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rhythm_dualMod.m
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rhythm_dualMod.m
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function rhythm
% % close all; clc;
%% RHYTHM (01/27/2012)
% Matlab software for analyzing optical mapping data
%
% By Matt Sulkin, Jake Laughner, Xinyuan Sophia Cui, Jed Jackoway
% Washington University in St. Louis -- Efimov Lab
%
% Currently maintained by: Christopher Gloschat [Jan. 2015 - Present]
%
% For any questions and suggestions, please email us at:
%
% Modification Log:
% Jan. 23, 2015 - 1) Size of tools adjusted for MATLAB 2014a to constrain
% all tools and labels to their groups. Mostly cosmetic adjustment. 2) I
% built in fail safes to prevent the GUI from doing undesired things. For
% example, if cancel was selected after clicking get directory it set the
% directory to root. Now it will only set the directory if a directory is
% set.
%
% Jan. 26, 2015 - The invert_cmap function was added to facilitate the
% inversion of the default colormap used for maps of activation time and
% action potential duration.
%
% Feb. 9, 2015 - With the MATLAB2014b release multiple commands in the
% visualization toolkit were changed. Among these were the video writer
% commands and the command for tracking mouse clicks on the GUI. These
% commands have been updated and RHYTHM should now be functional on 2014b.
%
% Feb. 24, 2016 - The GUI has been streamlined to reduce clutter and create
% a space for plugins created by future users.
%
%
%% Create GUI structure
scrn_size = get(0,'ScreenSize');
f = figure('Name','RHYTHM','Visible','off','Position',[scrn_size(3),scrn_size(4),1250,730],'NumberTitle','Off');
% set(f,'Visible','off')
% Load Data
p1 = uipanel('Title','Display Data','FontSize',12,'Position',[.01 .01 .98 .98]);
filelist = uicontrol('Parent',p1,'Style','listbox','String','Files','Position',[10 240 150 450],'Callback',{@filelist_callback});
selectdir = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Select Directory','Position',[10 205 150 30],'Callback',{@selectdir_callback});
loadfile = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Load','Position',[10 175 150 30],'Callback',{@loadfile_callback});
refreshdir = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Refresh Directory','Position',[10 145 150 30],'Callback',{@refreshdir_callback});
% Movie Screen for Optical Data
movie_scrn = axes('Parent',p1,'Units','Pixels','YTick',[],'XTick',[],'Position',[170, 190, 500,500]);
% Movie Slider for Controling Current Frame
movie_slider = uicontrol('Parent',f, 'Style', 'slider','Position', [183, 180, 502, 20],'SliderStep',[.001 .01],'Callback',{@movieslider_callback});
addlistener(movie_slider,'ContinuousValueChange',@movieslider_callback);
% Mouse Listening Function
set(f,'WindowButtonDownFcn',{@button_down_function});
set(f,'WindowButtonUpFcn',{@button_up_function});
set(f,'WindowButtonMotionFcn',{@button_motion_function});
% Signal Display Screens for Optical Action Potentials
signal_scrn1 = axes('Parent',p1,'Units','Pixels','Color','w','XTick',[],'Position',[710,572,498,120]);
signal_scrn2 = axes('Parent',p1,'Units','Pixels','Color','w','XTick',[],'Position',[710,444,498,120]);
signal_scrn3 = axes('Parent',p1,'Units','Pixels','Color','w','XTick',[],'Position',[710,316,498,120]);
signal_scrn4 = axes('Parent',p1,'Units','Pixels','Color','w','XTick',[],'Position',[710,188,498,120]);
signal_scrn5 = axes('Parent',p1,'Units','Pixels','Color','w','Position',[710,60,498,120]);
xlabel('Time (sec)');
expwave_button = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Export OAPs','Position',[1115 1 100 30],'Callback',{@expwave_button_callback});
starttimesig_text = uicontrol('Parent',p1,'Style','text','FontSize',12,'String','Start Time','Position',[830 9 55 15]);
starttimesig_edit = uicontrol('Parent',p1,'Style','edit','FontSize',14,'Position',[890 5 55 23],'Callback',{@starttimesig_edit_callback});
endtimesig_text = uicontrol('Parent',p1,'Style','text','FontSize',12,'String','End Time','Position',[965 9 52 15]);
endtimesig_edit = uicontrol('Parent',p1,'Style','edit','FontSize',14,'Position',[1022 5 55 23],'Callback',{@endtimesig_edit_callback});
% Sweep Bar Display for Optical Action Potentials
sweep_bar = axes ('Parent',p1,'Units','Pixels','Layer','top','Position',[710,55,500,735]);
set(sweep_bar,'NextPlot','replacechildren','Visible','off')
% Video Control Buttons and Optical Action Potential Display
play_button = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Play Movie','Position',[215 141 100 30],'Callback',{@play_button_callback});
stop_button = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Stop Movie','Position',[315 141 100 30],'Callback',{@stop_button_callback});
dispwave_button = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Display Wave','Position',[415 141 100 30],'Callback',{@dispwave_button_callback});
expmov_button = uicontrol('Parent',p1,'Style','pushbutton','FontSize',12,'String','Export Movie','Position',[515 141 100 30],'Callback',{@expmov_button_callback});
% Signal Conditioning Button Group and Buttons
cond_sig = uibuttongroup('Parent',p1,'Title','Condition Signals','FontSize',12,'Position',[0.01 0.015 .255 .18]);
removeBG_button = uicontrol('Parent',cond_sig,'Style','checkbox','FontSize',12,'String','Remove Background','Position',[5 92 150 25]);
