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InteractiveGUI.m
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classdef InteractiveGUI < AutoTipTrackDataClass
properties
UIFig; %figure handle for the GUI
Interface = struct(); %structure containing handles to the individual gui elements
Tabs; %Cellstring of tab names
end
methods
function I = InteractiveGUI(Config)
I@AutoTipTrackDataClass(Config);
I.UIFig = figure('DockControls','off','IntegerHandle','off','MenuBar','none','Name',...
'evaluateManyExperiments - Interactive UI','NumberTitle','off','Tag','InteractiveGUI');
fPlaceFig(I.UIFig,'big');
set(I.UIFig,'Units','pixels');
end
function I=setupInteractivePanel(I,varargin)
p = inputParser;
p.addParameter('Threshold', true, @islogical);
p.addParameter('Patterns', false, @islogical);
p.parse(varargin{:});
I.Interface.TabGroup=uitabgroup('Parent',I.UIFig,...
'Position',[0 0 1 1],...
'Tag','TabGroup',...
'SelectionChangedFcn',@I.refresh);
if p.Results.Threshold
I.setupThresholdTab;
I.refreshThresholdTab;
end
if p.Results.Patterns
I.setupPatternTab;
I.refreshPatternTab;
end
end
function refresh(I,~,~)
TabName=get(I.Interface.TabGroup.SelectedTab,'Tag');
if strcmp(TabName, 'PatternTab')
I.refreshPatternTab;
else
I.refreshThresholdTab;
end
end
%% pattern identification tab
function I=setupPatternTab(I)
I.Interface.PatternTab=struct();
I.Interface.PatternTab.Rotation = 0;
I.Interface.PatternTab.Flip = false;
I.Interface.PatternTab.MainTab=uitab(I.Interface.TabGroup,...
'Title','PatternIdentification','Tag','PatternTab');
if isempty(I.Stack)
h = waitbar(0,'Loading stack, please wait...');
I.loadFile;
close(h)
end
BtnH = 0.05;
BtnW = 0.18;
BtnSpacing = 0.06;
BtnX = 0.81;
I.Interface.PatternTab.SRScaleSlider = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'String','Scaling',...
'Style','slider',...
'Position',[0 0.5 0.05 0.5],...
'Callback',@I.rescaleMaximumProjection,...
'Tag','SRScaleSlider');
I.labelSlider(I.Interface.PatternTab.SRScaleSlider,'PatternTab')
I.Interface.PatternTab.MaximumProjPanel = uipanel(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'Title','Maximum projection',...
'Position',[0.15 0.5 0.65 0.5],...
'Tag','MaximumProjPanel');
I.Interface.PatternTab.MaximumProjAxes = axes(...
'Parent',I.Interface.PatternTab.MaximumProjPanel,...
'Position',[0 0 1 1],...
'Visible','off');
I.Interface.PatternTab.CorrelationThreshSlider = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'Max',1,...
'Min',0,...
'Value',0.5,...
'SliderStep',[0.01 0.1],...
'String','Correlation Threshold',...
'Style','slider',...
'Position',[0 0 0.05 0.5],...
'Callback',@I.updateRectangles,...
'Tag','CorrelationThreshSlider');
I.labelSlider(I.Interface.PatternTab.CorrelationThreshSlider,'PatternTab')
I.Interface.PatternTab.RegionPanel = uipanel(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'Title','Junction Regions',...
'Position',[0.15 0 0.65 0.5],...
'Tag','RegionPanel');
I.Interface.PatternTab.RegionImageAxes = axes(...
'Parent',I.Interface.PatternTab.RegionPanel,...
'Position',[0 0 1 1],...
'Visible','off');
I.Interface.PatternTab.ProjectionValue = 1;
I.Interface.PatternTab.ProjectionMethod = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Style','popupmenu','Units','normalized',...
'Position',[BtnX 16 * BtnSpacing - 0.02 BtnW BtnH],'Tag','ProjectionMethod','Fontsize',10,...
'String',{'Maximum','Median','Standard Deviation'},...
'Value', I.Interface.PatternTab.ProjectionValue,...
'Callback',@I.changeProjection);
I.Interface.PatternTab.RotateRightButton = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'String','Rotate Right',...
'Style','pushbutton',...
'Position',[BtnX 15 * BtnSpacing BtnW BtnH],...
'Callback',@I.rotateMaxProjRight,...
'Tag','SRCancelButton');
I.Interface.PatternTab.RotateLeftButton = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'String','Rotate Left',...
'Style','pushbutton',...
'Position',[BtnX 14 * BtnSpacing BtnW BtnH],...
'Callback',@I.rotateMaxProjLeft,...
'Tag','SRCancelButton');
I.Interface.PatternTab.FlipUDButton = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'String','Flip Up-Down',...
'Style','pushbutton',...
'Position',[BtnX 13 * BtnSpacing BtnW BtnH],...
'Callback',@I.flipMaxProj,...
'Tag','SRCancelButton');
I.Interface.PatternTab.RegionTabGroup=uitabgroup('Parent',I.Interface.PatternTab.MainTab,...
'Position',[0.8 2 * BtnSpacing .2 4 * BtnSpacing],...
