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ImagePro_v1p23_20231101_zc.m
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ImagePro_v1p23_20231101_zc.m
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function varargout = ImagePro_v1p23_20231101_zc(varargin)
% IMAGEPRO_V1P23_20231101_ZC M-file for ImagePro_v1p23_20231101_zc.fig
% IMAGEPRO_V1P23_20231101_ZC, by itself, creates a new IMAGEPRO_V1P23_20231101_ZC or raises the existing
% singleton*.
%
% H = IMAGEPRO_V1P23_20231101_ZC returns the handle to a new IMAGEPRO_V1P23_20231101_ZC or the handle to
% the existing singleton*.
%
% IMAGEPRO_V1P23_20231101_ZC('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in IMAGEPRO_V1P23_20231101_ZC.M with the given input arguments.
%
% IMAGEPRO_V1P23_20231101_ZC('Property','Value',...) creates a new IMAGEPRO_V1P23_20231101_ZC or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before ImagePro_v1p23_20231101_zc_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to ImagePro_v1p23_20231101_zc_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help ImagePro_v1p23_20231101_zc
% Last Modified by GUIDE v2.5 01-Nov-2023 12:53:23
% Begin initialization code - DO NOT EDIT
% Update Log:
% leiz 20231101
% fixed Movie button for saving current images in the listbox into .mp4
% fixed colorbar button
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ImagePro_v1p23_20231101_zc_OpeningFcn, ...
'gui_OutputFcn', @ImagePro_v1p23_20231101_zc_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 ImagePro_v1p23_20231101_zc is made visible.
function ImagePro_v1p23_20231101_zc_OpeningFcn(hObject, eventdata, handles, varargin) %#ok<*INUSL>
% This function has no output args, see OutputFcn.
% hObject handle to figure
% varargin command line arguments to ImagePro_v1p23_20231101_zc (see VARARGIN)
% Choose default command line output for ImagePro_v1p23_20231101_zc
handles.output = hObject;
%
colorTmp=[1,0,0;
0,1,0;
0,0,1;
0.502,0,1;
0,1,1;
1,0,1;
0.3,0.3,0.7;
0.5,1/2,1/2];
handles.appBG = [];
handles.colorTmp=colorTmp;
handles.filePathMat={};
handles.fileNameMat={};
handles.fileMat=[];
handles.pMat=[];
handles.appHome = fileparts(which(mfilename));
handles.bgColor=get(gcf,'color');
if exist([handles.appHome,filesep,'zfhc.png'])
axis(handles.axes_rawImg);
imshow(imread([handles.appHome,filesep,'zfhc.png']));
else
text(0.5, 0.6, {'\bfKindt Lab';'\fontsize{36}For Fish Fun'},...
'interpreter','tex','Units','normalized',...
'horizontalAlignment','center','Fontsize',52,'Color',[0.75,0.75,0.75]);
end
handles.fileType = 'png';
axis off;
hold off;
guidata(hObject, handles);
% UIWAIT makes ImagePro_v1p23_20231101_zc wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = ImagePro_v1p23_20231101_zc_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pb_imgLoad.
function pb_imgLoad_Callback(hObject, eventdata, handles)
% hObject handle to pb_imgLoad (see GCBO)
cdDefault=cd;
set(handles.pb_imgLoad,'backgroundcolor',handles.bgColor);
% t=get(gcf,'children');
% set(findobj(t,'style','text'),'backgroundcolor',c1);
% set(findobj(t,'style','checkbox'),'backgroundcolor',c1);
% set(findobj(t,'style','pushbutton'),'backgroundcolor',c1);
% set(findobj(t,'type','uipanel'),'backgroundcolor',c1)
method='imgLoad';
handles=imgLoadInitial(hObject,handles,method);
if strcmp(handles.fileType,'mat')~=1
cd(handles.filePath)
imgInfo=imfinfo(handles.fileName(1).name);
uint8Flag=imgInfo.BitDepth;
if uint8Flag==24
uint8Flag=8;
elseif uint8Flag==16*3
uint8Flag=16;
elseif uint8Flag==1
uint8Flag=8;
end
handles.imgDepth=['uint',num2str(uint8Flag)];
else
handles.imgDepth='uint8';
end
handles=pp_spfilterMethod_Callback(handles.pp_spfilterMethod, eventdata, handles);
% handles=pp_2filterMethod_outside(hObject,handles);
% handles=filterInfoRead2_spatial(handles);
% cd(cdDefault);
%set(allchild(gcf),'unit','normalized')
set(handles.pb_imgLoad,'BackgroundColor',[0.3,0.75,0.93]);
guidata(hObject,handles);
function handles=imgLoadInitial(hObject,handles,method)
pathWhich=which(mfilename);
dotNO=strfind(pathWhich,filesep);
dotNO=dotNO(end);
pathWhich=pathWhich(1:dotNO-1);
path(pathWhich,path);
cdDef=cd;
%% reset .mat file list
handles.filePathMat={};
handles.fileNameMat={};
handles.fileMat=[];
%%
if strcmp(method,'imgLoad')
if isfield(handles,'filePath_output')
cd(handles.filePath_output)
end
if get(handles.cb_cdCurrent,'value')
cd(cdDef)
end
[file,filePath]=uigetfile('*.*');
if filePath==0
filePath=handles.filePath_output;
file=handles.file;
end
cd(filePath);
indexNO=strfind(file,'.');
fileType=file(indexNO(end)+1:end);
fileName=dir(['*.',fileType]);
for iss=length(fileName):-1:1
if strcmp(fileName(iss).name(1:2),'._')
fileName(iss)=[];
end
end
p=length(fileName);
elseif strcmp(method,'userInput')
filePath=get(handles.et_fileName_path,'string');
file1=get(handles.et_fileName_file,'string');
file2=get(handles.et_fileName_start,'string');
file3=get(handles.et_fileName_format,'string');
% check whether file3 contains dot
indexNO=strfind(file3,'.');
if isempty(indexNO)
file3=['.',file3];
end
fileType=file3(2:end);
file=[file1,file2,file3];
p=eval(get(handles.et_fileName_to,'string'))-eval(file2)+1;
zeroPadding=length(file2);
fileName=struct;
startNO=eval(file2);
step=eval(get(handles.et_step,'string'));
ss=1;
if get(handles.cb_NoZero,'value')
for ii=1:step:p
jj=startNO+ii-1;
file2=num2str(jj);
fileName(ss).name=[file1,file2,file3];
ss=ss+1;
end
else
for ii=1:step:p
jj=startNO+ii-1;
file2=num2str(jj,['%0',num2str(zeroPadding),'d']);
fileName(ss).name=[file1,file2,file3];
ss=ss+1;
end
end
file=fileName(1).name;
end
p=length(fileName);
%%
%show images' name
handles.p=p;
handles.fileType=fileType;
handles.filePath_output = filePath;
handles.filePathOri = filePath;
handles.file=file;
handles.filePath=filePath;
handles.fileName=fileName;
handles.filePath_movie = [filePath,filesep,'Movies'];
switch fileType
case ('mat')
handles.filePathMat=filePath;
handles.fileNameMat=fileName;
handles.fileMat=fileName(1).name;
handles.filePath_output = fileparts(fileparts(filePath));
end
listName=cell(p,1);
for ii=1:p
listName{ii}=fileName(ii).name;
end
set(handles.lb_curFileNames,'value',1);
set(handles.lb_curFileNames,'string',listName);
% filePathWrap=textwrap(handles.st_curFilePath,{filePath});
filePathWrap=filePath;
set(handles.st_curFilePath,'string',filePathWrap);
set(handles.t_curFile,'string',file)
handles=imageShow(handles,'replace');
set(handles.et_IOSresultPath,'string',handles.filePath_output);
contents = cellstr(get(handles.pm_groupNO,'String'));
if isfield(handles,'pointPst')==0
handles.pointPst=cell(str2num(contents{get(handles.pm_groupNO,'Value')}),1);
end
set(handles.dt_IntestedImg,'string',['[1:',num2str(p),']'])
%% for showing point coordinateions
set(allchild(gca),'ButtonDownFcn', ...
