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Re: [Spasm-devel] Spasm 2.0, discrete grids
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From: Phil S. <sa...@gm...> - 2006-07-03 01:39:26
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Thanks Paul,
I'm sure if I read i a few times i'll get my head around it. Thanks for
writing it out clearly.
Would the iterating be a lot faster using this method? so far, the way I was
doing it was not as fast as I had hoped.
Cheers
Phil Sammons
Today's Topics:
>
> 1. Re: Spasm 2.0, discrete grids (Paul Thompson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 30 Jun 2006 17:20:01 +1000
> From: "Paul Thompson" <p.t...@ca...>
> Subject: Re: [Spasm-devel] Spasm 2.0, discrete grids
> To: <spa...@li...>
> Message-ID: <200...@tr...>
> Content-Type: text/plain; charset="us-ascii"
>
> Phil,
>
> There's boost::multi_array, which is templated by the number of
> dimensions.
>
> Construction with different numbers of cells in each dimension, and
> iterating over the cells are helped using boost::array
>
> This allows one to write _dimension-independent code_ .
> This would seem to be more flexible than matrices of matrices or vectors
> of
> vectors of vectors...
>
> Perhaps this would be a good base for the spasm discrete grid stuff.
> I'm not actually working with discrete grids, so this never progressed
> beyond looking at the multi-dimensional array iteration.
>
> Hope it helps.
>
> Paul Thompson.
>
>
>
>
>
>
> #include "boost/multi_array.hpp"
> #include <cassert>
> #include <cmath>
>
> ...
>
> //construction of multi-dimensional array,
> const int numdims = 4;
> const int cells_per_dim = 20;
> typedef double valuetype;
> typedef boost::multi_array<valuetype, numdims> array_type;
>
> boost::array<array_type::index, numdims> shape;
> shape[0] = 10; shape[1] = 11; shape[2] = 12; shape[3] = 14; //size
> of
> the dimensions
>
> //construct the multi-dim array (10 x 11 x 12 x 14 4 dimensional
> array
> !)
> array_type A(shape);
>
> boost::array<array_type::index,numdims> idx;
> idx[0] = 5; idx[1] = 6; idx[2] = 7; idx[3] = 8;
>
> //set the (5,6,7,8) entry in the matrix:
> A(idx) = 0.0;
>
>
>
>
>
>
> The boost::array idx can be used to iterate over the matrix:
>
>
> void iterate_multidimarray_do_something_func(
> int numdims,
> int cells_per_dim,
> array_type &A, void
> (*do_something_func)(boost::array<array_type::index,numdims>, array_type
> &)
> )
> {
> boost::array<array_type::index,numdims> idx;
>
> //reset idx to zeros
> for (int dim = 0; dim < numdims; dim++)
> {
> idx[dim] = 0;
> }
>
> bool done = false;
>
> //this loop considers idx as a base:cells_per_dim number, where
> idx[i] is a digit
> // and counts from 00000 to the maximum... Calling
> do_something_func on the whole grid.
> while(!done)
> {
> do_something_func(idx,A);
>
> // increment the first dimension every time.
> idx[numdims-1]++;
>
> // check all other dimensions for overflow, propagate the carry.
> for (int dim = numdims-1; dim >= 0 ; dim--)
> {
> // overflow this dimension, 'carry' over to the next
> dimension.
> if (idx[dim] >= cells_per_dim)
> {
> idx[dim] = 0;
> idx[dim-1]++;
> }
>
> // if the final dimension is past the final cell number,
> finish
> if (idx[0] >= cells_per_dim)
> {
> done = true;
> break;
> }
> }
> }
>
> return;
> }
>
>
>
> -----Original Message-----
> From: Phil [mailto:sa...@un...]
> Sent: Friday, 30 June 2006 3:26 PM
> To: Ben Upcroft
> Cc: Bertrand Douillard; Lee Ling (Sharon) Ong; Matt Ridley; 'Paul
> Thompson';
> Suresh Kumar; Tim Bailey; Tobias Kaupp; Alex Makarenko; Ryan Cross
> Subject: Re: Fwd: Spasm 2.0
>
> Hi Ben,
>
> This sounds like a good plan.
>
> I have managed to get some grid based Bayesian stuff working to some
> extent.
> In the coming weeks I hope to start refining it a little and moving it
> into a more spasm like structure. I am a little unfamiliar with the
> template structure that spasm is using so I'll have to some more learning
> on
> that side. What changed will be made if we move away from templates to an
> inference model?
>
> also, to enable me to do some calculations, I have added the following
> line
> to my /ulapack/matrix_types.hpp to enable me to use 4 Dimensional
> matrices.
> Is there an obvious and better way of doing this so I do not have to
> change
> uLapack?
>
> typedef ublas::matrix<ublas::matrix<double, ublas::column_major>,
> ublas::column_major> Matrix4d;
>
> Cheers
> Phil
>
> Ben Upcroft wrote:
> > Has everyone signed up to the mailing list? If you didn't get the
> > message below and wish to get similar messages, please sign up.
> >
> > Ben
> >
> > ---------- Forwarded Message ----------
> >
> > Subject: Spasm 2.0
> > Date: Friday 30 June 2006 10:08
> > From: Matthew Ridley <mr...@me...>
> > To: spa...@li...
> > Cc: Ben Upcroft <b.u...@ca...>
> >
> > I wanted to kick off some discussion with regards to what we want
> > spasm 2.0 to look like.
> >
> > some of my thoughts are:
> >
> > - Remove Particles from PDF, i.e. create a Sample/WeightedSample class
> > and associated utilities.
> > - Make conversion between PDF types use global functions, this means
> > that these are independent of class definitions.
> > - spasm-filters to use inheritance instead of templates for various
> > PDF types.
> >
> > - spasm-gl for rending PDF's in OpenGL ?
> >
> > Ben: is everyone on the list yet ?
> >
> > Matt
> > --
> >
> > -------------------------------------------------------
> >
> >
>
>
>
>
>
>
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> End of Spasm-devel Digest, Vol 2, Issue 1
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