diff --git a/src/MATLAB/+Editor/CreateMitosisAction.m b/src/MATLAB/+Editor/CreateMitosisAction.m
index c4ca7dbbac402e82224872102dff652629ad7ebd..c16ce02198cf7b4cc7e6b2f481e2beadcaf92e63 100644
--- a/src/MATLAB/+Editor/CreateMitosisAction.m
+++ b/src/MATLAB/+Editor/CreateMitosisAction.m
@@ -3,83 +3,42 @@
%
% Create user identified mitosis events and add to current tree.
-function historyAction = CreateMitosisAction(trackID, dirFlag, treeID, time, linePoints)
- global CellFamilies CellTracks HashedCells
+function historyAction = CreateMitosisAction(trackID, dirFlag, time, linePoints)
+ global CellTracks
if ( time < 2 )
error('Mitosis event cannot be defined in the first frame');
end
- treeTracks = [CellFamilies(treeID).tracks];
-
- bInTracks = Helper.CheckInTracks(time, treeTracks, 0, 0);
- checkTracks = treeTracks(bInTracks);
- if ( isempty(checkTracks) )
- error('No valid tracks to add a mitosis onto');
- end
-
- startTimes = [CellTracks(checkTracks).startTime];
- [minTime minIdx] = min(startTimes);
-
- forceParents = [];
- % If a mitosis is specified RIGHT after another one, we have a problem
- % so force old mitosis children into the list
- if ( minTime == time-1 )
- forceParents = arrayfun(@(x)(CellTracks(x).hulls(1)), checkTracks);
- end
-
+ treeID = CellTracks(trackID).familyID;
linePoints = clipToImage(linePoints);
-
% Find or create hulls to define mitosis event
childHulls = Segmentation.MitosisEditor.FindChildrenHulls(linePoints, time);
- parentHull = Segmentation.MitosisEditor.FindParentHull(childHulls, linePoints, time-1, forceParents);
-
-% costMatrix = Tracker.GetCostMatrix();
-
-% bLeafTrack = arrayfun(@(x)(isempty(x.childrenTracks)), CellTracks(treeTracks));
-% leafTracks = treeTracks(bLeafTrack);
-
- Helper.SetTreeLocked(treeID, 0);
+ parentHull = Segmentation.MitosisEditor.FindParentHull(childHulls, linePoints, time-1);
- % NOTE: This just makes the tree as balanced as possible, it is probably not correct
- balancedTrack = checkTracks(minIdx);
- parentTrack = Hulls.GetTrackID(parentHull);
+ chkDropHull = Helper.GetNearestTrackHull(trackID, time+1,+1);
- % TODO: Don't change things up if parentTrack is already complete and on
- % the correct family
- if ( CellTracks(parentTrack).familyID == treeID )
- balancedTrack = parentTrack;
+ parentTrackID = Hulls.GetTrackID(parentHull);
+ if ( parentTrackID ~= trackID )
+ parentTrackID = Tracks.TearoffHull(parentHull);
+
+ Tracks.ChangeTrackID(parentTrackID, trackID, time-1);
end
- if ( ~isempty(trackID) && dirFlag > 0 )
- balancedTrack = trackID;
- else
- error('Adding mitosis event above edit is currently unsupported!');
+ chkTrackID = Hulls.GetTrackID(childHulls(1));
+ if ( chkTrackID ~= trackID )
+ chkTrackID = Tracks.TearoffHull(childHulls(1));
+ Tracks.ChangeLabel(chkTrackID, trackID, time);
end
- if ( balancedTrack ~= parentTrack )
- attemptLockedChangeLabel(parentTrack, balancedTrack, time-1);
- end
+ newTrackID = Tracks.TearoffHull(childHulls(2));
+ Families.AddMitosis(newTrackID, trackID, time);
- childTrack = Hulls.GetTrackID(childHulls(1));
- if ( balancedTrack ~= childTrack )
- attemptLockedChangeLabel(childTrack, balancedTrack, time);
- end
-
- childTrack = Hulls.GetTrackID(childHulls(2));
- if ( Helper.CheckTreeLocked(childTrack) )
- error('Not yet implemented: Locked "addMitosis"');
- else
- Families.AddMitosis(childTrack, balancedTrack, time);
- end
-
- % TODO: Make this respect the endTime from start of state
- if ( time < length(HashedCells) )
- for i=1:2
- childTrack = Hulls.GetTrackID(childHulls(i));
- Helper.DropSubtree(childTrack);
- end
+ if ( chkDropHull > 0 )
+ leftChildTrackID = Hulls.GetTrackID(childHulls(1));
