Dynamic alterations in cardiac autonomic regulation during recurrent generalized seizures.

Code ↔ Paper

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The 2 matches

[1] § STAR★Methods › Quantification and statistical analysis ↔ Source Code - OWS and dFdt update/ElectroMap.m, lines 64–134 · score 0.52 · spatially filtered, ElectroMap, Gaussian, signals, mapping
[2] § STAR★Methods › Quantification and statistical analysis ↔ Source Code/ElectroMap.m, lines 64–131 · score 0.52 · spatially filtered, ElectroMap, Gaussian, signals, mapping

Paper

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The authors' code

MATLAB · 4,115 lines · 134 KB · BSD-3-Clause · 1 match

function varargout = ElectroMap(varargin)
% Main function for running ElectroMap.
% Chris O'Shea and Ting Yue Yu, University of Birmingham
% Maintained by Chris O'Shea - Email [email hidden] for any queries
% Version 1.0
% Release Date -
% For license information, please see 'license.txt' at ...
% Last Updated -
% Update Summary
% ElectroMap MATLAB code for ElectroMap.fig
% ElectroMap, by itself, creates a new ElectroMap or raises the existing
% singleton*.
%
% H = ElectroMap returns the handle to a new ElectroMap or the handle to
% the existing singleton*.
%
% ElectroMap('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in ElectroMap.M with the given input arguments.
%
% ElectroMap('Property','Value',...) creates a new ALLM or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before ElectroMap_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% NUstop. All inputs are passed to ElectroMap_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)"
%
% See also: GUIDE, GUIDATA, GUIHANDLESF
% Edit the above text to modify the response to help ElectroMap
% Last Modified by GUIDE v2.5 27-Nov-2019 18:13:25
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ElectroMap_OpeningFcn, ...
'gui_OutputFcn', @ElectroMap_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before ElectroMap is made visible.
function ElectroMap_OpeningFcn(hObject, ~, handles, varargin)
% Fucnction for setting values on interface intialisation
handles.output = hObject;
set(handles.invertopt,'Value',1); %inversion of signal
set(handles.sfilt,'Value',2); %spatial filtering (gaussian)
set(handles.velout, 'Value', 4); %Velociy outlier removal
handles.bgon=1; %background on/off switch
handles.bgcol='w'; %backgroung colour
handles.folder_name=[]; %filled when directory folder chosen
handles.fname='opening of GUI hold';
handles.lastprocessedfname='opening of GUI hold'; %holds for loaded and processed files
warning('off','all')
handles.drawcon=0;
handles.conbon=[];
handles.medifilt=1;
masterdir=cd;
if isdeployed == 0
addpath(masterdir,'-frozen');
end
handles.ttpstart=10;
handles.ttpend=90; %time to peak defualt settings
handles.roinum=1;
handles.roisum=0; %roi defualt settings
handles.snrt1=10;
handles.snrt2=30;
handles.pbefore=5;
handles.pafter=5;
handles.ep=0;
handles.herefromroiload=0; %switch for load roi from .txt file
set(handles.manthresh,'Enable','off') %slider off unless manual trheshold level set
handles.rect=[];
handles.loadedmask=[];
set(handles.resegment,'Enable','off')
set(handles.B2B,'Enable','off')
set(handles.pushprocess,'Enable','off')
set(handles.producemaps,'Enable','off')
handles.herefromsegmentpush=0;
handles.filming = 0; %switch for saving maps to video files
%axis not visible until something is in them
axes(handles.mapaxes); axis off
axes(handles.bgimage);axis off
axes(handles.axes2);axis off
axes(handles.cb); axis off
axes(handles.imageaxes); axis off
zoom xon
handles.isZoomed=0;
handles.dFlevel=0;
handles.i_framerate=16;
handles.fmin=0.5;handles.fmax=10;handles.fbin=0.05;handles.dfwin=0; %Frequency mapping defaults
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes ElectroMap wait for user response (see UIRESUME)
% uiwait(handles.ElectroMap);
% --- Outputs from this function are returned to the command line.
function varargout = ElectroMap_OutputFcn(~, ~, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushselect.
function pushselect_Callback(hObject, ~, ~)
% hObject handle to pushselect (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
%% Populate listbox with .mat and .tif files
set(handles.listbox1,'Value',1); %set value to 1 on each new file chosen to stop error
[handles.folder_name]=uigetdir;
workingdir=handles.folder_name;
if isdeployed == 0
cd(workingdir);
end
%get all files in directory
allfiles = dir(handles.folder_name);
if isdeployed == 0
addpath(handles.folder_name);
end
file_list= {};
count=0;
%Find tif and mat files
for i=1:length(allfiles)
k = strfind(allfiles(i).name, '.TIF');
d = strfind(allfiles(i).name, '.tif');
m = strfind(allfiles(i).name, '.mat');
%l = isfolder(allfiles(i).name);
if isempty(k) ~= 1 %&& l ~= 1
count=count+1;
file=allfiles(i).name;
file_list{count}=file;
end
if isempty(d) ~= 1 %&& l ~= 1
count=count+1;
file=allfiles(i).name;
file_list{count}=file;
end
if isempty(m) ~= 1 %&& l ~= 1
count=count+1;
file=allfiles(i).name;
file_list{count}=file;
end
end
set(handles.listbox1,'String',file_list);
guidata(hObject, handles);
% --- Executes on selection change in listbox1.
function listbox1_Callback(~, ~, ~)
% hObject handle to listbox1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes during object creation, after setting all properties.
function listbox1_CreateFcn(hObject, ~, ~)
% hObject handle to listbox1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushload.
function pushload_Callback(hObject, ~, ~)
handles = guidata(hObject);
set(handles.listbox2,'Value',1);
set(handles.pushprocess,'Enable','on')
set(handles.producemaps,'Enable','off')
%% Get image info from GUI
%image
handles.threshop=get(handles.threshopt,'Value'); %thershold choice
handles.threshman=(get(handles.manthresh,'Value')); %manual thershold setting
imchoice=get(handles.imagedisp,'Value'); %image to display
cropchoice=get(handles.cropbox,'Value'); %crop image setting
handles.cropchoice=cropchoice; %0 means no crop, 1 mean new crop, 2 means crop from before
if cropchoice == 1
handles.rect = [];
end
quinnieopt=get(handles.squareROI,'Value'); %custom ROI setting
%% file info
chosenfilecontents=cellstr(get(handles.listbox1,'String'));
choice=get(handles.listbox1,'Value');
fname=chosenfilecontents{choice};
if ispc == 1 %change of file setting it mac or pc
handles.fnamenew=[handles.folder_name,'\',fname];
else
handles.fnamenew=[handles.folder_name,'/',fname];
end
tf = strcmp(handles.fname,handles.fnamenew);
if tf == 0
handles.rect = [];
handles.images=[];
handles.lastprocessedfname='Pressing load or changing threshold hold';
end
handles.fname=handles.fnamenew;
%% If custom roi chosen, get rid off manual thresholding
if quinnieopt == 1 || handles.herefromroiload == 1
handles.threshop = 2;
handles.threshman = -50000;
if handles.herefromroiload == 1
quinnieopt = 0;
end
end
%% load, crop and reset opt, threshold image
inversion=get(handles.invertopt,'Value');
camopt=0;
axes(handles.imageaxes)
set(handles.resegment,'Enable','off')
set(handles.B2B,'Enable','off')
%% Load new image using OMimload function
if tf == 0
[num_images,handles.newrect,mask,im,handles.I,boundaries,handles.camopt,handles.frame1,handles.fluoim,handles.rois,handles.rhsn,handles.tstack] = OMimload(handles.fname,cropchoice,quinnieopt,handles.threshop,handles.threshman,handles.rect,inversion,camopt,get(handles.imagedisp,'Value'),handles.roinum,handles.roisum);
handles.mask=[];
handles.mask=mask;
handles.im=im; handles.num_images=num_images; handles.rect=handles.newrect;
%handles.loadedmask=[];
%handles.herefromroiload = 0;
if isempty(handles.loadedmask) == 0 && handles.herefromroiload == 1
handles.mask=[];
handles.I=[];
mask=handles.loadedmask;
mask=uint16(mask);
boundaries = bwboundaries(mask);
handles.mask=mask;
if size(im,1) ~= size(mask,1) || size(im,2) ~= size(mask,2)
if abs(size(im,1)-size(mask,1)) <= 2 && abs(size(im,2)-size(mask,2)) <= 2
choice = questdlg('ROI dimensons do not match Image but only slighty off. Would you like to reshape ROI?', ...
'ROI mismatch', ...
'Yes','No','Yes');
switch choice
case 'Yes'
[rows,cols]=size(im);
[rows2,cols2]=size(mask);
if rows<=rows2
rows3=rows;
else
rows3=rows2;
end
if cols<=cols2
cols3=cols;
else
cols3=cols2;
end
newmask=zeros(rows,cols);
for r=1:rows3
for c=1:cols3
newmask(r,c)=mask(r,c);
end
end
mask=uint16(newmask);
end
else
handles.herefromroiload = 0;
handles.loadedmask=[];
guidata(hObject,handles)
h=errordlg('Loaded ROI dimensions do not match Image');
waitfor(h)
end
end
handles.I=im.*mask;
handles.mask=mask;
end
set(handles.cropbox,'Value',0);
handles.boundaries=boundaries;
end
%% Rethreshold loaded image set
if tf == 1
[num_images,handles.newrect,mask,im,handles.I,boundaries,handles.camopt,handles.frame1,handles.fluoim,handles.rois,handles.rhsn] = OMimload(handles.fname,cropchoice,quinnieopt,handles.threshop,handles.threshman,handles.rect,inversion,camopt,get(handles.imagedisp,'Value'),handles.roinum,handles.roisum);;
handles.mask=[];
handles.mask=mask;
handles.im=im; handles.num_images=num_images; handles.rect=handles.newrect;
%handles.loadedmask=[];
%handles.herefromroiload = 0;
if isempty(handles.loadedmask) == 0 && handles.herefromroiload == 1
handles.mask=[];
handles.I=[];
mask=handles.loadedmask;
mask=uint16(mask);
boundaries = bwboundaries(mask);
handles.mask=mask;
if size(im,1) ~= size(mask,1) || size(im,2) ~= size(mask,2)
if abs(size(im,1)-size(mask,1)) <= 2 && abs(size(im,2)-size(mask,2)) <= 2
choice = questdlg('ROI dimensons do not match Image but only slighty off. Would you like to reshape ROI?', ...
'ROI mismatch', ...
'Yes','No','Yes');
switch choice
case 'Yes'
[rows,cols]=size(im);
[rows2,cols2]=size(mask);
if rows2>rows && cols2>cols
newmask=zeros(rows,cols);
for r=1:rows
for c=1:cols
newmask(r,c)=mask(r,c);
end
end
end
if rows>rows2 && cols>cols2
newmask=zeros(rows,cols);
for r=1:rows2
for c=1:cols2
newmask(r,c)=mask(r,c);
end
end
end
mask=uint16(newmask);
end
else
handles.herefromroiload = 0;
handles.loadedmask=[];
guidata(hObject,handles);
h=errordlg('Loaded ROI dimensions do not match Image');
waitfor(h)
end
end
handles.I=im.*mask;
handles.mask=mask;
end
set(handles.cropbox,'Value',0);
handles.boundaries=boundaries;
end
%% change pic in GUI
axes(handles.imageaxes);
cla;
if imchoice == 1
imshow(handles.frame1,[],'InitialMagnification', 400)
colormap('gray')
freezeColors
hold on
for i=1:size(boundaries,1)
plot(boundaries{i}(:,2),boundaries{i}(:,1),'r','LineWidth',2);
end
hold off
end
if imchoice == 2
imshow(handles.fluoim,[],'InitialMagnification', 400)
colormap('jet')
freezeColors
hold on
for i=1:size(boundaries,1)
plot(boundaries{i}(:,2),boundaries{i}(:,1),'k','LineWidth',2);
end
hold off
end
set(handles.pushprocess,'Enable','on')
set(handles.producemaps,'Enable','off')
guidata(hObject, handles);
% --- Executes on button press in pushprocess.
function pushprocess_Callback(hObject, ~, handles)
% hObject handle to pushprocess (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%handles = guidata(hObject);
%% get processing options from GUI
%segmentation
minpeakdist = str2double(get(handles.minpeak,'String'));
minpeakdist = ceil(minpeakdist/(1/str2double(get(handles.framerate,'String'))));
handles.minpeakdist=minpeakdist;
segchoice = get(handles.segchoice,'Value');
div=str2double(get(handles.segsize,'String'));
minboundary=str2double(get(handles.minbound,'String'));
minmumofpeaks=str2double(get(handles.minnum,'String'));
handles.avgCL=[];
%Baseline
BLopt=(get(handles.BLopt,'Value'));
%filtering
tfilt=get(handles.tfilt,'Value');
sfilt=get(handles.sfilt,'Value');
sfiltsize=str2double(get(handles.sfiltsize,'String'));
%outlieropts
handles.outlier=get(handles.apdout,'Value');
handles.outliervel=get(handles.velout,'Value');
%inversion
inversion=get(handles.invertopt,'Value');
% frame removal
handles.frameremove=get(handles.removef,'Value');
%% is same file check and process images
chosenfilecontents=cellstr(get(handles.listbox1,'String'));
choice=get(handles.listbox1,'Value');
newfname=chosenfilecontents{choice};
tf = strcmp(newfname,handles.lastprocessedfname);
if tf == 0
loadnewims=1;
handles.lastprocessedfname=newfname;
elseif tf == 1 && handles.herefromsegmentpush == 0
newsettingschoice = questdlg('Re-Process?', ...
'Re-Load same file', ...
'Yes','No - Just segment','No - Just segment');
switch newsettingschoice
case 'Yes'
loadnewims = 1;
case 'No - Just segment'
loadnewims = 0;
num_images=handles.num_images;
end
elseif tf == 1 && handles.herefromsegmentpush == 1
loadnewims = 0;
end
if loadnewims == 1
if isempty(handles.rect) == 0
handles.cropchoice = 1;
end
handles.averages=[];
tic
[handles.preimages,images,averages,mask] = OMimprocess(handles.fname,handles.im,handles.rect,handles.num_images,handles.cropchoice,handles.mask,sfilt,sfiltsize,inversion,tfilt,handles.frameremove,handles.camopt,str2double(get(handles.sfiltsigma,'String')),handles.pbefore,handles.pafter,handles.rhsn,handles.tstack);
toc
handles.waverages=averages;
handles.images=images;
handles.averages=averages;
num_images=handles.num_images;
handles.mask=mask;
end
set(handles.resegment,'Enable','on')
set(handles.B2B,'Enable','on')
if loadnewims == 0
averages=handles.averages;
images=handles.images;
num_images=handles.num_images;
end
%% Baseline Drift Correction
%Top hat filter
if BLopt == 1 || BLopt == 4
th_len=str2double(get(handles.thlen,'String'));
th_len=(th_len)/str2double(get(handles.framerate,'String'));
th_len=round(th_len);
se = strel('line', th_len, 0.5);
BLAV = imopen(averages, se);
%figure, plot(BL)
end
%Poly 4th degree
if BLopt == 2 || BLopt == 5
[p,~,mu]=polyfit(1:length(averages),averages,4);
BLAV=polyval(p,1:length(averages),[],mu);
end
%Poly 11th degree
if BLopt == 3 || BLopt == 6
[p,~,mu]=polyfit(1:length(averages),averages,11);
BLAV=polyval(p,1:length(averages),[],mu);
end
% No BL correction
if BLopt == 7
BLAV=min(averages);
end
handles.averages = (averages-BLAV); %Baseline subtraction
%% Remove baseline from each pixel
BLAV=BLAV-min(BLAV);
if BLopt == 4 || BLopt == 5 || BLopt == 6
for t = 1:size(images,3)
images(:,:,t)=images(:,:,t)+BLAV(t);
end
end
wb=waitbar(0.5,'Removing Baseline');
signal=zeros(1,size(images,3));
if BLopt == 1 || BLopt == 2 || BLopt == 3
for row=1:size(images,1) %%MY BL REMOVAL
for col=1:size(images,2)
for frame = 1:size(images,3)
signal(frame)=images(row,col,frame);
end
if inversion == 1
signal=imcomplement(signal);
end
if BLopt == 1
se = strel('line', th_len, 0.5);
BL = imopen(signal, se);
end
if BLopt == 2
[p,~,mu]=polyfit(1:length(signal),signal,4);
BL=polyval(p,1:length(images(row,col,:)),[],mu);
end
if BLopt == 3
[p,~,mu]=polyfit(1:length(signal),signal,11);
BL=polyval(p,1:length(signal),[],mu);
end
for frame = 1:size(images,3)
