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CSTCheckResults.m
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CSTCheckResults.m
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function CSTCheckResults(videoIdxToLoad, wormIdxToLoad)
% Copyright (c) 2013 Rutgers
% Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
% The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
% THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
global filenames fileDB colFtlWell mainPnlW mainPnlH filterNames filterSelection listOfWorms;
thresholdDistPixel = 4;
flagShowCurvaturePlots = false;
flagPlotCurvOnly = false;
totalWormsChecked = 0;
allMeasures = struct();
tmpDraw = [];
% ----------
% Variables storing the currently displayed video, frame, worm
% ----------
listOfWorms = cell(1,0);
nbOfWorms = 0;
nbOfFrames = 0;
imageFiles = [];
currentFrame = 1;
currentImage = [];
currentWorm = 0;
currentVideo = 0;
xImage = 0;
yImage = 0;
nbSamplesCBL = 24;
% ----------
% Measures to be computed
% ----------
listOfWorms.status = cell(1,0);
measures.highThr = [];
measures.lowThr = [];
measures.prevThr = [];
measures.highThrDef = [];
measures.lowThrDef = [];
measures.prevThrDef = [];
measures.usability = [];
centerMovedSignificantly = [];
% ----------
% Flag indicating that new glare zones have been defined
% ----------
flagNewZones = true;
% ----------
% Variables to switch worms
% ----------
valueStartFrame = 1;
valueEndFrame = 1;
idxOtherWorm = 1;
wormSwitchIdx =[];
% ----------
% Variables to define blocks and validity
% ----------
listOfWorms.manualInvalid = [];
listOfWorms.manualValid = [];
measures.manualSeparators = [];
measures.separators = [];
tmpAfterSelfOverlap = [];
% ============
% CREATE THE INTERFACE
% ============
% ----------
% Colors for display
% ----------
colorRejected = [0.8 0 0];
colorAccepted = [0.1 0.8 0.1];
colorTrajectory = [0.4 0.4 1];
colorThrash = [1 0.3 0.3];
% ----------
% Flag to display measures superimposed on the videos
% ----------
flagShowCBLSub = false;
flagShowTrajectory = false;
flagShowThrash = false;
% ----------
% Handles for the graphic objects to update for animation
% ----------
hLineHighThr = [];
hLineLowThr = [];
hLinePrevThr = [];
hRectCurrentFrame = [];
hSubImage = [];
hMainImage = [];
hShowHead = [];
hShowTail = [];
hMainAllWorms = [];
hMainTextWorms = [];
hMainBox = [];
hSubWorm = [];
displayAroundWorms = 10;
hTraj = [];
hGlareZones = cell(0);
hCBLSub = [];
hThrash = [];
% ----------
% Main figure and sliders
% ----------
scrsz = get(0,'ScreenSize');
mainW = min(mainPnlW, scrsz(3) - 10);
mainH = min(mainPnlH, scrsz(4) - 70);
mainPanelPosition = [2 , mainH-mainPnlH-2 , mainPnlW+50 , mainPnlH+50];
mainFigure = figure('Visible','off','Position',[5,40,mainW,mainH],'Name','CeleST: Compute Measures - Select videos, inspect their validity, compute the measures','numbertitle','off', 'menubar', 'none', 'resizefcn', @resizeMainFigure);
mainPanel = uipanel('parent', mainFigure,'BorderType', 'none','units','pixels', 'position', mainPanelPosition);
sliderHoriz = uicontrol('parent',mainFigure,'style','slider','position',[0 0 mainW-20 20],'max', 1,'min',0, 'value',0,'callback',@setMainPanelPositionBySliders);
sliderVert = uicontrol('parent',mainFigure,'style','slider','position',[mainW-20 20 20 mainH-20],'max', max(1,-mainPanelPosition(2)),'min',0, 'value',max(1,-mainPanelPosition(2)),'callback',@setMainPanelPositionBySliders);
set(mainFigure, 'color', get(mainPanel,'backgroundcolor'), 'keypressfcn', @keyboardShortcuts);
% ----------
% Filters
% ----------
filterH = 100;
filterW = 150;
hFilters = filterH + 20;
yFilters = mainPanelPosition(4) - hFilters - 5;
pnlFilters = uipanel('parent', mainPanel,'BorderType', 'none','units','pixels', 'position', [1 yFilters mainPnlW hFilters]);
for idxtmp = 0:length(filterNames)-1
uicontrol('parent',pnlFilters,'style','text','string',filterNames{idxtmp+1},'position',[idxtmp*filterW filterH filterW 20])
flt.(filterNames{idxtmp+1}) = uicontrol('parent',pnlFilters,'style','listbox','String',{''},'max',2,'min',0,'position',[idxtmp*filterW 0 filterW filterH],'callback',@setFilteredList);
end
% ----------
% List of videos
% ----------
txtListVideos = uicontrol('parent',mainPanel,'style','text','HorizontalAlignment', 'left','String','Select a video (0 filtered)','position',[0 yFilters-25 2*filterW 20]);
listVideos = uicontrol('parent',mainPanel,'style','listbox','String',{''},'position',[0 yFilters-2*filterH-25 2*filterW 2*filterH],'callback', @checkSelectedVideo);
listVideosIdx = [];
closeBtn = uicontrol('parent', mainPanel, 'style', 'pushbutton', 'string', 'Close (not saving)','position', [0 yFilters-filterH-165 filterW 30],'callback', @closeWindow);
% ----------
% List of worms
% ----------
pnlLoad = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [320 yFilters-filterH-185 2*filterW+120 270]);
txtVideoLoaded = uicontrol('parent',pnlLoad,'style','text','HorizontalAlignment', 'center','String','< Please Click a Video From the List to Load >','fontweight','bold','position',[0 210 2*filterW+100 20]);
listWorms = uicontrol('parent',pnlLoad,'style','listbox','String',{''},'max',1,'min',0,'position',[1 70 filterW filterH],'callback', @selectWorm);
validateWormBtn = uicontrol('parent',pnlLoad,'style','pushbutton','string','Validate', 'position', [0 40 75 30],'callback', @validateWorm);
rejectWormBtn = uicontrol('parent',pnlLoad,'style','pushbutton','string','Reject', 'position', [75 40 75 30],'callback', @rejectWorm);
saveAndComputeMeasuresBtn = uicontrol('parent', pnlLoad, 'style', 'pushbutton', 'string', 'Save and Compute measures','position', [0 0 2*filterW 30],'callback', @updateMeasureForCurrentVideo);
glareZonesBtn = uicontrol('parent', pnlLoad, 'style', 'pushbutton', 'string', 'Glare zones','position', [180 180 120 20],'callback', @manageGlareZones);
% ----------
% Switch trajectories
% ----------
pnlSwitch = uipanel('parent',pnlLoad,'BorderType', 'none','units','pixels', 'position', [180 50 120 filterH+15]);
uicontrol('parent',pnlSwitch,'style','text','HorizontalAlignment', 'left','String','From frame','position',[0 80 80 20]);
editFrameCutStart = uicontrol('parent',pnlSwitch,'style','edit','string','1','position',[70 80 50 25]);
uicontrol('parent',pnlSwitch,'style','text','HorizontalAlignment', 'left','String','to frame','position',[0 60 80 20]);
editFrameCutEnd = uicontrol('parent',pnlSwitch,'style','edit','string','1','position',[70 60 50 25]);
