Mailman 3 April 2017 - NumPy-Discussion

Invalid value encoutered : how to prevent numpy.where to do this?
by Eric Emsellem 18 Feb '23

18 Feb '23

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

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Re: [Numpy-discussion] example reading binary Fortran file
by Neil Martinsen-Burrell 22 Jul '21

22 Jul '21

David Froger <david.froger.info <at> gmail.com> writes: > Hy,My question is about reading Fortran binary file (oh no this question > again...) I've posted this before, but I finally got it cleaned up for the Cookbook. For this purpose I use a subclass of file that has methods for reading unformatted Fortran data. See http://www.scipy.org/Cookbook/FortranIO/FortranFile. I'd gladly see this in numpy or scipy somewhere, but I'm not sure where it belongs. > program makeArray > implicit none > integer,parameter:: nx=10,ny=20 > real(4),dimension(nx,ny):: ux,uy,p > integer :: i,j > open(11,file='uxuyp.bin',form='unformatted') > do i = 1,nx > do j = 1,ny > ux(i,j) = real(i*j) > uy(i,j) = real(i)/real(j) > p (i,j) = real(i) + real(j) > enddo > enddo > write(11) ux,uy > write(11) p > close(11) > end program makeArray When I run the above program compiled with gfortran on my Intel Mac, I can read it back with:: >>> import numpy as np >>> from fortranfile import FortranFile >>> f=FortranFile('uxuyp.bin', endian='<') >>> uxuy = f.readReals(prec='f') # 'f' for default reals >>> len(uxuy) 400 >>> ux = np.array(uxuy[:200]).reshape((20,10)).T >>> uy = np.array(uxuy[200:]).reshape((20,10)).T >>> p = f.readReals('f').reshape((20,10)).T >>> ux array([[ 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20.], [ 2., 4., 6., 8., 10., 12., 14., 16., 18., 20., 22., 24., 26., 28., 30., 32., 34., 36., 38., 40.], [ 3., 6., 9., 12., 15., 18., 21., 24., 27., 30., 33., 36., 39., 42., 45., 48., 51., 54., 57., 60.], [ 4., 8., 12., 16., 20., 24., 28., 32., 36., 40., 44., 48., 52., 56., 60., 64., 68., 72., 76., 80.], [ 5., 10., 15., 20., 25., 30., 35., 40., 45., 50., 55., 60., 65., 70., 75., 80., 85., 90., 95., 100.], [ 6., 12., 18., 24., 30., 36., 42., 48., 54., 60., 66., 72., 78., 84., 90., 96., 102., 108., 114., 120.], [ 7.,Proxy-Connection: keep-alive Cache-Control: max-age=0 14., 21., 28., 35., 42., 49., 56., 63., 70., 77., 84., 91., 98., 105., 112., 119., 126., 133., 140.], [ 8., 16., 24., 32., 40., 48., 56., 64., 72., 80., 88., 96., 104., 112., 120., 128., 136., 144., 152., 160.], [ 9., 18., 27., 36., 45., 54., 63., 72., 81., 90., 99., 108., 117., 126., 135., 144., 153., 162., 171., 180.], [ 10., 20., 30., 40., 50., 60., 70., 80., 90., 100., 110., 120., 130., 140., 150., 160., 170., 180., 190., 200.]]) >>> uy array([[ 1. , 0.5 , 0.33333334, 0.25 , 0.2 , 0.16666667, 0.14285715, 