Mailman 3 June 2014 - yt-users

Porting .ply files to Blender with colors?
by Jill P. Naiman 15 Aug '22

15 Aug '22

Hi All, I was curious if anyone has had any luck porting .ply files generated with yt into Blender with colors? It seems to port in the surfaces just fine, but they are a uniform color. From what I can gather, Blender imports .ply files with face color instead of vertex so I tried the surf.export_ply routine with "face" instead of "vertex" for sample_type, but no luck ("vertex" doesn't work either). Let me know if I can provide any more useful info. Thanks for any help, -J

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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

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Variance in phase/profiles
by david collins 11 Apr '20

11 Apr '20

Hi, Everybody! Does anyone out there have a technique for getting the variance out of a profile object? A profile object is good at getting <X> vs. B, I'd then like to get < (X - <X>)^2 > vs B. Matt and I had spittballed the possibility some time ago, but I was wondering if anyone out there had successfully done it. Thanks, d. -- Sent from my computer.

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Using yt to build simulation initial conditions
by Stuart Mumford 08 Jul '14

08 Jul '14

Hello, I have a use case for yt that I do not know if anyone else has encountered (though somehow I think they might have done!). I need to build background conditions for my code, this for me entails complex stratified density and magnetic field geometry see this: http://labs.adsabs.harvard.edu/adsabs/abs/2013MNRAS.435..689G/ to get an idea of the problem. The yt derived field and other abstractions would make doing this much easier, however I don't know if there is a framework for creating base fields in yt in memory and then computing derived fields based on those and then saving a mix of input fields and derived fields to disk? To make this more complex I have some weird save out requirements, so being able to change array order and do mpi decomposition at save time would be very useful. Any suggestions or people telling me that this is obvious are welcome :) Thanks Stuart

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issues with bbox filtering
by Desika Narayanan 25 Jun '14

25 Jun '14

Hi All, I'm playing around with filtering out particles from an SPH data set using the bounding box. I have a (somewhat lengthy but not complicated) notebook that highlights some of the capabilities (and an issue that I've found) here: http://nbviewer.ipython.org/gist/dnarayanan/517b736c9bb0cd72a6fa The notebook does 3 things: 1. It first loads a snapshot from a cosmological simulation, and does a projection plot. 2. It then sets a smaller bounding box, and attempts to zoom in on that region (centered on the max density). This works great. 3. Perplexingly, though, when I try basically the exact same code (the section after the second image) but with a different snapshot in the same simulation, I get a particle out of bounds error. One relevant clue is that this error only comes when trying to access smoothed quantities (i.e. the snippets where I try to access [as an example] the SFR gives no problems). Probably obvious, but this is the bleeding edge yt (most recent update). Any thoughts would definitely be welcome. thanks, desika

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grid background for camera snapshot
by Remy Indebetouw 25 Jun '14

25 Jun '14

yt newbie here - nice software, thanks for all your hard work! I really like the matplotlib 3d axis background, as e.g. http://yt-project.org/doc/cookbook/complex_plots.html#plotting-isocontours But I can't figure out how to get something remotely like that with a rendered camera snapshot. Is this possible? Thanks. Remy

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halo finding on gadget snapshots
by Desika Narayanan 24 Jun '14

24 Jun '14

Hi All, I'm having some issues with really basic halo finding on gadget snapshots in the bleeding edge version. What I want to do is ID halos in a volume, save a list of the halos, and plot a projection plot with circles over the halos (all of which I think should be possible). The principle script is: http://paste.yt-project.org/show/4824/ The error I get when trying to save the halos is: http://paste.yt-project.org/show/4822/ and in trying to annotate the halos on the projection plot is: http://paste.yt-project.org/show/4823/ Am I either doing something wrong in my commands? (hopefully as simple as that...) or are these not supported yet in the bleeding edge yt? thanks desika ps. On another (related) note, is it possible to manually draw circles on a projection plot? Or arrows, or tick marks, or anything that I could use to visually show off individual halos?

