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Copy pathAllDaysPhraseLockedSingleROIimage.m
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AllDaysPhraseLockedSingleROIimage.m
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%% Folders that contain data
% Folders on laptop:
laptop_mov_folder = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs';
laptop_wav_folder = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs/wav';
laptop_gif_folder = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs/wav/gif';
laptop_storage_folder = '/Volumes/CanaryData/DATA/lrb853_15/movs/';
laptop_annotated_dir = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs/wav/annotated';
laptop_annotated_images_dir = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/movs/wav/annotated/images';
DamagedFolder = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/too_large_or_damaged/';
laptop_manualROI_folder = '/Users/yardenc/Documents/Experiments/Imaging/Data/CanaryData/lrb853_15/ManualROIs';
%% Folders on desktop:
addpath(genpath('/Users/yardenc/Documents/GitHub/small-utils'));
laptop_manualROI_folder = '/Users/yardenc/Documents/Experiments/Imaging/CanaryData/lrb853_15/ManualROIs';
desktop_results_folder = '/Users/yardenc/Documents/Experiments/Imaging/CanaryData/lrb853_15/ManualROIs/SingleROIalignments';
%% Single bird
time_padding = 2; %seconds around phrase
bird_name = 'lrb85315';
cd (laptop_manualROI_folder);
load lrb85315template;
syllables = [[templates.wavs.segType] -1 102 103];
syls = [templates.wavs.segType];
n_syllables = numel(syllables);
freq_min = 300; freq_max = 8000;
colors = distinguishable_colors(n_syllables,'k');
load lrb85315auto_annotation5;
ord = [];
dates = [];
datenums = [];
for i = 1:numel(keys)
tokens = regexp(keys{i},'_','split');
ord = [ord; str2num(tokens{2})];
dates = [dates; char(join(tokens(3:5),'_'))];
datenums = [datenums; datenum(char(join(tokens(3:5),'_')))];
end
datenums = unique(datenums);
[locs,indx] = sort(ord);
elements = elements(indx);
keys = keys(indx);
dates = dates(indx,:);
%% Single day, selected ROIs
conds = [0 1;0 0; 1 1];
bg_lim = 0.5;
n_del_frames = 4;
%for dayn = 1:numel(datenums)
%Day = datestr(datenums(dayn),'yyyy_mm_dd'); %'2017_03_20';
Day = '2017_03_19';
if ~exist(fullfile(desktop_results_folder,Day),'dir')
mkdir(fullfile(desktop_results_folder,Day));
end
cd([laptop_manualROI_folder '/ROIdata/' Day]);
FILES = dir('ROIdata*.mat');
FILES = {FILES.name};
for sylcnt = 1:numel(syls) %[templates.wavs.segType]
sylnum = syls(sylcnt);
%%
hits = [];
durations = [];
%s = [];
for fnum = 1:numel(FILES)
fname = FILES{fnum};
tokens = regexp(fname,'_','split');
loc = find(locs == str2num(tokens{3}));
phrases = return_phrase_times(elements{loc});
if ismember(sylnum,phrases.phraseType)
load(fname);
% s = [s; zscore(dff(ROIs,n_del_frames+1:end)')];
phrase_locs = find(phrases.phraseType == sylnum);
for phrase_loc = 1:numel(phrase_locs)
phrasenum = phrase_locs(phrase_loc);
tonset = phrases.phraseFileStartTimes(phrasenum);
toffset = phrases.phraseFileEndTimes(phrasenum);
hits = [hits; fnum phrasenum];
durations = [durations; toffset-tonset];
end
end
end
% maxs = max(s);
[durations,dur_idx] = sort(durations);
hits = hits(dur_idx,:);
for ROIs = 1:size(dff,1) %18; %[5 6 7]; %[3 9 13];%
h=figure('Visible','off','Position',[77 91 1840 600]);
for cond = 1:3
subplot(1,3,cond);
warp = conds(cond,1);
locktoonset = conds(cond,2);
% for i = 1:numel(ROIs)
% h=figure('Visible','on','Position',[77 91 2215 420]);
% hs = [hs; h];
% end
%%
if warp == 0
I = zeros(size(hits,1),ceil(max(durations)*1000+4200),3);
else
