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AutoAOMontagingGUI.m
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AutoAOMontagingGUI.m
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function varargout = AutoAOMontagingGUI(varargin)
% AUTOAOMONTAGINGGUI MATLAB code for AutoAOMontagingGUI.fig
% AUTOAOMONTAGINGGUI, by itself, creates a new AUTOAOMONTAGINGGUI or raises the existing
% singleton*.
%
% H = AUTOAOMONTAGINGGUI returns the handle to a new AUTOAOMONTAGINGGUI or the handle to
% the existing singleton*.
%
% AUTOAOMONTAGINGGUI('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in AUTOAOMONTAGINGGUI.M with the given input arguments.
%
% AUTOAOMONTAGINGGUI('Property','Value',...) creates a new AUTOAOMONTAGINGGUI or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before AutoAOMontagingGUI_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to AutoAOMontagingGUI_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 AutoAOMontagingGUI
% Last Modified by GUIDE v2.5 31-Aug-2017 14:05:51
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @AutoAOMontagingGUI_OpeningFcn, ...
'gui_OutputFcn', @AutoAOMontagingGUI_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 AutoAOMontagingGUI is made visible.
function AutoAOMontagingGUI_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 AutoAOMontagingGUI (see VARARGIN)
% Choose default command line output for AutoAOMontagingGUI
handles.output = hObject;
%allocate variables and defaults
handles.outputFolder_name=[];
handles.combinedFile_names=[];
handles.postionFile_name=[];
handles.imgfolder_name=[];
handles.imageFile_names=[];
handles.modalitiesInfo = {'Confocal' 'confocal';
'Split Detection' 'split';
'Dark Field' 'avg';
'Modality 4' '';
'Modality 5' '';};
handles.inputExt = 1;
handles.device_mode = 'multi_modal';
%default to .tif
%add path and setup vl_feat
currentFile = mfilename('fullpath');
[currentFileLoc,name,ext] = fileparts(currentFile);
genpath(fullfile(currentFileLoc,'SupportFunctions'));
addpath(genpath(fullfile(currentFileLoc,'SupportFunctions')));
vl_setup;
% If we've set up photoshop, then enable and check the export to photoshop
% buttons.
if exist('psnewdoc')
set(handles.pshop_cbox,'Enable','on');
set(handles.pshop_cbox,'Value',1.0);
end
% Check this version of AO Montaging against git.
fid = fopen(fullfile(getparent(which(mfilename)),'.VERSION'),'r');
if fid ~= -1
thisver = fscanf(fid,'%s');
fclose(fid);
git_version_check( 'BrainardLab','AOAutomontaging', thisver )
else
warning('Failed to detect .VERSION file, unable to determine if running the newest version.')
end
%set default options
set(handles.uibuttongroup1,'selectedobject',handles.radiobutton3);
set(handles.radiobutton4,'enable','off');
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes AutoAOMontagingGUI wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = AutoAOMontagingGUI_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;
% --------------------------------------------------------------------
function filemenu_Callback(hObject, eventdata, handles)
% hObject handle to filemenu (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 imageList.
function imageList_Callback(hObject, eventdata, handles)
% hObject handle to imageList (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 imageList contents as cell array
% contents{get(hObject,'Value')} returns selected item from imageList
if(~isempty(handles.imgfolder_name) && ~isempty(handles.imageFile_names))
index_selected = get(handles.imageList,'Value');
axes(handles.canvas);
img = imread(fullfile(handles.imgfolder_name,handles.imageFile_names{index_selected}));
imagesc(img); colormap gray; axis equal; axis off;
end
% --- Executes during object creation, after setting all properties.
function imageList_CreateFcn(hObject, eventdata, handles)
% hObject handle to imageList (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 imagefolder.
