function [ dataset, metadata, success, errMessage ] = loadGeneric( fileName, seriesNumber, metadataOnly )
% loadGeneric tries to recognize and load any supported file format
%
% You should call this function within a try ... catch block.
%
% SYNOPSIS   dataset = loadGeneric( filename )
%
% INPUT      filename: String containing the full name with path
%            seriesNumber: (optional), default: []. In case of files with
%                          more than one series, specify which one to read.
%                          The first series has number = 1!
%                          If seriesNumber is [], a dialog will pop up with
%                          the choice of the series to pick.
%            metadataOnly: {0|1}, default: 0. If 1, only the metadata is
%                          returned
%
% OUTPUT     dataset :   cell array dataset{ timepoints, channels } with
%                        all stacks
%            metadata:   structure containing selected metadata extracted 
%                        from the OME XML metadata
%            success   : 1 if success, 0 otherwise.
%            errMessage: in case the bio-formats library fails reading
%                        file,  excMessage contains the text of the thrown
%                        exception.
%
% Aaron Ponti, 2009/10/15
%              2013/01/24: Changes to be compatible with loci_tools 4.4.4
%                          Extended metadata reading

%--------------------------------------------------------------------------
%
%   The contents of this file are subject to the Mozilla Public License
%   Version 1.1 (the "License"); you may not use this file except in
%   compliance with the License. You may obtain a copy of the License at
%   http://www.mozilla.org/MPL/
%
%   Software distributed under the License is distributed on an "AS IS"
%   basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
%   License for the specific language governing rights and limitations
%   under the License.
%
%   The Original Code is "Qu for MATLAB".
%
%   The Initial Developer of the Original Code is Aaron Ponti.
%   All Rights Reserved.
%
%--------------------------------------------------------------------------

import loci.formats.*;
import loci.formats.FormatTools;
import loci.formats.MetadataTools.*;
import ij.ImagePlus;

% Initialize success to 0
success = 0;

% Check inputs
switch nargin
    case 1,
        seriesNumber = [];
        metadataOnly = 0;
    case 2,
        metadataOnly = 0;
    case 3,
        % All set
    otherwise
        error( '1, 2 or 3 input parameters expected.' );
end

% Initialize output parameter dataset and metadata
dataset = { }; metadata = [ ]; errMessage = '';

% Create the reader
reader = loci.formats.ChannelSeparator( loci.formats.ChannelFiller( ) );

% Control the handling of files with similar names
% reader = loci.formats.FileStitcher( reader );
% reader.setGroupFiles( false() );

% Add metadata container
reader.setMetadataStore( loci.formats.MetadataTools.createOMEXMLMetadata( ) );
        
% Set the file name
try
    reader.setId( fileName );
catch e
    errMessage = e.message;
    return;
end

% Which series to read?
nSeries = reader.getSeriesCount( );

if nSeries == 1
    seriesNumber = 1;
else
    if isempty(seriesNumber)
        choices = cell(1, nSeries);
        for i = 1 : nSeries
            choices{i} = ['Series ',num2str(i)];
        end
        [s, v] = listdlg('PromptString', 'Select the series to open:',...
            'SelectionMode', 'single', 'ListString', choices);
        if v == 0
            return;
        end
        seriesNumber = s;
    else
        if seriesNumber < 1 || seriesNumber > nSeries
            if nSeries == 1
                errMessage = 'The file contains only one series!';
                return;
            else
                errMessage = ['Please specify a series number between ', ...
                    '1 and ', num2str(nSeries), '!'];
                return;
            end
        end
    end
end

% Make the seriesNumber index 0-based
seriesNumber = seriesNumber - 1;

% Set the reader onto the selected series
reader.setSeries( seriesNumber );

% Get sizes
X = reader.getSizeX( );
Y = reader.getSizeY( );
Z = 25; %reader.getSizeZ( );
C = reader.getSizeC( );
T = reader.getSizeT( );
N = reader.getImageCount( );

% Get the pixel type
pixelType = reader.getPixelType( );

% Is the datatype signed?
isSigned = loci.formats.FormatTools.isSigned( pixelType );

% Endianity
isLittleEndian = reader.isLittleEndian( );

