Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (feat_muscle_subdivisions) Browse

importSCase.m
ec80aabdeafffeat_muscle_subdivisions

importSCase.m
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			function varargout = importSCase(varargin)
			% IMPORTSCASE MATLAB code for importSCase.fig
			% IMPORTSCASE, by itself, creates a new IMPORTSCASE or raises the existing
			% singleton*.
			%
			% H = IMPORTSCASE returns the handle to a new IMPORTSCASE or the handle to
			% the existing singleton*.
			%
			% IMPORTSCASE('CALLBACK',hObject,eventData,handles,...) calls the local
			% function named CALLBACK in IMPORTSCASE.M with the given input arguments.
			%
			% IMPORTSCASE('Property','Value',...) creates a new IMPORTSCASE or raises the
			% existing singleton*. Starting from the left, property value pairs are
			% applied to the GUI before importSCase_OpeningFcn gets called. An
			% unrecognized property name or invalid value makes property application
			% stop. All inputs are passed to importSCase_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 importSCase

			% Last Modified by GUIDE v2.5 20-Feb-2019 10:59:13

			%% Begin initialization code - DO NOT EDIT
			gui_Singleton = 1;
			gui_State = struct('gui_Name', mfilename, ...
			'gui_Singleton', gui_Singleton, ...
			'gui_OpeningFcn', @importSCase_OpeningFcn, ...
			'gui_OutputFcn', @importSCase_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
			% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

			% From here this script has been edited by Jorge Solana Mu?oz, working at
			% the Laboratory of Biomechanical Orthopedics at EPFL (4.4.2019)

			% This function opens the grafical interfaces using the FIG file with the
			% same name of the current one
			function importSCase_OpeningFcn(hObject, eventdata, handles, varargin)
			%% --- Executes just before importSCase is made visible.
			% 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 importSCase (see VARARGIN)
			%--------------------------------------------------------------------------
			% Choose default command line output for importSCase
			handles.output = hObject;
			% Update handles structure
			guidata(hObject, handles);
			% UIWAIT makes importSCase wait for user response (see UIRESUME)
			% uiwait(handles.figure1);
			movegui('center')

			%--------------------------------------------------------------------------
			%% Customized by JSM 2019/04/04
			% Setting default values for some global variables

			% Default directory = the current directory
			handles.script_dir = pwd;

			% Radiobuttons default values
			set(handles.radiobutton_right,'Value',1);
			% handles.acquisition_stage => might be 'Preop' or 'Postop'
			set(handles.radiobutton_preop,'Value',1);
			% handles.output_dir => importation folder. By default the current dir.
			set(handles.output_dir,'String',pwd);
			% handles.body => might be 'Shoulder', 'Elbow' or 'Other[]'
			set(handles.radiobutton_shoulder,'Value',1);
			% handles.CTlabel_text => might be '-1', '-2', ..., '-1p', '-2p', ...
			set(handles.CTlabel_text,'String','-xxx');
			% Information extra added to the output README file
			handles.extra_info='.';
			% Updates global variables
			guidata(hObject,handles);

			% Function definition needed for the interface. Don't edit it.
			function varargout = importSCase_OutputFcn(hObject, eventdata, handles)
			%% --- Outputs from this function are returned to the command line.
			% 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;

			%% ======================================================================
			%% "Create Functions" execute during object creation, after setting all properties.
			% Those functions define graphical parameters

			%% --- Executes during object creation, after setting all properties.
			function patient_num_CreateFcn(hObject, eventdata, handles)
			% hObject handle to patient_num (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 during object creation, after setting all properties.
			function slider_2Dslice_CreateFcn(hObject, eventdata, handles)
			% hObject handle to slider_2Dslice (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called

			% Hint: slider controls usually have a light gray background.
			if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
			set(hObject,'BackgroundColor',[.9 .9 .9]);
			end
			% Updates global variables
			guidata(hObject,handles);


			%% --- Executes during object creation, after setting all properties.
			function edit_otherBody_CreateFcn(hObject, eventdata, handles)
			% hObject handle to edit_otherBody (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
			% Updates global variables
			guidata(hObject,handles);


			%% --- Executes during object creation, after setting all properties.
			function edit_extra_CreateFcn(hObject, eventdata, handles)
			% hObject handle to edit_extra (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
			set(hObject,'String','Write here every extra info...');
			% Updates global variables
			guidata(hObject,handles);


			%% ======================================================================
			%% **********************************************************************
			%% "CALLBACK Functions" execute on hObject's action events

			%% ******** Start Pending Directory / potentialy new SCase ************
			%% --- Executes on button press in Select_Pending_Directory.
			function Select_Pending_Directory_Callback(hObject, eventdata, handles)
			% hObject handle to Select_Pending_Directory (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			% This button lunch the initial check of a pending folder containing a
			% group of CTs. It counts the files per subfolder to clasify them

			%% Choose the main folder for the desired case
			% This open a navigation window allowing the user to choose a new directory
			if isfield(handles,'home_dir')
			% After the first use of this button, the software remembers the home
			% directory, saving time to the user
			newPath = uigetdir(handles.home_dir,'Chose the folder containing the all the CT sets');
			else
			% If the home directory saved is wrong or is the first CT load the
			% current working directory is temporaly used as home directory
			newPath = uigetdir(pwd,'Chose the folder containing all the CT sets');
			end

			% The new directory is saved as "patient directory" (handles.patien_dir)
			current_dir = pwd;
			cd([newPath '/..']);
			handles.patient_dir = pwd;
			cd(current_dir);

			% Finding "data" directory from "patient directory" and defining "home" and
			% "data" directories
			% All those paths will be needed further in this script
			handles.home_dir = extractBefore(handles.patient_dir,'data');
			data_dir_name = extractAfter(handles.patient_dir,handles.home_dir);
			data_dir_name = extractBefore(data_dir_name,'\');
			handles.data_dir = sprintf('%s%s',handles.home_dir,data_dir_name);
			handles.home_path = handles.home_dir;


			%% Set the patient group from directory
			% Since the patient group is coded in the directory path, the folowing
			% lines extract the patient group information from it and define the
			% correspondign global variable (handles.patient_group)
			patient_group = newPath;
			patient_group = extractAfter(patient_group,'\data');
			patient_group = extractAfter(patient_group,'\');
			patient_group = extractBefore(patient_group,'\');
			handles.patient_group = patient_group;

			% Call to another function which ask the user whether the 3D visualization
			% should be activated or not
			act3Dview_Callback(handles.act3Dview, eventdata, handles);

			% Updates the field "patient_num" with the "patient group" information
			patient_num = get(handles.patient_num,'String');
			set(handles.patient_num,'String',[handles.patient_group patient_num(2:end)]);


			%% Select a limit of minimun dicom files to discard scout scans & other
			% small scans as elbows
			% every CT with <30 DICOM files will be considered a scout scan
			scoutScanLimit = 30;
			% every CT with >29 and <90 DICOM files will be considered a potential
			% elbow scan
			smallScanLimit = 90;

			%% Check the chosen path and extract data from every folder and file inside
			dirList = dir(newPath);
			% Select only the folders from the current path and create a list
			folderN = 0;
			for k=3:length(dirList)
			folderN = folderN + dirList(k).isdir
			if folderN * dirList(k).isdir >0
			folderList(folderN) = dirList(k);
			folderN,folderList(folderN).name
			end
			end

			% Check how many dicom files are in each folder
			% A "waitbar" is prompted showing the progres to the user
			wb = waitbar(0,'Checking folders size');
			for k=1:folderN
			% files will contain a struct with data of files in the desired
			% folder
			% updating the "waitbar"
			waitbar(k/folderN,wb,sprintf('%s%s%s%i%s%i',"Checking directory ",...
			string(folderList(k).name),": ",k,"/",folderN));
			% Creates a list of files present in the folder
			files=dir([folderList(k).folder '/' folderList(k).name]);
			filesDicom = 0; % Initialitation of dicom files counter
			for n=1:length(files)
			% if there is a file and this file is a DICOM file, counts it
			if isfile([files(n).folder '/' files(n).name]) & ...
			isdicom([files(n).folder '/' files(n).name])
			files(n).isdicom = 1; % noting down that it is a dicom file
			filesDicom = filesDicom +1; % counting the dicom files
			% Next line builds a list of dicom file names in cell mode
			folderList(k).dicomList(filesDicom) = cellstr(files(n).name);
			else
			% Otherwise, is not a dicom file and don't count it
			files(n).isdicom = 0;
			end
			end
			% Each folder has its own counter of dicom files
			folderList(k).dicomN = filesDicom;
			% Adds a prefix with the number of files per CT, helping to prioritize
			% the importation order
			if ~contains(folderList(k).name,['s' char(string(folderList(k).dicomN))])
			movefile([folderList(k).folder '/' folderList(k).name],...
			[folderList(k).folder '/' 's'...
			char(string(folderList(k).dicomN)) '-' folderList(k).name]);
			folderList(k).name = ['s' char(string(folderList(k).dicomN))...
			'-' folderList(k).name];
			end

			%% This part could be removed since with the count of DICOM files per
			% folder should be enough information for the user

