function varargout = ARPESView(varargin)
% ARPESVIEW M-file for ARPESView.fig
%      ARPESVIEW, by itself, creates a new ARPESVIEW or raises the existing
%      singleton*.
%      H = ARPESVIEW returns the handle to a new ARPESVIEW or the handle to
%      the existing singleton*.
%      ARPESVIEW('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in ARPESVIEW.M with the given input arguments.
%      ARPESVIEW('Property','Value',...) creates a new ARPESVIEW or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before EasyLineSetup_OpeningFunction gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to ARPESView_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 ARPESView
% Last Modified by GUIDE v2.5 03-Mar-2021 15:31:22
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @ARPESView_OpeningFcn, ...
                   'gui_OutputFcn',  @ARPESView_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 ARPESView is made visible.
function ARPESView_OpeningFcn(hObject,~,handles,varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% varargin   command line arguments to ARPESView (see VARARGIN)
clear global; global IniDir RunFile CubePos EWin valPre hGUI
% choose default command line output for ARPESView
handles.output = hObject;
% update handles structure
guidata(hObject, handles);
% initial directory
IniDir='X:\';
% run file and pushbutton visibility
if exist('C:\ARPES Tools','dir')==7
   RunFile='C:\temp\LastRun.h5';
else
   set(handles.pushbuttonRunFile,'Visible','Off');
end
% openGL rendering necessary for R2013a or some graphics drivers
try opengl software; end
% data cube
axis(handles.axesCube,[-1 1 -1 1 -1 1]);
set(gca,'layer','top','box','on','Projection','Orthographic','TickLength',[0 0],'XTick',[],'YTick',[],'ZTick',[]); 
axis square tight; view(-86,6);
set(gca,'PlotBoxAspectRatio',[5 1 1]);
try set(gca,'boxstyle','full'); end % R2017b
CubePos=get(handles.axesCube,'Position');
% initial viewMode value
%viewMode=1;
% initial iso-energy window
EWin=[-0.1 0]; valPre=0; %set(handles.editEnergy,'String',sprintf('%g+-%g',[mean(EWin) diff(EWin)/2]));
% Setup panels
% - LockSetup
global feat_Lock featIni setTo_Lock setToIni % dEWin_Lock dEWinIni dESm_Lock dESmIni
% dEWinIni=[]; dEWin_Lock=dEWinIni; dESmIni=[]; dESm_Lock=dESmIni; 
featIni='Edge'; feat_Lock=featIni; setToIni=0.0; setTo_Lock=setToIni;
% - NormSetup
global scCoeffIni scCoeff
scCoeffIni=0.75; scCoeff=scCoeffIni;
% - ImgProcSetup initializes in itself because the image processing is activated by selecting XTra which calls ImgProcSetup 
% - ViewSetup
global FracView FracViewIni gamma gammaIni render renderIni %XRange YRange
FracViewIni=[1e-2 1-1e-4]; FracView=FracViewIni; 
gammaIni=1; gamma=gammaIni;
renderIni='Flat'; render=renderIni;
% XRange=[]; YRange=[];
% % - NaviSetup
% % global hvNorm_Navi hvNormIni kxNorm_Navi kxNormIni thtANorm_Navi thtANormIni thtMNorm_Navi thtMNormIni surfNx
% % hvNormIni=0; hvNorm_Navi=hvNormIni; kxNormIni=0; kxNorm_Navi=kxNormIni; thtANormIni=0; thtANorm_Navi=thtANormIni; 
% % thtMNormIni=0; thtMNorm_Navi=thtMNormIni; surfNx=0;
% global surfNx surfNx=[];
% % position of the Kz-transform fields
% PosHvKz=get(handles.radiobuttonHvKz,'Position'); PosTextVo=get(handles.textVo,'Position'); PosEditVo=get(handles.editVo,'Position');
% PosSurfNy=get(handles.editSurfNy,'Position'); shift=PosHvKz(2)-PosSurfNy(2);
% set(handles.radiobuttonHvKz,'Position',[PosHvKz(1) PosHvKz(2)-shift PosHvKz(3:4)]);
% set(handles.textVo,'Position',[PosTextVo(1) PosTextVo(2)-shift PosTextVo(3:4)]);
% set(handles.editVo,'Position',[PosEditVo(1) PosEditVo(2)-shift PosEditVo(3:4)]);
% % initial state of menus
% global valMenuLockPre; valMenuLockPre=1;
% GUI handle
hGUI=gcf;

% --- Outputs from this function are returned to the command line.
function varargout = ARPESView_OutputFcn(~,~,handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% Get default command line output from handles structure
varargout{1} = handles.output;

% --- Executes on button press in pushbuttonDirFile
function pushbuttonDirFile_Callback(~,~,handles)
% Hint: get(hObject,'Value') returns toggle state of togglebutton2
global FullName IniDir DataFull DataXC FullList
% loading filename
[filename,pathname]=uigetfile({'*.h5;*.sp2'},'Data File',IniDir);
if isequal(filename,0) || isequal(path,0); return; end % return if Cancel pressed
IniDir=pathname; FullName=[pathname filename];
% reset data and load file
DataFull=[]; DataXC=[]; LoadFile(handles,FullName);
% file list
% - trim filename to show in menu
lenMax=37; if length(FullName)>lenMax TrimName=['...' FullName(max(1,end-(lenMax-4)):end)]; else TrimName=FullName; end
% - full- and trimmed-name lists
TrimList=get(handles.menuFileList,'String');
if isempty(TrimList); FullList={FullName}; TrimList={TrimName};
else
   FullList=[{FullName};FullList]; TrimList=[{TrimName};TrimList];
end
% remove previous identical filenames
for iList=2:size(FullList,1)
%   [num2str(iList) '   ' FullList{iList} '   ' FullName '   ' num2str(strcmp(FullList{iList},FullName))]
   if strcmp(FullList{iList},FullName)==1; FullList(iList,:)=[]; TrimList(iList,:)=[]; break; end 
end
% - max number of last files 
maxList=5; FullList=FullList(1:min(end,maxList)); TrimList=TrimList(1:min(end,maxList));
% - set menu 
set(handles.menuFileList,'String',TrimList,'Value',1);

% --- Executes on selection change in menuFileList.
function menuFileList_Callback(hObject,~,handles)
% Hints: contents = cellstr(get(hObject,'String')) returns menuFileList contents as cell array
%        contents{get(hObject,'Value')} returns selected item from menuFileList
global DataFull DataXC FullList FullName
n=get(hObject,'Value'); FullName=FullList(n); FullName=FullName{1};
% reset data and load file
DataFull=[]; DataXC=[]; LoadFile(handles,FullName);

% --- Executes on button press in pushbuttonRunFile
function pushbuttonRunFile_Callback(~,~,handles)
% hObject    handle to menuFileList (see GCBO)
global RunFile FullName DataFull DataXC
% check if exists
if exist(RunFile,'file')~=2
   msgbox('Run File Inavailable','modal'); return;
end
FullName=RunFile;
% reset data and load file
DataFull=[]; DataXC=[]; LoadFile(handles,FullName);

% --- Executes on selection change in radiobuttonEqImages.
function radiobuttonEqImages_Callback(~,~,handles)
% hObject    handle to radiobuttonEqImages (see GCBO)
global FullName
if isempty(FullName); return; else; LoadFile(handles,FullName); end