0.125 , 0.11111111, 0.1 , 0.09090909, 0.08333334, 0.07692308, 0.07142857, 0.06666667, 0.0625 , 0.05882353, 0.05555556, 0.05263158, 0.05 ], [ 2. , 1. , 0.66666669, 0.5 , 0.40000001, 0.33333334, 0.2857143 , 0.25 , 0.22222222, 0.2 , 0.18181819, 0.16666667, 0.15384616, 0.14285715, 0.13333334, 0.125 , 0.11764706, 0.11111111, 0.10526316, 0.1 ], [ 3. , 1.5 , 1. , 0.75 , 0.60000002, 0.5 , 0.42857143, 0.375 , 0.33333334, 0.30000001, 0.27272728, 0.25 , 0.23076923, 0.21428572, 0.2 , 0.1875 , 0.17647059, 0.16666667, 0.15789473, 0.15000001], [ 4. , 2. , 1.33333337, 1. , 0.80000001, 0.66666669, 0.5714286 , 0.5 , 0.44444445, 0.40000001, 0.36363637, 0.33333334, 0.30769232, 0.2857143 , 0.26666668, 0.25 , 0.23529412, 0.22222222, 0.21052632, 0.2 ], [ 5. , 2.5 , 1.66666663, 1.25 , 1. , 0.83333331, 0.71428573, 0.625 , 0.55555558, 0.5 , 0.45454547, 0.41666666, 0.38461539, 0.35714287, 0.33333334, 0.3125 , 0.29411766, 0.27777779, 0.2631579 , 0.25 ], [ 6. , 3. , 2. , 1.5 , 1.20000005, 1. , 0.85714287, 0.75 , 0.66666669, 0.60000002, 0.54545456, 0.5 , 0.46153846, 0.42857143, 0.40000001, 0.375 , 0.35294119, 0.33333334, 0.31578946, 0.30000001], [ 7. , 3.5 , 2.33333325, 1.75 , 1.39999998, 1.16666663, 1. , 0.875 , 0.77777779, 0.69999999, 0.63636363, 0.58333331, 0.53846157, 0.5 , 0.46666667, 0.4375 , 0.41176471, 0.3888889 , 0.36842105, 0.34999999], [ 8. , 4. , 2.66666675, 2. , 1.60000002, 1.33333337, 1.14285719, 1. , 0.8888889 , 0.80000001, 0.72727275, 0.66666669, 0.61538464, 0.5714286 , 0.53333336, 0.5 , 0.47058824, 0.44444445, 0.42105263, 0.40000001], [ 9. , 4.5 , 3. , 2.25 , 1.79999995, 1.5 , 1.28571427, 1.125 , 1. , 0.89999998, 0.81818181, 0.75 , 0.69230771, 0.64285713, 0.60000002, 0.5625 , 0.52941179, 0.5 , 0.47368422, 0.44999999], [ 10. , 5. , 3.33333325, 2.5 , 2. , 1.66666663, 1.42857146, 1.25 , 1.11111116, 1. , 0.90909094, 0.83333331, 0.76923078, 0.71428573, 0.66666669, 0.625 , 0.58823532, 0.55555558, 0.52631581, 0.5 ]]) >>> p array([[ 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21.], [ 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22.], [ 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23.], [ 5., 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24.], [ 6., 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25.], [ 7., 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26.], [ 8., 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27.], [ 9., 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28.], [ 10., 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29.], [ 11., 12., 13., 14., 15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27., 28., 29., 30.]]) Note that you have to provide the shape information for ux and uy because fortran writes them together as a stream of 400 numbers. -Neil