uicontrol('parent',pnlSwitch,'style','text','HorizontalAlignment', 'left','String','switch ','position',[0 40 50 20]);
txtSelectedWorm = uicontrol('parent',pnlSwitch,'style','text','String','< n/a >','position',[45 40 60 20]);
uicontrol('parent',pnlSwitch,'style','text','HorizontalAlignment', 'left','String','and','position',[0 20 40 20]);
popWormSwitch = uicontrol('parent',pnlSwitch,'style','popupmenu','String',{'< n/a >'},'value',idxOtherWorm,'position',[25 25 90 20],'callback',@setWormSwitch);
switchWormsBtn = uicontrol('parent',pnlSwitch,'style','pushbutton','String','Switch','position',[1 1 120 20],'callback', @switchWorms);
% ----------
% Switch head and tail
% ----------
pnlSwitchHeadTail = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [320 yFilters-335 2*filterW 50]);
toggleLabelHeadTail = uicontrol('parent',pnlSwitchHeadTail,'Style','checkbox','String','Label Head/Tail','position',[0 25 150 25], 'Callback', @labelHeadTail);
uicontrol('parent',pnlSwitchHeadTail,'style','text','HorizontalAlignment', 'left','String','From ','position',[0 0 40 20]);
editFrameSwitchHTStart = uicontrol('parent',pnlSwitchHeadTail,'Style','edit','String','1','position',[40 2 50 25]);
uicontrol('parent',pnlSwitchHeadTail,'style','text','HorizontalAlignment', 'left','String','to ','position',[90 0 20 20]);
editFrameSwitchHTEnd = uicontrol('parent',pnlSwitchHeadTail,'Style','edit','String','-','position',[110 2 50 25]);
switchHTBtn = uicontrol('parent',pnlSwitchHeadTail,'style','pushbutton','String','Switch H / T','position',[160 2 120 25],'callback', @switchHeadTail);
% ----------
% Video of all field
% ----------
hAxeAllVideo = axes('parent', mainPanel, 'units','pixels','position',[4*filterW+560 yFilters-filterH-235 500 320],'xtick',[],'ytick',[],'color',[.5 .5 .5]);
axis('image','ij')
% ----------
% Video of selected worm
% ----------
hAxeCurrentWorm = axes('parent', mainPanel, 'units','pixels','position',[4*filterW+120 yFilters-filterH-190 410 275],'xtick',[],'ytick',[],'color',[.5 .5 .5]);
axis('image','ij')
% ----------
% Navigation through the frames
% ----------
pnlNavigate = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [4*filterW+100 yFilters-335 460 40]);
uicontrol('parent',pnlNavigate,'style','text','HorizontalAlignment', 'left','string','1','position',[5 6 10 20]);
btnFirstFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','<<<','position',[15 1 40 35],'callback',@selectFrameByClick);
editStartFrame = uicontrol('parent',pnlNavigate,'style','edit','string','-','position',[55 1 40 35],'callback',@selectFrameByClick);
btnRewindFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','<<','position',[95 1 40 35],'callback',@selectFrameByClick);
btnPrevFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','<','position',[135 1 40 35],'callback',@selectFrameByClick);
editCurrentFrame = uicontrol('parent',pnlNavigate,'style','edit','string','-','position',[175 1 40 35],'callback',@selectFrameByClick);
btnNextFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','>','position',[275 1 40 35],'callback',@selectFrameByClick);
btnForwardFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','>>','position',[315 1 40 35],'callback',@selectFrameByClick);
editEndFrame = uicontrol('parent',pnlNavigate,'style','edit','string','-','position',[355 1 40 35],'callback',@selectFrameByClick);
btnLastFrame = uicontrol('parent',pnlNavigate,'style','pushbutton','string','>>>','position',[395 1 40 35],'callback',@selectFrameByClick);
txtMaxFrame = uicontrol('parent',pnlNavigate,'style','text','HorizontalAlignment', 'left','string','-','position',[435 6 40 20]);
btnPlayVideo = uicontrol('parent',pnlNavigate,'style','togglebutton','string','Play','position',[215 1 60 35],'callback',@playPauseVideo);
% ----------
% Panel for validity
% ----------
pnlValidity = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 525 3*544+25 90]);
hAxeValid = axes('parent', pnlValidity, 'units','pixels','position',[25 10 3*544 30],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlValidity,'style','text','HorizontalAlignment', 'left','string','Validity of the segmented body: ','position',[25 55 250 20]);
txtValid = uicontrol('parent',pnlValidity,'style','text','HorizontalAlignment', 'left','string','Valid frames: - / - = - %','position',[300 55 275 20], 'foregroundcolor', [0.1 0.5 0.1]);
txtReject = uicontrol('parent',pnlValidity,'style','text','HorizontalAlignment', 'left','string','Rejected frames: - / - = - %','position',[575 55 275 20], 'foregroundcolor' , [0.7 0 0]);
nextBlockBtn = uicontrol('parent',pnlValidity,'style','pushbutton','string','Next block','position',[875 55 100 35],'callback',@selectNextBlock);
switchValidityBtn = uicontrol('parent',pnlValidity,'style','pushbutton','string','Switch validity (right click)','position',[1015 55 190 35],'callback',@switchValidity);
splitBlockBtn = uicontrol('parent',pnlValidity,'style','pushbutton','string','Split block (double click)','position',[1215 55 190 35],'callback',@splitBlock);
isolateFrameBtn = uicontrol('parent',pnlValidity,'style','pushbutton','string','Isolate frame (triple click)','position',[1415 55 190 35],'callback',@isolateFrame);
% ----------
% Panel for glare zones
% ----------
pnlGlare = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 460 3*544+25 60]);
hAxeGlare = axes('parent', pnlGlare, 'units','pixels','position',[25 10 3*544 30],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlGlare,'style','text','HorizontalAlignment', 'left','string','Within glare zones: ','position',[25 42 200 20]);
% ----------
% Panel for lost
% ----------
pnlLost = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 395 3*544+25 60]);
hAxeLost = axes('parent', pnlLost, 'units','pixels','position',[25 10 3*544 30],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlLost,'style','text','HorizontalAlignment', 'left','string','Lost during tracking: ','position',[25 42 200 20]);
% ----------
% Panel for overlap
% ----------
pnlOverlap = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 330 3*544+25 60]);
hAxeOverlap = axes('parent', pnlOverlap, 'units','pixels','position',[25 10 3*544 30],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlOverlap,'style','text','HorizontalAlignment', 'left','string','Overlap with other worm: ','position',[25 42 200 20]);
% ----------
% Panel for self-overlap
% ----------