bg_thresh_label = uicontrol('Parent',cond_sig,'Style','text','FontSize',12,'String','BG Threshold','Position',[32 67 77 25]);
perc_ex_label = uicontrol('Parent',cond_sig,'Style','text','FontSize',12,'String','EX Threshold','Position',[33 47 76 25]);
bg_thresh_edit = uicontrol('Parent',cond_sig,'Style','edit','FontSize',12,'String','0.3','Position',[112 75 35 18]);
perc_ex_edit = uicontrol('Parent',cond_sig,'Style','edit','FontSize',12,'String','0.5','Position',[112 55 35 18]);
bin_button = uicontrol('Parent',cond_sig,'Style','checkbox','FontSize',12,'String','Bin','Position',[160 92 150 25]);
filt_button = uicontrol('Parent',cond_sig,'Style','checkbox','FontSize',12,'String','Filter','Position',[160 64 150 25]);
removeDrift_button = uicontrol('Parent',cond_sig,'Style','checkbox','FontSize',12,'String','Drift','Position',[160 36 150 25]);
norm_button = uicontrol('Parent',cond_sig,'Style','checkbox','FontSize',12,'String','Normalize','Position',[5 36 125 15]);
apply_button = uicontrol('Parent',cond_sig,'Style','pushbutton','FontSize',12,'String','Apply','Position',[3 2 150 30],'Callback',{@cond_sig_selcbk});
%Pop-up menu options
bin_popup = uicontrol('Parent',cond_sig,'Style','popupmenu','FontSize',12,'String',{'3 x 3', '5 x 5', '7 x 7'},'Position',[234 88 75 25]);
filt_popup = uicontrol('Parent',cond_sig,'Style','popupmenu','FontSize',12,'String',{'[0 50]','[0 75]', '[0 100]', '[0 150]'},'Position',[219 61 90 25]);
drift_popup = uicontrol('Parent',cond_sig,'Style','popupmenu','FontSize',12,'String',{'1st Order','2nd Order', '3rd Order', '4th Order'},'Position',[210 34 99 25]);
export_button = uicontrol('Parent',cond_sig,'Style','pushbutton','FontSize',12,'String','Export Data','Position',[160 2 145 30],'Callback',{@export_callback});
set(filt_popup,'Value',3)
% Optical Action Potential Analysis Button Group and Buttons
% Create Button Group
anal_data = uibuttongroup('Parent',p1,'Title','Analyze Data','FontSize',12,'Position',[0.275 0.015 .150 .180]);
anal_select = uicontrol('Parent',anal_data,'Style','popupmenu','FontSize',12,'String',{'-----','Activation','Conduction','APD','Phase','Dominant Frequency'},'Position',[5 85 165 25],'Callback',{@anal_select_callback});
sig_noise = uicontrol('Parent', anal_data,'Style','pushbutton','FontSize',12,'String','Calculate SNR', 'Position',[5 50 165 25],'Callback',{@sig2noise});
% Invert Color Map Option
invert_cmap = uicontrol('Parent',anal_data,'Style','checkbox','FontSize',12,'String','Invert Colormaps','Position',[175 88 150 25],'Visible','on','Callback',{@invert_cmap_callback});
% Mapping buttons
starttimemap_text = uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','Start Time','Position',[12 57 57 25],'Visible','on');
starttimemap_edit = uicontrol('Parent',anal_data,'Style','edit','FontSize',14,'Position',[72 62 45 22],'Visible','on','Callback',{@maptime_edit_callback});
endtimemap_text = uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','End Time','Position',[12 30 54 25],'Visible','on');
endtimemap_edit = uicontrol('Parent',anal_data,'Style','edit','FontSize',14,'Position',[72 35 45 22],'Visible','on','Callback',{@maptime_edit_callback});
createmap_button = uicontrol('Parent',anal_data,'Style','pushbutton','FontSize',12,'String','Calculate Map','Position',[10 2 110 30],'Visible','on','Callback',{@createmap_button_callback});
% APD specific buttons
minapd_text = uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','Min APD','Visible','on','Position',[125 57 57 25]);
minapd_edit = uicontrol('Parent',anal_data,'Style','edit','FontSize',12,'String','0','Visible','on','Position',[180 62 45 22],'Callback',{@minapd_edit_callback});
maxapd_text = uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','Max APD','Visible','on','Position',[125 30 54 25]);
maxapd_edit = uicontrol('Parent',anal_data,'Style','edit','FontSize',12,'String','1000','Visible','on','Position',[180 35 45 22],'Callback',{@maxapd_edit_callback});
percentapd_text= uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','%APD','Visible','on','Position',[230 57 45 25]);
percentapd_edit= uicontrol('Parent',anal_data,'Style','edit','FontSize',12,'String','0.8','Visible','on','Position',[275 62 45 22],'callback',{@percentapd_edit_callback});
remove_motion_click = uicontrol('Parent',anal_data,'Style','checkbox','FontSize',12,'String','Remove','Visible','on','Position',[230 35 100 25]);
remove_motion_click_txt = uicontrol('Parent',anal_data,'Style','text','FontSize',12,'String','Motion','Visible','on','Position',[248 15 50 25]);
calc_apd_button = uicontrol('Parent',anal_data,'Style','pushbutton','FontSize',12,'String','Regional APD','Position',[125 2 103 30],'Callback',{@calc_apd_button_callback});
% Check boxes to allow choice of voltage plot, Ca plot, or both
plot_choice = uibuttongroup('Parent',p1,'Title','Plot Choice','FontSize',12,'Position',[0.435 0.038 .100 .160]);
volt_choice = uicontrol('Parent',plot_choice,'Style','checkbox','FontSize',12,'String','Plot Voltage','Position',[5 60 165 25],'Callback',@checkbox_volt);
set(volt_choice, 'Value', 1);
cal_choice = uicontrol('Parent',plot_choice,'Style','checkbox','FontSize',12,'String','Plot Calcium','Position',[5 30 165 25],'Callback',@checkbox_cal);
set(cal_choice, 'Value', 1);
% Allow all GUI structures to be scaled when window is dragged
set([f,p1,filelist,selectdir,refreshdir,loadfile,movie_scrn,movie_slider, signal_scrn1,signal_scrn2,signal_scrn3,...
