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readEllipseROIs.m
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readEllipseROIs.m
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function [roiIdx roishapeIdx xmlStruct] = readEllipseROIs(roifile)
%Point this to an ROI file to read out the ROI and ROIShapes in it. Will
%return roiIdx containing the indexes of the true ROIs and the T, Z, X, Y,
%Width and Height information for each ROI Shape withing each ROI.
%
%Author Michael Porter
% Copyright (C) 2009-2014 University of Dundee.
% All rights reserved.
%
% 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.
%[filename filepath] = uigetfile('*.xml');
%Read the ROI xml file into a Matlab struct
xmlStruct = xml2struct(roifile);
%Get the ROI elements from the struct and store their index in roiIdx. Use
%these to get the roiShapes from the struct too.
roiIdx = [];
thisroishapeIdx = [];
counter = 1;
for i = 1:length(xmlStruct.children)
if strcmpi(xmlStruct.children(i).name, 'roi')
roiIdx = [roiIdx i];
numROIShapes = length(xmlStruct.children(i).children);
for j = 1:numROIShapes
if strcmpi(xmlStruct.children(i).children(j).name, 'roishape')
thisroishapeIdx = [thisroishapeIdx j];
end
end
roishapeIdx{counter}.R = thisroishapeIdx;
counter = counter + 1;
thisroishapeIdx = [];
end
end
%For each roishape fetch out the Z and T information and store it in the
%same struct as the roishape.R (R = ROI) index. Then dig deeper and get the
%svg data for the x and y centres of the ROI, and the width and
%height. Since this is ellipse we also need the angle of rotation and the
%name of the ROI.
thisroishapeT = [];
thisroishapeZ = [];
thisroishapeX = [];
thisroishapeY = [];
thisroishapeWidth = [];
thisroishapeHeight = [];
for thisROIIdx = 1:length(roishapeIdx)
for thisROIShapeIdx = 1:length(roishapeIdx{thisROIIdx}.R)
thisroishapeT = [thisroishapeT str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).attributes(1).value)];
thisroishapeZ = [thisroishapeZ str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).attributes(2).value)];
%Check if the ROI is an ellipse and get the rotation angle from the
%transform if it exists. From the SVG section of the xml.
for thisSVG = 1:length(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children)
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).name, 'svg')
for thisShape = 1:length(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).children)
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).children(thisShape).name, 'ellipse')
roishapeIdx{thisROIIdx}.shape = 'ellipse';
for thisShapeAttr = 1:length(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).children(thisShape).attributes)
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).children(thisShape).attributes(thisShapeAttr).name, 'transform')
thisroishapeTransformMatrix = xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(thisSVG).children(thisShape).attributes(thisShapeAttr).value;
partText = thisroishapeTransformMatrix(8:end);
[firstPart theRest] = strtok(partText);
if str2double(firstPart) >0 && str2double(firstPart) <1
rotAngle = acosd(str2double(firstPart)); %Get the angle in degress by taking the inverse cos (acosd) of the first part of the transformation matrix.
continue;
else
[firstPart theRest] = strtok(theRest);
if str2double(firstPart) >0 && str2double(firstPart) <1
rotAngle = asind(str2double(firstPart)); %Get the angle in degress by taking the inverse sin (asind) of the second part of the transformation matrix.
continue;
else
[firstPart theRest] = strtok(theRest);
if str2double(firstPart) >0 && str2double(firstPart) <1
rotAngle = -asind(str2double(firstPart)); %Get the angle in degress by taking the negative inverse sin (-asind) of the third part of the transformation matrix.
continue;
else
[firstPart theRest] = strtok(theRest, ')');
if str2double(firstPart) >0 && str2double(firstPart) <1
rotAngle = acosd(str2double(firstPart)); %Get the angle in degress by taking the inverse cos (acosd) of the forth part of the transformation matrix.
continue;
end
end
end
end
end
end
end
end
end
end
%Find the name of the ROI and the cx, cy etc. from the Annotation section of the xml.
for this3rdGen = 1:length(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children)
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).name, 'annotation')
for thisAnnotation = 1:length(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children)
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).name, 'basicTextAnnotation')
thisroishapeName = xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).attributes(2).value;
if ~strcmp(thisroishapeName, ' ')
roishapeIdx{thisROIIdx}.ROIName = thisroishapeName;
end
end
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).name, 'measurementCentreX')
thisroishapeX = str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).attributes(2).value);
end
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).name, 'measurementCentreY')
thisroishapeY = str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).attributes(2).value);
end
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).name, 'measurementWidth')
thisroishapeWidth = str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).attributes(2).value);
end
if strcmpi(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).name, 'measurementHeight')
thisroishapeHeight = str2double(xmlStruct.children(roiIdx(thisROIIdx)).children(roishapeIdx{thisROIIdx}.R(thisROIShapeIdx)).children(this3rdGen).children(thisAnnotation).attributes(2).value);
end
end
end
end
roishapeIdx{thisROIIdx}.T(thisROIShapeIdx) = thisroishapeT;
roishapeIdx{thisROIIdx}.Z(thisROIShapeIdx) = thisroishapeZ;
roishapeIdx{thisROIIdx}.X(thisROIShapeIdx) = thisroishapeX;
roishapeIdx{thisROIIdx}.Y(thisROIShapeIdx) = thisroishapeY;
roishapeIdx{thisROIIdx}.Width(thisROIShapeIdx) = thisroishapeWidth;
roishapeIdx{thisROIIdx}.Height(thisROIShapeIdx) = thisroishapeHeight;
if exist('rotAngle') %If the ellipse is circular then there may be no transform matrix and therefore no rotAngle. Insert a zero.
roishapeIdx{thisROIIdx}.Angle(thisROIShapeIdx) = rotAngle;
else
roishapeIdx{thisROIIdx}.Angle(thisROIShapeIdx) = 0;
end
thisroishapeT = [];
thisroishapeZ = [];
thisroishapeX = [];
thisroishapeY = [];
thisroishapeWidth = [];
thisroishapeHeight = [];
end
end
end