+ fixupChildTrackID = Hulls.GetTrackID(chkDropHull);
+ Tracks.ChangeLabel(fixupChildTrackID, leftChildTrackID, time+1);
end
Helper.SetTreeLocked(treeID, 1);
@@ -87,14 +46,6 @@ function historyAction = CreateMitosisAction(trackID, dirFlag, treeID, time, lin
historyAction = 'Push';
end
-function attemptLockedChangeLabel(changeTrack, desiredTrack, time)
- if ( Helper.CheckTreeLocked(changeTrack) )
- Tracks.LockedChangeLabel(changeTrack, desiredTrack, time);
- else
- Tracks.ChangeLabel(changeTrack, desiredTrack, time);
- end
-end
-
function newPoints = clipToImage(linePoints)
global CONSTANTS
diff --git a/src/MATLAB/+Editor/MitosisEditInitializeAction.m b/src/MATLAB/+Editor/MitosisEditInitializeAction.m
index bf3f3596a1bafa27b12fda57cf7767278ed2dbdf..c139554d0132b4fdd339a4d965ad4cd7d7ff876a 100644
--- a/src/MATLAB/+Editor/MitosisEditInitializeAction.m
+++ b/src/MATLAB/+Editor/MitosisEditInitializeAction.m
@@ -14,5 +14,5 @@ function historyAction = MitosisEditInitializeAction(treeID, endTime)
CellFamilies(treeID).bLocked = 1;
- historyAction = 'Push';
+ historyAction = '';
end
diff --git a/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m b/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m
new file mode 100644
index 0000000000000000000000000000000000000000..8aea85b38b6bf6a7c4b51d3c9904c3fdc1070113
--- /dev/null
+++ b/src/MATLAB/+Editor/MitosisHullPhenotypeAction.m
@@ -0,0 +1,20 @@
+% [historyAction newTrack] = MitosisHullPhenotypeAction()
+% Edit Action:
+
+function [historyAction hullID] = MitosisHullPhenotypeAction(clickPoint, time, trackID)
+
+ hullID = Hulls.FindHull(time, clickPoint);
+ if ( hullID <= 0 )
+ newTrackID = Segmentation.AddNewSegmentHull(clickPoint, time);
+ hullID = Tracks.GetHullID(time, newTrackID);
+ else
+ newTrackID = Hulls.GetTrackID(hullID);
+ end
+
+ if ( newTrackID ~= trackID )
+ newTrackID = Tracks.TearoffHull(hullID);
+ Tracks.ChangeLabel(newTrackID, trackID, time);
+ end
+
+ historyAction = '';
+end
diff --git a/src/MATLAB/+Tracks/TearoffHull.m b/src/MATLAB/+Tracks/TearoffHull.m
new file mode 100644
index 0000000000000000000000000000000000000000..b14dc68d0c532a31aeafa2428593728c2e0225eb
--- /dev/null
+++ b/src/MATLAB/+Tracks/TearoffHull.m
@@ -0,0 +1,38 @@
+function newTrackID = TearoffHull(hullID)
+ global CellHulls CellTracks
+
+ time = CellHulls(hullID).time;
+ trackID = Hulls.GetTrackID(hullID);
+
+ if ( length(CellTracks(trackID).hulls) == 1 )
+ newTrackID = trackID;
+ return;
+ end
+
+ bLeafTrack = isempty(CellTracks(trackID).childrenTracks);
+
+ bStartHull = (CellTracks(trackID).startTime == time);
+ bEndHull = (CellTracks(trackID).endTime == time);
+
+ droppedTracks = Families.RemoveFromTree(trackID, time);
+
+ newTrackID = Hulls.GetTrackID(hullID);
+ if ( bEndHull )
+ % Tearoff both children since can't reconstruct mitosis without
+ % this hull
+ if ( ~bLeafTrack )
+ Families.RemoveFromTreePrune(CellTracks(newTrackID).childrenTracks(1));
+ end
+ return;
+ end
+
+ % Tearoff rest of subtree if this is root or the start of a track
+ % (can't reattach mitosis events without a new hull)
+ if ( bStartHull )
+ Families.RemoveFromTreePrune(newTrackID,time+1);
+ return;
+ end
+
+ % Reattach the rest of the track
+ Tracks.ChangeLabel(newTrackID, trackID, time+1);
+end
diff --git a/src/MATLAB/+UI/CreateContextMenuCells.m b/src/MATLAB/+UI/CreateContextMenuCells.m
index 53d2b9d4ecc490c518cfb7ab17bf17f6975ded87..d9150b8dec82f2952b114b0b83524356917a3b01 100644
--- a/src/MATLAB/+UI/CreateContextMenuCells.m
+++ b/src/MATLAB/+UI/CreateContextMenuCells.m
@@ -81,10 +81,6 @@ uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Remove Cell (this frame)',...
