masiv.m

classdef masiv < handle
    % masiv
    %
    % MaSIV is a MATLAB-based viewer for very large 3D image stacks
    % https://github.com/alexanderbrown/masiv


    properties(Access=protected, Hidden)        
        %% Internal tracking
        numScrolls=0
        panxInt=0
        panyInt=0
        %% open plugin windows that override close requests
        openPluginsOverridingCloseReq={}
    end %protected properties

    
    properties
        %% Handles to visible objects
        hFig
        hMainImgAx
        hAxContrastHist
        hAxContrastMin
        hAxContrastMax
        hjSliderContrast
        hAxContrastAuto
        
        infoPanels
        
        %% Menus
        mnuMain
        mnuImage
        mnuPlugins
        mnuTutPlugins

        %% Data
        Meta      
        MainStack 
        mainDisplay
        additionalDisplays
        contrastMode=0
        dragOrigin=NaN 
    end %properties

    
    events
        CacheChanged
        ViewChanged
        Scrolled
        Panned
        Zoomed
        CursorPositionChangedWithinImageAxes
        CursorPositionChangedOutsideImageAxes
        ViewClicked
        KeyPress
        ViewerClosing
    end %events
   

    methods
        function obj=masiv(MetaIn, idx)
            % Constructor
            obj=obj@handle; % base class initialisation
            
            startDebugOutput;
            runStartupTests;
            masiv.utils.setupMaSIV_path
            
            if nargin<1 ||isempty(MetaIn)
                chooseDataset(obj)
                if isempty(obj.Meta)
                    return
                end
            else
                obj.Meta=MetaIn;
            end
            
            if nargin<2||isempty(idx)
                getDownsampledStackChoice(obj)
            else
                obj.MainStack=obj.Meta.masivStacks(idx);
            end
            
            if isempty(obj.MainStack)
                return
            end
            
            setupGUI(obj)
            setupMenus(obj)
            setupPlugins(obj)
            setupContrastController(obj)
            initialiseDisplay(obj)
            setupInfoBoxes(obj)          
            setupResources(obj)
            setupContrast(obj)
            startParallelPool()
            
            %% Show the figure, we're done here!
            obj.hFig.Visible='on';
        end % close constructor


        function delete(obj)
             % Destructor
            notify(obj, 'ViewerClosing')
            delete(obj.MainStack)
            deleteInfoPanel(obj, 'all')
            delete(timerfind);
            if ishandle(obj.hFig)
                masivSetting('viewer.mainFigurePosition', obj.hFig.Position)
                delete(obj.hFig);
            end
        end %destructor

    end %methods
    

    methods(Access=protected)
        
        %% ---Scrolling
        function formatKeyScrollAndAddToQueue(obj, eventdata)
            masivDebugTimingInfo(0, 'masiv: KeyScroll event fired',toc, 's')
            mods=eventdata.Modifier;
            if ~isempty(mods)&& any(~cellfun(@isempty, strfind(mods, 'shift')))
                p=masivSetting('navigation.scrollIncrement');p=p(1);
            else
                p=masivSetting('navigation.scrollIncrement');p=p(2);
            end
            switch eventdata.Key
                case 'leftarrow'
                    obj.keyScrollQueue(-p)
                case 'rightarrow'
                    obj.keyScrollQueue(+p);
            end
        end
        
        function keyScrollQueue(obj, dir)
            masivDebugTimingInfo(0, 'masiv: Scroll queue update beginning',toc, 's')
            obj.numScrolls=obj.numScrolls+dir;
            pause(masivSetting('navigation.keyboardUpdatePeriod'))
            if obj.numScrolls~=0
                p=obj.numScrolls;
                obj.numScrolls=0;
                obj.executeScroll(p,'zAxisScroll')
            end
        end
        
        function executeScroll(obj, nScrolls, scrollAction)
            %nScroll - scalar defining how many wheel clicks the user has produced (signed)
            %scrollAction - string defining which action to take. 

            %Set focus to main axes after a scroll. The UI interaction works better this way.
            %i.e. you can pan without having click on the figure window.
            axes(obj.hMainImgAx); 
            
            switch scrollAction
            case 'zAxisScroll'
                if masivSetting('navigation.scrollLayerInvert')==1
                    nScrolls=nScrolls*-1;
                end

                masivDebugTimingInfo(0, 'masiv:Calling mDisplay.seekZ',toc, 's')
                stdout=obj.mainDisplay.seekZ(nScrolls);
                if stdout
                    for ii=obj.additionalDisplays
                        ii.seekZ(nScrolls);
                    end
                    obj.changeAxes;
                    notify(obj, 'Scrolled')
                else
                    masivDebugTimingInfo(0, 'masiv: Scroll did not cause an axis change',toc, 's')
                end
            case 'zoomScroll'
                zoomRate=masivSetting('navigation.zoomRate'); %to zoom out
                if masivSetting('navigation.scrollZoomInvert')==1
                    nScrolls=nScrolls*-1;
                end
                if nScrolls<0
                    zoomRate=1/zoomRate; %to zoom out
                end
                for ii=1:abs(nScrolls)
                    obj.executeZoom(zoomRate) 
                end
            end
        end 