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[NumPy-discussion] Wish List of Possible ufunc Enhancements
by Matthew Harrigan 29 Apr '17

29 Apr '17

Here is a link <https://gist.github.com/mattharrigan/b784b50b451a41f327b3a990ec043557> to a wish list of possible ufunc enhancements. I would like to know what the community thinks. Thank you, Matt Harrigan

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[ANN] 10ᵀᴴ Advanced Scientific Programming in Python in Nikiti, Greece, August 28—September 2, 2017
by Tiziano Zito 28 Apr '17

28 Apr '17

10ᵀᴴ Advanced Scientific Programming in Python ============================================== a Summer School by the G-Node and the Municipality of Sithonia Scientists spend more and more time writing, maintaining, and debugging software. While techniques for doing this efficiently have evolved, only few scientists have been trained to use them. As a result, instead of doing their research, they spend far too much time writing deficient code and reinventing the wheel. In this course we will present a selection of advanced programming techniques and best practices which are standard in the industry, but especially tailored to the needs of a programming scientist. Lectures are devised to be interactive and to give the students enough time to acquire direct hands-on experience with the materials. Students will work in pairs throughout the school and will team up to practice the newly learned skills in a real programming project — an entertaining computer game. We use the Python programming language for the entire course. Python works as a simple programming language for beginners, but more importantly, it also works great in scientific simulations and data analysis. We show how clean language design, ease of extensibility, and the great wealth of open source libraries for scientific computing and data visualization are driving Python to become a standard tool for the programming scientist. This school is targeted at Master or PhD students and Post-docs from all areas of science. Competence in Python or in another language such as Java, C/C++, MATLAB, or Mathematica is absolutely required. Basic knowledge of Python and of a version control system such as git, subversion, mercurial, or bazaar is assumed. Participants without any prior experience with Python and/or git should work through the proposed introductory material before the course. We are striving hard to get a pool of students which is international and gender-balanced. You can apply online: https://python.g-node.org Application deadline: 23:59 UTC, May 31, 2017. There will be no deadline extension, so be sure to apply on time ;-) Be sure to read the FAQ before applying. Participation is for free, i.e. no fee is charged! Participants however should take care of travel, living, and accommodation expenses by themselves. Date & Location =============== August 28—September 2, 2017. Nikiti, Sithonia, Halkidiki, Greece Program ======= → Best Programming Practices • Best practices for scientific programming • Version control with git and how to contribute to open source projects with GitHub • Best practices in data visualization → Software Carpentry • Test-driven development • Debugging with a debuggger • Profiling code → Scientific Tools for Python • Advanced NumPy → Advanced Python • Decorators • Context managers • Generators → The Quest for Speed • Writing parallel applications • Interfacing to C with Cython • Memory-bound problems and memory profiling • Data containers: storage and fast access to large data → Practical Software Development • Group project Preliminary Faculty =================== • Francesc Alted, freelance consultant, author of Blosc, Castelló de la Plana, Spain • Pietro Berkes, NAGRA Kudelski, Lausanne, Switzerland • Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University, Fairfax, VA USA • Eilif Muller, Blue Brain Project, École Polytechnique Fédérale de Lausanne Switzerland • Juan Nunez-Iglesias, Victorian Life Sciences Computation Initiative, University of Melbourne, Australia • Rike-Benjamin Schuppner, Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Germany • Nicolas P. Rougier, Inria Bordeaux Sud-Ouest, Institute of Neurodegenerative Disease, University of Bordeaux, France • Bartosz Teleńczuk, European Institute for Theoretical Neuroscience, CNRS, Paris, France • Stéfan van der Walt, Berkeley Institute for Data Science, UC Berkeley, CA USA • Nelle Varoquaux, Berkeley Institute for Data Science, UC Berkeley, CA USA • Tiziano Zito, freelance consultant, Berlin, Germany Organizers ========== For the German Neuroinformatics Node of the INCF (G-Node) Germany: • Tiziano Zito, freelance consultant, Berlin, Germany • Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University, Fairfax, USA • Jakob Jordan, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Jülich GmbH, Germany • Etienne Roesch, Centre for Integrative Neuroscience and Neurodynamics, University of Reading, UK Website: https://python.g-node.org Contact: python-info(a)g-node.org

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Re: [Numpy-discussion] proposal: smaller representation of string arrays
by Chris Barker 27 Apr '17

