[yt-users] Error slicing 2D spherical FLASH data
Luke Zoltan Kelley
lkelley at cfa.harvard.edu
Mon Jun 23 14:15:55 PDT 2014
Sure, thanks Nathan!
I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharing
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
> For some reason it's falling over when it's trying to construct the colorbar for the plot. I'm not sure why and would need to look closer at the data file. If you'd be willing to share it with me I'm happy to do that.
>
> If you want to debug this on your own my first suggestion would be to run the script under gdb and try to figure out why the colorbar construction is going wonky.
>
> -Nathan
>
>
> On Mon, Jun 23, 2014 at 2:02 PM, Luke Zoltan Kelley <lkelley at cfa.harvard.edu> wrote:
> They seem fine:
>
> In [33]: dens = pf.all_data()['density']
>
> In [34]: print dens.min()
> 9.99999968266e-20 g/cm**3
>
> In [35]: print dens.max()
> 157.337768555 g/cm**3
>
> These are the values I expected.
>
>
> On Jun 23, 2014, at 4:47 PM, Nathan Goldbaum <nathan12343 at gmail.com> wrote:
>
>> Hey Luke,
>>
>> What do the raw density values in your data look like?
>>
>> dens = ds.all_data()['density']
>> print dens.max()
>> print dens.min()
>>
>> -Nathan
>>
>>
>> On Mon, Jun 23, 2014 at 1:37 PM, Luke Zoltan Kelley <lkelley at cfa.harvard.edu> wrote:
>> 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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