'CallBack', @removeHull);
-uimenu(Figures.cells.contextMenuHandle,...
- 'Label', 'Delete Track',...
- 'CallBack', @removeTrackPrevious);
-
uimenu(Figures.cells.contextMenuHandle,...
'Label', 'Remove From Tree',...
'CallBack', @removeFromTree);
diff --git a/src/MATLAB/+UI/DrawCells.m b/src/MATLAB/+UI/DrawCells.m
index 593360e970aaf80fd5a46350d4541f7f255bf23f..d4b6f8bd7dde924f3587c3cfecc475efc3949163 100644
--- a/src/MATLAB/+UI/DrawCells.m
+++ b/src/MATLAB/+UI/DrawCells.m
@@ -102,13 +102,13 @@ if(strcmp(get(Figures.cells.menuHandles.imageMenu, 'Checked'),'off'))
set(im,'Visible','off');
end
-bDrawLabels = isempty(Figures.tree.movingMitosis);
+bDrawLabels = true;
drawHullFilter = [];
if ( strcmpi(Figures.cells.editMode, 'mitosis') )
% Filter so we only draw family "mitosis" hulls when editing
bDrawLabels = 0;
- drawHullFilter = arrayfun(@(x)(CellTracks(x).hulls(1)),...
+ drawHullFilter = arrayfun(@(x)(CellTracks(x).hulls(CellTracks(x).hulls~=0)),...
CellFamilies(Figures.tree.familyID).tracks, 'UniformOutput',0);
drawHullFilter = [drawHullFilter{:}];
end
@@ -131,14 +131,6 @@ if(strcmp(get(Figures.cells.menuHandles.labelsMenu, 'Checked'),'on'))
curHullID = HashedCells{Figures.time}(i).hullID;
curTrackID = HashedCells{Figures.time}(i).trackID;
- %if dragging a mitosis, only show the siblings: Draws faster
- %and makes it easier to follow what is changing
- if(Figures.tree.movingMitosis)
- if(Figures.tree.movingMitosis ~= curTrackID)
- continue;
- end
- end
-
if ( ~isempty(drawHullFilter) && ~any(curHullID == drawHullFilter ) )
continue;
end
@@ -262,13 +254,7 @@ end
Figures.cells.axesHandle = curAx;
-if(~isempty(Figures.cells.PostDrawHookOnce))
- for i=1:length(Figures.cells.PostDrawHookOnce)
- hook = Figures.cells.PostDrawHookOnce{i};
- hook(curAx);
- end
- Figures.cells.PostDrawHookOnce = {};
-end
+
drawnow();
end
diff --git a/src/MATLAB/+UI/DrawTree.m b/src/MATLAB/+UI/DrawTree.m
index af969d2a962c3a8dfcc13d866368e34e91268a6e..d51b5ab365ce8d2d47ceb5f5a780ffd047770804 100644
--- a/src/MATLAB/+UI/DrawTree.m
+++ b/src/MATLAB/+UI/DrawTree.m
@@ -351,6 +351,7 @@ function drawCellLabel(curAx, trackID, xVal, bDrawLabels)
'FontSize',fontSize,...
'color',textColor,...
'UserData',trackID,...
+ 'ButtonDownFcn',@(src,evnt)(UI.FigureTreeDown(src,evnt,trackID)),...
'uicontextmenu',Figures.tree.contextMenuHandle);
% Draw a dead cell marker
@@ -362,6 +363,7 @@ function drawCellLabel(curAx, trackID, xVal, bDrawLabels)
'MarkerEdgeColor','r',...