			% When a folder has few DICOM files we can consider that it was a scan
			% scout instead of an interesting CT
			if folderList(k).dicomN < scoutScanLimit
			folderList(k).scanMode = 'scoutScan';
			% Changing the folder name to mark it as scoutScan (if not marked
			% before)
			if ~contains(folderList(k).name,'scout')
			movefile([folderList(k).folder '/' folderList(k).name],...
			[folderList(k).folder '/' folderList(k).name '_scoutScan']);
			end
			elseif folderList(k).dicomN < smallScanLimit
			folderList(k).scanMode = 'smallScan';
			% Changing the folder name to mark it as scoutScan (if not marked
			% before)
			if ~contains(folderList(k).name,'small')
			movefile([folderList(k).folder '/' folderList(k).name],...
			[folderList(k).folder '/' folderList(k).name '_smallScan']);
			end
			else
			folderList(k).scanMode = 'CT';
			end
			% Until here, the removable part%%
			end

			% This shows the path to the database used, in an info-box
			set(handles.text_data_dir,'String',...
			sprintf('%s%s','Database directory ',string(handles.data_dir)));
			% Updates global variables
			guidata(hObject,handles);


			%% ************ Select CT scan ************
			%% --- Executes on button press in Select_CT_Scan.
			function Select_CT_Scan_Callback(hObject, eventdata, handles)
			% hObject handle to Select_CT_Scan (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			% Before loading a new set of CTs we should remove the last one
			clear handles.data

			% Also remove the fields 'myinfo' and 'mydicom'
			if isfield(handles, 'myinfo');
			handles = rmfield(handles, 'myinfo'); % Removing 'myinfo' field from structure in handles
			else if isfield(handles, 'mydicom');
			handles = rmfield(handles, 'mydicom');% Removing 'mydicom' field from structure in handles
			end
			end

			if isfield(handles,'dicomSet')
			handles = rmfield(handles,'dicomSet');
			end
			if isfield(handles,'dicomSetSorted')
			handles = rmfield(handles,'dicomSetSorted');
			end

			%% Loading CT files
			% A navigator windows askes the user to select the DICOM files to be loaded
			% Using last patient directory
			if isfield(handles,'patient_dir')
			[handles.dicomlist, handles.dicomdir] = uigetfile('.',...
			'Select the images to load',handles.patient_dir,'MultiSelect', 'on');
			% When no "patient directory" is present, this uses the "database" path
			elseif isfield(handles,'data_dir')
			[handles.dicomlist, handles.dicomdir] = uigetfile('.',...
			'Select the images to load',handles.data_dir,'MultiSelect', 'on');
			% Finding patient_dir
			current_dir = pwd;
			cd([handles.dicomdir '/../..']);
			handles.patient_dir = pwd;
			cd(current_dir);
			% If neither the "database" path is recorded, this uses the "home
			% directory"
			elseif isfield(handles,'home_dir')
			[handles.dicomlist, handles.dicomdir] = uigetfile('.',...
			'Select the images to load',handles.home_dir,'MultiSelect', 'on');
			% Finding patient_dir
			current_dir = pwd;
			cd([handles.dicomdir '/../..']);
			handles.patient_dir = pwd;
			cd(current_dir);

			% Finding "data" directory from patient directory
			data_dir_name = extractAfter(handles.patient_dir,handleshome_dir);
			data_dir_name = extractBefore(data_dir_name,'\');
			handles.data_dir = sprintf('%s%s',handles.home_dir,data_dir_name);
			handles.home_path = handles.home_dir;
			else
			% When even the "home directory" is missing, this uses the current
			% working directory
			[handles.dicomlist, handles.dicomdir] = uigetfile('.',...
			'Select the images to load',pwd,'MultiSelect', 'on');

			% Finding patient_dir
			current_dir = pwd;
			cd([handles.dicomdir '/../..']);
			handles.patient_dir = pwd;
			cd(current_dir);

			% Finding "data" directory from patient directory
			handles.home_dir = extractBefore(handles.patient_dir,'data');
			data_dir_name = extractAfter(handles.patient_dir,handles.home_dir);
			data_dir_name = extractBefore(data_dir_name,'\');
			handles.data_dir = sprintf('%s%s',handles.home_dir,data_dir_name);
			handles.home_path = handles.home_dir;
			end

			% If the "patient group" has not been obtained yet, this gets it from the
			% chosen path
			if ~isfield(handles,'patient_group')
			%% Set the patient group from directory
			patient_group = handles.dicomdir;
			patient_group = extractAfter(patient_group,'\data');
			patient_group = extractAfter(patient_group,'\');
			patient_group = extractBefore(patient_group,'\');
			handles.patient_group = patient_group;

			% Call to another function which ask the user whether the 3D visualization
			% should be activated or not
			act3Dview_Callback(handles.act3Dview, eventdata, handles);
			patient_num = get(handles.patient_num,'String');
			set(handles.patient_num,'String',[handles.patient_group patient_num(2:end)]);
			end

			% When only one DICOM files is selected this selects all DICOMs present
			% This is a quick way to select the whole CT scan
			if length(string(handles.dicomlist))==1
			files=dir(handles.dicomdir);
			filesDicom = 0; % Initialitation of dicom files counter
			handles.dicomlist=[];
			for n=1:length(files)
			% if is a file and this file is a dicom file, note it
			% (files.isdicom) and count it
			if isfile([files(n).folder '/' files(n).name]) & ...
			isdicom([files(n).folder '/' files(n).name])
			handles.dicomlist = [handles.dicomlist {files(n).name}];
			end
			end
			end

			% Showing the dicom name in the interface
			set(handles.text_dicom_name,'String',...
			sprintf('%s%s',string(handles.dicomdir),string(handles.dicomlist(1))));

			% Number of dicom files
			handles.N = length(handles.dicomlist);

			% Set parametres for 2D visualization
			set(handles.slider_2Dslice, 'Max', handles.N);
			set(handles.slider_2Dslice, 'Value', int32(handles.N/2));
			set(handles.slider_2Dslice, 'SliderStep',[1/handles.N 10/handles.N]);
			set(handles.slider_2Dslice, 'Min', 1);

			set(handles.info_text, 'ForegroundColor', 'black', 'FontWeight', 'normal');

			% Read dicom data
			try
			% This loop reads all the DICOM files and builds a new struct with the
			% information from each row and the data (the images)
			wb = waitbar(0,'Loading DICOM files'); %This creates a waitbar
			L = length(handles.dicomlist); % number of DICOM files to load
			for n=1:L
			waitbar(n/L,wb,sprintf('%s%i%s%i',"Loading DICOM metadata ",n,"/",L));
			% Reads the info from each dicomfile
			handles.dicomSet(n) = dicominfo(sprintf('%s%s',...
			handles.dicomdir, char(handles.dicomlist(n))),'UseDictionaryVR',true);
			end
			for n=1:L
			waitbar(n/L,wb,sprintf('%s%i%s%i',"Loading DICOM images ",n,"/",L));
			handles.dicomSet(n).data = dicomread(sprintf('%s%s', ...
			handles.dicomdir, char(handles.dicomlist(int32(n)))));
			end

			handles.myinfo = handles.dicomSet(1); % To be removed (JSM 25102018)

			% Temporal storing of metadata
			tempInfo=handles.dicomSet(1);
			save('tempInfo.mat','tempInfo');

			% Shows few metadata in the interface:
			% - IPP identification number and Patient Initials
			set(handles.IPP_text, 'String', handles.dicomSet(1).PatientID)
			set(handles.initials_text,'String',sprintf('(%s%s)',...
			handles.dicomSet(1).PatientName.FamilyName(1),...
			handles.dicomSet(1).PatientName.GivenName(1)));
			set(handles.birthdate_text,'String',handles.dicomSet(1).PatientBirthDate);
			set(handles.gender_text,'String',handles.dicomSet(1).PatientSex);
			% - CT resolution in mm
			set(handles.Resolution_text, 'String', sprintf('%f mm', handles.dicomSet(1).PixelSpacing(1)));
			% - CT date
			set(handles.CTdate_text, 'String', sprintf('%s', handles.dicomSet(1).AcquisitionDate));

			% The following function sort the dicomFiles by their slice location
			handles.dicomSetSorted=sortStructByField(handles.dicomSet,{'InstanceNumber'},handles);
			handles.dicomSetOld=handles.dicomSet;
			handles.dicomSet=handles.dicomSetSorted;
			'load finished'

			catch except
			except
			except.identifier
			if strcmp(except.identifier,'Error identifier: MATLAB:nonExistentField')
			errordlg(except.message,'Loading Error')
			else
			errordlg(sprintf('%s%s','Error identifier: ',except.identifier))
			end
			end

			%% Updating the radioButtons "NONE", "BONE"('BONE'), "SOFT"('STANDARD')
			if isfield(handles.dicomSet(1), 'ConvolutionKernel')
			if strfind(handles.dicomSet(1).ConvolutionKernel, 'BONE')
			set(handles.radiobutton_none, 'Value', 0);
			set(handles.radiobutton_sharp, 'Value', 1);
			set(handles.radiobutton_smooth, 'Value', 0);
			elseif strfind(handles.dicomSet(1).ConvolutionKernel, 'STANDARD')
			set(handles.radiobutton_none, 'Value', 0);
			set(handles.radiobutton_sharp, 'Value', 0);
			set(handles.radiobutton_smooth, 'Value', 1);
			else
			set(handles.radiobutton_none, 'Value', 1);
			set(handles.radiobutton_sharp, 'Value', 0);
			set(handles.radiobutton_smooth, 'Value', 0);
			end
			else
			set(handles.radiobutton_none, 'Value', 1);
			set(handles.radiobutton_sharp, 'Value', 0);
			set(handles.radiobutton_smooth, 'Value', 0);
			end