% Bytes per pixel
BytesPerPixel = loci.formats.FormatTools.getBytesPerPixel( pixelType );
switch BytesPerPixel
    case 1,
        datatype = 'uint8';
    case 2,
        datatype = 'uint16';
    case 4,
        % This is 32-bit floating point
        datatype = 'single';
    otherwise,
        errMessage = 'Unsupported data type.';
        return
end

% =========================================================================
%
% Get metadata
%
% =========================================================================

voxelX = reader.getMetadataStore.getPixelsPhysicalSizeX( 0 );
if isempty( voxelX )
    voxelX = 0;
else
    voxelX = voxelX.getValue();
end
voxelY = reader.getMetadataStore.getPixelsPhysicalSizeY( 0 );
if isempty( voxelY )
    voxelY = 0;
else
    voxelY = voxelY.getValue();
end
voxelZ = reader.getMetadataStore.getPixelsPhysicalSizeZ( 0 );
if isempty( voxelZ )
    voxelZ = 0;
else
    voxelZ = voxelZ.getValue();
end
voxels = [ voxelX voxelY voxelZ ];
if all( voxels( voxels ~= 0 ) < 1 )
    voxels = 1000 .* voxels;
end

metadata = struct( ...
    'width',           reader.getSizeX( ), ...
    'height',          reader.getSizeY( ), ...
    'nPlanes',         reader.getSizeZ( ), ...
    'nChannels',       reader.getSizeC( ), ...
    'nTimepoints',     reader.getSizeT( ), ...
    'seriesNumber',    seriesNumber + 1, ... % MATLAB 1-based array
    'nImagesInSeries', reader.getImageCount( ), ...
    'voxelX',          voxels( 1 ), ...
    'voxelY',          voxels( 2 ), ...
    'voxelZ',          voxels( 3 ), ...
    'datatype',        datatype, ...
    'stagePosition',   [ ], ...
    'acquisitionDate', ...
    reader.getMetadataStore( ).getImageAcquisitionDate( 0 ).getValue( ), ...
    'timeInterval',  ...
    double(reader.getMetadataStore( ).getPixelsTimeIncrement( 0 )), ...
    'timestamps',      getTimeStamps(), ...
    'color',           [ ] );

metadata.datatype = datatype;

if metadataOnly == 1
    
    %Close the reader and return here
    reader.close();
    return
    
end

% =========================================================================
%
% Get pixel data
%
% =========================================================================

% Initialize the dataset
dataset = cell( T, C );

% Allocate space for the individual stacks
stack = zeros( [ Y X Z ], datatype );
for t = 1 : T
    for c = 1 : C
        dataset{ t, c } = stack;
    end
end

% Global image counter
n = 0;

% Open a waitbar
if N > 1
    hWaitbar = waitbar( 0, 'Loading ...' );
end

% Go over all images and arrange them by plane, channel and time index
switch char( reader.getDimensionOrder( ) )
    case 'XYZCT',

        for t = 1 : T
            
            for c = 1 : C
                    
                for z = 1 : Z
                    
                    % Load the pixel data
                    arr = loci.common.DataTools.makeDataArray( ...
                        reader.openBytes( n ), ...
                        BytesPerPixel, isSigned, isLittleEndian);

                    
                    % Java does not have explicitly unsigned datatypes
                    if ~isSigned
                        switch class(arr)
                            case 'int8'
                                arr = typecast(arr, 'uint8');
                            case 'int16'
                                arr = typecast(arr, 'uint16');
                            case 'single',
                                % Do nothing
                            otherwise,
                                errMessage = 'Unsupported datatype.';
                                dataset = { }; metadata = [ ];
                                return;
                        end
                    end
                    
                    % Reshape into 2D
                    arr = reshape( arr, [ X Y ] )';
                    
                    % Store the plane
                    dataset{ t, c }( :, :, z ) = arr;
                    
                    % Update the global image counter
                    n = n + 1;
                    
                    if N > 1
                        % Update waitbar
                        waitbar( n / N, hWaitbar );
                    end
                    
                end
                
            end
            
        end

    case 'XYCZT',

        for t = 1 : T
            
            for z = 1 : Z

                for c = 1 : C

                    % Load the pixel data
                    arr = loci.common.DataTools.makeDataArray( ...
                        reader.openBytes( n ), ...
                        BytesPerPixel, isSigned, isLittleEndian);
                    