'MarkerSize',circleSize,...
'UserData',trackID,...
+ 'ButtonDownFcn',@(src,evnt)(UI.FigureTreeDown(src,evnt,trackID)),...
'uicontextmenu',Figures.tree.contextMenuHandle);
UI.DrawPool.SetDrawOrder(Figures.tree.axesHandle, [hMarker hLabel]);
@@ -379,6 +381,7 @@ function drawCellLabel(curAx, trackID, xVal, bDrawLabels)
'MarkerEdgeColor','w',...
'MarkerSize',phenoScale*circleSize,...
'UserData',trackID,...
+ 'ButtonDownFcn',@(src,evnt)(UI.FigureTreeDown(src,evnt,trackID)),...
'uicontextmenu',Figures.tree.contextMenuHandle);
end
@@ -390,6 +393,7 @@ function drawCellLabel(curAx, trackID, xVal, bDrawLabels)
'MarkerEdgeColor',CellTracks(trackID).color.background,...
'MarkerSize',circleSize,...
'UserData',trackID,...
+ 'ButtonDownFcn',@(src,evnt)(UI.FigureTreeDown(src,evnt,trackID)),...
'uicontextmenu',Figures.tree.contextMenuHandle);
@@ -406,6 +410,7 @@ function drawCellLabel(curAx, trackID, xVal, bDrawLabels)
'MarkerEdgeColor','k',...
'MarkerSize',circleSize,...
'UserData',trackID,...
+ 'ButtonDownFcn',@(src,evnt)(UI.FigureTreeDown(src,evnt,trackID)),...
'uicontextmenu',Figures.tree.contextMenuHandle);
end
diff --git a/src/MATLAB/+UI/FigureCellUp.m b/src/MATLAB/+UI/FigureCellUp.m
index 7c1049f1891b4622d1933c0f3750fbeeda33c2ff..bdffa44d3b4ffc8fca6475f970ce95070255a0b8 100644
--- a/src/MATLAB/+UI/FigureCellUp.m
+++ b/src/MATLAB/+UI/FigureCellUp.m
@@ -28,7 +28,7 @@ if ( strcmpi(Figures.cells.editMode, 'mitosis') )
UI.DrawCells();
else
curFamID = Figures.tree.familyID;
- drawHullFilter = arrayfun(@(x)(CellTracks(x).hulls(1)), CellFamilies(curFamID).tracks, 'UniformOutput',0);
+ drawHullFilter = arrayfun(@(x)(CellTracks(x).hulls(CellTracks(x).hulls~=0)), CellFamilies(curFamID).tracks, 'UniformOutput',0);
drawHullFilter = [drawHullFilter{:}];
bCurHulls = ([CellHulls(drawHullFilter).time] == Figures.time);
@@ -103,6 +103,11 @@ function addMitosisEvent(treeID, time, dragCoords)
return
end
+ if ( isempty(MitosisEditStruct) || ~isfield(MitosisEditStruct,'selectedTrackID') || isempty(MitosisEditStruct.selectedTrackID) )
+ msgbox('No cells selected for mitosis identification','No Cell Selected','warn');
+ return;
+ end
+
treeTracks = [CellFamilies(treeID).tracks];
bInTracks = Helper.CheckInTracks(time, treeTracks, 0, 0);
@@ -124,7 +129,7 @@ function addMitosisEvent(treeID, time, dragCoords)
% end
dirFlag = UI.MitosisGetSelectedDirTo(time);
- bErr = Editor.ReplayableEditAction(@Editor.CreateMitosisAction, MitosisEditStruct.selectedTrackID, dirFlag, treeID, time, (dragCoords.'));
+ bErr = Editor.ReplayableEditAction(@Editor.CreateMitosisAction, MitosisEditStruct.selectedTrackID, dirFlag, time, (dragCoords.'));
if ( bErr )
return;
end
diff --git a/src/MATLAB/+UI/FigureKeyPress.m b/src/MATLAB/+UI/FigureKeyPress.m
