bfGetPlaneAtZCT.m

function [I,idx] = bfGetPlaneAtZCT( r, z, c, t, varargin )
%bfGetPlaneAtCZT Obtains an image plane for the Z, C, T
%
%   I = bfGetPlaneAtZCT(r, z, c, t) returns a specified plane from the input
%   format reader. The indices specifying the plane to retrieve should be
%   contained between 1 and the number of planes for each dimesnion.
%
%   I = bfGetPlaneAtZCT(r, z, c, t, ...) does as above but passes extra
%   arguments to bfGetPlane for tiling, etc.
%
% Examples
%
%    r = bfGetReader('example.tif');
%    I = bfGetPlaneAtZCT(r, 1, 1, 1) % First plane of the series
%    I = bfGetPlaneAtZCT(r,r.getSizeZ(),r.getSizeC(),r.getSizeT()) % Last plane of the series
%    I = bfGetPlaneAtZCT(r, 1, 1, 1, 1, 1, 1, 20, 20) % 20x20 tile originated at (0, 0)
%
% See also: BFGETREADER, BFGETPLANE, loci.formats.IFormatReader.getIndex

% OME Bio-Formats package for reading and converting biological file formats.
%
% Copyright (C) 2012 - 2017 Open Microscopy Environment:
%   - Board of Regents of the University of Wisconsin-Madison
%   - Glencoe Software, Inc.
%   - University of Dundee
%
% This program 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.
%
% This program 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 for more details.
%
% You should have received a copy of the GNU General Public License along
% with this program; if not, write to the Free Software Foundation, Inc.,
% 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.

% Input check
ip = inputParser;
isValidReader = @(x) isa(x, 'loci.formats.IFormatReader') && ...
    ~isempty(x.getCurrentFile());
ip.addRequired('r', isValidReader);
ip.parse(r);

ip = inputParser;
% No validation because we already checked
% Kept for positional errors
ip.addRequired('r');

% Check ZCT coordinates are within range
ip.addOptional('z',1,@(x) bfTestInRange(x,'z',r.getSizeZ()));
ip.addOptional('c',1,@(x) bfTestInRange(x,'c',r.getSizeC()));
ip.addOptional('t',1,@(x) bfTestInRange(x,'t',r.getSizeT()));

ip.parse(r, z, c, t);

javaIndex = r.getIndex(z-1, c-1, t-1);
I = bfGetPlane(r, javaIndex+1);

end