Re: [Swarm-Support] Basic Swarm to HDF5 question

[Marcus G. Daniels]

Hi Kerimcan,
> I want to create my experimental
> parameters and variable values (some agent variable
> values) in R. These parameters and variable values
> will be in the form of several vectors (e.g. a vector
> for the age of each agent) and matrices (e.g. a social
> network matrix) of possibly different types (integer,
> double, character etc.). Then I will save them as one
> HDF5 file (so that one file contains all
> parameters/variable values for one experimental
> configuration). Then I will read that file from within
> SWARM.
>   
Ok, here's how I'd do it.  First thing to note is that the Swarm 
reader/writer wants to work in objects. 
To make an object in R is just making a named list referencing your 
vectors:

expData <- list(pars=pars,net=net)

.. and then attaching a `type' attribute to that object.   The Swarm 
reader will use that type name to be the object name to instantiate.

attr(expData,"type") <- "ExpData"

Then it's just a matter of having `ExpData' ready on the Swarm end with 
the methods you want.  Actually you don't need to make this class at 
all, if you are willing to use probes to read and write its values.

[fyi, HDF5, the `objects' are stored as HDF5 groups and the fields 
(either scalars, vectors, or matrices) are stored as HDF5 datasets.
The R attributes, e.g. `type' are stored as HDF5 attributes on the group.]

Marcus

library(hdf5)

pars <- rnorm(10)
net <- rnorm(100)
dim(net) <- c(10,10)

expData <- list(pars=pars,net=net)
attr(expData,"type") <- "ExpData"

print(pars)
print(net)

hdf5save("sup-ex.hdf","expData")

#import <simtools.h> // initSwarm
#import <objectbase.h> // VarProbe
#import <defobj.h> // Archiver

#import <objectbase/SwarmObject.h>

@interface ExpData: SwarmObject

{
  double pars[10];
  double net[10][10];
}
- print;
@end

@implementation ExpData
- print
{
  unsigned i, j;

  printf ("pars:");
  for (i = 0; i < 10; i++)
    printf (" %.3f", pars[i]);

  printf ("\n\nnet:\n");
  for (i = 0; i < 10; i++) {
    for (j = 0; j < 10; j++)
      printf (" %.3f", net[i][j]);
    printf ("\n");
  }
}
@end

int
main (int argc, const char **argv)
{
  id <Archiver> archiver;
  id item;

  initSwarmBatch (argc, argv);

  archiver = [[[HDF5Archiver createBegin: globalZone]
                 setPath: "sup-ex.hdf"]
               createEnd];

  printf ("Getting object\n");
  item = [archiver getObject: "expData"];
  printf ("`%s'\n", [item getName]);
  [item print];
}
/*
Local Variables:
compile-command: "$HOME/packages/bin/libtool-swarm --mode=link gcc 
-I$HOME/packages/include -o test -g -Wno-import test.m -L$HOME/packages/lib 
-lswarm"
End:
*/