new file mode 100644
index 0000000000000000000000000000000000000000..845931b2a8f070732664394c2b702a5e9bd44cee
--- /dev/null
+++ b/src/MATLAB/+UI/FigureKeyPress.m
@@ -0,0 +1,152 @@
+function FigureKeyPress(src,evnt)
+ global Figures ResegState
+
+ if strcmp(evnt.Key,'downarrow') || strcmp(evnt.Key,'rightarrow')
+ if ( Figures.controlDown )
+ time = findMitosis(+1, Figures.time, Figures.tree.familyID);
+ UI.TimeChange(time);
+ else
+ time = Figures.time + 1;
+ UI.TimeChange(time);
+ end
+ elseif strcmp(evnt.Key,'uparrow') || strcmp(evnt.Key,'leftarrow')
+ if ( Figures.controlDown )
+ time = findMitosis(-1, Figures.time, Figures.tree.familyID);
+ UI.TimeChange(time);
+ else
+ time = Figures.time - 1;
+ UI.TimeChange(time);
+ end
+ elseif strcmp(evnt.Key,'pagedown')
+ time = Figures.time + 5;
+ UI.TimeChange(time);
+ elseif strcmp(evnt.Key,'pageup')
+ time = Figures.time - 5;
+ UI.TimeChange(time);
+ elseif strcmp(evnt.Key,'space')
+ if ( ~isempty(ResegState) )
+ % Toggle reseg playing
+ buttonHandles = get(ResegState.toolbar, 'UserData');
+ toggleFunc = get(buttonHandles(2), 'ClickedCallback');
+ toggleFunc(buttonHandles(2), []);
+ else
+ % standard movie playing
+ UI.TogglePlay(src,evnt);
+ end
+ elseif strcmp(evnt.Key,'period')
+ if ( ~isempty(ResegState) )
+ % Reseg Forward 1 Frame
+ buttonHandles = get(ResegState.toolbar, 'UserData');
+ toggleFunc = get(buttonHandles(3), 'ClickedCallback');
+ toggleFunc(buttonHandles(3), []);
+ else
+ % step forward one frame
+ time = Figures.time + 1;
+ UI.TimeChange(time);
+ end
+ elseif strcmp(evnt.Key,'comma')
+ if ( ~isempty(ResegState) )
+ % Reseg Backward 1 Frame
+ buttonHandles = get(ResegState.toolbar, 'UserData');
+ toggleFunc = get(buttonHandles(1), 'ClickedCallback');
+ toggleFunc(buttonHandles(1), []);
+ else
+ % step backward one frame
+ time = Figures.time - 1;
+ UI.TimeChange(time);
+ end
+ elseif ( strcmp(evnt.Key,'control') )
+ if(~Figures.controlDown)
+ %prevent this from getting reset when moving the mouse
+ Figures.controlDown = true;
+ end
+ elseif ( strcmp(evnt.Key,'delete') || strcmp(evnt.Key,'backspace') )
+ deleteSelectedCells();
+ elseif (strcmp(evnt.Key,'f12'))
+ Figures.cells.showInterior = ~Figures.cells.showInterior;
+ UI.DrawCells();
+ UI.DrawTree(Figures.tree.familyID);
+ elseif ( strcmp(evnt.Key,'return') )
+ mergeSelectedCells();
+ end
+end
+
+function mitTime = findMitosis(dirFlag, time, familyID)
+ global CellFamilies CellTracks HashedCells
+
+ mitTime = 1;
+ if ( dirFlag > 0 )
+ mitTime = length(HashedCells);
+ end
+
+ if ( isempty(familyID) )
+ return;
+ end
+
+ famTracks = CellFamilies(familyID).tracks;
+ if ( isempty(famTracks) )
+ return;
+ end
+
+ % Append start and end of family and movie to mitosis times list.