'IOS_Software(''axes_rawImg_ButtonDownFcn'',gco,[],guidata(gcbo))')
set(allchild(gca),'hitTest','on')
%% for spatial binning
cd(handles.filePath)
img=differentTypeRead(handles.file,handles.fileType);
[mm,nn,nnTrash]=size(img);
% set(handles.et_xBinningEnd,'string',num2str(nn))
% set(handles.et_yBinningEnd,'string',num2str(mm))
function img=differentTypeRead(file,fileType)
if strcmp(fileType,'txt')
img=load(file);
elseif strcmp(fileType,'mat')
img2=load(file);
img2Name=fieldnames(img2);
img=img2.(img2Name{1});
else
img=single(imread(file));
% img=double(imread(file));
% if size(img,3)~=1
% img=img(:,:,1);
% end
end
function img=differentTypeReadFilter(img,filterMethod2)
% if strcmp(fileType,'txt')
% img=load(file);
% elseif strcmp(fileType,'mat')
% img2=load(file);
% img2Name=fieldnames(img2);
% img=img2.(img2Name{1});
% else
% img=single(imread(file));
% % img=double(imread(file));
% % if size(img,3)~=1
% % img=img(:,:,1);
% % end
% end
sizNo=filterMethod2.sizNo;
sigmaNo=filterMethod2.sigmaNo;
nameNo=filterMethod2.name;
%% filterImg
if nameNo==0
%imgAvg=imgAvg;
elseif nameNo==1
w=fspecial('gaussian',[sizNo,sizNo],sigmaNo);
img=imfilter(img(:,:,1),w,'replicate');
elseif nameNo==2
img=medfilt2(img(:,:,1),[sizNo,sizNo]);
elseif nameNo==3
img=wiener2(img(:,:,1),[sizNo,sizNo]);
elseif nameNo==4
imgAvg2=maxFilter2(img(:,:,1),sizNo);
img=single(imgAvg2);
% imgAvg2=edge(img(:,:,1),'canny',[.05,.4],sigmaNo);
% img=single(imgAvg2);
elseif nameNo==5
order=filterMethod2.order;
fcut=filterMethod2.fcut;
img=butter_fcut(img,fcut,1,order,'abs');
end
function [zoFilter,varargout]=butter_fcut(z0,fcut,method,butterN,rc)
% method=1 butterworth;
[m,n]=size(z0);
mm=1:m;
nn=1:n;
m0=m/2;
if mod(m0,2)==0
m0=m0+0.5;
else
m0=floor(m0)+1;
end
n0=n/2;
if mod(n0,2)==0
n0=n0+0.5;
else
n0=floor(n0)+1;
end
[xx,yy]=meshgrid(nn,mm);
yy=yy-m0;
xx=xx-n0;
dist=sqrt(yy.^2+xx.^2);
if method==1
map=1 ./ (1.0 + (dist ./ (fcut*m)).^(2*butterN));
zoFilter=ifft2(ifftshift(map.*fftshift(fft2(z0))));
elseif method==2
map=dist<fcut*m;
zoFilter=ifft2(ifftshift(map.*fftshift(fft2(z0))));
end
if strcmp(rc,'abs')
zoFilter=abs(zoFilter);
end
if nargout>=2
varargout{1}=map;
end
function img2=maxFilter2(img1,sizNo)
[mm,nn]=size(img1);
sizNo=floor(sizNo/2);
edgeY=sizNo;
edgeX=sizNo;
%% make the images bigger; replicate padding
% img1_big=zeros(mm+2*edgeY,nn+2*edgeX);
% img1_big(edgeY+1:edgeY+mm,edgeX+1:edgeX+nn)=img1;
img1_big=zeros(mm+2*edgeY,nn+2*edgeX);
img1_big(edgeY+1:edgeY+mm,edgeX+1:edgeX+nn)=img1;
img1_big(1:edgeY,:)=ones(edgeY,1)*img1_big(1+edgeY,:);
img1_big(edgeY+mm+1:end,:)=ones(edgeY,1)*img1_big(mm,:);
img1_big(:,1:edgeX)=img1_big(:,edgeX+1)*ones(1,edgeX);
img1_big(:,nn+1+edgeX:end)=img1_big(:,nn)*ones(1,edgeX);
sizeY1=edgeY;
sizeX1=edgeX;
%% initialize matrix
img2=zeros(mm,nn);
for iiTmp=1:mm
% waitbar(iiTmp/mm,h_wait,[num2stimageShowr(100*iiTmp/mm,'%04.1f'),'%completed']);
ii=edgeY+iiTmp;
for jjTmp=1:nn
jj=edgeX+jjTmp;
ROI=img1_big(ii-sizeY1:ii+sizeY1,jj-sizeX1:jj+sizeX1); %#ok<*PFBNS>
img2(iiTmp,jjTmp)=max(ROI(:));
% disp(['y',num2str(iiTmp,'%03d'),'jj',num2str(jjTmp,'%03d')])
end
end
function handles=imageShow(handles,varargin)
contents = cellstr(get(handles.pm_colormap_raw,'String'));
colorSelectedTmp=contents(get(handles.pm_colormap_raw,'value'));
if get(handles.cb_uint16,'value')
colorSelectedTmp{1}=[colorSelectedTmp{1}(1:end-5),'(2^16)'];
end
colorSelected=eval(colorSelectedTmp{1});
% cd(handles.filePath)
handles.newIntensity=inline(get(handles.et_inline,'string'));
fileType=handles.fileType;
file=handles.file;
img=differentTypeRead(fullfile(handles.filePath,file),fileType);
handles.imgRaw=img;
newImg=handles.newIntensity(img);
%% further processing
if get(handles.cb_eval,'value')
x=newImg;
eval(get(handles.et_eval,'string')) ;
newImg=x;
end
handles.img=newImg;
d3=size(newImg,3);
if nargin==2 && strcmp(varargin{1},'replace')
axes(handles.axes_rawImg);
% set(gcf,'currentAxes',handles.axes_rawImg)
hold off;
if d3==3
if get(handles.cb_uint16,'value')
imshow(uint16(newImg));
newImgColor=uint16(newImg);
else
imshow(uint8(newImg))
