eventTimerAndCrop.m

function roiShapes = eventTimerAndCrop(theImage, imageId, origImageName, roiShapes, pixels, frames, channelLabels, saveMasks)
%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');
%Process the ROI file for cropping the images and passing the ROI's back to
%selectROIFiles.m

global session;
global progBar;

framesBefore = frames(1);
framesAfter = frames(2);
numROI = length(roiShapes);

maxX = pixels.getSizeX.getValue;
maxY = pixels.getSizeY.getValue;
fullZ = pixels.getSizeZ.getValue;
fullT = pixels.getSizeT.getValue;
numC = pixels.getSizeC.getValue;
pixelsType = char(pixels.getPixelsType.getValue.getValue);
pixelsId = pixels.getId.getValue;
theImage = pixels.getImage;
imageId = theImage.getId.getValue;


%Find the linear indices of the ROI's position on each frame (x,y,t,z).
%Use these indices to map intensity pixels from the original image to the
%new "Events" image. Also gather the 'deltaT' info for the first and last
%frames.

extraTBefore{numROI} = [];
extraTAfter{numROI} = [];
actualT{numROI} = [];
actualZ{numROI} = [];


for thisROI = 1:numROI
    allZ = [];
    allT = [];
    numShapes = roiShapes{thisROI}.numShapes;
    for thisShape = 1:numShapes
        allZ = [allZ roiShapes{thisROI}.(['shape' num2str(thisShape)]).getTheZ.getValue];
        allT = [allT roiShapes{thisROI}.(['shape' num2str(thisShape)]).getTheT.getValue];
    end
    numZ(thisROI) = length(unique(allZ));
    numT(thisROI) = length(unique(allT));
    for thisT = 1:numT(thisROI)
        for thisZ = 1:numZ(thisROI)
            indices{thisROI}{thisT}{thisZ} = [];
        end
    end

    actualZ{thisROI} = unique(allZ); %indices of the Z and T of the original image that this ROI points to.
    actualT{thisROI} = unique(allT);
    %If the user specified, add frames to the start and end of
    %actualT{thisROI}. Don't let it go below 0 or over max T.
    if framesBefore > 0
        minActualT = min(actualT{thisROI});
        newMinActualT = minActualT - framesBefore;
        for newT = newMinActualT:minActualT-1
            if newT <= 0
                continue;
            end
            actualT{thisROI} = [actualT{thisROI} newT];
            extraTBefore{thisROI} = [extraTBefore{thisROI} newT];
        end
    end
    if framesAfter > 0
        maxActualT = max(actualT{thisROI});
        newMaxActualT = maxActualT + framesAfter;
        for newT = maxActualT+1:newMaxActualT
            if newT > fullT
                continue;
            end
            actualT{thisROI} = [actualT{thisROI} newT];
            extraTAfter{thisROI} = [extraTAfter{thisROI} newT];
        end
    end
    extraT{thisROI} = [extraTBefore{thisROI} extraTAfter{thisROI}];
   
    firstPlaneInfo = getPlaneInfo(session, imageId, 0, 0, roiShapes{thisROI}.shape1.getTheT.getValue);
    secondPlaneInfo = getPlaneInfo(session, imageId, 0, 0, roiShapes{thisROI}.(['shape' num2str(numShapes)]).getTheT.getValue);
    firstDeltaT = firstPlaneInfo.getDeltaT.getValue;
    lastDeltaT = secondPlaneInfo.getDeltaT.getValue;
    roiShapes{thisROI}.deltaT = lastDeltaT - firstDeltaT;
    roiShapes{thisROI}.name = [origImageName '_event_' num2str(thisROI)];
    roiShapes{thisROI}.origName = origImageName;
end

%If the user has chosen so, save the mask to the server.

if saveMasks == 1
    store = session.createRawPixelsStore();
    currPlane = 0;
    numPlanes = fullZ * fullT * (numC+1);
    for thisROI = 1:numROI
        for thisT = 1:numT(thisROI)
            for thisZ = 1:numZ(thisROI)
                X = roiShapes{thisROI}.(['shape' num2str(thisT*thisZ)]).getX.getValue + 1;
                Y = roiShapes{thisROI}.(['shape' num2str(thisT*thisZ)]).getY.getValue + 1;
                width = roiShapes{thisROI}.(['shape' num2str(thisT*thisZ)]).getWidth.getValue;
                height = roiShapes{thisROI}.(['shape' num2str(thisT*thisZ)]).getHeight.getValue;
                ROIMaxX = X+width;
                ROIMaxY = Y+height;
                
                if X < 1
                    X = 1;
                end
                if Y < 1
                    Y = 1;
                end
                if ROIMaxX > maxX
                    ROIMaxX = maxX;
                end
                if ROIMaxY > maxY
                    ROIMaxY = maxY;
                end
                indices{thisROI}{thisT}{thisZ}.X = X:ROIMaxX;
                indices{thisROI}{thisT}{thisZ}.Y = Y:ROIMaxY;
            end
        end
    end
    
    
    %Create the new Image on the server so we can upload planes to it.
    %channelLabels = getChannelLabelsFromPixels(pixels);
    channelLabels{end+1} = 1000;
    newImage = createNewImageFromOldPixels(imageId, channelLabels, [origImageName, '_events'], 'uint16');
    newImageId = newImage.getId.getValue;
    newPixels = newImage.getPrimaryPixels;
    newPixelsId = newPixels.getId.getValue;
    store.setPixelsId(newPixelsId, false);
    