% ---  Function to load data file
function LoadFile(handles,FullName)
% LoadFile loads data file with the full name FullName
global Energy Angle ScanFull Scan SWin DataFull DataXC Data Note RawTable HV thtM tltM aDef ScanType ACorr ECorr ...
          dEWinIni dESmIni EAlign dESm_Lock dEWin_Lock feat_Lock ERange ARange AutoAWin AKx Kx KxRange ...
          AutoKxWin AKxRange AKxWin IDiv ISubtr CubePos setTo_Lock alpha % RangeIni RangeNorm 
% clear arrays
Kx=[]; IDiv=[]; ISubtr=[]; ScanType=[];
disp('- cleared Kx IDiv ISubtr ScanType')
% clear Scan field
set(handles.editScan,'String','')
% enable summation
set(handles.radiobuttonEqImages,'Enable','On')
% load file if new filename
if isempty(DataFull)
   try
      h=waitbar(0.5,'Reading In','Windowstyle','Modal'); 
      [Angle,Energy,ScanFull,DataFull,ep,Note,RawTable]=ReadARPES(FullName); 
      close(h);
   catch
      msgbox('Data Input Error','modal'); return;
   end
end
Data=DataFull; Scan=ScanFull;
% equivalent scans
if ~isempty(Scan)&&~all(diff(Scan))
   if get(handles.radiobuttonEqImages,'Value')==1
% - cross-correlated summation
      if isempty(DataXC)
         h=waitbar(0.5,'Reducing Equivalent Scans','Windowstyle','Modal');
         maxLagE=0.2; DataXC=SumScanXC(Energy,Data,maxLagE);
         close(h)
      end
      Data=DataXC; Scan=[];
   else
% - artificial Scan of the image numbers
      Scan=1:1:length(ScanFull); ScanType='Number';
   end
else
   set(handles.radiobuttonEqImages,'Enable','Off') 
end
% scan name
if isempty(ScanType)
PosColon=strfind(Note,':');
   if ~isempty(PosColon)
      PosEqual=strfind(Note,'='); PosEqual=PosEqual(PosEqual<PosColon(1)); posEqual=PosEqual(end);
      ScanType=Note(posEqual-8:posEqual-1); ScanType=deblank(ScanType);
%      if isequal(ScanType,'ADef'); ScanType='Tilt'; end % added at the upgrade to PHOIBOS225
   end
end
% HV
HV=[]; try
   pos1=strfind(Note,'hv'); pos2=strfind(Note,'Pol'); eval(['HV=' Note(pos1+10:pos2-2) ';']); HV=HV(1,:);
   if isempty(Scan) HV=HV(1); else HV=HV(1:length(Scan)); end % if the scan incomplete
end
% thtM
thtM=[]; try
   pos1=strfind(Note,'Theta   = '); pos2=strfind(Note,'Tilt'); eval(['thtM=' Note(pos1+9:pos2-2) ';']);
   if length(thtM)>1
      if isequal(ScanType,'Number'); thtM=mean(thtM); else thtM=[]; end
   end
end
% tltM
tltM=[];
try
   pos1=strfind(Note,'Tilt    = '); pos2=strfind(Note,'Azimuth'); eval(['tltM=' Note(pos1+9:pos2-2) ';']);
   if length(tltM)>1; tltM=[]; end
end
% aDef (added at the upgrade to PHOIBOS225)
aDef=[];
try
   pos1=strfind(Note,'ADef    = '); pos2=strfind(Note,'Gain'); pos3=strfind(Note,'dt'); % 'Gain' in new files and 'dt' in older files 
   eval(['aDef=' Note(pos1+9:min(pos2,pos3)-2) ';']);
   if length(aDef)>1; aDef=[]; end
end
% % adding up tltM and aDef if scalars, otherwise empty 
% tltM=tltM+aDef;
% % adding scalar tltM and aDef to Scan  
% if isequal(ScanType,'Tilt')
%    Scan=Scan+tltMAdd+aDefAdd;
% end
% alpha
alpha=20; try
   pos1=strfind(Note,'alpha'); pos2=strfind(Note,'Grating'); eval(['alpha=' Note(pos1+9:pos2-2) ';']);
end
% select compatible modes and show Scan range 
if isempty(Scan)||length(Scan)<2
   if get(handles.menuViewMode,'Value')>2; set(handles.menuViewMode,'Value',1); end 
   set(handles.menuViewMode,'String',{'Image';'Angle-Int Img'})
   SWin=[0 0.5];
else
   set(handles.menuViewMode,'String',{'Image';'Angle-Int Img';'Image Series';'Iso-E';'Iso-Angle/Kx'})
   SWin=[Scan(1) Scan(end)];
end
% select curvature and warping correction modes
pos=strfind(Note,'Corr');
if isequal(lower(Note(pos+10:pos+13)),'true')
   set(handles.radiobuttonCurvatureCorr,'Value',0,'Visible','Off')
   set(handles.radiobuttonWarpingCorr,'Value',0,'Visible','Off')
else
%    set(handles.radiobuttonCurvatureCorr,'Value',1,'Visible','On')
%    set(handles.radiobuttonWarpingCorr,'Value',1,'Visible','On')
   set(handles.radiobuttonCurvatureCorr,'Visible','On')
   set(handles.radiobuttonWarpingCorr,'Visible','On')
   % disable curvature correction if HV unknown (edited in raw table) 
   if any(isnan(HV)); set(handles.radiobuttonWarpingCorr,'Value',0,'Visible','Off'); end
end
% curvature and warping correction
% - check if the data already corrected
if contains(FullName,'_Export') && ...
(get(handles.radiobuttonCurvatureCorr,'Value')==1||get(handles.radiobuttonWarpingCorr,'Value')==1)
   waitfor(warndlg('Data may be already corrected','')); 
end
% - curvature corrected energy: 2D array
if get(handles.radiobuttonCurvatureCorr,'Value')==1
   ECorr=CurveCorr(Angle,Energy,ep);   
else ECorr=repmat(Energy,1,length(Angle)); 
end
% - warping corrected angles: 2D array for images and angle scans/ 3D for hv scans
if get(handles.radiobuttonWarpingCorr,'Value')==1
   ACorr=WarpCorr(Angle,Energy,HV);
else
   ACorr=repmat(Angle,length(Energy),1);
   if length(HV)>1; ACorr=repmat(ACorr,[1 1 length(HV)]); end
end
% % - - correcting average Angle
%    Angle=mean(ACorr,3); Angle=mean(Angle,1);
% angle range and auto window
ARange=[min(min(ACorr(:,1,:))) max(max(ACorr(:,end,:)))];
aMin=max(max(ACorr(:,1,:))); aMax=min(min(ACorr(:,end,:))); AutoAWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax];
AKx=ACorr; AKxRange=ARange; AKxWin=AutoAWin;
% aligned energy and its range 
% In the case the aligment fails, should it be left here or better disactivate the menu? Left here, consistently with Angle->Kx and Norm/Subtr 
% set(handles.menuLock,'Value',1)
if get(handles.menuLock,'Value')>1
   h=waitbar(0.5,'Aligning EF','Windowstyle','Modal'); % waitbar
% - alignment
   eWin=field2num(handles.editLockEF,0); if length(eWin)>1; eWin=linspace(eWin(1),eWin(2),size(Data,3)); end
   EAlign=AlignEF(Data,ECorr,eWin,dEWin_Lock,dESm_Lock,feat_Lock); EAlign=EAlign+setTo_Lock;
%   if ~isempty(Fail); uiwait(msgbox(['Warning: Failed to Lock EF in ' num2str(length(Fail)) ' images'],'modal')); end  
   close(h) % close waitbar
else
EAlign=repmat(ECorr,[1 1 max(1,length(Scan))]);
end
% - update energy range
ERange=[min(min(EAlign(:,1,:))) max(max(EAlign(:,end,:)))];
% ERange=[min(ECorr(1,:)) max(ECorr(end,:))];
% Kx-transform and auto Kx range if selected
if get(handles.radiobuttonAKx,'Value')==1
    surfNx=str2num(get(handles.editSurfNx,'String')); Kx=Kxx(HV,EAlign,thtM,ACorr,surfNx,alpha);
% - Kx range and auto window 
   KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))];
   aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax];
   AKx=Kx; AKxRange=KxRange; AKxWin=AutoKxWin;
end
% draw data cube
axes(handles.axesCube); cla
% - 2D case
if isempty(Scan)||length(Scan)<2
   axis([0 1 -0.5 0.5 ERange]);
   set(gca,'Position',[1.01*CubePos(1) CubePos(2) 0.8*CubePos(3:4)],'PlotBoxAspectRatio',[0.5 1 1]);
% - 3D case
else
   axis([Scan([1 end]) -0.5 0.5 ERange]); % axis square tight;
   set(gca,'Position',CubePos,'PlotBoxAspectRatio',[5 1 1])
end
% ranges and auto windows
% - Angle/Kx
if get(handles.radiobuttonAKx,'Value')==0
   set(handles.textAKx,'String',[sprintf('%0.1f',ARange(1)) '<Angle<' sprintf('%0.1f',ARange(2))])
   set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AutoAWin))
else
   set(handles.textAKx,'String',[sprintf('%0.1f',KxRange(1)) '<Kx<' sprintf('%0.1f',KxRange(2))])
   set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AutoKxWin))
end
% - Energy
set(handles.textEnergy,'String',[sprintf('%0.1f',ERange(1)) '<Eb/k<' sprintf('%0.1f',ERange(end))]);
% - Scan
if ~isempty(Scan); set(handles.textScan,'String',[sprintf('%0.1f',Scan(1)) '<Scan<' sprintf('%0.1f',Scan(end))]); end
% switch fields and visualize slices
SwitchFields(handles); DrawCubeSlice(handles)
% auto setup for LockSetup
dEWinIni=0.1*diff(ERange); dEWin_Lock=dEWinIni; dESmIni=0.01*diff(ERange); dESm_Lock=dESmIni;
% % auto energy range for NormSetup
% RangeIni=[0.9*ERange(1)+0.1*ERange(2) 0.1*ERange(1)+0.9*ERange(2)]; RangeNorm=RangeIni;

% reset export mode to data
set(handles.menuExport,'Value',1,'Enable','Off')

% ---  Function to switch fields depending on the view mode
function SwitchFields(handles)
global EWin Scan ScanType SWin Scan
viewMode=get(handles.menuViewMode,'Value');
% if isempty(Data); beep; return; end % return if no data
% control groups
ShowEnergy=[handles.textEnergy handles.pushbuttonEMinus handles.editEnergy handles.pushbuttonEPlus]; set(ShowEnergy,'Enable','Off')
ShowAKx=[handles.textAKx handles.pushbuttonAKxMinus handles.editAKx handles.pushbuttonAKxPlus]; set(ShowAKx,'Enable','Off')
ShowScan=[handles.textScan handles.pushbuttonScanMinus handles.editScan handles.pushbuttonScanPlus handles.textOddEven handles.menuOddEven]; % set(ShowScan,'Enable','Off')
ShowNorm=[handles.textNorm handles.menuNorm]; set(ShowNorm,'Enable','On');
ShowNormScans=[handles.textNormScans handles.menuNormScans]; set(ShowNormScans,'Enable','Off')
ShowImgProc=[handles.textImgProc handles.menuImgProcMode]; set(ShowImgProc,'Enable','On');
set(handles.menuReadout,'Value',1,'Enable','Off')
% initially switch off the surfNy and the Kz-transform fields
set([handles.textSurfNy handles.editSurfNy],'Visible','Off');
set([handles.radiobuttonHvKz handles.textVo handles.editVo],'Visible','Off');
% switch fields between modes
switch viewMode
   case 1  % Image
   % - fields
   if ~isempty(Scan); set(ShowScan ,'Enable','On'); set(handles.editScan,'String',sprintf('%g:%g',SWin)); end
   case 2  % Angle-Int Image
   % - fields
   set(ShowAKx,'Enable','On')
   if ~isempty(Scan); set(ShowScan,'Enable','On'); set(handles.editScan,'String',sprintf('%g:%g',SWin)); end
   set(ShowImgProc,'Enable','Off');
   set(handles.menuNorm,'Value',1); set(ShowNorm,'Enable','Off');
   case 3   % Image Series
   if diff(SWin)==0; SWin=Scan([1 end]); end; % full scan replaces single image 
   % - fields
   set(ShowScan,'Enable','On'); set(handles.editScan,'String',sprintf('%g:%g',SWin));
   case 4   % Iso-E
   if diff(SWin)==0; SWin=Scan([1 end]); end; % full scan replaces single image    
   % - fields
   set(ShowScan,'Enable','On'); set(handles.editScan,'String',sprintf('%g:%g',SWin));
   set(handles.editEnergy,'String',sprintf('%g+-%g',[mean(EWin) diff(EWin)/2]));
   set(ShowEnergy,'Enable','On'); set(ShowNormScans,'Enable','On')
   if isequal(ScanType,'Tilt')||isequal(ScanType,'ADef') set(handles.menuReadout,'Enable','On'); end
%   if ~isempty(Scan); set(handles.editScan,'String',sprintf('%g:%g',Scan([1 end]))); end % Full Scan can be changed to SWin
   if ~isempty(SWin); set(handles.editScan,'String',sprintf('%g:%g',SWin)); end % Full Scan can be changed to SWin
   % K-transform fields
   if get(handles.radiobuttonAKx,'Value')==1&&(isequal(ScanType,'Tilt')||isequal(ScanType,'ADef')||(isequal(ScanType,'hv')&&get(handles.radiobuttonHvKz,'value')==1))
      set([handles.textSurfNy handles.editSurfNy],'Visible','On')
   end
   if get(handles.radiobuttonAKx,'Value')==1&&isequal(ScanType,'hv')
      set(handles.radiobuttonHvKz,'Visible','On')
      if get(handles.radiobuttonHvKz,'Value')==1; set([handles.textVo handles.editVo],'Visible','On'); end
   end
   case 5   % Angle-Int Scan
   if diff(SWin)==0; SWin=Scan([1 end]); end; % full scan replaces single image       
   % - fields
   set(ShowScan,'Enable','On'); set(handles.editScan,'String',sprintf('%g:%g',SWin));
   % set(handles.menuNorm,'Value',1); set(ShowNorm,'Enable','Off'); % the normalization/subtraction can be useful for E(kz)
   set(ShowAKx,'Enable','On'); set(ShowNormScans,'Enable','On')
%   set(ShowScan,'Enable','On')
%   if ~isempty(Scan); set(handles.editScan,'String',sprintf('%g:%g',Scan([1 end]))); end % Full Scan can be changed to SWin
%   if ~isempty(SWin); set(handles.editScan,'String',sprintf('%g:%g',SWin)); end % Full Scan can be changed to SWin   
   % K-transform fields
   if get(handles.radiobuttonAKx,'Value')==1&&(isequal(ScanType,'Tilt')||isequal(ScanType,'ADef')||(isequal(ScanType,'hv')&&get(handles.radiobuttonHvKz,'value')==1))
      set([handles.textSurfNy handles.editSurfNy],'Visible','On')
   end
   if get(handles.radiobuttonAKx,'Value')==1&&isequal(ScanType,'hv')
      set(handles.radiobuttonHvKz,'Visible','On')
      if get(handles.radiobuttonHvKz,'Value')==1; set([handles.textVo handles.editVo],'Visible','On'); end
   end
end
% switch scan between 2D and 3D
if isempty(Scan)||length(Scan)<2; set(ShowScan,'Visible','Off'); else set(ShowScan,'Visible','On'); end