27 Apr '17

I just re-read the "Utf-8" manifesto, and it helped me clarify my thoughts: 1) most of it is focused on utf-8 vs utf-16. And that is a strong argument -- utf-16 is the worst of both worlds. 2) it isn't really addressing how to deal with fixed-size string storage as needed by numpy. It does bring up Python's current approach to Unicode: """ This lead to software design decisions such as Python’s string O(1) code point access. The truth, however, is that Unicode is inherently more complicated and there is no universal definition of such thing as *Unicode character*. We see no particular reason to favor Unicode code points over Unicode grapheme clusters, code units or perhaps even words in a language for that. """ My thoughts on that-- it's technically correct, but practicality beats purity, and the character concept is pretty darn useful for at least some (commonly used in the computing world) languages. In any case, whether the top-level API is character focused doesn't really have a bearing on the internal encoding, which is very much an implementation detail in py 3 at least. And Python has made its decision about that. So what are the numpy use-cases? I see essentially two: 1) Use with/from Python -- both creating and working with numpy arrays. In this case, we want something compatible with Python's string (i.e. full Unicode supporting) and I think should be as transparent as possible. Python's string has made the decision to present a character oriented API to users (despite what the manifesto says...). However, there is a challenge here: numpy requires fixed-number-of-bytes dtypes. And full unicode support with fixed number of bytes matching fixed number of characters is only possible with UCS-4 -- hence the current implementation. And this is actually just fine! I know we all want to be efficient with data storage, but really -- in the early days of Unicode, when folks thought 16 bits were enough, doubling the memory usage for western language storage was considered fine -- how long in computer life time does it take to double your memory? But now, when memory, disk space, bandwidth, etc, are all literally orders of magnitude larger, we can't handle a factor of 4 increase in "wasted" space? Alternatively, Robert's suggestion of having essentially an object array, where the objects were known to be python strings is a pretty nice idea -- it gives the full power of python strings, and is a perfect one-to-one match with the python text data model. But as scientific text data often is 1-byte compatible, a one-byte-per-char dtype is a fine idea, too -- and we pretty much have that already with the existing string type -- that could simply be enhanced by enforcing the encoding to be latin-9 (or latin-1, if you don't want the Euro symbol). This would get us what scientists expect from strings in a way that is properly compatible with Python's string type. You'd get encoding errors if you tried to stuff anything else in there, and that's that. Yes, it would have to be a "new" dtype for backwards compatibility. 2) Interchange with other systems: passing the raw binary data back and forth between numpy arrays and other code, written in C, Fortran, or binary flle formats. This is a key use-case for numpy -- I think the key to its enormous success. But how important is it for text? Certainly any data set I've ever worked with has had gobs of binary numerical data, and a small smattering of text. So in that case, if, for instance, h5py had to encode/decode text when transferring between HDF files and numpy arrays, I don't think I'd ever see the performance hit. As for code complexity -- it would mean more complex code in interface libs, and less complex code in numpy itself. (though numpy could provide utilities to make it easy to write the interface code) If we do want to support direct binary interchange with other libs, then we should probably simply go for it, and support any encoding that Python supports -- as long as you are dealing with multiple encodings, why try to decide up front which ones to support? But how do we expose this to numpy users? I still don't like having non-fixed-width encoding under the hood, but what can you do? Other than that, having the encoding be a selectable part of the dtype works fine -- and in that case the number of bytes should be the "length" specifier. This, however, creates a bit of an impedance mismatch between the "character-focused" approach of the python string type. And requires the user to understand something about the encoding in order to even know how many bytes they need -- a utf-8-100 string will hold a different "length" of string than a utf-16-100 string. So -- I think we should address the use-cases separately -- one for "normal" python use and simple interoperability with python strings, and one for interoperability at the binary level. And an easy way to convert between the two. For Python use -- a pointer to a Python string would be nice. Then use a native flexible-encoding dtype for everything else. Thinking out loud -- another option would be to set defaults for the multiple-encoding dtype so you'd get UCS-4 -- with its full compatibility with the python string type -- and make folks make an effort to get anything else. One more note: if a user tries to assign a value to a numpy string array that doesn't fit, they should get an error: EncodingError if it can't be encoded into the defined encoding. ValueError if it is too long -- it should not be silently truncated. -CHB -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker(a)noaa.gov

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__array_ufunc__ final review
by Charles R Harris 21 Apr '17

21 Apr '17

Hi All, The __array_ufunc__ <https://github.com/numpy/numpy/pull/8247> PR is ready for final review. If there are no complaints, I plan to put it in tomorrow. Chuck

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proposal: smaller representation of string arrays
by Julian Taylor 21 Apr '17