                    % Java does not have explicitly unsigned datatypes
                    if ~isSigned
                        switch class(arr)
                            case 'int8'
                                arr = typecast(arr, 'uint8');
                            case 'int16'
                                arr = typecast(arr, 'uint16');
                            otherwise,
                                errMessage = 'Unsupported datatype.';
                                dataset = { }; metadata = [ ];
                                return;
                        end
                    end
                    
                    % Reshape into 2D
                    arr = reshape( arr, [ X Y ] )';
                    
                    % Store the plane
                    dataset{ t, c }( :, :, z ) = arr;
                    
                    % Update the global image counter
                    n = n + 1;
                    
                    if N > 1
                        % Update waitbar
                        waitbar( n / N, hWaitbar );
                    end
                    
                end
                
            end
            
        end

    case 'XYZTC',

        for c = 1 : C
            
            for t = 1 : T
            
                for z = 1 : Z

                    % Load the pixel data
                    arr = loci.common.DataTools.makeDataArray( ...
                        reader.openBytes( n ), ...
                        BytesPerPixel, isSigned, isLittleEndian);
                    
                    % Java does not have explicitly unsigned datatypes
                    if ~isSigned
                        switch class(arr)
                            case 'int8'
                                arr = typecast(arr, 'uint8');
                            case 'int16'
                                arr = typecast(arr, 'uint16');
                            otherwise,
                                errMessage = 'Unsupported datatype,';
                                dataset = { }; metadata = [ ];
                                return;
                        end
                    end
                    
                    % Reshape into 2D
                    arr = reshape( arr, [ X Y ] )';

                    % Store the plane
                    dataset{ t, c }( :, :, z ) = arr;

                    % Update the global image counter
                    n = n + 1;
                    
                    if N > 1
                        % Update waitbar
                        waitbar( n / N, hWaitbar );
                    end
                    
                end
                
            end
            
        end
        
    otherwise,
        
        errMessage = [ 'Dimension order (', ...
            char( reader.getDimensionOrder( ) ), ') not supported.' ];
        dataset = { }; metadata = [ ];
        return
end

if N > 1
    % Close waitbar
    close( hWaitbar );
end

% =========================================================================
%
% Convert if necessary
%
% =========================================================================

if isa( dataset{ 1, 1 }, 'single' )
    mx = -Inf;
    for i = 1 : T
        for j = C
            nmx = max( dataset{ T, C }( : ) );
            if nmx > mx
                mx = nmx;
            end
        end
    end

    newDatatype = 'uint16';
    msg = [ 'The dataset is in 32-bit floating format, which is not ', ...
        'supported by Qu. '; ];
    if nmx > 2 ^ 16
        msg = [ msg, 'Since the maximum intensity is above 2^16, the ', ...
            'highest intensities will saturate. ' ];
    else
        if nmx < 255
            newDatatype = 'uint8';
            msg = [ msg, 'Since the maximum intensity falls into the 8 ', ...
                'bit range, the dataset can be safely converted to 8 bit ', ...
                '(with just a minor loss of precision due to rounding). ' ];
        else
            msg = [ msg, 'Since the maximum intensity falls into the 16 ', ...
                'bit range, the dataset can be safely converted to 16 bit ', ...
                '(with just a minor loss of precision due to rounding). ' ];
        end
    end
    msg = [ msg, 'Do you want to proceed?' ];

    choice = questdlg( msg, 'Qu :: Question', 'Yes', 'No', 'Yes' );
    switch choice,
        case 'Yes',
            for i = 1 : T
                for j = 1 : C
                    dataset{ i, j } = cast( dataset{ i, j }, newDatatype );
                end
            end
        otherwise,
            dataset = { };
            metadata = [ ];
            return;
   end % switch

end

% Close the reader
reader.close();

% Set success to 1
success = 1;

% Functions

% Extract the time stamps for all timepoints
    function timestamps = getTimeStamps()
        
        % Get the series metadata (Java) hash table and its keys
        table = reader.getSeriesMetadata();

        % Number of time stamps to retrieve
        nTimepoints = reader.getSizeT();
        
        % Allocate space to store the time stamps
        timestamps = zeros(1, nTimepoints);
        
        % Iterate over the keys and get the values
        for tp = 1 : nTimepoints

            try
                timestamps(tp) = table.get(['timestamp ', num2str(tp - 1)]); 
            catch e
                timestamps(tp) = NaN;
            end
            
        end

    end

end