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Error slicing 2D spherical FLASH data
by Luke Zoltan Kelley 24 Jun '14

24 Jun '14

Hello again yt-users, I'm trying to plot density from a FLASH simulation in 2D spherical. I assumed that a 'SlicePlot' would be the natural choice, slicing along axis '2'/'z'/'phi'. pf = load('starwind_hdf5_plt_cnt_0000') slc = SlicePlot(pf, 2, "density") However, I get the error: yt : [INFO ] 2014-06-23 16:31:42,631 xlim = -400000000000.000000 400000000000.000000 yt : [INFO ] 2014-06-23 16:31:42,632 ylim = -400000000000.000000 400000000000.000000 yt : [INFO ] 2014-06-23 16:31:42,632 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2014-06-23 16:31:42,698 xlim = -400000000000.000000 400000000000.000000 yt : [INFO ] 2014-06-23 16:31:42,698 ylim = -400000000000.000000 400000000000.000000 yt : [INFO ] 2014-06-23 16:31:42,699 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 yt : [INFO ] 2014-06-23 16:31:42,703 Making a fixed resolution buffer of (('gas', 'density')) 800 by 800 ERROR: ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() [numpy.ma.core] astropy: [ERROR ] 2014-06-23 16:31:42,864 ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-26-62c5de6a0872> in <module>() ----> 1 slc = SlicePlot(pf, 2, "density") /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in SlicePlot(pf, normal, fields, axis, *args, **kwargs) 1872 del kwargs['north_vector'] 1873 -> 1874 return AxisAlignedSlicePlot(pf, normal, fields, *args, **kwargs) /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in __init__(self, pf, axis, fields, center, width, axes_unit, origin, fontsize, field_parameters, window_size, aspect) 1093 if axes_unit is None: 1094 axes_unit = get_axes_unit(width, pf) -> 1095 self.set_axes_unit(axes_unit) 1096 1097 class ProjectionPlot(PWViewerMPL): /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_container.pyc in newfunc(*args, **kwargs) 67 rv = f(*args, **kwargs) 68 args[0]._plot_valid = False ---> 69 args[0]._setup_plots() 70 return rv 71 return newfunc /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in _setup_plots(self) 836 self._colormaps[f], extent, zlim, 837 self.figure_size, fp.get_size(), --> 838 self.aspect, fig, axes, cax) 839 840 axes_unit_labels = ['', ''] /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.pyc in __init__(self, data, cbname, cmap, extent, zlim, figure_size, fontsize, unit_aspect, figure, axes, cax) 1703 size, axrect, caxrect, zlim, figure, axes, cax) 1704 -> 1705 self._init_image(data, cbname, cmap, extent, unit_aspect) 1706 1707 self.image.axes.ticklabel_format(scilimits=(-2, 3)) /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/visualization/base_plot_types.pyc in _init_image(self, data, cbnorm, cmap, extent, aspect) 114 extent=extent, norm=norm, vmin=self.zmin, 115 aspect=aspect, vmax=self.zmax, cmap=cmap) --> 116 self.cb = self.figure.colorbar(self.image, self.cax) 117 118 def _repr_png_(self): /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/figure.pyc in colorbar(self, mappable, cax, ax, use_gridspec, **kw) 1449 cax, kw = cbar.make_axes(ax, **kw) 1450 cax.hold(True) -> 1451 cb = cbar.colorbar_factory(cax, mappable, **kw) 1452 1453 self.sca(current_ax) /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colorbar.pyc in colorbar_factory(cax, mappable, **kwargs) 1272 cb = ColorbarPatch(cax, mappable, **kwargs) 1273 else: -> 1274 cb = Colorbar(cax, mappable, **kwargs) 1275 1276 mappable.callbacksSM.connect('changed', cb.on_mappable_changed) /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colorbar.pyc in __init__(self, ax, mappable, **kw) 875 kw['alpha'] = mappable.get_alpha() 876 --> 877 ColorbarBase.__init__(self, ax, **kw) 878 879 def on_mappable_changed(self, mappable): /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colorbar.pyc in __init__(self, ax, cmap, norm, alpha, values, boundaries, orientation, ticklocation, extend, spacing, ticks, format, drawedges, filled, extendfrac, extendrect, label) 315 # The rest is in a method so we can recalculate when clim changes. 316 self.config_axis() --> 317 self.draw_all() 318 319 def _extend_lower(self): /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colorbar.pyc in draw_all(self) 336 and do all the drawing. 337 ''' --> 338 self._process_values() 339 self._find_range() 340 X, Y = self._mesh() /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colorbar.pyc in _process_values(self, b) 650 self.norm.vmin = 0 651 self.norm.vmax = 1 --> 652 b = self.norm.inverse(self._uniform_y(self.cmap.N + 1)) 653 if self._extend_lower(): 654 b[0] = b[0] - 1 /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/colors.pyc in inverse(self, value) 1001 if cbook.iterable(value): 1002 val = ma.asarray(value) -> 1003 return vmin * ma.power((vmax / vmin), val) 1004 else: 1005 return vmin * pow((vmax / vmin), value) /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/ma/core.pyc in __mul__(self, other) 3705 def __mul__(self, other): 3706 "Multiply other by self, and return a new masked array." -> 3707 return multiply(self, other) 3708 # 3709 def __rmul__(self, other): /Users/lzkelley/Library/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/numpy/ma/core.pyc in __call__(self, a, b, *args, **kwargs) 936 # Case 1. : scalar 937 if not result.ndim: --> 938 if m: 939 return masked 940 return result ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() yt instinfo Version = 3.0-dev Changeset = 90a724768665 Any help would be greatly appreciated, Thanks so much! Luke

