Hi Pavel
The question was the complement of this i.e. if I ask to normalize a vector v then I return
v/|v|
If |v| == 0 then we do have 0/0 happiness
I am certain that (0,0,0).length() will return 0
http://stackoverflow.com/questions/722073/how-do-you-normalize-a-zero-vector
In *almost every useful case* if you ask to normalize a 0 vector you probably did not want a 0 vector in the first place, else you would have tested this, so any error (even if obscure) is a useful pointer
Cheers Graeme
On 2 May 2017, at 06:44, Pavel Afonine mailto:[email protected]> wrote:
If memory serves norm of a zero vector is zero, isn't it? So naively I'd expect that function to return zero, not fail in obscure way..
Broadly speaking, norm is length. Length of a zero vector is zero.
So my proposal would be to treat zero vectors as special case and do the right thing for it.
Pavel
On 5/1/17 22:18, [email protected]mailto:[email protected] wrote:
Dear Oleg
philosophy question: what do you think is the correct result for (0,0,0).normalize()?
If |x|=0 I would probably expect a /0 error from this - is this your proposal below?
I would say that this has not been a problem so far and is used extensively so the current behaviour is probably OK... but that is one opinion of many
Documenting this is a good idea though!
Best wishes Graeme
________________________________
From: [email protected]mailto:[email protected] [[email protected]mailto:[email protected]] on behalf of Oleg Sobolev [[email protected]mailto:[email protected]]
Sent: 01 May 2017 19:10
To: cctbx mailing list
Subject: [cctbxbb] normalize() is not safe
Dear colleagues,
I recently discovered that normalize() function of scitbx::vec3<double> is not safe, i.e. this case
scitbx::vec3<double> a(0,0,0);
a.normalize();
it will produce division by zero and fail. If function contains this being called from python the traceback would be rather vague:
<...>
Floating-point error (Python and libc call stacks above)
This crash may be due to a problem in any imported
Python module, including modules which are not part
of the cctbx project. To disable the traps leading
to this message, define these environment variables
(e.g. assign the value 1):
BOOST_ADAPTBX_FPE_DEFAULT
BOOST_ADAPTBX_SIGNALS_DEFAULT
This will NOT solve the problem, just mask it, but
may allow you to proceed in case it is not critical.
The code that generates this error sits in scitbx/vec3.h, lines 143-153 with a comment that this was done intentionally and a pointer to an appropriate function to do safe normalization. This function is not wrapped to be available in python directly.
Similar functionality (but coded in a different place) accessible via python by:
from scitbx import matrix
b = matrix.col([0,0,0])
b.normalize()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 270, in normalize
return self / abs(self)
File "/net/anaconda/raid1/olegs/phenix_queue/modules/cctbx_project/scitbx/matrix/__init__.py", line 158, in __truediv__
return rec([e/other for e in self.elems], self.n)
ZeroDivisionError: float division by zero
Fast grepping shows that normalize() is widely used in xfel, smtbx, rstbx, dxtbx, mmtbx/hydrogens, scitbx/rigid_body, and in some other places.
My questions to CCTBX community are:
1. Were you aware of this issue?
2. Should we do something about it:
- make the function more safe and slow;
- leave it like it is and let everybody know about the issue and let developers deal with it individually;
3. Any other input on the matter?
Best regards,
Oleg Sobolev.
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