Error slicing 2D spherical FLASH data
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
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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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@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@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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Sure, thanks Nathan! I've uploaded the file here https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin... Luke On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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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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@cfa.harvard.edu
wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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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The NaNs are on purpose, to blank out the regions that hadn't been seen by the pixelizer. I grabbed Luke's data and played around with it, and I think I figured out the problem. The dimensionality shows up as 2, although Luke ran a 1D simulation. The blocks are all 8x8x1, too. Now, if I set the right edge of the grids in axis one to be pi, I get a plot like the one attached. If we can figure out in what situations dimensionality will be reported as 2, but the left/right edges arent' set correctly, we can get this working out of the box. Ideas, Luke, John, or anyone else? On Mon, Jun 23, 2014 at 4:46 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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@cfa.harvard.edu> wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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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AFAIK this is partially due to undesirable behavior in the way that FLASH writes bounding boxes in spherical coordinates when one or more dimension is suppressed. Buried deep within the code somewhere (which I cannot remember but I have run into before) there is logic that sets the bounding box along the suppressed dimensions to pi/nblock[xyz], where nblock[xyz] is the corresponding value of the number of blocks on a side for that dimension, even though the value of nblock[xyz] is completely irrelevant. My suggestion would be that within yt we should re-set the bounding boxes in 1D/2D datasets to be 0 -> pi or 0 -> 2*pi for theta and phi. This will also help us get cell_volume right. Are you sure that Luke's simulation is 1D? It can't be if the blocks are 8x8x1. On Jun 23, 2014, at 6:17 PM, Matthew Turk <matthewturk@gmail.com> wrote:
The NaNs are on purpose, to blank out the regions that hadn't been seen by the pixelizer.
I grabbed Luke's data and played around with it, and I think I figured out the problem. The dimensionality shows up as 2, although Luke ran a 1D simulation. The blocks are all 8x8x1, too.
Now, if I set the right edge of the grids in axis one to be pi, I get a plot like the one attached.
If we can figure out in what situations dimensionality will be reported as 2, but the left/right edges arent' set correctly, we can get this working out of the box. Ideas, Luke, John, or anyone else?
On Mon, Jun 23, 2014 at 4:46 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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@cfa.harvard.edu> wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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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<starwind_hdf5_plt_cnt_0000_Slice_phi_dens.png>_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I'm very confused. When I load this file (that I uploaded earlier), I get In [2]: pf = load('starwind_hdf5_plt_cnt_0000') yt : [WARNING ] 2014-06-23 20:55:08,536 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: current_time = 0.0 yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: domain_dimensions = [ 8 16 1] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_right_edge = [ 4.00000000e+11 3.14159265e+00 1.74532925e-02] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: cosmological_simulation = 0.0 so it seems to think it is 2D (which is *correct*), and the axis-0 (rad) and axis-1 (theta) bounds seem correct. The phi bound is pi/180 for some reason (but this can be overwritten in the FLASH parameter file). I tried manually resetting the pf.domain_right_edge to be [4e11, pi, pi] but I still get the exact same error --- I don't understand Matt's fix. On Jun 23, 2014, at 6:38 PM, John ZuHone <jzuhone@gmail.com> wrote:
AFAIK this is partially due to undesirable behavior in the way that FLASH writes bounding boxes in spherical coordinates when one or more dimension is suppressed. Buried deep within the code somewhere (which I cannot remember but I have run into before) there is logic that sets the bounding box along the suppressed dimensions to pi/nblock[xyz], where nblock[xyz] is the corresponding value of the number of blocks on a side for that dimension, even though the value of nblock[xyz] is completely irrelevant.
My suggestion would be that within yt we should re-set the bounding boxes in 1D/2D datasets to be 0 -> pi or 0 -> 2*pi for theta and phi. This will also help us get cell_volume right.
Are you sure that Luke's simulation is 1D? It can't be if the blocks are 8x8x1.