images(row,col,frame)=images(row,col,frame)+BL(frame);
end
images(row,col,:)=images(row,col,:) - min(images(row,col,:)); %make all mins zero
end
end
end
handles.images=images;
waitbar(0.95,wb,'Segmenting Signal');
wholav=handles.averages;
%% Display Signal
schoice = 1
if schoice == 1
handles.averages=handles.waverages;
end
if schoice == 2 || schoice == 3 || schoice == 4
if schoice == 2 || schoice == 4
figure,
imshow(handles.frame1, [],'InitialMagnification', 800)
title('Make your selection and press enter');
[~,rec]=imcrop;
cropfig=gcf;
close(cropfig)
rec=floor(rec);
r1=rec(2);
c1=rec(1);
if r1 == 0
r1=1;
end
if c1 == 0
c1=1;
end
r2=floor(rec(2)+rec(4));
c2=floor(rec(1)+rec(3));
[ar,ac,numim]=size(handles.images);
rmask=zeros(ar,ac);
for r=r1:r2
for c=c1:c2
rmask(r,c)=1;
end
end
rmask=uint16(rmask);
newav=zeros(1,numim);
for j=1:numim
class(handles.images)
class(rmask)
roiim=handles.images(:,:,j).*rmask;
newav(j)=sum(sum(roiim));
end
% figure,
newav=imcomplement(newav);
newav=newav-min(newav);
end
if schoice == 3 || schoice == 4
if schoice == 3
newav=handles.waverages;
end
dnewav=smooth(newav);
dnewav=smooth(diff(dnewav));
dnewav(1:10)=0;
dnewav=dnewav-min(dnewav);
dnewav(1:10)=0;
newav=[0,dnewav'];
end
%save overall average for later
wholav=handles.averages;
handles.averages=newav;
end
set(handles.listbox2,'Value',1)
axes(handles.axes2)
plot(handles.averages)
drawnow()
%% BLremoval
%% Baseline Drift Correction
if schoice == 1 || schoice == 2
if schoice == 1
handles.averages=wholav;
end
if BLopt == 1 || BLopt == 4
th_len=str2double(get(handles.thlen,'String'));
th_len=(th_len)/str2double(get(handles.framerate,'String'));
th_len=round(th_len);
se = strel('line', th_len, 0.5);
BLAV = imopen(handles.averages, se);
%figure, plot(BL)
end
if BLopt == 2 || BLopt == 5
[p,~,mu]=polyfit(1:length(handles.averages),handles.averages,4);
BLAV=polyval(p,1:length(handles.averages),[],mu);
end
if BLopt == 3 || BLopt == 6
[p,~,mu]=polyfit(1:length(handles.averages),handles.averages,11);
BLAV=polyval(p,1:length(handles.averages),[],mu);
end
if BLopt == 7
BLAV=min(handles.averages);
end
handles.averages = (handles.averages-BLAV);
end
axes(handles.axes2)
plot(handles.averages)
drawnow()
%% DETECT PEAKS
before=str2double(get(handles.beforeGUI,'String'));
before=before*str2double(get(handles.framerate,'String'));
before=round(before);
after=str2double(get(handles.afterGUI,'String'));
after=after*str2double(get(handles.framerate,'String'));
after=round(after);
handles.locs=[];handles.q2locs=[];handles.avgCL=[];
[handles.locs,~,handles.q2locs,handles.avgCL,handles.numofpeaksoverall,handles.peakheight]=Omseg2...
(handles.averages,str2double(get(handles.peakhigh,'String')),minpeakdist,str2double(get(handles.peakhigh,'String')),minpeakdist,minboundary,segchoice,minmumofpeaks,num_images,div,before,after);
%% Zoomed Section
axes(handles.axes2);
origInfo = getappdata(gca, 'matlab_graphics_resetplotview');
handles.isZoomed = 0;
if isempty(origInfo)
handles.isZoomed = 0;
else
handles.isZoomed = 1;
end
exposure=1/str2double(get(handles.framerate,'String'));
handles.newlim=get(gca,'XLim')/exposure;
handles.newlim(1)=floor(handles.newlim(1));
handles.newlim(2)=ceil(handles.newlim(2));
%% axes2
handles.avgCL=handles.avgCL.*(1/str2double(get(handles.framerate,'String')));
axes(handles.axes2)
cla
CM =['b','r','g','y','c','m','k'];
exposure=1/str2double(get(handles.framerate,'String'));
handles.averagestime=(0:1:(length(handles.averages)-1))*exposure;
plot(handles.averagestime, handles.averages,'k'),
xlabel('time (ms) \rightarrow');
ylabel('Fluorescence Intensity');
xlim([0 length(handles.averages)*exposure]);
hold on
plot(handles.averagestime(handles.locs),handles.averages(handles.locs), 'or');
before=round(str2double(get(handles.beforeGUI,'String'))/exposure);
after=round(str2double(get(handles.afterGUI,'String'))/exposure);
if length(handles.locs) < 2
handles.q2locs=handles.locs;
handles.avgCL(2,1)=0;
end
for i = 1:length(handles.q2locs(:,1))
c=mod(i,6);
if c == 0
c=6;
end
handles.q2locs;
A=(handles.q2locs(i,:));
if isempty(A) == 1
errordlg('No constant cycle length regions found. Please adjust pre-process settings')
end
if min(A(A>0)) < before %if first peak v.close to beginning it is ignored to stop dim error
k = find(A);
A(k(1))=0;
end
tstart=min(A(A>0))-before;
if tstart == 0
tstart = 1;
end
tend=max(A)+after;
if tend > length(handles.averagestime)
if length(A)>1
tend = A(end-1)+after;
elseif length(A) == 1
tend=length(handles.averagestime);
c=7;
end
end
if tend>length(handles.averagestime)
tend=length(handles.averagestime);
end
plot(handles.averagestime(tstart:tend),handles.averages(tstart:tend),'color',CM(c));
end
%end
colorbar off
hold off
set(gca,'FontSize',8);
ax=gca;
line(get(ax,'XLim'),[handles.peakheight handles.peakheight],'Color','b')
%populate section listbox
section = {};
if handles.numofpeaksoverall == 1
section{1}=('N/A');
else
for i = 1:length(handles.q2locs(:,1))
length(handles.q2locs(:,1));
handles.q2locs;
handles.avgCL;
section{i}=[num2str(i),' (',num2str((handles.avgCL(2,i))),'ms)'];
end
end
%% add zoomed section
if handles.isZoomed == 1
handles.q2locs
if length(handles.q2locs(1,:)) < 2 %for single peak seg
handles.q2locs(:,end+1)=0;
end
newline=zeros(1,length(handles.q2locs(1,:)));
newline(1)=handles.newlim(1);
newline(2)=handles.newlim(2);
handles.q2locs=[handles.q2locs;newline];
newsection='Zoomed Section';
section{length(section)+1}=newsection;
end
handles.section=section;
%% Couple sections to auto windows
%peak count set to 1 because of first ignored peak, should be changes
handles.winopt=1;
if length(handles.locs) == 1 || length(handles.locs) == 2
if length(handles.locs) == 1
handles.q2locs(1,1)=handles.locs;
end
if length(handles.locs) == 2
handles.q2locs=[];
handles.q2locs=handles.locs;
CL2=handles.locs(2)-handles.locs(1)*exposure;
handles.section;
handles.section{1}=[num2str(CL2),'ms'];
section=handles.section;
end
end
set(handles.listbox2,'String',section);
axes(handles.mapaxes);
pretty=get(handles.colmap,'String');
jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
delete(wb);
if schoice == 2 || schoice == 3
handles.averages=wholav;
end
set(handles.pushprocess,'Enable','on')
set(handles.producemaps,'Enable','on')
guidata(hObject, handles);
% --- Executes on selection change in listbox2.
function listbox2_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
axes(handles.axes2)
%handles.filming = 0;
exposure=1/str2double(get(handles.framerate,'String'));
handles.averagestime=(0:1:(length(handles.averages(1,:))-1))*exposure;
plot(handles.averagestime, handles.averages,'k'),
xlabel('time (ms) \rightarrow');
ylabel('Fluorescence Intensity');
xlim([0 length(handles.averages)*exposure]);
hold on
plot(handles.averagestime(handles.locs),handles.averages(handles.locs), 'or');
before=round(str2double(get(handles.beforeGUI,'String'))/exposure);
after=round(str2double(get(handles.afterGUI,'String'))/exposure);
section_choice=get(handles.listbox2,'Value');
A=(handles.q2locs(section_choice,:));
if isempty(A) == 1
errordlg('No constant cycle length regions found. Please adjust pre-process settings')
end
if min(A(A>0)) < before %if first peak v.close to beginning it is ignored to stop dim error
k = find(A);
A(k(1))=0;
end
tstart=min(A(A>0))-before;
if tstart == 0
tstart = 1;
end
tend=max(A)+after;
if tend > length(handles.averagestime)
tend = length(handles.averagestime);
end
plot(handles.averagestime(tstart:tend),handles.averages(tstart:tend),'color','r');
ax=gca;
line(get(ax,'XLim'),[handles.peakheight handles.peakheight],'Color','b')
set(gca,'FontSize',8);
producemaps_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function listbox2_CreateFcn(hObject, ~, ~)
% hObject handle to listbox2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in tfilt.
function segchoice_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function segchoice_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function segsize_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function segsize_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in BLopt.
function BLopt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function BLopt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in tfilt.
function tfilt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function tfilt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function minpeak_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function minpeak_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function minnum_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function minnum_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function minbound_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function minbound_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in invertopt.
function invertopt_Callback(~, ~, ~)
% hObject handle to invertopt (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hint: get(hObject,'Value') returns toggle state of invertopt
% --- Executes on selection change in sfilt.
function sfilt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function sfilt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function sfiltsize_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function sfiltsize_CreateFcn(hObject, ~, ~)
% hObject handle to sfiltsize (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in Mapchoice.
function Mapchoice_Callback(hObject, ~, ~)
% hObject handle to Mapchoice (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
choice=get(handles.Mapchoice,'Value');
axes(handles.bgimage);
if handles.bgon == 0
imshow(handles.frame1,[],'InitialMagnification', 400)
colormap('gray')
freezeColors
else
cla reset
axis off
end
[rows,cols]=size(handles.frame1)
axes(handles.mapaxes);
cla reset
axis off
drawnow()
imshow(zeros(rows,cols))
isochoice=get(handles.isoopt,'Value');
CVmap=[];
if choice == 10
cla reset
set(handles.meanchange,'String','');
set(handles.textchange,'String','');
[map,~,alll,~]=snrs(handles.averageBeat,handles.mask,handles.snrt1,handles.snrt2,(get(handles.tfilt,'Value')));
if isempty(map) == 1
map=0;
alll=0;
end
dmap=map; %displau map. values altered so displyaed so bg=white etc. Display and expoterd stats NOT based on this map.
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN;
him=imshow(dmap,[], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([floor(min(min(alll))) ceil(max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)=NaN;
him=imshow(dmap,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
end
title('SNR Map')
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
pretty=get(handles.colmap,'String');
colormap(colormap(pretty{get(handles.colmap,'Value')}));
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
if get(handles.apdscale,'Value') == 1
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=(floor(min(min(alll))):stepp:ceil(max(max(alll))));
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Signal/Noise';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Signal/Noise';
axis off
end
pos = get(hcb,'Position');
hcb.Label.Position=[pos(1) pos(2)-1.2];
stdall=std(alll);
palll=prctile(alll,[5,50,95]);
handles.rdata(4,1)=mean(alll);handles.rdata(4,2)=stdall;handles.rdata(4,3)=stdall/sqrt(numel(alll));handles.rdata(4,4)=stdall*stdall;handles.rdata(4,5)=((palll(3)-palll(1))/palll(2));
rownames{1}='APD';rownames{2}='CV';rownames{3}='Amp';rownames{4}='SNR';
axes(handles.mapaxes);
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
if choice == 1
cla reset
set(handles.meanchange,'String','');
set(handles.textchange,'String','');
t=str2double(get(handles.t,'String'));
map=handles.apdmap;
alll=handles.apalll;
if isempty(map) == 1
map=0;
alll=0;
end
dmap=map; %displau map. values altered so displyaed so bg=white etc. Display and expoterd stats NOT based on this map.
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN;
him=imshow(dmap,[], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([floor(min(min(alll))) ceil(max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)=NaN;
him=imshow(dmap,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
end
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
pretty=get(handles.colmap,'String');
colormap(colormap(pretty{get(handles.colmap,'Value')}));
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
if get(handles.apdscale,'Value') == 1
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=[floor(min(min(alll))):stepp:ceil(max(max(alll)))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Duration (ms)';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Duration (ms)';
axis off
end
pos = get(hcb,'Position');
hcb.Label.Position=[pos(1) pos(2)-1.2];
stdall=std(alll);
palll=prctile(alll,[5,50,95]);
handles.rdata(1,1)=mean(alll);handles.rdata(1,2)=stdall;handles.rdata(1,3)=stdall/sqrt(numel(alll));handles.rdata(1,4)=stdall*stdall;handles.rdata(1,5)=((palll(3)-palll(1))/palll(2));
[~,~,allSNRr,allSNRdb]=snrs(handles.averageBeat,handles.mask,handles.snrt1,handles.snrt2,(get(handles.tfilt,'Value')));
handles.rdata(4,1)=mean(allSNRr);handles.rdata(4,2)=mean(allSNRdb);
rownames=get(handles.rtable,'RowName');
rownames{4}='SNR';
axes(handles.mapaxes);
title(['APD', num2str(t)]);
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
if choice == 2
cla
set(handles.meanchange,'String','');
set(handles.textchange,'String','');
map=handles.actmap;
if isochoice == 1
mini=0;
maxi=max(max(map));
elseif isochoice == 2
mini=str2double(get(handles.isomin,'String'));
maxi=str2double(get(handles.isomax,'String'));
end
dmap=map;
dmap(dmap==0)= NaN;
him=imshow(dmap, [0 maxi], 'InitialMagnification', 800);
hold on
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
caxis([mini maxi]);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
title('Activation Map');
freezeColors
%colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
stepp=(maxi-mini)/5;
hcb.TickLabels=[mini:stepp:maxi];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Time of activation (ms)';
axis off
handles.rdata(4,1)=NaN;handles.rdata(4,2)=NaN;handles.rdata(4,3)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,5)=NaN;
rownames=get(handles.rtable,'RowName');
rownames{4}='';
set(handles.rtable,'RowName',rownames);
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
end
if choice == 3
cla
set(handles.meanchange,'String','');
set(handles.textchange,'String','');
map=handles.actmap;
quivers_X=handles.quivers_X;
quivers_Y=handles.quivers_Y;
quivers_vx=handles.quivers_vx;
quivers_vy=handles.quivers_vy;
if isochoice == 1
mini=0;
maxi=max(max(map));
elseif isochoice == 2
mini=str2double(get(handles.isomin,'String'));
maxi=str2double(get(handles.isomax,'String'));
end
dmap=map;
dmap(dmap==0)= NaN;