% ---  Function to draw data cube and slice depending on the view mode 
function DrawCubeSlice(handles)
global AKxRange AKxWin EWin SWin ERange % Scan
% draw patch in the cube
axes(handles.axesCube);
% switch between modes
viewMode=get(handles.menuViewMode,'Value');
try switch viewMode
   case 1  % Image
      DrawPatch((AKxRange-mean(AKxRange))/diff(AKxRange),ERange,SWin);
   case 2  % Angle-Int Image
      DrawPatch((AKxWin-mean(AKxRange))/diff(AKxRange),ERange,SWin);
   case 3   % Image Series
      DrawPatch((AKxRange-mean(AKxRange))/diff(AKxRange),ERange,SWin);
   case 4   % Iso-E
%      DrawPatch((AKxRange-mean(AKxRange))/diff(AKxRange),EWin,Scan);
      DrawPatch((AKxRange-mean(AKxRange))/diff(AKxRange),EWin,SWin);
   case 5   % Angle-Int Scan
%      DrawPatch((AKxWin-mean(AKxRange))/diff(AKxRange),ERange,Scan);
      DrawPatch((AKxWin-mean(AKxRange))/diff(AKxRange),ERange,SWin);
end; end

% --- Function to draw patch in data cube
function DrawPatch(AWin,EWin,SWin)
cla
vert = [SWin(end) AWin(end) EWin(1); SWin(1) AWin(end) EWin(1); ...
        SWin(1) AWin(end) EWin(end); SWin(end) AWin(end) EWin(end); ...
        SWin(1) AWin(1) EWin(end); SWin(end) AWin(1) EWin(end); ...
        SWin(end) AWin(1) EWin(1); SWin(1) AWin(1) EWin(1)];
fac = [1 2 3 4; 4 3 5 6; 6 7 8 5; 1 2 8 7; 6 7 1 4; 2 3 5 8];
patch('Faces',fac,'Vertices',vert,'FaceColor','g','FaceAlpha',0.65,'EdgeColor','k');

% --- Executes on button press in pushbuttonInfo.
function pushbuttonInfo_Callback(~,~,~)
% hObject    handle to pushbuttonInfo (see GCBO)
global Note; msgbox(Note)

% --- Executes on button press in pushbuttonRawTab.
function pushbuttonRawTab_Callback(~,~,~)
% hObject    handle to pushbuttonRawTab (see GCBO)
global  RawTable; RawTableDisplay(RawTable);

% --- Executes on selection change in menuViewMode.
function menuViewMode_Callback(hObject,~,handles)
% hObject    handle to menuViewMode (see GCBO)
global XRange YRange presmdX presmdY structMode sharp postsmdX postsmdY % RangeNorm scCoeff hNormSetup hViewSetup hImgProcSetup
% viewMode=get(hObject,'Value');
% % clear norm/subtr settings and close NormSetup window
% RangeNorm=[]; scCoeff=[]; % try close(hNormSetup); end
% disp('- cleared RangeNorm scCoeff')
% clear image processing settings
presmdX=[]; presmdY=[]; structMode=1; sharp=[]; postsmdX=[]; postsmdY=[]; set(handles.menuImgProcMode,'Value',1) % try close(hImgProcSetup); end 
disp('- cleared presmdX presmdY structMode sharp postsmdX postsmdY')
% clear plot ranges and close ViewSetup window
XRange=[]; YRange=[]; % try close(hViewSetup); end
disp('- cleared XRange YRange')
% restore full Scan range if not single-image modes
% switch fields and draw cube
SwitchFields(handles); DrawCubeSlice(handles)
% set Export mode
if get(hObject,'Value')==2; set(handles.pushbuttonExport,'Enable','Off'); else set(handles.pushbuttonExport,'Enable','On'); end   

% --- Executes on button press in radiobuttonCurvatureCorr.
function radiobuttonCurvatureCorr_Callback(~,~,handles)
% clear correction
global FullName ECorr EAlign Kx; ECorr=[]; EAlign=[]; Kx=[];
disp('- cleared ECorr EAlign Kx')
% re-process file
LoadFile(handles,FullName);

% --- Executes on button press in radiobuttonWarpingCorr.
function radiobuttonWarpingCorr_Callback(~,~,handles)
% clear correction
global FullName ACorr Kx ; ACorr=[]; Kx=[]; disp('- cleared ACorr Kx')
% re-process file
LoadFile(handles,FullName);

% --- Executes on edit of editScan.
function editScan_Callback(hObject,~,handles)
global Scan SWin % hFig createNewFig
% read in
ScanStr=get(hObject,'String'); ScanStr=strrep(ScanStr,':',' '); ScanStr=strrep(ScanStr,'end','1e6');
SWin=sort(str2num(ScanStr));
% check validity and substitute by the last if invalid
if isempty(SWin); SWin=Scan(end); end
% substitute by actual scan values
[~,n1]=min(abs(Scan-SWin(1))); [~,n2]=min(abs(Scan-SWin(end))); SWin=Scan([n1 n2]);
% display
if diff(SWin)==0; set(hObject,'String',sprintf('%g',SWin(1))); 
else set(hObject,'String',sprintf('%g:%g',SWin)); 
end
% re-draw cube
DrawCubeSlice(handles)
% % re-draw the existing view window
% try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonScanMinus.
function pushbuttonScanMinus_Callback(~,~,handles)
global Scan SWin hFig createNewFig
% read in scan window
SWin=sort(field2num(handles.editScan));
% calculate and write new energy window
dS=diff(SWin); if isempty(dS); dS=(Scan(end)-Scan(1))/(length(Scan)-1); end 
SWin=SWin-dS;
if isempty(SWin)||SWin(1)<min(Scan); return; end
if length(SWin)==1; set(handles.editScan,'String',sprintf('%g',SWin)); else set(handles.editScan,'String',sprintf('%g:%g',SWin)); end
% hide/popup controls and re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonScanPlus.
function pushbuttonScanPlus_Callback(~,~,handles)
global Scan SWin hFig createNewFig
% read in scan window
SWin=sort(field2num(handles.editScan));
% calculate and write new energy window
dS=diff(SWin); if isempty(dS); dS=(Scan(end)-Scan(1))/(length(Scan)-1); end 
SWin=SWin+dS;
if SWin(end)>max(Scan); return; end
if length(SWin)==1; set(handles.editScan,'String',sprintf('%g',SWin)); else set(handles.editScan,'String',sprintf('%g:%g',SWin)); end
% re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end

% --- Executes on edit of editAKx.
function editAKx_Callback(hObject,~,handles)
global AutoAWin AutoKxWin AKxWin % hFig createNewFig
% read in
%AKxWin=sort( sscanf( get(hObject,'String'),'%g:%g') );
AKxWin=sort(field2num(hObject));
% check validity and substitute by automatic range if invalid
if isempty(AKxWin)
   if get(handles.radiobuttonAKx,'Value')==0; set(hObject,'String',sprintf('%g:%g',AutoAWin));
   else set(hObject,'String',sprintf('%g:%g',AutoKxWin)); end  
end
% display
set(hObject,'String',sprintf('%g:%g',AKxWin))
% re-draw cube
DrawCubeSlice(handles)
% % re-draw the existing view window
% try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonAKxMinus.
function pushbuttonAKxMinus_Callback(~,~,handles)
global AKxRange AKxWin hFig createNewFig
% read in Angle/Kx
AKxWin=sort(field2num(handles.editAKx));
% calculate and write new Angle/Kx
AKxWin=AKxWin-diff(AKxWin);
if AKxWin(1)<AKxRange(1); return; end
set(handles.editAKx,'String',sprintf('%g:%g',AKxWin))
% re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonAKxPlus.
function pushbuttonAKxPlus_Callback(~,~,handles)
global AKxRange AKxWin hFig createNewFig
% read in Angle/Kx window
AKxWin=sort(field2num(handles.editAKx));
% calculate and write new Angle/Kx window
AKxWin=AKxWin+diff(AKxWin);
if AKxWin(2)>AKxRange(2); return; end
set(handles.editAKx,'String',sprintf('%g:%g',AKxWin))
% re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end

% --- Executes on selection change in radiobuttonAKx.
function radiobuttonAKx_Callback(hObject,~,handles)
global HV ECorr ACorr ARange AutoAWin thtM Kx KxRange AutoKxWin AKx AKxRange AKxWin alpha
if get(hObject,'Value')==0
   set([handles.textSurfNx handles.editSurfNx handles.pushbuttonFindSurfNx],'Visible','Off');
else
      set([handles.textSurfNx handles.editSurfNx handles.pushbuttonFindSurfNx],'Visible','On');
end
if isempty(HV); return; end % return if no data
% change between angle and Kx modes
if get(hObject,'Value')==0
% - display angle range
   AKx=ACorr; AKxRange=ARange; AKxWin=AutoAWin;
   set(handles.textAKx,'String',[sprintf('%0.1f',ARange(1)) '<Angle<' sprintf('%0.1f',ARange(2))])
else
% - calculate Kx, its ranges and auto window
   if isempty(Kx)
      % surfNx=str2num(get(handles.editSurfNx,'String')); 
      surfNx=field2num(handles.editSurfNx); Kx=Kxx(HV,ECorr,thtM,ACorr,surfNx,alpha);
      KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))];
      aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax];
   end
% - display Kx range
   AKx=Kx; AKxRange=KxRange; AKxWin=AutoKxWin;
   set(handles.textAKx,'String',[sprintf('%0.1f',KxRange(1)) '<Kx<' sprintf('%0.1f',KxRange(2))])
end
% display auto window
set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AKxWin))
% hide/popup controls and re-draw cube
SwitchFields(handles); DrawCubeSlice(handles)

% --- Executes on buttonpress in editSurfNx.
function editSurfNx_Callback(hObject,~,handles)
global HV ECorr ACorr thtM Kx KxRange AutoKxWin AKxRange AKxWin alpha
% calculate Kx and display Kx-ranges
%surfNx=str2num(get(hObject,'String'));
surfNx=field2num(hObject);
Kx=Kxx(HV,ECorr,thtM,ACorr,surfNx,alpha); KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))]; AKxRange=KxRange;
set(handles.textAKx,'String',[sprintf('%0.1f',KxRange(1)) '<Kx<' sprintf('%0.1f',KxRange(2))])
%set(handles.textAKx,'String',[{'Angle'};{[sprintf('%0.1f',AKxRange(1)) '<Kx<' sprintf('%0.1f',AKxRange(2))]}])
% calculate and display auto Kx window
aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax]; AKxWin=AutoKxWin; 
set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AKxWin))
% re-draw cube
DrawCubeSlice(handles)

% --- Executes on button press in pushbuttonFindSurfNx.
function pushbuttonFindSurfNx_Callback(~,~,handles)
global hFig CurrentXY ScanType SWin hv_N thtA_N eB_N surfNx_Navi HV ECorr EWin ...
          ACorr thtM Kx KxRange AutoKxWin AKxRange AKxWin createNewFig alpha
% graphics readout for surfNx input
viewMode=get(handles.menuViewMode,'Value');
% if (viewMode==1 && (isempty(ScanType) || isequal(ScanType,'Number')) ) || (viewMode==4 && isequal(ScanType,'Tilt'))
if (viewMode==1 && (isempty(ScanType) || diff(SWin)==0) ) || (viewMode==4 && (isequal(ScanType,'Tilt')||isequal(ScanType,'ADef')))
% - select Angle mode and XY readout
   set(handles.radiobuttonAKx,'Value',0);
   readoutIni=get(handles.menuReadout,'Value'); set(handles.menuReadout,'Value',1)
% - popup figure and graphics input till the figure is deleted
   createNewFig=1; ProcessView(handles); waitfor(hFig); XY=CurrentXY;
% - back to Kx mode and initial readout    
   set(handles.radiobuttonAKx,'Value',1); set(handles.menuReadout,'Value',readoutIni)
% - parameters   
   thtA_N=XY(1);
%   hv_N=mean(HV); % in case ScanType='Number' is defined through hv
  if  isequal(ScanType,'hv');  hv_N=SWin(1); else  hv_N=HV; end
% - other parameters 
  if viewMode==1; eB_N=XY(2);
  else eB_N=mean(EWin); set(handles.editSurfNy,'String',sprintf('%0.3f',XY(2)))
  end
else
   msgbox('Select a single image or an iso-E(Angle,Tlt) map','modal'); return
end
% position of the popup window
% PosFig=get(hObject,'Position'); PosPanel=get(handles.PanelProcessing,'Position'); PosButton=get(hObject,'Position');
% xPos_Navi=PosFig(1)+PosPanel(1)+PosButton(1)+PosButton(3); yPos_Navi=PosFig(2)+PosPanel(2)+PosButton(2);
% PosFig=get(hFig,'Position'); xPos_Navi=PosFig(1)+PosFig(3); yPos_Navi=PosFig(2)-PosFig(4);
% popup the panel to find surfNx and wait for the value
h=NaviSetup; set(h,'WindowStyle','modal'); uiwait(h);
if ~isempty(surfNx_Navi) set(handles.editSurfNx,'String',sprintf('%0.3f',surfNx_Navi)); end
% calculate Kx and display Kx-ranges
Kx=Kxx(HV,ECorr,thtM,ACorr,surfNx_Navi,alpha); KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))]; AKxRange=KxRange; 
set(handles.textAKx,'String',[sprintf('%0.1f',AKxRange(1)) '<Kx<' sprintf('%0.1f',AKxRange(2))])
% calculate and display auto Kx window
aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax]; AKxWin=AutoKxWin; 
set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AutoKxWin))
% re-draw cube
DrawCubeSlice(handles)

