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QUARTZ.m
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QUARTZ.m
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function varargout = QUARTZ(varargin)
% QUARTZ MATLAB code for QUARTZ.fig
% QUARTZ, by itself, creates a new QUARTZ or raises the existing
% singleton*.
%
% H = QUARTZ returns the handle to a new QUARTZ or the handle to
% the existing singleton*.
%
% QUARTZ('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in QUARTZ.M with the given input arguments.
%
% QUARTZ('Property','Value',...) creates a new QUARTZ or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before QUARTZ_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to QUARTZ_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 QUARTZ
% Last Modified by GUIDE v2.5 03-Dec-2013 05:51:20
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @QUARTZ_OpeningFcn, ...
'gui_OutputFcn', @QUARTZ_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 QUARTZ is made visible.
function QUARTZ_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to QUARTZ (see VARARGIN)
% Choose default command line output for QUARTZ
QUARTZ_setup(true);
handles.output = hObject;
handles.vessel_data = Vessel_Data;
centerfig(handles.fig_QUARTZ_MAIN);
warning('off');
global proc_settings;
global ui_settings;
iniFileName = 'QUARTZ_CONFIG.MAT';
bSavevsSetting = 0;
%Load up the initial values from the mat file.
strIniFile = fullfile(cd, '\QUARTZ_settings\' , iniFileName);
mkdir([cd, '\QUARTZ_settings\']);
if exist(strIniFile, 'file')
load(strIniFile);
%retVal = exist (ui_settings ,'var');
else
[ui_settings, proc_settings] = getDefaultSettings();
bSavevsSetting = 1;
end
%if(retVal == 0)
% [ui_settings, settings] = getDefaultSettings();
% bSavevsSetting = 1;
%end
if(bSavevsSetting)
save(strIniFile ,'ui_settings' , 'proc_settings');
end
%if exist(settings, 'class')
handles.proc_settings = proc_settings;
%end
set(handles.txtFolder, 'string', ui_settings.ImageFolder);
%uiwait(msgbox(structMainUI.ImageFolder));
% Load list of images in the image folder.
tdata = LoadImageList();
set(handles.tbl_ImagesData,'Data',tdata);
% Select none of the items in the listbox.
%set(handles.lst_ImageList, 'value', []);
handles.cI = [];
if(isempty(handles.cI))
updateInteractiveModeUI(handles,'off');
end
% Update handles structure
guidata(hObject, handles);
% --- Outputs from this function are returned to the command line.
function varargout = QUARTZ_OutputFcn(hObject, eventdata, 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 btnBrowse.
function btnBrowse_Callback(hObject, eventdata, handles)
% hObject handle to btnBrowse (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global ui_settings;
returnValue = uigetdir(ui_settings.ImageFolder,'Select folder');
% returnValue will be 0 (a double) if they click cancel.
% returnValue will be the path (a string) if they clicked OK.
%msgbox(ui_settings.ImageFolder);
if returnValue ~= 0
% Assign the value if they didn't click cancel.
ui_settings.ImageFolder = [returnValue '\'];
tdata = LoadImageList();
set(handles.tbl_ImagesData,'Data',tdata);
set(handles.txtFolder, 'string' ,ui_settings.ImageFolder);
if(ui_settings.isFovMaskDefaultDir)
ui_settings.maskFolder = [ui_settings.ImageFolder 'MASK\'];
end
guidata(hObject, handles);
% Save the image folder in our ini file.
%configValues.lastUsedImageFolder = ui_settings.ImageFolder;
strIniFile = fullfile([cd, '\QUARTZ_settings\'], ui_settings.iniFileName);
ui_settings.batchBeginIndex =1;
%if exist (strIniFile)
% load(ui_settings.iniFileName);
%end
%configValues.lastUsedImageFolder = ui_settings.ImageFolder;
save( strIniFile , 'ui_settings' , '-append');
end
% --- Executes on button press in btnVisualize.