him=imshow(dmap, [0 maxi], 'InitialMagnification', 800);
hold on
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
caxis([mini maxi]);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
scal = str2double(get(handles.scal,'String'));
hold on
quiver(quivers_X,quivers_Y,scal*quivers_vx,scal*quivers_vy,0,'k')
% Compile CV map
% factor=str2double(get(handles.pixelsize,'String'))/10;
% [rows,cols] = size(map);
% CVXmap=zeros(rows,cols);
% CVXmap(sub2ind(size(CVXmap),quivers_Y,quivers_X)) = quivers_vx;
% sCVXmap=CVXmap.*CVXmap;
% CVYmap=zeros(rows,cols);
% CVYmap(sub2ind(size(CVYmap),quivers_Y,quivers_X)) = quivers_vy;
% sCVYmap=CVYmap.*CVYmap;
% %construct cv map
% CVmap=sqrt(sCVXmap+sCVYmap);
% CVmap=CVmap*factor;
hold off
title('Activation Map');
freezeColors
%colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual'; hcb.TickLabelsMode='manual';
stepp=(maxi-mini)/5;
hcb.TickLabels=[mini:stepp:maxi];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Time of activation (ms)';
axis off
handles.rdata(4,1)=NaN;handles.rdata(4,2)=NaN;handles.rdata(4,3)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,5)=NaN;
rownames=get(handles.rtable,'RowName');
rownames{4}='';
set(handles.rtable,'RowName',rownames);
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
map=CVmap;
end
if choice == 4
cla
set(handles.meanchange,'String','');
set(handles.textchange,'String','');
map=handles.actmap;
quivers_Xout=handles.quivers_Xout;
quivers_Yout=handles.quivers_Yout;
quivers_vxout=handles.quivers_vxout;
quivers_vyout=handles.quivers_vyout;
if isochoice == 1
mini=0;
maxi=max(max(map));
elseif isochoice == 2
mini=str2double(get(handles.isomin,'String'));
maxi=str2double(get(handles.isomax,'String'));
end
axes(handles.mapaxes)
dmap=map;
dmap(dmap==0)= NaN;
him=imshow(dmap, [0 maxi], 'InitialMagnification', 800);
hold on
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
caxis([mini maxi]);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
scal = str2double(get(handles.scal,'String'));
hold on
quiver(quivers_Xout,quivers_Yout,scal*quivers_vxout,scal*quivers_vyout,0,'k')
hold off
% Compile CV map
% factor=str2double(get(handles.pixelsize,'String'))/10;
% [rows cols] = size(map);
% CVmap=zeros(rows,cols);
% CVXmap=zeros(rows,cols);
% CVXmap(sub2ind(size(CVXmap),quivers_Yout,quivers_Xout)) = quivers_vxout;
% sCVXmap=CVXmap.*CVXmap;
% CVYmap=zeros(rows,cols);
% CVYmap(sub2ind(size(CVYmap),quivers_Yout,quivers_Xout)) = quivers_vyout;
% sCVYmap=CVYmap.*CVYmap;
% %construct cv map
% CVmap=sqrt(sCVXmap+sCVYmap);
% CVmap=CVmap*factor;
title('Activation Map');
freezeColors
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
stepp=(maxi-mini)/5;
hcb.TickLabels=[mini:stepp:maxi];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Time of activation (ms)';
axis off
handles.rdata(4,1)=NaN;handles.rdata(4,2)=NaN;handles.rdata(4,3)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,5)=NaN;
rownames=get(handles.rtable,'RowName');
rownames{4}='';
set(handles.rtable,'RowName',rownames);
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
map=CVmap;
end
if choice == 5
cla
axes(handles.mapaxes);
axis off
%wb=waitbar(0.9,'Calculating Frequencies');
tic
[map]=domfreq(handles.mask,handles.imagerange,str2double(get(handles.framerate,'String')),handles.fmin,handles.fmax,handles.fbin,handles.dfwin,get(handles.tfilt,'Value'));
toc
dfs=map(map>0);
dmap=map;
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN;
him=imshow(dmap,[min(min(dfs)) max(max(dfs))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([floor(min(min(dfs))) ceil(max(max(dfs)))])
title('Dominant Frequency Map')
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
hcb.TickLabels=[min(min(dfs)) max(max(dfs))];
hcb.Ticks=[0 1];
hcb.Label.String='Dominant Frequency (Hz)';
end
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)= NaN;
him=imshow(dmap,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
hcb.TickLabels=[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0 1];
hcb.Label.String='Dominant Frequency (Hz)';
end
freezeColors
axis off
dfs=map(map>0);
dfsp=prctile(dfs,[5,50,95]);
handles.rdata(4,1)=mean(dfs);handles.rdata(4,2)=std(dfs);handles.rdata(4,3)=std(dfs)/numel(dfs);handles.rdata(4,4)=std(dfs)*std(dfs);handles.rdata(4,4)=std(dfs)*std(dfs);handles.rdata(4,5)=((dfsp(3)-dfsp(1))/dfsp(2));
rownames=get(handles.rtable,'RowName');
rownames{4}='DF';
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
if choice == 6
wb=waitbar(0.5,'Producing Diastolic Map');
section_choice=get(handles.listbox2,'Value');
A=handles.q2locs(section_choice,:);
A=A(A~=0);
frame_1=A(1);
frame_last=A(end);
exposure = 1/str2double(get(handles.framerate,'String'));
after=str2double(get(handles.afterGUI,'String'));
after=round(after/exposure);
if frame_last+after>handles.num_images
frame_last=A(end-1);
end
[map,~,alll]=DInt(str2double(get(handles.framerate,'String')),handles.I,handles.images,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.afterGUI,'String')),str2double(get(handles.minpeak,'String')),frame_1,frame_last,str2double(get(handles.t,'String')));
if isempty(alll) == 1
map=0;
alll=0;
end
numel(alll)
map(isnan(map)) = 0;
axes(handles.mapaxes);
imshow(map,[], 'InitialMagnification', 800);
title(['Diastolic Interval Distribution']);
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 1
caxis([floor(min(min(alll))) ceil(max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
end
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
if get(handles.apdscale,'Value') == 1
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=(floor(min(min(alll))):stepp:ceil(max(max(alll))));
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Diastolic Interval (ms)';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Diastolic Interval (ms)';
axis off
end
dis=alll;
disper=prctile(dis,[5,50,95]);
handles.rdata(4,1)=mean(dis);handles.rdata(4,2)=std(dis);handles.rdata(4,3)=std(dis)/numel(dis);handles.rdata(4,4)=std(dis)*std(dis);handles.rdata(4,4)=std(dis)*std(dis);handles.rdata(4,5)=((disper(3)-disper(1))/disper(2));
rownames=get(handles.rtable,'RowName');
rownames{4}='DI';
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
delete(wb)
end
if choice == 7
cla
t=str2double(get(handles.t,'String'));
[map,~,alll]=ttpnew(handles.ttpstart,handles.ttpend,str2double(get(handles.framerate,'String')),t,handles.I,handles.images,handles.averageBeat,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.beforeGUI,'String')),get(handles.apdbl,'Value'),str2double(get(handles.apdblnum,'String')));
dmap=map;
title('TTP');
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
dmap(dmap==0)= NaN;
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN;
him=imshow(dmap,[], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([floor(min(min(alll))) ceil(max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)=NaN;
him=imshow(dmap,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
end
title('Time to peak Map');
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
hcb.TicksMode='manual';hcb.TickLabelsMode='manual';
if get(handles.apdscale,'Value') == 1
max(max(alll))
min(min(alll))
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=[floor(min(min(alll))):stepp:ceil(max(max(alll)))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Duration (ms)';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Time to Peak (ms)';
axis off
end
ttps=alll;
ttpsp=prctile(ttps,[5,50,95]);
handles.rdata(4,1)=mean(ttps);handles.rdata(4,2)=std(ttps);handles.rdata(4,3)=std(ttps)/numel(ttps);handles.rdata(4,4)=std(ttps)*std(ttps);handles.rdata(4,4)=std(ttps)*std(ttps);handles.rdata(4,5)=((ttpsp(3)-ttpsp(1))/ttpsp(2));
rownames=get(handles.rtable,'RowName');
rownames{4}='TTP';
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
if choice == 8
cla
wb=waitbar(0.5,'Producing tau map');
[map,~,alll,~,~,~,~]=tautest3(str2double(get(handles.taustart,'String')),str2double(get(handles.taufinish,'String')),str2double(get(handles.framerate,'String')),handles.I,handles.images,handles.averageBeat,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.r2cut,'String')));
map(isnan(map)) = 0;
cla
axes(handles.mapaxes);
imshow(map,[], 'InitialMagnification', 800);
title('Relaxation Constant Map');
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 1
caxis([floor(min(min(alll))) ceil(max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
caxis([str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))])
end
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
if get(handles.apdscale,'Value') == 1
max(max(alll));
min(min(alll));
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=[floor(min(min(alll))):stepp:ceil(max(max(alll)))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Relaxation Constant (ms)';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Relaxation Constant (ms)';
axis off
end
delete(wb)
taus=alll;
tausp=prctile(taus,[5,50,95]);
handles.rdata(4,1)=mean(taus);handles.rdata(4,2)=std(taus);handles.rdata(4,3)=std(taus)/numel(taus);handles.rdata(4,4)=std(taus)*std(taus);handles.rdata(4,4)=std(taus)*std(taus);handles.rdata(4,5)=((tausp(3)-tausp(1))/tausp(2));
rownames=get(handles.rtable,'RowName');
rownames{4}='Tau';
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
if choice == 9
[map]=fluo_map(str2double(get(handles.framerate,'String')),handles.I,handles.images,get(handles.tfilt,'Value'),handles.averageBeat);
map(isnan(map)) = 0;
alll=map(map>0);
cla
axes(handles.mapaxes)
if get(handles.apdscale,'Value') == 1
imshow(map,[floor(min(min(alll))) ceil(max(max(alll)))], 'InitialMagnification', 800);
end
if get(handles.apdscale,'Value') == 2
imshow(map,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
end
title('Amplitude Map');
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
if get(handles.apdscale,'Value') == 1
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=[floor(min(min(alll))):stepp:ceil(max(max(alll)))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Relaxation Constant (ms)';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Relaxation Constant (ms)';
axis off
end
hcb.Label.String='Signal Level';
axis off
handles.rdata(4,1)=NaN;handles.rdata(4,2)=NaN;handles.rdata(4,3)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,5)=NaN;
rownames=get(handles.rtable,'RowName');
rownames{4}='';
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
end
if choice == 11
tic
beforeframes = str2num(get(handles.beforeGUI,'String'))*str2num(get(handles.framerate,'String'));
sdsd=handles.wsmat;
[dmap]=wavesim(handles.wsmat,handles.mask,handles.ep,beforeframes);
%[dmap]=wavesim(handles.wsmat,handles.mask,ep(i),beforeframes);
toc
alll=dmap(dmap>0);
dmap(isnan(dmap)) = 0;
cla
axes(handles.mapaxes)
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN
x=handles.wsmat;
handles.ep
dmap=medfilt2(dmap);
him=imshow(dmap,[], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
if (min(min(min(alll)))-(max(max(alll)))) ~= 0
caxis([(min(min(alll))) (max(max(alll)))])
else
caxis([min(min(alll))-0.1 min(min(alll))+0.1])
end
end
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)=NaN;
dmap=medfilt2(dmap);
him=imshow(dmap,[str2num(get(handles.cmin,'String')) str2num(get(handles.cmax,'String'))], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([str2num(get(handles.cmin,'String')) str2num(get(handles.cmax,'String'))])
end
title('Wave Similarity Map');
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
%jetcolormap(1,:) = [1, 1, 1];
colormap(flipud(jetcolormap));
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(flipud(jetcolormap));
hcb.Location = 'southoutside';
ax = gca;
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
if get(handles.apdscale,'Value') == 1
stepp=((max(max(alll)))-(min(min(alll))))/5;
hcb.TickLabels=[(min(min(alll)))-1:stepp:(max(max(alll)))-1];
hcb.Ticks=[0.01,0.2:0.2:1];
if handles.ep == 0;
hcb.Label.String='Optical Wave Similarity';
else
hcb.Label.String='Regularity Index';
end
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2num(get(handles.cmax,'String'))-str2num(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2num(get(handles.cmin,'String')):stepp:str2num(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Wave Similarity AU';
axis off
end
axis off
handles.rdata(4,1)=NaN;handles.rdata(4,2)=NaN;handles.rdata(4,3)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,4)=NaN;handles.rdata(4,5)=NaN;
rownames=get(handles.rtable,'RowName');
rownames{4}='';
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
map=dmap-1;
alll=map(map>-0.1); % return to actual map to get results
palll=prctile(alll,[5,50,95]);
handles.rdata(4,1)=mean(alll);handles.rdata(4,2)=std(alll);handles.rdata(4,3)=std(alll)/sqrt(numel(alll));handles.rdata(4,4)=std(alll)^2;handles.rdata(4,5)=((palll(3)-palll(1))/palll(2));
handles.wsm(1)=mean(alll);handles.wsm(2)=std(alll);handles.wsm(3)=std(alll)/sqrt(numel(alll));handles.wsm(4)=std(alll)^2;handles.wsm(5)=((palll(3)-palll(1))/palll(2));
guidata(hObject, handles);
if exist('handles.wscount') == 0
handles.wscount=1
end
xx1=get(handles.listbox2,'Value');
assignin('base',['WS_',num2str(xx1)],handles.wsm)
rownames=get(handles.rtable,'RowName');
if handles.ep == 0;
rownames{4}='OWS';
else
rownames{4}='RI';
end
guidata(hObject, handles);
set(handles.meanchange,'String',rownames{4});
set(handles.rtable,'data',handles.rdata);
set(handles.rtable,'RowName',rownames);
end
if choice == 12
cla reset
map=dFmap(handles.averageBeat,handles.mask,handles.dFlevel,str2double(get(handles.framerate,'String')),handles.i_framerate,get(handles.tfilt,'Value'),get(handles.invertopt,'Value'),0.55,0.45);
dmap=map;
alll=map(map>0);
alll=reshape(alll,1,numel(alll));
cla
axes(handles.mapaxes);
imshow(dmap,[], 'InitialMagnification', 800);
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
colormap(jetcolormap);
if get(handles.apdscale,'Value') == 1
dmap(dmap==0)= NaN;
him=imshow(dmap,[], 'InitialMagnification', 800);
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
caxis([(min(min(alll))) (max(max(alll)))])
end
if get(handles.apdscale,'Value') == 2
dmap(dmap==0)= NaN;
him=imshow(dmap,[str2double(get(handles.cmin,'String')) str2double(get(handles.cmax,'String'))], 'InitialMagnification', 800);
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='Relaxation Constant (ms)';
axis off
set(him, 'AlphaData', ~isnan(dmap))
if handles.bgon == 1
axis on
set(gca, 'XColor', 'none', 'yColor', 'none', 'xtick', [], 'ytick', [], 'Color', handles.bgcol)
end
end
if handles.dFlevel > 0
title(['dFdt ',num2str(handles.dFlevel), ' Map']);
else
title(['dFdt max Map']);
end
freezeColors
% colorbar
axes(handles.cb);
cla reset
hcb=colorbar;
hcb.Location = 'southoutside';
cpos = hcb.Position;
cpos(4) = 4*cpos(4);
hcb.Position = cpos;
if get(handles.apdscale,'Value') == 1
