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SiBoRG/analysis/analyze_ROI.m
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analyze_ROI.m
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% ANALYZE_ROI parses the ImageJ/Fiji ROIs to compute the requested
% properties and return the corresponding path.
%
% [PROPS, PATHS] = ANALYZE_ROI(ROIs, TYPES) parses the ROIs to calculate
% the requested TYPES of properties. Available TYPES are
% 'Slice', 'Area', 'Perimeter', 'Centroid', 'BoundingBox',
% and 'PCA'. TYPES are provided as string arguments. PROPS
% is then a NxP matrix with N ROIs and P properties. PATHS
% is a Nx1 cell matrix.
%
% [...] = ANALYZE_ROI(ROIs, RESOL, ...) provides the pixel size to scale the
% properties.
%
% Blanchoud Group, UNIFR
% Simon Blanchoud
% 08/06/2020
function [props, coords] = analyze_ROI(ROIs, varargin)
do_props = false(1,6);
resol = 1;
for i=1:nargin-1
if (isnumeric(varargin{i}))
resol = varargin{i};
elseif (ischar(varargin{i}))
switch varargin{i}
case 'Slice'
do_props(1) = true;
case 'Area'
do_props(2) = true;
case {'Perimeter', 'Length'}
do_props(3) = true;
case 'BoundingBox'
do_props(4) = true;
case 'Centroid'
do_props(5) = true;
case 'PCA'
do_props(6) = true;
otherwise
disp(['Unknown property ''' varargin{i} ''', skipping.']);
end
end
end
nROIs = length(ROIs);
props_indx = cumsum(do_props .* [1 1 1 4 2 4]);
props = NaN(nROIs, props_indx(end));
coords = cell(nROIs, 1);
resol = [resol(:); ones(nROIs - numel(resol), 1)*resol(1)];
for i=1:nROIs
type = ROIs{i}.strType;
if (strncmp(type, 'Line', 4))
pos = ROIs{i}.vnLinePoints([1 2; 3 4]) * resol(i);
elseif (strncmp(type, 'Points', 4))
pos = ROIs{i}.mfCoordinates * resol(i);
else
pos = ROIs{i}.mnCoordinates * resol(i);
end
if (do_props(1))
props(i, 1) = ROIs{i}.nPosition;
end
if (do_props(2) && strncmp(type, 'Polygon', 7))
props(i, props_indx(2)) = polyarea(pos(:,1), pos(:,2));
end
if (do_props(3) && ~strncmp(type, 'Point', 5))
props(i, props_indx(3)) = sum(sqrt(sum(diff(pos).^2, 2)));
end
if (do_props(4))
props(i, props_indx(4)-[3:-1:0]) = [min(pos, [], 1) max(pos, [], 1)];
end
if (do_props(5))
props(i, props_indx(5)-[1 0]) = mean(pos, 1);
end
if (do_props(6))
if (size(pos, 1) > size(pos, 2))
[eig, vect] = pca(pos);
props(i, props_indx(6)-[3:-1:0]) = vect(:).';
end
end
coords{i} = pos;
end
return;
end
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