Fix bug in FileStimGroup

.travis.yml

@@ -12,6 +12,6 @@ script:
 notifications:
     email:
         recipients: 
-            - [email protected]
+            - [email protected]
         on_success: change
         on_failure: always

AUTHORS

@@ -1,17 +1,17 @@
-Auryn package created by Friedemann Zenke <[email protected]>
+Auryn package created by Friedemann Zenke <[email protected]>
 
 Contributors: 
 Lorric Ziegler <[email protected]>
 Ankur Sinha <[email protected]>
 Emre Neftci <[email protected]>
+Anders Lansner <[email protected]>
+Alexandre Payeur <[email protected]>
 
 
 
 
 
 
-
-
-Copyright 2014-2018 Friedemann Zenke.
+Copyright 2014-2023 Friedemann Zenke.
 Copying and distribution of this file, with or without modification, are
 permitted provided the copyright notice and this notice are preserved.

CMakeLists.txt

@@ -2,7 +2,7 @@ CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
 PROJECT(Auryn)
 
 # The version number.
-SET(Auryn_VERSION_MAJOR 0)
+SET(Auryn_VERSION_MAJOR 1)
 SET(Auryn_VERSION_MINOR 8)
 
 # Important GCC Compiler flags for Auryn's performance

README.md

@@ -85,7 +85,7 @@ Bibtex:
 License & Copyright 
 -------------------
 
-Copyright 2014-2018 Friedemann Zenke
+Copyright 2014-2023 Friedemann Zenke
 
 Auryn is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

build/release/run_benchmark.sh

@@ -13,6 +13,8 @@ DATE=`date +"%Y-%m-%d"`
 # REVISION=`git log --pretty=oneline -1 | cut -d " " -f 1`
 REVISION=`git describe`
 TMPDIR=`mktemp -d`
+echo "temp dir= $TMPDIR"
+trap "{ rm -rf $TMPDIR; }" EXIT
 
 # Function declaration
 function fun_benchmark() 
@@ -39,18 +41,16 @@ fun_benchmark "$CMD_BENCHMARK1"
 RESULT_BENCHMARK1=$FUNCTION_RESULT
 
 # Zenke plasticity benchmark, single core
-CMD_BENCHMARK2="examples/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
+CMD_BENCHMARK2="examples/plasticity/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
 fun_benchmark "$CMD_BENCHMARK2"
 RESULT_BENCHMARK2=$FUNCTION_RESULT
 
 # Zenke plasticity benchmark, two cores
-CMD_BENCHMARK3="mpirun -n 2 examples/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
+CMD_BENCHMARK3="mpirun -n 2 examples/plasticity/sim_background --fast --tau 10 --simtime $SIMTIME --dir $TMPDIR"
 fun_benchmark "$CMD_BENCHMARK3"
 RESULT_BENCHMARK3=$FUNCTION_RESULT
 
 
 # Writ result to file
 echo "$HOSTNAME $REVISION $RESULT_BENCHMARK1 $RESULT_BENCHMARK2 $RESULT_BENCHMARK3 $DATE" >> benchmark_results.dat
 
-# Clean up
-rm -r $TMPDIR

examples/CMakeLists.txt

@@ -1,3 +1,10 @@
+ADD_SUBDIRECTORY(currents)
+ADD_SUBDIRECTORY(misc)
+ADD_SUBDIRECTORY(plasticity)
+ADD_SUBDIRECTORY(poisson)
+ADD_SUBDIRECTORY(tutorials)
+ADD_SUBDIRECTORY(monitoring)
+
 FILE( GLOB SIM_SOURCES *.cpp )
 FOREACH( sourcepath ${SIM_SOURCES} )
 	GET_FILENAME_COMPONENT( sourcefile ${sourcepath} NAME )

examples/currents/CMakeLists.txt

@@ -0,0 +1,9 @@
+FILE( GLOB SIM_SOURCES *.cpp )
+FOREACH( sourcepath ${SIM_SOURCES} )
+	GET_FILENAME_COMPONENT( sourcefile ${sourcepath} NAME )
+	STRING( REPLACE ".cpp" "" simname ${sourcefile} )
+	ADD_EXECUTABLE( ${simname} ${sourcefile} )
+	TARGET_LINK_LIBRARIES( ${simname} auryn ${AURYN_EXT_LINKLIBS} )
+ENDFOREACH( sourcepath ${SIM_SOURCES} )
+
+CONFIGURE_FILE(inject_current.txt inject_current.txt COPYONLY)

