zero-size array error when following Introduction code

[RolfeySBG]

Hello,

https://lifelines.readthedocs.io/en/latest/Survival%20Analysis%20intro.html

I was using a piece of code from the introduction page, which was working fine a few days ago, but when I run it now I get this error: ValueError: zero-size array to reduction operation minimum which has no identity

from lifelines.plotting import plot_lifetimes
import numpy as np
from numpy.random import uniform, exponential

N = 25

CURRENT_TIME = 10

actual_lifetimes = np.array([
    exponential(12) if (uniform() < 0.5) else exponential(2) for i in range(N)
])
observed_lifetimes = np.minimum(actual_lifetimes, CURRENT_TIME)
death_observed = actual_lifetimes < CURRENT_TIME

ax = plot_lifetimes(observed_lifetimes, event_observed=death_observed)

ax.set_xlim(0, 25)
ax.vlines(10, 0, 30, lw=2, linestyles='--')
ax.set_xlabel("time")
ax.set_title("Births and deaths of our population, at $t=10$")
print("Observed lifetimes at time %d:\n" % (CURRENT_TIME), observed_lifetimes)

I think the error relates to something in the ax = plot_lifetimes(observed_lifetimes, event_observed=death_observed) section.

Any ideas welcome.

Thanks,

Neptune

[CamDavidsonPilon]

Hey @Neptune444! Hm, I wonder if it has to do with a numpy 0.20.0? Can you confirm your version of numpy and pandas for me? pip freeze will display it

[CamDavidsonPilon]

can you post the entire stacktrace?

[RolfeySBG]

Sure. I've also updated Pandas and Numpy to the latest versions, but still getting the below error:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
~\Anaconda\lib\site-packages\IPython\core\formatters.py in __call__(self, obj)
    339                 pass
    340             else:
--> 341                 return printer(obj)
    342             # Finally look for special method names
    343             method = get_real_method(obj, self.print_method)

~\Anaconda\lib\site-packages\IPython\core\pylabtools.py in <lambda>(fig)
    246 
    247     if 'png' in formats:
--> 248         png_formatter.for_type(Figure, lambda fig: print_figure(fig, 'png', **kwargs))
    249     if 'retina' in formats or 'png2x' in formats:
    250         png_formatter.for_type(Figure, lambda fig: retina_figure(fig, **kwargs))

~\Anaconda\lib\site-packages\IPython\core\pylabtools.py in print_figure(fig, fmt, bbox_inches, **kwargs)
    130         FigureCanvasBase(fig)
    131 
--> 132     fig.canvas.print_figure(bytes_io, **kw)
    133     data = bytes_io.getvalue()
    134     if fmt == 'svg':

~\Anaconda\lib\site-packages\matplotlib\backend_bases.py in print_figure(self, filename, dpi, facecolor, edgecolor, orientation, format, bbox_inches, pad_inches, bbox_extra_artists, backend, **kwargs)
   2191                            else suppress())
   2192                     with ctx:
-> 2193                         self.figure.draw(renderer)
   2194 
   2195                     bbox_inches = self.figure.get_tightbbox(

~\Anaconda\lib\site-packages\matplotlib\artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     39                 renderer.start_filter()
     40 
---> 41             return draw(artist, renderer, *args, **kwargs)
     42         finally:
     43             if artist.get_agg_filter() is not None:

~\Anaconda\lib\site-packages\matplotlib\figure.py in draw(self, renderer)
   1861 
   1862             self.patch.draw(renderer)
-> 1863             mimage._draw_list_compositing_images(
   1864                 renderer, self, artists, self.suppressComposite)
   1865 

~\Anaconda\lib\site-packages\matplotlib\image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    129     if not_composite or not has_images:
    130         for a in artists:
--> 131             a.draw(renderer)
    132     else:
    133         # Composite any adjacent images together

~\Anaconda\lib\site-packages\matplotlib\artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     39                 renderer.start_filter()
     40 
---> 41             return draw(artist, renderer, *args, **kwargs)
     42         finally:
     43             if artist.get_agg_filter() is not None:

~\Anaconda\lib\site-packages\matplotlib\cbook\deprecation.py in wrapper(*inner_args, **inner_kwargs)
    409                          else deprecation_addendum,
    410                 **kwargs)
--> 411         return func(*inner_args, **inner_kwargs)
    412 
    413     return wrapper

~\Anaconda\lib\site-packages\matplotlib\axes\_base.py in draw(self, renderer, inframe)
   2746             renderer.stop_rasterizing()
   2747 
-> 2748         mimage._draw_list_compositing_images(renderer, self, artists)
   2749 
   2750         renderer.close_group('axes')

~\Anaconda\lib\site-packages\matplotlib\image.py in _draw_list_compositing_images(renderer, parent, artists, suppress_composite)
    129     if not_composite or not has_images:
    130         for a in artists:
--> 131             a.draw(renderer)
    132     else:
    133         # Composite any adjacent images together

~\Anaconda\lib\site-packages\matplotlib\artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     39                 renderer.start_filter()
     40 
---> 41             return draw(artist, renderer, *args, **kwargs)
     42         finally:
     43             if artist.get_agg_filter() is not None:

~\Anaconda\lib\site-packages\matplotlib\collections.py in draw(self, renderer)
    929     def draw(self, renderer):
    930         self.set_sizes(self._sizes, self.figure.dpi)
--> 931         Collection.draw(self, renderer)
    932 
    933 

~\Anaconda\lib\site-packages\matplotlib\artist.py in draw_wrapper(artist, renderer, *args, **kwargs)
     39                 renderer.start_filter()
     40 
---> 41             return draw(artist, renderer, *args, **kwargs)
     42         finally:
     43             if artist.get_agg_filter() is not None:

~\Anaconda\lib\site-packages\matplotlib\collections.py in draw(self, renderer)
    383             else:
    384                 combined_transform = transform
--> 385             extents = paths[0].get_extents(combined_transform)
    386             if (extents.width < self.figure.bbox.width
    387                     and extents.height < self.figure.bbox.height):

~\Anaconda\lib\site-packages\matplotlib\path.py in get_extents(self, transform, **kwargs)
    601                 xys.append(curve([0, *dzeros, 1]))
    602             xys = np.concatenate(xys)
--> 603         return Bbox([xys.min(axis=0), xys.max(axis=0)])
    604 
    605     def intersects_path(self, other, filled=True):

~\Anaconda\lib\site-packages\numpy\core\_methods.py in _amin(a, axis, out, keepdims, initial, where)
     41 def _amin(a, axis=None, out=None, keepdims=False,
     42           initial=_NoValue, where=True):
---> 43     return umr_minimum(a, axis, None, out, keepdims, initial, where)
     44 
     45 def _sum(a, axis=None, dtype=None, out=None, keepdims=False,

ValueError: zero-size array to reduction operation minimum which has no identity

[CamDavidsonPilon]

I don't know... I can't reproduce it either. Last shot: what version of matplotlib is installed?

[CamDavidsonPilon]

BTW, don't upgrade to latest numpy just yet: #1220

[RolfeySBG]

Ok, I'll regress my numpy. Matplotlib is '3.3.1'.