newImgColor=uint8(newImg);
end
elseif d3==1
%imshow(uint8(newImg),colorSelected)
if get(handles.cb_uint16,'value')
newImgColor=ind2rgb(uint16(newImg),colorSelected);
imshow(newImgColor)
else
newImgColor=ind2rgb(uint8(newImg),colorSelected);
imshow(newImgColor)
end
end
else
h_img=findobj(handles.axes_rawImg,'type','image');
%set(h_img,'CData',uint16(img))
if d3==3
if get(handles.cb_uint16,'value')
set(h_img,'CData',uint16(newImg))
newImgColor=uint16(newImg);
else
set(h_img,'CData',uint8(newImg))
newImgColor=uint8(newImg);
end
elseif d3==1
newImgColor=ind2rgb(uint8(newImg),colorSelected);
set(h_img,'CData',newImgColor)
if get(handles.cb_uint16,'value')
newImgColor=ind2rgb(uint16(newImg),colorSelected);
set(h_img,'CData',newImgColor)
else
newImgColor=ind2rgb(uint8(newImg),colorSelected);
set(h_img,'CData',newImgColor)
end
% set(h_img,'CData',uint8(newImg))
end
end
% axes(handles.axes_rawImg);
% colormap(colorSelected);
% colorbar;
img=newImg;
img=double(img);
[m,n,nn_trash]=size(img);
imgQuality=cell(5,1);
imgQuality{1}=[num2str(m),'x',num2str(n)];
imgQuality{2}=num2str(mean(img(:)));
imgQuality{3}=num2str(std(img(:)));
imgQuality{4}=num2str(max(img(:)));
imgQuality{5}=num2str(min(img(:)));
set(handles.imgQuality,'data',imgQuality)
handles.newImgColor=newImgColor;
% --- Executes on selection change in lb_curFileNames.
function handles=lb_curFileNames_Callback(hObject, eventdata, handles)
% hObject handle to lb_curFileNames (see GCBO)
contents = get(hObject,'String');
if length(contents)<get(hObject,'Value')
set(hObject,'value',1)
end
file=contents{get(hObject,'Value')};
handles.file=file;
handles=imageShow(handles);
set(handles.t_curFile,'string',file);
set(handles.et_file,'string',num2str(get(hObject,'Value')));
if isfield(handles,'pointer')
if ~isempty(handles.pointer)
handles=IOS_time_plotCurve(hObject,handles);
end
end
guidata(hObject,handles);
function lb_curFileNames_CreateFcn(hObject, eventdata, handles)
% hObject handle to lb_curFileNames (see GCBO)
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox controls usually have a white background on Windows.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function et_file_Callback(hObject, eventdata, handles)
% hObject handle to et_file (see GCBO)
fileNO=str2double(get(hObject,'String'));
set(handles.lb_curFileNames,'value',fileNO);
lb_curFileNames_Callback(handles.lb_curFileNames, eventdata, handles);
guidata(hObject,handles);
% et_file as text
% str2double(get(hObject,'String')) returns contents of et_file as a double
function et_file_CreateFcn(hObject, eventdata, handles) %#ok<*INUSD>
% hObject handle to et_file (see GCBO)
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function et_inline_Callback(hObject, eventdata, handles)
% hObject handle to et_inline (see GCBO)
handles=lb_curFileNames_Callback(handles.lb_curFileNames, eventdata, handles);
guidata(hObject,handles)
% et_inline as text
% str2double(get(hObject,'String')) returns contents of et_inline as a double
function et_inline_CreateFcn(hObject, eventdata, handles)
% hObject handle to et_inline (see GCBO)
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function et_IOSresultPath_Callback(hObject, eventdata, handles)
function et_IOSresultPath_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function et_pre1_Callback(hObject, eventdata, handles)
function et_pre1_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function et_pre2_Callback(hObject, eventdata, handles)
function et_pre2_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%%
function handles=IOS_time_parameterRead(handles)
handles.IOSresultPath=get(handles.et_IOSresultPath,'string');
handles.pre1=round(eval(get(handles.et_pre1,'string')));
handles.pre2=round(eval(get(handles.et_pre2,'string')));
% handles.x1=eval(get(handles.et_x1,'string'));
% handles.x2=eval(get(handles.et_x2,'string'));
% handles.NO=round(eval(get(handles.et_NO,'string')));
% handles.method=get(handles.pm_method,'value');
function et_rawIOSfolderName_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pb_rawIOS_mat.
