log of negative real numbers -> RuntimeWarning: invalid value encountered in log

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log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Brian Racey
Why does numpy produce a runtime warning (invalid value encountered in log) when taking the log of a negative number? I noticed that if you coerce the argument to complex by adding 0j to the negative number, the expected result is produced (i.e. ln(-1) = pi*i).

I was surprised I couldn't find a discussion on this, as I would have expected others to have come across this before. Packages like Matlab handle negative numbers automatically by doing the complex conversion.

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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Eric Wieser

One explanation for this behavior is that doing otherwise would be slow.

Consider an array like

arr = np.array([1]*10**6 + [-1])
ret = np.log(arr)

Today, what happens is:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

For what you describe to happen, the behavior would have to be either:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

  • If any negative element is encountered, allocate a new array as np.cdouble, copy all the data over, then continue. This results in the whole array being promoted.

or:

  • The input array is iterated over, and checked to see if all the values are positive
  • The output array is allocated as np.double or np.cdouble based on this result

  • The input array is iterated over, and log evaluated on each element in turn

In either case, you’ve converted a 1-pass iteration to a 2-pass one.

There are static-typing-based explanations for this behavior too, but I’ll let someone else present one of those.

Eric


On Mon, 25 May 2020 at 14:33, Brian Racey <[hidden email]> wrote:
Why does numpy produce a runtime warning (invalid value encountered in log) when taking the log of a negative number? I noticed that if you coerce the argument to complex by adding 0j to the negative number, the expected result is produced (i.e. ln(-1) = pi*i).

I was surprised I couldn't find a discussion on this, as I would have expected others to have come across this before. Packages like Matlab handle negative numbers automatically by doing the complex conversion.
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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Brian Racey
Thanks. That is for performance and memory which of course is valid for most use cases. Would it really be much different than doing type/size checking of all the np.array arguments to a function to ensure the appropriate final np.array sizes are allocated? I'm not trying to question current practice, just trying to understand as performance will eventually be important to me.

Would a "complex default" mode ever make it into numpy, to behave more like Matlab and other packages with respect to complex number handling? Sure it would make it marginally slower if enabled, but it might open the door to better compatibility when porting code to Python.

On Mon, May 25, 2020 at 9:49 AM Eric Wieser <[hidden email]> wrote:

One explanation for this behavior is that doing otherwise would be slow.

Consider an array like

arr = np.array([1]*10**6 + [-1])
ret = np.log(arr)

Today, what happens is:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

For what you describe to happen, the behavior would have to be either:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

  • If any negative element is encountered, allocate a new array as np.cdouble, copy all the data over, then continue. This results in the whole array being promoted.

or:

  • The input array is iterated over, and checked to see if all the values are positive
  • The output array is allocated as np.double or np.cdouble based on this result

  • The input array is iterated over, and log evaluated on each element in turn

In either case, you’ve converted a 1-pass iteration to a 2-pass one.

There are static-typing-based explanations for this behavior too, but I’ll let someone else present one of those.

Eric


On Mon, 25 May 2020 at 14:33, Brian Racey <[hidden email]> wrote:
Why does numpy produce a runtime warning (invalid value encountered in log) when taking the log of a negative number? I noticed that if you coerce the argument to complex by adding 0j to the negative number, the expected result is produced (i.e. ln(-1) = pi*i).

I was surprised I couldn't find a discussion on this, as I would have expected others to have come across this before. Packages like Matlab handle negative numbers automatically by doing the complex conversion.
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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Brian Racey
Being relatively new to numpy, I'm learning as I go. Your typing suggestion helped me come to the conclusion that I need to type and coerce my input arguments as I'm doing complex math. My test arguments were real, and thus numpy was producing real results. Doing .astype(np.complex128) to my input values that are generally complex resolved my issue.

On Mon, May 25, 2020 at 10:09 AM Brian Racey <[hidden email]> wrote:
Thanks. That is for performance and memory which of course is valid for most use cases. Would it really be much different than doing type/size checking of all the np.array arguments to a function to ensure the appropriate final np.array sizes are allocated? I'm not trying to question current practice, just trying to understand as performance will eventually be important to me.

Would a "complex default" mode ever make it into numpy, to behave more like Matlab and other packages with respect to complex number handling? Sure it would make it marginally slower if enabled, but it might open the door to better compatibility when porting code to Python.

