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detect_ripple_demo.m
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detect_ripple_demo.m
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function spikes_in_ripple_all = detect_ripple_demo(animal, day, epoch)
%% Detect ripple and spikes in ripples from specified EEG file(s)
animal_data_path = fullfile('../dataset', animal);
% day = 4; epoch = 4; % tetrode = 18;
eeg_data_path = fullfile(animal_data_path, 'EEG');
eeg_file_all = dir(eeg_data_path);
eeg_file_all = {eeg_file_all(~[eeg_file_all(:).isdir]).name};
eeg_file_chosen = eeg_file_all(contains(eeg_file_all, sprintf('%02d-%d', day, epoch)));
animal_file_all = dir(fullfile(animal_data_path));
animal_file_all = {animal_file_all(~[animal_file_all(:).isdir]).name};
spike_file_chosen = animal_file_all(contains(animal_file_all, sprintf('spikes%02d', day)));
if length(spike_file_chosen) ~= 1
fprintf('Spike file not unique!');
end
load(fullfile(animal_data_path, spike_file_chosen{1}), 'spikes');
tetrode_file = animal_file_all(contains(animal_file_all,'tetinfo'));
load(fullfile(animal_data_path, tetrode_file{1}), 'tetinfo');
ripples_by_tetrode = struct('tetrode', nan, 'area', '', 'depth', nan, 'ripples', []);
lfp_ripple_band_by_tetrode = struct('tetrode', nan, 'lfp_ripple_band', []);
for i=1:length(eeg_file_chosen)
load(fullfile(eeg_data_path, eeg_file_chosen{i}), 'eeg');
lfp_data_idxs = regexp(eeg_file_chosen{i}, '\d*','match');
lfp_data_idxs = cellfun(@str2num, lfp_data_idxs);
smpl_rate = eeg{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.samprate;
start_time = eeg{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.starttime;
lfp_data_idxs = regexp(eeg_file_chosen{i}, '\d*','match');
lfp_data_idxs = cellfun(@str2num, lfp_data_idxs);
ripples_by_tetrode(i).tetrode = lfp_data_idxs(3);
lfp_ripple_band_by_tetrode(i).tetrode = lfp_data_idxs(3);
if isempty(tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)})
continue;
elseif ~tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.numcells
continue;
elseif ~any(strcmp(fieldnames(tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}), 'area'))
continue;
elseif strcmp(tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.area, 'Reference')
continue;
end
ripples_by_tetrode(i).area = tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.area;
ripples_by_tetrode(i).depth = tetinfo{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.depth{1} * 0.0265; % depth in mm
% Detect ripples on the tetrode
lfp_data = eeg{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)}.data;
[lfp_ripple_band, ripples] = detect_ripple(lfp_data, smpl_rate, start_time, 'karlsson09', false);
% Examine number of spikes during the ripples on the same tetrode
putative_neurons = spikes{lfp_data_idxs(1)}{lfp_data_idxs(2)}{lfp_data_idxs(3)};
for k=1:length(ripples)
spike_locs_cell = cell(length(putative_neurons), 1);
neuron_id_mat = zeros(length(putative_neurons), 2);
for j=1:length(putative_neurons)
if isempty(putative_neurons{j}) || isempty(putative_neurons{j}.data)
spike_locs_cell{j} = [];
neuron_id_mat(j, :) = [lfp_data_idxs(3), j];
else
spike_locs = putative_neurons{j}.data(:, 1);
spike_locs = spike_locs(bitand(spike_locs>=ripples(k).start_sec, spike_locs<ripples(k).end_sec));
spike_locs_cell{j} = spike_locs;
neuron_id_mat(j, :) = [lfp_data_idxs(3), j];
end
end
ripples(k).spike_locs = spike_locs_cell(~cellfun(@isempty, spike_locs_cell));
ripples(k).neuron_ids = neuron_id_mat(~cellfun(@isempty, spike_locs_cell), :); % First col tetrode, second col neuron index
end
ripples_by_tetrode(i).ripples = ripples;
lfp_ripple_band_by_tetrode(i).lfp_ripple_band = lfp_ripple_band;
end
ripples_by_tetrode(cellfun(@isempty,{ripples_by_tetrode(:).ripples})) = []; % Remove tetrodes where there is no ripple
% Combine ripples on different tetrodes
ripples_by_tetrode_table = struct2table(ripples_by_tetrode);
ripples_by_tetrode_table = sortrows(ripples_by_tetrode_table, 'depth');
ripples_by_tetrode = table2struct(ripples_by_tetrode_table);
tetrode_dist = diff([ripples_by_tetrode(:).depth]);
ripples_by_group_tetrode = struct('tetrodes', [], 'depths', [], 'area', {}, 'ripples', []);
ripples_by_group_tetrode(1).tetrodes = ripples_by_tetrode(1).tetrode;
ripples_by_group_tetrode(1).depths = ripples_by_tetrode(1).depth;
ripples_by_group_tetrode(1).ripples = ripples_by_tetrode(1).ripples;
ripples_by_group_tetrode(1).area = ripples_by_tetrode(1).area;