examples/currents/inject_current.txt

@@ -0,0 +1,100 @@
+0.000000 0.000000
+0.050000 0.125333
+0.100000 0.248690
+0.150000 0.368125
+0.200000 0.481754
+0.250000 0.587785
+0.300000 0.684547
+0.350000 0.770513
+0.400000 0.844328
+0.450000 0.904827
+0.500000 0.951057
+0.550000 0.982287
+0.600000 0.998027
+0.650000 0.998027
+0.700000 0.982287
+0.750000 0.951057
+0.800000 0.904827
+0.850000 0.844328
+0.900000 0.770513
+0.950000 0.684547
+1.000000 0.587785
+1.050000 0.481754
+1.100000 0.368125
+1.150000 0.248690
+1.200000 0.125333
+1.250000 0.000000
+1.300000 -0.125333
+1.350000 -0.248690
+1.400000 -0.368125
+1.450000 -0.481754
+1.500000 -0.587785
+1.550000 -0.684547
+1.600000 -0.770513
+1.650000 -0.844328
+1.700000 -0.904827
+1.750000 -0.951057
+1.800000 -0.982287
+1.850000 -0.998027
+1.900000 -0.998027
+1.950000 -0.982287
+2.000000 -0.951057
+2.050000 -0.904827
+2.100000 -0.844328
+2.150000 -0.770513
+2.200000 -0.684547
+2.250000 -0.587785
+2.300000 -0.481754
+2.350000 -0.368125
+2.400000 -0.248690
+2.450000 -0.125333
+2.500000 -0.000000
+2.550000 0.125333
+2.600000 0.248690
+2.650000 0.368125
+2.700000 0.481754
+2.750000 0.587785
+2.800000 0.684547
+2.850000 0.770513
+2.900000 0.844328
+2.950000 0.904827
+3.000000 0.951057
+3.050000 0.982287
+3.100000 0.998027
+3.150000 0.998027
+3.200000 0.982287
+3.250000 0.951057
+3.300000 0.904827
+3.350000 0.844328
+3.400000 0.770513
+3.450000 0.684547
+3.500000 0.587785
+3.550000 0.481754
+3.600000 0.368125
+3.650000 0.248690
+3.700000 0.125333
+3.750000 0.000000
+3.800000 -0.125333
+3.850000 -0.248690
+3.900000 -0.368125
+3.950000 -0.481754
+4.000000 -0.587785
+4.050000 -0.684547
+4.100000 -0.770513
+4.150000 -0.844328
+4.200000 -0.904827
+4.250000 -0.951057
+4.300000 -0.982287
+4.350000 -0.998027
+4.400000 -0.998027
+4.450000 -0.982287
+4.500000 -0.951057
+4.550000 -0.904827
+4.600000 -0.844328
+4.650000 -0.770513
+4.700000 -0.684547
+4.750000 -0.587785
+4.800000 -0.481754
+4.850000 -0.368125
+4.900000 -0.248690
+4.950000 -0.125333

examples/sim_current_inject.cpp → examples/currents/sim_current_inject.cpp

@@ -1,5 +1,5 @@
 /* 
-* Copyright 2014-2018 Friedemann Zenke
+* Copyright 2014-2020 Friedemann Zenke
 *
 * This file is part of Auryn, a simulation package for plastic
 * spiking neural networks.

examples/sim_current_steps.cpp → examples/currents/sim_current_steps.cpp

@@ -1,5 +1,5 @@
 /* 
-* Copyright 2014-2018 Friedemann Zenke
+* Copyright 2014-2020 Friedemann Zenke
 *
 * This file is part of Auryn, a simulation package for plastic
 * spiking neural networks.

examples/sim_current_stim.cpp → examples/currents/sim_current_stim.cpp

@@ -1,5 +1,5 @@
 /* 
-* Copyright 2014-2018 Friedemann Zenke
+* Copyright 2014-2020 Friedemann Zenke
 *
 * This file is part of Auryn, a simulation package for plastic
 * spiking neural networks.