signal_scrn4,signal_scrn5,sweep_bar,play_button,stop_button,dispwave_button,expmov_button,cond_sig,removeBG_button,...
bg_thresh_label,perc_ex_label,bg_thresh_edit,perc_ex_edit,bin_button,filt_button,removeDrift_button,norm_button,...
apply_button,bin_popup,filt_popup,drift_popup,export_button,anal_data,anal_select,invert_cmap,starttimemap_text,...
starttimemap_edit,endtimemap_text,endtimemap_edit,createmap_button,minapd_text,minapd_edit,maxapd_text,maxapd_edit,...
percentapd_text,percentapd_edit,remove_motion_click,remove_motion_click_txt,calc_apd_button,expwave_button,...
starttimesig_text,starttimesig_edit,sig_noise,endtimesig_text,endtimesig_edit],'Units','normalized')
% Disable buttons that will not be needed until data is loaded
set([removeBG_button,bg_thresh_edit,bg_thresh_label,perc_ex_edit,perc_ex_label,bin_button,filt_button,removeDrift_button,norm_button,...
apply_button,bin_popup,filt_popup,drift_popup,anal_select,starttimemap_edit,starttimemap_text,endtimemap_edit,endtimemap_text,...
createmap_button,minapd_edit,minapd_text,maxapd_edit,maxapd_text,percentapd_edit,percentapd_text,remove_motion_click,remove_motion_click_txt,...
calc_apd_button,play_button,stop_button,dispwave_button,expmov_button,starttimesig_edit,endtimesig_edit,expwave_button,loadfile,...
refreshdir,invert_cmap,export_button,volt_choice,cal_choice,sig_noise],'Enable','off')
% Hide all analysis buttons
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,createmap_button,minapd_text,minapd_edit,maxapd_text,...
maxapd_edit,percentapd_text,percentapd_edit,remove_motion_click,...
calc_apd_button,remove_motion_click_txt],'Visible','off')
% %
% Center GUI on screen
movegui(f,'center')
set(f,'Visible','on')
%% Create handles
handles.filename = [];
handles.cmosData = [];
handles.rawData = [];
handles.time = [];
handles.wave_window = 1;
handles.normflag = 0;
handles.Fs = 1000; % this is the default value. it will be overwritten
handles.starttime = 0;
handles.fileLength = 1;
handles.endtime = 1;
handles.grabbed = -1;
handles.M = []; % this handle stores the locations of the markers
handles.slide=-1; % parameter for recognize clicking location
%%minimum values pixels require to be drawn
handles.minVisible = 6;
handles.normalizeMinVisible = .3;
handles.cmap = colormap('jet'); %saves the default colormap values
handles.apdC = []; % variable for storing apd calculations
%% All Callback functions
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% USER FUNCTIONALITY
%% Listen for mouse clicks for the point-dragger
% When mouse button is clicked and held find associated marker
function button_down_function(obj,~)
set(obj,'CurrentAxes',movie_scrn)
ps = get(gca,'CurrentPoint');
i_temp = round(ps(1,1));
j_temp = round(ps(2,2));
% if one of the markers on the movie screen is clicked
if i_temp<=size(handles.cmosData,1) || j_temp<size(handles.cmosData,2) || i_temp>1 || j_temp>1
if size(handles.M,1) > 0
for i=1:size(handles.M,1)
if i_temp == handles.M(i,1) && handles.M(i,2) == j_temp
handles.grabbed = i;
break
end
end
end
end
end
%% When mouse button is released
function button_up_function(~,~)
handles.grabbed = -1;
end
%% Update appropriate screens or slider when mouse is moved
function button_motion_function(obj,~)
% Update movie screen marker location
if handles.grabbed > -1
set(obj,'CurrentAxes',movie_scrn)
ps = get(gca,'CurrentPoint');
i_temp = round(ps(1,1));
j_temp = round(ps(2,2));
if i_temp<=size(handles.cmosData,1) && j_temp<=size(handles.cmosData,2) && i_temp>1 && j_temp>1
handles.M(handles.grabbed,:) = [i_temp j_temp];
i = i_temp;
j = j_temp;
switch handles.grabbed
case 1
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'b','LineWidth',2,'Parent',signal_scrn1)
handles.M(1,:) = [i j];
case 2
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'g','LineWidth',2,'Parent',signal_scrn2)
handles.M(2,:) = [i j];
case 3
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'m','LineWidth',2,'Parent',signal_scrn3)
handles.M(3,:) = [i j];
case 4
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'k','LineWidth',2,'Parent',signal_scrn4)
handles.M(4,:) = [i j];
case 5
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'c','LineWidth',2,'Parent',signal_scrn5)
handles.M(5,:) = [i j];
end
cla
currentframe = handles.frame;
drawFrame(currentframe);
M = handles.M; colax='bgmkc'; [a,~]=size(M);
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn);
set(movie_scrn,'YTick',[],'XTick',[]);% Hide tick markes
end
hold off
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% LOAD DATA
%% List that contains all files in directory
function filelist_callback(source,~)
str = get(source, 'String');
val = get(source,'Value');
file = char(str(val));
handles.filename = file;
end
%% Load selected files in filelist
function loadfile_callback(~,~)
if isempty(handles.filename)
msgbox('Warning: No data selected','Title','warn')
else
% Clear off all images from previous set of data
cla(movie_scrn); cla(signal_scrn1); cla(signal_scrn2); cla(signal_scrn3)