On Mon, May 25, 2020 at 9:49 AM Eric Wieser <[hidden email]> wrote:

One explanation for this behavior is that doing otherwise would be slow.

Consider an array like

arr = np.array([1]*10**6 + [-1])
ret = np.log(arr)

Today, what happens is:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

For what you describe to happen, the behavior would have to be either:

  • The output array is allocated as np.double
  • The input array is iterated over, and log evaluated on each element in turn

  • If any negative element is encountered, allocate a new array as np.cdouble, copy all the data over, then continue. This results in the whole array being promoted.

or:

  • The input array is iterated over, and checked to see if all the values are positive
  • The output array is allocated as np.double or np.cdouble based on this result

  • The input array is iterated over, and log evaluated on each element in turn

In either case, you’ve converted a 1-pass iteration to a 2-pass one.

There are static-typing-based explanations for this behavior too, but I’ll let someone else present one of those.

Eric


On Mon, 25 May 2020 at 14:33, Brian Racey <[hidden email]> wrote:
Why does numpy produce a runtime warning (invalid value encountered in log) when taking the log of a negative number? I noticed that if you coerce the argument to complex by adding 0j to the negative number, the expected result is produced (i.e. ln(-1) = pi*i).

I was surprised I couldn't find a discussion on this, as I would have expected others to have come across this before. Packages like Matlab handle negative numbers automatically by doing the complex conversion.
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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Sebastian Berg
In reply to this post by Brian Racey
On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:

> Thanks. That is for performance and memory which of course is valid
> for
> most use cases. Would it really be much different than doing
> type/size
> checking of all the np.array arguments to a function to ensure the
> appropriate final np.array sizes are allocated? I'm not trying to
> question
> current practice, just trying to understand as performance will
> eventually
> be important to me.
>
> Would a "complex default" mode ever make it into numpy, to behave
> more like
> Matlab and other packages with respect to complex number handling?
> Sure it
> would make it marginally slower if enabled, but it might open the
> door to
> better compatibility when porting code to Python.
>

I think the SciPy versions may have such a default, or there is such a
functionality hidden somewhere (maybe even the switching behaviour).
I am not sure anyone actually uses those, so it may not be a good idea
to use them to be honest.

The type safety aspects are that you do can get float or complex
results randomly, which of course is fine for much code...

From my side main argument in favor of the current behaviour is that
you, as someone working with complex numbers, likely immediately knows
that what you want is to use `np.log(..., dtype=...)` or cast the input
to complex.  But someone not used to complex numbers may be very
surprised if they suddenly have a complex result after a long
calculation.

That said, there is a problem here, since it is a bit clumsy to force a
complex result. `np.log(..., dtype=np.complex128)` works, but hard-
codes double precision. `np.log(arr + 0j)` works, but may look strange
(I will assume that `log` is so slow that the overhead is not very
relevant).  I am not sure that if the use case is actually big enough
to worry about it, i.e. if you work with complex numbers, you may be
fine with just converting to complex once early on...

- Sebastian



> On Mon, May 25, 2020 at 9:49 AM Eric Wieser <
> [hidden email]>
> wrote:
>
> > One explanation for this behavior is that doing otherwise would be
> > slow.
> >
> > Consider an array like
> >
> > arr = np.array([1]*10**6 + [-1])
> > ret = np.log(arr)
> >
> > Today, what happens is:
> >
> >    - The output array is allocated as np.double
> >    - The input array is iterated over, and log evaluated on each
> > element
> >    in turn
> >
> > For what you describe to happen, the behavior would have to be
> > either:
> >
> >    - The output array is allocated as np.double
> >    -
> >
> >    The input array is iterated over, and log evaluated on each
> > element in
> >    turn
> >    -
> >
> >    If any negative element is encountered, allocate a new array as
> >    np.cdouble, copy all the data over, then continue. This results
> > in the
> >    whole array being promoted.
> >
> > or:
> >
> >    - The input array is iterated over, and checked to see if all
> > the
> >    values are positive
> >    -
> >
> >    The output array is allocated as np.double or np.cdouble based
> > on this
> >    result
> >    -
> >
> >    The input array is iterated over, and log evaluated on each
> > element in
> >    turn
> >
> > In either case, you’ve converted a 1-pass iteration to a 2-pass
> > one.
> >
> > There are static-typing-based explanations for this behavior too,
> > but I’ll
> > let someone else present one of those.
> >
> > Eric
> >
> > On Mon, 25 May 2020 at 14:33, Brian Racey <[hidden email]>
> > wrote:
> >
> > > Why does numpy produce a runtime warning (invalid value
> > > encountered in
> > > log) when taking the log of a negative number? I noticed that if
> > > you coerce
> > > the argument to complex by adding 0j to the negative number, the
> > > expected
> > > result is produced (i.e. ln(-1) = pi*i).
> > >
> > > I was surprised I couldn't find a discussion on this, as I would
> > > have
> > > expected others to have come across this before. Packages like
> > > Matlab
> > > handle negative numbers automatically by doing the complex
> > > conversion.
> > > _______________________________________________
> > > NumPy-Discussion mailing list
> > > [hidden email]
> > > https://mail.python.org/mailman/listinfo/numpy-discussion
> > >
> > _______________________________________________
> > NumPy-Discussion mailing list
> > [hidden email]
> > https://mail.python.org/mailman/listinfo/numpy-discussion
> >
>
> _______________________________________________
> NumPy-Discussion mailing list
> [hidden email]
> https://mail.python.org/mailman/listinfo/numpy-discussion