function btnVisualize_Callback(hObject, eventdata, handles)
% hObject handle to btnVisualize (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.rb_vis_seg,'Value') == 1 )
vis_seg = handles.cI;
%vis_seg.binaryImage = handles.vessel_data.vessel_data.bw;
setappdata(0,'vis_seg',vis_seg);
VisualizeSegmentation;
elseif (get(handles.rb_vis_ana,'Value') == 1)
vdobj.vessel_data = handles.vessel_data;
vdobj.visualize = 1;
vdobj.settings = handles.proc_settings.vessel_settings;
setappdata(0,'vdobj',vdobj);
visAnalysis;
end
% --- Executes on button press in btnProcess.
function btnProcess_Callback(hObject, eventdata, handles)
% hObject handle to btnProcess (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
prepareProcessing(1, hObject, handles);
%=====================================================================
% --- Load up the listbox with tif files in folder handles.ui_settings.ImageFolder
function [tab_data] = LoadImageList()
global ui_settings;
tab_data = {};
folder = ui_settings.ImageFolder;
if ~isempty(ui_settings.ImageFolder)
if exist(folder,'dir') == false
warningMessage = sprintf('Note: the folder used when this program was last run:\n%s\ndoes not exist on this computer.\nPlease run Step 1 to select an image folder.', ui_settings.ImageFolder);
msgbox(warningMessage);
return;
end
else
msgboxw('No folder specified as input for function LoadImageList.');
return;
end
% If it gets to here, the folder is good.
ImageFiles = dir([ui_settings.ImageFolder ui_settings.ext]);
for Index = 1:length(ImageFiles)
if(ImageFiles(Index).isdir)
continue;
end
imgName = ImageFiles(Index).name;
[folder, name, extension] = fileparts(imgName);
extension = upper(extension);
%disp([num2str(Index-2) ':' name extension]);
switch lower(extension)
case {'.png', '.bmp', '.jpg', '.tif', '.avi'}
% Allow only PNG, TIF, JPG, or BMP images
tab_data{end+1,1} = imgName;
tab_data{end,2} = 'false';
tab_data{end,3} = 'false';
tFile = [ui_settings.segPath name '.png'];
if(exist (tFile , 'file'))
tab_data{end,2} = 'true';
end
tFile = [ui_settings.anaPath name '.mat'];
if(exist (tFile , 'file'))
tab_data{end,3} = 'true';
end
otherwise
end
end
return
%=====================================================================
%=====================================================================
% Reads FullImageFileName from disk into the axesImage axes.
function cI = DisplayImage(handles, imgPath)
% Read in image.
global ui_settings;
cI = [];
try
cI = readImage(imgPath , '', ui_settings.maskFolder,ui_settings.genFOVruntime );
anaFile = [ui_settings.segPath cI.StemName '.' ui_settings.segExt];
if(exist(anaFile,'file') )
binImg = imread(anaFile);
if(~islogical(binImg))
binImg = im2bw(binImg , graythresh(binImg));
end
cI.ves_seg = binImg;
%handles.cI.ves_seg = binImg;
end
%imgOriginal = imread(imgPath);
%cI.img = imgOriginal;
%[folder, name, extension] = fileparts(imgPath);
%cI.path = [folder '\'];
%cI.StemName = name;
%cI.extension = extension;
%cI.mask = imread([ui_settings.maskFolder cI.StemName '.png']);
catch ME
errorMessage = sprintf('Error opening image file with imread():\n%s\n%s', imgPath , ME.message);
set(handles.txtStatus, 'String', errorMessage);
msgbox(errorMessage);
return; % Skip the rest of this function
end
try
% Display image array in a window on the user interface.
set(handles.axesImage, 'parent',gcf);
%set(gcf,'CurrentAxes',handles.axesImage);
handleRGB = imshow(cI.img,[],'parent',handles.axesImage);
% Display a title above the image.
[folder, basefilename, extension] = fileparts(imgPath);
extension = lower(extension);
% Convert any underlines in the name into spaces because otherwise the character after the underline would be a subscript.
caption = strrep([basefilename extension], '_', ' ');
% Display the title.
title(handles.axesImage, caption, 'FontSize', 8);
%expandAxes(handles.axesImage);
catch ME
errorMessage = sprintf('Error in function DisplayImage.\nError Message:\n%s', ME.message);
msgbox(errorMessage , 'Warning' , 'warn' , 'modal');
end
return; % from DisplayImage
% --- Executes when selected cell(s) is changed in tbl_ImagesData.
