Invalid value encoutered : how to prevent numpy.where to do this?
Dear all, I have a code using lots of "numpy.where" to make some constrained calculations as in: data = arange(10) result = np.where(data == 0, 0., 1./data) # or data1 = arange(10) data2 = arange(10)+1.0 result = np.where(data1 > data2, np.sqrt(data1-data2), np.sqrt(data2-data2)) which then produces warnings like: /usr/bin/ipython:1: RuntimeWarning: invalid value encountered in sqrt or for the first example: /usr/bin/ipython:1: RuntimeWarning: divide by zero encountered in divide How do I avoid these messages to appear? I know that I could in principle use numpy.seterr. However, I do NOT want to remove these warnings for other potential divide/multiply/sqrt etc errors. Only when I am using a "where", to in fact avoid such warnings! Note that the warnings only happen once, but since I am going to release that code, I would like to avoid the user to get such messages which are irrelevant here (because I am testing, with the where, when NOT to divide by zero or take a sqrt of a negative number). thanks! Eric
On Sat, Jan 5, 2013 at 2:15 PM, Eric Emsellem <eric.emsellem@eso.org> wrote:
Dear all,
I have a code using lots of "numpy.where" to make some constrained calculations as in:
data = arange(10) result = np.where(data == 0, 0., 1./data)
# or data1 = arange(10) data2 = arange(10)+1.0 result = np.where(data1 > data2, np.sqrt(data1-data2), np.sqrt(data2-data2))
which then produces warnings like: /usr/bin/ipython:1: RuntimeWarning: invalid value encountered in sqrt
or for the first example:
/usr/bin/ipython:1: RuntimeWarning: divide by zero encountered in divide
How do I avoid these messages to appear?
I know that I could in principle use numpy.seterr. However, I do NOT want to remove these warnings for other potential divide/multiply/sqrt etc errors. Only when I am using a "where", to in fact avoid such warnings! Note that the warnings only happen once, but since I am going to release that code, I would like to avoid the user to get such messages which are irrelevant here (because I am testing, with the where, when NOT to divide by zero or take a sqrt of a negative number).
You can't avoid it while using np.where like this, because the warning is being issued before np.where is even called. It's basically doing: # Calculate all possible sqrts tmp1 = np.sqrt(data1-data2) tmp2 = np.sqrt(data2-data2) # let's pretend this isn't just all zeros... # Use np.where to pick out the useful ones and put them together into one array mashed_up = np.where(data1 > data2, tmp1, tmp2) So you need to somehow apply the indexing while doing the sqrt. In this case the easiest way would just be np.sqrt(np.where(data1 > data2, data1 - data2, data2 - data2)) Or, slightly faster (avoiding some temporaries): np.sqrt(np.where(data1 > data2, data1, data2) - data2) If your operation doesn't factor like this though then you can always use something more cumbersome like result = np.empty_like(data) mask = (data == 0) result[mask] = 0 result[~mask] = 1.0/data[~mask] Or in 1.7 this could be written result = np.zeros_like(data) np.divide(1.0, data, where=(data != 0), out=result) -n
I agree. The problem can be avoided in a very inelegant way by turning warnings off before calling where() and turning them back on afterward, like this warnings.filterwarnings("ignore", category=RuntimeWarning) result = np.where(x == 0.0, 0.0, 1./data) warnings.filterwarnings("always", category=RuntimeWarning) But it would be MUCH nicer if there were an optional keyword argument in the where() call. Thanks, Dave
Hi! You can use a context manager: with np.errstate(all=”ignore”): … Best regards, Hameer Abbasi Von meinem iPhone gesendet
Am 18.02.2023 um 16:00 schrieb David Pine <pine@nyu.edu>:
I agree. The problem can be avoided in a very inelegant way by turning warnings off before calling where() and turning them back on afterward, like this
warnings.filterwarnings("ignore", category=RuntimeWarning) result = np.where(x == 0.0, 0.0, 1./data) warnings.filterwarnings("always", category=RuntimeWarning)
But it would be MUCH nicer if there were an optional keyword argument in the where() call.
Thanks, Dave _______________________________________________ NumPy-Discussion mailing list -- numpy-discussion@python.org To unsubscribe send an email to numpy-discussion-leave@python.org https://mail.python.org/mailman3/lists/numpy-discussion.python.org/ Member address: einstein.edison@gmail.com
FWIW, scipy has a small utility just for this: https://github.com/scipy/scipy/blob/main/scipy/_lib/_util.py#L36 Not to be used in performance critical loops, of course. Cheers, Evgeni сб, 18 февр. 2023 г., 17:02 David Pine <pine@nyu.edu>:
I agree. The problem can be avoided in a very inelegant way by turning warnings off before calling where() and turning them back on afterward, like this
warnings.filterwarnings("ignore", category=RuntimeWarning) result = np.where(x == 0.0, 0.0, 1./data) warnings.filterwarnings("always", category=RuntimeWarning)
But it would be MUCH nicer if there were an optional keyword argument in the where() call.
Thanks, Dave _______________________________________________ NumPy-Discussion mailing list -- numpy-discussion@python.org To unsubscribe send an email to numpy-discussion-leave@python.org https://mail.python.org/mailman3/lists/numpy-discussion.python.org/ Member address: evgeny.burovskiy@gmail.com
participants (5)
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David Pine -
Eric Emsellem -
Evgeni Burovski -
Hameer Abbasi -
Nathaniel Smith