examples/currents/sim_file_current_inject.cpp

@@ -0,0 +1,77 @@
+/* 
+* Copyright 2014-2020 Friedemann Zenke
+*
+* This file is part of Auryn, a simulation package for plastic
+* spiking neural networks.
+* 
+* Auryn is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+* 
+* Auryn is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+* 
+* You should have received a copy of the GNU General Public License
+* along with Auryn.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include "auryn.h"
+
+#define N 1
+
+/*!\file 
+ *
+ * \brief Example simulation which demonstrates the use of FileCurrentInjector 
+ * */
+
+using namespace auryn;
+
+namespace po = boost::program_options;
+
+int main(int ac, char* av[]) 
+{
+
+	int errcode = 0;
+	string simname = "fcur_inject";
+	string logfile = simname;
+	string tmpstr;
+
+	// BEGIN Global definitions
+	auryn_init( ac, av );
+	sys->set_simulation_name(simname);
+	// END Global definitions
+
+	// define receiving group
+	IFGroup * neurons = new IFGroup(3);
+
+	// define monitors
+	VoltageMonitor * vmon0 = new VoltageMonitor( neurons, 0, sys->fn("neuron",0,"mem"), 1e-3 );
+	VoltageMonitor * vmon1 = new VoltageMonitor( neurons, 1, sys->fn("neuron",1,"mem"), 1e-3 );
+
+	// define FileCurrentInjector
+	FileCurrentInjector * injector = new FileCurrentInjector( neurons, "inject_current.txt", "mem" );
+	injector->set_scale(1.2); // Scales all current values by this factor
+
+	// To repeat the input current enable looping by uncommenting the following lines
+	// injector->loop = true;
+	// injector->set_loop_grid(10.0); // align time series to 1s grid (should be larger or equal to the input time series)
+
+	// To only inject current in some neurons uncomment the following code 
+	// injector->mode = LIST;
+	// injector->target_neuron_ids->push_back(0);
+	// injector->target_neuron_ids->push_back(2);
+
+	// run simulation
+	logger->msg("Running ...",PROGRESS);
+	sys->run(15.0);
+
+	if (errcode)
+		auryn_abort(errcode);
+
+	logger->msg("Freeing ...",PROGRESS,true);
+	auryn_free();
+	return errcode;
+}

examples/misc/CMakeLists.txt

@@ -0,0 +1,8 @@
+FILE( GLOB SIM_SOURCES *.cpp )
+FOREACH( sourcepath ${SIM_SOURCES} )
+	GET_FILENAME_COMPONENT( sourcefile ${sourcepath} NAME )
+	STRING( REPLACE ".cpp" "" simname ${sourcefile} )
+	ADD_EXECUTABLE( ${simname} ${sourcefile} )
+	TARGET_LINK_LIBRARIES( ${simname} auryn ${AURYN_EXT_LINKLIBS} )
+ENDFOREACH( sourcepath ${SIM_SOURCES} )
+

examples/misc/sim_delay_connection.cpp

@@ -0,0 +1,78 @@
+/* 
+* Copyright 2014-2020 Friedemann Zenke
+*
+* This file is part of Auryn, a simulation package for plastic
+* spiking neural networks.
+* 
+* Auryn is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+* 
+* Auryn is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+* 
+* You should have received a copy of the GNU General Public License
+* along with Auryn.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#include "auryn.h"
+
+#define N 1
+
+/*!\file 
+ *
+ * \brief Example simulation illustrating the effect of delay connection.
+ *
+ * The simulation sets up a single input neuron and connects it to a single output neuron via a SparseConnection
+ * (which only has the axonal delay from IFGroup) and via a DelayConnection which has both the axonal delay plus
+ * an added 10ms dendritic delay. The latter connection is GABAergic to make it easily differntiable in the 
+ * membrane trace.
+ * */
+
+using namespace auryn;
+
+int main(int ac, char* av[]) 
+{
+
+	int errcode = 0;
+	string simname = "delay_connection";
+	string logfile = simname;
+	string tmpstr;
+	AurynWeight w = 1.0;
+
+	// BEGIN Global definitions
+	auryn_init( ac, av );
+	sys->set_simulation_name(simname);
+	// END Global definitions
+
+	// define input group
+	PoissonGroup * poisson = new PoissonGroup(N,1.);
+
+	// define receiving group
+	IFGroup * neuron = new IFGroup(1);
+
+	// define connections
+	SparseConnection * con = new SparseConnection(poisson, neuron, w, 1.0, GLUT);
+	DelayConnection * dly_con = new DelayConnection(poisson, neuron, w,  1.0, GABA);
+	dly_con->set_delay(10e-3); // 10ms delay added
+
+	// define monitors
+	SpikeMonitor * smon = new SpikeMonitor( neuron, sys->fn("ras") );
+	VoltageMonitor * vmon = new VoltageMonitor( neuron, 0, sys->fn("mem"), 1e-3 );
+	StateMonitor * amon = new StateMonitor( neuron, 0, "g_ampa", sys->fn("ampa") );
+	StateMonitor * nmon = new StateMonitor( neuron, 0, "g_gaba", sys->fn("gaba") );
+
+	// run simulation
+	logger->msg("Running ...",PROGRESS);
+	sys->run(10);
+
+	if (errcode)
+		auryn_abort(errcode);
+
+	logger->msg("Freeing ...",PROGRESS,true);
+	auryn_free();
+	return errcode;
+}

examples/sim_epsp.cpp → examples/misc/sim_epsp.cpp

@@ -1,5 +1,5 @@
 /* 
-* Copyright 2014-2018 Friedemann Zenke
+* Copyright 2014-2020 Friedemann Zenke
 *
 * This file is part of Auryn, a simulation package for plastic
 * spiking neural networks.