[Numpy-discussion] how to efficiently build an array of x, y, z points

Brennan Williams brennan.williams@visualreservoir....
Wed Mar 3 14:05:43 CST 2010


Bruce Southey wrote:
> On 03/02/2010 09:47 PM, David Goldsmith wrote:
>> On Tue, Mar 2, 2010 at 6:59 PM, Brennan Williams 
>> <brennan.williams@visualreservoir.com 
>> <mailto:brennan.williams@visualreservoir.com>> wrote:
>>
>>     David Goldsmith wrote:
>>     >
>>     > On Tue, Mar 2, 2010 at 6:29 PM, Brennan Williams
>>     > <brennan.williams@visualreservoir.com
>>     <mailto:brennan.williams@visualreservoir.com>
>>     > <mailto:brennan.williams@visualreservoir.com
>>     <mailto:brennan.williams@visualreservoir.com>>> wrote:
>>     >
>>     >     I'm reading a file which contains a grid definition. Each
>>     cell in the
>>     >     grid, apart from having an i,j,k index also has 8 x,y,z
>>     coordinates.
>>     >     I'm reading each set of coordinates into a numpy array. I
>>     then want to
>>     >     add/append those coordinates to what will be my large
>>     "points" array.
>>     >     Due to the orientation/order of the 8 corners of each
>>     hexahedral
>>     >     cell I
>>     >     may have to reorder them before adding them to my large
>>     points array
>>     >     (not sure about that yet).
>>     >
>>     >     Should I create a numpy array with nothing in it and then
>>     .append
>>     >     to it?
>>     >     But this is probably expensive isn't it as it creates a new
>>     copy
>>     >     of the
>>     >     array each time?
>>     >
>>     >     Or should I create a zero or empty array of sufficient size and
>>     >     then put
>>     >     each set of 8 coordinates into the correct position in that
>>     big array?
>>     >
>>     >     I don't know exactly how big the array will be (some cells are
>>     >     inactive
>>     >     and therefore don't have a geometry defined) but I do know
>>     what its
>>     >     maximum size is (ni*nj*nk,3).
>>     >
>>     >
>>     > Someone will correct me if I'm wrong, but this problem - the "best"
>>     > way to build a large array whose size is not known beforehand -
>>     came
>>     > up in one of the tutorials at SciPyCon '09 and IIRC the answer was,
>>     > perhaps surprisingly, build the thing as a Python list (which is
>>     > optimized for this kind of indeterminate sequence building) and
>>     > convert to a numpy array when you're done.  Isn't that what was
>>     > recommended, folks?
>>     >
>>     Build a list of floating point values, then convert to an array and
>>     shape accordingly? Or build a list of small arrays and then somehow
>>     convert that into a big numpy array?
>>
>>
>> My guess is that either way will be better than iteratively 
>> "appending" to an existing array.
>>
>>
> Hi,
> Christopher Barker provided some code last last year on appending 
> ndarrays eg:
> http://mail.scipy.org/pipermail/numpy-discussion/2009-November/046634.html
>
> A lot depends on your final usage of the array otherwise there are no 
> suitable suggestions. That is do you need just to index the array 
> using i, j, k indices (this gives you either an i by j by k array that 
> contains the x, y, z coordinates) or do you also need to index the x, 
> y, z coordinates as well (giving you an i by j by k by x by y by z 
> array). If it is just plain storage then perhaps just a Python list, 
> dict or sqlite object may be sufficient.
>
Ultimately I'm trying to build a tvtk unstructured grid to view in a 
Traits/tvtk/Mayavi app. The grid is ni*nj*nk cells with 8 xyz's per cell 
(hexahedral cell with 6 faces). However some cells are inactive and 
therefore don't have geometry. Cells also have "connectivity" to other 
cells, usually to adjacent cells (e.g. cell i,j,k connected to cell 
i-1,j,k) but not always.

I'll post more comments/questions as I go.

Brennan

> There are also time and memory constraints as you can spend large 
> effort just to get the input into a suitable format and memory usage. 
> If you use a secondary storage like a Python list then you need memory 
> to storage the list, the ndarray and all intermediate components and 
> overheads.
>
> If you use scipy then you should look at using sparse arrays where 
> space is only added as you need it.
>
>
> Bruce
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