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Analyses_create_cross_validated_PSTs.m
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Analyses_create_cross_validated_PSTs.m
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function hndls = Analyses_create_cross_validated_PSTs(birdnum)
%% Create PSTs for canaries lrb85314, lbr3022, (lbr3009)
% This script creates the PSTs and figures
% To reduce noise some rare syllables are removed (the variable 'ignore_entries') and the criterion for
% removal is described for each bird (since the number of files changes
% between them)
% some dates are ignored (the 'ignore_dates' list) because of data
% corruption.
% Some entries are joined (the list 'join_entries') because they belong to
% the same syllable class and were separated due to user OCD.. :)
% 'include_zero' is 0/1 for including the label '0' (in birds 853 and
% 3022), 'min_phrases' sets the minimal # of phrases per song bout to
% include
%% repos. requirements: pst, BirdSongBout
addpath(genpath('/Users/yardenc/Documents/Experiments/Code and Hardware Dev/GitHub/pst'),'-end');
addpath(genpath('/Users/yardenc/Documents/Experiments/Code and Hardware Dev/GitHub/BirdSongBout/BirdSongBout'),'-end');
global colors color_tags;
%colors = [];
%color_tags = [];
switch birdnum
case 1
%% lrb85315
path_to_annotation = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs/wav/lrb85315auto_annotation5_fix.mat';
ignore_dates = {'2017_04_18' '2017_04_19' '2017_04_20'};
ignore_entries = [-1 100 102 101 103 202 406 408 409 402 403];
join_entries = {[207 307 407] [404 405] [200 309] [208 209]};
include_zero = 1;
min_phrases = 2;
load('/Users/yardenc/Documents/Projects/CohenGardner2017_CanaryHVCImaging/Figures/lrb853_colors.mat');
case 2
%% lbr3022
% ignore_dates = {'2017_04_05' '2017_04_06' '2017_04_11' '2017_04_12' '2017_04_14' ...
% '2017_04_16' '2017_04_20' '2017_04_21' '2017_04_23' '2017_04_25' '2017_04_26' ...
% '2017_04_27' '2017_04_30' '2017_05_03'};
ignore_dates = {'2017_04_14' '2017_04_27'};
ignore_entries = [-1 100 102 101 103];
join_entries = {[2 206]}; %{[207 307 407] [404 405] [208 209] [200 309]};
path_to_annotation = fullfile('/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lbr3022/movs/wav','lbr3022auto_annotation5_alexa.mat');
include_zero = 1;
min_phrases = 2;
load('/Users/yardenc/Documents/Projects/CohenGardner2017_CanaryHVCImaging/Figures/lbr3022_colors.mat');
case 3
%% lbr3009
ignore_dates = {'2017_04_27' '2017_04_28' '2017_06_05' '2017_06_06' '2017_06_07' '2017_06_08' '2017_06_09' '2017_06_12' '2017_06_13' ...
'2017_06_14' '2017_06_15' '2017_06_16' '2017_06_19' '2017_06_20' '2017_06_21' '2017_06_22' '2017_06_27' ...
'2017_06_28' '2017_06_29' '2017_06_30' '2017_07_03' '2017_07_04' '2017_07_06' '2017_07_07' '2017_07_10' ...
'2017_07_11' '2017_07_12' '2017_07_13' '2017_07_14' '2017_07_18' '2017_07_19' '2017_07_20' '2017_07_21'};
ignore_entries = [-1 100 102 101 103];
join_entries = {};
path_to_annotation = fullfile('/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lbr3009/movs/wav','lbr3009auto_annotation1_fix.mat');
include_zero = 0;
min_phrases = 2;
load('/Users/yardenc/Documents/Projects/CohenGardner2017_CanaryHVCImaging/Figures/lbr3009_colors.mat');
end
%%
[DATA, syls] = convert_annotation_to_pst(path_to_annotation,ignore_dates,ignore_entries,join_entries,1*(birdnum<3),2);
cv_store=pst_cross_validate(DATA,'L',5);
%
% [F_MAT ALPHABET N PI]=pst_build_trans_mat(DATA,5);
% TREE = pst_learn(F_MAT,ALPHABET,N,'L',5);
%%
syl_labels = mat2cell(syls',ones(numel(syls),1),1);
%%
[ni,nj,nk] = size(cv_store.tree);
for i = 1:ni
for j = 1:nj
for k = 1:nk
TREE = cv_store.tree{i,j,k};
hndls = [];
for rootnode = 1:numel(TREE(2).string)
display(['Main branch: Syllble #' num2str(syls(TREE(2).string{rootnode}))]);
figure; h_pie=pie(double(TREE(2).g_sigma_s(:,rootnode)),zeros(1,numel(syls)),cellfun(@num2str,syl_labels,'UniformOutput',0));
for cnt = 2:2:numel(h_pie)
h_pie(cnt).FontSize = 16;
h_pie(cnt-1).FaceColor = colors(color_tags == str2num(h_pie(cnt).String),:);
end
title(['Root: ' num2str(syls(TREE(2).string{rootnode}))]);
hndls = [hndls h_pie];
explore_branch(birdnum,TREE,syls,2,rootnode);
end
'8';
end
end
end
function explore_branch(bnum,TREE,syls,level_num,branch_num)
% switch bnum
% case 1
%
% load('/Users/yardenc/Documents/Projects/CohenGardner2017_CanaryHVCImaging/Figures/lrb853_colors.mat');
% case 2
% load('/Users/yardenc/Documents/Projects/CohenGardner2017_CanaryHVCImaging/Figures/lbr3022_colors.mat');
% end
syl_labels = mat2cell(syls',ones(numel(syls),1),1);
if (level_num < numel(TREE) & ~isempty(TREE(level_num + 1).parent))
branches = find(TREE(level_num + 1).parent(1,:) == branch_num);
for next_branch_num = 1:numel(branches)
%display([level_num next_branch_num])
display(['level ' num2str(level_num) ' Branch: ' num2str(syls(TREE(level_num + 1).string{branches(next_branch_num)}))]);
figure; h_pie=pie(double(TREE(level_num+1).g_sigma_s(:,branches(next_branch_num))),zeros(1,numel(syls)),cellfun(@num2str,syl_labels,'UniformOutput',0));
for cnt = 2:2:numel(h_pie)
h_pie(cnt).FontSize = 16;
h_pie(cnt-1).FaceColor = colors(color_tags == str2num(h_pie(cnt).String),:);
end
title(['Branch: ' num2str(syls(TREE(level_num + 1).string{branches(next_branch_num)}))]);
hndls = [hndls h_pie];
explore_branch(bnum,TREE,syls,level_num + 1,branches(next_branch_num));
end
end
end
end