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CellSummary_NDB.m
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CellSummary_NDB.m
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%% CellSummary_gt
% Make a raster with solo and nspike data.
%
% USAGE: [fig_handle, raster_info] = CellSummary_gt(behav_file, spk_file, align_ind, window,...
% by_mixture_ratio_flag, trials_to_include)
% EXAMPLE: h = CellSummary_gt(behav_fname, spk_fname, 3, [-2 1], 0, [1:145]);
%
% INPUTS: behav_file - path and filename of ratbase file
% spk_file - path and filename of spike file
% align_ind - which trial event to align rasters/psth to (indicated in
% GetSCGlobals.m)
% OdorPokeIn = 1
% OdorValveOn = 2
% OdorPokeOut = 3
% WaterPokeIn = 4
% WaterValveOn = 5
% WaterPokeOut = 6
% NextOdorPokeIn = 7
% window - 2x1 vector of times to rasterize spikes, relative to
% event_times ([START STOP]) (e.g., [-1 1])
% by_mixture_ratio_flag - whether to consider separate mixture
% ratios to be separate stimuli, or not (1 - yes; 0 - no)
% trials_to_include - which behavioral trials to include in
% analysis (OPTIONAL, default includes all trials)
%
% OUTPUTS: fig_handle - handle to figure of rasters, psths
% raster_info - structure containing info capable of
% reconstructing rasters
%
% Adapted from CellSummary for use w/ go tone data. Differs in that trials are grouped by
% response (L/R), mixture ratio, and go tone
% delay.
%
% 5/19/08 - GF
% Updates:
% $ 12/24/08 - added by_mixture_ratio flag - can be set to 0 for raster
% display, 1 for calculation of raster_info
function [raster_info] = CellSummary_NDB(behav_file, spk_file, align_ind, window,...
by_mixture_ratio_flag, trials_to_include)
% MIN_TRIAL_PLOTS = 6; % for psths
%PSTH_SMOOTH_FACTOR = (window(2) - window(1)) * 10; % this is the "standard value" as of 8/2011
PSTH_SMOOTH_FACTOR = (window(2) - window(1)) * 5;
%% load spike file
spike_times = spk_file/1000000; % converts to time in seconds
odorid = [95 5 60 40 80 20 50];
%% load behavioral file
before_trial_res = length(behav_file.start);
if exist('trials_to_include','var') % don't include all trials
behav_file = RestrictSession(behav_file, trials_to_include);
end
after_trial_res = length(behav_file.start);
GetNeuroGlobals;
global RESOLUTION; % set to 1000 to plot spike times to 1 msec resolution
global TRIAL_EVENTS;
trial_events = fieldnames(TRIAL_EVENTS);
trial_events{2} = 'DIO'; %DIO is OdorValveOn
trial_events{5} = 'WaterDeliv'; %WaterDeliv is WaterValveOn
trial_events{8} = 'cue'; %WaterDeliv is WaterValveOn
% PresentationFigSetUp; %%% THIS IS WHERE trial_events comes from (weird)
% fig_handle = gcf;
%% get event timings of each trial type
if by_mixture_ratio_flag == 0
[raster_events, stim_params] = TrialClassification_dispatcher2test(behav_file, trial_events);
% temp = 0;
elseif by_mixture_ratio_flag == 1
[raster_events, stim_params] = TrialClassification_dispatcher_previousTrial(behav_file, trial_events);
% temp = 1;
else
error('by_mixture_ratio_flag must be 0 or 1');
end
%% determine the total number of (performed) trials
num_stim = length(raster_events.L.trial_start);
total_num_trials = 0; % initialize
for stim_num = 1:num_stim
total_num_trials = total_num_trials + length(raster_events.L.trial_start{stim_num}) + length(raster_events.R.trial_start{stim_num});
end
%% Raster setup constants
raster_l = 0.08;
raster_w = 0.8;
raster_u_buff = 0.033;
total_rasters_h = 0.72; % fraction of total figure height to devote to rasters
intrastim_space = 0.005;
intrachoice_space = intrastim_space / 3;
available_rasters_h = total_rasters_h - (((num_stim - 1) * intrastim_space) + (num_stim * intrachoice_space));
textbuff = 0.04;
%% choice bar setup constants
choicebar_hor_buff = 0.01;
choicebar_w = 0.005;
choicebar_l = raster_l - (choicebar_hor_buff + choicebar_w);
%% stimulus bar setup constants
% stimbar_hor_buff = choicebar_hor_buff;
% stimbar_w = choicebar_w;
% stimbar_l = raster_l + raster_w + stimbar_hor_buff;
raster_u = 1 - raster_u_buff; % initialize
SECONDARY_EVENTS_COLORS = [...