num_tetrode_group = length(ripples_by_group_tetrode);
for i=1:length(tetrode_dist)
if tetrode_dist(i) > 3*0.0265 % depth in mm
num_tetrode_group = num_tetrode_group + 1;
ripples_by_group_tetrode(num_tetrode_group).tetrodes = ripples_by_tetrode(i+1).tetrode;
ripples_by_group_tetrode(num_tetrode_group).depths = ripples_by_tetrode(i+1).depth;
ripples_by_group_tetrode(num_tetrode_group).ripples = ripples_by_tetrode(i+1).ripples;
ripples_by_group_tetrode(num_tetrode_group).area = ripples_by_tetrode(i+1).area;
else
ripples_by_group_tetrode(num_tetrode_group).tetrodes = [ripples_by_group_tetrode(num_tetrode_group).tetrodes, ripples_by_tetrode(i+1).tetrode];
ripples_by_group_tetrode(num_tetrode_group).depths = [ripples_by_group_tetrode(num_tetrode_group).depths, ripples_by_tetrode(i+1).depth];
ripples_by_group_tetrode(num_tetrode_group).ripples = [ripples_by_group_tetrode(num_tetrode_group).ripples, ripples_by_tetrode(i+1).ripples];
ripples_by_group_tetrode(num_tetrode_group).area = [ripples_by_group_tetrode(num_tetrode_group).area, {ripples_by_tetrode(i+1).area}];
end
end
for i=1:length(ripples_by_group_tetrode)
ripples_table = struct2table(ripples_by_group_tetrode(i).ripples);
ripples_table = sortrows(ripples_table, 'start_idx');
ripples_struct = table2struct(ripples_table);
rows_to_remove = [];
for j=length(ripples_struct):-1:2
if (ripples_struct(j).start_idx >= ripples_struct(j-1).start_idx && ripples_struct(j).start_idx < ripples_struct(j-1).end_idx)
ripples_struct(j-1).end_idx = max(ripples_struct(j-1).end_idx, ripples_struct(j).end_idx);
ripples_struct(j-1).end_sec = max(ripples_struct(j-1).end_sec, ripples_struct(j).end_sec);
ripples_struct(j-1).length_idx = ripples_struct(j-1).end_idx - ripples_struct(j-1).start_idx;
ripples_struct(j-1).length_sec = ripples_struct(j-1).end_sec - ripples_struct(j-1).start_sec;
ripples_struct(j-1).spike_locs = [ripples_struct(j-1).spike_locs;ripples_struct(j).spike_locs];
ripples_struct(j-1).neuron_ids = [ripples_struct(j-1).neuron_ids; ripples_struct(j).neuron_ids];
rows_to_remove = [rows_to_remove, j];
end
end
ripples_struct(rows_to_remove) = [];
ripples_by_group_tetrode(i).ripples = ripples_struct;
end
% Remove ripples that are too long (currently, >200ms)
for i=1:length(ripples_by_group_tetrode)
rows_to_remove = [];
ripples_struct = ripples_by_group_tetrode(i).ripples;
for j=1:length(ripples_struct)
if ripples_struct(j).length_sec > 0.2
rows_to_remove = [rows_to_remove, j];
end
end
ripples_struct(rows_to_remove) = [];
ripples_by_group_tetrode(i).ripples = ripples_struct;
end
save(sprintf('../results/%sripples-day_%d-epoch_%d.mat', animal, day, epoch), 'ripples_by_group_tetrode');
spikes_in_ripple_all = convert_ripple_mat(ripples_by_group_tetrode);
save(sprintf('../results/%sspikes_in_ripple_all-day_%d-epoch_%d.mat', animal, day, epoch), 'spikes_in_ripple_all');
%% Visualize ripples during which there are several neurons firing together
% plot_window_offset = 0.5;
% num_neuron_thres = 3;
% for j=1:length(ripples_by_group_tetrode)
% ripples = ripples_by_group_tetrode(j).ripples;
% ripple_sel_mask = find(arrayfun(@(s) length(s.spike_locs)>=num_neuron_thres, ripples));
% for k=1:length(ripple_sel_mask)
% i = ripple_sel_mask(k);
% figure();
% subplot(2,1,1);
% hold on;
% for l=1:length(ripples_by_group_tetrode(j).tetrodes)
% tetrode_idx = find([lfp_ripple_band_by_tetrode(:).tetrode]==ripples_by_group_tetrode(j).tetrodes(l));
% plot(linspace(ripples(i).start_sec-plot_window_offset, ripples(i).end_sec+plot_window_offset, ripples(i).length_idx+1), ...
% lfp_ripple_band_by_tetrode(tetrode_idx).lfp_ripple_band(ripples(i).start_idx:ripples(i).end_idx));
% end
% hold off
% xlim([ripples(i).start_sec-plot_window_offset, ripples(i).end_sec+plot_window_offset]);
% legend(strcat('Tetrode ', cellstr(num2str(ripples_by_group_tetrode(j).tetrodes'))));
% xlabel('Time (sec)');
% ylabel('Voltage ')
% subplot(2,1,2);
% hold on;
% for l=1:length(ripples(i).spike_locs)
% raster(ripples(i).spike_locs{l}, l-1, 'k', []);
% end
% hold off;
% xlim([ripples(i).start_sec-plot_window_offset, ripples(i).end_sec+plot_window_offset]);
% ylim([0, length(ripples(i).spike_locs)]);
% yticks((1:length(ripples(i).spike_locs))-0.5);
% yticklabels(cellfun(@(p) sprintf('Tet.%dNeu.%d', p(1), p(2)), num2cell(ripples(i).neuron_ids, 2), 'UniformOutput', false));
% xlabel('Time (sec)');
% ylabel('Putative neuron')
% end
% end
end