			%% Extracting data for interface representation
			handles.slice = int32(handles.N / 2); % Chooses the central slice
			% removes previous object "mydicom" if existed
			if isfield(handles,'mydicom')
			handles=rmfield(handles,'mydicom');
			end
			% load handles.mydicom with the current slice image
			handles.mydicom(:,:,handles.slice) = handles.dicomSet(handles.slice).data;

			% Setting some visualization parammeters
			handles.CTmin = -200;
			handles.CTmax = 2000;
			handles.bigmax = 3000;
			handles.bigmin = -2000;

			set(handles.slider_2Dcontrast, 'Max', handles.bigmax - handles.bigmin - 1);
			set(handles.slider_2Dcontrast, 'Min', 0);
			set(handles.slider_2Dcontrast, 'Value', 900);

			set(handles.slider_2Dbrightness, 'Max', handles.bigmax);
			set(handles.slider_2Dbrightness, 'Min', handles.bigmin);
			set(handles.slider_2Dbrightness, 'Value', 1100);

			set(handles.slice_num, 'String', handles.slice);

			axes(handles.axes_2Dviewer); % Set current axes
			% finaly shows the current CT slice image
			imshow(handles.dicomSet(handles.slice).data, [handles.CTmin handles.CTmax]);

			%% ISOSURFACE section ==== 3D ========================================
			% Call to another function which ask the user whether the 3D visualization
			% should be activated or not
			act3Dview_Callback(handles.act3Dview, eventdata, handles);

			axes(handles.axes_2Dviewer); % Set current axes
			% Updates global variables
			guidata(hObject,handles);

			%% Reset the DB chech result info box
			set(handles.text_coincidences_info,'String',"Check DB for coincidences...");
			set(handles.info_text, 'String', 'CT loaded');
			set(handles.info_add_SCase, 'String', '');
			set(handles.text_data_dir,'String',...
			sprintf('%s%s','Database directory ',string(handles.data_dir)));
			guidata(hObject,handles);


			function act3Dview_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in act3Dview.
			% hObject handle to act3Dview (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 act3Dview
			% handles.enable_3Dview = get(hObject,'Value')
			if get(hObject,'Value')
			C=questdlg(['The 3D viewer might create memory problems when the CT'...
			' contains more than 300 slices. Do you want to activate it?'],...
			'3D viewer activation','Yes, Display 3D view','Abort','Abort')
			switch C
			case 'Yes, Display 3D view'
			handles.enable_3Dview = 1
			otherwise
			handles.enable_3Dview = 0
			set(hObject,'Value',0)
			end
			else
			handles.enable_3Dview = 0
			end
			% clear handles.data
			axes(handles.isosurface); % Set current axes
			cla

			if isfield(handles,'N') & handles.enable_3Dview
			if handles.N>1
			directory=handles.dicomdir;
			% Preparing list of dicom full names (including address)
			for k=1:handles.N
			dicomListFullName(k)="";
			dicomListFullName(k)=[directory char(handles.dicomlist(k))];
			end
			try
			[V,spatial,dim] = dicomreadVolume(dicomListFullName);
			v = squeeze(V);
			v = double(v);
			v2= imresize3(v,0.2);
			handles.v2 = v2;
			handles.isoValue = 1400; % default limit for isosurface rendering
			p = patch(isosurface(v2,handles.isoValue));
			Sv2 = size(v2);
			M = max(max(max(v2)));
			m = min(min(min(v2)));

			handles.bigmax = M;
			handles.bigmin = m;
			set(handles.slider_3Dviewer, 'Max', handles.bigmax);
			set(handles.slider_3Dviewer, 'Min', handles.bigmin);
			set(handles.slider_3Dviewer, 'Value', handles.isoValue);

			d1=(M-m)/Sv2(1);
			d2=(M-m)/Sv2(2);
			d3=(M-m)/Sv2(3);
			[x,y,z]=meshgrid(m:d1:M,m:d2:M,m:d3:M);
			handles.x=x(1:Sv2(1),1:Sv2(2),1:Sv2(3));
			handles.y=y(1:Sv2(1),1:Sv2(2),1:Sv2(3));
			handles.z=z(1:Sv2(1),1:Sv2(2),1:Sv2(3));
			isocolors(handles.x,handles.y,handles.z,v2,p);
			p.FaceColor='interp';
			p.EdgeColor='none';
			view(-20, 10);
			% isosurface(v2,1400);
			rotate3d on;
			catch except
			if strcmp(except.identifier,'images:dicomread:differentPatientOrientations')
			f = errordlg(sprintf('%s\n\n%s\n%s', ' CT SCAN WITH UNEXPECTED ORIENTATION.',...
			'Suggestion: mark the current folder as "Wrong_Orientation"',...
			'and try with another set of CTs'),'Loading Error');
			% We change the folder name to mark it as scoutScan (if not marked before)
			if ~contains(handles.dicomdir,'wrong')
			movefile([handles.dicomdir(1:end-1)],...
			[handles.dicomdir(1:end-1) '_wrongOrientatedScan']);
			end
			return
			else
			errordlg(sprintf('%s%s','Error identifier: ',except.identifier));
			end
			end
			end
			end
			guidata(hObject,handles);


			function slider_3Dviewer_Callback(hObject, eventdata, handles)
			%% --- Executes on slider movement.
			% hObject handle to slider_3Dviewer (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,'Value') returns position of slider
			% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
			guidata(hObject,handles);


			function radiobutton_left_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in radiobutton_left.
			% hObject handle to radiobutton_left (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 radiobutton_left
			handles.shoulder_side = 'Left';
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			% --- Executes on button press in radiobutton_both.
			function radiobutton_both_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_both (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 radiobutton_both
			handles.shoulder_side = 'Both';
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);

			function radiobutton_right_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in radiobutton_right.
			% hObject handle to radiobutton_right (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 radiobutton_right
			handles.shoulder_side = 'Right';
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			%% --- Executes on button press in radiobutton_preop.
			function radiobutton_preop_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_preop (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 radiobutton_preop
			handles.acquisition_stage = 'Preop';
			update_readme_Callback(handles.update_readme,eventdata,handles);
			% update_infoFields(handles);
			guidata(hObject,handles);

			function radiobutton_postop_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in radiobutton_postop.
			% hObject handle to radiobutton_postop (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 radiobutton_postop
			handles.acquisition_stage = 'Postop';
			update_readme_Callback(handles.update_readme,eventdata,handles);
			% update_infoFields(handles);
			guidata(hObject,handles);


			function Check_Database_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in Check_Database.
			% hObject handle to Check_Database (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			% New way of reading the Excel Database:
			try
			DBpath = sprintf('%s%s',handles.data_dir,'\Excel\xlsFromMatlab\');
			excelDB= "SCaseImport.xlsx";
			catch
			[excelDB, DBpath, ~] = uigetfile('*.xlsx','Select the Excel Database File',pwd);
			end

			wb = waitbar(0,'Checking Excel DataBase');
			"Openning Excel Database"

			E = exist(sprintf('%s%s',DBpath,excelDB));
			% We store the Excel file adress and name for further use
			handles.ExcelDB_path = DBpath;
			handles.ExcelDB_fullname = sprintf('%s%s',DBpath,excelDB);
			tic
			if E == 2 % Only if the file exist as a known format (XLS)
			[~,txt,raw,dates]=xlsread(handles.ExcelDB_fullname,'SCaseImport','','',@convertSpreadsheetExcelDates);
			% The dates cell array will have NaN in every cell not containing a "date"
			dates(~cellfun(@(x) isnumeric(x) \|\| islogical(x), dates)) = {NaN};
			handles.data.headers = string(txt(1,:));
			% Conversion of dates's cell array to numeric matrix
			dates=cell2mat(dates);
			% Finding columns with dates
			dates_CperR=find(~isnan(dates(1,:)));
			date_Cells{1}= dates_CperR;
			txt_Cells{1} = [];
			for p=2:size(txt,1)
			dates_CperR=find(~isnan(dates(p,:)));
			date_Cells{p}= dates_CperR;
			txt_CperR = find(~ismissing(txt(p,:)));
			txt_Cells{p} = txt_CperR;
			end
			date_columns = [];
			txt_columns = [];
			for p=1:length(date_Cells)
			date_columns= union(date_columns,date_Cells{p});
			txt_columns = union(txt_columns,txt_Cells{p});
			end
			num_columns = setdiff(1:size(raw,2),txt_columns);
			txt_columns = setdiff(txt_columns,date_columns);
			% Inverting the "date to number" convertion done during the importation
			dates_only = datetime(dates(2:end,[date_columns]),'ConvertFrom','Excel','Format','dd-MM-yyy');

			for n=1:size(txt,2) % for each text headers (column)
			[data.(raw{1,n})]=raw(2:end,n);
			end
			k=1;
			for n=date_columns' % for the date columns
			[data.(raw{1,n})]=dates_only(:,k);
			k=k+1;
			end

			elseif E == 0
			warndlg("Excel file not found!")
			else
			warndlg("Database file has unrecognized format. It should be an Excel file")
			end
			toc
			handles.data=data;

