// tdt2mat_data.hoc
// creates tdt2mat_data files that can be read by matlab to allow the simulation to
// be analysed like the experiments
/* excerpts from diagnostic_script_5.m
tdt2mat_data.streams.BRTH.data = BRTH_data;
tdt2mat_data.streams.BRTH.fs = fs;
tdt2mat_data.snips.eNeu.ts=spike_times;
tdt2mat_data.snips.eNeu.sortcode=ones(1, length(spike_times)); % arbitrarily assign a sortcode of 1 for each spike time
tdt2mat_data.epocs.SOFF.onset = SOFF;
duplicates_S_ON = kron(S_ON, [1 1]);
tdt2mat_data.epocs.S_ON.onset=duplicates_S_ON;
stimids=1:length(S_ON); % arbitrarily assign whole numbers as stimids
duplicates_stimids = kron(stimids, [1 1]);
tdt2mat_data.epocs.S_ON.data = duplicates_stimids;
----
use the following filenames where _d_ means _dot_ i.e. is a "." (see above)
tdt2mat_data_d_streams_d_BRTH_d_data.dat
tdt2mat_data_d_streams_d_BRTH_d_fs.dat
tdt2mat_data_d_snips_d_eNeu_d_ts.dat
tdt2mat_data_d_snips_d_eNeu_d_sortcode.dat
tdt2mat_data_d_epocs_d_SOFF_d.dat
tdt2mat_data_d_epocs_d_S_ON_d.dat
tdt2mat_data_d_epocs_d_S_ON_d_data.dat
*/
// first BRTH_data
// Make a sine wave lined up with the breath pulses:
objref BRTH_data, fs_vec, ts_vec, sortcode_vec, SOFF_vec, S_ON_vec, S_ON_data_vec
strdef tmpfilename // used by NSG to find run_X/tdt2mat_data for each simulation
proc save_tank() {
breath_zero_time = 0 // ThetaStim[0].outer_start+ThetaStim[0].start // arbitrarily choose the start time of the breath pulses as zero
// in the breath cycle
breath_period = breathing_period // ThetaStim[0].outer_interval
// assume that t_vec already exists and is the recorded time for the entire simulation
// comment in when want the big breath trace otherwise use shared breath trace to save space
// BRTH_data=t_vec.c.sin(1/(breath_period/1000),PI/2-2*PI*breath_zero_time/breath_period, dt) // freq in Hz
// uncomment the below if want to write the big file:
///// BRTH_data=t_vec.append(0) // store one number just to make a file
///// BRTH_data.c.mul(20).line(v_graph,t_vec,5,1)
///// sprint(tmpfilename, "%s_d_streams_d_BRTH_d_data.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
// skip writing these big identical files:
// write_vec(tmpfilename, BRTH_data)
fs_vec = new Vector()
fs_vec.append(1000/dt) // if dt is 0.025 us this will be 40k Hz
sprint(tmpfilename, "%s_d_streams_d_BRTH_d_fs.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename,fs_vec)
/////////////////////////////////////////
// augmented section for more possible activity traces
// ***************************** variants - this one is the original m1 activity
// ts_vec is a vector of the time's of the spikes: this comes in NEURON in ms so needs conversion to seconds
ts_vec=m1_events.c.div(1000) //
sprint(tmpfilename, "%s_d_snips_d_eNeu_d_ts_m1.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, ts_vec)
// ***************************** variants - this one is the pg reciprocal synapse - will try this first as main pg activity indicator
// ts_vec is a vector of the time's of the spikes: this comes in NEURON in ms so needs conversion to seconds
ts_vec=pg1_to_m1tuft_events.c.div(1000) //
sprint(tmpfilename, "%s_d_snips_d_eNeu_d_ts.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, ts_vec)
// ***************************** variants - this one is the pg1 axon to m2 priden and should match the recip synapse above
// ts_vec is a vector of the time's of the spikes: this comes in NEURON in ms so needs conversion to seconds
ts_vec=pg1_axon_to_m2_events.c.div(1000) //
sprint(tmpfilename, "%s_d_snips_d_eNeu_d_ts_pg1_to_m2.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, ts_vec)
// ***************************** variants - this one recorded the pg2 to m1 priden
// ts_vec is a vector of the time's of the spikes: this comes in NEURON in ms so needs conversion to seconds
ts_vec=pg2_axon_to_m1priden_events.c.div(1000) //
sprint(tmpfilename, "%s_d_snips_d_eNeu_d_ts_pg2_to_m1.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, ts_vec)
//////////////////////////////////////////////
sortcode_vec = ts_vec.c // make a vector the same length as the vector of spikes
sortcode_vec.fill(1) // make the sortcode arbitrarily set to 1
sprint(tmpfilename, "%s_d_snips_d_eNeu_d_sortcode.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, sortcode_vec)
SOFF_vec = new Vector()
S_ON_vec = new Vector()
S_ON_data_vec = new Vector()
/*
num_of_points = light1_events.size()
points_per_burst = ThetaStim[2].number // for light stimulation of mitral 1
stimid=1
for (i=0; i<num_of_points; i = i+ points_per_burst) {
// note that the S_ON and SOFF times are duplicated because the analysis code expects them to be duplicated
S_ON_vec.append(light1_events.x[i], light1_events.x[i])
SOFF_vec.append(light1_events.x[i+points_per_burst-1], light1_events.x[i+points_per_burst-1])
S_ON_data_vec.append(stimid, stimid)
stimid = stimid + 1
}
*/
// recreate the S_ON, SOFF vectors from the gauss light parameters
stimid = 1
current_S_ON_time = light_gauss_center - light_half_width
current_SOFF_time = light_gauss_center + light_half_width
while (current_S_ON_time < tstop) { // keep going until past tstop
// note that the S_ON and SOFF times are duplicated because the analysis code expects them to be duplicated
if (current_S_ON_time>0) {
S_ON_vec.append(current_S_ON_time, current_S_ON_time)
}
if (current_SOFF_time<tstop) {
SOFF_vec.append(current_SOFF_time, current_SOFF_time)
}
S_ON_data_vec.append(stimid, stimid)
// increment variables for next stimulus
current_S_ON_time += light_period
current_SOFF_time += light_period
stimid = stimid + 1
}
sprint(tmpfilename, "%s_d_epocs_d_SOFF_d_onset.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, SOFF_vec.c.div(1000)) // divide by 1000 to convert from ms to seconds
sprint(tmpfilename, "%s_d_epocs_d_S_ON_d_onset.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, S_ON_vec.c.div(1000))
sprint(tmpfilename, "%s_d_epocs_d_S_ON_d_data.dat", tank_folder) // looks like run_X/tdt2mat_data/_d_...
write_vec(tmpfilename, S_ON_data_vec)
/**/
}