I = zeros(size(hits,1),ceil(max(durations)/min(durations)*1000+4200),3);
end
for cnt = 1:size(hits,1)
fnum = hits(cnt,1);
phrasenum = hits(cnt,2);
fname = FILES{fnum};
tokens = regexp(fname,'_','split');
loc = find(locs == str2num(tokens{3}));
phrases = return_phrase_times(elements{loc});
load(fname);
display(fname);
s = zscore(dff(:,n_del_frames+1:end)')';
t = vidTimes;
tonset = phrases.phraseFileStartTimes(phrasenum);
toffset = phrases.phraseFileEndTimes(phrasenum);
signal = smooth(s(ROIs,:),3);
signal(signal < quantile(signal,bg_lim)) = 0;
signal = signal / max(signal); %maxs
timetag = (t(n_del_frames+1:end)-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
t_temp = t(n_del_frames+1:end);
durfactor = 1;
%if warp == 0
signal = interp1(timetag,signal,timetag(1):0.001:timetag(end)+1/30);
t_temp = interp1(timetag,t_temp,timetag(1):0.001:timetag(end)+1/30);
timetag = interp1(timetag,timetag,timetag(1):0.001:timetag(end)+1/30);
% else
% durfactor = max(durations)/durations(cnt);
% signal = interp1(timetag,signal,timetag(1):1/durfactor/1000:timetag(end)+1/30);
% t_temp = interp1(timetag,t_temp,timetag(1):1/durfactor/1000:timetag(end)+1/30);
% timetag = interp1(timetag,timetag,timetag(1):1/durfactor/1000:timetag(end)+1/30);
% end
idxmap = [1:numel(timetag)] - min(find(abs(timetag) == min(abs(timetag))))+2100+round((1-locktoonset)*max(durations)*(1000*(1-warp)+warp*durfactor));
for currphrase = 1:numel(phrases.phraseType)
t_on = (phrases.phraseFileStartTimes(currphrase)-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
t_off = (phrases.phraseFileEndTimes(currphrase)-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
idxs = find((timetag >= t_on) & (timetag <= t_off) & ...
(timetag >= -2*locktoonset + (-max(durations)*(1-warp)-2-warp)*(1-locktoonset)) & ...
(timetag <= 2*(1-locktoonset)+locktoonset*(2+max(durations)*(1-warp)+warp)));
if ~isempty(idxs)
%plot(timetag(idxs),signal(idxs),'Color',colors(find(syllables == phrases.phraseType(currphrase)),:));
% hold on;
I(cnt,idxmap(idxs),:) = signal(idxs)'*colors(find(syllables == phrases.phraseType(currphrase)),:);% + ...
%(1-signal(idxs)')*(1-colors(find(syllables == phrases.phraseType(currphrase)),:));
end
end
t_on = (phrases.phraseFileEndTimes(currphrase)-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
t_off = (phrases.phraseFileEndTimes(currphrase)+2-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
idxs = find((timetag >= t_on) & (timetag <= t_off) & ...
(timetag >= -2*locktoonset + (-max(durations)*(1-warp)-2-warp)*(1-locktoonset)) & ...
(timetag <= 2*(1-locktoonset)+locktoonset*(2+max(durations)*(1-warp)+warp)));
if ~isempty(idxs)
%plot(timetag(idxs),signal(idxs),'Color',colors(find(syllables == phrases.phraseType(currphrase)),:));
%hold on;
I(cnt,idxmap(idxs),:) = signal(idxs)'*[0.5 0.5 0.5];% + ...
%(1-signal(idxs)')*(1-colors(find(syllables == phrases.phraseType(currphrase)),:));
end
end
%%
image([-2.1-max(durations)*(1-locktoonset) 2.1+max(durations)*(locktoonset)],[1 cnt],I);
if warp
image(([1 size(I,2)]-2100)/1000,[1 cnt],I);
end
title(['Phrase #' num2str(sylnum) ' locked Ca signals from ' datestr(Day,'yyyy-mm-dd')])
set(gca,'XTick',[0 1]*locktoonset+(1-locktoonset)*[-1 0]);
set(gca,'YTick',[]);
ylabel(['ROI# ' num2str(ROIs)]);
if warp == 1
xlabel('Warped Time');
else
xlabel('Real Time');
end
set(gca,'FontSize',16);
end
figname = [bird_name ' Day ' Day ' syl #' num2str(sylnum) ' ManualROI #' num2str(ROIs) '.png'];
saveas(h,fullfile(desktop_results_folder,Day,figname));
hgclose(h);
end
end
%end
% plot(timetag(t(n_del_frames+1:end) >= phrases.phraseFileStartTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)), ...