			% *Obtain the first row available for a new case*
			% Get the colum of sCase.id, including those from rows available
			sCase_list = handles.data.SCase_ID;
			% Cut the list from the end untill found an existing sCases
			[s1,s2]=size(sCase_list);
			s0=0;
			while string(sCase_list(end,:))=="" \| ismissing(string(sCase_list(end,:)))% Last position empty...
			sCase_list = sCase_list(1:end-1,:);
			s0=s0+1;
			waitbar(s0/s1,wb,'Checking Excel Database');
			end
			handles.DB_length=length(sCase_list);

			sCase_N=[];
			sCase_P=[];
			sCase_list_sorted=string(sCase_list); % This have to be cleaned
			for n=1:s1-s0
			if sCase_list_sorted(n,:)~="" & ~ismissing(sCase_list_sorted(n,:))
			L = length(char(extractAfter(sCase_list_sorted(n,:),1)));
			while L<3
			sCase_list_sorted(n,:)=sprintf('%s%s%s',...
			extractBefore(sCase_list_sorted(n,:),2),...
			'0',extractAfter(sCase_list_sorted(n,:),1));
			L = length(char(extractAfter(sCase_list_sorted(n,:),1)));
			end
			if extractBefore(sCase_list_sorted(n,:),2)=="N"
			sCase_N=[sCase_N; sCase_list_sorted(n,:)];
			elseif extractBefore(sCase_list_sorted(n,:),2)=="P"
			sCase_P=[sCase_P; sCase_list_sorted(n,:)];
			else
			"there is a row without identification (N or P) in the DataBase"
			end
			waitbar(s1-s0+n/s1,wb,'Checking Excel Database');
			end
			end
			sCase_N=sort(sCase_N);
			sCase_P=sort(sCase_P);

			% Build the next sCase.id for a potential new sCase
			% by extracting the 'id' number of the last sCase and adding '1'
			if handles.patient_group=="N"
			new_sCase = str2num(extractAfter(char(sCase_N(end)),1))+1;
			% Finaly convert to string and add a 'P' for 'Pathological'
			new_sCase = string(['N' num2str(new_sCase)]);
			elseif handles.patient_group=="P"
			new_sCase = str2num(extractAfter(char(sCase_P(end)),1))+1;
			% Finaly convert to string and add a 'N' for 'Normal'
			new_sCase = string(['P' num2str(new_sCase)]);
			end
			handles.data.anonymity_IPP=cell2mat(handles.data.anonymity_IPP(1:handles.DB_length));
			handles.data.shoulder_side=cell2mat(handles.data.shoulder_side(1:handles.DB_length));

			% * Q1: Does the new IPP exist in the Database yet? *
			% Extract the list of patient IDs from Excel database
			IPP_list_DB = handles.data.anonymity_IPP;
			% Extracting patient ID from dicom-set info
			IPP_sCase = str2num(handles.myinfo(1).PatientID)

			% If the IPP of the current case already exist in the database,
			% it finds the position of the current patient ID in the list.
			% And for this position it extracts the case name "sCase", otherwise it
			% leave the variables empty
			% handles.patientIndex=find(handles.data.anonymityIPP==str2num(handles.myinfo(1).PatientID))
			handles.patientIndex=find(IPP_list_DB==IPP_sCase);
			handles.sCase = handles.data.SCase_ID(handles.patientIndex);

			% Determine how many sCases exits with the same IPP as the current CT
			Ncoincidences=length(handles.sCase);

			% * We start the decision tree *
			if Ncoincidences==0
			% This is a new sCase!! So we write a short message and set the sCase
			set(handles.dataCheck_text,'String', sprintf('This is a new case'));
			set(handles.dataCheck_panel,'BackgroundColor','g');
			handles.current_sCase=new_sCase;
			set(handles.patient_num,'String',sprintf('%s',handles.current_sCase));
			set(handles.text_coincidences_info,'String',"Current IPP not found in DB");

			% If the IPP exists in the Excel Database in more than one sCase we first
			% can discriminate by the shoulder side (rigth or left)
			elseif Ncoincidences>1
			% Launch a warning message
			set(handles.dataCheck_text,'String',...
			['Patient found in ' num2str(Ncoincidences) ' sCase(s)']);
			set(handles.dataCheck_panel,'BackgroundColor','y');

			% Shows information of the 2 first coincidences
			coincidences = sprintf("%s \t%s \t%s \t%s \n%s \t%s \t%s \t\t%s \n%s \t%s \t%s \t\t%s",...
			"SCase"," IPP "," CT_date ","Side",...
			string(handles.sCase(1)),...
			string(IPP_list_DB(handles.patientIndex(1))),...
			handles.data.CT_date(handles.patientIndex(1)),...
			handles.data.shoulder_side(handles.patientIndex(1)),...
			string(handles.sCase(2)),...
			string(IPP_list_DB(handles.patientIndex(2))),...
			handles.data.CT_date(handles.patientIndex(2)),...
			handles.data.shoulder_side(handles.patientIndex(2)));
			set(handles.text_coincidences_info,'String',coincidences);

			% *** Q2: is the current CT from the same side of one of the existing?
			% Get the side of the coincident sCases
			side_sCase = handles.data.shoulder_side(handles.patientIndex);
			% Launch 'question dialog' to let the user choose if one the coincident
			% sCases matches with the side (rigth or left) of the current CT
			question = sprintf("%s %s %s \n%s\n%s",...
			"The SCase",string(IPP_sCase),...
			"was found in the more than one case in the database.",...
			"Please, check the shoulder side of the currently loaded CT",...
			"and choose between the following options");
			title = "SCase found in database";
			btn1 = ['Existing case:' char(handles.sCase(1)) ' side:' char(side_sCase(1))];
			btn2 = ['Existing case:' char(handles.sCase(2)) ' side:' char(side_sCase(2))];
			btn3 = ['New case:' char(new_sCase) ' side: ?'];
			dfltbtn = btn3;
			answer = questdlg(question,title,btn1,btn2,btn3,dfltbtn);
			switch answer
			case btn1
			handles.current_sCase=handles.sCase(1);
			answerN = 1;
			case btn2
			handles.current_sCase=handles.sCase(2);
			answerN = 2;
			case btn3
			handles.current_sCase=string(new_sCase);
			answerN = 3;
			otherwise
			disp("Auto Check DB -ABORTED-");
			return;
			end
			disp(sprintf("%s %s",string(handles.current_sCase),"chosen"));

			% Update the list of sCases after selection
			handles.sCase=handles.current_sCase;
			Ncoincidences=1;

			% *** Q3: is the current CT date similar to the CT_date from any of the
			% concident sCases in the Database? ***

			% Get the CT's date from the coincident sCase from the Database
			try
			CTdate_DB = datestr(handles.data.CT_date(handles.patientIndex),'dd-mmm-yyyy');
			catch error
			message = sprintf("%s\n%s\n%s\n\n%s\n%s\n%s",...
			"Suggested solution:",...
			"Opt1. Update InfoCT.xlsx and repeat the 'Auto Check DB'",...
			"Opt2. Check the CT_date yourself and use 'Manual sCase'",...
			"Error details:",...
			error.identifier,error.message);
			errordlg(message,"Not valid CT_date found in Database");
			CTdate_DB = NaT;
			end
			% Get the CT's date from the new CT set
			current_CTdate = handles.myinfo.AcquisitionDate
			% Adapt date format to make it comparable
			current_CTdate=datestr([current_CTdate(1:4),'-',...
			current_CTdate(5:6),'-',current_CTdate(7:8)],'dd-mmm-yyyy')
			% Compare CT's dates
			if isequal(current_CTdate,CTdate_DB)
			% The sCase already exits so the user will have to decide if the CT
			% must be added to the case of it is already added.
			set(handles.dataCheck_text,'String',...
			['Current CT matches in IPP, side and CTdate with others in the database']);
			set(handles.dataCheck_panel,'BackgroundColor','r');
			set(handles.patient_num,'String',string(handles.current_sCase));
			else
			% The user must check if the current CT set corresponds to a
			% post-op shoulder
			set(handles.dataCheck_text,'String',...
			['Check if the CT is from a post-op. Current CT matches in IPP, side']);
			set(handles.dataCheck_panel,'BackgroundColor','r');
			set(handles.patient_num,'String',string(handles.current_sCase));
			end

