[yt-users] Error annotating particles

[Nathan Goldbaum]

Hi Jose,

I'm able to reproduce this error on yt 3.3.5, thank you for the report.

It looks like this was fixed in the development branch a few months ago:

https://github.com/yt-project/yt/commit/7606a8e38cae62dcc84d2b14fc20e8933bb302b1

Unfortunately that fix didn't make it into yt 3.3.5. We're planning to get
yt 3.4 out ASAP, which will include this fix.

To work around this you can explicitly set stride=1 (not 1.0) in your call
to annotate_particles.

Downgrading to numpy 1.11 would also fix this (using a float to index a
numpy array was made an error in numpy 1.12). Compiling yt from source on
the git master branch would also fix it.

Hope that helps,

Nathan

On Tue, Jul 18, 2017 at 1:47 PM, José Mauricio Utreras <
jutreras at ug.uchile.cl> wrote:

> Hi yt-users,
>
> I'm using an old and simple script to overplot particles but now is not
> working.
>
> Cheers!
>
> José Utreras
>
> slc=yt.SlicePlot(ds, 'z','density', width=(25,'kpc'))
> slc.annotate_particles(width=20*kpc)
>
>
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self)   1006                 try:-> 1007                     callback(cbw)   1008                 except YTDataTypeUnsupported as e:
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in _check_geometry(self, plot)     53         if supp is None or geom in supp:---> 54             return func(self, plot)     55         if cs in ("axis", "figure") and "force" not in supp:
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in __call__(self, plot)   1574         px, py = self.convert_to_plot(plot,-> 1575                     [np.array(particle_x[gg][::self.stride]),   1576                      np.array(particle_y[gg][::self.stride])])
> ~/miniconda3/lib/python3.6/site-packages/yt/units/yt_array.py in __getitem__(self, item)   1162     def __getitem__(self, item):-> 1163         ret = super(YTArray, self).__getitem__(item)   1164         if ret.shape == ():
> TypeError: slice indices must be integers or None or have an __index__ method
>
> During handling of the above exception, another exception occurred:
> YTPlotCallbackError                       Traceback (most recent call last)~/miniconda3/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj)    334             method = get_real_method(obj, self.print_method)    335             if method is not None:--> 336                 return method()    337             return None    338         else:
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_container.py in newfunc(*args, **kwargs)     76             # it is the responsibility of _setup_plots to     77             # call args[0].run_callbacks()---> 78             args[0]._setup_plots()     79         rv = f(*args, **kwargs)     80         return rv
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in _setup_plots(self)    954     955         self._set_font_properties()--> 956         self.run_callbacks()    957         self._plot_valid = True    958
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self)   1011                     six.reraise(YTPlotCallbackError,   1012                                 YTPlotCallbackError(callback._type_name, e),-> 1013                                 sys.exc_info()[2])   1014             for key in self.frb.keys():   1015                 if key not in keys:
> ~/miniconda3/lib/python3.6/site-packages/six.py in reraise(tp, value, tb)    683             value = tp()    684         if value.__traceback__ is not tb:--> 685             raise value.with_traceback(tb)    686         raise value    687
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_window.py in run_callbacks(self)   1005                 callback = CallbackMaker(*args[1:], **kwargs)   1006                 try:-> 1007                     callback(cbw)   1008                 except YTDataTypeUnsupported as e:   1009                     six.reraise(YTDataTypeUnsupported, e)
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in _check_geometry(self, plot)     52         cs = getattr(self, "coord_system", None)     53         if supp is None or geom in supp:---> 54             return func(self, plot)     55         if cs in ("axis", "figure") and "force" not in supp:     56             return func(self, plot)
> ~/miniconda3/lib/python3.6/site-packages/yt/visualization/plot_modifications.py in __call__(self, plot)   1573             if gg.sum() == 0: return   1574         px, py = self.convert_to_plot(plot,-> 1575                     [np.array(particle_x[gg][::self.stride]),   1576                      np.array(particle_y[gg][::self.stride])])   1577         plot._axes.scatter(px, py, edgecolors='None', marker=self.marker,
> ~/miniconda3/lib/python3.6/site-packages/yt/units/yt_array.py in __getitem__(self, item)   1161    1162     def __getitem__(self, item):-> 1163         ret = super(YTArray, self).__getitem__(item)   1164         if ret.shape == ():   1165             return YTQuantity(ret, self.units, bypass_validation=True)
> YTPlotCallbackError: annotate_particles callback failed with the following error: slice indices must be integers or None or have an __index__ method
>
>
>
>
>
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