+ chkTimes = unique([1 CellTracks(famTracks).startTime CellFamilies(familyID).endTime length(HashedCells)]);
+
+ if ( dirFlag < 0 )
+ idx = find(chkTimes < time, 1, 'last');
+ else
+ idx = find(chkTimes > time, 1, 'first');
+ end
+
+ if ( isempty(idx) )
+ return;
+ end
+
+ mitTime = chkTimes(idx);
+end
+
+function deleteSelectedCells()
+ global Figures CellFamilies
+
+ bErr = Editor.ReplayableEditAction(@Editor.DeleteCells, Figures.cells.selectedHulls);
+ if ( bErr )
+ return;
+ end
+
+ UI.ClearCellSelection();
+ Error.LogAction(['Removed selected cells [' num2str(Figures.cells.selectedHulls) ']'],Figures.cells.selectedHulls);
+
+ %if the whole family disappears with this change, pick a diffrent family to display
+ if(isempty(CellFamilies(Figures.tree.familyID).tracks))
+ for i=1:length(CellFamilies)
+ if(~isempty(CellFamilies(i).tracks))
+ Figures.tree.familyID = i;
+ break
+ end
+ end
+ end
+
+ UI.DrawTree(Figures.tree.familyID);
+ UI.DrawCells();
+end
+
+function mergeSelectedCells()
+ global Figures
+
+ [bErr deletedCells replaceCell] = Editor.ReplayableEditAction(@Editor.MergeCells, Figures.cells.selectedHulls);
+ if ( bErr )
+ return;
+ end
+
+ if ( isempty(replaceCell) )
+ msgbox(['Unable to merge [' num2str(Figures.cells.selectedHulls) '] in this frame'],'Unable to Merge','help','modal');
+ return;
+ end
+
+
+ UI.ClearCellSelection();
+ Error.LogAction('Merged cells', [deletedCells replaceCell], replaceCell);
+
+ UI.DrawTree(Figures.tree.familyID);
+ UI.DrawCells();
+end
+
diff --git a/src/MATLAB/+UI/FigureScroll.m b/src/MATLAB/+UI/FigureScroll.m
new file mode 100644
index 0000000000000000000000000000000000000000..cdd78c75af4aab69210747b8ab50a17e11e75abf
--- /dev/null
+++ b/src/MATLAB/+UI/FigureScroll.m
@@ -0,0 +1,7 @@
+function FigureScroll(src,evnt)
+ global Figures
+
+ time = Figures.time + evnt.VerticalScrollCount;
+
+ UI.TimeChange(time);
+end
diff --git a/src/MATLAB/+UI/FigureTreeDown.m b/src/MATLAB/+UI/FigureTreeDown.m
new file mode 100644
index 0000000000000000000000000000000000000000..3e82161a359fa1fdb18676b57c016f02f0a06562
--- /dev/null
+++ b/src/MATLAB/+UI/FigureTreeDown.m
@@ -0,0 +1,20 @@
+function FigureTreeDown(src,evnt, trackID)
+ global Figures CellTracks
+
+ if ( ~exist('trackID','var') )
+ trackID = [];
+ end
+
+ if ( ~isempty(trackID) && strcmpi(Figures.cells.editMode, 'mitosis') )
+ time = CellTracks(trackID).startTime;
+
+ UI.MitosisSelectTrackingCell(trackID, time);
+ return;
+ end
+
+ if(strcmp(get(Figures.tree.handle,'SelectionType'),'normal'))
+ set(Figures.tree.handle, 'WindowButtonMotionFcn',@UI.FigureTreeDrag);
+
+ UI.MoveLine();
+ end
+end
diff --git a/src/MATLAB/+UI/FigureTreeDrag.m b/src/MATLAB/+UI/FigureTreeDrag.m
new file mode 100644
index 0000000000000000000000000000000000000000..3c1a7c383863bcc628282c52a84dafd0efa61947
--- /dev/null
+++ b/src/MATLAB/+UI/FigureTreeDrag.m
@@ -0,0 +1,5 @@
+function FigureTreeDrag(src,evnt)
+
+ UI.MoveLine();
+ UI.DrawCells();
+end
diff --git a/src/MATLAB/+UI/FigureTreeUp.m b/src/MATLAB/+UI/FigureTreeUp.m
new file mode 100644
index 0000000000000000000000000000000000000000..8b67a68445e4f3342679dd63bf5f616cea40ffa8
--- /dev/null
+++ b/src/MATLAB/+UI/FigureTreeUp.m
@@ -0,0 +1,9 @@
+function FigureTreeUp(src,evnt)
+ global Figures
+
+ set(Figures.tree.handle, 'WindowButtonMotionFcn','');
+
+ if(strcmp(get(Figures.tree.handle,'SelectionType'),'normal'))
+ UI.TimeChange(Figures.time);
+ end
+end
diff --git a/src/MATLAB/+UI/InitializeFigures.m b/src/MATLAB/+UI/InitializeFigures.m
index d16d45ddf46de85882e1959529372e5cb5c185e3..fb52d444eba250b1d23a1e996f570cea1f4aeef7 100644
--- a/src/MATLAB/+UI/InitializeFigures.m
+++ b/src/MATLAB/+UI/InitializeFigures.m
@@ -47,7 +47,6 @@ Figures.tree.handle = figure();
Figures.cells.selectedHulls = [];
Figures.controlDown = false; %control key is currently down? for selecting cells and fine adjustment
-Figures.cells.PostDrawHookOnce = {}; %list of functions to call post DrawCells. Cleared on every draw
Figures.downHullID = -1;
Figures.downClickPoint = [0 0];
@@ -56,14 +55,14 @@ whitebg(Figures.cells.handle,'k');
whitebg(Figures.tree.handle,'w');
Figures.advanceTimerHandle = timer(...