pnlSelfOverlap = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 265 3*544+25 60]);
hAxeSelfOverlap = axes('parent', pnlSelfOverlap, 'units','pixels','position',[25 10 3*544 30],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlSelfOverlap,'style','text','HorizontalAlignment', 'left','string','End of self-overlap: ','position',[25 42 200 20]);
% ----------
% Panel for prev overlap
% ----------
pnlPrevOverlap = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [1 160 3*544+25 110]);
hAxePrevOverlap = axes('parent', pnlPrevOverlap, 'units','pixels','position',[25 20 3*544 60],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlPrevOverlap,'style','text','HorizontalAlignment', 'left','string','Self-overlap with previous frame (in %): ','position',[25 82 250 20]);
uicontrol('parent',pnlPrevOverlap,'style','text','HorizontalAlignment', 'right','string','Threshold: ','position',[275 82 90 20]);
btnPrevThrUp = uicontrol('parent',pnlPrevOverlap,'style','pushbutton','string','^','position',[365 82 40 25],'callback',@selectThreshold);
editPrevThr = uicontrol('parent',pnlPrevOverlap,'style','edit','string','25','position',[405 82 45 25],'callback',@selectThreshold);
btnPrevThrDown = uicontrol('parent',pnlPrevOverlap,'style','pushbutton','string','v','position',[450 82 40 25],'callback',@selectThreshold);
btnPrevThrDefault = uicontrol('parent',pnlPrevOverlap,'style','pushbutton','string','Undo','position',[490 82 40 25],'callback',@selectThreshold);
% ----------
% Panel for body length
% ----------
pnlBodyLength = uipanel('parent',mainPanel,'BorderType', 'none','units','pixels', 'position', [0 40 3*544+25 130]);
hAxeLength = axes('parent', pnlBodyLength, 'units','pixels','position',[25 20 3*544 60],'xtick',[],'ytick',[],'color',[.5 .5 .5],'ButtonDownFcn', @selectFrameByClick);
uicontrol('parent',pnlBodyLength,'style','text','HorizontalAlignment', 'left','string','Length of the segmented body: ','position',[25 81 200 20]);
uicontrol('parent',pnlBodyLength,'style','text','HorizontalAlignment', 'right','string','High threshold: ','position',[225 106 140 20]);
btnHighThrUp = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','^','position',[365 106 40 25],'callback',@selectThreshold);
editHighThr = uicontrol('parent',pnlBodyLength,'style','edit','string','0','position',[405 106 45 25],'callback',@selectThreshold);
btnHighThrDown = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','v','position',[450 106 40 25],'callback',@selectThreshold);
btnHighThrDefault = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','Undo','position',[490 106 40 25],'callback',@selectThreshold);
uicontrol('parent',pnlBodyLength,'style','text','HorizontalAlignment', 'right','string','Low threshold: ','position',[225 82 140 20]);
btnLowThrUp = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','^','position',[365 82 40 25],'callback',@selectThreshold);
editLowThr = uicontrol('parent',pnlBodyLength,'style','edit','string','0','position',[405 82 45 25],'callback',@selectThreshold);
btnLowThrDown = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','v','position',[450 82 40 25],'callback',@selectThreshold);
btnLowThrDefault = uicontrol('parent',pnlBodyLength,'style','pushbutton','string','Undo','position',[490 82 40 25],'callback',@selectThreshold);
% ============
% SHOW THE INTERFACE
% ============
populateFilters
set(mainFigure,'visible','on')
setMainPanelPositionBySliders
pause(0.1)
if flagShowCurvaturePlots
hPlots = figure('Position',[5,40,mainW,mainH]);
if flagPlotCurvOnly
hOnlyCurv = figure('Position',[5,600,mainW,250]);
end
end
% ------------
% Case where this function was called from the visualization GUI, and needs to load a specific video and worm
% ------------
if nargin >= 2
loadVideoContents
set(listWorms, 'value', wormIdxToLoad);
selectWorm
end
flagRemoveTempMeasures = true;
% ----------
% UI elements to block
% ----------
listToDisable = {listVideos,listWorms, validateWormBtn, rejectWormBtn, saveAndComputeMeasuresBtn, glareZonesBtn, switchWormsBtn, switchHTBtn, switchValidityBtn, splitBlockBtn, isolateFrameBtn, nextBlockBtn,...
btnFirstFrame, editStartFrame, btnRewindFrame, btnPrevFrame, editCurrentFrame, btnNextFrame, btnForwardFrame, editEndFrame, btnLastFrame, txtMaxFrame, btnPlayVideo, closeBtn};
% ------------
% Waiting for closure
% ------------
waitfor(mainFigure,'BeingDeleted','on');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% SUBFUNCTIONS
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function switchHeadTail(hObject, eventdata)
try
if currentWorm~=0
for ff = max(1,min(nbOfFrames, floor(str2double(get(editFrameSwitchHTStart, 'string'))))):max(1,min(nbOfFrames, floor(str2double(get(editFrameSwitchHTEnd, 'string')))))
listOfWorms.skel{currentWorm}{ff} = listOfWorms.skel{currentWorm}{ff}(:,end:-1:1);
listOfWorms.width{currentWorm}{ff} = listOfWorms.width{currentWorm}{ff}(end:-1:1);
end
selectWorm;
CSTwriteSegmentationToTXT(listOfWorms, fileDB(currentVideo).name);
else
warndlg('Please select a video','No Video Selected');
end
catch exception
generateReport(exception)
end
end
function labelHeadTail(hObject, eventdata)
try
if ~isempty(tmpDraw)
if get(toggleLabelHeadTail, 'Value')
hold(hAxeCurrentWorm, 'on')
if isempty(hShowHead) || ~ishandle(hShowHead)
hShowHead = text(tmpDraw(1,1),tmpDraw(2,1),'\leftarrow Head','Color','r','FontWeight','bold','Parent',hAxeCurrentWorm);
hShowTail = text(tmpDraw(1,round(length(tmpDraw)/2)),tmpDraw(2,round(length(tmpDraw)/2)),'\leftarrow Tail','Color','r','FontWeight','bold','Parent',hAxeCurrentWorm);
else
set(hShowHead, 'Position', [tmpDraw(1,1),tmpDraw(2,1)], 'Visible', 'on');
set(hShowTail, 'Position', [tmpDraw(1,round(length(tmpDraw)/2)),tmpDraw(2,round(length(tmpDraw)/2))], 'Visible', 'on');
end
set(hShowHead, 'Visible', 'on');
set(hShowTail, 'Visible', 'on');
else
set(hShowHead, 'Visible', 'off');
set(hShowTail, 'Visible', 'off');
end
end
catch exception
generateReport(exception)
end
end
function setAllEnable(action)
for item = 1:length(listToDisable)
set(listToDisable{item}, 'enable', action);
end
end
function updateMeasureForCurrentVideo(hObject, eventdata)
try
if currentVideo == 0
return
end
setAllEnable('off');
hTmp = waitbar(0,'Saving the results...');
pause(0.001)
finalNames = {'Wave_Initiation_Rate_Median', 'Wave_Initiation_Rate_Range', 'Body_Wave_Number_Median', 'Body_Wave_Number_Range', 'Asymmetry_Median', 'Asymmetry_Range', ...
