver(X,Y, pixX, pixY, scale=self.scale, scale_units=self.scale_units) 151 plot._axes.set_xlim(xx0,xx1) 152 plot._axes.set_ylim(yy0,yy1) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/axes.pyc in quiver(self, *args, **kw) 5873 def quiver(self, *args, **kw): 5874 if not self._hold: self.cla() -> 5875 q = mquiver.Quiver(self, *args, **kw) 5876 self.add_collection(q, False) 5877 self.update_datalim(q.XY) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/quiver.pyc in __init__(self, ax, *args, **kw) 392 transOffset=ax.transData, 393 closed=False, --> 394 **kw) 395 self.polykw = kw 396 self.set_UVC(U, V, C) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, verts, sizes, closed, **kwargs) 664 %(Collection)s 665 """ --> 666 Collection.__init__(self,**kwargs) 667 self._sizes = sizes 668 self.set_verts(verts, closed) /home/taskere/yt/lib/python2.6/site-packages/matplotlib/collections.pyc in __init__(self, edgecolors, facecolors, linewidths, linestyles, antialiaseds, offsets, transOffset, norm, cmap, pickradius, urls, **kwargs) 106 107 self._pickradius = pickradius --> 108 self.update(kwargs) 109 110 /home/taskere/yt/lib/python2.6/site-packages/matplotlib/artist.pyc in update(self, props) 624 func = getattr(self, 'set_'+k, None) 625 if func is None or not callable(func): --> 626 raise AttributeError('Unknown property %s'%k) 627 func(v) 628 changed = True AttributeError: Unknown property scale_units Is there an easy fix for this? If it helps, an example data set is at: http://www.physics.mcmaster.ca/~taskere/GT_RotFrame_128AMR8_stars_0200.tar.… (about 650 Mb) and the yt script: http://paste.yt-project.org/show/1816/ Elizabeth

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yt-users September 2011