max(max(alll))
min(min(alll))
stepp=(ceil(max(max(alll)))-floor(min(min(alll))))/5;
hcb.TickLabels=[(min(min(alll))):stepp:(max(max(alll)))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='dFdt';
axis off
end
if get(handles.apdscale,'Value') == 2
stepp=(str2double(get(handles.cmax,'String'))-str2double(get(handles.cmin,'String')))/5;
hcb.TickLabels=[str2double(get(handles.cmin,'String')):stepp:str2double(get(handles.cmax,'String'))];
hcb.Ticks=[0.01,0.2:0.2:1];
hcb.Label.String='dFdt';
axis off
end
taus=alll;
tausp=prctile(taus,[5,50,95]);
handles.rdata(4,1)=mean(taus);handles.rdata(4,2)=std(taus);handles.rdata(4,3)=std(taus)/numel(taus);handles.rdata(4,4)=std(taus)*std(taus);handles.rdata(4,4)=std(taus)*std(taus);handles.rdata(4,5)=((tausp(3)-tausp(1))/tausp(2));
rownames=get(handles.rtable,'RowName');
rownames{4}='dFdt';
set(handles.rtable,'RowName',rownames);
set(handles.rtable,'data',handles.rdata);
end
% Draw Contours
drawcon = handles.drawcon;
if drawcon == 1
axes(handles.mapaxes);
hold on
for j = 0:str2double(handles.conbon):max(max(map))+str2double(handles.conbon)
mapmask=(map<=j);
A=map.*mapmask;
[cons]=bwboundaries(A);
for i=1:size(cons,1)
plot(cons{i}(:,2),cons{i}(:,1),'k','LineWidth',1);
end
end
end
% handles.mask=handles.hold_mask; %keep and reinsate overall mask at end
handles.holdmap=map;
handles.holdcvmap=CVmap;
drawnow()
guidata(hObject, handles);
drawnow()
% Hints: contents = cellstr(get(hObject,'String')) returns apdvaluechoice contents as cell array
% contents{get(hObject,'Value')} returns selected item from apdvaluechoice
% --- Executes during object creation, after setting all properties.
function Mapchoice_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in mapoptions.
function mapoptions_Callback(~, ~, ~)
% hObject handle to mapoptions (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns mapoptions contents as cell array
% contents{get(hObject,'Value')} returns selected item from mapoptions
% --- Executes during object creation, after setting all properties.
function mapoptions_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in ExportMap.
function ExportMap_Callback(~, ~, handles)
GUI_fig_children=get(gcf,'children');
Fig_Axes=findobj(GUI_fig_children,'type','Axes');
fig=figure;ax=axes;clf;
new_handle=copyobj(handles.mapaxes,fig);
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
set(gca,'ActivePositionProperty','outerposition')
set(gca,'Units','normalized')
set(gca,'OuterPosition',[0 0 1 1])
set(gca,'position',[0.1300 0.1100 0.7750 0.8150])
% --- Executes on button press in actpoints.
function actpoints_Callback(hObject, ~, ~)
% hObject handle to actpoints (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
if get(handles.actfittimes,'Value') == 1
[~,act_x,act_y,act_t,~,~,~,~,~,~,~,~,~, ~,~,~,~,~] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,100,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
if get(handles.actfittimes,'Value') == 2
[~,act_x,act_y,act_t,~,~,~,~,~,~,~,~, ~,~,~,~,~] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
str2double(get(handles.MINt,'String')),str2double(get(handles.MAXt,'String')),str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
figure, hold on
plot3(act_x,act_y,act_t,'.k')
title('activation points');
zlabel('time (ms)', 'FontSize', 20);
xlabel('x', 'FontSize', 20);
ylabel('y', 'FontSize', 20);
zlim([0 15])
hold off
% --- Executes on button press in velhist.
function velhist_Callback(hObject, ~, ~)
% hObject handle to velhist (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
if get(handles.actfittimes,'Value') == 1
[~,~,~,~,~,~,~,~,~,~,vout,~,~,~,~,~,~,~] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,100,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
if get(handles.actfittimes,'Value') == 2
[~,~,~,~,~,~,~,~,~,~,vout,~,~,~,~,~,~,~] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
str2double(get(handles.MINt,'String')),str2double(get(handles.MAXt,'String')),str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
figure, histogram(vout,str2double(get(handles.binnumber,'String')));
hold on
%line([mean(vout) mean(vout)],[0 300],'Color','r','Linewidth',3)
xlabel('Conduction Velocity (cm/s)')
ylabel('Number of Pixels')
hold off
% --- Executes on button press in APDdist.
function APDdist_Callback(hObject, ~, ~)
% hObject handle to APDdist (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
alll=handles.apalll;
figure, histogram(alll,str2double(get(handles.binnumber,'String')));
hold on
xlabel('Action Potential Duration (ms)')
ylabel('Number of Pixels')
hold off
% --- Executes on selection change in apdout.
function apdout_Callback(hObject, eventdata, ~)
% hObject handle to apdout (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
Mapchoice_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function apdout_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function cmin_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function cmin_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function cmax_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function cmax_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in velout.
function velout_Callback(~, ~, handles)
% hObject handle to velout (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if get(handles.velout, 'Value') == 9
set(handles.minvel,'String','0.2')
set(handles.maxvel,'String','0.8')
set(handles.text64,'String','(0-1)');
elseif get(handles.velout, 'Value') == 2
set(handles.minvel,'String','0')
set(handles.maxvel,'String','100')
set(handles.text64,'String','cm/s');
end
% Hints: contents = cellstr(get(hObject,'String')) returns velout contents as cell array
% contents{get(hObject,'Value')} returns selected item from velout
% --- Executes during object creation, after setting all properties.
function velout_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function minvel_Callback(~, ~, ~)
% hObject handle to minvel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of minvel as text
% str2double(get(hObject,'String')) returns contents of minvel as a double
% --- Executes during object creation, after setting all properties.
function minvel_CreateFcn(hObject, ~, ~)
% hObject handle to minvel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function maxvel_Callback(~, ~, ~)
% hObject handle to maxvel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of maxvel as text
% str2double(get(hObject,'String')) returns contents of maxvel as a double
% --- Executes during object creation, after setting all properties.
function maxvel_CreateFcn(hObject, ~, ~)
% hObject handle to maxvel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushrecal.
function pushrecal_Callback(hObject, eventdata, ~)
% hObject handle to pushrecal (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
contents = cellstr(get(handles.Mapchoice,'String'));
choice=get(handles.Mapchoice,'Value');
axes(handles.mapaxes);
handles.outlier=get(handles.apdout,'Value');
handles.outliervel=get(handles.velout,'Value');
wb=waitbar(0.4,'Calculating APD');
t=str2double(get(handles.t,'String'));
[apmap,meanapd,alll,onedev]=mapsbaby(get(handles.aptime1,'Value'),str2double(get(handles.framerate,'String')),t,handles.I,handles.images,handles.averageBeat,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.beforeGUI,'String')),get(handles.apdbl,'Value'),str2double(get(handles.apdblnum,'String')),handles.medifilt);
stdall=std(alll);
palll=prctile(alll,[5,50,95]);
handles.rdata(4,1)=mean(alll);handles.rdata(4,2)=stdall;handles.rdata(4,3)=stdall/sqrt(numel(alll));handles.rdata(4,4)=stdall*stdall;handles.rdata(4,5)=((palll(3)-palll(1))/palll(2));
waitbar(0.6,wb,'Calculating conduction velocity');
if get(handles.actfittimes,'Value') == 1
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevcv,varicv,SEcv] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,100,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
if get(handles.actfittimes,'Value') == 2
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevcv,varicv,SEcv] =...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
str2double(get(handles.MINt,'String')),str2double(get(handles.MAXt,'String')),str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
%save AP,CV maps and vectors
handles.apdmap=apmap;
handles.apalll=alll;
handles.actmap=actmap;
handles.act_t=act_t;
handles.vout=vout;
handles.quivers_X=quivers_X;
handles.quivers_Y=quivers_Y;
handles.quivers_vx=quivers_vx;
handles.quivers_vy=quivers_vy;
handles.quivers_Xout=quivers_Xout;
handles.quivers_Yout=quivers_Yout;
handles.quivers_vxout=quivers_vxout;
handles.quivers_vyout=quivers_vyout;
%% update rtable
rdata=handles.rdata;
APp=prctile(alll,[5,50,95]);
CVp=prctile(vout,[5,50,95]);
handles.errCV=[onedevcv,SEcv,varicv,((CVp(3)-CVp(1))/CVp(2))];
guidata(hObject, handles);
rdata(1,1)=mean(alll);rdata(1,2)=handles.err(1);rdata(1,3)=handles.err(2);rdata(1,4)=handles.err(3);rdata(1,5)=handles.err(4);
rdata(2,1)=mean(vout);rdata(2,2)=handles.errCV(1);rdata(2,3)=handles.errCV(2);rdata(2,4)=handles.errCV(3);rdata(2,5)=handles.errCV(4);
handles.rdata=rdata;
set(handles.rtable,'data',handles.rdata);
%activation time
tim=act_t;
tim=tim-min(tim);
allpts=numel(tim);
xbins=0:0.01:max(tim);
tissueact=100*cumsum(hist(tim,xbins))/allpts;
actmax=str2double(get(handles.actmax,'String'));
actmin=str2double(get(handles.actmin,'String'));
Imax = find(tissueact > actmax);
Imin = find(tissueact > actmin);
if actmax < 100
Imax=Imax(1);
else Imax=max(tim);
end
Imin=Imin(1);
if actmax < 100
timmax=Imax*0.01;
else timmax=Imax
end
timmin=Imin*0.01;
timdiff=timmax-timmin;
if actmin == 0
timdiff=timmax;
end
if get(handles.checkbox8,'Value')==1
pixar=str2double(get(handles.pixelsize,'String'));
pixar=pixar*pixar;
pixar=pixar/1000000; %convert to mm2
normfac=pixar*allpts;
timdiff=timdiff/normfac;
end
set(handles.actquote, 'String', [num2str(timdiff),' ms']);
delete(wb)
%maps
Mapchoice_Callback(hObject, eventdata, handles)
% hold off
%scales the values to work with out camera frame rate and resolution
%factor = pix/exposure*100; % converts to cm/sec
%CV = mean(v)*factor;
% disp(['mean_cv: ', num2str(CV), 'cm/sec']);
%
% text(0,1,['CV: ',num2str(CV), 'cm/sec'], 'Units', 'Normalized')
guidata(hObject, handles);
% --- Executes on button press in pushmapapply.
function pushmapapply_Callback(hObject, eventdata, handles)
% hObject handle to pushmapapply (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
Mapchoice_Callback(hObject, eventdata, handles)
% --- Executes on button press in producemaps.
function producemaps_Callback(hObject, eventdata, ~)
% hObject handle to producemaps (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
%handles.filming=0;
%% Store each peak into array
before=str2double(get(handles.beforeGUI,'String'));
after=str2double(get(handles.afterGUI,'String'));
exposure=1/str2double(get(handles.framerate,'String'));
before = round(before/exposure); %1000 because we are dealing with ms
after = round(after/exposure);
if handles.filming == 0
wb=waitbar(0.1,'Preparing Images');
section_choice=get(handles.listbox2,'Value');
end
handles.filming
if handles.filming == 1
handles.filmcount=handles.filmcount+1;
section_choice=handles.filmcount;
section_choice
end
if strcmp(handles.section{section_choice},'Zoomed Section') == 1 && handles.filming ~= 1
sig=handles.averages(handles.q2locs(section_choice,1):handles.q2locs(section_choice,2));
%Peak Parameters
maxfluo = max(handles.averages);
mo = mode(handles.averages);
handles.peakheight = maxfluo*str2double(get(handles.peakhigh,'String'));
minpeakdist = str2double(get(handles.minpeak,'String'));
minpeakdist = ceil(minpeakdist/(1/str2double(get(handles.framerate,'String'))));
% find peaks
[~,m] = findpeaks(sig, 'MINPEAKHEIGHT', handles.peakheight, 'MINPEAKDISTANCE', minpeakdist)
m;
m=m+handles.q2locs(section_choice,1)-1;
else
m=handles.q2locs(section_choice,:);
end
f=m(m~=0);
peaks = (length(f)); % ignores last peak as the signal may cut out
%% OVERLAYING ALL BEATS TO MAKE AN AVERAGE BEAT
% total action potential duration
APtime = before+after;
[~,~,num]=size(handles.images(:,:,:))
% create empty matrix to fill later on
if APtime <= num
overlay = zeros(size(handles.im,1), size(handles.im,2), APtime);
else
overlay = zeros(size(handles.im,1), size(handles.im,2), num);
end
% skip the first and last AP to forgo any possible errors exceeding matrix
% dimensions
if f(1) <= before
startloc =2;
else startloc =1;
end
if f(end)+after > num
endloc=numel(f)-1;
else endloc = numel(f);
end
locRange = startloc:endloc;
if length(handles.q2locs) >1
end
% fill matrix
if isempty(locRange)== 1
errordlg('Peak too close to start/end of file to be analysed with current window settings, next peak analysed')
end
if f(locRange(end))+after > length(handles.images(1,1,:))
locRange=locRange(1:end-1);
end
wsmat=[];
tic
f1=f(locRange);
f1start=(f1(1)-before);
f1end=(f1(end)-after);
handles.imagerange=handles.images(:,:,f1start:f1end);
if length(locRange) > 1 %only need to overlay if more than 1 peak
wsmat=zeros(size(handles.images,1),size(handles.images,2),numel(-before:after),numel(locRange));
for x = -before:after
if f(locRange)+after < length(handles.images(1,1,:))
overlay(:,:,x+before+1) = sum(handles.images(:,:,f(locRange)+x),3)./numel(f);
overlay(:,:,x+before+1) = overlay(:,:,x+before+1).*double(handles.mask);
wsmat(:,:,x+before+1,locRange)=handles.images(:,:,f(locRange)+x);
end
end
end
handles.wsmat=wsmat;
toc
if length(locRange) == 1 %1 beat
for x = -before:after
overlay(:,:,x+before+1) = (handles.images(:,:,f(locRange)+x));
overlay(:,:,x+before+1) = overlay(:,:,x+before+1).*double(handles.mask);
end
end
handles.cvimages=overlay;
inversion=get(handles.invertopt,'Value');
%% WRITE TO TIFF STACK
% % normalise
%cos = 26/11/16 with new BL removal overlay all negative, so min and max
if handles.numofpeaksoverall > 1
minI = min(overlay(:));
maxI = max(overlay(:));
%
averageBeat = overlay - minI;
averageBeat = (2^16-1)*averageBeat./(maxI);
%
%make 16 bit
handles.averageBeat = uint16(averageBeat);
end
if handles.numofpeaksoverall == 1
disp('hi')
handles.averageBeat=handles.images;
%handles.cvimages=handles.images;
end
%% Get numbers
handles.outlier=get(handles.apdout,'Value');
if handles.filming == 0
waitbar(0.4,wb,'Producing APD map');
t=str2double(get(handles.t,'String'));
[apmap,meanapd,alll,onedev,var,SE]=mapsbaby(get(handles.aptime1,'Value'),str2double(get(handles.framerate,'String')),t,handles.I,handles.images,handles.averageBeat,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.beforeGUI,'String')),get(handles.apdbl,'Value'),str2double(get(handles.apdblnum,'String')),handles.medifilt);
waitbar(0.6,wb,'Producing Isochronal map');
if get(handles.actfittimes,'Value') == 1
