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Copy pathJACK_Analyze_Template.m
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JACK_Analyze_Template.m
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function [] = JACK_Analyze_Template(rootdir)
%% Analyze_Template: Reads in all raw trials, transforms data, and saves in organized structure
% INPUTS:
% root : directory where .mat files are located
% OUTPUTS:
% -
%---------------------------------------------------------------------------------------------------------------------------------
% EXAMPLE INPUT %
rootdir = 'E:\Jack\Experiment_Wing_CL_Figure\mat';
%---------------------------------------------------------------------------------------------------------------------------------
%% Setup Directories %%
%---------------------------------------------------------------------------------------------------------------------------------
% Select files
[FILES, PATH] = uigetfile({'*.mat', 'DAQ-files'}, 'Select files', rootdir, 'MultiSelect','on');
FILES = cellstr(FILES)'; % if only one character array >> store in cell
[~,I,N,U] = GetFileData(FILES,false,'Fly','Trial','HGain','WGain');
%% Get Data %%
%---------------------------------------------------------------------------------------------------------------------------------
TIME = cell(N{1,1},1);
HEAD.Pos = cell(N{1,1},1);
WING.Pos = cell(N{1,1},1);
PAT.XPos = cell(N{1,1},1);
PAT.YPos = cell(N{1,1},1);
HEAD.All.Pos = cell(N{1,4},N{1,3});
WING.All.Pos = cell(N{1,4},N{1,3});
PAT.All.XPos = cell(N{1,4},N{1,3});
PAT.All.YPos = cell(N{1,4},N{1,3});
for kk = 1:N{1,1} % fly
for jj = 1:N{1,4} % wing gain
for ii = 1:N{1,3} % head gain
TIME {kk,1}{jj,ii} = [];
HEAD.Pos{kk,1}{jj,ii} = [];
WING.Pos{kk,1}{jj,ii} = [];
PAT.XPos{kk,1}{jj,ii} = [];
PAT.YPos{kk,1}{jj,ii} = [];
end
end
end
fly = [];
FlyState = [];
AI = [];
fly.Fc = 20;
span = 20:1:2000;
for kk = 1:N{1,end} % all trials
filename = fullfile(PATH,FILES{kk}); % full file name
load(filename,'FlyState','AI','VidTime') % load in fly kinematics & arena voltages
vid.time = VidTime;
fly.time = FlyState{:,1};
fly.Ts = mean(diff(fly.time));
fly.Fs = 1/fly.Ts;
[fly.b,fly.a] = butter(2,fly.Fc/(fly.Fs/2),'low'); % 2nd-order low-pass butterworth filter
fly.head.pos = filtfilt(fly.b,fly.a,FlyState{:,2});
fly.wing.pos = filtfilt(fly.b,fly.a,filtfilt(fly.b,fly.a,FlyState{:,3}) - filtfilt(fly.b,fly.a,FlyState{:,4}));
fly.head.vel = [diff(fly.head.pos)./fly.Ts ; 0];
fly.wing.vel = [diff(fly.wing.pos)./fly.Ts ; 0];
pat.time = AI{:,1};
pat.Ts = mean(diff(pat.time));
pat.Fs = 1/pat.Ts;
pat.Fc = 30;
[pat.b,pat.a] = butter(2,pat.Fc/(pat.Fs/2),'low'); % 2nd-order low-pass butterworth filter
pat.xpos = filtfilt(pat.b,pat.a,AI{:,2});
pat.xpos = 3.75*(round((AI{:,2})*(96/4.9)));
% pat.xpos = FitPanel(pat.xpos,pat.time,vid.time,false,false); % true does debugging, false does not
% pat.xpos = medfilt1(pat.xpos,5);
% pat.xpos = rad2deg(wrapToPi(deg2rad(pat.xpos)));
pat.xpos = pat.xpos/3.75 - 90;
pat.xpos(pat.xpos<((96/2)-96)) = pat.xpos(pat.xpos<((96/2)-96)) + (96);
pat.xpos = pat.xpos * 3.75;
pat.ypos = (round((AI{:,3})*(96/5)));
fly.time = vid.time (span);
fly.head.pos = fly.head.pos (span);
fly.wing.pos = fly.wing.pos (span);
fly.head.vel = fly.head.vel (span);
fly.wing.vel = fly.wing.vel (span);
pat.xpos = pat.xpos (span);
pat.ypos = pat.ypos (span);
TIME {I{kk,1}}{I{kk,4},I{kk,3}}(:,end+1) = fly.time;
HEAD.Pos {I{kk,1}}{I{kk,4},I{kk,3}}(:,end+1) = fly.head.pos;
WING.Pos {I{kk,1}}{I{kk,4},I{kk,3}}(:,end+1) = fly.wing.pos;
PAT.XPos {I{kk,1}}{I{kk,4},I{kk,3}}(:,end+1) = pat.xpos ;
PAT.YPos {I{kk,1}}{I{kk,4},I{kk,3}}(:,end+1) = pat.ypos;
HEAD.All.Pos {I{kk,4},I{kk,3}}(:,end+1) = fly.head.pos;
WING.All.Pos {I{kk,4},I{kk,3}}(:,end+1) = fly.wing.pos;
PAT.All.XPos {I{kk,4},I{kk,3}}(:,end+1) = pat.xpos;
PAT.All.YPos {I{kk,4},I{kk,3}}(:,end+1) = pat.ypos;
end
%% Plot pattern position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (100) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Head Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
xlim([0 20])
ylim([1 96])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel({['Head Gain = ' num2str(U{1,3}{1}(ii))],['Pattern Position(' char(176) ')']},...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel('Time (s)','FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
time = TIME{kk}{jj,ii};
pos = (PAT.XPos{kk}{jj,ii});
plot(time,pos)
pp = pp + 1;
end
end
end
%% Plot head position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (1) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Head Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
xlim([0 20])
ylim(20*[-1 1])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel({['Head Gain = ' num2str(U{1,3}{1}(ii))],['Head Position(' char(176) ')']},...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel('Time (s)','FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
time = TIME{kk}{jj,ii};
pos = rad2deg(HEAD.Pos{kk}{jj,ii});