function tbl_ImagesData_CellSelectionCallback(hObject, eventData, handles)
% hObject handle to tbl_ImagesData (see GCBO)
% eventdata structure with the following fields (see UITABLE)
% Indices: row and column indices of the cell(s) currently selecteds
% handles structure with handles and user data (see GUIDATA)
if( isempty(eventData.Indices) )
return;
end
global ui_settings;
% Get image name
selectedItem = eventData.Indices(1);
% If more than one is selected, bail out.
if selectedItem < 0
return;
end
tbldata = get(handles.tbl_ImagesData,'Data');
imgName = tbldata(selectedItem,1);
imgName = cell2mat(imgName);
imgPath = [ui_settings.ImageFolder imgName]; % Prepend folder.
[folder, baseFileName, extension] = fileparts(imgPath);
switch lower(extension)
case {'.tif', '.png', '.jpg'}
cI = DisplayImage(handles, imgPath);
handles.cI = cI;
clear cI;
if(isempty(handles.cI)==0)
updateInteractiveModeUI(handles,'on');
end
anaFile = [ui_settings.segPath imgName(1:end-3) ui_settings.segExt];
if(exist(anaFile,'file') )
set(handles.rb_vis_seg , 'Enable' , 'on');
binImg = imread(anaFile);
if(~islogical(binImg))
binImg = im2bw(binImg , graythresh(binImg));
end
handles.cI.ves_seg = binImg;
else
set(handles.rb_vis_seg , 'Enable' , 'off');
end
anaFile = [ui_settings.anaPath imgName(1:end-3) ui_settings.anaExt];
if(exist(anaFile,'file') )
vd = load(anaFile);
handles.vessel_data = vd.vessel_data;
set(handles.rb_vis_ana , 'Enable' , 'on');
else
set(handles.rb_vis_ana , 'Enable' , 'off');
handles.vessel_data = [];%Vessel_Data;
end
if (strcmp(tbldata(selectedItem,2) ,'false') && strcmp(tbldata(selectedItem,3) ,'false' ) )
set(handles.btnVisualize , 'Enable' , 'off');
end
otherwise
msgboxw(['"' extension '"' ' is not supported.']);
return;
end
% Update handles structure
guidata(hObject, handles);
% --------------------------------------------------------------------
function Tools_Callback(hObject, eventdata, handles)
% hObject handle to Tools (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function directories_Callback(hObject, eventdata, handles)
% hObject handle to directories (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global ui_settings;
setappdata(0,'ui_settings',ui_settings);
f = vessel_segmentation_settings;
waitfor(f);
if( isappdata(0,'vui_settings') )
vd = getappdata(0,'vui_settings');
ui_settings.segPath = vd.segPath;
ui_settings.anaPath = vd.anaPath;
ui_settings.maskFolder = vd.maskFolder;
ui_settings.segExt = vd.segExt;
ui_settings.anaExt = vd.anaExt;
ui_settings.exportMode = vd.exportMode;
ui_settings.exportDir = vd.exportDir;
ui_settings.exportFile = vd.exportFile;
ui_settings.saperateFile4EachImage = vd.saperateFile4EachImage;
ui_settings.overwriteFile = vd.overwriteFile;
ui_settings.writeCommulative = vd.writeCommulative;
ui_settings.isFovMaskDefaultDir = vd.isFovMaskDefaultDir;
ui_settings.genFOVruntime = vd.genFOVruntime;
if( ui_settings.isFovMaskDefaultDir )
ui_settings.maskFolder = [ui_settings.ImageFolder , 'MASK\'];
end
rmappdata(0,'vui_settings');
iniFileName = 'QUARTZ_CONFIG.MAT';
strIniFile = fullfile(cd, '\QUARTZ_settings\' , iniFileName);
save(strIniFile ,'ui_settings' , '-append');
end
% --------------------------------------------------------------------
function preferences_Callback(hObject, eventdata, handles)
% hObject handle to preferences (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on selection change in lstStatusMsg.
function lstStatusMsg_Callback(hObject, eventdata, handles)
% hObject handle to lstStatusMsg (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 lstStatusMsg contents as cell array
% contents{get(hObject,'Value')} returns selected item from lstStatusMsg
% --- Executes during object creation, after setting all properties.
function lstStatusMsg_CreateFcn(hObject, eventdata, handles)
% hObject handle to lstStatusMsg (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 listbox2.