% --- Executes on selection change in radiobuttonHvKz.
function radiobuttonHvKz_Callback(hObject,~,handles)
global YRange; YRange=[]; disp ('- clear YRange')
if get(hObject,'Value')==0
   set([handles.textVo handles.editVo],'Visible','Off'); set(handles.textSurfNy,'Visible','Off'); set(handles.editSurfNy,'Visible','Off');
else
   set([handles.textVo handles.editVo],'Visible','On'); set(handles.textSurfNy,'Visible','On'); set(handles.editSurfNy,'Visible','On');
end

% --- Executes on button press in editEnergy.
function editEnergy_Callback(hObject,~,handles)
global ERange EWin % hFig createNewFig
% read in energy window
eStr=get(hObject,'String'); pmPos=strfind(deblank(eStr),'+-');
eSlice=str2num(eStr(1:pmPos-1)); dE=str2num(eStr(pmPos+2:end));
% validity check
if isempty(eSlice*dE); EWin=[]; msgbox('Check energy-window format E+-dE','modal'); return; end
if eSlice-dE<ERange(1)||eSlice+dE>ERange(2); EWin=[]; msgbox('Check energy-window ranges','modal'); return; end
EWin=[eSlice-dE eSlice+dE];
% re-draw cube
DrawCubeSlice(handles)
% % re-draw the existing view window
% try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonEMinus.
% Note: Replacement of malfunctioning Slider
function pushbuttonEMinus_Callback(~,~,handles)
global ERange EWin hFig createNewFig
% read in energy window
eStr=get(handles.editEnergy,'String'); pmPos=strfind(deblank(eStr),'+-');
eSlice=str2num(eStr(1:pmPos-1)); dE=str2num(eStr(pmPos+2:end));
% calculate and write new energy window
eSlice=eSlice-dE;
if eSlice-dE<ERange(1); return; end    % leave the previous window if below the range
EWin=[eSlice-dE eSlice+dE];
set(handles.editEnergy,'String',[num2str(eSlice) '+-' num2str(dE)])
% re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end
% --- Executes on button press in pushbuttonEPlus.
function pushbuttonEPlus_Callback(~,~,handles)
global ERange EWin hFig createNewFig
% read in energy window
eStr=get(handles.editEnergy,'String'); pmPos=strfind(deblank(eStr),'+-');
eSlice=str2num(eStr(1:pmPos-1)); dE=str2num(eStr(pmPos+2:end));
% calculate and write new energy window
eSlice=eSlice+dE;
if eSlice+dE>ERange(2); return; end    % leave the previous window if above the range
EWin=[eSlice-dE eSlice+dE];
set(handles.editEnergy,'String',[num2str(eSlice) '+-' num2str(dE)])
% re-draw cube
DrawCubeSlice(handles)
% re-draw the existing view window
try Pos=get(hFig,'Position'); createNewFig=0; ProcessView(handles); set(hFig,'Position',Pos); end

% --- Executes on selection change in menuLock.
function menuLock_Callback(hObject,~, handles)
% Hints: contents = cellstr(get(hObject,'String')) returns menuLock contents as cell array
%        contents{get(hObject,'Value')} returns selected item from menuLock
global hGUI Data HV thtM ACorr ECorr EAlign ERange Kx KxRange AutoKxWin AKxRange AKxWin ...
          dEWin_Lock dEWinIni dESm_Lock dESmIni  feat_Lock featIni setTo_Lock setToIni IDiv ISubtr CubePos Scan alpha
% % return if no change in selection
% if get(hObject,'Value')==valMenuLockPre; return; else valMenuLockPre=get(hObject,'Value'); end
% reset
IDiv=[]; ISubtr=[]; disp('- cleared IDiv ISubtr')
if get(hObject,'Value')==1
   EAlign=repmat(ECorr,[1 1 max(1,length(Scan))]);
else
% set initial parameters if 'Auto'
   if get(hObject,'Value')==2
      dEWin_Lock=dEWinIni; dESm_Lock=dESmIni; feat_Lock=featIni; setTo_Lock=setToIni; 
% draw the popup window and wait for initial parameters if 'XTra'
   else
% position of the popup window      
      PosGUI=get(hGUI,'Position'); PosPanel=get(handles.PanelProcessing,'Position'); PosButton=get(hObject,'Position');
      xPos_Lock=PosGUI(1)+PosPanel(1)+PosButton(1)+PosButton(3); yPos_Lock=PosGUI(2)+PosPanel(2)+PosButton(2);
% popup window   
      h=LockSetup; 
      Pos=get(h,'Position'); Pos=[xPos_Lock yPos_Lock-Pos(4)-30 Pos(3) Pos(4)]; 
      set(h,'Position',Pos,'WindowStyle','modal'); uiwait(h); 
   end
% aligned energy and energy range
   h=waitbar(0.5,'Aligning EF','WindowStyle','Modal'); % open waitbar
% - alignment
   eWin=field2num(handles.editLockEF,0); if length(eWin)>1; eWin=linspace(eWin(1),eWin(2),size(Data,3)); end
   EAlign=AlignEF(Data,ECorr,eWin,dEWin_Lock,dESm_Lock,feat_Lock); EAlign=EAlign+setTo_Lock;
%   if ~isempty(Fail); uiwait(msgbox(['Warning: Failed to Lock EF in ' num2str(length(Fail)) ' images'],'modal')); end
   close(h) % close waitbar
end 
% update energy range
   ERange=[min(min(EAlign(:,1,:))) max(max(EAlign(:,end,:)))];
   set(handles.textEnergy,'String',[sprintf('%0.1f',ERange(1)) '<Eb/k<' sprintf('%0.1f',ERange(end))]);
% update Kx range if Auto
if get(handles.radiobuttonAKx,'Value')==1 && all(AKxWin==AutoKxWin)
   surfNx=field2num(handles.editSurfNx); Kx=Kxx(HV,EAlign,thtM,ACorr,surfNx,alpha);
   KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))];
   aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax];
   set(handles.textAKx,'String',[sprintf('%0.1f',KxRange(1)) '<Kx<' sprintf('%0.1f',KxRange(2))])
   set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AutoKxWin))
   AKxRange=KxRange; AKxWin=AutoKxWin;
end
% draw data cube
axes(handles.axesCube); cla
% - 2D case
if isempty(Scan)||length(Scan)<2
   axis([0 1 -0.5 0.5 ERange]);
   set(gca,'Position',[1.01*CubePos(1) CubePos(2) 0.8*CubePos(3:4)],'PlotBoxAspectRatio',[0.5 1 1]);
% - 3D case
else
   axis([Scan([1 end]) -0.5 0.5 ERange]); % axis square tight;
   set(gca,'Position',CubePos,'PlotBoxAspectRatio',[5 1 1])
end
% switch fields and visualize slices
DrawCubeSlice(handles)

function editLockEF_Callback(~,~,handles)
% hObject    handle to editLockEF (see GCBO)
%global EAlign Kx IDiv ISubtr; EAlign=[]; Kx=[]; IDiv=[]; ISubtr=[]; disp('- cleared EAlign Kx IDiv ISubtr')
global Data HV thtM ACorr ECorr EAlign ERange Kx KxRange AutoKxWin AKxRange AKxWin ...
          dEWin_Lock dESm_Lock feat_Lock setTo_Lock IDiv ISubtr CubePos Scan alpha
 % exit if menuLock set to None
 if get(handles.menuLock,'Value')==1; return; end
% reset
IDiv=[]; ISubtr=[]; disp('- cleared IDiv ISubtr')
% aligned energy and energy range
h=waitbar(0.5,'Aligning EF','WindowStyle','Modal'); % open waitbar
% - alignment
eWin=field2num(handles.editLockEF,0); if length(eWin)>1; eWin=linspace(eWin(1),eWin(2),size(Data,3)); end
EAlign=AlignEF(Data,ECorr,eWin,dEWin_Lock,dESm_Lock,feat_Lock); EAlign=EAlign+setTo_Lock;
%   if ~isempty(Fail); uiwait(msgbox(['Warning: Failed to Lock EF in ' num2str(length(Fail)) ' images'],'modal')); end
close(h) % close waitbar
% update energy range
ERange=[min(min(EAlign(:,1,:))) max(max(EAlign(:,end,:)))];
set(handles.textEnergy,'String',[sprintf('%0.1f',ERange(1)) '<Eb/k<' sprintf('%0.1f',ERange(end))]);
% update Kx range
if get(handles.radiobuttonAKx,'Value')==1
   surfNx=field2num(handles.editSurfNx); Kx=Kxx(HV,EAlign,thtM,ACorr,surfNx,alpha);
   KxRange=[min(min(Kx(:,1,:))) max(max(Kx(:,end,:)))];
   aMin=max(max(Kx(:,1,:))); aMax=min(min(Kx(:,end,:))); AutoKxWin=[0.95*aMin+0.05*aMax 0.05*aMin+0.95*aMax];
   set(handles.textAKx,'String',[sprintf('%0.1f',KxRange(1)) '<Kx<' sprintf('%0.1f',KxRange(2))])
   set(handles.editAKx,'String',sprintf('%0.1f:%0.1f',AutoKxWin))
   AKxRange=KxRange; AKxWin=AutoKxWin;
end
% draw data cube
axes(handles.axesCube); cla
% - 2D case
if isempty(Scan)||length(Scan)<2
   axis([0 1 -0.5 0.5 ERange]);
   set(gca,'Position',[1.01*CubePos(1) CubePos(2) 0.8*CubePos(3:4)],'PlotBoxAspectRatio',[0.5 1 1]);
% - 3D case
else
   axis([Scan([1 end]) -0.5 0.5 ERange]); % axis square tight;
   set(gca,'Position',CubePos,'PlotBoxAspectRatio',[5 1 1])
end
% switch fields and visualize slices
DrawCubeSlice(handles)