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ZeroDivisionError accessing field from ray in spherical 1D FLASH data
by Luke Zoltan Kelley 23 Jun '14

23 Jun '14

Hello yt-users, Just starting using YT, please forgive simple problems. I have 1D spherical FLASH data which I'm trying to plot. I thought I should use a 'ray', so I created one as such and try to access the data but I'm getting a ZeroDivision Error: from yt.mods import * pf = load('starwind_hdf5_plt_cnt_0000') In [141]: ray = pf.h.ray([0.0,0.0,0.0],[1.0e11,0.0,0.0], fields=["Density"]) In [142]: ray['Density'] yt : [INFO ] 2014-06-23 12:40:51,841 Getting field t from 138 ERROR: ZeroDivisionError: float division [IPython.core.interactiveshell] astropy: [ERROR ] 2014-06-23 12:40:51,846 ZeroDivisionError: float division --------------------------------------------------------------------------- ZeroDivisionError Traceback (most recent call last) <ipython-input-142-c8a80a171d35> in <module>() ----> 1 ray['Density'] /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in __getitem__(self, key) 316 if key not in self.fields: 317 self.fields.append(key) --> 318 self.get_data(key) 319 return self.field_data[key] 320 /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in get_data(self, fields, in_grids) 523 self[field] = np.concatenate( 524 [self._get_data_from_grid(grid, field) --> 525 for grid in self._grids]) 526 if not self.field_data.has_key(field): 527 continue /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in save_state(self, grid, field, *args, **kwargs) 79 old_keys = grid.field_data.keys() 80 grid.field_parameters = self.field_parameters ---> 81 tr = func(self, grid, field, *args, **kwargs) 82 grid.field_parameters = old_params 83 grid.field_data = YTFieldData( [(k, grid.field_data[k]) for k in old_keys] ) /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_data_from_grid(self, grid, field) 689 @restore_grid_state 690 def _get_data_from_grid(self, grid, field): --> 691 mask = np.logical_and(self._get_cut_mask(grid), 692 grid.child_mask) 693 if field == 'dts': return self._dts[grid.id][mask] /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in check_cache(self, grid) 109 elif grid.id not in self._cut_masks or \ 110 hasattr(self, "_boolean_touched"): --> 111 cm = func(self, grid) 112 self._cut_masks[grid.id] = cm 113 return self._cut_masks[grid.id] /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.pyc in _get_cut_mask(self, grid) 704 ts = np.zeros(grid.ActiveDimensions, dtype='float64') 705 VoxelTraversal(mask, ts, dts, grid.LeftEdge, grid.RightEdge, --> 706 grid.dds, self.center, self.vec) 707 self._dts[grid.id] = np.abs(dts) 708 self._ts[grid.id] = np.abs(ts) /Users/lzkelley/Applications/yt/yt-x86_64/src/yt-hg/yt/utilities/lib/RayIntegrators.so in yt.utilities.lib.RayIntegrators.VoxelTraversal (yt/utilities/lib/RayIntegrators.c:3408)() ZeroDivisionError: float division yt instinfo Version = 2.6.1 Changeset = c7bae05dd4ef Any ideas what I'm doing wrong? Thanks! Luke

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Volume rendering with gadget data
by Fernando Becerra 20 Jun '14

20 Jun '14

Dear all, I'm trying to make a volume rendering of one of my binary Gadget dataset. I'm following this tutorial: http://yt-project.org/docs/dev-3.0/cookbook/simple_volume_rendering.py, which has been working great for my Enzo outputs. But the same script is not working with the Gadget ones. The error I'm getting is "Failed to split grids" when I try to do "cam = pf.h.cam()". I checked if yt is reading the Gadget file in the right way by plotting the particles, and it looks good. Any ideas of what can be causing that problem? Best, Fernando.

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