cla(signal_scrn4); cla(signal_scrn5); cla(sweep_bar)
% Initialize handles
handles.M = []; % this handle stores the locations of the markers
handles.normflag = 0;% this handle indicate if normalize is clicked
handles.wave_window = 1;% this handle indicate the window number of the next wave displayed
handles.frame = 1;% this handles indicate the current frame being displayed by the movie screen
handles.slide=-1;% this handle indicate if the movie slider is clicked
% Check for *.mat file, if none convert
filename = [handles.dir,'/',handles.filename];
% Check for existence of already converted *.mat file
if ~exist([filename(1:end-3),'mat'],'file')
% Convert data and save out *.mat file
CMOSconverter(handles.dir,handles.filename);
end
% Load data from *.mat file
Data = load([filename(1:end-3),'mat']);
% Check for dual camera data
if isfield(Data,'cmosData2')
handles.cmosData = double(Data.cmosData(:,:,2:end));
handles.cmosData2 = double(Data.cmosData2(:,:,2:end));
handles.bg = double(Data.bgimage);
handles.bg2 = double(Data.bgimage2);
else
% Load from single camera
handles.cmosData = double(Data.cmosData(:,:,2:end));
handles.bg = double(Data.bgimage);
% Save out pacing spike
handles.ecg = Data.channel{1}(2:end)*-1;
% Save out frequency
handles.Fs = double(Data.frequency);
end
% Save out the frequency, cameras alternate, divide by 2
handles.Fs = double(Data.frequency);
% Save out pacing spike. Note: Data.channel1 is not
% necessarily the ecg channel. Correspondes to analog1
% input to SciMedia box
handles.ecg = Data.channel{1}(1:size(Data.channel{1},2)/2)*-1;
% Save a variable to preserve the raw cmos data
handles.cmosRawData = handles.cmosData;
% Convert background to grayscale
handles.bgRGB = real2rgb(handles.bg, 'gray');
%%%%%%%%% WINDOWED DATA %%%%%%%%%%
handles.matrixMax = .9 * max(handles.cmosData(:));
% Initialize movie screen to the first frame
set(f,'CurrentAxes',movie_scrn)
G = real2rgb(handles.bg, 'gray');
Mframe = handles.cmosData(:,:,handles.frame);
J = real2rgb(Mframe, 'jet');
A = real2rgb(Mframe >= handles.minVisible, 'gray');
I = J .* A + G .* (1-A);
handles.movie_img = image(I,'Parent',movie_scrn);
set(movie_scrn,'NextPlot','replacechildren','YTick',[],'XTick',[])
% Scale signal screens and sweep bar to appropriate time scale
timeStep = 1/handles.Fs;
handles.time = 0:timeStep:size(handles.cmosData,3)*timeStep-timeStep;
set(signal_scrn1,'XLim',[min(handles.time) max(handles.time)])
set(signal_scrn1,'NextPlot','replacechildren')
set(signal_scrn2,'XLim',[min(handles.time) max(handles.time)])
set(signal_scrn2,'NextPlot','replacechildren')
set(signal_scrn3,'XLim',[min(handles.time) max(handles.time)])
set(signal_scrn3,'NextPlot','replacechildren')
set(signal_scrn4,'XLim',[min(handles.time) max(handles.time)])
set(signal_scrn4,'NextPlot','replacechildren')
set(signal_scrn5,'XLim',[min(handles.time) max(handles.time)])
set(signal_scrn5,'NextPlot','replacechildren')
set(sweep_bar,'XLim',[min(handles.time) max(handles.time)])
set(sweep_bar,'NextPlot','replacechildren')
% Fill times into activation map editable textboxes
handles.starttime = 0;
handles.endtime = max(handles.time);
set(starttimesig_edit,'String',num2str(handles.starttime))
set(endtimesig_edit,'String',num2str(handles.endtime))
set(starttimemap_edit,'String',num2str(handles.starttime))
set(endtimemap_edit,'String',num2str(handles.endtime))
% Initialize movie slider to the first frame
set(movie_slider,'Value',0)
drawFrame(1);
% Enable signal processing and analysis tools
set([removeBG_button,bg_thresh_edit,bg_thresh_label,perc_ex_edit,...
perc_ex_label,bin_button,filt_button,removeDrift_button,norm_button,...
apply_button,bin_popup,filt_popup,drift_popup,play_button,anal_select,...
stop_button,dispwave_button,expmov_button,starttimesig_edit,...
endtimesig_edit,expwave_button,export_button,volt_choice,cal_choice,sig_noise],'Enable','on')
end
end
%% Select directory for optical files
function selectdir_callback(~,~)
dir_name = uigetdir;
if dir_name ~= 0
handles.dir = dir_name;
search_name = [dir_name,'/*.rsh'];
search_nameNew = [dir_name,'/*.gsh'];
files = struct2cell(dir(search_name));
filesNew = struct2cell(dir(search_nameNew));
handles.file_list = [files(1,:)'; filesNew(1,:)'];
set(filelist,'String',handles.file_list)
handles.filename = char(handles.file_list(1));
% enable the refresh directory and load file buttons
set([loadfile,refreshdir],'Enable','on')
% reset analysis window
set(anal_select,'Value',1)
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,createmap_button,minapd_text,minapd_edit,maxapd_text,...
maxapd_edit,percentapd_text,percentapd_edit,remove_motion_click,...
remove_motion_click_txt],'Visible','off','Enable','on')
% turn off all other buttons
set([removeBG_button,bg_thresh_edit,bg_thresh_label,perc_ex_edit,...
perc_ex_label,bin_button,filt_button,removeDrift_button,norm_button,...
apply_button,bin_popup,filt_popup,drift_popup,anal_select,...
starttimemap_edit,starttimemap_text,endtimemap_edit,endtimemap_text,...
