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Re: Looking for tetrahedra. Searching sorted lists. [message #45179 is a reply to message #45015]

Tue, 16 August 2005 07:13

James Kuyper
Messages: 425
Registered: March 2000

Senior Member

cgguido wrote:
> Hi Karl,
>
> thanks for replying.
>
>> One thing worth pointing out is that nearly all mesh-related functions
>> in IDL are implemented in C because those algorithms call for a lot of
>> looping and other operations that are not efficient in IDL.
>
> Am not sure what you mean by mesh-related... my data comes from the 3D
> positions of ~5000 brownian particles diffusing around (each tagged
> with an id). I can determine whether particles are nearest neighbours
> two by two (which gives me the input matrix I mention in the original
> post) and now am looking for quadruplets of mutually nearest neighbours
> particles...

The links you've made between nearest neighbors define a mesh.

>> Since you've got an algorithm implemented in IDL and an apparent need to
>> run it repeatedly on lots of data that takes hours to process with IDL,
>> this may be a good example of something to translate to C and package up
>> as a DLM.
>
> That's a possibility I would have never thought of, thanks! Although I
> extensively use 'where' and 'uniq' and I don't know if they exist in C.
> (at the very least, they must be available as a library...)

Possibly, but nothing quite like 'where' or 'uniq' are available as
part of the C standard library. That's because you don't write C code
the same way you do IDL, mainly because of the huge performance penalty
for explicit loops in IDL. In most instances where IDL code uses where
or uniq, C code would use a loop, and therefore usually doesn't need to
store the complete list of indices; it just needs one index at a time:

IDL:
i = where(array eq 3)
; use 'i'
j = uniq(sorted_array)
; use 'j'

C:
int i;
for(i=0; i<n1; i++)
{
if (array[i] == 3)
{
/* use i */
}
}

int j;
for(j=0; j<n2; j++)
{
if(j==n2-1 || sorted_array[j] != sorted_array[j+1])
{
/* use j */
}
}

C code could store the complete list of matches, if needed, but then it
would need to explicitly allocate the memory to store that list, and it
would also need to explicitly deallocate it when the code is done with
that list, which makes the user code more complicated than it would be
in IDL. There's no free lunch here; those same issues apply to IDL,
it's just handled internally by IDL itself. The cost of doing it
internally is that's its done less efficiently, in some cases, than it
could be if done under user control (by a sufficiently competent
user!).

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[Message index]

		Looking for tetrahedra. Searching sorted lists. By: cgguido on Sun, 07 August 2005 21:37
		Re: Looking for tetrahedra. Searching sorted lists. By: cgguido on Thu, 11 August 2005 07:33
		Re: Looking for tetrahedra. Searching sorted lists. By: James Kuyper on Tue, 16 August 2005 07:13
		Re: Looking for tetrahedra. Searching sorted lists. By: cgguido on Mon, 15 August 2005 20:15
		Re: Looking for tetrahedra. Searching sorted lists. By: cgguido on Mon, 15 August 2005 20:12
		Re: Looking for tetrahedra. Searching sorted lists. By: Richard French on Mon, 15 August 2005 20:09
		Re: Looking for tetrahedra. Searching sorted lists. By: cgguido on Mon, 15 August 2005 19:53
		Re: Looking for tetrahedra. Searching sorted lists. By: Karl Schultz on Mon, 15 August 2005 09:43

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