			% If only one sCase was found in the Database
			elseif Ncoincidences==1
			% Launch a warning message
			set(handles.dataCheck_text,'String',...
			['Patient found in one sCase(s)']);
			set(handles.dataCheck_panel,'BackgroundColor','r');
			handles.current_sCase=handles.sCase;

			coincidences = sprintf("%s \t%s \t%s \t%s \n%s \t%s \t%s \t\t%s",...
			"SCase"," IPP "," CT_date ","Side",...
			string(handles.sCase(1)),...
			string(IPP_list_DB(handles.patientIndex(1))),...
			handles.data.CT_date(handles.patientIndex(1)),...
			handles.data.shoulder_side(handles.patientIndex(1)));
			set(handles.text_coincidences_info,'String',coincidences);

			side_sCase=handles.data.shoulder_side(handles.patientIndex);
			% Creating question dialog to let the user choose between the found
			% SCase and a new SCase label
			question = sprintf("%s %s %s \n%s\n%s",...
			"The loaded SCase",string(IPP_sCase),...
			"was found in the SCase list in the database.",...
			"Please, check the shoulder side of the currently loaded CT",...
			"and choose between the following options");
			title = "SCase found in database";
			btn1 = ['Existing case:' char(handles.sCase(1)) ' side:' char(side_sCase(1))];
			btn2 = ['New case:' char(new_sCase) ' side: ?'];
			dfltbtn = btn2;
			answer= questdlg(question,title,btn1,btn2,dfltbtn);

			switch answer
			case btn1
			handles.current_sCase=handles.sCase(1)
			answerN=1;
			case btn2
			handles.current_sCase=string(new_sCase);
			answerN=2;
			otherwise
			disp("Auto Check DB -ABORTED-");
			return;
			end
			disp(sprintf("%s %s",string(handles.current_sCase),"chosen"));

			if answerN==1

			% *** Q3: is the current CT date similar to the CT_date from any of the
			% concident sCases in the Database? ***

			% Get the CT's date from the coincident sCase from the Database
			try
			CTdate_DB = datestr(handles.data.CT_date(handles.patientIndex),'dd-mmm-yyyy');
			catch error
			message = sprintf("%s\n%s\n%s\n\n%s\n%s\n%s",...
			"Suggested solution:",...
			"Opt1. Update InfoCT.xlsx and repeat the 'Auto Check DB'",...
			"Opt2. Check the CT_date yourself and use 'Manual sCase'",...
			"Error details:",...
			error.identifier,error.message);
			errordlg(message,"Not valid CT_date found in Database");
			CTdate_DB = NaT;
			end
			% Get the CT's date from the new CT set
			current_CTdate = handles.myinfo.AcquisitionDate
			% Adapt date format to make it comparable
			current_CTdate=datestr([current_CTdate(1:4),'-',...
			current_CTdate(5:6),'-',current_CTdate(7:8)],'dd-mmm-yyyy')
			% Compare CT's dates
			if isequal(current_CTdate,CTdate_DB)
			% The sCase already exits so the user will have to decide if the CT
			% must be added to the case of it is already added.
			set(handles.dataCheck_text,'String',...
			['Current CT matches in IPP, side and CTdate with others in the database']);
			set(handles.dataCheck_panel,'BackgroundColor','r');
			set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
			else
			% The user must check if the current CT set corresponds to a
			% post-op shoulder
			set(handles.dataCheck_text,'String',...
			['Check if the CT is from a post-op. Current CT matches in IPP, side']);
			set(handles.dataCheck_panel,'BackgroundColor','r');
			set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
			end
			else
			% This is a new sCase!! So we write a short message and set the sCase
			set(handles.dataCheck_text,'String', sprintf('This is a new case'));
			set(handles.dataCheck_panel,'BackgroundColor','g');
			handles.current_sCase=new_sCase;
			set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
			end
			end

			F1=extractBefore(char(handles.current_sCase),2);
			F2=extractBetween(char(handles.current_sCase),2,2);
			F3=extractBetween(char(handles.current_sCase),3,3);

			current_dir = cd(char(strcat(handles.data_dir,'/',F1,'/',F2,'/',F3))); % saving current directory and changing to the output dir
			output_dir = pwd; % needed to update the output directory
			cd(current_dir); % back to the current directory
			set(handles.output_dir,'String',output_dir);
			% set(handles.output_dir,'String',strcat(handles.data_dir,F1,'/',F2,'/',F3));%sprintf('%s%s\%s\%s',data_dir,F1,F2,F3));
			waitbar(1,wb,'Checking Excel Database');
			guidata(hObject,handles);


			%% --- Executes on button press in Manual_SCase.
			function Manual_SCase_Callback(hObject, eventdata, handles)
			% hObject handle to Manual_SCase (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)
			sCase_dir = uigetdir(handles.data_dir, "Select the output directory",handles.data_dir);
			set(handles.output_dir,'String',sCase_dir);
			update_readme_Callback(handles.update_readme,eventdata,handles);
			warndlg('Please uptade the sCase.id accordingly with the chosen output directory')
			guidata(hObject,handles);


			%% Executes with 'Enter' in patient_num
			function patient_num_Callback(hObject, eventdata, handles)
			% hObject handle to patient_num (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 patient_num as text
			% str2double(get(hObject,'String')) returns contents of patient_num as a double

			% The output directory is stablish by the automatic Check of the DB or the
			% manual selection. Hence, here we only check whether the sCase number
			% matches with the selected output directory
			% From "patient_num" which corresponds to sCase number
			patient_num = get(handles.patient_num,'String'); % Get the sCase number
			F0=char(extractBefore(char(patient_num),1))
			F0=char(extractBefore(char(patient_num),2)) % Extract the 'N' or 'P'
			F1=char(extractBetween(char(patient_num),2,2)) % Extract the first digit (1 to 9)
			F2=char(extractBetween(char(patient_num),3,3)) % Extract the second digit (0to9)
			% From "output_dir" which corresponds to output directory
			output_dir = get(handles.output_dir,'String'); % Get the ourput directory
			L = length(output_dir); % lenght of the string that contains the directory
			D0=char(extractBetween(char(output_dir),L-4,L-4)) % Extact the 'N' or 'P'
			D1=char(extractBetween(char(output_dir),L-2,L-2)) % Extract the first digit (1 to 9)
			D2=char(extractAfter(char(output_dir),L-1)) % Extract the second digit (0 to 9)

			if F0==D0 & F1==D1 & F2==D2
			handles.enable_importation = 1
			else
			handles.enable_importation = 0
			warndlg('Importation cancelled. The sCase (patient number) must be consistant with the Output Directory')
			end

			guidata(hObject,handles);



			%% --- Executes on slider movement.
			function slider_2Dslice_Callback(hObject, eventdata, handles)
			% hObject handle to slider_2Dslice (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,'Value') returns position of slider
			% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
			handles.slice = int32(get(hObject,'Value'));
			set(handles.slice_num, 'String', handles.slice);
			handles.mydicom(:,:,handles.slice) = handles.dicomSet(handles.slice).data;
			axes(handles.axes_2Dviewer) % Set current axes
			imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax])
			% update slice name info
			set(handles.text_dicom_name,'String',...
			sprintf('%s%s%s','DICOM File Full-name: ',string(handles.dicomdir),...
			string(handles.dicomlist(str2num(handles.slice_num.String)))));
			guidata(hObject,handles);


			%% --- Executes on button press in Anonymise_Import.
			function Anonymise_Import_Callback(hObject, eventdata, handles)
			% hObject handle to Anonymise_Import (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			sortPictures = 1;

			set(handles.info_text, 'String', 'Preparing DICOM images to be imported...');
			drawnow

			% Warning message in info panel when no patient's number is found
			if isempty(get(handles.patient_num,'String'))
			set(handles.info_text, 'ForegroundColor', 'red', 'FontWeight', 'bold', 'String', 'Please give a patient number')
			return
			else
			patient = get(handles.patient_num,'String');
			end

			% Warning message in info panel when no output dir is found
			if isempty(get(handles.output_dir,'String'))
			outputdir = uigetdir(handles.home_path,"Select the output directory where the CT must be imported");
			if outputdir
			set(handles.output_dir,'String', outputdir);
			end
			else
			outputdir = get(handles.output_dir,'String');
			end

			if ~outputdir
			set(handles.info_text, 'ForegroundColor', 'red', 'FontWeight', 'bold',...
			'String', 'Please select an output directoy');
			return
			end

			set(handles.info_text, 'ForegroundColor', 'black', 'FontWeight', 'normal');

			% Create name string
			newname = [patient, '-', handles.dicomSet(1).PatientID, '_',...
			handles.dicomSet(1).PatientName.FamilyName(1),...
			handles.dicomSet(1).PatientName.GivenName(1)];
			if get(handles.radiobutton_sharp,'Value')
			newname = [newname, '-bone.'];
			elseif get(handles.radiobutton_smooth,'Value')
			newname = [newname, '-soft.'];
			else
			newname = [newname, '.'];
			end

			% Checking the existance of a folder with similar SCase_ID and different
			% IPP
			if exist(outputdir)==7
			f=dir(outputdir);
			if length(f)>2 % When a subfolder is present this length is >=3
			for n=3:length(f)
			SC{n-2}=extractBefore(f(n).name,'-');
			IPP{n-2}=extractAfter(f(n).name,'-');
			end
			SC=string(SC);
			IPP=string(IPP);
			SC_dx = find(SC==string(patient));
			if ~isempty(SC_dx)
			if IPP(SC_dx(1))~=string(handles.dicomSet(1).PatientID)
			errordlg(sprintf("%s %s %s %s", "SCase =",string(patient),...
			"present with a IPP = ", IPP(SC_dx)),...
			'Current SCase_ID already in the directories database');
			set(handles.info_text, 'String', 'Preparing DICOM images to be imported...');
			drawnow
			return
			end
			end
			end
			end

			suggested_outputdir = sprintf('%s%s%s%s%s%s%s%s%s%s%s',outputdir,'/', patient,'-',...
			handles.dicomSet(1).PatientID,'/','CT-',patient,'-',...
			handles.dicomSet(1).PatientID,handles.CTlabel_text.String,'/dicom/');
			if exist(suggested_outputdir)==7
			outputdir = sprintf('%s%s%s%s%s%s%s%s%s%s%s',outputdir,'/', patient,'-',...
			handles.dicomSet(1).PatientID,'/','CT-',patient,'-',...
			handles.dicomSet(1).PatientID,'xxx','/dicom/');
			else
			outputdir = suggested_outputdir;
			end
			% Creating the output directory
			mkdir(outputdir);