'Curling', 'Stretch_Median', 'Stretch_Range', 'Traveling_Speed_Mean', 'Brush_Stroke_Median', 'Brush_Stroke_Range', 'Activity_Index_Median', 'Activity_Index_Range'...
, 'Wave_Initiation_Rate_10' 'Body_Wave_Number_10', 'Asymmetry_10', 'Stretch_10', 'Brush_Stroke_10', 'Activity_Index_10'...
};
for measureIdx = 1:length(finalNames)
allMeasures.(finalNames{measureIdx}) = NaN(1,nbOfWorms);
end
finalNamesAllValues = {'Wave_Initiation_Rate_All', 'Body_Wave_Number_All', 'Asymmetry_All', ...
'Curling_All', 'Stretch_All', 'Traveling_Speed_All', 'Brush_Stroke_All', 'Activity_Index_All'...
};
for measureIdx = 1:length(finalNamesAllValues)
allMeasures.(finalNamesAllValues{measureIdx}) = zeros(nbOfWorms,2*nbOfFrames);
end
allMeasures.('Curling_All') = NaN(nbOfWorms, nbOfFrames);
allMeasures.usability = NaN(1,nbOfWorms);
oldNames = {'status', 'highThr', 'lowThr', 'prevThr', 'highThrDef', 'lowThrDef', 'prevThrDef', 'usability', 'manualSeparators', 'separators'};
for oldIdx = 1:length(oldNames)
if strcmp(oldNames{oldIdx}, 'status')
allMeasures.(oldNames{oldIdx}) = listOfWorms.status;
else
allMeasures.(oldNames{oldIdx}) = measures.(oldNames{oldIdx});
end
end
totWorms = 0;
for wormToMeasure = 1:nbOfWorms
if isgraphics(hTmp); waitbar(wormToMeasure/nbOfWorms,hTmp,['Calculating Measures for Worm:' num2str(wormToMeasure) ' of ' num2str(nbOfWorms)]); end
if strcmp(listOfWorms.status{wormToMeasure}, 'rejected')
continue
end
totWorms = totWorms + 1;
%-----------------
% Usability
%-----------------
allMeasures.usability(wormToMeasure) = mean(listOfWorms.valid(wormToMeasure, :));
%-----------------
% Curvature
%-----------------
flagSmoothCurvature = true;
flagSuperSampleCurvature = true;
[ temporalFreq , spatialFreq , dynamicAmplitude , curvature ] = CSTComputeMeasuresFromBody(listOfWorms.skel{wormToMeasure}, flagSmoothCurvature, flagSuperSampleCurvature, listOfWorms.valid(wormToMeasure,:));
rangeUsable = ~isnan(temporalFreq);
if isempty(rangeUsable)
return
end
%-----------------
% Wave Initiation Rate
%-----------------
allMeasures.('Wave_Initiation_Rate_All')(wormToMeasure,rangeUsable) = fileDB(currentVideo).frames_per_second * 60 * temporalFreq(rangeUsable);
allMeasures.('Wave_Initiation_Rate_Median')(wormToMeasure) = fileDB(currentVideo).frames_per_second * 60 * median(temporalFreq(rangeUsable));
allMeasures.('Wave_Initiation_Rate_Range')(wormToMeasure) = fileDB(currentVideo).frames_per_second * 60 * ( prctile(temporalFreq(rangeUsable),90) - prctile(temporalFreq(rangeUsable),10) );
allMeasures.('Wave_Initiation_Rate_10')(wormToMeasure) = fileDB(currentVideo).frames_per_second * 60 * prctile(temporalFreq(rangeUsable),10);
%-----------------
% Body Wave Number
%-----------------
allMeasures.('Body_Wave_Number_All')(wormToMeasure,rangeUsable) = spatialFreq(rangeUsable);
allMeasures.('Body_Wave_Number_Median')(wormToMeasure) = median(abs(spatialFreq(rangeUsable)));
allMeasures.('Body_Wave_Number_Range')(wormToMeasure) = ( prctile(abs(spatialFreq(rangeUsable)),90) - prctile(abs(spatialFreq(rangeUsable)),10) );
allMeasures.('Body_Wave_Number_10')(wormToMeasure) = prctile(abs(spatialFreq(rangeUsable)),10);
%-----------------
% Symmetry / Lateral preference
%-----------------
totalCurvature = mean(curvature(:,3:end),2);
averCurvature = zeros(1,length(totalCurvature));
for ff = 1:length(totalCurvature)
if temporalFreq(ff) > 0
period = max(3,min(50,fix(1/temporalFreq(ff))));
else
period = 50;
end
timeRange = max(1, min(length(totalCurvature), ff-period)):max(1, min(length(totalCurvature), ff+period));
averCurvature(ff) = mean(totalCurvature(timeRange));
end
rangeUsable2 = ~isnan(averCurvature(:) .* totalCurvature(:));
tmpAverCurvature = averCurvature(rangeUsable2);
allMeasures.('Asymmetry_All')(wormToMeasure,rangeUsable2) = tmpAverCurvature;
allMeasures.('Asymmetry_Median')(wormToMeasure) = median(tmpAverCurvature);
allMeasures.('Asymmetry_Range')(wormToMeasure) = ( prctile(tmpAverCurvature,90) - prctile(tmpAverCurvature,10) );
allMeasures.('Asymmetry_10')(wormToMeasure) = prctile(tmpAverCurvature,10);
%-----------------
% Curling
%-----------------
usableFrames = 0;
for ff = 1:nbOfFrames
if listOfWorms.valid(wormToMeasure, ff)
usableFrames = usableFrames + 1;
% distance head to lower-body
idxHd = 1;
idxTail = size(listOfWorms.skel{wormToMeasure}{ff}, 2);
idxMid = round(idxTail / 2);
xx = listOfWorms.skel{wormToMeasure}{ff}(1,:);
yy = listOfWorms.skel{wormToMeasure}{ff}(2,:);
minDistHead = min(hypot(xx(idxHd) - xx(idxMid:idxTail), yy(idxHd) - yy(idxMid:idxTail)));
minDistTail = min(hypot(xx(idxTail) - xx(idxHd:idxMid), yy(idxTail) - yy(idxHd:idxMid)));
allMeasures.('Curling_All')(wormToMeasure, ff) = min(minDistHead, minDistTail);
end
end
allMeasures.('Curling')(wormToMeasure) = sum( allMeasures.('Curling_All')(wormToMeasure, :) <= thresholdDistPixel ) / usableFrames * 60; % in seconds(of curling) per minute(of swimming)
%-----------------
% Stretch
%-----------------
allMeasures.('Stretch_All')(wormToMeasure,rangeUsable) = dynamicAmplitude(rangeUsable);