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevCV,varCV,SECV]=...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,400,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
if get(handles.actfittimes,'Value') == 2
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevCV,varCV,SECV]=...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
str2double(get(handles.MINt,'String')),str2double(get(handles.MAXt,'String')),str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
APp=prctile(alll,[5,50,95]);
CVp=prctile(vout,[5,50,95]);
handles.err=[onedev,SE,var,((APp(3)-APp(1))/APp(2))];
handles.errCV=[onedevCV,SECV,varCV,((CVp(3)-CVp(1))/CVp(2))];
rdata=zeros(4,4);
rdata(1,1)=mean(alll);rdata(1,2)=handles.err(1);rdata(1,3)=handles.err(2);rdata(1,4)=handles.err(3);rdata(1,5)=handles.err(4);
rdata(2,1)=mean(vout);rdata(2,2)=handles.errCV(1);rdata(2,3)=handles.errCV(2);rdata(2,4)=handles.errCV(3);rdata(2,5)=handles.errCV(4);
[fmap]=fluo_map(str2double(get(handles.framerate,'String')),handles.I,handles.images,get(handles.tfilt,'Value'),handles.averageBeat);
fmap(isnan(fmap))=0;
salll=fmap(fmap>0);
sp=prctile(salll,[5,50,95]);
rdata(3,1)=mean(salll);
rdata(3,2)=std(salll);
rdata(3,3)=std(salll)/sqrt(numel(salll));
rdata(3,4)=std(salll)*std(salll);
rdata(3,5)=((sp(3)-sp(1))/sp(2));
rdata(rdata==0)=NaN;
handles.rdata=rdata;
set(handles.rtable,'Data',rdata);
disp('2218')
%save AP,CV maps and vectors
handles.apdmap=apmap;
handles.apalll=alll;
handles.actmap=actmap;
handles.act_t=act_t;
handles.vout=vout;
handles.quivers_X=quivers_X;
handles.quivers_Y=quivers_Y;
handles.quivers_vx=quivers_vx;
handles.quivers_vy=quivers_vy;
handles.quivers_Xout=quivers_Xout;
handles.quivers_Yout=quivers_Yout;
handles.quivers_vxout=quivers_vxout;
handles.quivers_vyout=quivers_vyout;
%activation time
tim=act_t;
tim=tim-min(tim);
allpts=numel(tim);
xbins=0:0.01:max(tim);
tissueact=100*cumsum(hist(tim,xbins))/allpts;
actmax=str2double(get(handles.actmax,'String'));
actmin=str2double(get(handles.actmin,'String'));
Imax = find(tissueact > actmax);
Imin = find(tissueact > actmin);
if actmax < 100
Imax=Imax(1);
else Imax=max(tim);
end
Imin=Imin(1);
if actmax < 100
timmax=Imax*0.01;
else timmax=Imax
end
timmin=Imin*0.01;
timdiff=timmax-timmin;
if actmin == 0
timdiff=timmax;
end
if get(handles.checkbox8,'Value')==1
pixar=str2double(get(handles.pixelsize,'String'));
pixar=pixar*pixar;
pixar=pixar/1000000; %convert to mm2
normfac=pixar*allpts;
timdiff=timdiff/normfac;
end
set(handles.actquote, 'String', [num2str(timdiff),' ms']);
if strcmp(handles.section{1},'N/A') == 1
set(handles.CLdisp,'String',('N/A - only one peak'));
end
if strcmp(handles.section{1},'N/A') == 0
if strcmp(handles.section{section_choice},'Zoomed Section') == 1
set(handles.CLdisp,'String','N/A - Custom Section');
else
set(handles.CLdisp,'String',[num2str((handles.avgCL(2,section_choice))),' ms (Frequency = ',num2str(1000/round(handles.avgCL(2,section_choice),-1)),' Hz)']);
end
end
delete(wb)
end
guidata(hObject, handles);
axes(handles.mapaxes);
%% Upadte roi selector
% Make MAPS!!!!!
Mapchoice_Callback(hObject, eventdata, handles)
drawnow()
guidata(hObject, handles);
% --- Executes on selection change in threshopt.
function threshopt_Callback(hObject, ~, handles)
% hObject handle to threshopt (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if get(handles.threshopt,'Value') == 1
set(handles.manthresh,'Enable','off')
end
if get(handles.threshopt,'Value') == 2
set(handles.manthresh,'Enable','on')
end
guidata(hObject, handles);
% Hints: contents = cellstr(get(hObject,'String')) returns threshopt contents as cell array
% contents{get(hObject,'Value')} returns selected item from threshopt
% --- Executes during object creation, after setting all properties.
function threshopt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function manthresh_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
pushload_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function manthresh_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in cropimage.
function cropimage_Callback(~, ~, ~)
% --- Executes on selection change in imagedisp.
function imagedisp_Callback(hObject, ~, ~)
handles = guidata(hObject);
imchoice=get(handles.imagedisp,'Value');
axes(handles.imageaxes);
cla;
[boundaries] = bwboundaries(handles.mask);
if imchoice == 1
imshow(handles.frame1,[],'InitialMagnification', 400)
colormap('gray')
freezeColors
hold on
for i=1:size(boundaries,1)
plot(boundaries{i}(:,2),boundaries{i}(:,1),'r','LineWidth',2);
end
hold off
end
if imchoice == 2
imshow(handles.fluoim,[],'InitialMagnification', 400)
colormap('jet')
freezeColors
hold on
for i=1:size(boundaries,1)
plot(boundaries{i}(:,2),boundaries{i}(:,1),'k','LineWidth',2);
end
hold off
end
axes(handles.mapaxes);
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
guidata(hObject, handles);
% Hints: contents = cellstr(get(hObject,'String')) returns imagedisp contents as cell array
% contents{get(hObject,'Value')} returns selected item from imagedisp
% --- Executes during object creation, after setting all properties.
function imagedisp_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in cropbox.
function cropbox_Callback(~, ~, ~)
% --- Executes on button press in exportvalues.
function exportvalues_Callback(hObject, ~, ~)
handles = guidata(hObject);
[filename,pathname] = uiputfile({'*.csv';'*.txt';'*.mat'}, 'Save Map values (Isochronal maps with vector overlay can only be saved as .mat files)');
[~,~,ext] = fileparts(filename);
file=[pathname,filename];
choice=get(handles.Mapchoice,'Value');
map=handles.holdmap;
% mat file save
if strcmp('.mat',ext) == 1
if choice == 1
APD_Dist=map;
save(file,'APD_Dist');
end
if choice == 2;
activation_time=map;
save(file,'activation_time');
end
if choice == 3;
activation_time=map;
xpositions=X_pos;
ypositions=Y_pos;
xvelocities=X_vel;
yvelocities=Y_vel;
velocities=total_vel;
save(file,'activation_time','xpositions','ypositions','xvelocities','yvelocities','velocities','fractional_up');
end
if choice == 4;
activation_time=map;
xpositions=Xout_pos;
ypositions=Yout_pos;
xvelocities=Xout_vel;
yvelocities=Yout_vel;
velocities=total_velout;
save(file,'activation_time','xpositions','ypositions','xvelocities','yvelocities','velocities','fractional_up');
end
if choice == 6
DI=handles.holdmap;
save(file,'DI')
end
if choice == 8
tau=handles.holdmap;
save(file,'tau')
end
if choice == 9
[~,~,~,act_t,~,~,~,~,~,~,vout,~,~,~,~, onedevCV,varCV,SECV]=...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,200,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
cvmean = mean(vout);
CVdev=onedevCV;
save(file,'RT50','t1080','signal_level','gofmap1080','cvmean','CVdev')
disp('done')
end
end
% csv and txt files
if strcmp('.csv',ext) == 1 || strcmp('.txt',ext) == 1
cho = questdlg('How would you like to export the values?', ...
'Export', ...
'Map','List','List');
switch cho
case 'Map'
T=table(map);
writetable(T,file,'Delimiter',',','WriteVariableNames',false);
if choice == 2 || choice == 3 || choice == 4
cvfile=[pathname,'CV_',filename];
T2=table(handles.holdcvmap);
writetable(T2,cvfile,'Delimiter',',','WriteVariableNames',false);
end
case 'List'
listmap=reshape(map,numel(map),1);
listmap=listmap(listmap>0);
listmap=listmap(isnan(listmap)==0);
T=table(listmap);
writetable(T,file,'Delimiter',',','WriteVariableNames',false);
if choice == 2 || choice == 3 || choice == 4
cvfile=[pathname,'CV_',filename];
CVmap=handles.holdcvmap;
listcvmap=reshape(CVmap,numel(CVmap),1);
listcvmap=listcvmap(listcvmap>0);
listcvmap=listcvmap(isnan(listcvmap)==0);
T=table(listcvmap);
writetable(T,cvfile,'Delimiter',',','WriteVariableNames',false);
end
end
end
% --- Executes on button press in act_movie.
function act_movie_Callback(hObject, ~, ~)
handles = guidata(hObject);
meme=0;
gifsave=questdlg('Save File?','Gif Save','Yes','No','Yes');
switch gifsave
case 'Yes'
meme=1;
case 'No'
meme=0;
end
map=handles.actmap;
if meme == 1
[a,b]=uiputfile('*.gif');
filename=[b,a];
end
h=figure;
hold on
imshow(map,[],'InitialMagnification', 800);
map=map;
if get(handles.isoopt,'Value') == 1
mini=0;
maxi=max(max(map)); %ms
end
if get(handles.isoopt,'Value') == 2
maxi=str2double(get(handles.isomax,'String'));
mini=str2double(get(handles.isomin,'String'));
end
maxiall=max(max(map));
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [0, 0, 0];
colormap(jetcolormap);
caxis([0 maxi]);
delay=0.01;
for j = 1:0.1:ceil(maxiall);
mapmask=(map<j);
A=map.*mapmask;
imshow(A, [mini ceil(maxi)], 'Colormap',jetcolormap, 'InitialMagnification', 400)
if meme == 1
frame = getframe(h);
im = frame2im(frame);
[imind,cm] = rgb2ind(im,256);
% Write to the GIF File
if j == 1
imwrite(imind,cm,filename,'gif', 'Loopcount',inf,'DelayTime',delay);
else
imwrite(imind,cm,filename,'gif','WriteMode','append','DelayTime',delay);
end
end
end
function isomin_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function isomin_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function isomax_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function isomax_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in isoopt.
function isoopt_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function isoopt_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in applyiso.
function applyiso_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
listbox2_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --- Executes on button press in pushbutton17.
function pushbutton17_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
axes(handles.mapaxes);
choice = questdlg('Video or Image?', ...
'Thing', ...
'Video','Image','Video');
switch choice
case 'Video'
[filename,pathname] = uiputfile({'*.avi'}, 'Save .avi image video file of currently displayed maps across all sections' );
[~,~,ext] = fileparts(filename);
file=[pathname,filename];
% if isdepolyed == 0
% cd(pathname)
% end
handles.filming = 1;
numsec=length(handles.section);
vidobj = VideoWriter(file);
vidobj.FrameRate=1;
open(vidobj);
set(gca,'nextplot','replacechildren');
guidata(hObject, handles);
%wb=waitbar(0.1,'Producing video file','WindowStyle', 'modal');
for k=1:numsec
handles.filmcount = k;
guidata(hObject,handles);
producemaps_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
axes(handles.mapaxes);
currFrame = getframe;
writeVideo(vidobj,currFrame);
0.1+0.9*(k/numsec)
%waitbar((0.1+0.9*(k/numsec)),wb);
end
close(vidobj);
%delete(wb)
set(handles.listbox2,'Value',numsec)
handles.filming = 0;
case 'Image'
handles.filming = 1;
numsec=length(handles.section);
for i=1:numsec
handles.filmcount = i;
handles.b2bimage=1;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles);
GUI_fig_children=get(gcf,'children');
Fig_Axes=findobj(GUI_fig_children,'type','Axes');
fig=figure;
ax=axes;clf;
new_handle=copyobj(handles.mapaxes,fig);
pretty=get(handles.colmap,'String'); jetcolormap = (colormap(pretty{get(handles.colmap,'Value')}));
jetcolormap(1,:) = [1, 1, 1];
colormap(jetcolormap);
set(gca,'ActivePositionProperty','outerposition')
set(gca,'Units','normalized')
set(gca,'OuterPosition',[i/numsec-0.2 i/numsec-0.2 i/numsec i/numsec])
%set(gca,'position',[0.1300 0.1100 0.7750 0.8150])
guidata(hObject, handles);
end
handles.filming=0
guidata(hObject, handles);
end
% --- Executes on button press in segEP.
function segEP_Callback(~, ~, ~)
segEP
% --- Executes on button press in fold.
function fold_Callback(~, ~, ~)
function framerate_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function framerate_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function pixelsize_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function pixelsize_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function binnumber_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function binnumber_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in getpixelinfo.
function getpixelinfo_Callback(hObject, ~, handles)
% hObject handle to getpixelinfo (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
compare
guidata(hObject, handles);
% --- Executes on button press in phasemap.
function phasemap_Callback(~, ~, ~)
% hObject handle to phasemap (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
phasemapping
% --- Executes on button press in compare.
function compare_Callback(~, ~, ~)
pixelinfo
% --- Executes on button press in pushbutton23.
function pushbutton23_Callback(~, ~, ~)
conduction
function beforeGUI_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function beforeGUI_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function afterGUI_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function afterGUI_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in velalgo.
function velalgo_Callback(hObject, eventdata, handles)
wb=waitbar(0.5,'Producing Isochronal map');
guidata(hObject, handles);
if get(handles.actfittimes,'Value') == 1
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevCV,varCV,SECV]=...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
0,400,str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
if get(handles.actfittimes,'Value') == 2
[actmap,~,~,act_t,quivers_X,quivers_Y,quivers_vx,quivers_vy,~,~,vout,quivers_Xout,quivers_Yout, quivers_vxout,quivers_vyout,onedevCV,varCV,SECV]=...
cvmap(str2double(get(handles.pixelsize,'String')),str2double(get(handles.framerate,'String')),handles.cvimages,handles.mask,get(handles.velout,'Value'),str2double(get(handles.minvel,'String')),str2double(get(handles.maxvel,'String')),get(handles.velalgo,'Value'),...
str2double(get(handles.MINt,'String')),str2double(get(handles.MAXt,'String')),str2double(get(handles.winsize,'String')),str2double(get(handles.beforeGUI,'String')),str2double(get(handles.wint,'String')),0,str2double(get(handles.t,'String')),get(handles.tfilt,'Value'),get(handles.usespline,'Value'),str2double(get(handles.splineN,'String')));
end
CVp=prctile(vout,[5,50,95]);
handles.errCV=[onedevCV,SECV,varCV,((CVp(3)-CVp(1))/CVp(2))];
rdata=handles.rdata;
rdata(2,1)=mean(vout);rdata(2,2)=handles.errCV(1);rdata(2,3)=handles.errCV(2);rdata(2,4)=handles.errCV(3);rdata(2,5)=handles.errCV(4);
handles.rdata=rdata;
set(handles.rtable,'Data',rdata);
disp('2768')
%save CV maps and vectors
handles.actmap=actmap;
handles.act_t=act_t;
handles.quivers_X=quivers_X;
handles.quivers_Y=quivers_Y;
handles.quivers_vx=quivers_vx;
handles.quivers_vy=quivers_vy;
handles.quivers_Xout=quivers_Xout;
handles.quivers_Yout=quivers_Yout;
handles.quivers_vxout=quivers_vxout;
handles.quivers_vyout=quivers_vyout;
delete(wb)
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% Hints: contents = cellstr(get(hObject,'String')) returns velalgo contents as cell array
% contents{get(hObject,'Value')} returns selected item from velalgo