function handles=pb_rawIOS_mat_Callback(hObject, eventdata, handles)
handles=IOS_time_parameterRead(handles);
pre1=handles.pre1;
pre2=handles.pre2;
file=handles.file;
filePath=handles.filePath;
fileType=handles.fileType;
fileName=handles.fileName;
cd(filePath);
img=differentTypeRead(file,fileType);
p=handles.p;
inverseNegative=get(handles.cb_inverseNegative,'value');
%% prestimulus mean
baselineImg=zeros(size(img));
for ii=pre1:pre2
file=fileName(ii).name;
img=differentTypeRead(file,fileType);
baselineImg=baselineImg+img;
end
baselineImg=baselineImg/(pre2-pre1+1);
baselineImg(baselineImg==0)=1;
%% IOS
IOSresultPath=handles.filePath_output;
resultName=get(handles.et_rawIOSfolderName_mat,'string');
resultPath=fullfile(IOSresultPath,resultName);
if exist(resultPath)~=7
% cd(IOSresultPath)
mkdir(resultPath)
end
fileTypeLength=length(fileType);
hh=waitbar(0,'just wait','name','Saving dF/F0 in .mat');
binningN=eval(get(handles.et_binning,'string'));
pp=floor(p/binningN);
for ii=1:pp
waitbar(ii/pp,hh, ...
[num2str(100*ii/pp,'%03.1f'),'% completed']);
cd(filePath)
imgAvg=img*0;
for jj=1:binningN
file=fileName((ii-1)*binningN+jj).name;
img=differentTypeRead(file,fileType);
imgAvg=imgAvg+img;
end
imgAvg=imgAvg/binningN;
if get(handles.cb_dF,'value')
imgIOStmp=(imgAvg-baselineImg);
else
imgIOStmp=(imgAvg-baselineImg)./baselineImg;
end
%imgIOStmp=(imgAvg-baselineImg);
if inverseNegative==1
imgIOStmp=abs(imgIOStmp);
end
imgIOS=single(imgIOStmp);
cd(resultPath)
saveName=[file(1:end-fileTypeLength),'mat'];
save(saveName,'imgIOS');
end
close(hh)
%% save them for other applications, i.e., creating grayscale & color images
handles.mat_resultPath=resultPath;
handles.mat_fileType='mat';
handles.mat_file=saveName;
guidata(hObject,handles)
function et_rawIOSfolderName_mat_Callback(hObject, eventdata, handles)
function et_rawIOSfolderName_mat_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
function et_rawIOSfolderName_Callback(hObject, eventdata, handles)
function edit8_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in pb_g1.
function pb_g1_Callback(hObject, eventdata, handles)
gN=1;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
% --- Executes on button press in pb_g2.
function pb_g2_Callback(hObject, eventdata, handles)
gN=2;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
% --- Executes on button press in pb_g3.
function pb_g3_Callback(hObject, eventdata, handles)
gN=3;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
% --- Executes on button press in pb_g4.
function pb_g4_Callback(hObject, eventdata, handles)
gN=4;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
% --- Executes on button press in pb_g5.
function pb_g5_Callback(hObject, eventdata, handles)
gN=5;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
function pushbutton10_Callback(hObject, eventdata, handles)
gN=handles.pointCurrent_group;
handles.pointPst{gN(end)}(end)=[];
delete(handles.pointCurrent_h(end));
handles.pointCurrent_h(end)=[];
handles.pointCurrent_group(end)=[];
handles.pointPstH{gN(end)}(end)=[];
handles=GroupROITag(handles);
guidata(hObject,handles)
% --- Executes on button press in pb_g6.
function pb_g6_Callback(hObject, eventdata, handles)
gN=6;
handles=getPointG1(handles,gN);
guidata(hObject,handles);
function pm_groupNO_Callback(hObject, eventdata, handles)
contents = cellstr(get(handles.pm_groupNO,'String'));
if get(handles.pm_groupNO,'value')<7
groupNO=eval(contents{get(handles.pm_groupNO,'Value')});
handles.pointPst=cell(groupNO,1);
handles.pointPstH=cell(groupNO,1);
if groupNO==1
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','off')
set(handles.pb_g3,'visible','off')
set(handles.pb_g4,'visible','off')
set(handles.pb_g5,'visible','off')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
elseif groupNO==2
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','on')
set(handles.pb_g3,'visible','off')
set(handles.pb_g4,'visible','off')
set(handles.pb_g5,'visible','off')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
elseif groupNO==3
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','on')
set(handles.pb_g3,'visible','on')
set(handles.pb_g4,'visible','off')
set(handles.pb_g5,'visible','off')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
elseif groupNO==4
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','on')
set(handles.pb_g3,'visible','on')
set(handles.pb_g4,'visible','on')
set(handles.pb_g5,'visible','off')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
elseif groupNO==5
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','on')
set(handles.pb_g3,'visible','on')
set(handles.pb_g4,'visible','on')
set(handles.pb_g5,'visible','on')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
elseif groupNO==6
set(handles.pb_g1,'visible','on')
set(handles.pb_g2,'visible','on')
set(handles.pb_g3,'visible','on')
set(handles.pb_g4,'visible','on')
set(handles.pb_g5,'visible','on')
set(handles.pb_g6,'visible','on')
set(handles.pb_g7,'visible','off')
set(handles.pb_g7_et,'visible','off')
end
elseif get(handles.pm_groupNO,'value')==7
set(handles.pb_g1,'visible','off')
set(handles.pb_g2,'visible','off')
set(handles.pb_g3,'visible','off')
set(handles.pb_g4,'visible','off')
set(handles.pb_g5,'visible','off')
set(handles.pb_g6,'visible','off')
set(handles.pb_g7,'visible','on')
set(handles.pb_g7_et,'visible','on')
handles.pointPst=cell(7,1);
handles.pointPstH=cell(7,1);
end
guidata(hObject,handles)
function pm_groupNO_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function handles=getPointG1(handles,gN)
colorTmp=handles.colorTmp;
pointPst=handles.pointPst;
axes(handles.axes_rawImg);
% set(gcf,'currentAxes',handles.axes_rawImg)
% zoom on
% h=zoom;
% set(h,'ActionPostCallback','uiresume(gcbf)');
% uiwait(gcf);
if gN==7
annularPar=eval(get(handles.pb_g7_et,'string'));
y0=annularPar(1);
x0=annularPar(2);
r1=annularPar(3);
r2=annularPar(4);
r1_tmp=min([r1,r2]);