allMeasures.('Stretch_Median')(wormToMeasure) = median(dynamicAmplitude(rangeUsable));
allMeasures.('Stretch_Range')(wormToMeasure) = ( prctile(dynamicAmplitude(rangeUsable) ,90) - prctile(dynamicAmplitude(rangeUsable) ,10) );
allMeasures.('Stretch_10')(wormToMeasure) = prctile(dynamicAmplitude(rangeUsable) ,10);
%-----------------
% Travel speed
%-----------------
deltas = zeros(1,nbOfFrames);
positionCenterX = zeros(1,nbOfFrames);
positionCenterY = zeros(1,nbOfFrames);
ff0 = 1;
if temporalFreq(ff0) > 0
period = max(3,min(50,fix(1/temporalFreq(ff0))));
else
period = 50;
end
timeWindowForSweptAreas = period;
while ff0 + timeWindowForSweptAreas < nbOfFrames
% -----------
% find the next frame with a complete usable range
% -----------
while (ff0 + timeWindowForSweptAreas <= nbOfFrames) && any( ~ listOfWorms.valid(wormToMeasure, ff0 + (0:timeWindowForSweptAreas)))
ff0 = ff0 + 1;
end
if temporalFreq(ff0) > 0
period = max(3,min(50,fix(1/temporalFreq(ff0))));
else
period = 50;
end
timeWindowForSweptAreas = period;
if ff0 + timeWindowForSweptAreas <= nbOfFrames
% -----------
% Initialize mask
% -----------
totalUsed = 0;
for ff = ff0 + (0:timeWindowForSweptAreas)
if listOfWorms.valid(wormToMeasure, ff)
totalUsed = totalUsed + 1;
totalWidth = sum(listOfWorms.width{wormToMeasure}{ff}(:));
positionCenterX(ff0) = positionCenterX(ff0) + sum(listOfWorms.width{wormToMeasure}{ff}(:)' .* listOfWorms.skel{wormToMeasure}{ff}(1,:)) / totalWidth;
positionCenterY(ff0) = positionCenterY(ff0) + sum(listOfWorms.width{wormToMeasure}{ff}(:)' .* listOfWorms.skel{wormToMeasure}{ff}(2,:)) / totalWidth;
end
end
positionCenterX(ff0) = positionCenterX(ff0) / totalUsed;
positionCenterY(ff0) = positionCenterY(ff0) / totalUsed;
if (ff0 > 1) && (positionCenterX(ff0-1) > 0) && (positionCenterY(ff0-1) > 0) && positionCenterX(ff0) >0 && positionCenterY(ff0) >0
deltas(ff0) = hypot(positionCenterX(ff0)-positionCenterX(ff0-1), positionCenterY(ff0)-positionCenterY(ff0-1));
end
end
ff0 = ff0 + 1;
% -----------
% finished
% -----------
end
listOfWorms.positionCenterX(wormToMeasure,:) = positionCenterX;
listOfWorms.positionCenterY(wormToMeasure,:) = positionCenterY;
% mm / min
tmpFramesUsed = length(deltas) - length(find(isnan(deltas)));
rangeUsableDist = ~isnan(deltas);
tmpDistanceTraveled = sum(deltas(rangeUsableDist));
allMeasures.('Traveling_Speed_All')(wormToMeasure, rangeUsableDist) = cumsum(deltas(rangeUsableDist)) * fileDB(currentVideo). mm_per_pixel;
allMeasures.('Traveling_Speed_Mean')(wormToMeasure) = tmpDistanceTraveled / tmpFramesUsed * fileDB(currentVideo). mm_per_pixel * fileDB(currentVideo).frames_per_second * 60;
%-----------------
% Sweeping speed
%-----------------
maskAreaCovered = zeros(yImage, xImage);
averageWormBodyMask = zeros(yImage, xImage);
areaCoveredNorm = zeros(1,nbOfFrames);
sweeping_noTimeNorm = zeros(1, nbOfFrames);
ff0 = 1;
if temporalFreq(ff0) > 0
period = max(3,min(50,fix(1/temporalFreq(ff0))));
else
period = 50;
end
timeWindowForSweptAreas = period;
while ff0 + timeWindowForSweptAreas < nbOfFrames
% -----------
% find the next frame with a complete usable range
% -----------
while (ff0 + timeWindowForSweptAreas < nbOfFrames) && any( ~ listOfWorms.valid(wormToMeasure, ff0 + (0:timeWindowForSweptAreas)))
ff0 = ff0 + 1;
end
if temporalFreq(ff0) > 0
period = max(3,min(50,fix(1/temporalFreq(ff0))));
else
period = 50;
end
timeWindowForSweptAreas = min(period, nbOfFrames - ff0);
if ff0 + timeWindowForSweptAreas <= nbOfFrames
% -----------
% Initialize mask
% -----------
maskAreaCovered(:) = 0;
averageWormBodyArea = 0;
for ff = ff0 + (0:timeWindowForSweptAreas)
averageWormBodyMask(:) = 0;
for vv = 1:length(listOfWorms.width{wormToMeasure}{ff})
rr = max(1, min(yImage, round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
cc = max(1, min(xImage, round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
averageWormBodyMask(rr,cc) = 1 + averageWormBodyMask(rr,cc);
maskAreaCovered(rr,cc) = 1 + maskAreaCovered(rr,cc);
end
averageWormBodyArea = averageWormBodyArea + sum(averageWormBodyMask(:) > 0);
end
areaCoveredNorm(ff0) = sum(maskAreaCovered(:) > 0) / (averageWormBodyArea / (1+timeWindowForSweptAreas));
% -----------
% move to the next frame
% -----------
ff0 = ff0 + 1;
while (ff0 + timeWindowForSweptAreas < nbOfFrames) && listOfWorms.valid(wormToMeasure, ff0+timeWindowForSweptAreas)
% -----------
% remove previous frame
% -----------
ff = ff0 - 1;
averageWormBodyMask(:) = 0;
for vv = 1:length(listOfWorms.width{wormToMeasure}{ff})
rr = max(1, min(yImage, round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
cc = max(1, min(xImage, round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
averageWormBodyMask(rr,cc) = 1 + averageWormBodyMask(rr,cc);
maskAreaCovered(rr,cc) = -1 + maskAreaCovered(rr,cc);
end
averageWormBodyArea = averageWormBodyArea - sum(averageWormBodyMask(:) > 0);
% -----------
% add new frame
% -----------
ff = ff0 + timeWindowForSweptAreas;
averageWormBodyMask(:) = 0;
for vv = 1:length(listOfWorms.width{wormToMeasure}{ff})
rr = max(1, min(yImage, round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(2,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
cc = max(1, min(xImage, round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)-listOfWorms.width{wormToMeasure}{ff}(vv)):round(listOfWorms.skel{wormToMeasure}{ff}(1,vv)+listOfWorms.width{wormToMeasure}{ff}(vv))));
averageWormBodyMask(rr,cc) = 1 + averageWormBodyMask(rr,cc);
maskAreaCovered(rr,cc) = 1 + maskAreaCovered(rr,cc);
end
averageWormBodyArea = averageWormBodyArea + sum(averageWormBodyMask(:) > 0);
areaCoveredNorm(ff0) = sum(maskAreaCovered(:) > 0) / (averageWormBodyArea / (1+timeWindowForSweptAreas));
sweeping_noTimeNorm(ff0) = areaCoveredNorm(ff0) * temporalFreq(ff0*2) * fileDB(currentVideo).frames_per_second * 60;
% -----------
% move to the next frame
% -----------
ff0 = ff0 + 1;
end
end
% -----------
% finished
% -----------
end
tmp = sweeping_noTimeNorm;
allMeasures.('Activity_Index_All')(wormToMeasure,1:length(sweeping_noTimeNorm)) = sweeping_noTimeNorm;
allMeasures.('Activity_Index_Median')(wormToMeasure) = median(tmp(tmp > 0));
allMeasures.('Activity_Index_Range')(wormToMeasure) = ( prctile(tmp(tmp > 0), 90) - prctile(tmp(tmp > 0), 10) );
allMeasures.('Activity_Index_10')(wormToMeasure) = prctile(tmp(tmp > 0), 10);
tmp = areaCoveredNorm(areaCoveredNorm > 0) ./ timeWindowForSweptAreas;
allMeasures.('Brush_Stroke_All')(wormToMeasure, 1:length(tmp)) = tmp;
allMeasures.('Brush_Stroke_Median')(wormToMeasure) = median(tmp);
allMeasures.('Brush_Stroke_Range')(wormToMeasure) = ( prctile(tmp, 90) - prctile(tmp, 10) );
allMeasures.('Brush_Stroke_10')(wormToMeasure) = prctile(tmp, 10);
totalWormsChecked = totalWormsChecked + 1;
end
if flagRemoveTempMeasures
finalNamesAllValues = {'Wave_Initiation_Rate_All', 'Body_Wave_Number_All', 'Asymmetry_All', ...
'Curling_All', 'Stretch_All', 'Traveling_Speed_All', 'Brush_Stroke_All', 'Activity_Index_All'...
};
for measureIdx = 1:length(finalNamesAllValues)
allMeasures = rmfield(allMeasures, finalNamesAllValues{measureIdx});
end
end
pause(0.001);
if currentVideo~=0
if isgraphics(hTmp); waitbar(wormToMeasure/nbOfWorms,hTmp,'Writing Data...'); end
CSTwriteSegmentationToTXT(listOfWorms, fileDB(currentVideo).name)
CSTwriteMeasuresToTXT(allMeasures, fileDB(currentVideo).name, true, listOfWorms.status);
fileDB(currentVideo).measured = true;
fileDB(currentVideo).worms = totWorms;
populateFilters
end
if isgraphics(hTmp); close(hTmp); end
pause(0.001);
setAllEnable('on');
catch exception
generateReport(exception)
end
end
% *****************
% MEASURES
% *****************
% ============
% SHORTCUTS FOR NAVIGATION AND VALIDATION
% ============
function keyboardShortcuts(hObject, eventdata) %#ok<INUSL>
try
if strcmp(eventdata.Key, 'space') && ~isempty(eventdata.Modifier) && strcmp(eventdata.Modifier{1}, 'shift')
isolateFrame
switchValidity
elseif strcmp(eventdata.Key, 'space')
switchValidity
elseif strcmp(eventdata.Key, 'leftarrow')
selectFrameByClick(btnPrevFrame)
elseif strcmp(eventdata.Key, 'rightarrow')
selectFrameByClick(btnNextFrame)
elseif strcmp(eventdata.Key, 'uparrow')
selectNextBlock
elseif strcmp(eventdata.Key, 'pageup')
tmpNewWorm = get(listWorms, 'value') - 1;
if tmpNewWorm >= 1
set(listWorms, 'value', tmpNewWorm);
selectWorm
end
elseif strcmp(eventdata.Key, 'pagedown')
tmpNewWorm = get(listWorms, 'value') + 1;
if tmpNewWorm <= nbOfWorms
set(listWorms, 'value', tmpNewWorm)
selectWorm
end
elseif strcmp(eventdata.Key, 'return')
validateWorm
elseif strcmp(eventdata.Key, 'backspace')
rejectWorm
elseif strcmp(eventdata.Key, 'home')
selectFrameByClick(btnFirstFrame)
end
catch exception
generateReport(exception)
end
end
% ************************
% GLARE ZONES MANAGEMENT
% ************************
% ============
% MANAGE GLARE ZONES FROM A POP-UP WINDOW: DISPLAY, DEFINE, MODIFY, ERASE, SAVE
% ============
function manageGlareZones(hObject,eventdata) %#ok<*INUSD>
try
if currentVideo == 0
return
end
dimImage = 1.5*size(currentImage);
popupPosition = [5,40,dimImage(2)+10,dimImage(1)+50];
hPolygons = cell(1,length(fileDB(currentVideo).glareZones));
hEllipses = cell(1,0);
hPopup = figure('Visible','off','Position',popupPosition,'Name','CeleST: Define glare zone','numbertitle','off', 'menubar', 'none', 'windowstyle', 'modal');
pnlPopup = uipanel('parent', hPopup,'BorderType', 'none','units','pixels', 'position', [0 0 popupPosition(3) popupPosition(4)]);
hAxePopup = axes('parent', pnlPopup, 'units','pixels','position',[5 5 dimImage(2) dimImage(1)],'xtick',[],'ytick',[],'color',[.5 .5 .5]);
uicontrol('parent',pnlPopup,'style','pushbutton','string','New Ellipse','position',[105 dimImage(1)+10 100 35],'callback',@(a,b) newEllipse);
uicontrol('parent',pnlPopup,'style','pushbutton','string','New Polygon','position',[205 dimImage(1)+10 100 35],'callback',@(a,b) newPolygon);
uicontrol('parent',pnlPopup,'style','pushbutton','string','Save and Close','position',[405 dimImage(1)+10 150 35],'callback',@(a,b) saveAll);
uicontrol('parent',pnlPopup,'style','pushbutton','string','Erase zones','position',[655 dimImage(1)+10 100 35],'callback',@(a,b) eraseAll);