% --- Executes during object creation, after setting all properties.
function velalgo_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in actopt.
function actopt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function actopt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function actmin_Callback(hObject, ~, ~)
handles = guidata(hObject);
tim=handles.act_t;
tim=tim-min(tim);
allpts=numel(tim);
xbins=0:0.01:max(tim);
tissueact=100*cumsum(hist(tim,xbins))/allpts;
actmax=str2double(get(handles.actmax,'String'));
actmin=str2double(get(handles.actmin,'String'));
Imax = find(tissueact > actmax);
Imin = find(tissueact > actmin);
if actmax < 100
Imax=Imax(1);
else
Imax=max(tim);
end
Imin=Imin(1);
if actmax < 100
timmax=Imax*0.01;
else
timmax=Imax;
end
timmin=Imin*0.01;
timdiff=timmax-timmin;
if actmin == 0
timdiff=timmax;
end
if get(handles.checkbox8,'Value')==1
normfac=225/allpts; %why 225?
timdiff=timdiff*normfac;
end
set(handles.actquote, 'String', [num2str(timdiff),' ms']);
guidata(hObject, handles);
% Hints: get(hObject,'String') returns contents of actmin as text
% str2double(get(hObject,'String')) returns contents of actmin as a double
% --- Executes during object creation, after setting all properties.
function actmin_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function actmax_Callback(hObject, ~, ~)
handles = guidata(hObject);
tim=handles.act_t;
tim=tim-min(tim);
allpts=numel(tim);
xbins=0:0.01:max(tim);
tissueact=100*cumsum(hist(tim,xbins))/allpts;
actmax=str2double(get(handles.actmax,'String'));
actmin=str2double(get(handles.actmin,'String'));
Imax = find(tissueact > actmax);
Imin = find(tissueact > actmin);
if actmax < 100
Imax=Imax(1);
else Imax=max(tim);
end
Imin=Imin(1);
if actmax < 100
timmax=Imax*0.01;
else timmax=Imax
end
timmin=Imin*0.01;
timdiff=timmax-timmin;
if actmin == 0
timdiff=timmax;
end
if get(handles.checkbox8,'Value')==1
normfac=225/allpts;
timdiff=timdiff*normfac;
end
set(handles.actquote, 'String', [num2str(timdiff),' ms']);
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function actmax_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in checkbox8.
function checkbox8_Callback(hObject, ~, ~)
handles = guidata(hObject);
tim=handles.act_t;
tim=tim-min(tim);
allpts=numel(tim);
xbins=0:0.01:max(tim);
tissueact=100*cumsum(hist(tim,xbins))/allpts;
actmax=str2double(get(handles.actmax,'String'));
actmin=str2double(get(handles.actmin,'String'));
Imax = find(tissueact > actmax);
Imin = find(tissueact > actmin);
if actmax < 100
Imax=Imax(1);
else
Imax=max(tim);
end
Imin=Imin(1);
if actmax < 100
timmax=Imax*0.01;
else
timmax=Imax;
end
timmin=Imin*0.01;
timdiff=timmax-timmin;
if actmin == 0
timdiff=timmax;
end
if get(handles.checkbox8,'Value')==1
pixar=str2double(get(handles.pixelsize,'String'));
pixar=pixar*pixar;
pixar=pixar/1000000; %convert to mm2
normfac=pixar*allpts;
timdiff=timdiff/normfac;
end
set(handles.actquote, 'String', [num2str(timdiff),' ms']);
function t_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
t=str2double(get(handles.t,'String'));
[apmap,meanapd,alll,onedev,var,SE]=mapsbaby(get(handles.aptime1,'Value'),str2double(get(handles.framerate,'String')),t,handles.I,handles.images,handles.averageBeat,handles.outlier,str2double(get(handles.cmin,'String')),str2double(get(handles.cmax,'String')),get(handles.tfilt,'Value'),str2double(get(handles.beforeGUI,'String')),get(handles.apdbl,'Value'),str2double(get(handles.apdblnum,'String')),handles.medifilt);
%alll=apmap(apmap>0);
APp=prctile(alll,[5,50,95]);
handles.err=[onedev,SE,var,((APp(3)-APp(1))/APp(2))];
%save AP,CV maps and vectors
handles.apdmap=apmap;
handles.apalll=alll;
rdata=handles.rdata;
rdata(1,1)=mean(alll);rdata(1,2)=handles.err(1);rdata(1,3)=handles.err(2);rdata(1,4)=handles.err(3);rdata(1,5)=handles.err(4);
handles.rdata=rdata;
guidata(hObject,handles)
set(handles.rtable,'Data',rdata);
disp('2977')
mapcho=get(handles.Mapchoice,'Value');
if mapcho == 1
Mapchoice_Callback(hObject, eventdata, handles);
end
guidata(hObject,handles)
% --- Executes during object creation, after setting all properties.
function t_CreateFcn(hObject, ~, ~)
% hObject handle to t (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in apdscale.
function apdscale_Callback(hObject, eventdata, ~)
% hObject handle to apdscale (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
Mapchoice_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function apdscale_CreateFcn(hObject, ~, ~)
% hObject handle to apdscale (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: popupmenu controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function MINt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function MINt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function MAXt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function MAXt_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in actfittimes.
function actfittimes_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function actfittimes_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function winsize_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function winsize_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function taustart_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
contents = cellstr(get(handles.Mapchoice,'String'));
choice=get(handles.Mapchoice,'Value');
if choice == 8
Mapchoice_Callback(hObject, eventdata, handles)
end
% --- Executes during object creation, after setting all properties.
function taustart_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function r2cut_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
contents = cellstr(get(handles.Mapchoice,'String'));
choice=get(handles.Mapchoice,'Value');
if choice == 8
Mapchoice_Callback(hObject, eventdata, handles)
end
% --- Executes during object creation, after setting all properties.
function r2cut_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function apdblnum_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function apdblnum_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in apdbl.
function apdbl_Callback(hObject, eventdata, handles)
t_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function apdbl_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function taufinish_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function taufinish_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function peakhigh_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function peakhigh_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function scal_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function scal_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function wint_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function wint_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in altanal.
function altanal_Callback(hObject, ~, ~)
alternangui
% --- Executes on button press in removef.
function removef_Callback(~, ~, ~)
% --- Executes on selection change in aptime1.
function aptime1_Callback(hObject, eventdata, handles)
t_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function aptime1_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in configure.
function configure_Callback(~, ~, handles)
% Construct a questdlg
choice = questdlg('Would you like to load a configuration file or save current settings?', ...
'Config File', ...
'New File', 'Load Settings','Load Settings');
% Handle response
switch choice
case 'New File'
[fname,PathName] = uiputfile('*.txt')
filename=[PathName,fname];
% create file for writing too
fileID = fopen(filename,'w');
dt=datetime('now'); dt=datestr(dt);
fprintf(fileID,'Configuration File for use in ElectroMap\r\n');
fprintf(fileID,['Created: ',dt,'\r\n'])
fprintf(fileID,['Notes:\r\n\r\n\r\n'])
fprintf(fileID,['--- DO NOT EDIT VARIABLE NAMES OR REMOVE ! BELOW THIS POINT, {} = units, () = settings in ElectroMap or Notes ---\r\n\r\n'])
%cell arrays for popdown menu strings
threshopt_string=get(handles.threshopt,'String');
thershopt_string=threshopt_string{get(handles.threshopt,'Value')};
sfilt_string=get(handles.sfilt,'String');
sfilt_string=sfilt_string{get(handles.sfilt,'Value')};
segchoice_string=get(handles.segchoice,'String');
segchoice_string=segchoice_string{get(handles.segchoice,'Value')}
BLopt_string=get(handles.BLopt,'String');
BLopt_string=BLopt_string{get(handles.BLopt,'Value')}
tfilt_string=get(handles.tfilt,'String');
tfilt_string=tfilt_string{get(handles.tfilt,'Value')};
apdbl_string=get(handles.apdbl,'String');
apdbl_string=apdbl_string{get(handles.apdbl,'Value')};
aptime1_string=get(handles.aptime1,'String');
aptime1_string=aptime1_string{get(handles.aptime1,'Value')};
velalgo_string=get(handles.velalgo,'String');
velalgo_string=velalgo_string{get(handles.velalgo,'Value')};
actfittimes_string=get(handles.actfittimes,'String');
actfittimes_string=actfittimes_string{get(handles.actfittimes,'Value')};
velout_string=get(handles.velout,'String');
velout_string=velout_string{get(handles.velout,'Value')};
apdout_string=get(handles.apdout,'String');
apdout_string=apdout_string{get(handles.apdout,'Value')};
apdscale_string=get(handles.apdscale,'String');
apdscale_string=apdscale_string{get(handles.apdscale,'Value')};
% get settings and put into file
fprintf(fileID,['framerate=',get(handles.framerate,'String'),'! {kHz} !\r\n']);
fprintf(fileID,['pixelsize=',get(handles.pixelsize,'String'),'! {ms} !!\r\n']);
fprintf(fileID,['threshopt=',num2str(get(handles.threshopt,'Value')),'! (',thershopt_string,')',' !\r\n']);
fprintf(fileID,['manthresh=',get(handles.manthresh,'String'),'! {Percent} (Change from automatically generated threshold) !\r\n']);
fprintf(fileID,['sfilt=',num2str(get(handles.sfilt,'Value')),'! (',sfilt_string,') !\r\n']);
fprintf(fileID,['sfiltsize=',get(handles.sfiltsize,'String'),'! {Pixels} !\r\n']);
fprintf(fileID,['segchoice=',num2str(get(handles.segchoice,'Value')),'! (',segchoice_string,') !\r\n']);
fprintf(fileID,['segsize=',get(handles.segsize,'String'),'! !\r\n']);
fprintf(fileID,['invertopt=',num2str(get(handles.invertopt,'Value')),'! (1 means invert signal) !\r\n']);
fprintf(fileID,['BLopt=',num2str(get(handles.BLopt,'Value')),'! (',BLopt_string,') !\r\n']);
fprintf(fileID,['thlen=',get(handles.thlen,'String'),'! {ms}, (Length of top-hat filter) !\r\n']);
fprintf(fileID,['tfilt=',num2str(get(handles.tfilt,'Value')),'! (',tfilt_string,') !\r\n']);
fprintf(fileID,['minpeak=',get(handles.minpeak,'String'),'! {ms} !\r\n']);
fprintf(fileID,['peakhigh=',get(handles.peakhigh,'String'),'! !\r\n']);
fprintf(fileID,['minnum=',get(handles.minnum,'String'),'! !\r\n']);
fprintf(fileID,['minbound=',get(handles.minbound,'String'),'! {ms} !\r\n']);
fprintf(fileID,['beforeGUI=',get(handles.beforeGUI,'String'),'! {ms} !\r\n']);
fprintf(fileID,['afterGUI=',get(handles.afterGUI,'String'),'! {ms} !\r\n']);
fprintf(fileID,['apdbl=',num2str(get(handles.apdbl,'Value')),'! (',apdbl_string,') !\r\n']);
fprintf(fileID,['apdblnum=',get(handles.apdblnum,'String'),'! {ms} !\r\n']);
fprintf(fileID,['aptime1=',num2str(get(handles.aptime1,'Value')),'! (',aptime1_string,') !\r\n']);
fprintf(fileID,['taustart=',get(handles.taustart,'String'),'! {Percent} !\r\n']);
fprintf(fileID,['taufinish=',get(handles.taufinish,'String'),'! {Percent} !\r\n']);
fprintf(fileID,['r2cut=',get(handles.r2cut,'String'),'! !\r\n']);
fprintf(fileID,['velalgo=',num2str(get(handles.velalgo,'Value')),'! (',velalgo_string,') (Activation Measure) !\r\n']);
fprintf(fileID,['isoopt=',num2str(get(handles.isoopt,'Value')),'! !\r\n']);
fprintf(fileID,['isomin=',get(handles.isomin,'String'),'! {ms} !\r\n']);
fprintf(fileID,['isomax=',get(handles.isomax,'String'),'! {ms} !\r\n']);
fprintf(fileID,['actfittimes=',num2str(get(handles.actfittimes,'Value')),'! (',actfittimes_string,') !\r\n']);
fprintf(fileID,['MINt=',get(handles.MINt,'String'),'! {ms} (Minimum activation time for multi-vector fit) !\r\n']);
fprintf(fileID,['MAXt=',get(handles.MAXt,'String'),'! {ms} (Maximum activation time for multi-vector fit) !\r\n']);
fprintf(fileID,['velout=',num2str(get(handles.velout,'Value')),'! (',velout_string,') (Local Velocity outlier removal) !\r\n']);
fprintf(fileID,['minvel=',get(handles.minvel,'String'),'! {ms} (Minimum calcualted velocity that is not discarded) !\r\n']);
fprintf(fileID,['maxvel=',get(handles.maxvel,'String'),'! {ms} (Maximum calculated velocity that is not discarded) !\r\n']);
fprintf(fileID,['winsize=',get(handles.winsize,'String'),'!{Pixels} (Local window size) !\r\n']);
fprintf(fileID,['scal=',get(handles.scal,'String'),'! (Size of overlaid velocity vectors) !\r\n']);
fprintf(fileID,['wint=',get(handles.wint,'String'),'! (Maximum time diffrence allowed in local window fit) !\r\n']);
fprintf(fileID,['apdout=',num2str(get(handles.apdout,'Value')),'! (',apdout_string,') (APD/CaD outlier removal) !\r\n']);
fprintf(fileID,['apdscale=',num2str(get(handles.apdscale,'Value')),'! (',apdscale_string,') !\r\n']);
fprintf(fileID,['cmin=',get(handles.cmin,'String'),'! {ms} (manual colour map minimum)!\r\n']);
fprintf(fileID,['cmax=',get(handles.cmax,'String'),'! {ms} (manual colour map maximum)!\r\n']);
fprintf(fileID,['t=',get(handles.t,'String'),'! {Percent} (APD/CaD)!\r\n']);
fprintf(fileID,['checkbox8=',num2str(get(handles.checkbox8,'Value')),'! (1 means normalised to {ms/mm2}, 0 absoulte in {ms})!\r\n']);
fprintf(fileID,['actmin=',get(handles.actmin,'String'),'! {Percent}!\r\n']);
fprintf(fileID,['actmax=',get(handles.actmax,'String'),'! {Percent}!\r\n']);
fprintf(fileID,['binnumber=',get(handles.binnumber,'String'),'!!\r\n']);
% close file
fclose(fileID);
case 'Load Settings'
[fname,PathName] = uigetfile('*.txt');
filename=[PathName,fname];
%% open file for reading
fid=fopen(filename,'r','b')
fstr=fread(fid,'int8=>char')';
fclose(fid);
%% Update GUI
set(handles.framerate,'String',varEM(fstr,'framerate',0))
set(handles.pixelsize,'String',varEM(fstr,'pixelsize',0))
set(handles.threshopt,'Value',varEM(fstr,'threshopt',1))
set(handles.manthresh,'String',varEM(fstr,'manthresh',0))
set(handles.sfilt,'Value',varEM(fstr,'sfilt',1))
set(handles.sfiltsize,'String',varEM(fstr,'sfiltsize',0))
set(handles.segchoice,'Value',varEM(fstr,'segchoice',1))
set(handles.segsize,'String',varEM(fstr,'segsize',0))
set(handles.invertopt,'Value',varEM(fstr,'invertopt',1))
set(handles.BLopt,'Value',varEM(fstr,'BLopt',1))
set(handles.tfilt,'Value',varEM(fstr,'tfilt',1))
set(handles.minpeak,'String',varEM(fstr,'minpeak',0))
set(handles.peakhigh,'String',varEM(fstr,'peakhigh',0))
set(handles.minnum,'String',varEM(fstr,'minnum',0))
set(handles.minbound,'String',varEM(fstr,'minbound',0))
set(handles.beforeGUI,'String',varEM(fstr,'beforeGUI',0))
set(handles.afterGUI,'String',varEM(fstr,'afterGUI',0))