function imagefolder_Callback(hObject, eventdata, handles)
% hObject handle to imagefolder (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
selectedDir=uigetdir(handles.imgfolder_name);
if(selectedDir == 0)
return
end
handles.imgfolder_name = selectedDir;
set(handles.selectFolderText, 'String', handles.imgfolder_name) ;
set(handles.selectFolderText, 'TooltipString', handles.imgfolder_name) ;
Allfiles = dir(fullfile(handles.imgfolder_name,'*.tif'));
Allfiles = {Allfiles.name};
handles.imageFile_names =[];
%Use current identifiers to locate all images
dataSummary = cell(1,1);
dataSummary{1} = 'Input Data Summary:';
if strcmp(handles.device_mode, 'multi_modal')
for m = 1:size(handles.modalitiesInfo,1)
if (~isempty(handles.modalitiesInfo{m,2}))%check it's not empty
found = sort(Allfiles(~cellfun(@isempty, strfind(Allfiles, handles.modalitiesInfo{m,2}))));
handles.imageFile_names = [handles.imageFile_names, found];%search
dataSummary{end+1} =[num2str(size(found,2)),' ',char(handles.modalitiesInfo{m,1}),' image(s) found.'];
end
end
dataSummary{end+1} = '';
dataSummary{end+1} = 'Note: You can modify how to search for each modality under Preferences->Input Settings.';
elseif strcmp(handles.device_mode, 'canon')
found = sort(Allfiles(cellfun(@(s) strcmp(s(1:4),'206-'), Allfiles )));
handles.imageFile_names = [handles.imageFile_names, found];%search
dataSummary{end+1} =[num2str(size(found,2)),' image(s) found.'];
end
msgbox(dataSummary,'Input Complete');
set(handles.imageList,'String',handles.imageFile_names,...
'Value',1)
guidata(hObject, handles);
% --- Executes on button press in selectPosFile.
function selectPosFile_Callback(hObject, eventdata, handles)
% hObject handle to selectPosFile (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
defaultfolder = handles.imgfolder_name;
[FileName,PathName] = uigetfile(fullfile(defaultfolder,'*.xlsx'));
handles.postionFile_name = fullfile(PathName,FileName);
set(handles.posFileText, 'String', handles.postionFile_name);
set(handles.posFileText, 'TooltipString', handles.postionFile_name);
guidata(hObject, handles);
% --- Executes on selection change in montageList.
function montageList_Callback(hObject, eventdata, handles)
% hObject handle to montageList (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 montageList contents as cell array
% contents{get(hObject,'Value')} returns selected item from montageList
if(~isempty(handles.combinedFile_names) && ~isempty(handles.outputFolder_name))
index_selected = get(handles.montageList,'Value');
axes(handles.canvas);
img = imread(fullfile(handles.outputFolder_name,handles.combinedFile_names{index_selected}));
imagesc(img(:,:,1)); colormap gray; axis equal; axis off;
end
% --- Executes during object creation, after setting all properties.
function montageList_CreateFcn(hObject, eventdata, handles)
% hObject handle to montageList (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 montageAll.
function montageAll_Callback(hObject, eventdata, handles)
% hObject handle to montageAll (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
%Get Transformation Type
TransType=0;
switch get(get(handles.uibuttongroup1,'SelectedObject'),'Tag')
case 'radiobutton2', TransType=0;
case 'radiobutton3', TransType=1;
case 'radiobutton4', TransType=3;
end
%New Montage Or Append to Existing?
AppendToExisting=0;
MontageSave=[];
switch get(get(handles.uibuttongroup2,'SelectedObject'),'Tag')
case 'radiobutton5'
% If new check for existing save file exists
if(exist(fullfile(handles.outputFolder_name, 'AOMontageSave.mat'), 'file'))
choice = questdlg('AOMontageSave.mat file found in output folder. Overwrite existing montage?','Warrning');
if(~isequal(choice,'Yes'))
return;
end
end
AppendToExisting=0;
case 'radiobutton6',
%If appending check for existing save file
if(~exist(fullfile(handles.outputFolder_name, 'AOMontageSave.mat'), 'file'))
choice = questdlg('Appending Failed: AOMontageSave.mat file not found in output folder. Continue as New?','Error');
if(isequal(choice,'Yes'))
AppendToExisting = 0;
else
return;
end
else
MontageSave = fullfile(handles.outputFolder_name, 'AOMontageSave.mat');
AppendToExisting=1;
end
end
%read filename substrings to search for different modalities
tic
handles.combinedFile_names = AOMosiacAllMultiModal(handles.imgfolder_name, handles.postionFile_name, ...
handles.outputFolder_name, handles.device_mode, ...
handles.modalitiesInfo(:,2), TransType,AppendToExisting, ...
MontageSave, get(handles.pshop_cbox,'Value') );
toc
if(~isempty(handles.combinedFile_names))
set(handles.montageList,'String',handles.combinedFile_names,...