function listbox2_Callback(hObject, eventdata, handles)
% hObject handle to listbox2 (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 listbox2 contents as cell array
% contents{get(hObject,'Value')} returns selected item from listbox2
% --- Executes on button press in btnBreak.
function btnBreak_Callback(hObject, eventdata, handles)
% hObject handle to btnBreak (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global ui_settings;
ui_settings.broken = 1;
% --- Executes on button press in btnClearStatusMsg.
function btnClearStatusMsg_Callback(hObject, eventdata, handles)
% hObject handle to btnClearStatusMsg (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set(handles.txtStatus,'String','..');
function [ui_settings , proc_settings] = getDefaultSettings(mode)
userDir='C:\';
if(ispc)
userDir = winqueryreg('HKEY_CURRENT_USER',...
['Software\Microsoft\Windows\CurrentVersion\' ...
'Explorer\Shell Folders'],'Personal') ;
if(isempty(userDir))
userDir= getenv('USERPROFILE');
end
else
userDir= getenv('HOME');
end
userDir = [userDir '\'];
ui_settings.ImageFolder = userDir;
ui_settings.maskFolder = [ui_settings.ImageFolder '\MASK\'];
ui_settings.iniFileName = 'QUARTZ_CONFIG.MAT';
ui_settings.anaPath = 'C:\D\QUARTZ\TEST\Ana\';
ui_settings.segPath = 'C:\D\QUARTZ\TEST\Seg\';
ui_settings.ext = '*.*';
ui_settings.anaExt = 'mat';
ui_settings.segExt = 'png';
ui_settings.broken = 0;
ui_settings.mode = '';
ui_settings.batchBeginIndex = 1;
ui_settings.bWriteIntemediateImages = false;
ui_settings.interim_images_path = '';
ui_settings.batBeginIndex = 1;
ui_settings.batEndIndex = 73;
ui_settings.broken = 0;
ui_settings.bProcessAllFiles = 0;
ui_settings.exportMode = 1;
ui_settings.exportDir = 'C:\D\QUARTZ\TEST\';
ui_settings.exportFile = 'testFile';
ui_settings.saperateFile4EachImage = 0;
ui_settings.overwriteFile = 1;
ui_settings.writeCommulative = 0;
ui_settings.isFovMaskDefaultDir = 1;
ui_settings.genFOVruntime = 0;
ui_settings.procMode = 1;
ui_settings.procOption = 1;
args.image_large_size = [1024 , 1024];
args.image_resize_factor = 1;
args.mask_option = 'create';
args.mask_erode = 1;
args.iuwt_dark = 1;
args.iuwt_inpainting = 0;
args.iuwt_w_levels = 0.2;
args.iuwt_w_thresh = [3,4,5]
args.iuwt_px_remove = 0.05;
args.iuwt_px_fill = 0.05;
args.spline_piece_spacing = 10;
args.processor_function = 'QUARTZ_algorithm_general'
args.mask_dark_threshold = 30;
args.mask_bright_threshold = 255;
args.mask_largest_region = 1;
args.centre_spurs = 10;
args.centre_min_px = 10;
args.centre_remove_extreme = 1;
args.centre_clear_branches_dist_transform = 0;
args.smooth_parallel = 2;
args.smooth_perpendicular = 0.1;
args.enforce_connectivity = 1;
proc_settings.vessel_settings = Vessel_Settings;
proc_settings.vessel_settings.show_labels = false;
proc_settings.vessel_settings.show_optic_disc = true;
proc_settings.vs_args = args;
proc_settings.segment = [];
% --- Executes on button press in btnClose.
