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Merge pull request #3444 from mkitti/develop_matlab_bfGetPlaneAtZCT
MATLAB: Add function bfGetPlaneAtZCT.m and improve range checking for bfGetPlane
2 parents 02b3305 + 5e2382e commit 0544530

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3 files changed

+122
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‎components/formats-gpl/matlab/bfGetPlane.m‎

Lines changed: 8 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -49,25 +49,20 @@
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ip.parse(r);
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% Plane check
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isValidPlane = @(x) isscalar(x) && ismember(x, 1 : r.getImageCount());
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isValidPlane = @(p) bfTestInRange(p,'iPlane',r.getImageCount());
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% Optional tile arguments check
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isValidX = @(x) isscalar(x) && ismember(x, 1 : r.getSizeX());
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isValidY = @(x) isscalar(x) && ismember(x, 1 : r.getSizeY());
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isValidX = @(x) bfTestInRange(x,'x',r.getSizeX());
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isValidY = @(y) bfTestInRange(y,'y',r.getSizeY());
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isValidWidth = @(w) bfTestInRange(w,'width',r.getSizeX()-varargin{2}+1);
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isValidHeight = @(h) bfTestInRange(h,'height',r.getSizeY()-varargin{3}+1);
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ip.addRequired('iPlane', isValidPlane);
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ip.addOptional('x', 1, isValidX);
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ip.addOptional('y', 1, isValidY);
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ip.addOptional('width', r.getSizeX(), isValidX);
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ip.addOptional('height', r.getSizeY(), isValidY);
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ip.addOptional('width', r.getSizeX(), isValidWidth);
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ip.addOptional('height', r.getSizeY(), isValidHeight);
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ip.parse(r, varargin{:});
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% Additional check for tile size
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assert(ip.Results.x - 1 + ip.Results.width <= r.getSizeX(),...
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'MATLAB:InputParser:ArgumentFailedValidation',...
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'Invalid tile size');
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assert(ip.Results.y - 1 + ip.Results.height <= r.getSizeY(),...
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'MATLAB:InputParser:ArgumentFailedValidation',...
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'Invalid tile size');
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% Get pixel type
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pixelType = r.getPixelType();
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bpp = javaMethod('getBytesPerPixel', 'loci.formats.FormatTools', pixelType);

‎components/formats-gpl/matlab/bfGetPlaneAtZCT.m‎

Lines changed: 63 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
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function [I,idx] = bfGetPlaneAtZCT( r, z, c, t, varargin )
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%bfGetPlaneAtCZT Obtains an image plane for the Z, C, T
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%
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% I = bfGetPlaneAtZCT(r, z, c, t) returns a specified plane from the input
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% format reader. The indices specifying the plane to retrieve should be
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% contained between 1 and the number of planes for each dimesnion.
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%
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% I = bfGetPlaneAtZCT(r, z, c, t, ...) does as above but passes extra
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% arguments to bfGetPlane for tiling, etc.
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%
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% Examples
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%
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% r = bfGetReader('example.tif');
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% I = bfGetPlaneAtZCT(r, 1, 1, 1) % First plane of the series
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% I = bfGetPlaneAtZCT(r,r.getSizeZ(),r.getSizeC(),r.getSizeT()) % Last plane of the series
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% I = bfGetPlaneAtZCT(r, 1, 1, 1, 1, 1, 1, 20, 20) % 20x20 tile originated at (0, 0)
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%
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% See also: BFGETREADER, BFGETPLANE, loci.formats.IFormatReader.getIndex
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% OME Bio-Formats package for reading and converting biological file formats.
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%
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% Copyright (C) 2012 - 2017 Open Microscopy Environment:
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% - Board of Regents of the University of Wisconsin-Madison
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% - Glencoe Software, Inc.
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% - University of Dundee
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as
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% published by the Free Software Foundation, either version 2 of the
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% License, or (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License along
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% with this program; if not, write to the Free Software Foundation, Inc.,
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% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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% Input check
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ip = inputParser;
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isValidReader = @(x) isa(x, 'loci.formats.IFormatReader') && ...
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~isempty(x.getCurrentFile());
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ip.addRequired('r', isValidReader);
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ip.parse(r);
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ip = inputParser;
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% No validation because we already checked
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% Kept for positional errors
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ip.addRequired('r');
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% Check ZCT coordinates are within range
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ip.addOptional('z',1,@(x) bfTestInRange(x,'z',r.getSizeZ()));
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ip.addOptional('c',1,@(x) bfTestInRange(x,'c',r.getSizeC()));
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ip.addOptional('t',1,@(x) bfTestInRange(x,'t',r.getSizeT()));
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ip.parse(r, z, c, t);
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javaIndex = r.getIndex(z-1, c-1, t-1);
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I = bfGetPlane(r, javaIndex+1);
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end

‎components/formats-gpl/matlab/bfTestInRange.m‎

Lines changed: 51 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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function test = bfTestInRange(x,name,maxValue)
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%bfTestInRange A validation function that tests if the argument
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% is scalar integer between 1 and maxValue
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%
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% This should be faster than ismember(x, 1:maxValue) while also producing
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% more readable errors.
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% OME Bio-Formats package for reading and converting biological file formats.
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%
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% Copyright (C) 2012 - 2017 Open Microscopy Environment:
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% - Board of Regents of the University of Wisconsin-Madison
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% - Glencoe Software, Inc.
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% - University of Dundee
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%
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% This program is free software: you can redistribute it and/or modify
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% it under the terms of the GNU General Public License as
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% published by the Free Software Foundation, either version 2 of the
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% License, or (at your option) any later version.
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%
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% This program is distributed in the hope that it will be useful,
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% but WITHOUT ANY WARRANTY; without even the implied warranty of
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% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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% GNU General Public License for more details.
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%
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% You should have received a copy of the GNU General Public License along
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% with this program; if not, write to the Free Software Foundation, Inc.,
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% 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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% Check to see if x is a single value
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test = isscalar(x);
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if(~test)
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error('bfTestInRange:notScalar', ...
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[name ' value, [' num2str(x) '], is not scalar']);
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end
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% Check to see if x is a whole number
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test = mod(x,1) == 0;
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if(~test)
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error('bfTestInRange:notAnInteger', ...
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[name ' value, ' num2str(x) ', is not an integer']);
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end
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% Check to see if x is between 1 and maxValue
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test = x >= 1 && x <= maxValue;
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if(~test)
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error('bfTestInRange:notInSequence', ...
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[name ' value, ' num2str(x) ', is not between 1 and ', ...
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num2str(maxValue)]);
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end
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end

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