% --- Executes on button press in menuNorm.
function menuNorm_Callback(hObject,~,handles)
% hObject    handle to menuNorm (see GCBO)
global hGUI scCoeff scCoeffIni clipNormNeg RangeNorm % hNormSetup RangeIni
% try close(hNormSetup); end
% position of the popup window
PosGUI=get(hGUI,'Position'); PosPanel=get(handles.PanelProcessing,'Position'); PosButton=get(hObject,'Position');
xPos_Norm=PosGUI(1)+PosPanel(1)+PosButton(1)+PosButton(3); yPos_Norm=PosGUI(2)+PosPanel(2)+PosButton(2);
% select normalization modes
switch get(hObject,'Value')
% close the window if 'None'
case 1
%   try delete(hNormSetup); end
% close window and reset initial parameters if 'Auto'   
case 2
%   try delete(hNormSetup); end
   scCoeff=scCoeffIni; clipNormNeg=1; RangeNorm=[]; % RangeNorm=RangeIni; 
% raise the popup window if 'Xtra'
otherwise      
%   if isempty(hNormSetup)||~ishandle(hNormSetup)
      hNormSetup=NormSetup;
      Pos=get(hNormSetup,'position'); Pos=[xPos_Norm yPos_Norm-Pos(4)-30 Pos(3) Pos(4)];
      set(hNormSetup,'position',Pos,'Visible','On','WindowStyle','modal'); uiwait(hNormSetup);
%   end
end

% --- Executes on selection change in menuImgProcMode.
function menuImgProcMode_Callback(hObject,~,handles)
% Hints: contents = cellstr(get(hObject,'String')) returns menuView contents as cell array
%        contents{get(hObject,'Value')} returns selected item from menuView
global hGUI  presmdX presmdY structMode sharp postsmdX postsmdY % hImgProcSetup
% try close(hImgProcSetup); end
% position of the popup window
PosGUI=get(hGUI,'Position'); PosPanel=get(handles.PanelProcessing,'Position'); PosButton=get(hObject,'Position');
xPos_ImgProc=PosGUI(1)+PosPanel(1)+PosButton(1)+PosButton(3); yPos_ImgProc=PosGUI(2)+PosPanel(2)+PosButton(2);
% select normalization modes
switch get(hObject,'Value')
% close window and reset initial parameters if 'None'
case 1
%   try delete(hImgProcSetup); end
   presmdX=[]; presmdY=[]; structMode=1; sharp=[]; postsmdX=[]; postsmdY=[];
% raise the popup window if 'Xtra'
   otherwise      
% raise the popup window if 'Xtra'
%   if isempty(hImgProcSetup)||~ishandle(hImgProcSetup)
      hImgProcSetup=ImgProcSetup;
      Pos=get(hImgProcSetup,'position'); Pos=[xPos_ImgProc yPos_ImgProc-Pos(4)-30 Pos(3) Pos(4)];
      set(hImgProcSetup,'position',Pos,'Visible','On','WindowStyle','modal'); uiwait(hImgProcSetup);
%   end
end

% --- Executes on selection change in menuView.
function menuView_Callback(hObject,~,~)
% Hints: contents = cellstr(get(hObject,'String')) returns menuView contents as cell array
%        contents{get(hObject,'Value')} returns selected item from menuView
global hGUI FracView FracViewIni XRange YRange render renderIni gamma gammaIni % hViewSetup
% try close(hViewSetup); end
% position of the popup window
PosGUI=get(hGUI,'Position'); PosButton=get(hObject,'Position');
xPos_View=PosGUI(1)+PosButton(1)+PosButton(3); yPos_View=PosGUI(2)+PosButton(2);
% select view modes
switch get(hObject,'Value')
% close window and reset initial parameters if 'Auto'   
   case 1
%   try delete(hViewSetup); end
   FracView=FracViewIni; XRange=[]; YRange=[]; gamma=gammaIni; render=renderIni; 
otherwise
% raise the popup window if 'Xtra'
%   if isempty(hViewSetup)||~ishandle(hViewSetup)
      hViewSetup=ViewSetup;
      Pos=get(hViewSetup,'position'); Pos=[xPos_View yPos_View-Pos(4)-30 Pos(3) Pos(4)];
      set(hViewSetup,'position',Pos,'Visible','On','WindowStyle','modal'); uiwait(hViewSetup);
%   end
end

% --- Executes on button press in pushbuttonView.
function pushbuttonView_Callback(~,~,handles)
global createNewFig
createNewFig=1; ProcessView(handles);

