cutPatchesFromROI.m

function [patches, measureSegChannel] = cutPatchesFromROI(roiShapes, channels, channelsToFetch, pixels, thisROI, zctStack, thisT)
global session;

measureSegChannel = 1;


for thisFetchChannel = channelsToFetch
    %for thisROI = 1:numROI
    
    % Copyright (C) 2013-2014 University of Dundee & Open Microscopy Environment.
    % 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.
    numZ = roiShapes{thisROI}.numShapes;
    timePoints = getROITimePoints(roiShapes{thisROI});
    thisPatch = 1;
    X = floor(roiShapes{thisROI}.shape1.getX.getValue+1);    %svg entry in xml file indexes from (0, 0) instead of (1, 1), so +1
    Y = floor(roiShapes{thisROI}.shape1.getY.getValue+1);
    width = int32(roiShapes{thisROI}.shape1.getWidth.getValue);
    height = int32(roiShapes{thisROI}.shape1.getHeight.getValue);
    %Check to see if there's a tranform (translate) on the shape and
    %modify the XY coords
    transformCheck = roiShapes{thisROI}.shape1.getTransform;
    if isempty(transformCheck)
        transform = 'none';
    else
        transform = char(roiShapes{thisROI}.shape1.getTransform.getValue.getBytes');
    end
    
    if ~strcmp(transform, 'none') || ~isempty(transform)
        if strncmp(transform, 'trans', 5)
            closeBracket = findstr(transform, ')');
            openBracket = findstr(transform, '(');
            transformData = transform(openBracket+1:closeBracket-1);
            spaceChar = findstr(transformData, ' ');
            if isempty(spaceChar)
                firstTranslate = str2double(transformData(1:end));
                secondTranslate = 0;
            else
                firstTranslate = str2double(transformData(1:spaceChar-1));
                secondTranslate = str2double(transformData(spaceChar+1:end));
            end
            X = X + firstTranslate;
            Y = Y + secondTranslate;
        end
        if strncmp(transform, 'matrix', 6)
            closeBracket = findstr(transform, ')');
            openBracket = findstr(transform, '(');
            transformData = transform(openBracket+1:closeBracket-1);
            spaceChars = findstr(transformData, ' ');
            firstPart = transformData(1:spaceChars(1)-1);
            secondPart = transformData(spaceChars(1)+1:spaceChars(2)-1);
            thirdPart = transformData(spaceChars(2)+1:spaceChars(3)-1);
            fourthPart = transformData(spaceChars(3)+1:spaceChars(4)-1);
            fifthPart = transformData(spaceChars(4)+1:spaceChars(5)-1);
            sixthPart = transformData(spaceChars(5)+1:end);
            
            transX = str2double(fifthPart);
            transY = str2double(sixthPart);
            X = X + transX;
            Y = Y + transY;
        end
    end
    maxX = pixels.getSizeX.getValue;
    maxY = pixels.getSizeY.getValue;
    pixelsId = pixels.getId.getValue;
    imageId = pixels.getImage.getId.getValue;
    
    for thisZ = 1:numZ
        %for thisT = 1
            thisPlane = zctStack(:,:,roiShapes{thisROI}.(['shape' num2str(thisZ)]).getTheZ.getValue+1,thisFetchChannel,thisT);
            %thisPlane = getPlane(session, imageId, roiShapes{thisROI}.(['shape' num2str(thisZ)]).getTheZ.getValue, thisFetchChannel-1, roiShapes{thisROI}.(['shape' num2str(thisZ)]).getTheT.getValue);
            patch(:,:, thisPatch) = zeros(height,width);
            
            %Check for the ROI going outwith the image. If it does
            %the patch will be contructed pixel by pixel. Otherwise
            %it can be done with a quick matrix operation.
            ROIEndX = X+width;
            ROIEndY = Y+height;
            if ROIEndX > maxX || ROIEndY > maxY || X < 0 || Y < 0
                cropPatch = 1;
            else
                cropPatch = 0;
            end
            
            if cropPatch == 1
                if X < 1
                    X = 1;
                end
                if Y < 1
                    Y = 1;
                end
                for col = 1:width
                    posX = col+X-1;
                    if posX > maxX  %If the ROI was drawn to extend off the image, set the crop to the edge of the image only.
                        posX = maxX;
                    end
                    for row = 1:height
                        posY = row+Y-1;
                        if posY > maxY
                            posY = maxY;
                        end
                        patch(row, col, thisPatch) = thisPlane(posY, posX);
                    end
                end
            else
                posX = floor(X+width-1);
                posY = floor(Y+height-1);
                patch(:,:,thisPatch) = thisPlane(Y:posY,X:posX);
            end
            thisPatch = thisPatch + 1;
            patches{thisFetchChannel} = patch;
            
        %end %for thisT = 1
    end
    patch = [];
    
end
end