- 'TimerFcn', @play,...
+ 'TimerFcn', @UI.Play,...
'Period', .05,...
'ExecutionMode', 'fixedSpacing',...
'BusyMode', 'drop');
set(Figures.cells.handle,...
- 'WindowScrollWheelFcn', @figureScroll,...
- 'KeyPressFcn', @figureKeyPress,...
+ 'WindowScrollWheelFcn', @UI.FigureScroll,...
+ 'KeyPressFcn', @UI.FigureKeyPress,...
'Menu', 'none',...
'ToolBar', 'figure',...
'BusyAction', 'cancel',...
@@ -74,8 +73,7 @@ set(Figures.cells.handle,...
'Tag', 'cells',...
'ResizeFcn', @UI.UpdateSegmentationEditsMenu);
-addlistener(Figures.cells.handle, 'WindowKeyRelease', @figureKeyRelease);
- Figures.tree.movingMitosis = [];
+addlistener(Figures.cells.handle, 'WindowKeyRelease', @UI.KeyStateRelease);
Figures.cells.showInterior = false;
Figures.cells.editMode = 'normal';
@@ -94,6 +92,7 @@ Figures.cells.cellCountLabel = uicontrol(Figures.cells.handle,...
hPan = pan(Figures.cells.handle);
set(hPan,'ActionPostCallback',@forceRedrawCells);
+
hZoom = zoom(Figures.cells.handle);
set(hZoom,'ActionPostCallback',@forceRedrawCells);
@@ -101,10 +100,10 @@ UI.CreateMenuBar(Figures.cells.handle);
UI.CreateContextMenuCells();
set(Figures.tree.handle,...
- 'WindowButtonDownFcn', @figureTreeDown,...
- 'WindowButtonUpFcn', @figureTreeUp,...
- 'WindowScrollWheelFcn', @figureScroll,...
- 'KeyPressFcn', @figureKeyPress,...
+ 'WindowButtonDownFcn', @UI.FigureTreeDown,...
+ 'WindowButtonUpFcn', @UI.FigureTreeUp,...
+ 'WindowScrollWheelFcn', @UI.FigureScroll,...
+ 'KeyPressFcn', @UI.FigureKeyPress,...
'CloseRequestFcn', @UI.CloseFigure,...
'Menu', 'none',...
'ToolBar', 'figure',...
@@ -114,12 +113,8 @@ set(Figures.tree.handle,...
'Name', [CONSTANTS.datasetName ' Lineage'],...