plot(time,pos)
pp = pp + 1;
end
end
end
%% Plot wing position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (2) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Wing Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
xlim([0 20])
ylim(40*[-1 1])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel({['Head Gain = ' num2str(U{1,3}{1}(ii))],['\Delta WBA(' char(176) ')']},...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel('Time (s)','FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
time = TIME{kk}{jj,ii};
pos = rad2deg(WING.Pos{kk}{jj,ii});
plot(time,pos)
pp = pp + 1;
end
end
end
%% Histogram of Pattern Position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (3) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Pattern Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector = 1:96;
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
%xlim([0 20])
%ylim(120*[-1 1])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel('Pattern Position','FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = (PAT.XPos{kk}{jj,ii});
histogram(pos,1:96);
pp = pp + 1;
end
end
end
%% Histogram of HEAD Position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (4) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Head Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector1 = -20:1:20;
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
ylim([0 3500])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel(['Head Angle (' char(176) ')'],'FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = rad2deg(HEAD.Pos{kk}{jj,ii});
histogram(pos,vector1);
pp = pp + 1;
end
end
end
%% Histogram of WING Position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (5) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Wing Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector1 = -35:1:35;
for kk = 1:N{1,1}
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
ylim([0 1500])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel(['\Delta WBA(' char(176) ')'],'FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = rad2deg(WING.Pos{kk}{jj,ii});
histogram(pos,vector1);
pp = pp + 1;
end
end
end
%% Histogram of Head Position ALL FLIES %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (6) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Head Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector = -20:1:20;
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
% xlim([0 20])
ylim([0 12000])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel(['Head Angle (' char(176) ')'],'FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = rad2deg(HEAD.All.Pos{jj,ii});
histogram(pos,vector,'facecolor','k');
pp = pp + 1;
end
end
%% Histogram of Pattern Position ALL FLIES %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (7) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Pattern Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector = 3.75*(-96/2:1:96/2);
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
%xlim([0 20])
ylim([0 4000])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel(['Pattern Position (' char(176) ')'],'FontSize',12,'fontweight','bold')
else
xticklabels('')
end
pos = (PAT.All.XPos{jj,ii});
histogram(pos,vector,'facecolor','k');
pp = pp + 1;
end
end
%% Histogram of Wing Position ALL FLIES %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (8) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Wing Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector = -70:1:70;
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
%xlim([0 20])
ylim([0 6000])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel(['Head Gain = ' num2str(U{1,3}{1}(ii))],...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel(['\Delta WBA(' char(176) ')'],'FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = rad2deg(WING.All.Pos{jj,ii});
histogram(pos,vector,'facecolor','k');
pp = pp + 1;
end
end
%% Box Plot of Head Position %%
%---------------------------------------------------------------------------------------------------------------------------------
figure (9) ; clf ; hold on
set(gcf,'Color','w')
set(gcf,'Name','Histogram of Head Position')
set(gcf,'Position',[0 0 N{1,4}*400 N{1,3}*400])
movegui(gcf,'center')
vector = -20:1:20;
pp = 1;
for jj = 1:N{1,4}
for ii = 1:N{1,3}
subplot(N{1,3},N{1,4},pp) ; hold on
%xlim([0 20])
%ylim(120*[-1 1])
if any(pp==(1:N{1,4}))
title(['Wing Gain = ' num2str(U{1,4}{1}(jj))],'FontSize',12,'fontweight','bold')
end
if ((pp-1)/N{1,4}) == floor((pp-1)/N{1,4})
ylabel({['Head Gain = ' num2str(U{1,3}{1}(ii))],['Head Position(' char(176) ')']},...
'FontSize',13,'fontweight','bold')
else
yticks(0)
yticklabels('')
end
if any(pp==(N{1,4}*N{1,3}-N{1,4}+1):(N{1,4}*N{1,3}))
xlabel('Pattern Position','FontSize',12,'fontweight','bold')
else
xticks(0)
xticklabels('')
end
pos = rad2deg(HEAD.All.Pos{jj,ii});
histogram(pos,vector,'facecolor','k');
pp = pp + 1;
end
end
%% Box Plot of Wing Position
%% Box Plot of Pattern Position
end