r2_tmp=max([r1,r2]);
r1=r1_tmp;
r2=r2_tmp;
% circumference=2*pi*r1;
% pixel
section=360;
if 2*pi*r2>360
section=round(2*pi*r2);
end
theta=linspace(0,2*pi,section);
y1=sin(theta)*r1+y0;
x1=cos(theta)*r1+x0;
y2=sin(-theta)*r2+y0;
x2=cos(-theta)*r2+x0;
cx=[x1,x2,x1(end)].';
cy=[y1,y2,y1(end)].';
else
if length(pointPst)<gN
pointPst{gN}=[];
% handles.pointPst=cell(groupNO,1);
handles.pointPstH{gN}=[];
end
if get(handles.cb_ROIuserInput,'value')
dataPosition=get(handles.t_positions,'data');
dataPosition=dataPosition(1:2,1:2);
dataPosition2=dataPosition;
dataTrash=zeros(2,2);
dataTrash(1,1)=eval(dataPosition{1,1});
dataTrash(1,2)=eval(dataPosition{1,2});
dataTrash(2,1)=eval(dataPosition{2,1});
dataTrash(2,2)=eval(dataPosition{2,2});
dataPosition=dataTrash;
% dataPosition=cell2mat(dataPosition);
cy=[dataPosition(1,1)-.1,dataPosition(2,1)+.1,dataPosition(2,1)+.1,dataPosition(1,1)-.1]';
cx=[dataPosition(1,2)-.1,dataPosition(1,2)-.1,dataPosition(2,2)+.1,dataPosition(2,2)+.1]';
else
if get(handles.cb_circle,'value')
htrash=imellipse;
addNewPositionCallback(htrash,@(p) title(mat2str(p,3)));
fcn = makeConstrainToRectFcn('imellipse',get(gca,'XLim'),get(gca,'YLim'));
setPositionConstraintFcn(htrash,fcn);
% wait( hAll{ii});
% h = imellipse;
vertices = wait(htrash);
cx=vertices(:,1);
cy=vertices(:,2);
delete(htrash);
else
% [cx,cy,c]=improfile;
[c,cx,cy]=roipoly;
end
if length(cx)==1
cx=round(cx);
cy=round(cy);
cx=[cx-.1,cx-.1,cx+.1,cx+.1].';
cy=[cy-.1,cy+.1,cy+.1,cy-.1].';
end
end
end
if get(handles.cb_circle2,'value')
img=handles.img;
bw=roipoly(img(:,:,1),cx,cy);
t=regionprops(bw,'centroid');
ax=t.Centroid(1);
ay=t.Centroid(2);
rr=(cx-ax).^2+(cy-ay).^2;
r2=sqrt(rr);
r=min(r2);
r=r(1);
cx=(ax+cos(linspace(0,2*pi,100))*r).';
cy=(ay+sin(linspace(0,2*pi,100))*r).';
end
if get(handles.cb_gr11,'value')
if length(handles.pointPst)>=1
cx2=handles.pointPst{1};
if length(cx2)>=1
cx3=handles.pointPst{1}{1};
if length(cx3)>=1
img=handles.img;
bw=roipoly(img(:,:,1),cx,cy);
t=regionprops(bw,'centroid');
ax=t.Centroid(1);
ay=t.Centroid(2);
bw2=roipoly(img(:,:,1),cx3(:,1),cx3(:,2));
t2=regionprops(bw2,'centroid');
ax2=t2.Centroid(1);
ay2=t2.Centroid(2);
cx=cx3(:,1)+ax-ax2;
cy=cx3(:,2)+ay-ay2;
end
end
end
end
data=pointPst{gN};
if isempty(data)
data=cell(1,1);
data{1}=[cx,cy];
else
[m,n]=size(data);
data{m+1,1}=[cx,cy];
end
pointPst{gN}=data;
handles.pointPst=pointPst;
axes(handles.axes_rawImg);
% set(gcf,'currentAxes',handles.axes_rawImg)
% zoom out;
hold on;
% if get(handles.cb_ROIuserInput,'value') && abs(max(cy)-min(cy))<1 && abs(max(cx)-min(cx))<1
if abs(max(cy)-min(cy))<1 && abs(max(cx)-min(cx))<1
% get(handles.cb_ROIuserInput,'value') && abs(cy(2)-cy(1))<1 && abs(cx(2)-cx(1))<1
hh=plot(cx(1),cy(1),'+','color',colorTmp(gN,:));
else
hh=plot([cx;cx(1)],[cy;cy(1)],'color',colorTmp(gN,:));
end
if isfield(handles, 'pointCurrent_h')~=1
handles.pointCurrent_h=hh;
handles.pointCurrent_group=gN;
else
handles.pointCurrent_h=[handles.pointCurrent_h;hh];
handles.pointCurrent_group=[handles.pointCurrent_group;gN];
end
if isfield(handles, 'pointPstH')~=1
handles.pointPstH=cell(size(handles.pointPst));
else
handles.pointPstH{gN}=[handles.pointPstH{gN},hh];
end
handles=GroupROITag(handles);
function handles=GroupROITag(handles)