'Value',1)
img=imread(fullfile(handles.outputFolder_name,handles.combinedFile_names{1}));
axes(handles.canvas);
imagesc(img(:,:,1)); colormap gray; axis equal; axis off;
guidata(hObject, handles);
else
errordlg('Montage Interrupted!','Error');
end
% --------------------------------------------------------------------
function save_Callback(hObject, eventdata, handles)
% hObject handle to save (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function close_Callback(hObject, eventdata, handles)
% hObject handle to close (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
close all;
% --- Executes on button press in outputFolder.
function outputFolder_Callback(hObject, eventdata, handles)
% hObject handle to outputFolder (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
defaultfolder = handles.imgfolder_name;
selectedDir=uigetdir(defaultfolder);
if(selectedDir == 0)
return
end
handles.outputFolder_name = selectedDir;
set(handles.outputFolderText, 'String', handles.outputFolder_name) ;
set(handles.outputFolderText, 'TooltipString', handles.outputFolder_name) ;
guidata(hObject, handles);
% --- Executes on button press in radiobutton1.
function radiobutton1_Callback(hObject, eventdata, handles)
% hObject handle to radiobutton1 (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 radiobutton1
% --- Executes when selected object is changed in uibuttongroup1.
function uibuttongroup1_SelectionChangedFcn(hObject, eventdata, handles)
% hObject handle to the selected object in uibuttongroup1
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function prefmenu_Callback(hObject, eventdata, handles)
% hObject handle to prefmenu (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function inputsettings_Callback(hObject, eventdata, handles)
% hObject handle to inputsettings (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
prompt = {'Filename substrings for identifying each modality:','Image extension:'};
dlg_title = 'Input';
num_lines = [5 50;1 10];
%defaultsettings = {char({'confocal';'split';'avg';''});'.tif'};
defaultsettings = {'confocal\nsplit\navg\n','.tif'};
Title = 'Input Settings';
%%%% SETTING DIALOG OPTIONS
% Options.WindowStyle = 'modal';
Options.Resize = 'on';
Options.Interpreter = 'tex';
Options.CancelButton = 'on';
Options.ApplyButton = 'off';
Options.ButtonNames = {'Save','Cancel'}; %<- default names, included here just for illustration
Option.Dim = 4; % Horizontal dimension in fields
Prompt = {};
Formats = {};
DefAns = struct([]);
Prompt(1,:) = {'Filename substrings for identifying each modality:','modalitiesInfo',[]};
Formats(1,1).type = 'table';
Formats(1,1).format = {'char', 'char'}; % table (= table in main dialog) / window (= table in separate dialog)
Formats(1,1).items = {'Modality Name' 'Substring'};
Formats(1,1).size = [158.5 106];
Formats(1,1).margin = 2;
Formats(1,1).span = [1 1]; % item is 2 field x 1 fields
Formats(1,1).labelloc = 'topcenter';
Formats(1,1).unitsloc = 'bottomcenter';
DefAns(1).modalitiesInfo = handles.modalitiesInfo;
Prompt(end+1,:) = {'Input images extension:','inputExt',[]};
Formats(2,1).type = 'list';
Formats(2,1).style = 'popupmenu';
Formats(2,1).items = {'.tif','.png'};
DefAns(1).inputExt = handles.inputExt;
[Input,Cancelled] = inputsdlg(Prompt,Title,Formats,DefAns,Options);
if(~Cancelled)
handles.modalitiesInfo=Input.modalitiesInfo;
handles.inputExt=Input.inputExt;
guidata(hObject, handles);
end
% --------------------------------------------------------------------
function outputsettings_Callback(hObject, eventdata, handles)
% hObject handle to outputsettings (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --------------------------------------------------------------------
function multi_modal_device_Callback(hObject, eventdata, handles)
% hObject handle to multi_modal_device (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set(handles.canon_device, 'Checked', 'off');
set(handles.multi_modal_device, 'Checked', 'on');
set(handles.selectPosFile, 'Enable','on');
set(handles.inputsettings,'Enable','on');
handles.modalitiesInfo = {'Confocal' 'confocal';
'Split Detection' 'split';
'Dark Field' 'avg';
'Modality 4' '';
'Modality 5' '';};
handles.device_mode = 'multi_modal';
guidata(hObject, handles);
% --------------------------------------------------------------------
function canon_device_Callback(hObject, eventdata, handles)
% hObject handle to canon_device (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set(handles.canon_device, 'Checked', 'on');
set(handles.multi_modal_device, 'Checked', 'off');
set(handles.posFileText,'String','');
set(handles.selectPosFile, 'Enable','off');
set(handles.inputsettings,'Enable','off');
handles.modalitiesInfo = {'Canon confocal','206-'};
handles.device_mode = 'canon';
guidata(hObject, handles);
% --- Executes on button press in pshop_cbox.
function pshop_cbox_Callback(hObject, eventdata, handles)
% hObject handle to pshop_cbox (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 pshop_cbox