			% Sort pictures in correct order
			if sortPictures == 1
			for h = 1:handles.N
			infoTemp = dicominfo(sprintf('%s%s', handles.dicomdir,...
			char(handles.dicomlist(h))),'UseDictionaryVR',true);
			SliceLoc(h,1) = h;
			SliceLoc(h,2) = infoTemp.SliceLocation;
			end
			SliceSorted = sortrows(SliceLoc,2);
			end
			guidata(hObject,handles);

			% Read all data
			% at the importation we set the dicomSet as definitively sorted
			handles.dicomSet=handles.dicomSetSorted; % with this sentence we could avoid the very previous sorting...
			for i = 1:handles.N
			str = sprintf('Copying dicom...\n%d / %d\n', i, handles.N);
			set(handles.info_text, 'String', str);
			drawnow

			% This replace the Given Name by the patient inicials and kernel info
			if get(handles.radiobutton_sharp,'Value')
			handles.dicomSet(i).PatientName.GivenName = ...
			[handles.dicomSet(i).PatientName.FamilyName(1),...
			handles.dicomSet(i).PatientName.GivenName(1), '_bone'];
			elseif get(handles.radiobutton_smooth,'Value')
			handles.dicomSet(i).PatientName.GivenName = ...
			[handles.dicomSet(i).PatientName.FamilyName(1),...
			handles.dicomSet(i).PatientName.GivenName(1), '_soft'];
			else
			handles.dicomSet(i).PatientName.GivenName = ...
			[handles.dicomSet(i).PatientName.FamilyName(1),...
			handles.dicomSet(i).PatientName.GivenName(1)];
			end
			% This replace the Given Name by the IPP
			handles.dicomSet(i).PatientName.FamilyName = [patient, '_',...
			handles.dicomSet(1).PatientID];

			% Importation
			dicomwrite(handles.dicomSet(i).data,[outputdir, newname,...
			sprintf('%04d',i), '.dcm'], handles.dicomSet(i));
			end
			guidata(hObject,handles);

			% Create readme.txt file if it does not exist already
			localDir = string(get(handles.output_dir,'String'));
			localDir = sprintf('%s%s%s%s%s%s',localDir,'/', patient,'-', handles.dicomSet(1).PatientID,'/');
			if ~exist(sprintf('%s%s',localDir,'readme.txt'), 'file')
			readme_file=fopen(sprintf('%s%s',localDir,'readme.txt'), 'wt');
			fprintf(readme_file,sprintf('%s%s%s %s %s\r\n',patient,'-',...
			handles.dicomSet(1).PatientID,handles.initials_text.String,...
			handles.shoulder_side));
			fprintf(readme_file,sprintf('\r\n%s',get(handles.text_readme,'String')));
			fclose(readme_file);
			else
			readme_file=fopen(sprintf('%s%s',localDir,'readme.txt'), 'at'); % opening to append text
			fprintf(readme_file,sprintf('\r\n%s',get(handles.text_readme,'String')));
			fclose(readme_file);
			end

			set(handles.info_text, 'String', 'CT Imported');
			guidata(hObject,handles);


			function output_dir_Callback(hObject, eventdata, handles)
			%%
			% hObject handle to output_dir (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 output_dir as text
			% str2double(get(hObject,'String')) returns contents of output_dir as a double
			guidata(hObject,handles);



			function CTlabel_text_Callback(hObject, eventdata, handles)
			% hObject handle to CTlabel_text (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 CTlabel_text as text
			% str2double(get(hObject,'String')) returns contents of CTlabel_text as a double
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			function output_dir_CreateFcn(hObject, eventdata, handles)
			%% --- Executes during object creation, after setting all properties.
			% hObject handle to output_dir (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
			guidata(hObject,handles);



			%% --- Executes during object creation, after setting all properties.
			function info_text_CreateFcn(hObject, eventdata, handles)
			% hObject handle to info_text (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called
			guidata(hObject,handles);


			%% --- Executes during object creation, after setting all properties.
			function DicomInfoBox_CreateFcn(hObject, eventdata, handles)
			% hObject handle to info_text (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called
			guidata(hObject,handles);




			%% --- Executes during object creation, after setting all properties.
			function slider_3Dviewer_CreateFcn(hObject, eventdata, handles)
			% hObject handle to slider_3Dviewer (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called

			% Hint: slider controls usually have a light gray background.
			if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
			set(hObject,'BackgroundColor',[.9 .9 .9]);
			end
			guidata(hObject,handles);


			%% --- Executes on button press in DicomDetails.
			function DicomDetails_Callback(hObject, eventdata, handles)
			% hObject handle to DicomDetails (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)
			try
			load tempInfo.mat
			tempInfo
			handles.DicomInfoBox.String = ['Dicom Info: ',...
			'Patient Sex: ', handles.dicomSet(1).PatientSex,...
			'. Birthday: ', handles.dicomSet(1).PatientBirthDate];
			catch exception
			"Dicom info not available"
			end
			guidata(hObject,handles);


			%% --- Executes on button press in checkbox_CTdate.
			function checkbox_CTdate_Callback(hObject, eventdata, handles)
			% hObject handle to checkbox_CTdate (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 checkbox_CTdate
			if get(hObject,'Value') %the IPP must be added to the readme line
			try
			handles.readme.CTdate = string(handles.myinfo(1).AcquisitionDate);
			['CTdate info to be added to the Readme line := ' handles.readme.CTdate]
			catch except
			sprintf('%s%s','Error identifier: ',except.identifier)
			['CTdate info failed to be added to the Readme line.']
			handles.readme.CTdate = '';
			end
			else
			handles.readme.CTdate = '';
			['CTdate info not present in Readme line']
			end
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			%% --- Executes on button press in checkbox_resolution.
			function checkbox_resolution_Callback(hObject, eventdata, handles)
			% hObject handle to checkbox_resolution (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 checkbox_resolution
			if get(hObject,'Value') %the IPP must be added to the readme line
			try
			handles.readme.resolution = string(handles.myinfo(1).PixelSpacing(1));
			['Resolution info to be added to the Readme line := ' handles.readme.resolution]
			catch except
			sprintf('%s%s','Error identifier: ',except.identifier)
			['Resolution info failed to be added to the Readme line.']
			handles.readme.resolution = '';
			end
			else
			handles.readme.resolution = '';
			['Resolution info not present in Readme line']
			end
			% update_readme_line(handles)
			% update_infoFields(handles);
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			%% --- Executes on button press in radiobutton_shoulder.
			function radiobutton_shoulder_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_shoulder (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 radiobutton_shoulder
			handles.body = 'Shoulder';
			set(handles.checkbox_contralateral,'Value',0);
			handles.contralateral='';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);

			%% --- Executes on button press in radiobutton_elbow.
			function radiobutton_elbow_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_elbow (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 radiobutton_elbow
			handles.body = 'Elbow';
			set(handles.checkbox_contralateral,'Value',0);
			handles.contralateral='';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);


			%% --- Executes on button press in radiobutton_thorax.
			function radiobutton_thorax_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_thorax (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 radiobutton_thorax
			handles.body = 'Thorax';
			set(handles.checkbox_contralateral,'Value',0);
			handles.contralateral='';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);


			%% --- Executes on button press in checkbox_contralateral.
			function checkbox_contralateral_Callback(hObject, eventdata, handles)
			% hObject handle to checkbox_contralateral (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 checkbox_contralateral
			if get(handles.checkbox_contralateral,'Value')
			handles.contralateral = ['Contralateral '];
			else
			handles.contralateral = '';
			end
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);


			%% --- Executes on button press in radiobutton_otherBody.
			function radiobutton_otherBody_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_otherBody (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 radiobutton_otherBody
			set(handles.checkbox_contralateral,'Value',0);
			handles.contralateral='';
			set(handles.edit_otherBody,'Enable','On');
			handles.body = get(handles.edit_otherBody,'String');
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);

			function edit_otherBody_Callback(hObject, eventdata, handles)
			%%
			% hObject handle to edit_otherBody (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 edit_otherBody as text
			% str2double(get(hObject,'String')) returns contents of edit_otherBody as a double
			handles.body = get(handles.edit_otherBody,'String');
			guidata(hObject,handles);


			%% --- Executes on button press in radiobutton_sharp.
			function radiobutton_sharp_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_sharp (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 radiobutton_sharp

			handles.kernel='Sharp';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);

			%% --- Executes on button press in radiobutton_smooth.
			function radiobutton_smooth_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_smooth (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 radiobutton_smooth
			handles.kernel='Smooth';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);

