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peri_span_vel.m
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% Calculating lateral wave metrics across all movies and different treatments
% INPUT
% Just use the correct file address storing all the motility files upon prompt
% OUTPUT
% Data file storing motility metrics for individual treatment windows
clear all;
% This address has to be changed accorrdingly
path = uigetdir('E:\\Spandan\\New_Analysis\\kymo_files');
files = dir(fullfile(path,'**','*.mat'));
files = struct2cell(files);
names = files(1,:);
for i = 1:length(names)
name = char(names(i));
if string(name(5)) == '9'
j = 1:3;
elseif string(name(5)) == '1' && string(name(6)) == '0'
j = 1:3;
elseif string(name(5)) == '1' && string(name(6)) == '9'
j = 1:3;
elseif string(name(5)) == '2' && string(name(6)) == '1'
j = 1:3;
elseif string(name(5)) == '2' && string(name(6)) == '8'
j = 1:3;
elseif string(name(5)) == '3' && string(name(6)) == '6'
j = 1:3;
elseif string(name(5)) == '1' && string(name(6)) == '4' && string(name(end-4)) == '2'
j = 1:2;
elseif string(name(5)) == '1' && string(name(6)) == '5' && string(name(end-4)) == '2'
j = 1:2;
elseif string(name(5)) == '2' && string(name(6)) == '0' && string(name(end-4)) == '2'
j = 1:2;
elseif string(name(5)) == '2' && string(name(6)) == '2' && string(name(end-4)) == '2'
j = 1:2;
elseif string(name(5)) == '2' && string(name(6)) == '9' && string(name(end-4)) == '2'
j = 1:2;
elseif string(name(5)) == '3' && string(name(6)) == '7' && string(name(end-4)) == '2'
j = 1:2;
else
j = 1;
end
n_ph = length(j);
for k = j(1):j(end)
if name(5) == '6'
re_len = 24.12;
save_name = 'sv_exp'+string(name(5))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '7'
re_len = 24.12;
save_name = 'sv_exp'+string(name(5))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '8'
re_len = 23.51;
save_name = 'sv_exp'+string(name(5))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '9'
re_len = 23.51;
save_name = 'sv_exp'+string(name(5))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '0'
re_len = 24.11;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '1'
re_len = 22.45;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '2'
re_len = 22.45;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '3'
re_len = 22.52;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '4'
re_len = 24.81;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '5'
re_len = 24.81;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '6'
re_len = 24.20;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '7'
re_len = 24.23;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '8'
re_len = 24.50;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '1' && name(6) == '9'
re_len = 24.52;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '0'
re_len = 23.66;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '1'
re_len = 26.22;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '2'
re_len = 24.51;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '3'
re_len = 24.51;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '4'
re_len = 24.51;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '5'
re_len = 24.16;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '6'
re_len = 24.15;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '7'
re_len = 24.15;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '8'
re_len = 20.44;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '2' && name(6) == '9'
re_len = 20.84;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '0'
re_len = 22.30;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '2'
re_len = 21.06;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '3'
re_len = 24.84;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '4'
re_len = 24.06;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '5'
re_len = 24.92;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '6'
re_len = 19.66;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '7'
re_len = 17.78;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '8'
re_len = 25.14;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '3' && name(6) == '9'
re_len = 24.36;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
elseif name(5) == '4' && name(6) == '0'
re_len = 22.35;
save_name = 'sv_exp'+string(name(5))+string(name(6))+'_p'+string(name(end-4))+string(k);
end
filepath = string(path)+'\\'+string(name);
v = load(filepath); % loading data file corresponding to the treatment window
vy2avg = v.vy2avg; %% Motility map of mean vy(dorsal-ventral)-motion as a function of time
clear v;
% The 4 following experiments were imaged from the opposite side in comparison to the usual (hence the posterior and anterior directions are flipped)
if name(5) == '6' || name(5) == '7' || name(5) == '8' || name(5) == '9'
vy2avg = flip(vy2avg,1);
end
perist_new(vy2avg,3,re_len,k,n_ph,100,save_name);
% Fs (frame-rate) = 3Hz. and an area threshold(for identifying wave regions) of 100 pixels have been chosen for analysis.
end
end