0 1 0;... % Neon Green OdorPokeIn
1 0.5 1;... % Hot Pink OdorValveOn
0.75 0 0.75;... % Dark Pink OdorPokeOut
0 0.75 0.75;... % Turquoise WaterPokeIn
0 0 1;... % Navy Blue WaterValveOn
0.75 0 0;... % Red WaterPokeOut
0 1 0;... % Neon Green NextOdorPokeIn
0.87 0.49 0]; % Dark Purple Cue Signal
%% L & R Trials
% L trials
for stim_num = 1:num_stim
% determine height of raster window
num_trials = length(raster_events.L.trial_start{stim_num});
raster_h = (num_trials / total_num_trials) * available_rasters_h;
raster_u = raster_u - (raster_h + intrastim_space);
trial_start_L = raster_events.L.trial_start{stim_num};
align_event_time_L = raster_events.L.trial_events_time{stim_num}(align_ind, :);
secondary_event_time_L = raster_events.L.trial_events_time{stim_num};
raster_pos = [raster_l raster_u raster_w raster_h];
% set(gcf, 'CurrentAxes', whole_fig); % re-reference whole figure
% text(raster_l - textbuff, raster_u + raster_h/2, num2str(odorid(stim_num)));
if num_trials > 0 % make sure there are trials of this type
% axes('Position', raster_pos);
[ref_spike_times.L{stim_num}, trial_inds.L{stim_num}, plot_handle] =...
raster(spike_times, trial_start_L, align_event_time_L, window, secondary_event_time_L, 1);
% set(gca, 'XTick', [], 'YTick', []);
% Change colors of secondary event symbols
% for sec_event_ind = 1:size(SECONDARY_EVENTS_COLORS, 1)
% set(plot_handle.secondary_events(:, sec_event_ind), 'Color', SECONDARY_EVENTS_COLORS(sec_event_ind, :));
% end
% for first stim type, add the plot title
% if stim_num == 1
% f = findstr(spk_file, '\');
% title_str = [behav_file(end-14:end), ' - ', spk_file(f(end)+1:end)];
% title(ReplaceUnderscores(title_str));
% end
% make a color bar showing choice
% col = RASTER_COLORS.L;
% choicebar_pos = [choicebar_l raster_u choicebar_w raster_h];
% h = axes('Position', choicebar_pos);
% set(h, 'Color', col, 'XColor', col, 'YColor', col);
% set(h, 'YTick', [], 'XTick', []);
else
ref_spike_times.L{stim_num} = [];
trial_inds.L{stim_num} = [];
end
% R trials
% determine height of raster window
num_trials = length(raster_events.R.trial_start{stim_num});
raster_h = (num_trials / total_num_trials) * available_rasters_h;
raster_u = raster_u - (raster_h + intrachoice_space);
trial_start_R = raster_events.R.trial_start{stim_num};
align_event_time_R = raster_events.R.trial_events_time{stim_num}(align_ind, :);
secondary_event_time_R = raster_events.R.trial_events_time{stim_num};
raster_pos = [raster_l raster_u raster_w raster_h];
if num_trials > 0 % make sure there are trials of this type
% h = axes('Position', raster_pos);
% axes('Position', raster_pos);
[ref_spike_times.R{stim_num}, trial_inds.R{stim_num}, plot_handle] =...
raster(spike_times, trial_start_R, align_event_time_R, window, secondary_event_time_R, 1);
% set(gca, 'XTick', [], 'YTick', []);
% Change colors of secondary event symbols
% for sec_event_ind = 1:size(SECONDARY_EVENTS_COLORS, 1)
% set(plot_handle.secondary_events(:, sec_event_ind), 'Color', SECONDARY_EVENTS_COLORS(sec_event_ind, :));
% end
% make a color bar showing choice
% col = RASTER_COLORS.R;
% choicebar_pos = [choicebar_l raster_u choicebar_w raster_h];
% h = axes('Position', choicebar_pos);
% set(h, 'Color', col, 'XColor', col, 'YColor', col);
% set(h, 'YTick', [], 'XTick', []);
else
ref_spike_times.R{stim_num} = [];
trial_inds.R{stim_num} = [];
end
end
%% PSTHS
psth_l = raster_l;
psth_w = raster_w;
psth_h = 0.15;
psth_vertbuff = 0.01;
psth_u = raster_u - psth_h - psth_vertbuff;
psth_pos = [psth_l psth_u psth_w psth_h];
% axes('Position', psth_pos);
%
% hold on;
%
init_psth_window = window + [-((RESOLUTION/1000)/2) +((RESOLUTION/1000)/2)]; %b/c raster output has been padded
%% L & R Trials
for stim_num = 1:num_stim
% L trials
% if max(trial_inds.L{stim_num}) >= MIN_TRIAL_PLOTS % make sure there are enough trials of this type to plot
% no_plot_flag = 0;
% else
% no_plot_flag = 1;
% end
[ref_psth.L.correct{stim_num}, plot_handle] = psth(ref_spike_times.L{stim_num}, trial_inds.L{stim_num},...
init_psth_window, PSTH_SMOOTH_FACTOR, 1);
% set(plot_handle, 'Color', RASTER_COLORS.L);
% R trials
% if max(trial_inds.R{stim_num}) >= MIN_TRIAL_PLOTS % make sure there are enough trials of this type to plot
% no_plot_flag = 0;
% else
% no_plot_flag = 1;
% end
[ref_psth.R.correct{stim_num}, plot_handle] = psth(ref_spike_times.R{stim_num}, trial_inds.R{stim_num},...
init_psth_window, PSTH_SMOOTH_FACTOR, 1);
% set(plot_handle, 'Color', RASTER_COLORS.R);
% xlabel(['Time relative to ', trial_events{align_ind}, ' (s)']);
% ylabel('Firing rate (spks/s)');
end
%% package output structure
raster_info.ref_spike_times = ref_spike_times;
raster_info.trial_inds = trial_inds;
raster_info.raster_events = raster_events;
raster_info.stim_params = stim_params;
raster_info.align_ind = align_ind;
raster_info.window = window;
raster_info.beTI = before_trial_res;
raster_info.afTI = after_trial_res;
return