createmap_button,minapd_edit,minapd_text,maxapd_edit,maxapd_text,...
percentapd_edit,percentapd_text,remove_motion_click,remove_motion_click_txt,...
play_button,stop_button,dispwave_button,expmov_button,starttimesig_edit,...
endtimesig_edit,expwave_button,invert_cmap,export_button],'Enable','off')
end
end
%% Refresh file list (in case more files are open after directory is selected)
function refreshdir_callback(~,~)
dir_name = handles.dir;
search_name = [dir_name,'/*.rsh'];
search_nameNew = [dir_name,'/*.gsh'];
files = struct2cell(dir(search_name));
filesNew = struct2cell(dir(search_nameNew));
handles.file_list = [files(1,:)'; filesNew(1,:)'];
set(filelist,'String',handles.file_list)
handles.filename = char(handles.file_list(1));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% MOVIE SCREEN
%% Movie Slider Functionality
function movieslider_callback(source,~)
val = get(source,'Value');
i = round(val*size(handles.cmosData,3))+1;
handles.frame = i;
if handles.frame == size(handles.cmosData,3) + 1
i = size(handles.cmosData,3);
handles.frame = size(handles.cmosData,3);
end
% Update movie screen
set(movie_scrn,'NextPlot','replacechildren','YTick',[],'XTick',[]);
set(f,'CurrentAxes',movie_scrn)
drawFrame(i);
% Update markers on movie screen
M = handles.M; colax='bgmkc'; [a,~]=size(M);
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn);
set(movie_scrn,'YTick',[],'XTick',[]);% Hide tick markes
end
hold off
% Update sweep bar
set(f,'CurrentAxes',sweep_bar)
a = [handles.time(i) handles.time(i)];b = [0 1]; cla
plot(a,b,'r','Parent',sweep_bar)
axis([handles.starttime handles.endtime 0 1])
hold off; axis off
end
%% Draw
function drawFrame(frame)
G = handles.bgRGB;
Mframe = handles.cmosData(:,:,frame);
if handles.normflag == 0
Mmax = handles.matrixMax;
Mmin = handles.minVisible;
numcol = size(jet,1);
J = ind2rgb(round((Mframe - Mmin) ./ (Mmax - Mmin) * (numcol - 1)), 'jet');
A = real2rgb(Mframe >= handles.minVisible, 'gray');
else
J = real2rgb(Mframe, 'jet');
A = real2rgb(Mframe >= handles.normalizeMinVisible, 'gray');
end
I = J .* A + G .* (1 - A);
image(I,'Parent',movie_scrn);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% DISPLAY CONTROL
%% Play button functionality
function play_button_callback(~,~)
if isempty(handles.cmosData)
msgbox('Warning: No data selected','Title','warn')
else
handles.playback = 1; % if the PLAY button is clicked
startframe = handles.frame;
% Update movie screen with new frames
for i = startframe:5:size(handles.cmosData,3)
if handles.playback == 1 % recheck if the PLAY button is clicked
set(movie_scrn,'NextPlot','replacechildren','YTick',[],'XTick',[]);
set(f,'CurrentAxes',movie_scrn)
drawFrame(i);
handles.frame = i;
% Update markers with each frame
M = handles.M;[a,~]=size(M); colax='bgmkc';
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn)
end
pause(0.01)
% Update movie slider
set(movie_slider,'Value',(i-1)/size(handles.cmosData,3))
% Update sweep bar
set(f,'CurrentAxes',sweep_bar)
a = [handles.time(i) handles.time(i)];b = [0 1]; cla
plot(a,b,'r','Parent',sweep_bar)
axis([handles.starttime handles.endtime 0 1])
hold off; axis off
pause(0.01); pause(0.01)
else
break
end
end
handles.frame = min(handles.frame, size(handles.cmosData, 3));
set(movie_scrn,'NextPlot','replacechildren','YTick',[],'XTick',[]);
set(f,'CurrentAxes',movie_scrn)
drawFrame(i);
handles.frame = i;
% Update makers with each frame
M = handles.M;[a,~]=size(M); colax='bgmkc';
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn)
end
pause(0.01)
% Update movie slider
set(movie_slider,'Value',(i-1)/size(handles.cmosData,3))
% Update sweep bar
set(f,'CurrentAxes',sweep_bar)
a = [handles.time(i) handles.time(i)];b = [0 1]; cla
plot(a,b,'r','Parent',sweep_bar)
axis([handles.starttime handles.endtime 0 1])
hold off; axis off
end
end
%% Stop button functionality
function stop_button_callback(~,~)
handles.playback = 0;
end
%% Display Wave Button Functionality
function dispwave_button_callback(~,~)
set(f,'CurrentAxes',movie_scrn)
[i_temp,j_temp] = myginput(1,'circle');
i = round(i_temp); j = round(j_temp);
%make sure pixel selected is within movie_scrn
if i_temp>size(handles.cmosData,1) || j_temp>size(handles.cmosData,2) || i_temp<=1 || j_temp<=1
% tell user to pick new pixel
msgbox('Warning: Pixel Selection out of Boundary','Title','help')
else
check = 1;
end
if check == 1;
% Find the correct wave window
if handles.wave_window == 6
handles.wave_window = 1;
end
wave_window = handles.wave_window;
switch wave_window
case 1
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'b','LineWidth',2,'Parent',signal_scrn1)
hold on
plot(handles.time,squeeze(handles.cmosData2(j,i,:)),'b','LineWidth',2,'Parent',signal_scrn1)
handles.M(1,:) = [i j];
hold off
case 2
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'g','LineWidth',2,'Parent',signal_scrn2)
hold on
plot(handles.time,squeeze(handles.cmosData2(j,i,:)),'g','LineWidth',2,'Parent',signal_scrn2)
handles.M(2,:) = [i j];
hold off
case 3
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'m','LineWidth',2,'Parent',signal_scrn3)
hold on
plot(handles.time,squeeze(handles.cmosData2(j,i,:)),'m','LineWidth',2,'Parent',signal_scrn3)
handles.M(3,:) = [i j];
hold off
case 4
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'k','LineWidth',2,'Parent',signal_scrn4)
hold on
plot(handles.time,squeeze(handles.cmosData2(j,i,:)),'k','LineWidth',2,'Parent',signal_scrn4)