% --- Function to process the data for viewing
function ProcessView(handles)
global FullName ScanType EWin Scan SWin Data Data3 EAlign ERange ACorr AutoAWin Kx AKx AKxWin RangeNorm IDiv scCoeff ISubtr clipNormNeg ...
          X Y Z FracView switchAKx HV thtM tltM aDef presmdX presmdY structMode sharp postsmdX postsmdY clipImgProcNeg alpha
% Note: For processing of angular deflection, LoadData provides global tltM (scalar and empty if scan in Tlt), 
% aDef (scalar and empty if scan in ADef), Scan, and ScanType ('Tilt' or 'ADef')
viewMode=get(handles.menuViewMode,'Value');
% return if no data
if isempty(Data); return; end
% ePhi for Kz
ePhi=4.5;
% selecting between Angles and Kx
switchAKx=get(handles.radiobuttonAKx,'Value');
if switchAKx==0; AKx=ACorr; else surfNx=field2num(handles.editSurfNx); thtMPhys=thtM+surfNx; AKx=Kx; end
% AKxWin=sscanf(get(handles.editAKx,'String'),'%g:%g');
% AKxWin=field2num(handles.editAKx);
% odd/even switch
oddEven=get(handles.menuOddEven,'Value');
switch oddEven
   case 1; nOffset=0; nPeriod=1;
   case 2; nOffset=0; nPeriod=2;
   case 3; nOffset=1; nPeriod=2;
end
% scan window indices
if isempty(Scan); nS1=1; nS2=1;
else
   [~,nS1]=min(abs(Scan(1+nOffset:nPeriod:end)-SWin(1))); nS1=nOffset+1+(nS1-1)*nPeriod;
   [~,nS2]=min(abs(Scan(1+nOffset:nPeriod:end)-SWin(end))); nS2=nOffset+1+(nS2-1)*nPeriod;
end
% % align the energy scale at EF if EAlign empty (not yet calculated)
% if isempty(EAlign) 
%    if get(handles.menuLock,'Value')>1
%       h=waitbar(0.5,'Aligning EF','Windowstyle','Modal'); % waitbar
% % - parameters and alignment       
% %    eWin=str2num(get(handles.editLockEF,'String'));
%       eWin=field2num(handles.editLockEF);
%       [EAlign,dECorr,Fail]=AlignEF(Data,ECorr,eWin,dEWin_Lock,dESm_Lock,feat_Lock); EAlign=EAlign+setTo_Lock;
% %     if ~isempty(Fail); uiwait(msgbox(['Warning: Failed to Lock EF in ' num2str(length(Fail)) ' images'],'modal')); end  
%       close(h) % close waitbar  
%    else
%       EAlign=repmat(ECorr,[1 1 max(1,length(Scan))]);
%    end
% end
% % update energy range
% ERange=[min(min(EAlign(:,1,:))) max(max(EAlign(:,end,:)))];
set(handles.textEnergy,'String',[sprintf('%0.1f',ERange(1)) '<Eb/k<' sprintf('%0.1f',ERange(end))]);
% no need to calculate Kx-transform because it was already calculated 
% either in Load or in textAKx/editSurfNx/pushbuttonFind
% if isempty(Kx)&&get(handles.textAKx,'Value')==2
%    surfNx=str2num(get(handles.editSurfNx,'String')); Kx=Kxx(HV,ECorr,thtM,ACorr,surfNx,alpha);
% end
% normalize by intensity in the defined energy window into global Data3
Data3=Data;
if viewMode~=2&&get(handles.menuNorm,'Value')>1
   if isempty(IDiv)
      h=waitbar(0.5,'Forming Normalization Array','Windowstyle','Modal');
      if isempty(RangeNorm); IntEWin=[0.9*ERange(1)+0.1*ERange(2) 0.1*ERange(1)+0.9*ERange(2)];
      else IntEWin=RangeNorm; end
      IDiv=Slice(ACorr,EAlign,Data3,'isoE',IntEWin);
      close(h)
      if isempty(IDiv) msgbox('Error: Inconsistent normalization energy window','modal'); return; end
      IDiv=Gaco2(IDiv,5,0); % HWHM adjusted to suppress uneven sensitivity of the CCD channels
      IDiv=repmat(IDiv,1,1,size(Data3,1)); IDiv=permute(IDiv,[3 2 1]);
   end
   Data3=Data3./IDiv;
% subtract angle-integrated spectrum and clip negative values into global output Data3 
   if scCoeff~=0
      if isempty(ISubtr)
         h=waitbar(0.5,'Forming Subtraction Array','Windowstyle','Modal');
            ISubtr=Slice(ACorr,EAlign,Data3,'isoK',AutoAWin);
         close(h) 
         ISubtr=repmat(ISubtr,1,1,size(Data3,2)); ISubtr=permute(ISubtr,[1 3 2]);
      end
      Data3=Data3-scCoeff*ISubtr;
      if clipNormNeg==1; Data3(Data3<0)=0; end
   end
end
% processing and image modes into global output X,Y,Z
switch viewMode
%
% *** image *** (summation of images from 3D data ignores their energy shifts; in principle, should use remapping)   
case 1
   if size(AKx,3)>1; X=mean(AKx(:,:,nS1:nPeriod:nS2),3); else X=AKx; end
   Y=mean(EAlign(:,:,nS1:nPeriod:nS2),3);
   Z=mean(Data3(:,:,nS1:nPeriod:nS2),3);
%
case 2
% *** angle integrated image ***
%   [Y,X]=IntAngle(mean(Data3(:,:,nS1:nS2),3),Angle,mean(EAlign(:,:,nS1:nS2),3),AKxWin);
   if ismatrix(AKx); MeanAKx=AKx; else MeanAKx=mean(AKx(:,:,nS1:nPeriod:nS2),3); end
   [Y,X]=Slice(MeanAKx,mean(EAlign(:,:,nS1:nPeriod:nS2),3),mean(Data3(:,:,nS1:nPeriod:nS2),3),'isoK',AKxWin);
   Z=[];
%
% **** series of images mode ****
case 3
% plot images in the selected Scan range
   if size(AKx,3)>1; A=AKx(:,:,nS1:nPeriod:nS2); else A=AKx; end
%   if size(EAlign,3)>1; EAlignV=EAlign(:,:,nS1:nPeriod:nS2); else EAlignV=EAlign; end
   modeMap=get(handles.menuColormap,'Value'); modeMapC=get(handles.menuColormap,'String'); colorScheme=[char(modeMapC(modeMap)) '(256)'];  % color scheme
   nRows=3; nCols=3; ViewSeries(A,EAlign(:,:,nS1:nPeriod:nS2),Scan(nS1:nPeriod:nS2),Data3(:,:,nS1:nPeriod:nS2),nRows,nCols,colorScheme,FracView(1),FracView(2))
   X=[]; Y=[]; Z=[];
%
% *** iso-E mode ***
case 4
% - slice formation waitbar
   h=waitbar(0.5,'Forming Data Slice','Windowstyle','Modal');
% - slice within EWin
   if size(ACorr,3)>1; A=ACorr(:,:,nS1:nPeriod:nS2); else A=ACorr; end
   try [ISliceE,ASliceE]=Slice(A,EAlign(:,:,nS1:nPeriod:nS2),Data3(:,:,nS1:nPeriod:nS2),'isoE',EWin); catch; beep; close(h); return; end
%    try [ISliceE,ASliceE]=Slice(ACorr,EAlign(:,:,nS1:nPeriod:nS2),Data3(:,:,nS1:nPeriod:nS2),'isoE',EWin); catch; beep; close(h); return; end
% - close waitbar
   close(h)
% scan normalization
   normScanMode=get(handles.menuNormScans,'Value');
   switch normScanMode
% - no normalization
   case 1
      ISliceN=ISliceE;
   otherwise
% - integral intensity of scans over 90% of angular range
      nA=size(ISliceE,2); n1=round(0.05*nA); n2=round(0.95*nA);
      ISliceN=ISliceE(:,n1:n2); ISliceN=sum(ISliceN,2)/(n2-n1+1);
% - 2-order smoothing of integral intensity if normalization set to 'Smooth'
      if normScanMode==3; P=polyfit(Scan(nS1:nPeriod:nS2)',ISliceN,2); ISliceN=polyval(P,Scan(nS1:nPeriod:nS2)'); end
% - normalization
      ISliceN=ISliceE./repmat(ISliceN,1,nA);
% % - bilinear over 90% of angular range
%       [~,Coeffs]=Flat(AngleN,Scan,ISliceN);
%       [AngleM,ScanM]=meshgrid(Angle,Scan);
%       ISliceN=ISliceE./(Coeffs(1)*AngleM+Coeffs(2)*ScanM+Coeffs(3));
   end
% Kx-conversion   
   if switchAKx==0
      AKxSliceE=ASliceE;
   else   
      if isequal(ScanType,'Tilt')||isequal(ScanType,'ADef'); AKxSliceE=Kxx(HV,mean(EWin),thtM,ASliceE,surfNx,alpha); end 
      if isequal(ScanType,'hv'); AKxSliceE=Kxx(HV(nS1:nPeriod:nS2),mean(EWin),thtM,ASliceE,surfNx,alpha); end
   end   
% - image output
   X=AKxSliceE; Y=Scan(nS1:nPeriod:nS2)'; Z=ISliceN;
% K-space transformation if Kx activated
   if switchAKx==1
      surfNy=field2num(handles.editSurfNy);
% - Tilt scan       
      if isequal(ScanType,'Tilt')
         Ky=Kyy(HV,mean(EWin),ASliceE,thtM,Scan(nS1:nPeriod:nS2)-surfNy,surfNx,alpha); Y=Ky;
      end
% - ADef scan
      if isequal(ScanType,'ADef')
%         Ky=Kyy(HV,mean(EWin),ASliceE,thtM,Scan(nS1:nPeriod:nS2)+tltM-surfNy,surfNx,alpha);
         ADefM=repmat((Scan(nS1:nPeriod:nS2))',1,size(ASliceE,2));
         Ky=0.5124*sqrt(HV-ePhi+mean(EWin)).*sind(tltM+ADefM-surfNy).*cosd(ASliceE+thtMPhys)+2*pi*HV*sind(alpha+thtMPhys).*sind(tltM)/12400;
         Y=Ky;
      end
% - hv scan  
      if isequal(ScanType,'hv')
         if get(handles.radiobuttonHvKz,'Value')==1
            Vo=field2num(handles.editVo,-10);
            Kz=Kzz(HV(nS1:nPeriod:nS2),mean(EWin),thtM,ASliceE,tltM+aDef-surfNy,Vo,surfNx,alpha); Y=Kz;
         end
      end
   end   
%
% *** Iso-Angle/Kx mode ***  
case 5
% angle integration
   h=waitbar(0.5,'Angle Integrating','Windowstyle','Modal'); % waitbar
%    [ISliceA,ESliceA]=IntAngle(Data3,Angle,EAlign,AWin);
   if size(AKx,3)>1; A=AKx(:,:,nS1:nPeriod:nS2); else A=AKx; end
   try [ISliceA,ESliceA]=Slice(A,EAlign(:,:,nS1:nPeriod:nS2),Data3(:,:,nS1:nPeriod:nS2),'isoK',AKxWin); catch; beep; close(h); return; end
   close(h) % close waitbar
  % scan normalization
   normScanMode=get(handles.menuNormScans,'Value');
   ISliceZ=ISliceA';
   switch normScanMode
% - no normalization
   case {2,3}
% - integral intensity of scans over 80% of energy range
      nE=size(ISliceZ,2); n1=round(0.1*nE); n2=round(0.9*nE);
      ISliceN=ISliceZ(:,n1:n2); ISliceN=sum(ISliceN,2)/(n2-n1+1);
% - 2-order smoothing of integral intensity if normalization set to 'Smooth'
      if normScanMode==3; P=polyfit(Scan',ISliceN,2); ISliceN=polyval(P,Scan'); end
% - normalization
      ISliceZ=ISliceZ./repmat(ISliceN,1,nE);
   end
% image data
%   X=ESliceA'; Y=Scan'; Z=ISliceZ;
   X=ESliceA'; Y=Scan(nS1:nPeriod:nS2)'; Z=ISliceZ;
% interpolation to uniform energy grid if active energy alignment   
   if get(handles.menuLock,'Value')>1
      XGrid=linspace(min(X(:,1)),max(X(:,end)),size(X,2)); % energy grid column vector
      for iScan=1:length(Y)
         Z(iScan,:)=interp1(X(iScan,:),Z(iScan,:),XGrid); % interpolation to the same energy grid
      end
      X=XGrid;
   end
% K-space transformations if Kx activated
   if get(handles.radiobuttonAKx,'Value')==1
%       surfNx=str2num(get(handles.editSurfNx,'String')); 
%       surfNx=field2num(handles.editSurfNx); thtMPhys=thtM+surfNx;
%       surfNy=str2num(get(handles.editSurfNy,'String'));
       surfNy=field2num(handles.editSurfNy);
       kx=mean(AKxWin);
% - Tilt scan
      if isequal(ScanType,'Tilt') 
         Eb=X; TltM=repmat(Y,1,size(X,2))-surfNy;
         ThtA=asind((kx+2*pi*HV*cosd(alpha+thtMPhys)/12400)./(0.5124*sqrt(HV-ePhi+Eb)))-thtMPhys;
         Ky=0.5124*sqrt(HV-ePhi+Eb).*sind(TltM).*cosd(ThtA+thtMPhys)+2*pi*HV*sind(alpha+thtMPhys).*sind(TltM)/12400;
         Y=Ky;
      end
% - ADef scan
      if isequal(ScanType,'ADef') 
         Eb=X; ADefM=repmat(Y,1,size(X,2))-surfNy;
         ThtA=asind((kx+2*pi*HV*cosd(alpha+thtMPhys)/12400)./(0.5124*sqrt(HV-ePhi+Eb)))-thtMPhys;
         Ky=0.5124*sqrt(HV-ePhi+Eb).*sind(tltM+ADefM).*cosd(ThtA+thtMPhys)+2*pi*HV*sind(alpha+thtMPhys).*sind(tltM)/12400;
         Y=Ky;
      end
 % - hv scan
      if isequal(ScanType,'hv')
         if get(handles.radiobuttonHvKz,'Value')==1
%            Vo=str2num(get(handles.editVo,'String'));  
            Vo=field2num(handles.editVo,-10);
            Eb=X; HV2=repmat(Y,1,size(X,2));
            ThtA=asind((kx+2*pi*HV2*cosd(alpha+thtMPhys)/12400)./(0.5124*sqrt(HV2-ePhi+Eb)))-thtMPhys;
            Kxy_2=(HV2-ePhi+Eb).*(sind(ThtA+thtMPhys).^2+(sind(tltM+aDef-surfNy).*cosd(ThtA+thtMPhys)).^2); 
            Kz=0.5124*sqrt(HV2+Eb+Vo-Kxy_2)+2*pi*HV2*sind(alpha+thtMPhys)/12400;
            Y=Kz;
         end   
      end
   end
end
% image filter
if viewMode~=2
   if get(handles.menuImgProcMode,'Value')==2   
      dx=mean(mean(diff(X'))); dy=mean(mean(diff(Y)));
% - Gaussian pre-smoothing
      hwPtsX=0.5*presmdX/dx; hwPtsY=0.5*presmdY/dy;
      Z=Gaco2(Z,hwPtsX,hwPtsY,2*hwPtsX,2*hwPtsY);
% - image structure
      switch structMode
      case 2 % curvature along X
         if sharp==0; Z=-1*(DifC(Z',2))'; else; Z=-DiffFlt2(Z','1D',sharp)'; end
      case 3 % curvature along Y
         if sharp==0; Z=-1*DifC(Z,2); else; Z=-DiffFlt2(Z,'1D',sharp); end
      case 4 % curvature along XY
         if sharp==0; Z=-1*(DifC(Z,2)+(dy/dx)^2*(DifC(Z',2))'); else; Z=-DiffFlt2(Z,'2D',sharp,dx/dy); end  
      end
% - Gaussian post-smoothing
      hwPtsX=0.5*postsmdX/dx; hwPtsY=0.5*postsmdY/dy;
      Z=Gaco2(Z,hwPtsX,hwPtsY);      
 % - clipping negative values
      if clipImgProcNeg==1; Z(Z<0)=0; end
   end
end
% enable export
set(handles.menuExport,'Enable','On')
% % *** end 3D block ***
% end
%
% *** plot ***
Pos=strfind(FullName,'\'); if isempty(Pos); Pos=strfind(FullName,'/'); end  % parsing universal between Windows and Mac/Linux
FileName=FullName(Pos(end)+1:end); Opts.FileName=FileName; Opts.Scan=Scan; Opts.ScanType=ScanType;
PlotAll(X,Y,Z,Opts,handles)

% --- Plot and set callbacks function
function PlotAll(X,Y,Z,Opts,handles)
global switchAKx FracView render XRange YRange hFig createNewFig gamma ZView
            % presmdX presmdY structMode sharp postsmdX postsmdY clipImgProcNeg ScanType hIm hXDC hYDC
viewMode=get(handles.menuViewMode,'Value');
% reject image series
if viewMode==3; return; end
% color scheme
modeMap=get(handles.menuColormap,'Value'); modeMapC=get(handles.menuColormap,'String'); colorScheme=[char(modeMapC(modeMap)) '(256)'];
% scan type
ScanType=Opts.ScanType;
% deactivate slope readout
% set(handles.menuReadout,'Value',1,'Enable','Off');
% set previous or create new figure 
if createNewFig==0 
%   try delete(hFig); end
% - set previous figure as current
   figure(hFig)
%   clf(hFig)
% - retrieve previous image axes handle and set it active 
   UserData=get(hFig,'UserData'); hIm=UserData.hIm; axes(hIm)
else
% - new figure with callbacks  
   hFig=figure('WindowButtonDownFcn',{@window_Zoom,handles},'WindowButtonUpFcn',{@window_H,handles}); % default normalized units
end
% linear plot
if isempty(Z)
   plot(X,Y); axis tight; set(gca,'TickDir','Out')
% image plots   
else
% set image limits  
% - render 1D-X,Y to 2D-X,Y  
   if size(X,1)==1; XX=repmat(X,size(Y,1),1); else XX=X; end
   if size(Y,2)==1; YY=repmat(Y,1,size(X,2)); else YY=Y; end
% - set NaN outside the limits
   if ~isempty(XRange); Z(XX<XRange(1)|XX>XRange(2))=NaN; end
   if ~isempty(YRange); Z(YY<YRange(1)|YY>YRange(2))=NaN; end
% set contrast
   % RawZ=Z; 
   ZView=SetContrast(Z,FracView(1),FracView(2),gamma);
%   if get(handles.menuNorm,'Value')==1; Z=Z*scale; end
% different image modes
   switch viewMode
% - image
      case 1
         ImData(X,Y,ZView,render); axis tight; colorbar;  eval(['colormap ''' colorScheme ''''])
% - iso-E
      case 4
         ImData(X,Y,ZView,render); axis tight; colorbar; eval(['colormap ''' colorScheme ''''])
% - Iso-E(Angle)         
         if isequal(ScanType,'Tilt')||isequal(ScanType,'ADef')
            axis tight equal %set(gca,'YDir','Reverse'); 
            set(handles.menuReadout,'Enable','On');
         end
% - angle-integrated scan
      case 5
         ImData(X,Y,ZView,render); axis tight; colorbar; eval(['colormap ''' colorScheme ''''])
   end
end
% update image axes handle
hIm=gca;
% limitsOpts.Scan
if ~isempty(XRange); xlim(XRange); end
if ~isempty(YRange); ylim(YRange); end
% title and axes information
if switchAKx==0; titleAKx=', Angle='; else titleAKx=', Kx='; end
switch viewMode
   case 1
      if isempty(Opts.Scan); titleStr=Opts.FileName;   
      else titleStr=[Opts.FileName ', Scan=' get(handles.editScan,'string')]; 
      end
      if switchAKx==0; xlabel('Angle (deg)'); else xlabel('K_{x} (1/A)'); end 
      if min(Y)>100; ylabel('E_{k} (eV)'); else ylabel('E_{B} (eV)'); end
   case 2
      if isempty(Opts.Scan); titleStr=[Opts.FileName titleAKx get(handles.editAKx,'string')];   
      else titleStr=[Opts.FileName ', Scan=' get(handles.editScan,'string') titleAKx get(handles.editAKx,'string')]; 
      end
      if min(X)>100; xlabel('E_{k} (eV)'); else xlabel('E_{B} (eV)'); end
      ylabel('Intensity');
   case 4
      titleStr=[Opts.FileName ', E=' get(handles.editEnergy,'string')];
      if switchAKx==0; xlabel('Angle (deg)'); else xlabel('K_{x} (1/A)'); end
      switch(ScanType)
         case 'Number'; ylabel('Image Number');
         case 'hv'; if get(handles.radiobuttonHvKz,'Value')==0; ylabel('hv (eV)'); else ylabel('K_{z} (1/A)'); end 
         case {'Theta','Azimuth'}; ylabel([ScanType ' (deg)'])
         case {'Tilt','ADef'}; if switchAKx==0; ylabel([ScanType ' (deg)']); else ylabel('K_{y} (1/A)'); end   
         case {'X','Z'}; ylabel([ScanType ' (mm)'])
      end
   case 5
      titleStr=[Opts.FileName titleAKx get(handles.editAKx,'string')];
      if min(X)>100; xlabel('E_{k} (eV)'); else xlabel('E_{B} (eV)'); end
      switch(ScanType)
         case 'Number'; ylabel('Image Number');
         case 'hv'; if get(handles.radiobuttonHvKz,'Value')==0; ylabel('hv (eV)'); else ylabel('K_{z} (1/A)'); end
         case {'Theta','Azimuth'}; ylabel([ScanType ' (deg)'])
         case {'Tilt','ADef'}; if switchAKx==0; ylabel([ScanType ' (deg)']); else ylabel('K_{y} (1/A)'); end               
         case {'X','Z'}; ylabel([ScanType ' (mm)'])
      end
end
if get(handles.menuNorm,'value')>1; titleStr=[titleStr ', Subtr']; end
if isequal(get(handles.menuNormScans,'enable'),'on') && get(handles.menuNormScans,'value')~=1 
   titleStr=[titleStr ', NormScans']; 
end
title(titleStr,'Interpreter','none','fontweight','normal');
% white background
set(hFig,'color','w')
% user data for Zoom
UserData.viewMode=viewMode; UserData.Opts=Opts; UserData.X=X; UserData.Y=Y; UserData.Z=Z; UserData.hIm=hIm;
set(hFig,'UserData',UserData)
%
% *** add XDC/YDC panels ***
if viewMode~=2 && viewMode~=3 && get(handles.radiobuttonXYDC,'Value')==1
% switch off the Zoom callback on WindowButtonDownFcn   
    set(hFig,'WindowButtonDownFcn',[]);
% switch off resizing (resizing corrupts positioning of the panels)
   set(hFig,'resize','off')
% extend figure for the XYDC panels
   PosFig=get(hFig,'Position'); sizeFig=max(PosFig([3 4])); set(hFig,'Position',[PosFig(1) PosFig(2)+PosFig(4)-sizeFig sizeFig sizeFig])
% prepare the figure
   axis square; colorbar('off'); hIm=gca;
% remove old and draw new panels
   set(hIm,'position',[0.1 0.1 0.5 0.5]); 
%   XLim=get(hIm,'XLim'); YLim=get(hIm,'YLim');
%   hPlot=plot(hOver,XLim,YLim); set(hPlot,'visible','off')
   try delete(UserData.hXDC); end; hXDC=axes('position',[0.1 0.7 0.5 0.25],'box','on','XTick',[],'YTick',[]); 
   try delete(UserData.hYDC); end; hYDC=axes('position',[0.7 0.1 0.25 0.5],'box','on','XTick',[],'YTick',[]);
% X/Y edit fields
hY=uicontrol('Callback',@PlotXYDC,'Style','edit','fontsize',11,'units','normalized','position',[0.65 0.8 0.16 0.04], ...
                       'string',['-0.1' '+-' sprintf('%0.1f',0.1)]);
uicontrol('Style','text','string','Y=','units','normalized','position',[0.61 0.795 0.04 0.04],'BackgroundColor','w','fontsize',11);
hX=uicontrol('Callback',@PlotXYDC,'Style','edit','fontsize',11,'units','normalized','position',[0.76 0.625 0.16 0.04], ...
                       'string',['0.0' '+-' sprintf('%0.1f',0.1)]);
uicontrol('Style','text','string','X=','units','normalized','position',[0.72 0.62 0.04 0.04],'BackgroundColor','w','fontsize',11);
% set callback on cursor motion
set(hFig,'WindowButtonDownFcn',@Ginput_XYDC);
%      set(hFig,'WindowButtonMotionFcn',@window_XYDC,'BusyAction','Cancel');
% add user data
   %UserData.RawZ=RawZ; 
   UserData.hIm=hIm; UserData.hYDC=hYDC; UserData.hXDC=hXDC; UserData.hX=hX; UserData.hY=hY; 
   set(hFig,'UserData',UserData)  %UserData.hOver=hOver;   
% plot the ROI-cross and XYDCs
PlotXYDC
end

% --- Executes on button press in radiobuttonXYDC.
function radiobuttonXYDC_Callback(hObject, ~, handles)
% hObject    handle to radiobuttonXYDC (see GCBO)
if get(hObject,'Value')==0
   set(handles.menuExport,'String',{'Data';'Raw Image';'View Image'})
else
   set(handles.menuExport,'String',{'Data';'Raw Image';'View Image';'XDC';'YDC'})   
end

% graphical input of ROI for XYDCs
function Ginput_XYDC(~,~,~)
global hFig
% retrieve user data from the current figure 
UserData=get(hFig,'UserData'); hIm=UserData.hIm; 
try hX=UserData.hX; hY=UserData.hY; catch; return; end % return if the previous figure without edit fields
% remove previous lines
try delete([hLine1 hLine2 hLine3 hLine4]); end
%delete(hIm) deleting image makes the function reactive
% plot(hIm,[0 1],[0 1])
% current point
XY=get(hIm,'CurrentPoint'); x=XY(1,1); y=XY(1,2);
% XY=get(hOver,'CurrentPoint'); x=XY(1,1); y=XY(1,2);
% return if outside the image
XLim=get(hIm,'XLim'); YLim=get(hIm,'YLim');
if x<XLim(1) || x>XLim(2) || y<YLim(1) || y>YLim(2); return; end
% X- and Y-fields
xStr=get(hX,'String'); pmPos=strfind(deblank(xStr),'+-'); dX=str2num(xStr(pmPos+2:end)); set(hX,'String',[sprintf('%0.2f+-%0.2f',[x dX])]);
yStr=get(hY,'String'); pmPos=strfind(deblank(yStr),'+-'); dY=str2num(yStr(pmPos+2:end)); set(hY,'String',[sprintf('%0.2f+-%0.2f',[y dY])]);
% plot the ROI-cross and XYDCs
PlotXYDC

% plot the ROI-cross and XYDCs
function PlotXYDC(~,~,~)
global hLine1 hLine2 hLine3 hLine4 hFig XPts XDC YPts YDC
% remove previous lines
try delete([hLine1 hLine2 hLine3 hLine4]); end
% retrieve user data from the current figure
UserData=get(hFig,'UserData'); X=UserData.X; Y=UserData.Y; Z=UserData.Z; 
hIm=UserData.hIm; hXDC=UserData.hXDC; hYDC=UserData.hYDC; hX=UserData.hX; hY=UserData.hY; %hOver=UserData.hOver;
% x- and y-windows
xStr=get(hX,'String'); pmPos=strfind(deblank(xStr),'+-'); x=str2num(xStr(1:pmPos-1)); dX=abs(str2num(xStr(pmPos+2:end)));
if isempty(x*dX); msgbox('Check format X+-dX','modal'); return; end
yStr=get(hY,'String'); pmPos=strfind(deblank(yStr),'+-'); y=str2num(yStr(1:pmPos-1)); dY=abs(str2num(yStr(pmPos+2:end)));
if isempty(y*dY); msgbox('Check format Y+-dY','modal'); return; end
% return if outside the image
XLim=get(hIm,'XLim'); YLim=get(hIm,'YLim');
if x+dX<XLim(1) || x-dX>XLim(2) || y+dY<YLim(1) || y-dY>YLim(2); return; end
% cross
hLine1=line(hIm,[XLim(1) x-dX x-dX],[y-dY y-dY YLim(1)],'color','g');
hLine2=line(hIm,[x+dX x+dX XLim(2)],[YLim(1) y-dY y-dY ],'color','g');
hLine3=line(hIm,[x+dX x+dX XLim(2)],[YLim(2) y+dY y+dY ],'color','g');
hLine4=line(hIm,[XLim(1) x-dX x-dX],[y+dY y+dY YLim(2)],'color','g');
% XDC panel
[XPts,XDC]=Cut(X,Y,Z,'mdc',[y-dY y+dY]);
if isempty(XDC); cla(hXDC)
else plot(hXDC,XPts,XDC,'linewidth',1); set(hXDC,'xlim',XLim,'xtickmode','auto');
end
% YDC panel
[YPts,YDC]=Cut(X,Y,Z,'edc',[x-dX x+dX]);
if isempty(YDC); cla(hYDC)
else plot(hYDC,YDC,YPts,'linewidth',1); set(hYDC,'ylim',YLim,'ytickmode','auto')
end