set(handles.apdbl,'Value',varEM(fstr,'apdbl',1))
set(handles.apdblnum,'String',varEM(fstr,'apdblnum',0))
set(handles.aptime1,'Value',varEM(fstr,'aptime1',1))
set(handles.taustart,'String',varEM(fstr,'taustart',0))
set(handles.taufinish,'String',varEM(fstr,'taufinish',0))
set(handles.r2cut,'String',varEM(fstr,'r2cut',0))
set(handles.velalgo,'Value',varEM(fstr,'velalgo',1))
set(handles.isoopt,'Value',varEM(fstr,'isoopt',1))
set(handles.isomin,'String',varEM(fstr,'isomin',0))
set(handles.isomax,'String',varEM(fstr,'isomax',0))
set(handles.actfittimes,'Value',varEM(fstr,'actfittimes',1))
set(handles.MINt,'String',varEM(fstr,'MINt',0))
set(handles.MAXt,'String',varEM(fstr,'MAXt',0))
set(handles.velout,'Value',varEM(fstr,'velout',1))
set(handles.minvel,'String',varEM(fstr,'minvel',0))
set(handles.maxvel,'String',varEM(fstr,'maxvel',0))
set(handles.winsize,'String',varEM(fstr,'winsize',0))
set(handles.scal,'String',varEM(fstr,'scal',0))
set(handles.wint,'String',varEM(fstr,'wint',0))
set(handles.apdout,'Value',varEM(fstr,'apdout',1))
set(handles.apdscale,'Value',varEM(fstr,'apdscale',1))
set(handles.cmin,'String',varEM(fstr,'cmin',0))
set(handles.cmax,'String',varEM(fstr,'cmax',0))
set(handles.t,'String',varEM(fstr,'t',0))
set(handles.checkbox8,'Value',varEM(fstr,'checkbox8',1))
set(handles.actmin,'String',varEM(fstr,'actmin',0))
set(handles.actmax,'String',varEM(fstr,'actmax',0))
set(handles.binnumber,'String',varEM(fstr,'binnumber',0))
set(handles.thlen,'String',varEM(fstr,'thlen',0))
end
function thlen_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function thlen_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in colmap.
function colmap_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
Mapchoice_Callback(hObject, eventdata, handles)
% --- Executes during object creation, after setting all properties.
function colmap_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in drawcon.
function drawcon_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
Mapchoice_Callback(hObject, eventdata, handles)
% --- Executes on button press in roibutton.
function roibutton_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
choice = questdlg('Save Current ROI or load previous?', ...
'ROI', ...
'Save ROI','Load ROI','Save ROI');
% Handle response
switch choice
case 'Save ROI'
[filename,pathname] = uiputfile({'*.txt'}, 'Save ROI in text file');
file=[pathname,filename];
savemask=handles.mask;
figure,
imshow(savemask,[])
dlmwrite(file,savemask);
lmask=maskload(file)
figure,
imshow(lmask,[])
size(savemask)
size(lmask)
case 'Load ROI'
[filename,pathname] = uigetfile('*.txt','Select the ROI File');
file=[pathname,filename];
handles.loadedmask=maskload(file)
handles.herefromroiload=1;
guidata(hObject, handles);
pushload_Callback(hObject, eventdata, handles)
handles = guidata(hObject); %%update handles after doing OMimload
handles.herefromroiload=0;
guidata(hObject, handles);
end
guidata(hObject, handles);
% --- Executes on button press in rawvid.
function rawvid_Callback(hObject, ~, ~)
handles = guidata(hObject);
axes(handles.imageaxes)
[rows, cols]=size(handles.im);
images=handles.images;
mask=handles.mask;
images=imcomplement(images);
im=handles.im;
im=double(im);
im=im-min(min(im));
im=im./max(max(im));
im=im*65535;
im=uint16(im);
savegif=1;
if savegif == 1
[a,b]=uiputfile('*.gif');
filename=[b,a];
end
prompt = {'Fluorescence threshold (0-1):','Video Start (s):','Video End (s)','Normalise? (0=no, 1=yes)'};
dlg_title = 'Raw Video Options';
num_lines = 1;
exposure=1/str2double(get(handles.framerate,'String'));
defaultans = {'0.2','0',num2str(size(images,3)/1000*exposure),'1'};
opts = inputdlg(prompt,dlg_title,num_lines,defaultans);
flthresh=str2double(opts{1});
istart=str2double(opts{2});
iend=str2double(opts{3});
normF=str2double(opts{4});
%change is to frame #
istart=round((istart/exposure)*1000);
iend=round((iend/exposure)*1000);
if istart == 0
istart = 1;
end
if iend > size(images,3)
iend = size(images,3);
end
for r=1:rows
for c=1:cols
sig=squeeze(images(r,c,:));
sig=sig-min(sig);
sig=double(sig);
if normF == 1
sig=(sig./max(sig))*65535;
end
sig=uint16(sig);
images(r,c,:)=sig;
end
end
wb=waitbar(0,'Saving Raw Video');
images=double(images);
mask=double(mask);
maxval=max(max(max(images)));
background = repmat(im, [1, 1, 3]);
for i =istart:iend
waitbar(i/(iend-istart),wb,'Saving Raw Video');
combinedImage = background;
foreground=images(:,:,i).*mask;
foreground=foreground./maxval;
foreground(foreground < flthresh) = 0;
foregroundColourised = colouriseData(foreground, 'j',flthresh,1);
c1 = combinedImage(:, :, 1);
c2 = combinedImage(:, :, 2);
c3 = combinedImage(:, :, 3);
f1 = foregroundColourised(:, :, 1);
f2 = foregroundColourised(:, :, 2);
f3 = foregroundColourised(:, :, 3);
c1(sum(foreground, 3) ~= 0) = f1(sum(foreground, 3) ~= 0);
c2(sum(foreground, 3) ~= 0) = f2(sum(foreground, 3) ~= 0);
c3(sum(foreground, 3) ~= 0) = f3(sum(foreground, 3) ~= 0);
combinedImage(:, :, 1) = c1;
combinedImage(:, :, 2) = c2;
combinedImage(:, :, 3) = c3;
hold on
axis image;
axis off;
if savegif == 1
delay=0.01;
[imind,cm] = rgb2ind(combinedImage,256);
% Write to the GIF File
if i == istart
imwrite(imind,cm,filename,'gif', 'Loopcount',inf,'DelayTime',delay);
else
imwrite(imind,cm,filename,'gif','WriteMode','append','DelayTime',delay);
end
end
end
delete(wb)
% --- Executes on button press in resegment.
function resegment_Callback(hObject, eventdata, handles)
handles.herefromsegmentpush=1;
guidata(hObject, handles);
pushprocess_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
handles.herefromsegmentpush = 0;
guidata(hObject, handles);
producemaps_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
guidata(hObject, handles);
% --- Executes on button press in B2B.
function B2B_Callback(hObject, eventdata, handles)
handles.herefromsegmentpush=1;
set(handles.segsize,'String',1);
set(handles.segchoice,'Value',2);
guidata(hObject, handles);
pushprocess_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
handles.herefromsegmentpush = 0;
guidata(hObject, handles);
producemaps_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
guidata(hObject, handles);
% --- Executes on selection change in winopt.
function winopt_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function winopt_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in segsignal.
function segsignal_Callback(hObject, eventdata, handles)
handles.herefromsegmentpush=1;
guidata(hObject, handles);
pushprocess_Callback(hObject, eventdata, handles)
handles = guidata(hObject);
% --- Executes during object creation, after setting all properties.
function segsignal_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function sfiltsigma_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function sfiltsigma_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on selection change in usespline.
function usespline_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function usespline_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function splineN_Callback(~, ~, ~)
% --- Executes during object creation, after setting all properties.
function splineN_CreateFcn(hObject, ~, ~)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushbutton35.
function pushbutton35_Callback(~, ~, ~)
% --------------------------------------------------------------------
function freqmapopt_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
prompt = {'Minimum Frequency (Hz):','Maximum Frequency (Hz):','Frequency Bin Size (Hz)','Window? 0 = no, 1 = hann'};
dims = [1 35];
definput = {num2str(handles.fmin),num2str(handles.fmax),num2str(handles.fbin),num2str(handles.dfwin)};
answer = inputdlg(prompt,'Frequnecy Mapping Options',dims,definput)
handles.fmin=str2double(answer{1});
handles.fmax=str2double(answer{2});
handles.fbin=str2double(answer{3});
handles.dfwin=str2double(answer{4});
guidata(hObject, handles);
if get(handles.Mapchoice,'Value') == 5;
Mapchoice_Callback(hObject, eventdata, handles)
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function ROInum_Callback(hObject, ~, ~)
handles = guidata(hObject);
prompt = {'Number of ROIs:','Remove overlapping pixels? (0=Yes) (1=No)'};
dims = [1 35];
definput = {num2str(handles.roinum),num2str(handles.roisum)};
answer = inputdlg(prompt,'ROI options',dims,definput)
handles.roinum=str2double(answer{1});
handles.roisum=str2double(answer{2});
guidata(hObject, handles);
% --------------------------------------------------------------------
function Untitled_1_Callback(~, ~, ~)
% --------------------------------------------------------------------
function Untitled_5_Callback(~, ~, ~)
%% ColourMaps
function coljet_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',1);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colhsv_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',2);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colhot_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',3);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colcool_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',4);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colparula_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',5);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colspring_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',6);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colsummer_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',7);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colautumn_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',8);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function colwinter_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
set(handles.colmap,'Value',9);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function Untitled_3_Callback(~, ~, ~)
% --------------------------------------------------------------------
function Untitled_4_Callback(~, ~, ~)
% --------------------------------------------------------------------
function Untitled_6_Callback(~, ~, ~)
% --------------------------------------------------------------------
function bgblack_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.bgcol='k';
handles.bgon=1;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function bgwhite_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.bgcol='w';
handles.bgon=1;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function bgtran_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.bgon=0;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
guidata(hObject, handles);
% --------------------------------------------------------------------
function snrcalc_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
prompt = {'Signal before time (from peak) (ms):','Signal after time (from peak) (ms):'};
dims = [1 35];
definput = {num2str(handles.snrt1),num2str(handles.snrt2)};
answer = inputdlg(prompt,'Frequnecy Mapping Options',dims,definput);
handles.snrt1=str2double(answer{1});
handles.snrt2=str2double(answer{2});
guidata(hObject, handles);
if get(handles.Mapchoice,'Value') == 10 || get(handles.Mapchoice,'Value') == 1
Mapchoice_Callback(hObject, eventdata, handles)
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function ttpset_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
prompt = {'Start Point (%):','End Point (%):'};
dims = [1 35];
definput = {num2str(handles.ttpstart),num2str(handles.ttpend)};
answer = inputdlg(prompt,'Frequnecy Mapping Options',dims,definput);
handles.ttpstart=str2double(answer{1});
handles.ttpend=str2double(answer{2});
guidata(hObject, handles);
if get(handles.Mapchoice,'Value') == 7
Mapchoice_Callback(hObject, eventdata, handles)
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function Untitled_7_Callback(~, ~, ~)
% --------------------------------------------------------------------
function connnnnnnnnnn_Callback(~, ~, ~)
% --------------------------------------------------------------------
function conoff_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.drawcon=0;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function conon_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.drawcon=1;
prompt = {'Contour spacing (map units):'};
dims = [1 35];
if isempty(handles.conbon) == 1
handles.framerate
conbount=1/str2double(get(handles.framerate,'String'));
handles.conbon=num2str(conbount);
end
definput = {num2str(handles.conbon)};
answer = inputdlg(prompt,'Contour Setting',dims,definput);
handles.conbon=answer{1};
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function nomedifilt_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.medifilt=0;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
% --------------------------------------------------------------------
function yesmedifilt_Callback(hObject, eventdata, ~)
handles = guidata(hObject);
handles.medifilt=1;
guidata(hObject, handles);
Mapchoice_Callback(hObject, eventdata, handles)
function squareROI_Callback(~,~,~)
% --------------------------------------------------------------------
function frameremoval_Callback(hObject, eventdata, handles)
% hObject handle to frameremoval (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
handles.drawcon=1;
prompt = {'Frames before pulse to remove:','Frames after pulse to remove:'};
dims = [1 35];
definput = {num2str(handles.pbefore),num2str(handles.pafter)};
answer = inputdlg(prompt,'Contour Setting',dims,definput);
handles.pbefore=str2double(answer{1});
handles.pafter=str2double(answer{2});
guidata(hObject, handles);
% --------------------------------------------------------------------
function WS_mapping_Callback(hObject, eventdata, handles)
% hObject handle to WS_mapping (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
prompt = {'Set similarity thershold (radians)'};
dims = [1 35];
definput = {num2str(handles.ep)};
answer = inputdlg(prompt,'Frequnecy Mapping Options',dims,definput)
handles.ep=str2num(answer{1});
guidata(hObject, handles);
if get(handles.Mapchoice,'Value') == 11;
Mapchoice_Callback(hObject, eventdata, handles)
end
guidata(hObject, handles);
% --------------------------------------------------------------------
function dFdt_mapping_Callback(hObject, eventdata, handles)
% hObject handle to dFdt_mapping (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles = guidata(hObject);
prompt = {'dFdt level','Interpolation Framerate'};
dims = [1 35];
definput = {num2str(handles.dFlevel),num2str(handles.i_framerate)};
answer = inputdlg(prompt,'dFdt options',dims,definput)
handles.dFlevel=str2double(answer{1});
handles.i_framerate=str2double(answer{2});
guidata(hObject, handles);
if get(handles.Mapchoice,'Value') == 12;
Mapchoice_Callback(hObject, eventdata, handles)
end
guidata(hObject, handles);