handles.M(4,:) = [i j];
hold off
case 5
plot(handles.time,squeeze(handles.cmosData(j,i,:)),'c','LineWidth',2,'Parent',signal_scrn5)
hold on
plot(handles.time,squeeze(handles.cmosData2(j,i,:)),'c','LineWidth',2,'Parent',signal_scrn5)
handles.M(5,:) = [i j];
hold off
end
end
handles.wave_window = wave_window + 1; % Dial up the wave window count
% Update movie screen with new markers
cla
currentframe = handles.frame;
drawFrame(currentframe);
M = handles.M; colax='bgmkc'; [a,~]=size(M);
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn);
set(movie_scrn,'YTick',[],'XTick',[]);% Hide tick markes
end
hold off
end
%% Export movie to .avi file
%Construct a VideoWriter object and view its properties. Set the frame rate to 60 frames per second:
function expmov_button_callback(~,~)
% Save the movie to the same directory as the cmos data
% Request the directory for saving the file
dir = uigetdir;
% If the cancel button is selected cancel the function
if dir == 0
return
end
% Request the desired name for the movie file
filename = inputdlg('Enter Filename:');
filename = char(filename);
% Check to make sure a value was entered
if isempty(filename)
error = 'A filename must be entered! Function cancelled.';
msgbox(error,'Incorrect Input','Error');
return
end
filename = char(filename);
% Create path to file
movname = [handles.dir,'/',filename,'.avi'];
% Create the figure to be filmed
fig=figure('Name',filename,'NextPlot','replacechildren','NumberTitle','off',...
'Visible','off','OuterPosition',[170, 140, 556,715]);
% Start writing the video
vidObj = VideoWriter(movname,'Motion JPEG AVI');
open(vidObj);
movegui(fig,'center')
set(fig,'Visible','on')
axis tight
set(gca,'nextplot','replacechildren');
% Designate the step of based on the frequency
% Creat pop up screen; the start time and end time are determined
% by the windowing of the signals on the Rhythm GUI interface
% Grab start and stop time times and convert to index values by
% multiplying by frequency, add one to shift from zero
start = str2double(get(starttimesig_edit,'String'))*handles.Fs+1;
fin = str2double(get(endtimesig_edit,'String'))*handles.Fs+1;
% Designate the resolution of the video: ex. 5 = every fifth frame
step = 5;
for i = start:step:fin
% Plot sweep bar on bottom subplot
subplot('Position',[0.05, 0.1, 0.9,0.15])
a = [handles.time(i) handles.time(i)];
b = [min(handles.ecg) max(handles.ecg)];
cla
plot(a,b,'r','LineWidth',1.5);hold on
% Plot ecg data on bottom subplot
subplot('Position',[0.05, 0.1, 0.9,0.15])
% Create a variable for the endtime index
endtime = round(handles.endtime*handles.Fs);
% Plot the desired
plot(handles.time(start:endtime),handles.ecg(start:endtime));
%
axis([handles.time(start) handles.time(fin) min(handles.ecg) max(handles.ecg)])
% Set the xick mark to start from zero
xlabel('Time (sec)');hold on
% Image movie frames on the top subplot
subplot('Position',[0.05, 0.28, 0.9,0.68])
% Update image
G = handles.bgRGB;
Mframe = handles.cmosData(:,:,i);
if handles.normflag == 0
Mmax = handles.matrixMax;
Mmin = handles.minVisible;
numcol = size(jet,1);
J = ind2rgb(round((Mframe - Mmin) ./ (Mmax - Mmin) * (numcol - 1)), jet);
A = real2rgb(Mframe >= handles.minVisible, 'gray');
else
J = real2rgb(Mframe, 'jet');
A = real2rgb(Mframe >= handles.normalizeMinVisible, 'gray');
end
I = J .* A + G .* (1 - A);
image(I);
axis off; hold off
F = getframe(fig);
writeVideo(vidObj,F);% Write each frame to the file.
end
close(fig);
close(vidObj); % Close the file.
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% SIGNAL SCREENS
%% Start Time Editable Textbox for Signal Screens
function starttimesig_edit_callback(source,~)
%get the val01 (lower limit) and val02 (upper limit) plot values
val01 = str2double(get(source,'String'));
val02 = str2double(get(endtimesig_edit,'String'));
if val01 >= 0 && val01 <= (size(handles.cmosData,3)-1)*handles.Fs
set(signal_scrn1,'XLim',[val01 val02]);
set(signal_scrn2,'XLim',[val01 val02]);
set(signal_scrn3,'XLim',[val01 val02]);
set(signal_scrn4,'XLim',[val01 val02]);
set(signal_scrn5,'XLim',[val01 val02]);
set(sweep_bar,'XLim',[val01 val02]);
else
error = 'The START TIME must be greater than %d and less than %.3f.';
msgbox(sprintf(error,0,max(handles.time)),'Incorrect Input','Warn');
set(source,'String',0)
end
% Update the start time value
handles.starttime = val01;
end
%% End Time Editable Textbox for Signal Screens
function endtimesig_edit_callback(source,~)
val01 = str2double(get(starttimesig_edit,'String'));
val02 = str2double(get(source,'String'));
if val02 >= 0 && val02 <= (size(handles.cmosData,3)-1)*handles.Fs
set(signal_scrn1,'XLim',[val01 val02]);
set(signal_scrn2,'XLim',[val01 val02]);
set(signal_scrn3,'XLim',[val01 val02]);
set(signal_scrn4,'XLim',[val01 val02]);
set(signal_scrn5,'XLim',[val01 val02]);
set(sweep_bar,'XLim',[val01 val02]);
else
error = 'The END TIME must be greater than %d and less than %.3f.';
msgbox(sprintf(error,0,max(handles.time)),'Incorrect Input','Warn');
set(source,'String',max(handles.time))
end
% Update the end time value
handles.endtime = val02;
end
%% Export signal waves to new screen
function expwave_button_callback(~,~)
M = handles.M; colax='bgmkc'; [a,~]=size(M);
if isempty(M)
msgbox('No wave to export. Please use "Display Wave" button to select pixels on movie screen.','Icon','help')
else
w=figure('Name','Signal Waves','NextPlot','add','NumberTitle','off',...