function btnClose_Callback(hObject, eventdata, handles)
% hObject handle to btnClose (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
try
allFigs = findall(0,'Type','figure');
for idx = 1: length(allFigs)
if( strcmp(get(allFigs(idx) , 'tag' ) , 'figVesselSegmentTool'))
delete(allFigs(idx));
elseif( strcmp(get(allFigs(idx) , 'tag' ) , 'figVisualizeSegmentation'))
delete(allFigs(idx));
end
end
clear allFigs;
delete(handles.fig_QUARTZ_MAIN);
catch Ex
end
function doProcessing(hObject,handles)
global ui_settings;
mkdir(ui_settings.anaPath);
handles.proc_settings.vessel_settings.last_path = ui_settings.segPath;
try
if(ui_settings.procMode == 2 ) %Interactive Processing Mode
imgPath = [handles.cI.path , handles.cI.StemName, handles.cI.ext];
new_line = ['Started : ' handles.cI.StemName];
set(handles.txtStatus,'String',new_line);
pause (0.1);
% vessel segmentation only
if(ui_settings.procOption == 1)
ves_seg = vessel_segmentation(ui_settings, handles.cI);
handles.cI.ves_seg = ves_seg;
% vessel analysis only
elseif (ui_settings.procOption > 1)
if(ui_settings.procOption == 3)
ves_seg = vessel_segmentation(ui_settings , handles.cI);
handles.cI.ves_seg = ves_seg;
end
handles.proc_settings.vs_args.cI = handles.cI ;
% Load VESSEL_DATA from file
[handles.vessel_data, process_time] = Vessel_Data_IO.load_from_file(imgPath, ...
handles.proc_settings.vs_args, handles.proc_settings.vessel_settings);
[x_cord , y_cord] = od_localization(handles.cI.img);
handles.vessel_data.od_location = [x_cord , y_cord];
%////vess classification
AVClassification('' , handles.vessel_data);
%/////vess classification
fileName = [ui_settings.anaPath handles.cI.StemName '.mat' ];
Vessel_Data_IO.save_to_file(fileName, handles.vessel_data);
end
cur_msg=cellstr(get(handles.txtStatus,'String'));
new_line = ['Finished : ' handles.cI.StemName];
new_msg = [cur_msg;{new_line}];
set(handles.txtStatus,'String',new_msg);
elseif(ui_settings.procMode == 1 ) %Batch Processing Mode
tbldata = get(handles.tbl_ImagesData,'Data');
numImages = size(tbldata,1);
%these should be updates in a callback; not here
ui_settings.batBeginIndex = str2num(get(handles.edStart , 'String'));
ui_settings.batEndIndex = str2num(get(handles.edEnd , 'String'));
if(ui_settings.bProcessAllFiles)
begIdx = 1 ;
endIdx = numImages;
else
begIdx = ui_settings.batBeginIndex ;
endIdx = ui_settings.batEndIndex ;
end
set(handles.txtStatus,'String','. . .');
for (idx = begIdx:endIdx)
imgName = tbldata(idx,1);
imgName = cell2mat(imgName);
imgPath = [ui_settings.ImageFolder imgName];
cI = DisplayImage(handles, imgPath);
handles.cI = cI;
new_line = ['Started : ' num2str(idx) '-' cI.StemName];
if(idx > begIdx)
cur_msg = ['Finished : ' num2str(idx-1) '-' cell2mat(tbldata(idx-1,1))];
else
cur_msg=cellstr(get(handles.txtStatus,'String'));
end
new_msg = [cur_msg;{new_line}];
set(handles.txtStatus,'String',new_msg);
clear cur_msg;
pause(0.1);
if (ui_settings.broken == 1)
new_line = ['TERMINATED after completing ' num2str(idx) '-' cI.StemName];
cur_msg=cellstr(get(handles.txtStatus,'String'));
new_msg = [cur_msg;{new_line}];
set(handles.txtStatus,'String',new_msg);
%ui_settings.batchBeginIndex = idx+1;
%strIniFile = fullfile(cd, ui_settings.iniFileName);
%save(strIniFile ,'ui_settings' , '-append');
ui_settings.broken = 0;
break;
end
if(ui_settings.procOption == 1)
ves_seg = vessel_segmentation(ui_settings, handles.cI);
handles.cI.ves_seg = ves_seg;
elseif (ui_settings.procOption >1)
if( ui_settings.procOption == 3)
ves_seg = vessel_segmentation(ui_settings);
handles.cI.ves_seg = ves_seg;
end
handles.proc_settings.vs_args.cI = handles.cI ;
% Load VESSEL_DATA from file
[handles.vessel_data, process_time] = Vessel_Data_IO.load_from_file(imgPath, ...
