asd

asd

create_stimulus_file.m

@@ -0,0 +1,76 @@
+function create_stimulus_file
+% Generate stimulus files for SNT experiment
+
+%%%%%%%%%%%%%%%%%
+N_blocks = 3; % Number of blocks to calculate
+% EXP_TYPE = 'exp_1'; % 
+EXP_TYPE = 'exp_2'; % 
+
+
+% Define the stimuli in each experiment - In each block (of the N_blocks)
+% we will have each stimulus once, in a pseudorandom order
+% switch statement for experiment type
+switch EXP_TYPE  
+    case 'exp_1'
+        Stimuli{1} = 'MU_1';
+        Stimuli{2} = 'MU_2';
+        Stimuli{3} = 'MU_3';
+        Stimuli{4} = 'FU_1';
+        Stimuli{5} = 'FU_2';
+        Stimuli{6} = 'FU_3';                
+    case 'exp_2'
+        Stimuli{1} = 'PU_1';
+        Stimuli{2} = 'PU_2';
+        Stimuli{3} = 'PU_3';
+        Stimuli{4} = 'MU_1';
+        Stimuli{5} = 'MU_2';
+        Stimuli{6} = 'MU_3';    
+        Stimuli{7} = 'FU_1';
+        Stimuli{8} = 'FU_2';
+        Stimuli{9} = 'FU_3';    
+end
+
+[BASE_P,~,~] = fileparts(mfilename('fullpath'));
+STIM_FILE_PATH     = [BASE_P filesep 'stimulus_files'];
+if ~exist(STIM_FILE_PATH,'dir')
+    mkdir(STIM_FILE_PATH);
+end
+datestring = datestr(now,1); 
+fname = [STIM_FILE_PATH  filesep 'stimfile_' datestring '.txt'];
+
+
+
+if exist(fname,'file')
+    ButtonName=questdlg('File exists, overwrite?', ...
+        'make pseudo file', ...
+        'No','Yes','No');
+    switch ButtonName
+        case 'No'
+            return
+    end % switch
+end
+
+
+fid = fopen(fname,'w');
+
+% shuffle the random number generator (to avoid repeats in different MATLAB sessions)
+rng('shuffle')
+
+% Write stimuli to file
+for i = 1:N_blocks
+    ords = randperm(length(Stimuli));    
+    for j = 1:length(ords)
+        fprintf(fid,'%s\r\n',Stimuli{ords(j)});
+    end
+    fprintf(fid,['\r\n\r\n']);
+end
+
+
+fclose(fid);
+
+return
+
+
+
+
+

generate_single_SNT_stim_scan.m

@@ -0,0 +1,33 @@
+function [SOUND_chan,VNO_chan,VALVE_chan ] = generate_single_SNT_stim_scan(Params)
+% Generate a single SNT stimulation train
+
+% param fields are
+% SR sampling rate in Hz
+SR = Params.SR;
+
+samples_VNO_stim_duration            = Params.VNO_stim_duration * SR;
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% generate VNO stimulation train
+VNO_period_samples = ceil(SR / Params.VNO_stim_frequency) ;% in samples
+VNO_n_cycles = ceil(samples_VNO_stim_duration/VNO_period_samples);
+% positive, inter and negative pulse times in samples:
+VNO_ps  = ceil(SR*Params.VNO_stim_pulse_width/1000);
+VNO_ips = ceil(SR*Params.VNO_stim_interphase_delay/1000);
+VNO_samples_per_pulse = 2*VNO_ps + VNO_ips;
+VNO_samples_between_pulses = VNO_period_samples - VNO_samples_per_pulse;
+VNO_one_pulse = [zeros(1,VNO_samples_between_pulses) -Params.VNO_stim_amplitude*ones(1,VNO_ps) zeros(1,VNO_ips) Params.VNO_stim_amplitude*ones(1,VNO_ps)];
+VNO_stim_train = repmat(VNO_one_pulse,1,VNO_n_cycles);
+VNO_stim_train = VNO_stim_train(1:samples_VNO_stim_duration);
+VNO_stim_train = [VNO_stim_train(1:(end-5)) zeros(1,5)];
+
+
+trial_ints(1) = samples_VNO_stim_duration;
+
+
+SOUND_chan  =  0*ones(1,sum(trial_ints(1)))   ;
+VNO_chan   =  VNO_stim_train  ;
+VALVE_chan = 0*ones(1,sum(trial_ints(1))) ;
+
+