			%% --- Executes on button press in radiobutton_none.
			function radiobutton_none_Callback(hObject, eventdata, handles)
			% hObject handle to radiobutton_none (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 radiobutton_none
			handles.kernel='none';
			warndlg(char("IMPORTANT: The operator must choose between 'Sharp (Bone)' or 'Smooth (Soft Tissue)'"));
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			function checkbox_with_phantoms_Callback(hObject, eventdata, handles)
			%% --- Executes on button press in checkbox_with_phantoms.
			% hObject handle to checkbox_with_phantoms (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 checkbox_with_phantoms
			handles.phantoms = 'with';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);


			function radiobutton_without_phantoms_Callback(hObject, eventdata, handles)
			% --- Executes on button press in radiobutton_without_phantoms.
			% hObject handle to radiobutton_without_phantoms (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 radiobutton_without_phantoms
			handles.phantoms = 'without';
			update_readme_Callback(handles.update_readme, eventdata, handles);
			guidata(hObject,handles);


			function edit_extra_Callback(hObject, eventdata, handles)
			%%
			% hObject handle to edit_extra (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 edit_extra as text
			% str2double(get(hObject,'String')) returns contents of edit_extra as a double
			handles.extra_info=handles.edit_extra.String;
			update_readme_Callback(handles.update_readme,eventdata,handles);
			guidata(hObject,handles);


			%% --- Executes on button press in update_readme.
			function update_readme_Callback(hObject, eventdata, handles)
			% hObject handle to update_readme (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			if ~isfield(handles,'shoulder_side')
			handles.shoulder_side = 'Sh_Side';
			end
			if ~isfield(handles,'acquisition_stage')
			handles.acquisition_stage = 'Pre-o-Post_op';
			end

			if ~isfield(handles,'body')
			handles.body = 'body';
			end
			if ~isfield(handles,'kernel')
			handles.kernel = 'kernel';
			end
			if ~isfield(handles,'phantoms')
			handles.phantoms = 'phantoms';
			end
			if ~isfield(handles,'contralateral')
			handles.contralateral = '';
			end
			if ~isfield(handles,'N')
			handles.N = 0;
			end

			% choosing handles.CTlabel_text from radiobutton option chosen by user
			switch handles.acquisition_stage
			case 'Preop'
			if ~get(handles.checkbox_contralateral,'Value')
			switch handles.body
			case 'Shoulder'
			switch handles.phantoms
			case 'without'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-1';
			case 'Smooth'
			handles.CTlabel_text.String = '-2';
			otherwise
			handles.CTlabel_text.String = '-xxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			case 'with'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-3';
			case 'Smooth'
			handles.CTlabel_text.String = '-4';
			otherwise
			handles.CTlabel_text.String = '-xxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			otherwise
			handles.CTlabel_text.String = '-xxx';
			end
			case 'Elbow'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-5';
			case 'Smooth'
			handles.CTlabel_text.String = '-6';
			otherwise
			handles.CTlabel_text.String = '-xxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			case 'Thorax'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-7';
			case 'Smooth'
			handles.CTlabel_text.String = '-8';
			otherwise
			handles.CTlabel_text.String = '-xxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			otherwise
			handles.CTlabel_text.String = '-x11';
			end
			else
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-9';
			case 'Smooth'
			handles.CTlabel_text.String = '-10';
			otherwise
			handles.CTlabel_text.String = '-xxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			end
			case 'Postop'
			if ~get(handles.checkbox_contralateral,'Value')
			switch handles.body
			case 'Shoulder'
			switch handles.phantoms
			case 'without'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-p1';
			case 'Smooth'
			handles.CTlabel_text.String = '-p2';
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			case 'with'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-p3';
			case 'Smooth'
			handles.CTlabel_text.String = '-p4';
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			end
			case 'Elbow'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-p5';
			case 'Smooth'
			handles.CTlabel_text.String = '-p6';
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			case 'Thorax'
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-p7';
			case 'Smooth'
			handles.CTlabel_text.String = '-p8';
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			otherwise
			handles.CTlabel_text.String = '-px11';
			end
			else
			switch handles.kernel
			case 'Sharp'
			handles.CTlabel_text.String = '-p9';
			case 'Smooth'
			handles.CTlabel_text.String = '-p10';
			otherwise
			handles.CTlabel_text.String = '-pxxx';
			warndlg('Operator must choose between Sharp or Smooth kernel');
			end
			end
			otherwise
			handles.CTlabel_text.String = '-xxx';
			end

			RL = sprintf('%s%s%s%s%s %s %s %s %s %s %s %s %s ','CT-',...
			handles.patient_num.String,'-',...
			handles.IPP_text.String,...
			handles.CTlabel_text.String,...
			handles.contralateral,...
			handles.body,...
			handles.kernel,...
			handles.phantoms,'phantoms',...
			handles.Resolution_text.String,...
			string(handles.N),'slices',...
			handles.extra_info);
			set(handles.text_readme,'String',RL);
			guidata(hObject,handles);


			%% --- Executes on button press in add_SCase_toDB.
			function add_SCase_toDB_Callback(hObject, eventdata, handles)
			% hObject handle to add_SCase_toDB (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles structure with handles and user data (see GUIDATA)

			% This function writes a new line inside the file "SCaseImport.xlsx" (F1)
			% and launches the script "dicominfoSCase.m" (F2) which read one CT from
			% SCase present in the Database to fill the corresponding DICOM parameters
			% in the main Excel File "ShoulderDataBase.xlsx"

			%% F1 - writting the new line inside the file "SCaseImport.xlsx"
			% Collecting new row parameters and translation to Excel compatible format
			try
			new_SCase_ID = {handles.patient_num.String};
			IPP_number = str2num(handles.IPP_text.String);
			Initials={extractBefore(extractAfter(handles.initials_text.String,'('),')')};
			BirthDate = {[handles.birthdate_text.String(1:4) ...
			'-' handles.birthdate_text.String(5:6) ...
			'-' handles.birthdate_text.String(7:8)]};
			Patient_Gender = handles.gender_text.String;
			Shoulder_Side = handles.shoulder_side(1);
			CT_date = {[handles.CTdate_text.String(1:4) ...
			'-' handles.CTdate_text.String(5:6) ...
			'-' handles.CTdate_text.String(7:8)]}; %handles.dicomSet(1).AcquisitionDate;

			% Question dialog box to allow the user to validate the data or abort
			quest = sprintf('%s:\n%s, %s, %s, %s,\n%s, %s, %s, %s.\n %s',...
			"Please confirm if you want to add the followin line to the Excel Database",...
			string(new_SCase_ID),'SCase_idx*',string(IPP_number),...
			string(Initials),string(BirthDate),string(Patient_Gender),...
			string(Shoulder_Side),string(CT_date),'* to be determined while updating');
			btn1 = 'Confirm';
			btn2 = 'Abort';
			defbtn = 'Abort';

			catch error
			% A comun error arrives when the function is launched before selecting
			% every option in the script graphical interface
			warndlg("Some parameters are maybe missing. Action Aborted")
			error
			return
			end

			% The file SCaseImport.xlsx must be located inside the subfolder
			% xlsFromMatlab/ which is in the same directory of the main Database Excel
			try
			% If the Excel directory has been correctly stored before, we can
			% find the excel file without problems and continue
			if isfield(handles,'ExcelDB_path')
			ExcelImport_fullname = sprintf('%s%s',handles.ExcelDB_path,"SCaseImport.xlsx");
			sprintf("%s%s", "Writting in file ", ExcelImport_fullname)
			title = sprintf('%s %s','Adding new SCase row to Excel file:',ExcelImport_fullname);
			% A dialog box opens to let the operator validate the data
			answer = questdlg(quest,title,btn1,btn2,defbtn);
			% Else, if at least the "data" or "dataDev" directory has been stored,
			% we can still find the excel file and continue
			elseif isfield(handles,'data_dir')
			title = sprintf('%s %s','Adding new SCase row to Excel file:','FILE NOT FOUND');
			% A dialog box opens to let the operator validate the data
			answer = questdlg(quest,title,btn1,btn2,defbtn);
			[excelDB, DBpath, ~] = uigetfile('*.xlsx','Select the Excel Database File',handles.data_dir);
			handles.ExcelDB_path = DBpath;
			ExcelImport_fullname = sprintf('%s%s',handles.ExcelDB_path,"SCaseImport.xlsx");
			sprintf("%s%s", "Writting in file ", ExcelImport_fullname)
			else
			title = sprintf('%s %s','Adding new SCase row to Excel file:','FILE NOT FOUND');
			quest = sprintf('%s \n%s','WARNING abort action recommended. Any DICOM info loaded.',quest);
			answer = questdlg(quest,title,btn1,btn2,defbtn);
			[excelDB, DBpath, ~] = uigetfile('*.xlsx','Select the Excel Database File',pwd);
			handles.ExcelDB_path = DBpath;
			ExcelImport_fullname = sprintf('%s%s',handles.ExcelDB_path,"SCaseImport.xlsx");
			sprintf("%s%s", "Writting in file ", ExcelImport_fullname)
			end
			catch error
			errordlg("database directory not found");
			end

			switch answer
			case 'Abort'
			warningdlg("Action aborted");
			case 'Confirm'
			% Text info to the command window
			info=sprintf('%s:\n%s, %s, %s, %s,\n%s, %s, %s, %s %s.',...
			"The parameters to write in the Excel Database are",...
			"SCase_ID","SCase_idx","anonymity_IPP","anonymity_initials",...
			"anonymity_bithDate","patient_gender","shoulder_side",'and',"CT_date")
			set(handles.info_add_SCase,'String',info)