On Jun 23, 2014, at 6:17 PM, Matthew Turk <matthewturk@gmail.com> wrote:
The NaNs are on purpose, to blank out the regions that hadn't been seen by the pixelizer.
I grabbed Luke's data and played around with it, and I think I figured out the problem. The dimensionality shows up as 2, although Luke ran a 1D simulation. The blocks are all 8x8x1, too.
Now, if I set the right edge of the grids in axis one to be pi, I get a plot like the one attached.
If we can figure out in what situations dimensionality will be reported as 2, but the left/right edges arent' set correctly, we can get this working out of the box. Ideas, Luke, John, or anyone else?
On Mon, Jun 23, 2014 at 4:46 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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@cfa.harvard.edu> wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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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On Mon, Jun 23, 2014 at 7:59 PM, Luke Zoltan Kelley <lkelley@cfa.harvard.edu> wrote:
I'm very confused. When I load this file (that I uploaded earlier), I get
In [2]: pf = load('starwind_hdf5_plt_cnt_0000') yt : [WARNING ] 2014-06-23 20:55:08,536 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: current_time = 0.0 yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: domain_dimensions = [ 8 16 1] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_right_edge = [ 4.00000000e+11 3.14159265e+00 1.74532925e-02] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: cosmological_simulation = 0.0
so it seems to think it is 2D (which is *correct*), and the axis-0 (rad) and axis-1 (theta) bounds seem correct. The phi bound is pi/180 for some reason (but this can be overwritten in the FLASH parameter file). I tried manually resetting the pf.domain_right_edge to be [4e11, pi, pi] but I still get the exact same error --- I don't understand Matt's fix.
Ah, I misread your earlier email and thought it was supposed to be 1D. Now, that being said, I think yt is actually doing what John suggested after I made one minor change. The thing I'm a bit confused by is how it's setting the left/right edges of the grids inside yt. What seems to be right for Cartesian isn't right for non-Cartesian. John, the tricky logic seems to all be inside where we use ND and rdx to lock against integer multiples. I'm going to try again to take a look at this tomorrow (have to go tonight) but basically everything seems to be in place, there's just this confusion with blocks, etc, and the domain_dimensions not adding up to the domain_width. -Matt
On Jun 23, 2014, at 6:38 PM, John ZuHone <jzuhone@gmail.com> wrote:
AFAIK this is partially due to undesirable behavior in the way that FLASH writes bounding boxes in spherical coordinates when one or more dimension is suppressed. Buried deep within the code somewhere (which I cannot remember but I have run into before) there is logic that sets the bounding box along the suppressed dimensions to pi/nblock[xyz], where nblock[xyz] is the corresponding value of the number of blocks on a side for that dimension, even though the value of nblock[xyz] is completely irrelevant.
My suggestion would be that within yt we should re-set the bounding boxes in 1D/2D datasets to be 0 -> pi or 0 -> 2*pi for theta and phi. This will also help us get cell_volume right.
Are you sure that Luke's simulation is 1D? It can't be if the blocks are 8x8x1.
On Jun 23, 2014, at 6:17 PM, Matthew Turk <matthewturk@gmail.com> wrote:
The NaNs are on purpose, to blank out the regions that hadn't been seen by the pixelizer.
I grabbed Luke's data and played around with it, and I think I figured out the problem. The dimensionality shows up as 2, although Luke ran a 1D simulation. The blocks are all 8x8x1, too.
Now, if I set the right edge of the grids in axis one to be pi, I get a plot like the one attached.
If we can figure out in what situations dimensionality will be reported as 2, but the left/right edges arent' set correctly, we can get this working out of the box. Ideas, Luke, John, or anyone else?