21 Apr '17

Hello, As you probably know numpy does not deal well with strings in Python3. The np.string type is actually zero terminated bytes and not a string. In Python2 this happened to work out as it treats bytes and strings the same way. But in Python3 this type is pretty hard to work with as each time you get an item from a numpy bytes array it needs decoding to receive a string. The only string type available in Python3 is np.unicode which uses 4-byte utf-32 encoding which is deemed to use too much memory to actually see much use. What people apparently want is a string type for Python3 which uses less memory for the common science use case which rarely needs more than latin1 encoding. As we have been told we cannot change the np.string type to actually be strings as existing programs do interpret its content as bytes despite this being very broken due to its null terminating property (it will ignore all trailing nulls). Also 8 years of working around numpy's poor python3 support decisions in third parties probably make the 'return bytes' behaviour impossible to change now. So we need a new dtype that can represent strings in numpy arrays which is smaller than the existing 4 byte utf-32. To please everyone I think we need to go with a dtype that supports multiple encodings via metadata, similar to how datatime supports multiple units. E.g.: 'U10[latin1]' are 10 characters in latin1 encoding Encodings we should support are: - latin1 (1 bytes): it is compatible with ascii and adds extra characters used in the western world. - utf-32 (4 bytes): can represent every character, equivalent with np.unicode Encodings we should maybe support: - utf-16 with explicitly disallowing surrogate pairs (2 bytes): this covers a very large range of possible characters in a reasonably compact representation - utf-8 (4 bytes): variable length encoding with minimum size of 1 bytes, but we would need to assume the worst case of 4 bytes so it would not save anything compared to utf-32 but may allow third parties replace an encoding step with trailing null trimming on serialization. To actually do this we have two options both of which break our ABI when doing so without ugly hacks. - Add a new dtype, e.g. npy.realstring By not modifying an existing type the only break programs using the NPY_CHAR. The most notable case of this is f2py. It has the cosmetic disadvantage that it makes the np.unicode dtype obsolete and is more busywork to implement. - Modify np.unicode to have encoding metadata This allows use to reuse of all the type boilerplate so it is more convenient to implement and by extending an existing type instead of making one obsolete it results in a much nicer API. The big drawback is that it will explicitly break any third party that receives an array with a new encoding and assumes that the buffer of an array of type np.unicode will a character itemsize of 4 bytes. To ease this problem we would need to add API's to get the itemsize and encoding to numpy now so third parties can error out cleanly. The implementation of it is not that big a deal, I have already created a prototype for adding latin1 metadata to np.unicode which works quite well. It is imo realistic to get this into 1.14 should we be able to make a decision on which way to implement it. Do you have comments on how to go forward, in particular in regards to new dtype vs modify np.unicode? cheers, Julian

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Relaxed stride checking fixup
by Charles R Harris 20 Apr '17

20 Apr '17

Hi All, Currently numpy master has a bogus stride that will cause an error when downstream projects misuse it. That is done in order to help smoke out errors. Previously that bogus stride has been fixed up for releases, but that requires a special patch to be applied after each version branch is made. At this point I'd like to pick one or the other option and make the development and release branches the same in this regard. The question is: which option to choose? Keeping the fixup in master will remove some code and keep things simple, while not fixing up the release will possibly lead to more folks finding errors. At this point in time I am favoring applying the fixup in master. Thoughts? Chuck

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Long term plans for dropping Python 2.7
by Charles R Harris 16 Apr '17

16 Apr '17

Hi All, It may be early to discuss dropping support for Python 2.7, but there is a disturbance in the force that suggests that it might be worth looking forward to the year 2020 when Python itself will drop support for 2.7. There is also a website, http://www.python3statement.org, where several projects in the scientific python stack have pledged to be Python 2.7 free by that date. Given that, a preliminary discussion of the subject might be interesting, if only to gather information of where the community currently stands. Chuck

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testing needed for f2py with char/string arrays
by Julian Taylor 15 Apr '17

15 Apr '17

hi, we need to deprecate the NPY_CHAR typenumber [0] in order to enable us to add new core dtypes without adding ugly hacks to our ABI. Technically the typenumber was deprecated way back in 1.6 when it accidentally broke our ABI. But due to lack of time f2py never got updated to actually follow through. In order to unblock our dtype development cleanly we want to finally do the deprecation properly. As nobody really knows how f2py works and there are no existing unit tests covering the char dtype the change is very likely to break something. The change is available here: https://github.com/numpy/numpy/pull/8948 It attempts to map the NPY_CHAR dtype to the equivalent NPY_STRING with itemsize 1. I have only been able to come up with a test that covers one of the changed places. So if you have a f2py usecase that in some way involves passing arrays of strings back and forth between python and fortran, please test that branch or post a reproducable example here. Thanks, Julian [0] https://github.com/numpy/numpy/blob/master/numpy/core/include/numpy/ndarray…

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NumPy-Discussion April 2017