ElectroMap.m at commit a1fc5f2, under BSD-3-Clause · at the source

Overview

Authors: Anqi Du¹, Bo Li², Guangqi Chen³, Na Wang², Chuanyu Li¹, Shaowen Tian¹, Weichao Liu³, Junqing Sun¹

ORCID iDs: Junqing Sun

Institutions: Guilin Medical University (China); Southwest Medical University (China); Affiliated Hospital of Southwest Medical University (China)

Journal: iScience, volume 29, issue 8, article 117048

Dates: received 3 March 2026; accepted 17 July 2026; published online 3 August 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1016/j.isci.2026.117048 · PMID 42597762 · PMCID PMC13470416 · OpenAlex W7172320414

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: other (modality), epilepsy (population)

Methods: Statistics, Smoothing, state filtering, decompositions, Evoked potentials, Physiology & signal measures

Keywords: epilepsy, cardiac autonomic regulation, heart rate variability, generalized seizures

Topic: Heart Rate Variability and Autonomic Control (Cardiology and Cardiovascular Medicine, Medicine), according to OpenAlex

Funding: Sichuan Province Science and Technology Support Program (2024JDRC0034); National Natural Science Foundation of China (82160642, 32360220); Guangxi Science and Technology Plan Project (GK2025GXNSFAA069809)

Citations: not cited yet (Europe PMC); 26 references in the paper

Research resources: Mouse: C57BL/6J RRID:IMSR_JAX:000664

Abstract

Epileptic seizures are associated with cardiovascular disturbances, yet how cardiac autonomic regulation changes across repeated seizures remains unclear. Here, using a pentylenetetrazol-induced murine model, we combined ECG telemetry, heart rate variability (HRV) analysis, pharmacological intervention, optical mapping, and brainstem patch-clamp recordings to characterize seizure-associated autonomic responses. Acute seizures produced transient bradyarrhythmias and increased HRV indices that were attenuated by muscarinic blockade. In contrast, repeated seizures reduced HRV and decreased the excitability of cardiac vagal neurons in the nucleus ambiguus, whereas optical mapping detected no significant intrinsic myocardial electrophysiological abnormalities. Together, these findings identify dynamic, stage-dependent alterations in cardiac autonomic regulation during recurrent generalized seizures, with distinct autonomic changes observed following acute and repeated seizure exposure.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

CXO531/ElectroMap

License: BSD-3-Clause

State: the link answers, verified on 26 September 2026

Evidence: files inventoried

Commit: a1fc5f2ded39ec84ad49e38853b852a6fe1cc805, 25 June 2020

Languages: MATLAB (75)

Size: 98 files, 75 scripts

Software Heritage: not archived

Found in: the resources table

Holds: README, license file

Not found: CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Signal Processing Toolbox (39 files), Image Processing Toolbox (24 files), Statistics and Machine Learning Toolbox (8 files)

Availability: 1 check, the latest on 26 September 2026: the link answers

26 September 2026: the link answers

77 files

Source Code - OWS and dFdt update/DInt.m, MATLAB, 248 lines
Source Code - OWS and dFdt update/ElectroMap.m, MATLAB, 4,115 lines, 1 match
Source Code - OWS and dFdt update/OMimload.m, MATLAB, 274 lines
Source Code - OWS and dFdt update/OMimprocess.m, MATLAB, 207 lines
Source Code - OWS and dFdt update/OMimreload.m, MATLAB, 213 lines
Source Code - OWS and dFdt update/Omseg2.m, MATLAB, 218 lines
Source Code - OWS and dFdt update/TIFFStack.m, MATLAB, 1,891 lines
Source Code - OWS and dFdt update/activationmapoff.m, MATLAB, 389 lines
Source Code - OWS and dFdt update/alfn.m, MATLAB, 185 lines
Source Code - OWS and dFdt update/alternangui.m, MATLAB, 1,410 lines
Source Code - OWS and dFdt update/cbfreeze.m, MATLAB, 449 lines
Source Code - OWS and dFdt update/cbhandle.m, MATLAB, 228 lines
Source Code - OWS and dFdt update/colouriseData.m, MATLAB, 181 lines
Source Code - OWS and dFdt update/compare.m, MATLAB, 463 lines
Source Code - OWS and dFdt update/conduction.m, MATLAB, 1,084 lines
Source Code - OWS and dFdt update/cvmap.m, MATLAB, 616 lines
Source Code - OWS and dFdt update/dFmap.m, MATLAB, 88 lines
Source Code - OWS and dFdt update/deleteoutliers.m, MATLAB, 103 lines
Source Code - OWS and dFdt update/domfreq.m, MATLAB, 86 lines
Source Code - OWS and dFdt update/fluo_map.m, MATLAB, 64 lines
Source Code - OWS and dFdt update/fluo_map_raw.m, MATLAB, 25 lines
Source Code - OWS and dFdt update/freezeColors.m, MATLAB, 275 lines
Source Code - OWS and dFdt update/localfitt.m, MATLAB, 63 lines
Source Code - OWS and dFdt update/mapsbaby.m, MATLAB, 303 lines
Source Code - OWS and dFdt update/mapsbabyonepix.m, MATLAB, 429 lines
Source Code - OWS and dFdt update/maskload.m, MATLAB, 72 lines
Source Code - OWS and dFdt update/master_vel.m, MATLAB, 50 lines
Source Code - OWS and dFdt update/phasemapping.m, MATLAB, 340 lines
Source Code - OWS and dFdt update/pixelinfo.m, MATLAB, 352 lines
Source Code - OWS and dFdt update/segEP.m, MATLAB, 1,686 lines
Source Code - OWS and dFdt update/segapd.m, MATLAB, 345 lines
Source Code - OWS and dFdt update/snrs.m, MATLAB, 60 lines
Source Code - OWS and dFdt update/tautest3.m, MATLAB, 215 lines
Source Code - OWS and dFdt update/ttpnew.m, MATLAB, 183 lines
Source Code - OWS and dFdt update/upmap.m, MATLAB, 111 lines
Source Code - OWS and dFdt update/varEM.m, MATLAB, 34 lines
Source Code - OWS and dFdt update/velcalc2.m, MATLAB, 111 lines
Source Code - OWS and dFdt update/wavesim.m, MATLAB, 169 lines
Source Code/DInt.m, MATLAB, 248 lines
Source Code/ElectroMap.m, MATLAB, 3,887 lines, 1 match
Source Code/OMimload.m, MATLAB, 237 lines
Source Code/OMimprocess.m, MATLAB, 184 lines
Source Code/OMimreload.m, MATLAB, 213 lines
Source Code/Omseg2.m, MATLAB, 218 lines
Source Code/activationmapoff.m, MATLAB, 389 lines
Source Code/alfn.m, MATLAB, 185 lines
Source Code/alternangui.m, MATLAB, 1,410 lines
Source Code/cbfreeze.m, MATLAB, 449 lines
Source Code/cbhandle.m, MATLAB, 228 lines
Source Code/colouriseData.m, MATLAB, 181 lines
Source Code/compare.m, MATLAB, 463 lines
Source Code/conduction.m, MATLAB, 1,084 lines
Source Code/cvmap.m, MATLAB, 616 lines
Source Code/deleteoutliers.m, MATLAB, 103 lines
Source Code/domfreq.m, MATLAB, 86 lines
Source Code/fluo_map.m, MATLAB, 64 lines
Source Code/fluo_map_raw.m, MATLAB, 25 lines
Source Code/freezeColors.m, MATLAB, 275 lines
Source Code/localfitt.m, MATLAB, 63 lines
Source Code/mapsbaby.m, MATLAB, 303 lines
Source Code/mapsbabyonepix.m, MATLAB, 429 lines
Source Code/maskload.m, MATLAB, 72 lines
Source Code/master_vel.m, MATLAB, 50 lines
Source Code/phasemapping.m, MATLAB, 340 lines
Source Code/pixelinfo.m, MATLAB, 352 lines
Source Code/segEP.m, MATLAB, 1,686 lines
Source Code/segapd.m, MATLAB, 345 lines
Source Code/snrs.m, MATLAB, 60 lines
Source Code/tautest3.m, MATLAB, 215 lines
Source Code/ttpnew.m, MATLAB, 183 lines
Source Code/upmap.m, MATLAB, 111 lines
Source Code/varEM.m, MATLAB, 34 lines
Source Code/velcalc2.m, MATLAB, 111 lines
ghsnew.m, MATLAB, 54 lines
rhsnew.m, MATLAB, 120 lines
License.txt, License, 27 lines
README.md, Text, 46 lines

At the source: github.com/CXO531/ElectroMap

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
75 scripts, each with its path and the digest of its content;
2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data and code availability

The data reported in this paper will be shared by the lead contact upon reasonable request.

This paper does not report original code.

Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon reasonable request.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 3, 28 September 2026

Authors: added Junqing Sun (0009-0007-4884-0585); removed Junqing Sun

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 8 authors, 4 keywords, 3 funders, 26 references, 1 RRID.

Cite

This paper

Du, A., Li, B., Chen, G., Wang, N., Li, C., Tian, S., Liu, W., & Sun, J. (2026). Dynamic alterations in cardiac autonomic regulation during recurrent generalized seizures. iScience, 29(8), 117048. https://doi.org/10.1016/j.isci.2026.117048

BibTeX

@article{du2026dynamic, author = {Du, Anqi and Li, Bo and Chen, Guangqi and Wang, Na and Li, Chuanyu and Tian, Shaowen and Liu, Weichao and Sun, Junqing}, title = {{Dynamic alterations in cardiac autonomic regulation during recurrent generalized seizures}}, journal = {iScience}, year = {2026}, month = aug, volume = {29}, number = {8}, pages = {117048}, publisher = {Elsevier}, issn = {2589-0042}, doi = {10.1016/j.isci.2026.117048}, url = {https://doi.org/10.1016/j.isci.2026.117048}, pmid = {42597762}, pmcid = {PMC13470416} }

RIS

TY - JOUR AU - Du, Anqi AU - Li, Bo AU - Chen, Guangqi AU - Wang, Na AU - Li, Chuanyu AU - Tian, Shaowen AU - Liu, Weichao AU - Sun, Junqing TI - Dynamic alterations in cardiac autonomic regulation during recurrent generalized seizures T2 - iScience J2 - iScience PY - 2026 DA - 2026/08/03 VL - 29 IS - 8 SP - 117048 SN - 2589-0042 PB - Elsevier DO - 10.1016/j.isci.2026.117048 UR - https://doi.org/10.1016/j.isci.2026.117048 LA - en ER -

CSL-JSON

{ "id": "10.1016/j.isci.2026.117048", "type": "article-journal", "title": "Dynamic alterations in cardiac autonomic regulation during recurrent generalized seizures", "container-title": "iScience", "author": [ { "family": "Du", "given": "Anqi" }, { "family": "Li", "given": "Bo" }, { "family": "Chen", "given": "Guangqi" }, { "family": "Wang", "given": "Na" }, { "family": "Li", "given": "Chuanyu" }, { "family": "Tian", "given": "Shaowen" }, { "family": "Liu", "given": "Weichao" }, { "family": "Sun", "given": "Junqing" } ], "container-title-short": "iScience", "volume": "29", "issue": "8", "page": "117048", "DOI": "10.1016/j.isci.2026.117048", "PMID": "42597762", "PMCID": "PMC13470416", "ISSN": "2589-0042", "publisher": "Elsevier", "URL": "https://doi.org/10.1016/j.isci.2026.117048", "language": "en", "issued": { "date-parts": [ [ 2026, 8, 3 ] ] } }

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