'Visible','off','OuterPosition',[100, 50, 555,120*a+80]);
for x = 1:a
subplot('Position',[0.06 (120*(a-x)+70)/(120*a+80) 0.9 110/(120*a+80)])
plot(handles.time,squeeze(handles.cmosData(M(x,2),M(x,1),:)),'color',colax(x),'LineWidth',2)
xlim([handles.starttime handles.endtime]);
hold on
if x == a
else
set(gca,'XTick',[])
end
end
xlabel('Time (sec)')
hold off
movegui(w,'center')
set(w,'Visible','on')
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CONDITION SIGNALS
%% Condition Signals Selection Change Callback
function cond_sig_selcbk(~,~)
% Read check box
removeBG_state =get(removeBG_button,'Value');
bin_state = get(bin_button,'Value');
filt_state = get(filt_button,'Value');
drift_state = get(removeDrift_button,'Value');
norm_state = get(norm_button,'Value');
% Grab pop up box values
bin_pop_state = get(bin_popup,'Value');
% Create variable for tracking conditioning progress
trackProg = [removeBG_state filt_state bin_state drift_state norm_state];
trackProg = sum(trackProg);
counter = 0;
g1 = waitbar(counter,'Conditioning Signal');
% Return to raw unfiltered cmos data
cmosData = handles.cmosRawData;
handles.normflag = 0; % Initialize normflag
% Condition Signals
% Remove Background
if removeBG_state == 1
% Update counter % progress bar
counter = counter + 1;
waitbar(counter/trackProg,g1,'Removing Background');
bg_thresh = str2double(get(bg_thresh_edit,'String'));
perc_ex = str2double(get(perc_ex_edit,'String'));
cmosData = remove_BKGRD(cmosData,handles.bg,bg_thresh,perc_ex);
end
% Bin Data
if bin_state == 1
% Update counter % progress bar
counter = counter + 1;
waitbar(counter/trackProg,g1,'Binning Data');
if bin_pop_state == 3
bin_size = 7;
elseif bin_pop_state == 2
bin_size = 5;
else
bin_size = 3;
end
cmosData = binning(cmosData,bin_size);
end
% Filter Data
if filt_state == 1
% Update counter % progress bar
counter = counter + 1;
waitbar(counter/trackProg,g1,'Filtering Data');
filt_pop_state = get(filt_popup,'Value');
if filt_pop_state == 4
or = 100;
lb = 0.5;
hb = 150;
elseif filt_pop_state == 3
or = 100;
lb = 0.5;
hb = 100;
elseif filt_pop_state == 2
or = 100;
lb = 0.5;
hb = 75;
else
or = 100;
lb = 0.5;
hb = 50;
end
cmosData = filter_data(cmosData,handles.Fs, or, lb, hb);
end
% Remove Drift
if drift_state == 1
% Update counter % progress bar
counter = counter + 1;
waitbar(counter/trackProg,g1,'Removing Drift');
% Gather drift values and adjust for drift
ord_val = get(drift_popup,'Value');
ord_str = get(drift_popup,'String');
cmosData = remove_Drift(cmosData,ord_str(ord_val));
end
% Normalize Data
if norm_state == 1
% Update counter % progress bar
counter = counter + 1;
waitbar(counter/trackProg,g1,'Normalizing Data');
% Normalize data
cmosData = normalize_data(cmosData,handles.Fs);
handles.normflag = 1;
end
% Delete the progress bar
delete(g1)
% Save conditioned signal
handles.cmosData = cmosData;
% Update movie screen with the conditioned data
set(f,'CurrentAxes',movie_scrn)
cla
handles.matrixMax = .9 * max(handles.cmosData(:));
currentframe = handles.frame;
if handles.normflag == 0
drawFrame(currentframe);
hold on
else
drawFrame(currentframe);
caxis([0 1])
hold on
end
set(movie_scrn,'YTick',[],'XTick',[]);% Hide tick markes
% Update markers on movie screen
M = handles.M;colax='bgmkc';[a,~]=size(M);
hold on
for x=1:a
plot(M(x,1),M(x,2),'cs','MarkerSize',8,'MarkerFaceColor',colax(x),'MarkerEdgeColor','w','Parent',movie_scrn);
set(movie_scrn,'YTick',[],'XTick',[]);% Hide tick markes
end
hold off
% Update signal waves (yes this is ugly. if you find a better way, please change)
if a>=1
plot(handles.time,squeeze(handles.cmosData(M(1,2),M(1,1),:)),'b','LineWidth',2,'Parent',signal_scrn1)
if a>=2
plot(handles.time,squeeze(handles.cmosData(M(2,2),M(2,1),:)),'g','LineWidth',2,'Parent',signal_scrn2)
if a>=3
plot(handles.time,squeeze(handles.cmosData(M(3,2),M(3,1),:)),'m','LineWidth',2,'Parent',signal_scrn3)
if a>=4
plot(handles.time,squeeze(handles.cmosData(M(4,2),M(4,1),:)),'k','LineWidth',2,'Parent',signal_scrn4)
if a>=5
plot(handles.time,squeeze(handles.cmosData(M(5,2),M(5,1),:)),'c','LineWidth',2,'Parent',signal_scrn5)
end
end
end
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Data Analysis Selection
function anal_select_callback(~,~)
% Get the type of analysis
anal_state = get(anal_select,'Value');
% Adjustment of buttons based on analysis
if anal_state == 1
% Turn all buttons off and hide
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,minapd_text,minapd_edit,maxapd_text,...