'Tag','TabGroup');
I.Interface.PatternTab.GridTab=uitab(I.Interface.PatternTab.RegionTabGroup,...
'Title','Grid','Tag','GridTab');
TBtnH = 0.3;
TBtnW = 1;
TBtnSpacing = 0.33;
TBtnX = 0;
I.Interface.PatternTab.SelectLeftRegionButton = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','Select left anchor region',...
'Style','pushbutton',...
'Position',[TBtnX 2 * TBtnSpacing TBtnW TBtnH],...
'Callback',@I.selectJunctionRegion,...
'Tag','SelectLeftRegionButton');
I.Interface.PatternTab.SelectRightRegionButton = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','Select right anchor region',...
'Style','pushbutton',...
'Position',[TBtnX 1 * TBtnSpacing TBtnW TBtnH],...
'Callback',@I.selectJunctionRegion,...
'Tag','SelectRightRegionButton');
I.Interface.PatternTab.XSpacingL = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','X-Spacing (nm)',...
'Style','text',...
'Position',[TBtnX 0 * TBtnSpacing + TBtnH/2 TBtnW/2.1 TBtnH/2],...
'Tag','XSpacingL');
I.Interface.PatternTab.XSpacing = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','12000',...
'Style','edit',...
'Position',[TBtnX 0 * TBtnSpacing TBtnW/2.1 TBtnH/1.7],...
'Callback',@I.updatePatternGrid,...
'Tag','XSpacing');
I.Interface.PatternTab.YSpacingL = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','Y-Spacing (nm)',...
'Style','text',...
'Position',[TBtnX + 0.525 0 * TBtnSpacing + TBtnH/2 TBtnW/2.1 TBtnH/2],...
'Tag','YSpacingL');
I.Interface.PatternTab.YSpacing = uicontrol(...
'Parent',I.Interface.PatternTab.GridTab,...
'Units','normalized',...
'String','8805',...
'Style','edit',...
'Position',[TBtnX + 0.525 0 * TBtnSpacing TBtnW/2.1 TBtnH/1.7],...
'Callback',@I.updatePatternGrid,...
'Tag','YSpacing');
I.Interface.PatternTab.CorrelationTab=uitab(I.Interface.PatternTab.RegionTabGroup,...
'Title','Correlation','Tag','CorrelationTab');
I.Interface.PatternTab.SelectRegionButton = uicontrol(...
'Parent',I.Interface.PatternTab.CorrelationTab,...
'Units','normalized',...
'String','Select initial region',...
'Style','pushbutton',...
'Position',[TBtnX 2 * TBtnSpacing TBtnW TBtnH],...
'Callback',@I.selectJunctionRegion,...
'Tag','SelectRegionButton');
I.Interface.PatternTab.CorrelateRegionButton = uicontrol(...
'Parent',I.Interface.PatternTab.CorrelationTab,...
'Units','normalized',...
'String','Find Correlating Regions',...
'Style','pushbutton',...
'Position',[TBtnX 1 * TBtnSpacing TBtnW TBtnH],...
'Callback',@I.correlateRegion,...
'Tag','CorrelateRegionButton',...
'Enable','off');
I.Interface.PatternTab.EliminateOverlap = uicontrol(...
'Parent',I.Interface.PatternTab.CorrelationTab,...
'Units','normalized',...
'String','Eliminate Overlapping Rectangles',...
'Style','pushbutton',...
'Position',[TBtnX 0 * TBtnSpacing TBtnW TBtnH],...
'Callback',@I.eliminateRectanglesButton,...
'Tag','EliminateOverlap');
I.Interface.PatternTab.CancelButton = uicontrol(...
'Parent',I.Interface.PatternTab.MainTab,...
'Units','normalized',...
'String','Done',...
'Style','pushbutton',...
'Position',[BtnX 0 * BtnSpacing BtnW BtnH],...
'Callback',@I.closeFig,...