% --- Zoom and XY/slope readout function
function window_Zoom(~,~,handles)
global CurrentXY PSave ha hc hl hFig hGUI createNewFig
% return if GUI
if isequal(gcf,hGUI); return; end
% clear previous line
try delete([ha hc hl]); end
% retrieve user data from the figure
hFig=gcf;
UserData=get(hFig,'UserData');
viewMode=UserData.viewMode; Opts=UserData.Opts; X=UserData.X; Y=UserData.Y; Z=UserData.Z; 
% reject image series
if viewMode==3; return; end
% keep the plot figure handle which gets spoiled by rbbox
hhFig=hFig;
% previous limits
XLim0=get(gca,'XLim'); YLim0=get(gca,'YLim'); 
% rbbox and its borders
p1=get(gca,'CurrentPoint'); p1x=p1(1,1); p1y=p1(1,2); rbbox; p2=get(gca,'CurrentPoint'); p2x=p2(1,1); p2y=p2(1,2); 
% XY-coordinates if point click
if (p2x-p1x)==0 && (p2y-p1y)==0
% return if the coordinates outside the plot
   if p1x<XLim0(1)||p1x>XLim0(2)||p1y<YLim0(1)||p1y>YLim0(2); return; end
% readout set to XY   
   if get(handles.menuReadout,'Value')==1
%    hc=line(p1x-[-1 1 0 0 0]*diff(XLim0)/20,p1y-[0 0 0 1-1]*diff(YLim0)/20); set(hc,'color','g','linewidth',1.5) % draw cross
      hold on; hc=plot(p1x,p1y,'+g','markersize',20); hold off
      ha=annotation('textbox', [0.65, 0.02, 0.35, 0.05],'String',['X=' sprintf('%0.3f',p1x) '; Y=' sprintf('%0.3f',p1y)],'EdgeColor','W','FontSize',11);
      CurrentXY=[p1x p1y];
%      pause(1); delete(hc) 
      return
% readout set to Slope      
   else 
      if isempty(PSave)
         PSave=[p1x p1y];
         hold on; hc=plot(p1x,p1y,'*g','markersize',10); hold off
      else hl=line([PSave(1) p1x],[PSave(2) p1y]); set(hl,'color','g','linewidth',1.5);
         Fit=polyfit([PSave(1) p1x],[PSave(2) p1y],1); slope=atand(Fit(1));
         ha=annotation('textbox', [0.7, 0.02, 0.3, 0.05],'String',['Slope=' sprintf('%0.3f',slope)],'EdgeColor','W','FontSize',11);
%         pause(1); delete(hl)
         PSave=[];
      end
   end
end
% restore the plot figure handle
hFig=hhFig;
% process current point
XLim=sort([p1x p2x]); YLim=sort([p1y p2y]);
XLim=[max(XLim(1),XLim0(1)) min(XLim(2),XLim0(2))]; 
YLim=[max(YLim(1),YLim0(1)) min(YLim(2),YLim0(2))];
% return if rbbox is too small
% if diff(XLim)*diff(YLim)==0; return; end
if diff(XLim)<0.01*diff(XLim0) || diff(YLim)<0.01*diff(YLim0); return; end
% % return if not the last plotted figure
% if ~isequal(gcf,hhFig); 
%    hMsg=msgbox('Zooming Active Only in the Last Plot','modal'); pause(2); close(hMsg); return; 
% end
% trimming of images to re-colorscale
ZZ=Z;
switch viewMode
case 1
   ZZ(X<XLim(1)|X>XLim(2))=NaN; ZZ(Y<YLim(1)|Y>YLim(2))=NaN;
case 2
   ZZ=[];
case {4,5}
   if size(Y,2)==1; YY=repmat(Y,1,size(X,2)); else YY=Y; end % 1D vector of angles vs 2D array of k
   ZZ(X<XLim(1)|X>XLim(2))=NaN; ZZ(YY<YLim(1)|YY>YLim(2))=NaN;
% case 5
%    [XX,YY]=meshgrid(X,Y);
%    ZZ(X<XLim(1)|X>XLim(2))=NaN; ZZ(YY<YLim(1)|YY>YLim(2))=NaN;
end
% draw zoomed figure
% close(gcf) % replace previous figure
createNewFig=0; PlotAll(X,Y,ZZ,Opts,handles); set(gca,'XLim',XLim,'YLim',YLim)

% --- Function to set global handle of the active figure for readout
function window_H(~,~,handles)
global hFig hGUI
% return if GUI
if isequal(gcf,hGUI); return; end
hFig=gcf;
% set XDC/YDC of the figure 
hAllAxes=findobj(hFig,'Type','axes');
if length(hAllAxes)==1; set(handles.radiobuttonXYDC,'Value',0); else set(handles.radiobuttonXYDC,'Value',1); end 
% enable slope readout
A=daspect;
if isequal(A(1),A(2)); set(handles.menuReadout,'Enable','On'); 
else set(handles.menuReadout,'Value',1,'Enable','Off'); end

% --- Executes on selection change in menuColormap.
function menuColormap_Callback(~,~,handles)
% % colorscheme
% global colorScheme
% modeMap=get(hObject,'Value'); modeMapC=get(hObject,'String'); colorScheme=[char(modeMapC(modeMap)) '(256)'];
% % ['set(gca,''colormap'', ' colorScheme '(256))']; eval(['set(gca,''colormap'', ' colorScheme '(256))']) % does not work
% re-draw image
global createNewFig
createNewFig=0; ProcessView(handles);

% --- Executes on selection change in menuReadout.
function menuReadout_Callback(hObject,~,~)
global PSave
if get(hObject,'Value')==2; PSave=[]; end

% --- Executes on button press in CloseFigs.
function CloseFigs_Callback(~,~,~)
% hObject    handle to CloseFigs (see GCBO)
% handles of all figures
global hGUI
hPlots=findobj('Type','figure');
% remove the GUI handle
hPlots=hPlots(hPlots~=hGUI);
% close all plots
close(hPlots)

% --- Executes on button press in pushbuttonExport.
function pushbuttonExport_Callback(~,~,handles)
% hObject    handle to pushbuttonExport (see GCBO)
global Scan Data3 Note EAlign FullName AKx X Y Z ZView XPts XDC YPts YDC
global ExpX ExpY ExpZ % share output data
% DataX=Data; ECorrX=ECorr; EAlignX=EAlign; ACorrX=ACorr;
% check data and activated corrections
if isempty(Data3); errordlg('No Data','','modal'); return; end
if contains(FullName,'_Exp'); waitfor(warndlg('Data file seems already exported','')); end 
% filename to export
Dots=strfind(FullName,'.'); dot=Dots(end);
[filename,pathname]=uiputfile('*.h5','Export As',[FullName(1:dot-1) '_Exp.h5']);
if filename~=0; filename=[pathname filename];
else errordlg('Invalid Filename','','modal'); return
end
% select export mode
switch get(handles.menuExport,'Value')
% - current data generated by ProcessView (incl. energy alignment and normalization/subtraction)
   case 1; ExpX=AKx; ExpY=EAlign; ExpZ=Data3;
% - current image or plot (empty Z) generated by ProcessView (+ scan normalizaton and image filtering)
   case 2; ExpX=X; ExpY=Y; ExpZ=Z;
% - current image generated by PlotAll (+ contrast enhancement and X/Y ranges)  
   case 3; ExpX=X; ExpY=Y; ExpZ=ZView;
% - current XDC
   case 4; ExpX=XPts; ExpY=XDC; ExpZ=[];    
% - current YDC      
   case 5; ExpX=YPts; ExpY=YDC; ExpZ=[];
end
% remapping
% - linear plots
if isempty(ExpZ)
% - interpolate if non-equidistant
   if any(diff(diff(ExpX))~=0)
      LinX=linspace(ExpX(1),ExpX(end),length(ExpX));
      ExpY=interp1(ExpX,ExpY,LinX,'pchip'); ExpX=LinX;
   end
% - data or images   
else
% - remapping (3D data processed sequentally through the images)
   h=waitbar(0.5,'Remapping Data','Windowstyle','Modal');
   [ExpX,ExpY,ExpZ]=Remap(ExpX,ExpY,ExpZ);
   close(h)
end
% % conversion to int32 (normalized to use the full resolution of int32)
% ExpZ=int32(double(intmax('int32'))*ExpZ/max(max(max(ExpZ))) );
% IGOR's scales
xaxis = [ExpX(1) mean(diff(ExpX))];
if get(handles.menuExport,'Value')>=4; scale = [0 0; xaxis];
else
   yaxis = [ExpY(1) mean(diff(ExpY))];
   if get(handles.menuExport,'Value')>=2; scale = [0 0; xaxis; yaxis];
   else
% if repeated scans (such as hi-stat scans) the original Scan is ScanFull of the repeated parameters and Scan is their sequential numbers    
      scan = [Scan(1) mean(diff(Scan))]; 
      scale = [0 0; xaxis; yaxis; scan];
      ExpZ = permute(ExpZ, [3 1 2]);
   end
end
% open writing waitbar
h=waitbar(0.5,'Saving Data','Windowstyle','Modal');
% delete the file to overwrite which otherwise causes error in h5create
if exist(filename,'file'); delete(filename); end
% ExpY to ExpZ substitution for linear plots
if isempty(ExpZ); ExpZ=ExpY; end
% writing
h5create(filename, '/Matrix', size(ExpZ));
h5write(filename, '/Matrix', ExpZ);
h5writeatt(filename, '/Matrix', 'IGORWaveNote', Note,'TextEncoding', 'system');
h5writeatt(filename, '/Matrix', 'IGORWaveScaling', fliplr(scale)');
% close waitbar
close(h)

% % --- Executes on button press in pushbuttonExport.
% function pushbuttonExport_Callback(~,~,handles)
% % hObject    handle to pushbuttonExport (see GCBO)
% global ScanFull Scan Data3 Note EAlign FullName AKx hFig ExpX ExpY ExpZ
% % DataX=Data; ECorrX=ECorr; EAlignX=EAlign; ACorrX=ACorr;
% % check data and activated corrections
% if isempty(Data3); errordlg('No Data','','modal'); return; end
% if contains(FullName,'_Export'); waitfor(warndlg('Data file seems already exported','')); end 
% % filename to export
% Dots=strfind(FullName,'.'); dot=Dots(end);
% [filename,pathname]=uiputfile('*.h5','Export As',[FullName(1:dot-1) '_Export.h5']);
% if filename~=0; filename=[pathname filename];
% else errordlg('Invalid Filename','','modal'); return;
% end
% % select export of the current image  
% if get(handles.menuExport,'Value')==2
%    get(hFig,'UserData',UserData); 
%    ExpX=UserData.X; ExpY=UserData.Y; ExpZ=UserData.Z;
% % select export of the whole data
% else
%    ExpX=AKx; ExpY=EAlign; ExpZ=Data3;
% end
% % open waitbar
% h=waitbar(0.5,'Remapping Data','Windowstyle','Modal');
% % remapping (3D data processed sequentally through the images)
% [ExpX,ExpY,ExpZ]=Remap(ExpX,ExpY,ExpZ);
% % % conversion to int32 (normalization to use the full resolution of int32)
% % ExpZ=int32(double(intmax('int32'))*ExpZ/max(max(max(ExpZ))) );
% % arrays in the IGOR-compatible format
% % repeated Data (any acquisition with ones(XXX)) are saved as a sequence of numbered frames and can no more be summed up with correlation;
% % all normal scans are OK because Scan is saved
% xaxis = [ExpX(1) mean(diff(ExpX))];
% yaxis = [ExpY(1) mean(diff(ExpY))];
% if isempty(Scan)
%     scale = [0 0; xaxis; yaxis;];
% else
%    ExpZ = permute(ExpZ, [3 1 2]);
% % if repeated scans (such as hi-stat scans) the original Scan is ScanFull of the repeated parameters and Scan is their sequential numbers    
% %    scan = [Scan(1) mean(diff(Scan))];
%     scan = [ScanFull(1) mean(diff(ScanFull))];
%     scale = [0 0; xaxis; yaxis; scan];
% end
% close(h); h=waitbar(0.5,'Saving Data','Windowstyle','Modal');
% % delete the file to overwrite which otherwise causes error in h5create
% if exist(filename,'file'); delete(filename); end
% % write into HDF5 file
% h5create(filename, '/Matrix', size(ExpZ));
% h5write(filename, '/Matrix', ExpZ);
% h5writeatt(filename, '/Matrix', 'IGORWaveNote', Note);
% h5writeatt(filename, '/Matrix', 'IGORWaveScaling', fliplr(scale)');
% % close waitbar 
% close(h);

% --- Executes during object deletion, before destroying properties.
function figure1_DeleteFcn(~,~,~)
% handles of all figures
hPlots=findobj('Type','figure');
% close all figures including the GUI
close(hPlots)

% 07.01.2021
% X,Y,Z from ProcessView are written by PlotAll to UserData of each plot; after zooming, PlotAll updates Z where all values outside the X/Y range are set to NaN 
% RawZ excluded; contrast-enhanced ImZ deglobalized (it looks like previously zoom applied to already contrast-enhanced data)
% Global Z is set only in ProcessView