			% In order to avoid the repetition of any SCase we have to read and check
			% the SCaseImport.xlsx file:
			[~,txt,raw,dates]=xlsread(ExcelImport_fullname,'SCaseImport','','',@convertSpreadsheetExcelDates);
			% Looking for the "desired new SCase" in the existing list of SCases of
			% SCaseImport.xlsx
			% Removing void rows
			raw=raw(find(string(raw(:,1))~=''),:);

			% If there is no coincidence we set the desired SCase as a new one and can
			% allow to write the new line of Importation Parameters. Otherwise we will ask
			% to overwrite the existing line of parameters or doing nothing.
			found_SCase_Index = find(string(raw(:,1))==handles.patient_num.String);
			new_SCase_Index = handles.DB_length +2; %length(string(raw(:,1)))+1;
			if isempty(found_SCase_Index)
			SCase_Index = new_SCase_Index;
			else
			question = "The chosen SCase already exist. Do you want to overwrite it?";
			title = "WARNING: SCase repeated";
			btn1 = "Cancel";
			btn2 = "Overwrite";
			dfltbtn = "Cancel";
			answer = questdlg(question,title,btn1,btn2,dfltbtn);
			% Handle response
			switch answer
			case "Overwrite"
			SCase_Index = found_SCase_Index
			case "Cancel"
			disp("new SCase parameter line aborted")
			return;
			otherwise
			disp("new SCase parameter line aborted")
			return;
			end
			end

			rowNumber=SCase_Index;

			% Writting SCase_ID
			"Writting SCase_ID"
			SCaseCell = sprintf('%s%i','A',rowNumber);
			xlswrite(ExcelImport_fullname,new_SCase_ID,'SCaseImport',SCaseCell)
			% Writting SCase_idx
			"Writting SCase_idx"
			IdxCell = sprintf('%s%i','B',rowNumber);
			xlswrite(ExcelImport_fullname,rowNumber,'SCaseImport',IdxCell)
			% Writting anonymity_IPP
			IPPCell=sprintf('%s%i','C',rowNumber);
			xlswrite(ExcelImport_fullname,IPP_number,'SCaseImport',IPPCell)
			% Writting anonymity_initials
			InitialsCell=sprintf('%s%i','D',rowNumber);
			xlswrite(ExcelImport_fullname,Initials,'SCaseImport',InitialsCell)
			% Writting anonymity_birthDate
			BirthDateCell=sprintf('%s%i','E',rowNumber);
			xlswrite(ExcelImport_fullname,BirthDate,'SCaseImport',BirthDateCell)
			% Writting patient_gender
			GenderCell = sprintf('%s%i','F',rowNumber);
			xlswrite(ExcelImport_fullname,Patient_Gender,'SCaseImport',GenderCell)
			% Writting shoulder_side
			ShSideCell = sprintf('%s%i','G',rowNumber);
			xlswrite(ExcelImport_fullname,Shoulder_Side,'SCaseImport',ShSideCell)
			% Writting CT_date
			CTdateCell = sprintf('%s%i','H',rowNumber);
			xlswrite(ExcelImport_fullname,CT_date,'SCaseImport',CTdateCell)

			%% launch 'dicominfoSCase.m' to update CTdicomInfo CSV and XLS
			cd([handles.script_dir '/..'])
			dicominfoSCase % Lauched without arguments to avoid current error (1'20")
			cd(handles.script_dir)
			msgbox("Operation completed!")
			otherwise
			warndlg("Action aborted");
			end

			%%***********************************************
			%% Internal functions

			function update_readme_line(handles)
			%% -- Updates readme line
			% Complete the line to be writen in the readme file as:
			% CT-P454-513554-1 sharp shoulder without phantoms 0.351562 mm 137 slices
			try
			handles.readme.IPP = handle.myinfo.PatientID;
			handles.readme.CTdate = handles.myinfo.AcquisitionDate;
			handles.readme.CT_label = handles.CTlabel_text;
			if handles.radiobutton_sharp
			handles.readme.kernel = 'Sharp (BONE)';
			elseif handles.radiobutton_smooth
			handles.readme.kernel = 'Smooth (SOFT)';
			else
			handles.readme.kernel = 'None';
			end


			handles.readme.line = ['CT-' handles.readme.IPP '-' handles.readme.CT_label...
			' ' handles.readme.kernel ' ' handles.readme.body ' '...
			handles.readme.phantoms ' ' handles.readme.resolution ' ' ...
			handles.readme.slices ' ' handles.readme.stage ' ' handles.readme.extra...
			' ']
			catch except
			sprintf('%s%s','Error identifier: ',except.identifier)
			'fields lacking'

			end
			guidata(hObject,handles);

			function sortedST = sortStructByField(ST,field,handles)
			try
			"internal fuction activated"
			STfields = fieldnames(ST);
			STcell = struct2cell(ST);
			sz = size(STcell); % Notice that this is a 3 dimensional array.
			% For MxN structure array with P fields, the size
			% of the converted cell array is PxMxN

			% Once it's a cell array, you can sort using sortrows:

			% Convert to a matrix
			STcell = reshape(STcell, sz(1), []); % Px(MxN)

			% Make each field a column
			STcell = STcell'; % (MxN)xP

			column=0

			% Sort by field
			for k=1:length(STfields)
			if isequal(STfields(k),field)
			column = k;
			end
			end

			if column == 0
			['Warning: field ' char(field) ' not found in dicom metadata']
			sortedST = ST;
			return
			else
			fieldColumn = column;
			STcell = sortrows(STcell, fieldColumn);
			% And convert it back to a structure array:
			% Put back into original cell array format
			STcell = reshape(STcell', sz);

			% Convert to Struct
			STsorted = cell2struct(STcell, STfields, 1);
			sortedST = STsorted;
			end
			catch except
			except.identifier
			except.message
			['exception arised during dicom sorting by field']
			end


			%% Functions to be removed or reused
			function slider_2Dcontrast_Callback(hObject, eventdata, handles)
			%% --- Executes on slider movement.
			% hObject handle to slider_2Dcontrast (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,'Value') returns position of slider
			% get(hObject,'Min') and get(hObject,'Max') to determine range of slider

			if ~isfield(handles, 'mydicom');
			return
			end

			handles.CTmax = (get(handles.slider_2Dbrightness,'Max') + get(handles.slider_2Dbrightness,'Min') - get(handles.slider_2Dbrightness,'Value')) + (get(hObject,'Max') - get(hObject,'Value'))/2;
			handles.CTmin = (get(handles.slider_2Dbrightness,'Max') + get(handles.slider_2Dbrightness,'Min') - get(handles.slider_2Dbrightness,'Value')) - (get(hObject,'Max') - get(hObject,'Value'))/2;

			if handles.CTmax > handles.bigmax
			handles.CTmax = handles.bigmax;
			end

			if handles.CTmin < handles.bigmin
			handles.CTmin = handles.bigmin;
			end

			imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax]);

			guidata(hObject,handles)


			function slider_2Dcontrast_CreateFcn(hObject, eventdata, handles)
			%% --- Executes during object creation, after setting all properties.
			% hObject handle to slider_2Dcontrast (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called

			% Hint: slider controls usually have a light gray background.
			if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
			set(hObject,'BackgroundColor',[.9 .9 .9]);
			end
			guidata(hObject,handles);


			function slider_2Dbrightness_Callback(hObject, eventdata, handles)
			%% --- Executes on slider movement.
			% hObject handle to slider_2Dbrightness (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,'Value') returns position of slider
			% get(hObject,'Min') and get(hObject,'Max') to determine range of slider

			if ~isfield(handles, 'mydicom');
			return
			end

			handles.CTmax = (get(hObject,'Max') + get(hObject,'Min')...
			- get(hObject,'Value')) + (get(handles.slider_2Dcontrast,'Max')...
			- get(handles.slider_2Dcontrast,'Value'))/2;
			handles.CTmin = (get(hObject,'Max') + get(hObject,'Min')...
			- get(hObject,'Value')) - (get(handles.slider_2Dcontrast,'Max')...
			- get(handles.slider_2Dcontrast,'Value'))/2;

			if handles.CTmax > handles.bigmax
			handles.CTmax = handles.bigmax;
			end

			if handles.CTmin < handles.bigmin
			handles.CTmin = handles.bigmin;
			end

			imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax]);

			guidata(hObject,handles);


			function slider_2Dbrightness_CreateFcn(hObject, eventdata, handles)
			%% --- Executes during object creation, after setting all properties.
			% hObject handle to slider_2Dbrightness (see GCBO)
			% eventdata reserved - to be defined in a future version of MATLAB
			% handles empty - handles not created until after all CreateFcns called

			% Hint: slider controls usually have a light gray background.
			if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
			set(hObject,'BackgroundColor',[.9 .9 .9]);
			end
			guidata(hObject,handles);

R8218/ImportSCase/importSCase.mec80aabdeafffeat_muscle_subdivisions

importSCase.mView Options

R8218/ImportSCase/importSCase.m
ec80aabdeafffeat_muscle_subdivisions

importSCase.m
View Options