        
        %% ---Panning
        function formatKeyPanAndAddToQueue(obj, eventdata)
            masivDebugTimingInfo(0, 'masiv: KeyPan event fired',toc, 's')
            mods=eventdata.Modifier;
            if ~isempty(mods)&& any(~cellfun(@isempty, strfind(mods, 'shift')))
                p=masivSetting('navigation.panIncrement'); p=p(1);
            else
                p=masivSetting('navigation.panIncrement');p=p(2);
            end
            switch eventdata.Key
                case 'w'
                    obj.keyPanQueue(0, +range(ylim(obj.hMainImgAx))/p)
                case 'a'
                    obj.keyPanQueue(+range(xlim(obj.hMainImgAx))/p, 0)
                case 's'
                    obj.keyPanQueue(0, -range(ylim(obj.hMainImgAx))/p)
                case 'd'
                    obj.keyPanQueue(-range(xlim(obj.hMainImgAx))/p, 0)
            end
        end
        
        function keyPanQueue(obj, xChange, yChange)
           
            obj.panxInt=obj.panxInt+xChange;
            obj.panyInt=obj.panyInt+yChange;
            pause(masivSetting('navigation.keyboardUpdatePeriod'))
            
            if obj.panxInt~=0 || obj.panyInt~=0
                xOut=obj.panxInt;
                yOut=obj.panyInt;
                obj.panxInt=0;
                obj.panyInt=0;
                obj.executePan(xOut,yOut)
            end
        end
        
        function executePan(obj, xMove,yMove)
            if masivSetting('navigation.panModeInvert')==1
                xMove=-xMove;
                yMove=-yMove;
            end
            
            [xMove, yMove]=obj.checkPanWithinLimits(xMove, yMove);
            movedFlag=0;
            
            if xMove~=0
                newLim=xlim(obj.hMainImgAx)+xMove;
                xlim(obj.hMainImgAx,newLim)
                arrayfun(@(thisAxis) xlim(thisAxis.axes,newLim), obj.additionalDisplays)
                movedFlag=1;
            end
            if yMove~=0
                newLim=ylim(obj.hMainImgAx)+yMove;
                ylim(obj.hMainImgAx,newLim)
                arrayfun(@(thisAxis) ylim(thisAxis.axes,newLim), obj.additionalDisplays)
                movedFlag=1;
            end

            if movedFlag
                obj.changeAxes;
                notify(obj, 'Panned')
            else
                masivDebugTimingInfo(0, 'masiv: Pan did not cause an axis change',toc, 's')
            end
        end

        function [xMove,yMove]=checkPanWithinLimits(obj, xMove,yMove)
            xl=xlim(obj.hMainImgAx);
            yl=ylim(obj.hMainImgAx);

            if xl(1) + xMove < 0
                xMove = -xl(1);
            end
            if yl(1) + yMove < 0
                yMove = -yl(1);
            end
            if xl(2) + xMove > obj.mainDisplay.imageXLimOriginalCoords(2)
                xMove=obj.mainDisplay.imageXLimOriginalCoords(2) - xl(2);
            end
            if yl(2) + yMove > obj.mainDisplay.imageYLimOriginalCoords(2)
                yMove=obj.mainDisplay.imageYLimOriginalCoords(2) - yl(2);
            end
        end

        function pos=updateMouseCoordsInPanel(obj)
            %updates the position of the mouse and the pixel value in the right-hand panel
            C = get (obj.hMainImgAx, 'CurrentPoint');
            xl=xlim(obj.hMainImgAx);
            yl=ylim(obj.hMainImgAx);
            x=C(1, 1);
            y=C(2, 2);
            if x>=xl(1) && x<=xl(2) && y>=yl(1) && y<=yl(2)
                v=getPixelValueAtCoordinate(obj, x, y);
                notify(obj, 'CursorPositionChangedWithinImageAxes', CursorPositionData(C, v));
            else
                notify(obj, 'CursorPositionChangedOutsideImageAxes')
            end

            pos=[x,y];
        end

        %% --- Zooming
        function executeZoom(obj, zoomfactor)
            C = get (obj.hMainImgAx, 'CurrentPoint');
            zoom(obj.hMainImgAx,zoomfactor)
            for ii=obj.additionalDisplays
                zoom(ii.axes, zoomfactor);
            end
            obj.centreView(C);
            obj.changeAxes
            notify(obj, 'Zoomed')

        end
        function moved=centreView(obj, pointToCenterUpon)
            xl=xlim(obj.hMainImgAx);
            yl=ylim(obj.hMainImgAx);
            x=pointToCenterUpon(1, 1);
            y=pointToCenterUpon(2, 2);

            %% Calculate move
            centrePointX=mean(xl);
            centrePointY=mean(yl);

            xMove=round(x-centrePointX);
            yMove=round(y-centrePointY);
            %% Check move is within limits
            [xMove, yMove]=checkPanWithinLimits(obj, xMove, yMove);
            %% Do the move
            xlim(obj.hMainImgAx, xl+xMove);
            ylim(obj.hMainImgAx, yl+yMove);
            for ii=obj.additionalDisplays
                xlim(ii.axes, xl+xMove);
                ylim(ii.axes, yl+yMove);
            end

            if yMove~=0 || xMove~=0
                moved=1;
            else
                moved=0;
            end
        end

        %% ---Update axes
        function changeAxes(obj)
            masivDebugTimingInfo(0, 'masiv: Calling mainDisplay updateZoomedView...',toc, 's')
            obj.mainDisplay.updateZoomedView
            masivDebugTimingInfo(0, 'masiv: mainDisplay updateZoomedView complete',toc, 's')
            for ii=obj.additionalDisplays
                masivDebugTimingInfo(0, 'masiv: Calling additional display updateZoomedView...',toc, 's')
                ii.updateZoomedView
                masivDebugTimingInfo(0, 'masiv: additional display updateZoomedView complete',toc, 's')
            end
            masivDebugTimingInfo(0, 'masiv: Firing ViewChanged Event',toc, 's')
            obj.updateMouseCoordsInPanel;
            notify(obj, 'ViewChanged')
        end

        %% Info Panel Functions
        function addInfoPanel(obj, hPanel)
            if isempty(obj.infoPanels)
                obj.infoPanels={hPanel};
            else
                obj.infoPanels{end+1}=hPanel;
            end
        end

        function deleteInfoPanel(obj, hPanel)
            if ischar(hPanel)&&strcmp(hPanel, 'all')
                obj.deleteInfoPanel(1:numel(obj.infoPanels))
            else
                if isobject(hPanel)&&isscalar(hPanel)
                    idx=ismember(obj.infoPanels, hPanel);
                elseif isnumeric(hPanel)&&isvector(hPanel)
                   idx= hPanel;
                else
                    error('Unrecognised deleted panel specification')
                end
                for ii=1:numel(idx)
                    delete(obj.infoPanels{idx(ii)})
                end
                obj.infoPanels(idx)=[];
            end
        end
    end  %methods(Access=protected)


    methods 
        % Keep track of open plugins that want the viewer to cancel close requests
        function registerOpenPluginForCloseReqs(obj, plg)
            if isempty(obj.getCloseReqRegistrationIndexOfPlugin(plg))
                obj.openPluginsOverridingCloseReq{end+1}=plg;
            end
        end %registerOpenPluginForCloseReqs

        function deregisterOpenPluginForCloseReqs(obj, plg)
            plgIdx=obj.getCloseReqRegistrationIndexOfPlugin(plg);
            if ~isempty(plgIdx)
                obj.openPluginsOverridingCloseReq(plgIdx)=[];
            end
        end %deregisterOpenPluginForCloseReqs

        function idx=getCloseReqRegistrationIndexOfPlugin(obj, plg)
            idx=cellfun(@(x) eq(plg, x), obj.openPluginsOverridingCloseReq);
        end %getCloseReqRegistrationIndexOfPlugin


        function varargout=centreViewOnCoordinate(obj,xPos,yPos)
            % Public method for allowing plugins to centre the image on any desired locaion
            C=zeros(2);
            C(1,1)=xPos;
            C(2,2)=yPos;

            moved=obj.centreView(C);

            if moved
                obj.changeAxes;
                notify(obj, 'Panned')
                fprintf( sprintf('Centred on x=%d y=%d\n', round(xPos), round(yPos)) )
            end

            if nargout>0
                varargout{1}=moved;
            end
        end %centreViewOnCoordinate
    end %methods
    
end %MaSIV


function startDebugOutput
    tic
    clc
end    

%% Callbacks
function hFigMain_KeyPress(~, eventdata, obj)

    startDebugOutput

    %% What shall we do?
    ctrlMod=ismember('control', eventdata.Modifier);
    shiftMod=ismember('shift', eventdata.Modifier);
    if ~ctrlMod
        switch eventdata.Key
            case 'uparrow'
                obj.executeZoom(masivSetting('navigation.zoomRate'))
            case 'downarrow'
                obj.executeZoom(1/masivSetting('navigation.zoomRate'))
            case {'leftarrow', 'rightarrow'}
                obj.formatKeyScrollAndAddToQueue(eventdata);
            case {'w' 'a' 's' 'd'}
                obj.formatKeyPanAndAddToQueue(eventdata);
            case 'c'
                updateContrastHistogram(obj.mainDisplay, obj.hAxContrastHist)

            otherwise
                notify(obj, 'KeyPress', KeyPressEventData(eventdata))
        end
    else
        notify(obj, 'KeyPress', KeyPressEventData(eventdata))
    end
    if shiftMod
        if ~obj.contrastMode
            obj.contrastMode=1;
            obj.hFig.Pointer='custom';
        end
    end
end

function hFigMain_KeyRelease(~, eventdata, obj)
    shiftMod=ismember('shift', eventdata.Modifier);
    if ~shiftMod
        if obj.contrastMode
            obj.contrastMode=0;
            obj.hFig.Pointer='arrow';
        end
    end
end

function hFigMain_BtnDown(~, ~, obj)
    if obj.contrastMode;
        obj.dragOrigin=mouseMove([],[],obj);
    end
end

function hFigMain_BtnUp(~, ~, obj)
    obj.dragOrigin=NaN;
end

function pos=mouseMove(~, ~, obj)
    pos=obj.updateMouseCoordsInPanel;

    if obj.contrastMode && ~any(isnan(obj.dragOrigin))
        %% Contrast
        gain=2;
        delta=pos-obj.dragOrigin;
        delta(1)=delta(1)/range(xlim); % make it relative
        delta(2)=delta(2)/range(ylim);

        m=obj.hjSliderContrast.getLowValue();
        rng=obj.hjSliderContrast.getHighValue-m;
        newVal=obj.hjSliderContrast.getHighValue()+delta(2)*rng*gain; % scales quite nicely

        if newVal>m
            obj.hjSliderContrast.setHighValue(newVal);
        else
            obj.hjSliderContrast.setHighValue(m+0);
        end


        %% Brightness
        bAdj=delta(1)*(obj.hjSliderContrast.maximum-obj.hjSliderContrast.minimum);

        newLow=obj.hjSliderContrast.getLowValue()+bAdj;
        newHigh=obj.hjSliderContrast.getHighValue()+bAdj;

        if newLow<obj.hjSliderContrast.minimum
            newHigh=newHigh+obj.hjSliderContrast.minimum-newLow-1;
            newLow=obj.hjSliderContrast.minimum;
        end

        if newHigh>obj.hjSliderContrast.maximum
            newLow=newLow+obj.hjSliderContrast.maximum-newHigh-1;
            newHigh=obj.hjSliderContrast.maximum;
        end

        obj.hjSliderContrast.setHighValue(newHigh);
        obj.hjSliderContrast.setLowValue(newLow);

        %% Reset
        obj.dragOrigin=pos;
    end

end

function hFigMain_ScrollWheel(~, eventdata, obj)
    startDebugOutput

    masivDebugTimingInfo(0, 'masiv: WheelScroll event fired',toc, 's')

    modifiers = get(obj.hFig,'currentModifier');          
    %If user ctrl-scrolls we zoom instead of change z-level
    if ismember('control',modifiers)    
        obj.executeScroll(eventdata.VerticalScrollCount,'zoomScroll');    
        return
    end

    p=masivSetting('navigation.scrollIncrement');
    if ismember('shift',modifiers);
        p=p(1);
    else
        p=p(2);
    end
    obj.executeScroll(p*eventdata.VerticalScrollCount,'zAxisScroll'); %scroll through z-stack

end

function adjustContrast(~, ~, obj)
    %     if nargin<1
    %         hContrastLim=[];
    %     end
    %     if ~isempty(hContrastLim)&&~all(isstrprop(hContrastLim.String, 'digit')) %it's invalid, use the previous value
    %         if hContrastLim==obj.hAxContrastMin
    %             hContrastLim.String=obj.mainDisplay.contrastLims(1);
    %         elseif hContrastLim==obj.hAxContrastMax
    %             hContrastLim.String=obj.mainDisplay.contrastLims(2);
    %         end
    %     else
    %         obj.mainDisplay.contrastLims=[str2double(obj.hAxContrastMin.String) str2double(obj.hAxContrastMax.String)];
    %     end
    obj.mainDisplay.contrastLims=[obj.hjSliderContrast.getLowValue(), obj.hjSliderContrast.getHighValue()];
end

function closeRequest(~,~,obj)
    if isempty(obj.openPluginsOverridingCloseReq)
        % set contrast limits for this stack
        obj.MainStack.contrastLimits=[get(obj.hjSliderContrast,'Low') get(obj.hjSliderContrast,'High')];
        delete(obj)
    else
        msgbox('One or more plugins are open that require your attention before closing')
    end
end

function changeProcessingSteps(~, ~, obj)
    zvm=obj.mainDisplay.zoomedViewManager;
    newPipeline=setImageProcessingPipeline(zvm.imageProcessingPipeline);
    zvm.imageProcessingPipeline=newPipeline;
    zvm.clearCache;
end

function handleMouseClick(~,~, obj)
    notify(obj, 'ViewClicked');
end

function adjustXYPosClick(caller,~,obj)
    zvm=obj.mainDisplay.zoomedViewManager;
    if isempty(zvm.xyPositionAdjustProfile)
        zProfile=loadXYAlignmentProfile;
        if ~isempty(zProfile)
            zvm.xyPositionAdjustProfile=zProfile;
            caller.Checked='on';
            zvm.clearCache;
        end
    else
        caller.Checked='off';
        zvm.xyPositionAdjustProfile=[];
        zvm.clearCache;
    end
end