    %Make the full image from the ROI patches and send it to the server each
    %completed T at a time.
    pixelsType = char(pixels.getPixelsType().getValue().getValue());
    drawnow;
    for thisT = 1:fullT
        for thisZ = 1:fullZ
            for thisC = 1:numC+1
                newPlane = zeros(maxY, maxX);
                newPlane = setMatrixType(newPlane, pixelsType);
                labelPlane = zeros(maxY, maxX);
                for thisROI = 1:numROI
                    if any(actualT{thisROI}(:) == thisT-1) && any(actualZ{thisROI}(:) == thisZ-1)
                        ROIZ = find(actualZ{thisROI}== thisZ-1);
                        ROIT = find(setdiff(actualT{thisROI}, extraT{thisROI})== thisT);
                        if isempty(ROIT)
                            ROIT = 1;
                            if ismember(thisT, extraTAfter{thisROI})
                                Tdiff = setdiff(actualT{thisROI}, extraT{thisROI});
                                ROIT = length(Tdiff);
                            end
                        end
                        if thisC > numC   %Make the channel to number these events on the image itself.
                            if ~ismember(thisT-1, extraTBefore{thisROI}) && ~ismember(thisT-1, extraTAfter{thisROI}) %Don't put the event number on leading or trailing frames to the ROI.
                                ROIText = num2str(thisROI);
                                lenLabel = length(ROIText);
                                spacer = 0;
                                labelX = roiShapes{thisROI}.(['shape' num2str(ROIT*ROIZ)]).getX.getValue + 1;
                                if labelX <= 0
                                    labelX = 1;
                                end
                                if labelX > (maxX - 14)
                                    labelX = maxX - (lenLabel * 14);
                                end
                                labelY = roiShapes{thisROI}.(['shape' num2str(ROIT*ROIZ)]).getY.getValue + 1;
                                if labelY <= 0
                                    labelY = 1;
                                end
                                if labelY > (maxY - 13)
                                    labelY = maxY - 13;
                                end
                                for thisLabel = 1:lenLabel
                                    labelPlane = numberOverlay(labelPlane, labelX+spacer, labelY, str2double(ROIText(thisLabel)));
                                    spacer = spacer + 7;
                                end
                                newPlane = labelPlane;
                            end
                        else  %Copy the intensity patch from the original image to the new plane;
                            thisPlane = getPlane(session, imageId, thisZ-1, thisC-1, thisT-1);
                            newPlane(indices{thisROI}{ROIT}{ROIZ}.Y,indices{thisROI}{ROIT}{ROIZ}.X) = thisPlane(indices{thisROI}{ROIT}{ROIZ}.Y,indices{thisROI}{ROIT}{ROIZ}.X);
                        end
                        
                    end
                end
                
                planeType = class(newPlane);
                if ~strcmpi(planeType, pixelsType)
                    newPlane = setMatrixType(newPlane, pixelsType);
                end
                planeAsBytes = toByteArray(newPlane', pixels);
                store.setPlane(planeAsBytes, thisZ-1, thisC-1, thisT-1);
                drawnow;
                currPlane = currPlane + 1;
                waitbar(currPlane/numPlanes, progBar);
            end
        end
    end
    store.save();
    store.close();
    %Now make the channel to number these events on the image itself
    
    %Set the new image's start and end display values the same as the original.
    %Start by getting the start and end values for each channel
    renderingEngine = session.createRenderingEngine;
    renderingEngine.lookupPixels(pixelsId);
    renderingEngine.lookupRenderingDef(pixelsId);
    renderingEngine.load();
    for thisC = 1:numC
        channelStart(thisC) = renderingEngine.getChannelWindowStart(thisC-1);
        channelEnd(thisC) = renderingEngine.getChannelWindowEnd(thisC-1);
    end
    renderingEngine.close();
    
    %Now load the rendersettings for the new image and apply the settings.
    renderingEngine = session.createRenderingEngine;
    renderingEngine.lookupPixels(newPixelsId);
    renderingEngine.resetDefaultSettings(1);
    renderingEngine.lookupRenderingDef(newPixelsId);
    renderingEngine.load();
    for thisC = 1:numC
        renderingEngine.setActive(thisC-1,1);
        renderingEngine.setChannelWindow(thisC-1, channelStart(thisC), channelEnd(thisC));
    end
    pixServiceDescription = session.getPixelsService.retrievePixDescription(newPixelsId).getChannel(thisC).getLogicalChannel();
    pixServiceDescription.setName(omero.rtypes.rstring('Events'));
    iUpdate = session.getUpdateService();
    iUpdate.saveObject(pixServiceDescription);
    renderingEngine.setRGBA(thisC,255,255,255,200); %Set the label channel to grey, alpha 200;
    renderingEngine.saveCurrentSettings;
    renderingEngine.close();
    
    
    % Retrieve all datasets linked to image
    queryService = session.getQueryService();
    links = queryService.findAllByQuery(['select link from DatasetImageLink as link where link.child.id = ', num2str(imageId)], []);
    links = toMatlabList(links);
    datasetId = links(1).getParent().getId().getValue();
    
    % Link creation
    newLink = omero.model.DatasetImageLinkI();
    newLink.setParent(omero.model.DatasetI(datasetId, false));
    newLink.setChild(omero.model.ImageI(newImageId, false));
    session.getUpdateService().saveObject(newLink);
    
end