% signal(t(n_del_frames+1:end) >= phrases.phraseFileStartTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase))+cnt*mulcnt, ...
% 'LineWidth',2,'Color',[colors(find(syllables == phrases.phraseType(currphrase)),:) opacity_factor]);
% hold on;
%
% plot(timetag(t(n_del_frames+1:end) >= phrases.phraseFileEndTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)+2), ...
% signal(t(n_del_frames+1:end) >= phrases.phraseFileEndTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)+2)+cnt*mulcnt, ...
% 'LineWidth',2,'Color',[0 0 0 0.4],'LineStyle','--');
%
%
%
% %%
% for fnum = 1:numel(FILES)
% fname = FILES{fnum};
% tokens = regexp(fname,'_','split');
% loc = find(locs == str2num(tokens{3}));
% phrases = return_phrase_times(elements{loc});
% if ismember(sylnum,phrases.phraseType)
% load(fname);
% display(fname);
% s = zscore(dff(:,n_del_frames+1:end)')';
% t = vidTimes;
% phrase_locs = find(phrases.phraseType == sylnum);
% for phrase_loc = 1:numel(phrase_locs)
% phrasenum = phrase_locs(phrase_loc);
% tonset = phrases.phraseFileStartTimes(phrasenum);
% toffset = phrases.phraseFileEndTimes(phrasenum);
% for roi_n = 1:numel(ROIs)
% % if (phrasenum < numel(phrases.phraseFileStartTimes))
% % subplot(1,numel(ROIs)+1,roi_n);
% % else
% % subplot(1,numel(ROIs)+1,numel(ROIs)+1);
% % end
% subplot(1,numel(ROIs),roi_n);
% %axes(hs(roi_n));
% signal = smooth(s(ROIs(roi_n),:),3);
% timetag = (t(n_del_frames+1:end)-tonset*locktoonset-(1-locktoonset)*toffset)/((toffset-tonset)*warp+1-warp);
% %signal = (signal-quantile(signal,0.2))/max(signal);
% for currphrase = 1:numel(phrases.phraseType)
% plot(timetag(t(n_del_frames+1:end) >= phrases.phraseFileStartTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)), ...
% signal(t(n_del_frames+1:end) >= phrases.phraseFileStartTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase))+cnt*mulcnt, ...
% 'LineWidth',2,'Color',[colors(find(syllables == phrases.phraseType(currphrase)),:) opacity_factor]);
% hold on;
% end
% plot(timetag(t(n_del_frames+1:end) >= phrases.phraseFileEndTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)+2), ...
% signal(t(n_del_frames+1:end) >= phrases.phraseFileEndTimes(currphrase) & ...
% t(n_del_frames+1:end) <= phrases.phraseFileEndTimes(currphrase)+2)+cnt*mulcnt, ...
% 'LineWidth',2,'Color',[0 0 0 0.4],'LineStyle','--');
% %plot(,signal+cnt*0.0,'LineWidth',2,'Color',[0 0 0 0.3]);
% cnt = cnt+1;
% set(gca,'color','none');
% box off;
% if (roi_n == 1)
% title(['Phrase #' num2str(sylnum) ' locked Ca signals from ' datestr(Day,'yyyy-mm-dd')])
% end
% if (roi_n < numel(ROIs))
% set(gca,'XTick',[]);
% else
% set(gca,'XTick',[0 1]*locktoonset+(1-locktoonset)*[-1 0]);
% end
% set(gca,'YTick',[]);
% ylabel(['ROI# ' num2str(ROIs(roi_n))]);
% if (roi_n == numel(ROIs))
% if warp == 1
% xlabel('Warped Time');
% else
% xlabel('Real Time');
% end
% end
%
% set(gca,'FontSize',16);
% axis tight;
% xlim([-1 3]-(1-locktoonset));
% end
% end
%
% end
% end