%% Utilities
function updateContrastHistogram(dsStack,hContrastHist_Axes)
    data=dsStack.hImg.CData;
    n=hist(double(data(:)), numel(data)/100);n=n/max(n);
    bar(linspace(0, 1, length(n)), n, 'Parent', hContrastHist_Axes, 'FaceColor', [0.8 0.8 0.8])
    hContrastHist_Axes.Color=[0.1 0.1 0.1];
    hold(hContrastHist_Axes, 'on')

    % Overlay fake axes
    line([0 0], [-0.08 1.1], 'Color', [0.8 0.8 0.8],'Parent', hContrastHist_Axes) %y axis
    line([-0.05 0.01], [1 1],  'Color', [0.8 0.8 0.8],'Parent', hContrastHist_Axes) %top y axis tick
    line([1 1], [-0.08 0.001], 'Color', [0.8 0.8 0.8],'Parent', hContrastHist_Axes) %end x tick

    % rectangles cover any funny error pixels
    rectangle('Position', [-0.08 1 2 1], 'FaceColor',[0.1 0.1 0.1], 'EdgeColor', 'none','Parent', hContrastHist_Axes)
    rectangle('Position', [-1.001 -1.001 1 1], 'FaceColor', [0.1 0.1 0.1], 'EdgeColor', 'none','Parent', hContrastHist_Axes)
    rectangle('Position', [1.01 -1.001 1 1], 'FaceColor', [0.1 0.1 0.1],'EdgeColor', 'none','Parent', hContrastHist_Axes)

    % Ovelay limit lines
    %        line(ones(2, 1)*contrastMin, [-0.05 1], 'Parent', hContrastHist_Axes)
    %        line(ones(2, 1)*contrastMax, [-0.05 1], 'Parent', hContrastHist_Axes)
    hold(hContrastHist_Axes, 'off')
    set(hContrastHist_Axes, 'XTick', [], 'XColor', get(0, 'defaultuicontrolbackgroundcolor'))
    set(hContrastHist_Axes, 'YTick', [], 'YColor', get(0, 'defaultuicontrolbackgroundcolor'))
    xlim(hContrastHist_Axes, [-0.05 1.1])
    ylim(hContrastHist_Axes, [-0.1 1.1])
end

function exportViewToWorkspace(~,~,obj)
    if obj.mainDisplay.zoomedViewManager.imageVisible;
        I=obj.mainDisplay.zoomedViewManager.currentImageViewData;
    else
        I=obj.mainDisplay.currentImageViewData;
    end
    xView=round(obj.hMainImgAx.XLim);xView(xView<1)=1;
    yView=round(obj.hMainImgAx.YLim);yView(yView<1)=1;
    proposedImageName=sprintf('%s_%s_x%u_%u_y%u_%u_layer%04u',...
        obj.MainStack.stackName, ...
        obj.MainStack.channel, ...
        xView(1), xView(2), ...
        yView(1), yView(2), ...
        obj.mainDisplay.currentZPlaneOriginalLayerID);

    retry=1;
    while retry
        imageName=inputdlg('Image variable name:', 'Export Image to Base Workspace', 1, {proposedImageName});

        if isempty(imageName)
            return
        else
            imageName=imageName{1};
        end
            varExistsInBase=evalin('base', sprintf('exist(''%s'', ''var'');', imageName));
            if varExistsInBase
                if ~strcmp(questdlg(sprintf('A variable of name\n%s\n already exists. Overwrite?', imageName), ...
                               'Export Image to Base Workspace', 'Yes', 'No', 'No'), 'Yes')
                    continue
                end
            end
            assignin('base',  matlab.lang.makeValidName(imageName), I);
            retry=0;
    end
end

function zProfile=loadXYAlignmentProfile
    [f,p]=uigetfile({'*.zpfl', 'Z-Profile (*.zpfl)'; '*.csv', 'CSV-File (*.csv)'; '*.*', 'All Files (*.*)'}, 'Select Z Profile To Register To', masivSetting('defaultDirectory'));
    pathToCSVFile=fullfile(p,f);
    if exist(pathToCSVFile, 'file')
        zProfile=dlmread(pathToCSVFile);
    else
        zProfile=[];
    end
end

function v=getPixelValueAtCoordinate(obj, x, y)
    zoomedViewStatus=obj.mainDisplay.zoomedViewNeeded &&... %Are we at a zoom level?
                     obj.mainDisplay.zoomedViewManager.currentSliceFileExistsOnDisk && ... %Can we find the file?
                     ~strcmp(obj.mainDisplay.zoomedViewManager.hImg.Visible, 'off'); %Has it been successfully loaded?