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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Python School Organizers
In reply to this post by Brian Racey
>Would a "complex default" mode ever make it into numpy, to behave more like Matlab and other packages with respect to complex number handling? Sure it would make it marginally slower if enabled, but it might open the door to better compatibility when porting code to Python.

numpy already has the "complex default" log function: numpy.lib.scimath.log . There are other useful gems in that module, for example a "complex default" sqrt function

Ciao,
Tiziano
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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Robert Kern-2
In reply to this post by Sebastian Berg
On Mon, May 25, 2020 at 10:36 AM Sebastian Berg <[hidden email]> wrote:
On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:
> Would a "complex default" mode ever make it into numpy, to behave
> more like
> Matlab and other packages with respect to complex number handling?
> Sure it
> would make it marginally slower if enabled, but it might open the
> door to
> better compatibility when porting code to Python.
>

I think the SciPy versions may have such a default, or there is such a
functionality hidden somewhere (maybe even the switching behaviour).
I am not sure anyone actually uses those, so it may not be a good idea
to use them to be honest.

The versions in `np.lib.scimath` behave like this. Of course, people do use them when they want to deal with real numbers as subsets of the complex numbers.

--
Robert Kern

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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Sebastian Berg
On Mon, 2020-05-25 at 11:10 -0400, Robert Kern wrote:

> On Mon, May 25, 2020 at 10:36 AM Sebastian Berg <
> [hidden email]>
> wrote:
>
> > On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:
> > > Would a "complex default" mode ever make it into numpy, to behave
> > > more like
> > > Matlab and other packages with respect to complex number
> > > handling?
> > > Sure it
> > > would make it marginally slower if enabled, but it might open the
> > > door to
> > > better compatibility when porting code to Python.
> > >
> >
> > I think the SciPy versions may have such a default, or there is
> > such a
> > functionality hidden somewhere (maybe even the switching
> > behaviour).
> > I am not sure anyone actually uses those, so it may not be a good
> > idea
> > to use them to be honest.
> >
>
> The versions in `np.lib.scimath` behave like this. Of course, people
> do use
> them when they want to deal with real numbers as subsets of the
> complex
> numbers.
>

True, I guess I just used complex numbers too rarely in programs (i.e.
never central to any programming project).

It seems this is actually also exposed as `np.emath`, which is maybe a
better entry point? And I guess the scipy namespace uses them.

- Sebastian

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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Brian Racey
My Googling revealed none of this. I don't have anyone to talk to about using numpy, so Google (and this group) is all I have. This was extremely useful: https://numpy.org/devdocs/user/numpy-for-matlab-users.html so perhaps it could be extended to point out those modules and entry points if it isn't documented elsewhere.

On Mon, May 25, 2020 at 11:17 AM Sebastian Berg <[hidden email]> wrote:
On Mon, 2020-05-25 at 11:10 -0400, Robert Kern wrote:
> On Mon, May 25, 2020 at 10:36 AM Sebastian Berg <
> [hidden email]>
> wrote:
>
> > On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:
> > > Would a "complex default" mode ever make it into numpy, to behave
> > > more like
> > > Matlab and other packages with respect to complex number
> > > handling?
> > > Sure it
> > > would make it marginally slower if enabled, but it might open the
> > > door to
> > > better compatibility when porting code to Python.
> > >
> >
> > I think the SciPy versions may have such a default, or there is
> > such a
> > functionality hidden somewhere (maybe even the switching
> > behaviour).
> > I am not sure anyone actually uses those, so it may not be a good
> > idea
> > to use them to be honest.
> >
>
> The versions in `np.lib.scimath` behave like this. Of course, people
> do use
> them when they want to deal with real numbers as subsets of the
> complex
> numbers.
>

True, I guess I just used complex numbers too rarely in programs (i.e.
never central to any programming project).

It seems this is actually also exposed as `np.emath`, which is maybe a
better entry point? And I guess the scipy namespace uses them.

- Sebastian

> _______________________________________________
> NumPy-Discussion mailing list
> [hidden email]
> https://mail.python.org/mailman/listinfo/numpy-discussion


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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Ilhan Polat
In reply to this post by Sebastian Berg
I wasted a good 2 weeks because of that behavior of Matlab back in the day and I think that is one of the cardinal sins that matlab commits. If need be there are alternatives as mentioned before but I definitely do not prefer this coercion at all.

On Mon, May 25, 2020 at 5:18 PM Sebastian Berg <[hidden email]> wrote:
On Mon, 2020-05-25 at 11:10 -0400, Robert Kern wrote:
> On Mon, May 25, 2020 at 10:36 AM Sebastian Berg <
> [hidden email]>
> wrote:
>
> > On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:
> > > Would a "complex default" mode ever make it into numpy, to behave
> > > more like
> > > Matlab and other packages with respect to complex number
> > > handling?
> > > Sure it
> > > would make it marginally slower if enabled, but it might open the
> > > door to
> > > better compatibility when porting code to Python.
> > >
> >
> > I think the SciPy versions may have such a default, or there is
> > such a
> > functionality hidden somewhere (maybe even the switching
> > behaviour).
> > I am not sure anyone actually uses those, so it may not be a good
> > idea
> > to use them to be honest.
> >
>
> The versions in `np.lib.scimath` behave like this. Of course, people
> do use
> them when they want to deal with real numbers as subsets of the
> complex
> numbers.
>

True, I guess I just used complex numbers too rarely in programs (i.e.
never central to any programming project).

It seems this is actually also exposed as `np.emath`, which is maybe a
better entry point? And I guess the scipy namespace uses them.

- Sebastian

> _______________________________________________
> NumPy-Discussion mailing list
> [hidden email]
> https://mail.python.org/mailman/listinfo/numpy-discussion


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Re: log of negative real numbers -> RuntimeWarning: invalid value encountered in log

Robert Kern-2
In reply to this post by Sebastian Berg
On Mon, May 25, 2020 at 11:17 AM Sebastian Berg <[hidden email]> wrote:
On Mon, 2020-05-25 at 11:10 -0400, Robert Kern wrote:
> On Mon, May 25, 2020 at 10:36 AM Sebastian Berg <
> [hidden email]>
> wrote:
>
> > On Mon, 2020-05-25 at 10:09 -0400, Brian Racey wrote:
> > > Would a "complex default" mode ever make it into numpy, to behave
> > > more like
> > > Matlab and other packages with respect to complex number
> > > handling?
> > > Sure it
> > > would make it marginally slower if enabled, but it might open the
> > > door to
> > > better compatibility when porting code to Python.
> > >
> >
> > I think the SciPy versions may have such a default, or there is
> > such a
> > functionality hidden somewhere (maybe even the switching
> > behaviour).
> > I am not sure anyone actually uses those, so it may not be a good
> > idea
> > to use them to be honest.
> >
>
> The versions in `np.lib.scimath` behave like this. Of course, people
> do use
> them when they want to deal with real numbers as subsets of the
> complex
> numbers.
>

True, I guess I just used complex numbers too rarely in programs (i.e.
never central to any programming project).

It seems this is actually also exposed as `np.emath`, which is maybe a
better entry point? And I guess the scipy namespace uses them.

Ah, yes, that's the preferred alias, though the documentation page for it seems to be a little buggy (using `np.lib.scimath` instead `np.emath`; telling you to look at the docstrings for the individual functions, but they don't exist in the documentation).

--
Robert Kern

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