generate_single_VNS_trial_scan.m

@@ -0,0 +1,69 @@
+function [SOUND_chan,VNO_chan,VALVE_chan apply_sample] = generate_single_VNS_trial_scan(Params)
+% Generate output signals according to selected trial parameters
+% YBS 2017
+
+% param fields are
+% SR sampling rate in Hz
+SR = Params.SR;
+digoutV = 3.3; % scale factor for the valve channel
+
+
+[apply_sound,clean_sound, end_sound] = generate_trial_sounds(SR);
+
+samples_apply_sound = length(apply_sound);
+samples_clean_sound = length(clean_sound);
+samples_end_sound   = length(end_sound);
+samples_ES_stim_to_apply_delay = 0; % Params.ES_stim_to_apply_delay * SR;
+samples_ES_stim_duration       = 0; % Params.ES_stim_duration * SR;
+samples_application_to_stim_delay    = Params.application_to_stim_delay * SR;
+samples_ES_stim_to_VNO_stim_delay     = 0; % Params.ES_stim_to_VNO_stim_delay * SR;
+samples_VNO_stim_duration             = Params.VNO_stim_duration * SR;
+samples_stim_to_wash_delay            =  Params.stim_to_wash_delay * SR;
+samples_wash_start_to_wash_stim_delay = Params.wash_start_to_wash_stim_delay * SR;
+samples_wash_stim_to_wash_end_delay   = Params.wash_stim_to_wash_end_delay * SR;
+
+apply_sample = samples_apply_sound;
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% generate VNO stimulation train
+VNO_period_samples = ceil(SR / Params.VNO_stim_frequency) ;% in samples
+VNO_n_cycles = ceil(samples_VNO_stim_duration/VNO_period_samples);
+% positive, inter and negative pulse times in samples:
+VNO_ps  = ceil(SR*Params.VNO_stim_pulse_width/1000);
+VNO_ips = ceil(SR*Params.VNO_stim_interphase_delay/1000);
+VNO_samples_per_pulse = 2*VNO_ps + VNO_ips;
+VNO_samples_between_pulses = VNO_period_samples - VNO_samples_per_pulse;
+VNO_one_pulse = [zeros(1,VNO_samples_between_pulses) -Params.VNO_stim_amplitude*ones(1,VNO_ps) zeros(1,VNO_ips) Params.VNO_stim_amplitude*ones(1,VNO_ps)];
+VNO_stim_train = repmat(VNO_one_pulse,1,VNO_n_cycles);
+VNO_stim_train = VNO_stim_train(1:samples_VNO_stim_duration);
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% generate ES external stimulation train
+ES_stim_train = [];
+
+
+trial_ints(1) = samples_apply_sound - samples_ES_stim_to_apply_delay;
+trial_ints(2) = samples_ES_stim_to_apply_delay;
+trial_ints(3) = samples_ES_stim_duration - samples_ES_stim_to_apply_delay;
+trial_ints(4) = samples_application_to_stim_delay - samples_ES_stim_to_VNO_stim_delay - trial_ints(3);
+trial_ints(5) = samples_ES_stim_to_VNO_stim_delay;
+trial_ints(6) = samples_VNO_stim_duration;
+trial_ints(7) = samples_ES_stim_duration - trial_ints(5) - trial_ints(6);
+trial_ints(8) = samples_stim_to_wash_delay - trial_ints(7) - trial_ints(6) - samples_clean_sound;
+trial_ints(9) = samples_clean_sound;
+trial_ints(10) = samples_wash_start_to_wash_stim_delay;
+trial_ints(11) = samples_VNO_stim_duration;
+trial_ints(12) = samples_wash_stim_to_wash_end_delay - samples_VNO_stim_duration;
+trial_ints(13) = samples_end_sound;
+
+
+
+SOUND_chan  = [apply_sound zeros(1,sum(trial_ints([3:8])))  clean_sound zeros(1,sum(trial_ints([10:12]))-samples_end_sound)   end_sound zeros(1,sum(trial_ints([13])))] ;
+VNO_chan   = [zeros(1,sum(trial_ints([1:5]))) VNO_stim_train zeros(1,sum(trial_ints([7:10])))  VNO_stim_train zeros(1,sum(trial_ints([12:13])))] ;
+VALVE_chan = [zeros(1,sum(trial_ints([1:9]))) digoutV * ones(1,sum(trial_ints([10:12]))) zeros(1,sum(trial_ints([13])))];
+
+

generate_single_washvalve_scan.m

@@ -0,0 +1,15 @@
+function [SOUND_chan,VNO_chan,VALVE_chan]=generate_single_washvalve_scan(valveState)
+% open and close the valve - simply changing output level
+% YBS - 2017
+
+digoutV = 3.3;
+
+if  strcmp(valveState,'close')
+    samples_valve_duration=ones(1,100);
+elseif strcmp(valveState,'open')
+    samples_valve_duration=zeros(1,100);
+end
+SOUND_chan  =  0*samples_valve_duration   ;
+VNO_chan   =  0*samples_valve_duration  ;
+VALVE_chan = samples_valve_duration*digoutV ;
+

generate_trial_sounds.m

@@ -0,0 +1,51 @@
+function [apply_sound clean_sound  end_sound] = generate_trial_sounds(SR)
+% generate sounds for queing the user for stimulus application 
+% YBS 2017
+
+
+% Define the sound segment lengths
+% Sound factors for all sound waveforms generated
+sound_amp    = 5;
+sound_offset = 0;
+% apply sound parameters
+apply_sound_dur_per_step = 1;
+apply_sound_freq = 2*[130.81 146.83 164.81 174.61 196 220 246.94 261.63];
+
+% generate initial sound signal
+apply_sound = [];
+duration = apply_sound_dur_per_step * ones(size(apply_sound_freq)); % in seconds %duration = [1 0.5 1 1 1 0.5 0.2 0.5 1]
+for i = 1:length(apply_sound_freq)
+    samps_per_cycle = floor(SR/apply_sound_freq(i));
+    one_cycle = sin(linspace(0, 2*pi, samps_per_cycle));
+    cycles_per_second = SR/length(one_cycle);
+    apply_sound = [apply_sound   repmat(one_cycle,[1  ceil(cycles_per_second*duration(i))])  ];
+end
+% to shift voltage so that INTAN board can read it
+apply_sound = sound_amp*apply_sound + sound_offset;
+
+% clean sound parameters
+clean_sound_duration = 0.5;
+clean_sound_freq = fliplr(apply_sound_freq);
+clean_sound = [];
+duration = clean_sound_duration * ones(size(clean_sound_freq)); % in seconds %duration = [1 0.5 1 1 1 0.5 0.2 0.5 1]
+for i = 1:length(clean_sound_freq)
+    samps_per_cycle = floor(SR/clean_sound_freq(i));
+    one_cycle = sin(linspace(0, 2*pi, samps_per_cycle));
+    cycles_per_second = SR/length(one_cycle);
+    clean_sound = [clean_sound   repmat(one_cycle,1,ceil(cycles_per_second*duration(i)))];
+end
+clean_sound = sound_amp*clean_sound +sound_offset;
+
+% End of trial sound
+end_sound_duration = 0.1;
+end_sound_freq = fliplr(2 * [130.81 146.83 164.81 174.61 196 ]);
+end_sound_signal = [];
+duration = end_sound_duration * ones(size(end_sound_freq)); % in seconds %duration = [1 0.5 1 1 1 0.5 0.2 0.5 1]
+for i = 1:length(end_sound_freq)
+    samps_per_cycle = floor(SR/end_sound_freq(i));
+    one_cycle = sin(linspace(0, 2*pi, samps_per_cycle));
+    cycles_per_second = SR/length(one_cycle);
+    end_sound_signal = [end_sound_signal   repmat(one_cycle,[1  ceil(cycles_per_second*duration(i))]) ];
+end
+end_sound = sound_amp*end_sound_signal + sound_offset;
+

read_stimulus_file.m

@@ -0,0 +1,17 @@
+function Stimuli = read_stimulus_file(fname)
+% Read stimuli from stimulus file and return as char array
+
+fid = fopen(fname,'r');
+
+k = 0;
+while 1
+    tline = fgetl(fid); % This is the file name line
+    if ~ischar(tline), break, end    
+    if ~isempty(tline) % ignore empty lines
+        k = k + 1;
+        Stimuli{k} = tline;        
+    end
+end
+
+
+fclose(fid);