    %If despite this there are no image data in the zoomed view, we force ourselves to use the non-zoomed view
    if isfield(obj.mainDisplay.zoomedViewManager.hImg, 'CData')
        if isempty(obj.mainDisplay.zoomedViewManager.hImg.CData)
            v=0;
            masivDebugTimingInfo(0, 'ERROR: masiv.getPixelValueAtCoordinate - zoomed data are missing and should not be',toc, 's')
            zoomedViewStatus=0;
        end
    end

    %Ensure the pixel we are going to index is within range
    if zoomedViewStatus
        [~, xIdx]=min(abs(x-obj.mainDisplay.zoomedViewManager.hImg.XData));
        [~, yIdx]=min(abs(y-obj.mainDisplay.zoomedViewManager.hImg.YData));
        try
            v=obj.mainDisplay.zoomedViewManager.hImg.CData(yIdx, xIdx);
        catch
            v=0;
            msg = sprintf('ERROR in masiv.getPixelValueAtCoordinate - failed to index image of size %dx%d with x=%d and y=%d',...
                size(obj.mainDisplay.zoomedViewManager.hImg.CData), xIdx, yIdx);
            masivDebugTimingInfo(0, msg,toc, 's')            
        end
    else
        [~, xIdx]=min(abs(x-obj.mainDisplay.overviewStack.xCoordsVoxels));
        [~, yIdx]=min(abs(y-obj.mainDisplay.overviewStack.yCoordsVoxels));
        v=obj.mainDisplay.hImg.CData(yIdx, xIdx);
    end
end

function x=roundToSingleSigFig(x)
    lg=log10(abs(x));
    x= round(x/10^floor(lg))*10^floor(lg);
end

function y=roundToClosest(x, n)
    x=int32(x);
    n=int32(n);
    y=idivide(x, n, 'round')*n;
end

function sliderCallback(obj, ~)
    persistent chk
    if isempty(chk)
        chk = 1;
        pause(0.5)
        if chk == 1;
            chk = [];
        end
    else
        currentLims={num2str(obj.getMinimum), num2str(obj.getMaximum)};
        newLims=inputdlg({'Low', 'High'}, 'B/C Scale Limits', 1, currentLims);
        try
            lims=cellfun(@str2num,newLims);
        catch
            return
        end
        if ~isempty(lims)
            setSliderRange(obj, lims);
        end
    end
end

%% Plugins menu creation
function addPlugins(hMenuBase, obj, pluginsDir, separateFirstEntry)
    %Add plugins in a directory to the menu
    if nargin<4||isempty(separateFirstEntry)
        separateFirstEntry=0;
    end

    if ~exist(pluginsDir, 'dir')
        error('plugins directory not found')
    else
        fprintf('Adding plugins in directory %s to menu\n',pluginsDir) 
    end

    filesInPluginsDirectory=dir(fullfile(pluginsDir, '*.m'));
    if isempty(filesInPluginsDirectory)
        fprintf('Found no .m files that could be plugins in directory %s\n',pluginsDir)
        return
    end

    for ii=1:numel(filesInPluginsDirectory)
        if masiv.utils.isValidMasivPlugin(pluginsDir, filesInPluginsDirectory(ii).name)
            [pluginDisplayString, pluginStartCallback]=masiv.utils.getPluginInfo(filesInPluginsDirectory(ii));
            hItem=uimenu(hMenuBase, 'Label', pluginDisplayString, 'Callback', pluginStartCallback, 'UserData', obj);
            if separateFirstEntry && ii==1
                hItem.Separator='on';
            end
        end
    end

    fprintf('Finished adding plugins.\n')
end

%% Constructor functions
function runStartupTests()
    if verLessThan('matlab', '8.4.0')
        error('%s requires MATLAB 2014b or newer',mfilename)
    end
end

function chooseDataset(obj)
    obj.Meta=masivMeta;
    if isempty(obj.Meta.metadata)
        obj.Meta=[];
    end
end

function getDownsampledStackChoice(obj)
    obj.MainStack=selectMasivStack(obj.Meta);
end