'Tag','SRCancelButton');
end
function I=refreshPatternTab(I)
I.Interface.PatternTab.FlatStack = [];
I.maximumProject;
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
I.selectJunctionRegion;
end
function I = changeProjection(I,~,~)
I.Interface.PatternTab.ProjectionValue = get(I.Interface.PatternTab.ProjectionMethod, 'Value');
I.maximumProject;
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
I.selectJunctionRegion;
end
function I=maximumProject(I)
if ~isfield(I.Interface.PatternTab, 'FlatStack') || isempty(I.Interface.PatternTab.FlatStack)
if isfield(I.Interface,'ThresholdTab')
BallRadius=I.Config.SubtractBackground.BallRadius;
I.Config.SubtractBackground.BallRadius=0;
end
if isempty(I.Stack)
h = waitbar(0,'Loading stack, please wait...');
I.loadFile;
close(h)
end
StackLen=length(I.Stack);
if isfield(I.Interface,'ThresholdTab')
I.Config.SubtractBackground.BallRadius=BallRadius;
BallRadius=round(get(I.Interface.ThresholdTab.RadiusSlider,'Value'));
Smoothe=get(I.Interface.ThresholdTab.SmootheSlider,'Value');
if BallRadius > 0
h = waitbar(0,'Calculating flattened stack...');
FlatStack=zeros([size(I.Stack{1}),StackLen]);
Stack=I.Stack;
parfor n=1:StackLen
FlatStack(:,:,n)=flattenImage(Stack{n},BallRadius,Smoothe);
end
I.Interface.PatternTab.FlatStack = FlatStack;
close(h);
end
end
if ~isfield(I.Interface.PatternTab, 'FlatStack') || isempty(I.Interface.PatternTab.FlatStack)
I.Interface.PatternTab.FlatStack = zeros([size(I.Stack{1}),StackLen]);
for n=1:StackLen
I.Interface.PatternTab.FlatStack(:,:,n)=I.Stack{n};
end
end
end
I.Interface.PatternTab.Flip = false;
I.Interface.PatternTab.Rotation = 0;
switch I.Interface.PatternTab.ProjectionValue
case 1
I.Interface.PatternTab.MaxP=max(I.Interface.PatternTab.FlatStack,[],3);
case 2
h = waitbar(0,'Calculating median...');
if size(I.Interface.PatternTab.FlatStack,3) > 100
I.Interface.PatternTab.MaxP=median(I.Interface.PatternTab.FlatStack(:,:,1:100),3);
else
I.Interface.PatternTab.MaxP=median(I.Interface.PatternTab.FlatStack,3);
end
close(h);
case 3
h = waitbar(0,'Calculating standard deviation...');
I.Interface.PatternTab.MaxP=std(I.Interface.PatternTab.FlatStack,0,3);
close(h);
otherwise
I.Interface.PatternTab.MaxP=max(I.Interface.PatternTab.FlatStack,[],3);
end
end
function I=rotateMaxProj(I, Angle)
if mod(Angle,90) > 0
error('MATLAB:AutoTiptrack:InteractiveGUI:RotateMaxProj','Angle must be a multiple of 90 degrees')
end
Angle = mod(Angle,360);
if isstruct(I.Interface.PatternTab) && isfield(I.Interface.PatternTab, 'Rotation') && isfield(I.Interface.PatternTab, 'MaxP') && ~isempty(I.Interface.PatternTab.MaxP)
I.Interface.PatternTab.MaxP = rot90(I.Interface.PatternTab.MaxP, Angle / 90);
I.Interface.PatternTab.Rotation = I.Interface.PatternTab.Rotation + Angle;
I.Interface.PatternTab.Rotation = mod(I.Interface.PatternTab.Rotation,360);
if isfield(I.Interface.PatternTab, 'SelectedRegion') && ...
isa(I.Interface.PatternTab.SelectedRegion, 'imrect') && ...
~isempty(I.Interface.PatternTab.SelectedRegion)&& ...
isvalid(I.Interface.PatternTab.SelectedRegion)
ImageSize = size(I.Interface.PatternTab.MaxP);
RegionPos = I.Interface.PatternTab.SelectedRegion.getPosition;
[RegionPos(1:2), RegionPos(3:4), ~] = I.rotateRegions(RegionPos(1:2), Angle, RegionPos(3:4), ImageSize);
I.Interface.PatternTab.SelectedRegion.delete;
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
I.Interface.PatternTab.SelectedRegion=imrect(I.Interface.PatternTab.MaximumProjAxes,RegionPos);
I.selectJunctionRegion;
else
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
end
if isfield(I.Interface.PatternTab, 'Correlation')
I.Interface.PatternTab.Correlation = rot90(I.Interface.PatternTab.Correlation, Angle / 90);
I.updateRectangles(I.Interface.PatternTab.CorrelationThreshSlider,'PatternTab');
end
end
end
function I=rotateMaxProjRight(I,~,~)
if isstruct(I.Interface.PatternTab) && isfield(I.Interface.PatternTab, 'Flip') && I.Interface.PatternTab.Flip
I.flipMaxProj();
msgbox('Flipping has to be the last operation performed. Undoing previous flipping operation. Please rotate first and then perform any flipping required as the last operation.');
end
I.rotateMaxProj(-90);
end
function I=rotateMaxProjLeft(I,~,~)
if isstruct(I.Interface.PatternTab) && isfield(I.Interface.PatternTab, 'Flip') && I.Interface.PatternTab.Flip
I.flipMaxProj();
msgbox('Flipping has to be the last operation performed. Undoing previous flipping operation. Please rotate first and then perform any flipping required as the last operation.');
end
I.rotateMaxProj(90);
end
function I=flipMaxProj(I,varargin)
if isstruct(I.Interface.PatternTab) && isfield(I.Interface.PatternTab, 'Flip') && isfield(I.Interface.PatternTab, 'MaxP') && ~isempty(I.Interface.PatternTab.MaxP)
I.Interface.PatternTab.MaxP = flipud(I.Interface.PatternTab.MaxP);
I.Interface.PatternTab.Flip = ~I.Interface.PatternTab.Flip;
if isfield(I.Interface.PatternTab, 'SelectedRegion') && ...
isa(I.Interface.PatternTab.SelectedRegion, 'imrect') && ...
~isempty(I.Interface.PatternTab.SelectedRegion)&& ...
isvalid(I.Interface.PatternTab.SelectedRegion)
RegionPos = I.Interface.PatternTab.SelectedRegion.getPosition;
RegionPos(2) = size(I.Interface.PatternTab.MaxP, 1) - RegionPos(2) - RegionPos(4);
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
I.Interface.PatternTab.SelectedRegion=imrect(I.Interface.PatternTab.MaximumProjAxes,RegionPos);
I.selectJunctionRegion;
else
I.rescaleMaximumProjection(I.Interface.PatternTab.SRScaleSlider);
end
if isfield(I.Interface.PatternTab, 'Correlation')
I.Interface.PatternTab.Correlation = flipud(I.Interface.PatternTab.Correlation);
I.updateRectangles(I.Interface.PatternTab.CorrelationThreshSlider,'PatternTab');
end
end
end
function selectJunctionRegion(I,hObj,~)
Region = 'SelectedRegion';
if nargin > 1
if strcmp(hObj.Tag, 'SelectRightRegionButton')
if ~(isfield(I.Interface.PatternTab, Region) && ...
isa(I.Interface.PatternTab.(Region), 'imrect'))
msgbox('Please select the left region first.');
return;
end
Region = 'RightRegion';
XSpacing = str2double(I.Interface.PatternTab.XSpacing.String) / I.Config.PixSize;
end
end
if isfield(I.Interface.PatternTab, Region) && ...
isa(I.Interface.PatternTab.(Region), 'imrect') && ...
~isempty(I.Interface.PatternTab.(Region))&& ...
isvalid(I.Interface.PatternTab.(Region))
RegionPos=I.Interface.PatternTab.(Region).getPosition;
I.Interface.PatternTab.(Region).delete;
else
ImSize=size(I.Interface.PatternTab.MaxP);
if strcmp(Region, 'RightRegion')
RegionPos = I.Interface.PatternTab.SelectedRegion.getPosition;
RegionPos(1) = (floor( (ImSize(1) - RegionPos(1)) / XSpacing) - 1) * XSpacing;
else
RegionPos=round([ImSize/2 ImSize/10]);
end
end
I.Interface.PatternTab.(Region)=imrect(I.Interface.PatternTab.MaximumProjAxes,RegionPos);
if strcmp(Region, 'RightRegion')
I.Interface.PatternTab.(Region).setColor('r');
I.Interface.PatternTab.(Region).setResizable(false);
I.Interface.PatternTab.(Region).setPositionConstraintFcn(@I.constrainPositionToGrid);
else
I.Interface.PatternTab.(Region).setPositionConstraintFcn(@I.constrainPositionToImage);
end
RegionPos=I.Interface.PatternTab.(Region).getPosition;
I.redrawRegionImage(RegionPos);
I.Interface.PatternTab.(Region).addNewPositionCallback(@I.redrawRegionImage);
set(I.Interface.PatternTab.CorrelateRegionButton,'Enable','on');
I.updatePatternGrid;
end
function ConstrainedPos = constrainPositionToImage(I, Position)
ImSize=size(I.Interface.PatternTab.MaxP);
MaxX = ImSize(1) - Position(3);
MaxY = ImSize(2) - Position(4);
ConstrainedPos = Position;
if Position(1) < 0
ConstrainedPos(1) = 0;
elseif Position(1) > MaxX
ConstrainedPos(1) = MaxX;
end
if Position(2) < 0
ConstrainedPos(2) = 0;
elseif Position(2) > MaxY
ConstrainedPos(2) = MaxY;
end
end
function ConstrainedPos = constrainPositionToGrid(I, Position)
ReferencePos = I.Interface.PatternTab.SelectedRegion.getPosition;
XSpacing = str2double(I.Interface.PatternTab.XSpacing.String) / I.Config.PixSize;
%YSpacing = str2double(I.Interface.PatternTab.YSpacing.String) / I.Config.PixSize;
DiffPos = Position(1:2) - ReferencePos(1:2);
if all(DiffPos == 0)
ConstrainedPos = ReferencePos + [XSpacing 0 0 0];
Angle = 0;
else
Angle = atan(DiffPos(2) / DiffPos(1));
Distance = sqrt(sum(DiffPos .^ 2));
ConstrainedDistance = round(Distance ./ XSpacing) .* XSpacing;
ConstrainedX = cos(Angle) .* ConstrainedDistance;
ConstrainedY = sin(Angle) .* ConstrainedDistance;
ConstrainedPos = [ConstrainedX + ReferencePos(1) ConstrainedY + ReferencePos(2) ReferencePos(3:4)];
end
I.drawRectangleGrid(Angle);
end
function drawRectangleGrid(I,Angle)
ReferencePos = I.Interface.PatternTab.SelectedRegion.getPosition;
RightPos = I.Interface.PatternTab.RightRegion.getPosition;
XSpacing = str2double(I.Interface.PatternTab.XSpacing.String) / I.Config.PixSize;
YSpacing = str2double(I.Interface.PatternTab.YSpacing.String) / I.Config.PixSize;
DiffPos = RightPos(1:2) - ReferencePos(1:2);
if XSpacing <= 0
NumCols = 1;
else
NumCols = ceil(DiffPos(1) / XSpacing);
end
if YSpacing <= 0
NumRows = 1;
else
NumRows = floor(ReferencePos(2) / YSpacing);
end
X = ((0:NumCols) .* XSpacing)';
Y = -((0:NumRows) .* YSpacing)';
NumCols = NumCols + 1;
NumRows = NumRows + 1;
Coords = zeros(NumCols * NumRows,2);
for n = 1:NumRows
Coords((n - 1) * NumCols + 1 : n * NumCols, :) = [X repmat(Y(n),NumCols,1)];
end
R = [cos(-Angle) -sin(-Angle);...
sin(-Angle) cos(-Angle)];
Coords = Coords * R;
Coords(:, 1) = Coords(:, 1) + ReferencePos(1);
Coords(:, 2) = Coords(:, 2) + ReferencePos(2);
I.Interface.PatternTab.RectSize=ReferencePos(3:4);
I.Interface.PatternTab.RectPos=Coords;
I.drawRectangles;
end
function I = updatePatternGrid(I,~,~)
if isfield(I.Interface.PatternTab, 'RightRegion') && isa(I.Interface.PatternTab.RightRegion, 'imrect')
I.Interface.PatternTab.RightRegion.setPosition(I.constrainPositionToGrid(I.Interface.PatternTab.RightRegion.getPosition));
end
end
function redrawRegionImage(I,RegionPos)
RegionPos=round(RegionPos);
I.Interface.PatternTab.RegionImage=I.Interface.PatternTab.MaxP(RegionPos(2):RegionPos(2)+RegionPos(4),RegionPos(1):RegionPos(1)+RegionPos(3));
imshow(I.Interface.PatternTab.RegionImage,[0, get(I.Interface.PatternTab.SRScaleSlider,'Value') ],...
'Parent',I.Interface.PatternTab.RegionImageAxes,'Border','tight');
end
function correlateRegion(I,~,~)
ImSize=size(I.Interface.PatternTab.MaxP);
RegionPos=I.Interface.PatternTab.SelectedRegion.getPosition;
RegionPos=round(RegionPos);
Correlation=zeros(ImSize-[RegionPos(4) RegionPos(3)]);
NumRows=ImSize(1)-RegionPos(4);
NumCols=ImSize(2)-RegionPos(3);
Part=I.Interface.PatternTab.RegionImage;
MaxP=I.Interface.PatternTab.MaxP;
RegionHeight=RegionPos(4);
RegionWidth=RegionPos(3);
h = waitbar(0,'Searching image...');
parfor r=1:NumRows
for c=1:NumCols
Correlation(r,c)=corr2(Part,MaxP(r:r+RegionHeight,c:c+RegionWidth)); %#ok<PFBNS>
end
end
close(h);
I.Interface.PatternTab.Correlation=Correlation;
I.updateRectangles(I.Interface.PatternTab.CorrelationThreshSlider,'PatternTab');
end
function updateRectangles(I,hObj,~)
I.syncSliders(get(hObj,'Tag'),'PatternTab');
RegionPos=I.Interface.PatternTab.SelectedRegion.getPosition;
RegionPos=round(RegionPos);
Average=fspecial('average');
Maxima=imregionalmax(imfilter(I.Interface.PatternTab.Correlation,Average,'replicate'));
MaximaValues=I.Interface.PatternTab.Correlation.*Maxima;
[R,C]=find(MaximaValues>get(I.Interface.PatternTab.CorrelationThreshSlider,'Value'));
I.Interface.PatternTab.RectSize=RegionPos(3:4);
I.Interface.PatternTab.RectPos=[C,R];
I.drawRectangles;
end
function I=drawRectangles(I)
if isfield(I.Interface.PatternTab,'Rect')
R = findall(I.Interface.PatternTab.MaximumProjAxes, 'Tag', 'WhiteRect');
R.delete;
end
for n=size(I.Interface.PatternTab.RectPos,1):-1:1
I.Interface.PatternTab.Rect(n) = rectangle('Parent', I.Interface.PatternTab.MaximumProjAxes, ...
'Position',[I.Interface.PatternTab.RectPos(n,:) I.Interface.PatternTab.RectSize], 'EdgeColor', 'w', 'Tag', 'WhiteRect');
end
%drawnow;
end
function I = eliminateRectanglesButton(I,~,~)
I.eliminateOverlappingRectangles;
I.drawRectangles;
end
function [I, RectPos, RectSize, Rotation, Flip, ProjectionMethod] = eliminateOverlappingRectangles(I)
RectPos=[];
RectSize=[];
Rotation = I.Interface.PatternTab.Rotation;
Flip = I.Interface.PatternTab.Flip;
ProjectionMethod = 1;
if isfield(I.Interface,'PatternTab') && isfield(I.Interface.PatternTab,'RectPos') && isfield(I.Interface.PatternTab, 'ProjectionValue')
ProjectionMethod = I.Interface.PatternTab.ProjectionValue;
RectPos = I.Interface.PatternTab.RectPos;
RectSize = I.Interface.PatternTab.RectSize;
SD = squareform(pdist(RectPos));
NSquares = size(RectPos,1);
SD(1:NSquares + 1:end) = Inf(1, NSquares);
[R, ~] = find(SD < min(RectSize));
if length(R) > 1
Delete = zeros(1,length(R));
for n = 1:2:length(R) - 1
N1 = sort(SD(R(n),:));
N2 = sort(SD(R(n+1),:));
%find out which of the two overlapping rectangles is better
%centered within its 8 neighbors and delete the other one.
if length(N1) > 8
Dist1 = sum(N1(2:2:8) - N1(3:2:9));
Dist2 = sum(N2(2:2:8) - N2(3:2:9));
else
Dist1 = sum(N1(2:2:end - 1) - N1(3:2:end - 1));
Dist2 = sum(N1(2:2:end - 1) - N1(3:2:end - 1));
end
if Dist1 > Dist2
Delete(n) = R(n+1);
else
Delete(n) = R(n);
end
end
Delete(Delete == 0) = [];
RectPos(Delete,:) = [];
end
I.Interface.PatternTab.RectPos = RectPos;
end
end
function rescaleMaximumProjection(I,hObj,~)
I.syncSliders(get(hObj,'Tag'),'PatternTab');
I.rescaleSlider(I.Interface.PatternTab.SRScaleSlider,I.Interface.PatternTab.MaxP,'PatternTab')
imshow(I.Interface.PatternTab.MaxP,[0, get(I.Interface.PatternTab.SRScaleSlider,'Value') ],...
'Parent',I.Interface.PatternTab.MaximumProjAxes,'Border','tight');
end
%% threshold tab
function I=setupThresholdTab(I)
BtnH = 0.05;
BtnW = 0.18;
BtnSpacing = 0.06;
BtnX = 0.81;
I.Interface.ThresholdTab=struct();
I.Interface.ThresholdTab.MainTab=uitab(I.Interface.TabGroup,...
'Title','Threshold','Tag','ThresholdTab');
I.Interface.ThresholdTab.FrameSlider = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Max',2,...
'Min',1,...
'Value',1,...
'String','Frame',...
'Style','slider',...
'Position',[0 0.95 1 0.05],...
'Callback',@I.updateFlattenedImage,...
'Tag','FrameSlider');
I.labelSlider(I.Interface.ThresholdTab.FrameSlider)
I.Interface.ThresholdTab.ScaleSlider = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','Scaling',...
'Style','slider',...
'Position',[0 0.475 0.05 0.475],...
'Callback',@I.updateThresholdImages,...
'Tag','ScaleSlider');
I.labelSlider(I.Interface.ThresholdTab.ScaleSlider)
I.Interface.ThresholdTab.DisableBGButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','Disable background subtraction',...
'Style','pushbutton',...
'Enable', 'on',...
'Visible', 'on',...
'Position',[BtnX 0.80 BtnW BtnH],...
'Callback',@I.disableBGSubtraction,...
'Tag','DisableBGButton');
I.Interface.ThresholdTab.EnableBGButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','Enable background subtraction',...
'Style','pushbutton',...
'Enable', 'off',...
'Visible', 'off',...
'Position',[BtnX 0.80 BtnW BtnH],...
'Callback',@I.enableBGSubtraction,...
'Tag','EnableBGButton');
I.Interface.ThresholdTab.RadiusSlider = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Max',200,...
'Min',5,...
'Value',I.Config.SubtractBackground.BallRadius,...
'SliderStep',[1 5]/195,...
'String','BallRadius',...
'Style','slider',...
'Position',[0.05 0.475 0.05 0.475],...
'Callback',@I.updateFlattenedImage,...
'Tag','RadiusSlider');
I.labelSlider(I.Interface.ThresholdTab.RadiusSlider)
I.Interface.ThresholdTab.SmootheSlider = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Max',5,...
'Min',0,...
'Value',I.Config.SubtractBackground.Smoothe,...
'SliderStep',[0.1 1]/5,...
'String','Smoothe',...
'Style','slider',...
'Position',[0.1 0.475 0.05 0.475],...
'Callback',@I.updateFlattenedImage,...
'Tag','SmootheSlider');
I.labelSlider(I.Interface.ThresholdTab.SmootheSlider)
I.Interface.ThresholdTab.ThreshSlider = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Max',4000,...
'Min',100,...
'Value',imag(I.Config.Threshold.Value),...
'SliderStep',[1 10]/3900,...
'String','Threshold',...
'Style','slider',...
'Position',[0 0 0.05 0.475],...
'Callback',@I.updateThreshold,...
'Tag','ThreshSlider');
I.labelSlider(I.Interface.ThresholdTab.ThreshSlider)
I.Interface.ThresholdTab.FlattenedPanel = uipanel(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Title','Flattened image',...
'Position',[0.15 0.475 0.65 0.475],...
'Tag','FlattenedPanel');
I.Interface.ThresholdTab.FlattenedAxes = axes(...
'Parent',I.Interface.ThresholdTab.FlattenedPanel,...
'Position',[0 0 1 1],...
'Visible','off');
I.Interface.ThresholdTab.ThresholdPanel = uipanel(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'Title','Threshold image',...
'Position',[0.15 0 0.65 0.475],...
'Tag','ThresholdPanel');
I.Interface.ThresholdTab.ThresholdAxes = axes(...
'Parent',I.Interface.ThresholdTab.ThresholdPanel,...
'Position',[0 0 1 1],...
'Visible','off');
I.Interface.ThresholdTab.AnnotateTrainingButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','annotate training data',...
'Style','pushbutton',...
'Position',[BtnX 4 * BtnSpacing BtnW BtnH],...
'Callback',@I.annotateTrainingData,...
'Tag','AnnotateTrainingButton');
I.Interface.ThresholdTab.SaveThresholdButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','save threshold stack',...
'Style','pushbutton',...
'Position',[BtnX 3 * BtnSpacing BtnW BtnH],...
'Callback',@I.saveThreshold,...
'Tag','SaveThresholdButton');
I.Interface.ThresholdTab.CancelButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','cancel',...
'Style','pushbutton',...
'Position',[BtnX 2 * BtnSpacing BtnW BtnH],...
'Callback',@I.close,...
'Tag','CancelButton');
I.Interface.ThresholdTab.SaveFileSpecificButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','save as file specific config',...
'Style','pushbutton',...
'Position',[BtnX 1 * BtnSpacing BtnW BtnH],...
'Callback',@I.saveFileSpecificConfig,...
'Tag','SaveFileSpecificButton');
I.Interface.ThresholdTab.SaveGeneralButton = uicontrol(...
'Parent',I.Interface.ThresholdTab.MainTab,...
'Units','normalized',...
'String','save as general config',...
'Style','pushbutton',...
'Position',[BtnX 0 BtnW BtnH],...
'Callback',@I.saveGeneralConfig,...
'Tag','SaveGeneralButton');
end
function disableBGSubtraction(I, ~, ~)
I.Interface.ThresholdTab.RadiusSlider.Enable = 'off';
I.Interface.ThresholdTab.RadiusSlider.Min = 0;
I.Interface.ThresholdTab.RadiusSlider.Value = 0;
I.Interface.ThresholdTab.SmootheSlider.Enable = 'off';
I.Interface.ThresholdTab.DisableBGButton.Enable = 'off';
I.Interface.ThresholdTab.DisableBGButton.Visible = 'off';
I.Interface.ThresholdTab.EnableBGButton.Enable = 'on';
I.Interface.ThresholdTab.EnableBGButton.Visible = 'on';
I.updateFlattenedImage(I.Interface.ThresholdTab.FrameSlider);
end
function enableBGSubtraction(I, ~, ~)
I.Interface.ThresholdTab.RadiusSlider.Enable = 'on';
I.Interface.ThresholdTab.RadiusSlider.Min = 5;
I.Interface.ThresholdTab.RadiusSlider.Value = 30;
I.Interface.ThresholdTab.SmootheSlider.Enable = 'on';
I.Interface.ThresholdTab.DisableBGButton.Enable = 'on';
I.Interface.ThresholdTab.DisableBGButton.Visible = 'on';
I.Interface.ThresholdTab.EnableBGButton.Enable = 'off';
I.Interface.ThresholdTab.EnableBGButton.Visible = 'off';
I.updateFlattenedImage(I.Interface.ThresholdTab.FrameSlider);
end
function refreshThresholdTab(I)
BallRadius=I.Config.SubtractBackground.BallRadius;
I.Config.SubtractBackground.BallRadius=0;
if isempty(I.Stack)
h = waitbar(0,'Loading stack, please wait...');
I.loadFile;
close(h)
end
I.Config.SubtractBackground.BallRadius=BallRadius;
NumFrames=length(I.Stack);
if NumFrames>1
SliderStep=[1 round(NumFrames/10)]/(NumFrames-1);
set(I.Interface.ThresholdTab.FrameSlider,'Enable','on');
set(I.Interface.ThresholdTab.FrameNumber,'Enable','on');
else
SliderStep=[1 1];
set(I.Interface.ThresholdTab.FrameSlider,'Enable','off');
set(I.Interface.ThresholdTab.FrameNumber,'Enable','off');
end
set(I.Interface.ThresholdTab.FrameSlider,'Max',NumFrames,...
'SliderStep',SliderStep,...
