%'ima2netcdf': read image series and transform to netcdf
%------------------------------------------------------------------------

    
% function ParamOut=ima2netcdf(Param)
%
%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%OUTPUT
% ParamOut: sets options in the GUI series.fig needed for the function
%
%INPUT:
% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
% In batch mode, Param is the name of the corresponding xml file containing the same information
% when Param.Action.RUN=0 (as activated when the current Action is selected
% in series), the function ouput paramOut set the activation of the needed GUI elements
%
% Param contains the elements:(use the menu bar command 'export/GUI config' in series to 
% see the current structure Param)
%    .InputTable: cell of input file names, (several lines for multiple input)
%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
%    .OutputSubDir: name of the subdirectory for data outputs
%    .OutputDirExt: directory extension for data outputs
%    .Action: .ActionName: name of the current activated function
%             .ActionPath:   path of the current activated function
%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
%             .RUN =0 for GUI input, =1 for function activation
%             .RunMode='local','background', 'cluster': type of function  use
%             
%    .IndexRange: set the file or frame indices on which the action must be performed
%    .FieldTransform: .TransformName: name of the selected transform function
%                     .TransformPath:   path  of the selected transform function
%    .InputFields: sub structure describing the input fields withfields
%              .FieldName: name(s) of the field
%              .VelType: velocity type
%              .FieldName_1: name of the second field in case of two input series
%              .VelType_1: velocity type of the second field in case of two input series
%              .Coord_y: name of y coordinate variable
%              .Coord_x: name of x coordinate variable
%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%=======================================================================
% Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
%
%     This file is part of the toolbox UVMAT.
%
%     UVMAT is free software; you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published
%     by the Free Software Foundation; either version 2 of the license,
%     or (at your option) any later version.
%
%     UVMAT is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License (see LICENSE.txt) for more details.
%=======================================================================

function ParamOut=extract_multitif_parallel(Param)

%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
if isstruct(Param) && isequal(Param.Action.RUN,0)
    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
    ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes'))
    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    ParamOut.FieldTransform = 'off';%can use a transform function
    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
    ParamOut.OutputDirExt='.png';%set the output dir extension
    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
      ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
    %% root input file(s) and type
    % check the existence of the first file in the series
        first_j=[];% note that the function will propose to cover the whole range of indices
    if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end
    last_j=[];
    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
    PairString='';
    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
    if ~exist(FirstFileName,'file')
        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
    end

    %% check the validity of  input file types
    FileInfo=get_file_info(FirstFileName);
    if ~strcmp(FileInfo.FileType,'multimage')
        msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image'])
        return
    end
    %ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml');  
    return
end
%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%% 

%% read input parameters from an xml file if input is a file name (batch mode)
checkrun=1;
RUNHandle=[];
WaitbarHandle=[];
if ischar(Param)
    Param=xml2struct(Param);% read Param as input file (batch case)
    checkrun=0;
else
    hseries=findobj(allchild(0),'Tag','series');
    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
end

%% list of input images
% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2});
% ListStruct=dir(DirImages);
% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
% ListFile=ListCells(1,find(~check_dir & ~check_bad));

%% check file names
% RootName=regexprep(ListFile{1},'.tif$','')
% rank(1)=1;
% for ilist=2:numel(ListFile)
%     rank_str=regexprep(ListFile{ilist},'.tif$','');
%     rank(ilist)=regexprep(rank_str,['^' RootName '@'],'');
% %     if ~isequal(str2num(rank),ilist-1)
% %         disp(['error in the list of input file # ' num2str(ilist-1)])
% %         return
% %     end
% end