function setupGUI(obj)
    obj.hFig=figure(...
                'Name', sprintf('MaSIV: %s', obj.Meta.stackName), ...
                'NumberTItle', 'off', ...
                'MenuBar', 'none', ...
                'Position', masivSetting('viewer.mainFigurePosition'), ...
                'Color', masivSetting('viewer.mainBkgdColor'), ...
                'ColorMap', gray(256), ...
                'KeyPressFcn', {@hFigMain_KeyPress, obj}, ...
                'KeyReleaseFcn', {@hFigMain_KeyRelease, obj}, ...
                'WindowButtonMotionFcn', {@mouseMove, obj}, ...
                'WindowScrollWheelFcn', {@hFigMain_ScrollWheel, obj}, ...
                'WindowButtonDownFcn', {@hFigMain_BtnDown, obj}, ...
                'WindowButtonUpFcn', {@hFigMain_BtnUp, obj}, ...
                'CloseRequestFcn', {@closeRequest, obj}, ...
                'BusyAction', 'cancel', 'Visible', 'off');
    obj.hMainImgAx=axes(...
                'Box', 'on', ...
                'YDir', 'reverse', ...
                'Color', [0 0 0], ...
                'XTick', [], 'YTick', [], ...
                'Position', [0.02 0.02 0.8 0.96], ...
                'ButtonDownFcn', {@handleMouseClick, obj});
end

function setupMenus(obj)
    obj.mnuMain=uimenu(obj.hFig, 'Label', 'Main');
    uimenu(obj.mnuMain, 'Label', 'Quit', 'Callback', {@closeRequest, obj})
    
    obj.mnuImage=uimenu(obj.hFig, 'Label', 'Image');
    uimenu(obj.mnuImage, 'Label', 'Export Current View to Workspace', ...
        'Callback', {@exportViewToWorkspace, obj})
    uimenu(obj.mnuImage, 'Label', 'Detailed image processing steps...', ...
        'Callback', {@changeProcessingSteps, obj});
    uimenu(obj.mnuImage, 'Label', 'Adjust precise XY position', ...
        'Callback', {@adjustXYPosClick, obj});
end

function setupPlugins(obj)
     baseDir=fileparts(which('MaSIV')); %viewer installation base directory
     addPlugins(obj.mnuImage, obj, fullfile(baseDir,'code','masiv_resources','corePlugins'), 1);
     obj.mnuPlugins=uimenu(obj.hFig, 'Label', 'Plugins');
     
     %Optionally add tutorial plugins
     if ~masivSetting('plugins.hideTutorialPlugins')
         obj.mnuTutPlugins=uimenu(obj.mnuPlugins,'label','Tutorials');
         addPlugins(obj.mnuTutPlugins, obj, fullfile(baseDir,masivSetting('plugins.bundledPluginsDirPath'),'tutorials'))
     else
         fprintf('Skipping addition of tutorial plugins\n')
     end
     
     %Add bundled plugins
     addPlugins(obj.mnuPlugins, obj, fullfile(baseDir,masivSetting('plugins.bundledPluginsDirPath')));
     
     %Add external plugins
     for externalPlugin = masivSetting('plugins.externalPluginsDirs')
         thisExternalPluginDir=externalPlugin{1};

         if ~exist(thisExternalPluginDir,'dir')
             fprintf('Skipping missing plugin directory %s\n', thisExternalPluginDir)
             continue
         else
             fprintf('Searching for plugins in %s\n',thisExternalPluginDir)
         end

         pluginDirs=masiv.pluginManager.getPluginDirs(thisExternalPluginDir);
         
         %Loop through pluginDirs and add all directories to the path
         for ii=1:length(pluginDirs)
            if ~exist(pluginDirs{ii},'dir')
                fprintf('Expected to find plugin directory %s but failed to do so. Skipping\n',pluginDirs{ii})
                 continue
            end
            fprintf('Adding plugins in directory %s\n', pluginDirs{ii});
            addpath(pluginDirs{ii})
            addPlugins(obj.mnuPlugins, obj, pluginDirs{ii}); %register plugin in viewer
         end
     end
end

function setupContrastController(obj)
    obj.hAxContrastHist=axes(...
                'Box', 'on', ...
                'Color', masivSetting('viewer.panelBkgdColor'), ...
                'XTick', [], 'YTick', [], ...
                'Position', [0.83 0.89 0.16 0.09], ...
                'Color', [0.1 0.1 0.1]);
           
    sliderPanel=uipanel(...
                'Parent', obj.hFig, ...
                'Units', 'normalized', ...
                'Position', [0.83 0.81 0.16 0.07], ...
                'BackgroundColor', [0.1 0.1 0.1], ...
                'ForegroundColor', [0.8 0.8 0.8]);
            
    ppos=getpixelposition(sliderPanel);
    border=ppos(3:4)./[100 20]; border=[border border*2];
    
    
    obj.hjSliderContrast = com.jidesoft.swing.RangeSlider(-5000,15000,0,1000);  % min,max,low,high
    obj.hjSliderContrast = javacomponent(obj.hjSliderContrast, [border(1),border(2),ppos(3)-border(3),ppos(4)-border(4)], sliderPanel);
    