'Value',1);
I.syncSliders(get(I.Interface.ThresholdTab.FrameSlider,'Tag'),'ThresholdTab');
if isfield(I.Interface.ThresholdTab,'FlatImage')
I.Interface.ThresholdTab=rmfield(I.Interface.ThresholdTab,'FlatImage');
end
I.updateFlattenedImage(I.Interface.ThresholdTab.FrameSlider);
end
function ImageScaling=getImageScalingValue(I)
ImageScaling = struct('Mode','auto','Black',0,'White',0);
[~,White]=autoscale(I.Interface.ThresholdTab.FlatImage,0.2,0.05);
ScaleSliderValue = get(I.Interface.ThresholdTab.ScaleSlider,'Value');
if White ~= ScaleSliderValue
ImageScaling.Mode = 'manual';
ImageScaling.White = round(ScaleSliderValue);
end
end
function saveGeneralConfig(I,~,~)
ConfigPath=fullfile(I.FilePath,'config.mat');
if exist(ConfigPath,'file')==2
NewConf=ConfigClass;
NewConf.loadConfig(ConfigPath);
else
NewConfStruct=I.Config.exportConfigStruct;
NewConfStruct.FileName='';
NewConfStruct.StackName='';
NewConfStruct.Directory='';
NewConfStruct.StackType='TIFF';
NewConfStruct.LastFrame=1;
NewConfStruct.Times=[];
NewConfStruct.AcquisitionDate='';
NewConf=ConfigClass;
NewConf.importConfigStruct(NewConfStruct);
end
NewConf.SubtractBackground.BallRadius=get(I.Interface.ThresholdTab.RadiusSlider,'Value');
NewConf.SubtractBackground.Smoothe=get(I.Interface.ThresholdTab.SmootheSlider,'Value');
NewConf.Threshold.Value=I.getThresholdValue;
NewConf.ImageScaling=I.getImageScalingValue;
NewConf.save(ConfigPath);
msgbox(sprintf('Configuration saved as: %s',ConfigPath));
end
function saveFileSpecificConfig(I,~,~)
ConfigPath=fullfile(I.FilePath, [I.FileName '_conf.mat']);
I.Config.SubtractBackground.BallRadius=get(I.Interface.ThresholdTab.RadiusSlider,'Value');
I.Config.SubtractBackground.Smoothe=get(I.Interface.ThresholdTab.SmootheSlider,'Value');
I.Config.Threshold.Value=I.getThresholdValue;
I.Config.save(ConfigPath);
msgbox(sprintf('Configuration saved as: %s',ConfigPath));
end
function labelSlider(I,hSlider,TabName)
if nargin<3
TabName='ThresholdTab';
end
SliderPosition=get(hSlider,'Position');
if SliderPosition(3)>SliderPosition(4) %horizontal slider
NewSliderPosition=SliderPosition;
NewSliderPosition(3)=SliderPosition(3)-2*SliderPosition(4);
NewSliderPosition(1)=SliderPosition(1)+SliderPosition(4);
set(hSlider,'Position',NewSliderPosition);
NumberPosition=[SliderPosition(1) SliderPosition(2) SliderPosition(4) SliderPosition(4)];
LabelPosition=[SliderPosition(1)+SliderPosition(3)-SliderPosition(4) SliderPosition(2) SliderPosition(4) SliderPosition(4)];
LabelAlign='center';
else %vertical slider
NewSliderPosition=SliderPosition;
NewSliderPosition(4)=SliderPosition(4)-2*SliderPosition(3);
NewSliderPosition(2)=SliderPosition(2)+SliderPosition(3);
set(hSlider,'Position',NewSliderPosition);
NumberPosition=[SliderPosition(1) SliderPosition(2) SliderPosition(3) SliderPosition(3)];
LabelPosition=[SliderPosition(1) SliderPosition(2)+SliderPosition(4)-SliderPosition(3) SliderPosition(3) SliderPosition(3)];
LabelAlign='center';
end
Tag=get(hSlider,'Tag');
NumberName=[Tag(1:end-6) 'Number'];
LabelName=[Tag(1:end-6) 'Label'];
I.Interface.(TabName).(NumberName) = uicontrol(...
'Parent',get(hSlider,'Parent'),...
'Units',get(hSlider,'Units'),...
'String',num2str(get(hSlider,'Value')),...
'Style','edit',...
'Position',NumberPosition,...
'Callback',get(hSlider,'Callback'),...
'Tag',NumberName);
I.Interface.(TabName).(LabelName) = uicontrol(...
'Parent',get(hSlider,'Parent'),...
'Units',get(hSlider,'Units'),...
'String',get(hSlider,'String'),...
'Style','edit',...
'Enable','off',...
'HorizontalAlignment',LabelAlign,...
'Position',LabelPosition,...
'Tag',LabelName);
end
function syncSliders(I,Tag,TabName)
if nargin < 3
TabName='ThresholdTab';
end
if strendswith(Tag,'Number')
TargetTag=[Tag(1:end-6) 'Slider'];
Value=str2double(get(I.Interface.(TabName).(Tag),'String'));
MaxVal=get(I.Interface.(TabName).(TargetTag),'Max');
MinVal=get(I.Interface.(TabName).(TargetTag),'Min');
if Value>MaxVal
Value=MaxVal;
set(I.Interface.(TabName).(Tag),'String',num2str(Value));
elseif Value<MinVal
Value=MinVal;
set(I.Interface.(TabName).(Tag),'String',num2str(Value));
end
set(I.Interface.(TabName).(TargetTag),'Value',Value);
elseif strendswith(Tag,'Slider')
TargetTag=[Tag(1:end-6) 'Number'];
set(I.Interface.(TabName).(TargetTag),'String',num2str(get(I.Interface.(TabName).(Tag),'Value')));
end
end
function rescaleSlider(I,ScaleSlider,Image,TabName)
if nargin<4
TabName='ThresholdTab';
end
MaxScale=max(Image(:));
MinScale=min(Image(:));
Range=double(MaxScale-MinScale);
if Range>100
SliderStep=[1 round(Range/20)]/Range;
elseif Range>50
SliderStep=[1 round(Range/10)]/Range;
elseif Range>5
SliderStep=[1 round(Range/5)]/Range;
else