maxapd_edit,percentapd_text,percentapd_edit,remove_motion_click,...
remove_motion_click_txt,calc_apd_button],'Visible','off',...
'Enable','off')
% Turn createmap button off
set(createmap_button,'Enable','off')
elseif anal_state == 2
% Turn needed buttons on
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,createmap_button],'Visible','on','Enable','on')
% Turn unneeded buttons off
set([minapd_text,minapd_edit,maxapd_text,maxapd_edit,percentapd_text,...
percentapd_edit,remove_motion_click,remove_motion_click_txt,...
calc_apd_button],'Visible','off','Enable','off')
elseif anal_state == 3
% Turn needed buttons on
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,createmap_button],'Visible','on','Enable','on')
% Turn unneeded buttons off
set([minapd_text,minapd_edit,maxapd_text,maxapd_edit,percentapd_text,...
percentapd_edit,remove_motion_click,remove_motion_click_txt,...
calc_apd_button],'Visible','off','Enable','off')
elseif anal_state == 4
% Turn needed buttons on
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,createmap_button,minapd_text,minapd_edit,maxapd_text,...
maxapd_edit,percentapd_text,percentapd_edit,remove_motion_click,...
calc_apd_button,remove_motion_click_txt],'Visible','on','Enable','on')
elseif anal_state == 5
% Turn on create map button
set(createmap_button,'Visible','on','Enable','on')
% Turn all buttons off except the create map button
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,minapd_text,minapd_edit,maxapd_text,maxapd_edit,...
percentapd_text,percentapd_edit,remove_motion_click,calc_apd_button,...
remove_motion_click_txt],'Visible','off','Enable','off')
elseif anal_state == 6
% Turn on create map button
set(createmap_button,'Visible','on','Enable','on')
% Turn all buttons off except the create map button
set([invert_cmap,starttimemap_text,starttimemap_edit,endtimemap_text,...
endtimemap_edit,minapd_text,minapd_edit,maxapd_text,maxapd_edit,...
percentapd_text,percentapd_edit,remove_motion_click,calc_apd_button,...
remove_motion_click_txt],'Visible','off','Enable','off')
end
end
%% Regional APD Calculation
function calc_apd_button_callback(~,~)
% Read APD Parameters
handles.percentAPD = str2double(get(percentapd_edit,'String'));
handles.maxapd = str2double(get(maxapd_edit,'String'));
handles.minapd = str2double(get(minapd_edit,'String'));
% Read remove motion check box
remove_motion_state =get(remove_motion_click,'Value');
axes(movie_scrn)
coordinate=getrect(movie_scrn);
gg=msgbox('Creating Regional APD...');
apdCalc(handles.cmosData,handles.a_start,handles.a_end,handles.Fs,...
handles.percentAPD,handles.maxapd,handles.minapd,remove_motion_state,...
coordinate,handles.bg,handles.cmap);
close(gg)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% INVERT COLORMAP: inverts the colormaps for all isochrone maps
function invert_cmap_callback(~,~)
% Function Description: The checkbox function like toggle button.
% There are only 2 options and since the box starts unchecked,
% checking it will invert the map, uncheckecking it will invert it
% back to its original state. As such no additional code is needed.
% grab the current value of the colormap
cmap = handles.cmap;
% invert the existing colormap values
handles.cmap = flipud(cmap);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% ACTIVATION MAP
%% Callback for Start and End Time for Analysis
function maptime_edit_callback(~,~)
% get the bounds of the viewing window
vw_start = str2double(get(starttimesig_edit,'String'));
vw_end = str2double(get(endtimesig_edit,'String'));
% get the bounds of the activation window
a_start = str2double(get(starttimemap_edit,'String'));
a_end = str2double(get(endtimemap_edit,'String'));
if a_start >= 0 && a_start <= max(handles.time)
if a_end >= 0 && a_end <= max(handles.time)
set(f,'CurrentAxes',sweep_bar)
a = [a_start a_start];b = [0 1];cla
plot(a,b,'g','Parent',sweep_bar)
hold on
a = [a_end a_end];b = [0 1];
plot(a,b,'-g','Parent',sweep_bar)
axis([vw_start vw_end 0 1])
hold off; axis off
hold off
handles.a_start = a_start;
handles.a_end = a_end;
else
error = 'The END TIME must be greater than %d and less than %.3f.';
msgbox(sprintf(error,0,max(handles.time)),'Incorrect Input','Warn');
set(endtimemap_edit,'String',max(handles.time))
end
else
error = 'The START TIME must be greater than %d and less than %.3f.';
msgbox(sprintf(error,0,max(handles.time)),'Incorrect Input','Warn');
set(starttimemap_edit,'String',0)
end
end
%% %% Checkbox to manipulate plot on signal screens when VOLTAGE is checked
function checkbox_volt(source,~)
i_temp = handles.M(1);
j_temp = handles.M(2);
i = round(i_temp);
j = round(j_temp);
chkbx1 = get(source,'Value'); % gives value of 1 or 0 to indicate voltage checkbox status