    set(obj.hjSliderContrast,'PaintTicks',true, 'PaintLabels',true, ...
        'Background',java.awt.Color(0.1, 0.1, 0.1), 'Foreground', java.awt.Color(0.8, 0.8, 0.8), ...
        'StateChangedCallback',@(h,e) adjustContrast(h,e,obj));
    
end

function setupResources(obj)
    %% Setup Brightness / contrast icon
    try
        load bc.mat
        obj.hFig.PointerShapeCData=bcIco;
    catch
        warning('Unable to load custom brightness/contrast icon')
    end
end

function setupContrast(obj)
    
    fprintf('Choosing a reasonable value for the contrast scale...')
    numValues=1e5; %make histogram with this many values
    arraySize=numel(obj.MainStack.I);
    decimateBy=round(arraySize/numValues);
    if decimateBy<1
        decimateBy=1;
    end
    
    [n,x]=hist(single(obj.MainStack.I(1:decimateBy:end)),500);
    
    y=log10(n+0.5);
    y=y-min(y(:)); %in case of negative numbers
    m=y.*x;
    vals=cumsum(m)/sum(m);
    %% Set up limits
    highIdx=find(cumsum(y)>sum(y)*.99, 1);
    contrastLims=[0 x(highIdx)];
    contrastLims=contrastLims+[-1 1]*0.1*range(contrastLims); % dilate the range by 10% either side for safety
    
    %However, sometimes it chooses a high value that is too low, so stop it from choosing a too low value
    hardMaxLimit=10E3;
    fprintf(' Auto-selected %0.2f to %0.2f',contrastLims)
    if contrastLims(2)<hardMaxLimit;
        contrastLims(2)=hardMaxLimit;
        fprintf(', but forced the high value to be %0.2f\n',hardMaxLimit)
    else
        fprintf('\n')
    end

    
    %% Set up scale
    setSliderRange(obj.hjSliderContrast, contrastLims);

    %% Set up low and high values
    if isempty(obj.MainStack.contrastLimits)
        %% Set up high value
        if masivSetting('contrastSlider.doAutoContrast')
            thresh = masivSetting('contrastSlider.highThresh');
            if thresh>1 || thresh<0
                masivSetting('contrastSlider.highThresh', {}) %reset value to default
                thresh=masivSetting('contrastSlider.highThresh');
            end
            
            f=find(vals>thresh);
            threshVal=round(x(f(1)));
            fprintf('High contrast slider set to %d\n',threshVal)
            set(obj.hjSliderContrast,'High',threshVal)
        end
        
    else
        lims=obj.MainStack.contrastLimits;
        set(obj.hjSliderContrast,'Low',lims(1));
        set(obj.hjSliderContrast,'High',lims(2));
    end
    
    %% Set up callback to allow range changing
    set(obj.hjSliderContrast, 'MouseClickedCallback', @sliderCallback);
end

function setSliderRange(sliderObj, contrastLims)
    majorSpacing=roundToSingleSigFig(range(contrastLims/4)); % get 5 major ticks by default
    minorSpacing=majorSpacing/5;
    set(sliderObj,  'MajorTickSpacing',majorSpacing, 'MinorTickSpacing', minorSpacing)
    
    sliderObj.Minimum=min(-majorSpacing, double(roundToClosest(contrastLims(1), majorSpacing)));
    sliderObj.Maximum=roundToSingleSigFig(contrastLims(2));
end

function setupInfoBoxes(obj)
    obj.addInfoPanel(masivViewInfoPanel(obj, obj.hFig, [0.83 0.49 0.16 0.31], obj.mainDisplay));
    obj.addInfoPanel(masivPreLoader(obj, [0.83 0.39 0.16 0.09]));
    obj.addInfoPanel(masivReadQueueInfoPanel(obj.hFig, [0.83 0.29 0.16 0.09], obj.mainDisplay.zoomedViewManager));
    obj.addInfoPanel(masivCacheInfoPanel(obj, [0.83 0.19 0.16 0.09]));
    obj.addInfoPanel(masivSystemMemoryUsageInfoPanel(obj.hFig, [0.83 0.03 0.16 0.15], obj.mainDisplay.zoomedViewManager));
end

function startParallelPool()
     h=masiv.resources.splashWindow('Starting Parallel Pool', 'MaSIV');
     drawnow;
     G=gcp;
     G.IdleTimeout=inf;
     delete(h);
end

function initialiseDisplay(obj) 
    obj.mainDisplay=masivDisplay(obj, obj.MainStack, obj.hMainImgAx);
    obj.mainDisplay.drawNewZ();
    axis(obj.hMainImgAx, 'equal')
    set(findall(gcf, '-property','FontName'), 'FontName', masivSetting('font.name'));
end