[yt-users] Error slicing 2D spherical FLASH data
Nathan Goldbaum
nathan12343 at gmail.com
Mon Jun 23 14:46:03 PDT 2014
The issue seems to be that the pixelizer is returning NaNs:
ipdb> up
>
/Users/goldbaum/Documents/yt-hg/yt/visualization/base_plot_types.py(116)_init_image()
115 aspect=aspect,
vmax=self.zmax, cmap=cmap)
--> 116 self.cb = self.figure.colorbar(self.image, self.cax)
117
ipdb> l
111 norm = matplotlib.colors.Normalize()
112 extent = [float(e) for e in extent]
113 self.image = self.axes.imshow(data.to_ndarray(),
origin='lower',
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):
119 canvas = FigureCanvasAgg(self.figure)
120 f = StringIO()
121 canvas.print_figure(f)
ipdb> print data
[[ nan nan nan ..., nan nan nan]
[ nan nan nan ..., nan nan nan]
[ nan nan nan ..., nan nan nan]
...,
[ nan nan nan ..., nan nan nan]
[ nan nan nan ..., nan nan nan]
[ nan nan nan ..., nan nan nan]] g/cm**3
ipdb> print data.max()
nan g/cm**3
ipdb> print data.min()
nan g/cm**3
ipdb> print np.any(np.isfinite(data))
False
Unfortunately I'm not sure why this is happening. FWIW, Matt knows a lot
more than I do about how the pixelizer works for non-cartesian geometries.
On Mon, Jun 23, 2014 at 2:15 PM, Luke Zoltan Kelley <lkelley at cfa.harvard.edu
> wrote:
> 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
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> yt-users mailing list
>>> yt-users at lists.spacepope.org
>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>>
>>
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