handles.proc_settings.vs_args, handles.proc_settings.vessel_settings);
[x_cord , y_cord] = od_localization(handles.cI.img);
handles.vessel_data.od_location = [x_cord , y_cord];
%////vess classification
AVClassification('' , handles.vessel_data);
%/////vess classification
fileName = [ui_settings.anaPath cI.StemName '.mat' ];
Vessel_Data_IO.save_to_file(fileName, handles.vessel_data);
end
disp(['DONE : ' num2str(idx) '-' cI.StemName]);
end
end
catch Ex
errorMessage = sprintf('Error in function doProcessing.\nError Message:\n%s', Ex.message);
msgbox(errorMessage , 'Warning' , 'warn' , 'modal');
updateProcessingModeUI(handles,'on');
end
% Update handles structure
guidata(hObject, handles);
function updateInteractiveModeUI(handles, val)
set(handles.rb_int_proc,'Enable' , val);
set(handles.rb_vis_seg,'Enable' , val);
set(handles.rb_vis_ana,'Enable' , val);
set(handles.btnVisualize,'Enable' , val);
function updateProcessingModeUI(handles, val)
set(handles.rb_int_proc,'Enable' , val);
set(handles.rb_bat_proc,'Enable' , val);
set(handles.rb_vseg,'Enable' , val);
set(handles.rb_vana,'Enable' , val);
set(handles.rb_vseg_ana,'Enable' , val);
set(handles.rb_vis_seg,'Enable' , val);
set(handles.rb_vis_ana,'Enable' , val);
set(handles.btnVisualize,'Enable' , val);
set(handles.btnProcess,'Enable' , val);
set(handles.btnClearStatusMsg,'Enable' , val);
set(handles.tbl_ImagesData,'Enable' , val);
set(handles.chkAllFiles,'Enable' , val);
set(handles.edStart,'Enable' , val);
set(handles.edEnd,'Enable' , val);
set(handles.btnExport,'Enable' , val);
set(handles.btnPreprocess,'Enable' , val);
set(handles.btnBrowse,'Enable' , val);
% --- Executes on button press in btnExport.
function btnExport_Callback(hObject, eventdata, handles)
% hObject handle to btnExport (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
updateProcessingModeUI(handles,'off');
set(handles.txtStatus,'String','Start : Exporting vessel analysis');
pause(0.1);
global ui_settings;
path = ui_settings.anaPath;
D= dir([path '*.mat']);
expFile = [ui_settings.exportDir '\' ui_settings.exportFile];
if(ui_settings.overwriteFile == 0)
c = clock;
c = fix(c);
expFile = [expFile '_' num2str(c(1)) num2str(c(2)) num2str(c(3)) num2str(c(4)) num2str(c(5)) num2str(c(6))];
end
if(ui_settings.writeCommulative)
header = {'ImageName', 'OD X' , 'OD Y','Segment ID', 'Prob A' ,'Prob V', 'Num Diameters' , 'Mean Diameter' ,'std Diameter' ,'Min' , 'Max' ,'length', 'Diameter/Length' , 'Tortousity' ,'Centerline CoordinateX','Centerline CoordinateY','Diameter','Local Angle' };
else
header1 = {'ImageName', 'OD X' , 'OD Y','Segment ID', 'Prob A' ,'Prob V', 'Num Diameters' , 'Mean Diameter' ,'std Diameter' ,'Min' , 'Max' ,'length', 'Diameter/Length' , 'Tortousity' };
header2 = {'ImageName', 'Segment ID','Centerline CoordinateX','Centerline CoordinateY','Diameter','Local Angle' };
end
for(nIdx = 1:length(D))
filepath = [path , D(nIdx).name];
stemName = D(nIdx).name(1:end-4);
[vessel_data, process_time] = Vessel_Data_IO.load_from_file(filepath, ...
