[cctbxbb] repr for flex arrays

Fri Sep 14 11:08:30 PDT 2018

Hi Aaron

Yes I think this would be useful. I’d perhaps be more permissive say printing 10 or fewer items, but this is is the direction

The numpy illustration I gave was an unfortunate choice.

Thanks Graeme

On 14 Sep 2018, at 19:01, Aaron Brewster <asbrewster at lbl.gov<mailto:asbrewster at lbl.gov>> wrote:

Hi, I think avoiding a copy is good.  What about this:

Flex type <type(a)>, focus: <a.focus()>, size: <len(a)> memory address <address>, first and last element if len(a)>0: <a[0]>, <a[-1]>

Like numpy does, let's avoid printing every element.

On Fri, Sep 14, 2018 at 10:50 AM Nicholas Sauter <nksauter at lbl.gov<mailto:nksauter at lbl.gov>> wrote:
Yes, there is a philosophical objection to using .as_numpy_array().  Numpy only deals with a fixed number of data types, such as int, double, etc.  Flex arrays can be extended to many other types such as Bragg spots, 2-vectors, 3-vectors, and 3x3 matrices.  Therefore, if we are going to take the performance hit and do a copy, I would simply recommend using a Python list:

__repr__(a) :== list(a)

Nick

Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Fri, Sep 14, 2018 at 9:56 AM, Nicholas Devenish <ndevenish at gmail.com<mailto:ndevenish at gmail.com>> wrote:
I think as_numpy_array was just a suggestion of the simplest possible
starting implementation.

But is there a philosophical objection to them being added?

Nick

On Fri, Sep 14, 2018 at 5:27 PM Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk>
<Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>> wrote:
>
> Does it? Dang! Thought it would be fly weight and just make the data structures needed.
>
> If that’s the case then completely agree.
>
> Cheers Graeme
> ________________________________
> From: cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org> <cctbxbb-bounces at phenix-online.org<mailto:cctbxbb-bounces at phenix-online.org>> on behalf of Aaron Brewster <asbrewster at lbl.gov<mailto:asbrewster at lbl.gov>>
> Sent: 14 September 2018 17:23:41
> To: cctbx mailing list
> Subject: Re: [cctbxbb] repr for flex arrays
>
> Hi Graeme, I'm not sure what the right answer here is except I don't think it is as_numpy_array().__repr__ as that does a copy.  No good for big arrays.
>
>
>
>
> On Fri, Sep 14, 2018 at 7:30 AM Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk><mailto:Graeme.Winter at Diamond.ac.uk<mailto:Graeme.Winter at Diamond.ac.uk>> <Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk><mailto:Graeme.Winter at diamond.ac.uk<mailto:Graeme.Winter at diamond.ac.uk>>> wrote:
> Hi Folks,
>
> Is there a reason for not having a helpful __repr__ for flex arrays i.e.
>
> Grey-Area:002-decide-when graeme$ dials.python
> Python 2.7.14 (default, Apr 17 2018, 15:02:10)
> [GCC 4.2.1 Compatible Apple LLVM 9.1.0 (clang-902.0.39.1)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from dials.array_family import flex
> >>> a = flex.double([1, 2, 3])
> >>> print a
> <scitbx_array_family_flex_ext.double object at 0x1095673c0>
>
> (I have a feeling I asked this before but cannot find reference)
>
> For example
>
> >>> print a.as_numpy_array()
> [ 1.  2.  3.]
>
> is more useful… but annoying to type
>
> I appreciate a could be “big” but numpy seems to handle this OK
>
> even - could __repr__ be punned to as_numpy_array(),__repr__()?
>
> Currently it prints the type of the array and its location in ram, which are adequately served by
>
> >>> type(a)
> <class 'scitbx_array_family_flex_ext.double'>
> >>> print id(a)
> 4451627968
>
> If I print an array I more often want to see the content and less often the storage class and location (I humbly assert)
>
> Thoughts? I know this tends to confuse and annoy people who are new to flex arrays (and veterans who are busy debugging stuff…)
>
> Many thanks Graeme
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
> Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org><mailto:cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>>
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
> http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb

_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb