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

[David Goldsmith]

On Tue, Mar 2, 2010 at 6:59 PM, Brennan Williams <
brennan.williams at visualreservoir.com> wrote:

> David Goldsmith wrote:
> >
> > On Tue, Mar 2, 2010 at 6:29 PM, Brennan Williams
> > <brennan.williams at visualreservoir.com
> > <mailto:brennan.williams at 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.

I've got 24 floating point values which I've got in an array of shape
> (8,3) but I could easily have those in a list rather than an array and
> then just keep appending each small list of values to a big list and
> then do the final conversion to the array - I'll try that and see how it
> goes.
>

Great!  Be sure to report back. :-)

Dg

>
> Brennan
> > DG
> >
> >
> >
> >     Thanks
> >
> >     Brennan
> >
> >
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