#!/usr/bin/perl -w
#!/usr/bin/perl -d:ptkdb
#!
use strict;

$ENV{NEUROSPACES_NMC_MODELS} = '/usr/local/neurospaces/models/library';

$SIG{__DIE__}
    = sub {
	use Carp;
	confess @_;
    };

require GENESIS3;
package GENESIS3::Commands;

##########
# user workflow: create the model

my $NX = 2; # number of cells = NX*NY
my $NY = 2;

my $SEP_X = 0.001; # 1 mm
my $SEP_Y = 0.001;
my $SEP_Z = 1.0e-6; # give it a tiny z range in case of round off errors

my $syn_weight = 10; # synaptic weight, effectively multiplies gmax
my $cond_vel = 0.5; # m/sec - determines delay, based on distance
my $prop_delay = $SEP_X / $cond_vel;

# create a prototype cell in the namespace '::rscel::'
ndf_load_library('rscell', 'cells/RScell-nolib2.ndf');

# modify it to our taste
# with a soma area of 3.463609149e-08, this gives gmax = 1.5e-9
model_parameter_add('::rscell::/cell/soma/Ex_channel', 'G_MAX',
'0.04330736624');
# give a more realistic reversal potential
model_parameter_add('::rscell::/cell/soma/Ex_channel', 'Erev', '0');

# Reduce the default refractory period to a more reasonable 4 msec
model_parameter_add('::rscell::/cell/soma/spike', 'REFRACTORY', '0.004');

create('network', '/RSNet');
createmap('::rscell::/cell', '/RSNet/population', $NX, $NY, $SEP_X, $SEP_Y);

createprojection
    (
     {
      root => '/RSNet',
      projection => {
	  name => '/RSNet/projection',
# 	  source => '../population', # optional
# 	  target => '../population', # optional
		    },
      source => {
	  context => '/RSNet/population',
	  include => {
		     type => 'box', # type => 'all' would remove need for line below
		     coordinates => [ '-1', '-1', '-1', '1', '1', '1', ],
		    },
		},
      target => {
          context => '/RSNet/population',
          include => {
		     type => 'ellipse',
		     coordinates => [ 0, 0, 0, $SEP_X * 1.2, $SEP_Y * 1.2, $SEP_Z * 0.5, ],
		     },
          exclude => {
		     type => 'box',
		     coordinates => [ - $SEP_X * 0.5, - $SEP_Y * 0.5, - $SEP_Z * 0.5, 
                       $SEP_X * 0.5, $SEP_Y * 0.5, $SEP_Z * 0.5, ],
		    },
		},
      synapse => {
	  pre => 'spike',
	  post => 'Ex_channel',
	  weight => {
		     value => $syn_weight,
		    },
	  delay => {
		    value => $prop_delay,
		   },
		 },
      probability => '1.0',
      random_seed => '1212.0',
     },
    );


##########
# user workflow: create the experiment

# create a current injection protocol
inputclass_add('perfectclamp', 'current_injection_protocol', 'name', 'current_injection', 'command', '1e-9');
# Inject a corner cell 3
input_add('current_injection_protocol', '/RSNet/population/3/soma', 'INJECT');

ce('/RSNet/population');

for (my $counter = 0 ; $counter < $NX * $NY ; $counter++)
{
    output_add($counter . '/soma', 'Vm');
}

# The ndf_save funtion has not yet been fully implemented in the gshell
# ndf_save("/**", "/tmp/network-simple.ndf");

##########
# user workflow: configure the simulation

# configure the numerical solver

heccer_set_config('disassem_simple');

set_verbose('debug');

ce('/RSNet/population');

for (my $counter = 0 ; $counter < $NX * $NY ; $counter++)
{
    solverset($counter, 'heccer', '/RSNet');
}

solverset('/RSNet/projection', 'des', '/RSNet');

# run the simulation
run('/RSNet', '0.2');

# explore();