[Numpy-discussion] Raveling, reshape order keyword unnecessarily confuses index and memory ordering

Matthew Brett matthew.brett@gmail....
Sun Mar 31 14:54:29 CDT 2013


Hi,

On Sat, Mar 30, 2013 at 10:38 PM,  <josef.pktd@gmail.com> wrote:
> On Sun, Mar 31, 2013 at 12:50 AM, Matthew Brett <matthew.brett@gmail.com> wrote:
>> Hi,
>>
>> On Sat, Mar 30, 2013 at 9:37 PM,  <josef.pktd@gmail.com> wrote:
>>> On Sun, Mar 31, 2013 at 12:04 AM, Matthew Brett <matthew.brett@gmail.com> wrote:
>>>> Hi,
>>>>
>>>> On Sat, Mar 30, 2013 at 7:02 PM,  <josef.pktd@gmail.com> wrote:
>>>>> On Sat, Mar 30, 2013 at 8:29 PM, Matthew Brett <matthew.brett@gmail.com> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> On Sat, Mar 30, 2013 at 7:50 PM,  <josef.pktd@gmail.com> wrote:
>>>>>>> On Sat, Mar 30, 2013 at 7:31 PM, Bradley M. Froehle
>>>>>>> <brad.froehle@gmail.com> wrote:
>>>>>>>> On Sat, Mar 30, 2013 at 3:21 PM, Matthew Brett <matthew.brett@gmail.com>
>>>>>>>> wrote:
>>>>>>>>>
>>>>>>>>> On Sat, Mar 30, 2013 at 2:20 PM,  <josef.pktd@gmail.com> wrote:
>>>>>>>>> > On Sat, Mar 30, 2013 at 4:57 PM,  <josef.pktd@gmail.com> wrote:
>>>>>>>>> >> On Sat, Mar 30, 2013 at 3:51 PM, Matthew Brett
>>>>>>>>> >> <matthew.brett@gmail.com> wrote:
>>>>>>>>> >>> On Sat, Mar 30, 2013 at 4:14 AM,  <josef.pktd@gmail.com> wrote:
>>>>>>>>> >>>> On Fri, Mar 29, 2013 at 10:08 PM, Matthew Brett
>>>>>>>>> >>>> <matthew.brett@gmail.com> wrote:
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> Ravel and reshape use the tems 'C' and 'F" in the sense of index
>>>>>>>>> >>>>> ordering.
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> This is very confusing.  We think the index ordering and memory
>>>>>>>>> >>>>> ordering ideas need to be separated, and specifically, we should
>>>>>>>>> >>>>> avoid
>>>>>>>>> >>>>> using "C" and "F" to refer to index ordering.
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> Proposal
>>>>>>>>> >>>>> -------------
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> * Deprecate the use of "C" and "F" meaning backwards and forwards
>>>>>>>>> >>>>> index ordering for ravel, reshape
>>>>>>>>> >>>>> * Prefer "Z" and "N", being graphical representations of unraveling
>>>>>>>>> >>>>> in
>>>>>>>>> >>>>> 2 dimensions, axis1 first and axis0 first respectively (excellent
>>>>>>>>> >>>>> naming idea by Paul Ivanov)
>>>>>>>>> >>>>>
>>>>>>>>> >>>>> What do y'all think?
>>>>>>>>> >>>>
>>>>>>>>> >>>> I always thought "F" and "C" are easy to understand, I always thought
>>>>>>>>> >>>> about
>>>>>>>>> >>>> the content and never about the memory when using it.
>>>>>>>>> >>
>>>>>>>>> >> changing the names doesn't make it easier to understand.
>>>>>>>>> >> I think the confusion is because the new A and K refer to existing
>>>>>>>>> >> memory
>>>>>>>>> >>
>>>>>>>>>
>>>>>>>>> I disagree, I think it's confusing, but I have evidence, and that is
>>>>>>>>> that four out of four of us tested ourselves and got it wrong.
>>>>>>>>>
>>>>>>>>> Perhaps we are particularly dumb or poorly informed, but I think it's
>>>>>>>>> rash to assert there is no problem here.
>>>>>>>
>>>>>>> I think you are overcomplicating things or phrased it as a "trick question"
>>>>>>
>>>>>> I don't know what you mean by trick question - was there something
>>>>>> over-complicated in the example?  I deliberately didn't include
>>>>>> various much more confusing examples in "reshape".
>>>>>
>>>>> I meant making the "candidates" think about memory instead of just
>>>>> column versus row stacking.
>>>>
>>>> To be specific, we were teaching about reshaping a (I, J, K, N) 4D
>>>> array, it was an image, with time as the 4th dimension (N time
>>>> points).   Raveling and reshaping 3D and 4D arrays is a common thing
>>>> to do in neuroimaging, as you can imagine.
>>>>
>>>> A student asked what he would get back from raveling this array, a
>>>> concatenated time series, or something spatial?
>>>>
>>>> We showed (I'd worked it out by this time) that the first N values
>>>> were the time series given by [0, 0, 0, :].
>>>>
>>>> He said - "Oh - I see - so the data is stored as a whole lot of time
>>>> series one by one, I thought it would be stored as a series of
>>>> images'.
>>>>
>>>> Ironically, this was a Fortran-ordered array in memory, and he was wrong.
>>>>
>>>> So, I think the idea of memory ordering and index ordering is very
>>>> easy to confuse, and comes up naturally.
>>>>
>>>> I would like, as a teacher, to be able to say something like:
>>>>
>>>> This is what C memory layout is (it's the memory layout  that gives
>>>> arr.flags.C_CONTIGUOUS=True)
>>>> This is what F memory layout is (it's the memory layout  that gives
>>>> arr.flags.F_CONTIGUOUS=True)
>>>> It's rather easy to get something that is neither C or F memory layout
>>>> Numpy does many memory layouts.
>>>> Ravel and reshape and numpy in general do not care (normally) about C
>>>> or F layouts, they only care about index ordering.
>>>>
>>>> My point, that I'm repeating, is that my job is made harder by
>>>> 'arr.ravel('F')'.
>>>
>>> But once you know that ravel and reshape don't care about memory, the
>>> ravel is easy to predict (maybe not easy to visualize in 4-D):
>>
>> But this assumes that you already know that there's such a thing as
>> memory layout, and there's such a thing as index ordering, and that
>> 'C' and 'F' in ravel refer to index ordering.  Once you have that,
>> you're golden.  I'm arguing it's markedly harder to get this
>> distinction, and keep it in mind, and teach it, if we are using the
>> 'C' and 'F" names for both things.
>
> No, I think you are still missing my point.
> I think explaining ravel and reshape F and C is easy (kind of) because the
> students don't need to know at that stage about memory layouts.
>
> All they need to know is that we look at n-dimensional objects in
> C-order or in  F-order
> (whichever index runs fastest)

Would you accept that it may or may not be true that it is desirable
or practical not to mention memory layouts when teaching numpy?

You believe it is desirable, I believe that it is not - that teaching
numpy naturally involves some discussion of memory layout.

As evidence:

* My student, without any prompting about memory layouts, is asking about it
* Travis' numpy book has a very early section on this (section 2.3 -
memory layout)
* I often think about memory layouts, and from your discussion, you do
too.  It's uncommon that you don't have to teach something that
experienced users think about often.
* The most common use of 'order' only refers to memory layout.  For
example np.array "order" doesn't refer to index ordering but to memory
layout.
* The current docstring of 'reshape' cannot be explained without
referring to memory order.

Cheers,

Matthew


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