On Mon, Jun 23, 2014 at 4:46 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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@cfa.harvard.edu> wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hi all, Here's a pull request that should address the issue. https://bitbucket.org/yt_analysis/yt/pull-request/974/fixing-non-cartesian-f... Please leave a comment if it looks good to you. -Matt On Mon, Jun 23, 2014 at 9:08 PM, Matthew Turk <matthewturk@gmail.com> wrote:
On Mon, Jun 23, 2014 at 7:59 PM, Luke Zoltan Kelley <lkelley@cfa.harvard.edu> wrote:
I'm very confused. When I load this file (that I uploaded earlier), I get
In [2]: pf = load('starwind_hdf5_plt_cnt_0000') yt : [WARNING ] 2014-06-23 20:55:08,536 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: current_time = 0.0 yt : [INFO ] 2014-06-23 20:55:08,556 Parameters: domain_dimensions = [ 8 16 1] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_left_edge = [ 0. 0. 0.] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: domain_right_edge = [ 4.00000000e+11 3.14159265e+00 1.74532925e-02] yt : [INFO ] 2014-06-23 20:55:08,557 Parameters: cosmological_simulation = 0.0
so it seems to think it is 2D (which is *correct*), and the axis-0 (rad) and axis-1 (theta) bounds seem correct. The phi bound is pi/180 for some reason (but this can be overwritten in the FLASH parameter file). I tried manually resetting the pf.domain_right_edge to be [4e11, pi, pi] but I still get the exact same error --- I don't understand Matt's fix.
Ah, I misread your earlier email and thought it was supposed to be 1D.
Now, that being said, I think yt is actually doing what John suggested after I made one minor change. The thing I'm a bit confused by is how it's setting the left/right edges of the grids inside yt. What seems to be right for Cartesian isn't right for non-Cartesian.
John, the tricky logic seems to all be inside where we use ND and rdx to lock against integer multiples. I'm going to try again to take a look at this tomorrow (have to go tonight) but basically everything seems to be in place, there's just this confusion with blocks, etc, and the domain_dimensions not adding up to the domain_width.
-Matt
On Jun 23, 2014, at 6:38 PM, John ZuHone <jzuhone@gmail.com> wrote:
AFAIK this is partially due to undesirable behavior in the way that FLASH writes bounding boxes in spherical coordinates when one or more dimension is suppressed. Buried deep within the code somewhere (which I cannot remember but I have run into before) there is logic that sets the bounding box along the suppressed dimensions to pi/nblock[xyz], where nblock[xyz] is the corresponding value of the number of blocks on a side for that dimension, even though the value of nblock[xyz] is completely irrelevant.
My suggestion would be that within yt we should re-set the bounding boxes in 1D/2D datasets to be 0 -> pi or 0 -> 2*pi for theta and phi. This will also help us get cell_volume right.
Are you sure that Luke's simulation is 1D? It can't be if the blocks are 8x8x1.
On Jun 23, 2014, at 6:17 PM, Matthew Turk <matthewturk@gmail.com> wrote:
The NaNs are on purpose, to blank out the regions that hadn't been seen by the pixelizer.
I grabbed Luke's data and played around with it, and I think I figured out the problem. The dimensionality shows up as 2, although Luke ran a 1D simulation. The blocks are all 8x8x1, too.
Now, if I set the right edge of the grids in axis one to be pi, I get a plot like the one attached.
If we can figure out in what situations dimensionality will be reported as 2, but the left/right edges arent' set correctly, we can get this working out of the box. Ideas, Luke, John, or anyone else?
On Mon, Jun 23, 2014 at 4:46 PM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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@cfa.harvard.edu> wrote:
Sure, thanks Nathan! I've uploaded the file here
https://drive.google.com/file/d/0B4FXIXq2e3y4eVpHMHNPMVJCLVU/edit?usp=sharin...
Luke
On Jun 23, 2014, at 5:08 PM, Nathan Goldbaum <nathan12343@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@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@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@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@lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > _______________________________________________ > yt-users mailing list > yt-users@lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >
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participants (4)
-
John ZuHone -
Luke Zoltan Kelley -
Matthew Turk -
Nathan Goldbaum