handles.proc_settings.vs_args, handles.proc_settings.vessel_settings);
num_vessels = vessel_data.num_vessels;
total_diameters = vessel_data.total_diameters;
for(kdx = 1:num_vessels)
vess = vessel_data.vessel_list(kdx);
tdx = 1;
num_diameters = vess.num_diameters;
%do not write cumulative file
if(ui_settings.writeCommulative == 0)
adx = 1;
if(kdx==1)
mtW = header2;
aW = header1;
end
aW(kdx+1,adx) = cellstr(stemName);adx = adx+1;
aW(kdx+1,adx) = num2cell(vessel_data.od_location(1));adx = adx+1;
aW(kdx+1,adx) = num2cell(vessel_data.od_location(2));adx = adx+1;
aW(kdx+1,adx) = num2cell(vess.vesID,2); adx = adx+1;
if(isempty(vess.AV))
vess.AV = [0,0];
end
aW(kdx+1,adx) = num2cell(vess.AV(1)); adx = adx+1;
aW(kdx+1,adx) = num2cell(vess.AV(2)); adx = adx+1;
d = vess.diameters(vess.keep_inds);
aW(kdx+1,adx) = num2cell(numel(d)); adx = adx+1;
aW(kdx+1,adx) = num2cell(mean(d)); adx = adx+1;
aW(kdx+1,adx) = num2cell(std(d)); adx = adx+1;
aW(kdx+1,adx) = num2cell(min(d)); adx = adx+1;
aW(kdx+1,adx) = num2cell(max(d)); adx = adx+1;
% Calculate length
ind1 = find(vess.keep_inds, 1, 'first');
ind2 = find(vess.keep_inds, 1, 'last');
len = vess.offset(ind2) - vess.offset(ind1);
aW(kdx+1,adx) = num2cell(len); adx = adx+1;
% Calculate diameter / length
aW(kdx+1,adx) = num2cell(mean(d) / len); adx = adx+1;
% Calculate tortuosity
direct_len = sqrt(sum((vess.centre(ind2,:) - vess.centre(ind1,:)).^2)) * vess.scale_value;
tort = len / direct_len;
aW(kdx+1,adx) = num2cell(tort); adx = adx+1;
tW(1:num_diameters,tdx) = cellstr(stemName);tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vess.vesID,2); tdx = tdx+1;
else
if(kdx==1)
mtW=header;
end
tW(1:num_diameters,tdx) = cellstr(stemName);tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vessel_data.od_location(1));tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vessel_data.od_location(2));tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vess.vesID,2); tdx = tdx+1;
if(isempty(vess.AV))
vess.AV = [0,0];
end
tW(1:num_diameters,tdx) = num2cell(vess.AV(1)); tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vess.AV(2)); tdx = tdx+1;
d = vess.diameters(vess.keep_inds);
tW(1:num_diameters,tdx) = num2cell(numel(d)); tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(mean(d)); tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(std(d)); tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(min(d)); tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(max(d)); tdx = tdx+1;
% Calculate length
ind1 = find(vess.keep_inds, 1, 'first');
ind2 = find(vess.keep_inds, 1, 'last');
len = vess.offset(ind2) - vess.offset(ind1);
data{6,2} = len;
tW(1:num_diameters,tdx) = num2cell(len); tdx = tdx+1;
% Calculate diameter / length
data{7,2} = mean(d) / len;
tW(1:num_diameters,tdx) = num2cell(mean(d) / len); tdx = tdx+1;
% Calculate tortuosity
direct_len = sqrt(sum((vess.centre(ind2,:) - vess.centre(ind1,:)).^2)) * vess.scale_value;
tort = len / direct_len;
tW(1:num_diameters,tdx) = num2cell(tort); tdx = tdx+1;
end
tW(1:num_diameters,tdx) = num2cell(vess.centre(:,1));tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vess.centre(:,2));tdx = tdx+1;
tW(1:num_diameters,tdx) = num2cell(vess.diameters,2);tdx = tdx+1;
ang = vess.der;
angleInRadians = atan2(ang(:,1),ang(:,2));
angleInDegrees = (180/pi) * angleInRadians;
th = angleInDegrees * -1;
%th = (rad2deg(atan2(ang(:,1),ang(:,2))))*-1;
tW(1:num_diameters,tdx) = num2cell(th(1:num_diameters)); tdx = tdx+1;
mtW = cat(1,mtW , tW);
clear tW;
% for (nd = 1:num_diameters)
% cent_co = [ num2str(vess.centre(nd,1)) , ',' , num2str(vess.centre(nd,2))];
% tW (nd,2) = vess.centre(nd,1);
% tW (nd,3) = vess.centre(nd,2);
% tW (nd,4) = vess.diameters(nd);
% %tw (nd,4) = [ num2str(vess.angles(nd,1)) , ',' , num2str(vess.angles(nd,2))];
% tw (nd,5) = vess.angles(nd,1) ;
% end
%
% mtW = cat(1,mtW , tW);
% tW = [];
end
if(ui_settings.exportMode == 1) %do excel
if ui_settings.saperateFile4EachImage == 1
if ui_settings.writeCommulative
fileName = [expFile '_' stemName '.xls'];
xlswrite(fileName, mtW, 'A1');
else
fileName1 = [expFile '_' stemName '_1.xls'];
fileName2 = [expFile '_' stemName '_2.xls'];
xlswrite(fileName1, aW, 'A1');
xlswrite(fileName2, mtW, 'A1');
end
else
if ui_settings.writeCommulative
fileName = [expFile '.xls'];
xlswrite(fileName, mtW, stemName, 'A1');
else
fileName1 = [expFile '_1.xls'];
fileName2 = [expFile '_2.xls'];
xlswrite(fileName1, aW, stemName, 'A1');
xlswrite(fileName2, mtW, stemName, 'A1');
end
end
elseif(ui_settings.exportMode == 2) %do csv
if ui_settings.saperateFile4EachImage == 1
flag = 'w';
if ui_settings.writeCommulative
fileName = [expFile '_' stemName '.csv'];
else
fileName1 = [expFile '_' stemName '_1.csv'];
fileName2 = [expFile '_' stemName '_2.csv'];
end
elseif ui_settings.saperateFile4EachImage == 0
flag = 'a';
if ui_settings.writeCommulative
fileName1 = [expFile '.csv'];
else
fileName1 = [expFile '_1.csv'];
fileName2 = [expFile '_2.csv'];
end
end
if (ui_settings.writeCommulative == 1)
fid = fopen(fileName, flag);
for row=1:size(mtW,1)
if(row==1)
fprintf(fid, '%s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s \n', mtW{row,:});
else
fprintf(fid, '%s , %d , %d , %d , %f , %f , %d , %f , %f , %f , %f , %f , %f , %f , %f , %f , %f , %f \n', mtW{row,:});
end
end
fclose(fid);
elseif ui_settings.writeCommulative == 0
fid1 = fopen(fileName1, flag);
for row=1:size(aW,1)
if(row==1)
fprintf(fid1, '%s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s , %s \n', aW{row,:});
else
fprintf(fid1, '%s , %d , %d , %d , %f , %f , %d , %f , %f , %f , %f , %f , %f , %f \n', aW{row,:});
end
end
fclose(fid1);
fid2 = fopen(fileName2, flag);
for row=1:size(mtW,1)
if(row==1)
fprintf(fid2, '%s , %s , %s , %s , %s , %s \n', mtW{row,:});
else
fprintf(fid2, '%s , %d , %f , %f , %f , %f \n', mtW{row,:});
end
end
fclose(fid2);
end
%mtW(1,:) = [];
%dlmwrite(fileName,mtW,'-append');
%csvwrite(expFile,cell2mat(mtW));
end
clear mtW;
end
updateProcessingModeUI(handles,'on');
set(handles.txtStatus,'String','Finished : Export vessel analysis');
% --- Executes on button press in btnOpenExcel.
function btnOpenExcel_Callback(hObject, eventdata, handles)
% hObject handle to btnOpenExcel (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
system('climate.xls');
function edStart_Callback(hObject, eventdata, handles)
% hObject handle to edStart (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 edStart as text
% str2double(get(hObject,'String')) returns contents of edStart as a double
% --- Executes during object creation, after setting all properties.
function edStart_CreateFcn(hObject, eventdata, handles)
% hObject handle to edStart (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 edEnd_Callback(hObject, eventdata, handles)
% hObject handle to edEnd (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 edEnd as text
% str2double(get(hObject,'String')) returns contents of edEnd as a double
% --- Executes during object creation, after setting all properties.
function edEnd_CreateFcn(hObject, eventdata, handles)
% hObject handle to edEnd (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 chkAllFiles.
function chkAllFiles_Callback(hObject, eventdata, handles)
% hObject handle to chkAllFiles (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 chkAllFiles
global ui_settings;
ui_settings.bProcessAllFiles = get(hObject,'Value');
if( ui_settings.bProcessAllFiles )
else