image('parent', hAxePopup, 'cdata', currentImage);
axis(hAxePopup, 'equal', 'off', 'image', 'tight','ij');
colormap(gray(255));
for zz = 1:length(fileDB(currentVideo).glareZones)
hPolygons{zz} = impoly(hAxePopup, fileDB(currentVideo).glareZones{zz});
end
set(hPopup,'visible','on');
waitfor(hPopup,'BeingDeleted','on');
checkWormsAgainstGlare
computeBlockSeparatorsAndValidity;
selectWorm
catch exception
generateReport(exception)
end
function newEllipse
hEllipses{end+1} = imellipse(hAxePopup);
end
function newPolygon
hPolygons{end+1} = impoly(hAxePopup);
end
function eraseAll
choice = questdlg('Are you sure you want to erase all the zones?','Erase zones','Erase','Cancel','Cancel');
if strcmp(choice,'Erase')
for it = 1:length(hPolygons)
delete(hPolygons{it});
end
for it = 1:length(hEllipses)
delete(hEllipses{it});
end
hPolygons = cell(1,0);
hEllipses = cell(1,0);
end
end
function saveAll
fileDB(currentVideo).glareZones = cell(1,0);
for it = 1:length(hPolygons)
tmpVertices = round(getPosition(hPolygons{it}));
fileDB(currentVideo).glareZones{end+1} = tmpVertices([1:end,1],:);
end
for it = 1:length(hEllipses)
tmpVertices = round(getVertices(hEllipses{it}));
fileDB(currentVideo).glareZones{end+1} = tmpVertices(1:2:end,:);
end
flagNewZones = true;
set(hPopup,'visible','off');
delete(hPopup);
end
end
% ============
% CHECK WHETHER WORMS ARE WITHIN THE GLARE ZONES THROUGHOUT THE VIDEO
% ============
function checkWormsAgainstGlare
try
if isfield(fileDB, 'glareZones')
% Build a mask of glare regions
hWaitBar = waitbar(0,'Detecting the overlap of worms with glare zones...');
pause(0.001)
mask = false(yImage, xImage);
for zz = 1:length(fileDB(currentVideo).glareZones)
if ~isempty(fileDB(currentVideo).glareZones{zz})
mask = mask | poly2mask(fileDB(currentVideo).glareZones{zz}(:,1), fileDB(currentVideo).glareZones{zz}(:,2), yImage, xImage);
end
end
for ww = 1:nbOfWorms
if isgraphics(hWaitBar); waitbar(ww/nbOfWorms, hWaitBar); end
for ff = 1:nbOfFrames
skel = round(listOfWorms.skel{ww}{ff});
flagIn = false;
for vv = 1:size(skel,2)
if mask(max(1,min(yImage,skel(2,vv))), max(1,min(xImage,skel(1,vv))))
flagIn = true;
break
end
end
listOfWorms.inGlareZone(ww,ff) = flagIn;
end
end
if isgraphics(hWaitBar); close(hWaitBar); end
pause(0.001)
end
catch exception
generateReport(exception)
end
end
% ************************
% WORM SWITCHING
% ************************
% ============
% SELECT THE WORM TO BE SWITCHED FROM THE DROP-DOWN LIST IN THE GUI
% ============
function setWormSwitch(hObject,eventdata) %#ok<*INUSD>
try
valueSelected = get(popWormSwitch, 'value');
if valueSelected <= 0
set(popWormSwitch, 'value', idxOtherWorm);
else
idxOtherWorm = valueSelected;
end
catch exception
generateReport(exception)
end
end
% ============
% SWITCH THE TWO SELECTED WORMS
% ============
function switchWorms(hObject,eventdata)
try
frameCutStart = floor(str2double(get(editFrameCutStart, 'string')));
if isnan(frameCutStart) || frameCutStart < 1 || frameCutStart > nbOfFrames
return
end
frameCutEnd = floor(str2double(get(editFrameCutEnd, 'string')));
if isnan(frameCutEnd) || frameCutEnd < 1 || frameCutEnd > nbOfFrames
return
end
if (frameCutEnd < frameCutStart)
helpdlg('The frames defining the switch are not consistent. The initial frame index should be smaller than the final one.','CeleST');
return
end
choice = questdlg('Are you sure you want to switch the worms?','Switch worms','Switch','Cancel','Cancel');
if strcmp(choice,'Switch')
worm1 = currentWorm;
worm2 = wormSwitchIdx(get(popWormSwitch,'value'));
listBoolean = {'missed', 'lost', 'overlapped', 'valid', 'outOfLengths', 'outOfPrevious', 'inGlareZone', 'selfOverlap', 'manualInvalid', 'manualValid'};
listCell = {'skel', 'width', 'cblSubSampled'};
listCellSingle = {'localthreshold'};
listDouble = {'lengthWorms', 'positionCenterX', 'positionCenterY', 'widthCenter', 'overlapPrev', 'headThrashCount'};
% Removed deprecated fields from listDouble: 'angleHead', 'angleTail', 'I', 'J', 'C', 'S', 'O'
if worm2 < 0
disp('create new worm ')
% ---------
% Create a new worm
% ---------
nbOfWorms = 1 + nbOfWorms;
worm2 = nbOfWorms;
for idx = 1:length(listBoolean)
listOfWorms.(listBoolean{idx})(worm2,1:nbOfFrames) = false;
end
listOfWorms.lost(worm2,:) = true;
for idx = 1:length(listCell)
for ff = 1:nbOfFrames
listOfWorms.(listCell{idx}){worm2}{ff} = listOfWorms.(listCell{idx}){worm1}{frameCutStart};
end
end
for idx = 1:length(listCellSingle)
listOfWorms.(listCellSingle{idx}){worm2} = listOfWorms.(listCellSingle{idx}){worm1};
end
for idx = 1:length(listDouble)
listOfWorms.(listDouble{idx})(worm2,1:nbOfFrames) = listOfWorms.(listDouble{idx})(worm1,frameCutStart);
end
longMean = mean(listOfWorms.lengthWorms(worm2,~listOfWorms.lost(worm2,:) & ~listOfWorms.overlapped(worm2,:)));
longStd = std(listOfWorms.lengthWorms(worm2,~listOfWorms.lost(worm2,:) & ~listOfWorms.overlapped(worm2,:)));
measures.highThrDef(worm2) = ceil(longMean + 3*longStd);
measures.highThr(worm2) = measures.highThrDef(worm2);
measures.lowThrDef(worm2) = max(0,floor(longMean - 3*longStd));
measures.lowThr(worm2) = measures.lowThrDef(worm2);
listOfWorms.outOfLengths(worm2,:) = (listOfWorms.lengthWorms(worm2,:) > measures.highThr(worm2)) | (listOfWorms.lengthWorms(worm2,:) < measures.lowThr(worm2));
measures.prevThrDef(worm2) = 25;
measures.prevThr(worm2) = measures.prevThrDef(worm2);
listOfWorms.outOfPrevious(worm2,:) = (listOfWorms.overlapPrev(worm2,:)*100 < measures.prevThr(worm2));
listOfWorms.status{worm2} = '';
measures.manualSeparators{worm2} = [];
measures.separators{worm2} = [];
tmpAfterSelfOverlap(worm2,:) = false;
end
% ---------
% Switch the two worms
% ---------
for idx = 1:length(listCell)
buffer = listOfWorms.(listCell{idx}){worm1}(frameCutStart:frameCutEnd);
listOfWorms.(listCell{idx}){worm1}(frameCutStart:frameCutEnd) = listOfWorms.(listCell{idx}){worm2}(frameCutStart:frameCutEnd);
listOfWorms.(listCell{idx}){worm2}(frameCutStart:frameCutEnd) = buffer;
end
for idx = 1:length(listBoolean)
buffer = listOfWorms.(listBoolean{idx})(worm1,frameCutStart:frameCutEnd);
listOfWorms.(listBoolean{idx})(worm1,frameCutStart:frameCutEnd) = listOfWorms.(listBoolean{idx})(worm2,frameCutStart:frameCutEnd);
listOfWorms.(listBoolean{idx})(worm2,frameCutStart:frameCutEnd) = buffer;
end
for idx = 1:length(listDouble)
buffer = listOfWorms.(listDouble{idx})(worm1,frameCutStart:frameCutEnd);
listOfWorms.(listDouble{idx})(worm1,frameCutStart:frameCutEnd) = listOfWorms.(listDouble{idx})(worm2,frameCutStart:frameCutEnd);
listOfWorms.(listDouble{idx})(worm2,frameCutStart:frameCutEnd) = buffer;
end
% ---------
% Check if the extremities of each worm should be switched in the frames that were swapped
% ---------
for ww = [worm1, worm2]
if frameCutStart >= 2
if sum(hypot(listOfWorms.skel{ww}{frameCutStart-1}(1,:)-listOfWorms.skel{ww}{frameCutStart}(1,:), listOfWorms.skel{ww}{frameCutStart-1}(2,:)-listOfWorms.skel{ww}{frameCutStart}(2,:)))...
> sum(hypot(listOfWorms.skel{ww}{frameCutStart-1}(1,:)-listOfWorms.skel{ww}{frameCutStart}(1,end:-1:1), listOfWorms.skel{ww}{frameCutStart-1}(2,:)-listOfWorms.skel{ww}{frameCutStart}(2,end:-1:1)))
% Swap
for ff = frameCutStart:frameCutEnd
listOfWorms.skel{ww}{ff} = listOfWorms.skel{ww}{ff}(:, end:-1:1);
listOfWorms.width{ww}{ff} = listOfWorms.width{ww}{ff}(end:-1:1);
end
end
elseif frameCutEnd <= nbOfFrames-1
if sum(hypot(listOfWorms.skel{ww}{frameCutEnd}(1,:)-listOfWorms.skel{ww}{frameCutEnd+1}(1,:), listOfWorms.skel{ww}{frameCutEnd}(2,:)-listOfWorms.skel{ww}{frameCutEnd+1}(2,:)))...
> sum(hypot(listOfWorms.skel{ww}{frameCutEnd}(1,:)-listOfWorms.skel{ww}{frameCutEnd+1}(1,end:-1:1), listOfWorms.skel{ww}{frameCutEnd}(2,:)-listOfWorms.skel{ww}{frameCutEnd+1}(2,end:-1:1)))
% Swap
for ff = frameCutStart:frameCutEnd
listOfWorms.skel{ww}{ff} = listOfWorms.skel{ww}{ff}(:, end:-1:1);
listOfWorms.width{ww}{ff} = listOfWorms.width{ww}{ff}(end:-1:1);
end
end
end
end
listOfWorms.status{worm1} = 'unchecked';
listOfWorms.status{worm2} = 'unchecked';
computeBlockSeparatorsAndValidity
% ---------
% Update the interface
% ---------
nbOfWorms = length(listOfWorms.skel);
newListTmp = cell(1,nbOfWorms);
for tmp = 1:nbOfWorms
newListTmp{tmp} = ['Worm ', num2str(tmp), ' : ', listOfWorms.status{tmp}];
end
set(listWorms, 'string', newListTmp);
selectWorm;
end
catch exception
generateReport(exception)
end
end
% ************************
% BLOCK MANAGEMENT
% ************************
% ============
% COMPUTE THE BLOCK SEPARATORS USING THE MANUALLY DEFINED ONES AND THE AUTOMATICALLY DEFINES ONES
% ============
function computeBlockSeparatorsAndValidity
% ------------
% Ensure there are worms to compute Separators and Validity for
% ------------
if nbOfWorms == 0
return
end
% ------------
% Find the frames at the end of a self-overlap zone
% ------------
tmpAfterSelfOverlap = [false(nbOfWorms,1) , listOfWorms.selfOverlap(:,1:end-1) & ~listOfWorms.selfOverlap(:,2:end) ];
% ------------
% Compute the validity of the frames
% ------------
listOfWorms.valid = listOfWorms.manualValid | (~ (listOfWorms.manualInvalid...
| listOfWorms.outOfLengths | listOfWorms.outOfPrevious | listOfWorms.lost | listOfWorms.overlapped | listOfWorms.inGlareZone ...
| tmpAfterSelfOverlap));
% ------------
% Define the block separators
% ------------
for ww = 1:nbOfWorms
if ~strcmp(listOfWorms.status{ww}, 'rejected')
measures.separators{ww} = unique(sort([...
1, 1+nbOfFrames, ...
measures.manualSeparators{ww}(:)',...
1 + find(listOfWorms.manualValid(ww,1:end-1) ~= listOfWorms.manualValid(ww,2:end)),...
1 + find(listOfWorms.manualInvalid(ww,1:end-1) ~= listOfWorms.manualInvalid(ww,2:end)),...
1 + find(listOfWorms.outOfLengths(ww,1:end-1) ~= listOfWorms.outOfLengths(ww,2:end)),...
1 + find(listOfWorms.outOfPrevious(ww,1:end-1) ~= listOfWorms.outOfPrevious(ww,2:end)),...
1 + find(listOfWorms.lost(ww,1:end-1) ~= listOfWorms.lost(ww,2:end)),...
1 + find(listOfWorms.overlapped(ww,1:end-1) ~= listOfWorms.overlapped(ww,2:end)),...
1 + find(listOfWorms.inGlareZone(ww,1:end-1) ~= listOfWorms.inGlareZone(ww,2:end)),...
find(tmpAfterSelfOverlap(ww,:)), 1+find(tmpAfterSelfOverlap(ww,:)) ]));
end
end