pointPst=handles.pointPst;
if isfield(handles,'grTag')
grTag=handles.grTag;
for ii=1:length(grTag)
for jj=1:length(grTag{ii})
if ishandle(grTag{ii}{jj})
delete(grTag{ii}{jj})
end
end
end
end
grTag={};
img=differentTypeRead(fullfile(handles.filePath,handles.file),handles.fileType);
for ii=1:length(pointPst)
for jj=1:length(pointPst{ii})
% vv=vv+1;
cx=pointPst{ii}{jj}(:,1);
cy=pointPst{ii}{jj}(:,2);
bw=roipoly(img(:,:,1),cx,cy);
t=regionprops(bw,'centroid');
ax=t.Centroid(1);
ay=t.Centroid(2);
grTag{ii}{jj}=text(ax,ay,['(',num2str(ii),',',num2str(jj),')'],'color',handles.colorTmp(ii,:));
% ROItmp=img(bw);
% rawData(kk,vv)=mean(ROItmp(:));
end
end
handles.grTag=grTag;
function pushbutton12_Callback(hObject, eventdata, handles)
cd(handles.filePath)
[file,filePath]=uiputfile('parameterMat.mat');
cd(filePath)
%pointCurrent_h=handles.pointCurrent_h;
% pointCurrent_group=handles.pointCurrent_group;
pointPst=handles.pointPst;
colorTmp=handles.colorTmp;
save(file,'pointPst','colorTmp')
fileTmp=file;
filePathTmp=filePath;
filePath=handles.filePath;
fileType=handles.fileType;
cd(filePath)
img=differentTypeRead(handles.file,fileType);
[mm,nn,nnTrash]=size(img);
newImgColor=handles.newImgColor;
figure(78);imshow(newImgColor);hold on;
% handles=GroupROITag(handles);
cd(filePathTmp)
grTag={};
for ii=1:length(pointPst)
mapGroup=false(mm,nn);
for jj=1:length(pointPst{ii})
cx=pointPst{ii}{jj}(:,1);
cy=pointPst{ii}{jj}(:,2);
plot(cx,cy,'color',handles.colorTmp(ii,:))
bw=roipoly(img(:,:,1),cx,cy);
t=regionprops(bw,'centroid');
ax=t.Centroid(1);
ay=t.Centroid(2);
grTag{ii}{jj}=text(ax,ay,['(',num2str(ii),',',num2str(jj),')'],'color',handles.colorTmp(ii,:));
mapGroup=or(mapGroup, bw);
% pointPst{ii}{jj}(:,1)=pointPst{ii}{jj}(:,1)+3;
end
imwrite(mapGroup,[fileTmp(1:end-4),'Group',num2str(ii),'.tif'],'tif','compression','none');
end
saveas(78,'groupROITag.tif','tiff');
guidata(hObject,handles)
function pushbutton13_Callback(hObject, eventdata, handles)
[file,filePath]=uigetfile('*.mat','MultiSelect','on');
cd(filePath)
if iscell(file)==0
load(file)
else
p=length(file);
maxG=zeros(p,1);
for ii=1:p
load(file{ii});
maxG(ii)=length(pointPst);
end
pointPstTmp=cell(p,1);
for ii=1:p
load(file{ii});
for jj=1:maxG(ii)
pointPstTmp{jj}=[pointPstTmp{jj}; pointPst{jj}];
end
end
pointPst=pointPstTmp;
end
handles.pointPst=pointPst;
handles.colorTmp=colorTmp;
handles.pointCurrent_h=zeros(0,0);
handles.pointCurrent_group=zeros(0,0);
axes(handles.axes_rawImg)
% set(gcf,'currentAxes',handles.axes_rawImg)
hold on;
pointPstH=cell(size(pointPst));
for ii=1:length(pointPst)
for jj=1:length(pointPst{ii})
cx=pointPst{ii}{jj}(:,1);
cy=pointPst{ii}{jj}(:,2);
hh=plot([cx;cx(1)],[cy;cy(1)],'color',colorTmp(ii,:));
handles.pointCurrent_h=[handles.pointCurrent_h;hh];
handles.pointCurrent_group=[handles.pointCurrent_group;ii];
pointPstH{ii}=[pointPstH{ii},hh];
end
end
handles.pointPstH=pointPstH;
figure;
cd(handles.filePath)
img=differentTypeRead(handles.file,handles.fileType);
mapRange=eval(get(handles.et_fileRange,'string'));
contents = cellstr(get(handles.pp_fileColormap,'String'));
colorSelected=contents(get(handles.pp_fileColormap,'value'));
imshow(img,mapRange);
colormap(eval(colorSelected{1}))
colorbar
hold on;