%% output directory
OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);
OutputDirScan=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);
%% Timing
% XmlInputFile=Param.ActionInput.XmlFile;
% [XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera');
% if ~isempty(errormsg)
%     disp(['bad xml input file: ' errormsg])
%     return
% end
%ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices
count0=14;
Dtj=0.05;% time interval between frames
ImagesPerLevel=455;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions
Nbj=390; %Nbre of images kept at a given position
Dti=Dtj*ImagesPerLevel;
NbLevel=11;
NbScan=3;
TimeReturn=268.5; %time needed to return back to the first position (in sec)
NbReturn=round(TimeReturn/Dtj);
NbSkipReturn=NbReturn+1-NbLevel*ImagesPerLevel;
%% create the xml file of PCO camera if it does not exist
Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']);
if ~exist(Newxml,'file')
    XmlInput.Camera.CameraName='PCO';
    XmlInput.Camera.TimeUnit='s';
    XmlInput.Camera.BurstTiming.FrameFrequency=1;
   % XmlInput.Camera.BurstTiming.Time=-1;% for 180
   XmlInput.Camera.BurstTiming.Time=0;% for 200
    XmlInput.Camera.BurstTiming.Dtj=Dtj;
    XmlInput.Camera.BurstTiming.NbDtj=Nbj-1;
    XmlInput.Camera.BurstTiming.Dti=Dti;
    XmlInput.Camera.BurstTiming.NbDti=NbLevel-1;
    XmlInput.Camera.BurstTiming.Dtk=TimeReturn;
    XmlInput.Camera.BurstTiming.NbDtk=NbScan-1;
    %XmlInput=rmfield(XmlInput,'Time');
    %XmlInput=rmfield(XmlInput,'TimeUnit');
    t=struct2xml(XmlInput);
    t=set(t,1,'name','ImaDoc');
    save(t,Newxml);
end

%% Main loop


% count=0;
%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1
%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images
%% loop on the files
% include the first tiff file with no index in the first iteration
if Param.IndexRange.first_i==1% first slice of processing
    firstindex=0;
    count=0;
else
    firstindex=Param.IndexRange.first_i;
    ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif');
    NbFrames=numel(imfinfo(ImageName));
    count=Param.IndexRange.first_i*NbFrames;
end
for ifile=firstindex:Param.IndexRange.last_i
    if firstindex==0 && ifile==0% first slice of processing
        ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif')
    else
        ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif'])
    end
    NbFrames=numel(imfinfo(ImageName));
    for iframe=1:NbFrames
        iframe% = frame number inside a tif multimage
        checkkeep=1;
        count=count+1;
        if count<count0
            checkkeep=0;
        else
            countnew=count-count0+1;         
            if countnew<=ImagesPerLevel*NbLevel % first scan of 11 levels
                i_index=fix((countnew-1)/ImagesPerLevel)+1;
                j_index=mod(countnew-1,ImagesPerLevel)+1;
            elseif countnew<=NbReturn%skip 400 images during return
                checkkeep=0;
            elseif countnew<=NbReturn+ImagesPerLevel*NbLevel % =5930 second scan
                i_index=fix((countnew-NbSkipReturn)/ImagesPerLevel)+1;
                j_index=mod(countnew-NbSkipReturn,ImagesPerLevel)+1;
            elseif countnew<=2*NbReturn %skip images during second return, from 2763 to 3167
                checkkeep=0;
            elseif countnew<=2*NbReturn+ImagesPerLevel*NbLevel % =5930 third scan
                i_index=fix((countnew-2*NbSkipReturn)/ImagesPerLevel)+1;
                j_index=mod(countnew-2*NbSkipReturn,ImagesPerLevel)+1;
            end
        end
        if checkkeep
            if j_index>Nbj
                OutputFile='';
            else
                OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
            end
            if ~isempty(OutputFile)
                if Param.CheckOverwrite ||~exist(OutputFile,'file')
                    A=imread(ImageName,iframe);
                    imwrite(A,OutputFile,'BitDepth',16);
                    disp([OutputFile ' written'])
                else
                    disp([OutputFile ' already exists'])
                end
            end
%         else
%             OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
        end
    end
end



