runsim

#!/bin/bash
# This program runs the neuroprosthesis model.
#
# For more information, please contact Cliff Kerr on
# cliffk@neurosim.downstate.edu
# 
# Version: 2011sep28


# User-configurable options
cort_or_thal=1 # cortical (1) or thalamic (2) damage/prosthesis 
modelsize=1 # Sets the number of cells in the model. The paper used modelsize=10, but this takes up a lot of RAM and is quite slow.
simduration=20e3 # How many ms to run the model for. The paper used simulationtime=90e3, but this is also quite slow.
basefilename="neuropros" # Choose the base name of the files to output

tic=`date +%s` # Get current time, to check how long the simulation takes


# Save sim data
## First, input arguments
echo "~~~~~INPUT ARGUMENTS~~~~~" > $basefilename-sim.txt; echo "runsim $*" >> $basefilename-sim.txt # Save input arguments
for i in 1 2 3 4 5; do echo "" >> $basefilename-sim.txt; done # Make space
## Next, this file
echo "~~~~~RUNSIM~~~~~" >> $basefilename-sim.txt; cat runsim >> $basefilename-sim.txt # Save this file
for i in 1 2 3 4 5; do echo "" >> $basefilename-sim.txt; done # Make space
## All hoc files
for file in *.hoc
	do echo "~~~~~${file}~~~~~" >> $basefilename-sim.txt # Save this file
	cat $file >> $basefilename-sim.txt # Save all hoc files 
	for i in 1 2 3 4 5; do echo "" >> $basefilename-sim.txt; done # Make space
done
## All mod files
for file in *.mod
	do echo "~~~~~${file}~~~~~" >> $basefilename-sim.txt # Save this file
	cat $file >> $basefilename-sim.txt # Save all mod files 
	for i in 1 2 3 4 5; do echo "" >> $basefilename-sim.txt; done # Make space
done

# Figure out where the executable is living
if [ -f ./i686/special ]; then executable="./i686/special"; fi
if [ -f ./x86_64/special ]; then executable="./x86_64/special"; fi

if [ $executable ] # Only run if the executable is found!
	then
	for b_d_p in 1 2 3 # Loop over baseline (1), damage (2), and prosthesis (3) cases
		do
		
		# This line is what actually runs the model!!
		$executable -c "mytstop=$simduration" -c "strdef outfn1, outfn2" -c "outfn1=\"$basefilename$b_d_p-lfp.txt\"" -c "outfn2=\"$basefilename$b_d_p-spk.txt\"" -c "c_or_t=$cort_or_thal" -c "b_d_p=$b_d_p" -c "freq=20" -c "sigprct=80" -c "sigwt=20" -c "scale=$modelsize" batch.hoc 
		
		# Remove the stupid row/column info at the top of the matrix
		if [ -f $basefilename$b_d_p-spk.txt ] # Output files exist -- good
			then
			echo 'Removing empty first row...'
			sed -i 1d $basefilename$b_d_p-spk.txt
			sed -i 1d $basefilename$b_d_p-lfp.txt
		else
			echo 'Simulation aborted!' # Output files don't exist -- bad
		fi
	
	done

else
	echo "Executable not found! Please find 'special' manually."
fi

elapsed=$(( `date +%s` - tic )) # Find out elapsed time
echo "runsim: done; elapsed time: $elapsed s."
echo ""
echo "Performing analysis..."

python comparerasters.py & # Create Fig. 4/6 from the paper
python comparecausality.py & # Create Fig. 5/7 from the paper