'Tag', 'tree');
- addlistener(Figures.tree.handle, 'WindowKeyRelease', @figureKeyRelease);
-
-%WindowButtonMotionFcn callbacks cause 'CurrentPointer' to be updated
-%which is needed for dragging
-set(Figures.tree.handle, 'WindowButtonMotionFcn',@(src,evt)(src));
-Figures.tree.dragging = [];
+addlistener(Figures.tree.handle, 'WindowKeyRelease', @UI.KeyStateRelease);
+
Figures.tree.trackMap = [];
Figures.tree.trackingLine = [];
Figures.tree.trackingLabel = [];
@@ -166,288 +161,6 @@ end
%% Callback Functions
-function figureScroll(src,evnt)
-global Figures
-time = Figures.time + evnt.VerticalScrollCount;
-UI.TimeChange(time);
-end
-
-function play(src,event)
-global Figures HashedCells
-time = Figures.time + 1;
-if(time == length(HashedCells))
- time = 1;
-end
-UI.TimeChange(time);
-end
-
-function figureKeyPress(src,evnt)
-global Figures CellFamilies ResegState
-
-if strcmp(evnt.Key,'downarrow') || strcmp(evnt.Key,'rightarrow')
- time = Figures.time + 1;
- UI.TimeChange(time);
-elseif strcmp(evnt.Key,'uparrow') || strcmp(evnt.Key,'leftarrow')
- time = Figures.time - 1;
- UI.TimeChange(time);
-elseif strcmp(evnt.Key,'pagedown')
- time = Figures.time + 5;
- UI.TimeChange(time);
-elseif strcmp(evnt.Key,'pageup')
- time = Figures.time - 5;
- UI.TimeChange(time);
-elseif strcmp(evnt.Key,'space')
- if ( ~isempty(ResegState) )
- % Toggle reseg playing
- buttonHandles = get(ResegState.toolbar, 'UserData');
- toggleFunc = get(buttonHandles(2), 'ClickedCallback');
- toggleFunc(buttonHandles(2), []);
- else
- % standard movie playing
- UI.TogglePlay(src,evnt);
- end
-elseif strcmp(evnt.Key,'period')
- if ( ~isempty(ResegState) )
- % Reseg Forward 1 Frame
- buttonHandles = get(ResegState.toolbar, 'UserData');
- toggleFunc = get(buttonHandles(3), 'ClickedCallback');
- toggleFunc(buttonHandles(3), []);
- else
- % step forward one frame
- time = Figures.time + 1;
- UI.TimeChange(time);
- end
-elseif strcmp(evnt.Key,'comma')
- if ( ~isempty(ResegState) )
- % Reseg Backward 1 Frame
- buttonHandles = get(ResegState.toolbar, 'UserData');
- toggleFunc = get(buttonHandles(1), 'ClickedCallback');
- toggleFunc(buttonHandles(1), []);
- else
- % step backward one frame
- time = Figures.time - 1;
- UI.TimeChange(time);
- end
- elseif ( strcmp(evnt.Key,'control') )
- if(~Figures.controlDown)
- %prevent this from getting reset when moving the mouse
- Figures.controlDown = true;
- end
-elseif ( strcmp(evnt.Key,'delete') || strcmp(evnt.Key,'backspace') )
- deleteSelectedCells();
-elseif (strcmp(evnt.Key,'f12'))
- Figures.cells.showInterior = ~Figures.cells.showInterior;
- UI.DrawCells();
- UI.DrawTree(Figures.tree.familyID);
-elseif ( strcmp(evnt.Key,'return') )
- mergeSelectedCells();
-end
-end
-
-function figureKeyRelease(src,evnt)
- global Figures
-
- Figures.controlDown = false;
-end
-
-function figureTreeDown(src,evnt)
- global Figures indicatorMotionListener indicatorMouseUpListener;
-
- indicatorMotionListener = addlistener(Figures.tree.handle, 'WindowMouseMotion', @figureTreeMotion);
- indicatorMouseUpListener = addlistener(Figures.tree.handle, 'WindowMouseRelease', @indicatorMouseUp);
- if(strcmp(get(Figures.tree.handle,'SelectionType'),'normal'))
- moveLine();
- end
-end
-
-% NLS - 6/8/12
-% this actually returns the tracks that the hulls belong to
-% I'll Hopefully refactor DrawCells to allow drawing specific hulls soon
-function likelyHulls = FindLowestCostHulls(parentTrackID, time)
-global CellTracks HashedCells CellHulls Figures
- parentTrack = CellTracks(parentTrackID);
-
- fromHullID = Tracks.GetHullID(parentTrack.endTime, parentTrackID);
- potentialHulls = HashedCells{time};
- potentialHulls = [potentialHulls.hullID];
-
- timeDiff = time - CellHulls(fromHullID).time;
- [paths, costs] = mexDijkstra('matlabExtend', fromHullID, abs(timeDiff)+1, @(startID,endID)((any(endID == potentialHulls))), timeDiff);
-
- likelyHulls = [];
- if(length(paths) > 1)
- %if cost difference between {1} and {2} is really large, attempt to
- %split?
- likelyHulls = [paths{1}(end), paths{2}(end)];
- elseif (length(paths) == 1)
- likelyHulls = [paths{1}(end)];
- end
-
- if(length(likelyHulls) == 1) %attempt to split
- newHulls = Segmentation.ResegmentHull(CellHulls(likelyHulls(1)), 2, 1, 1);
- likelyHulls = [];
- if(isempty(newHulls)),return,end
- hull1 = newHulls(1);
- hull2 = newHulls(2);
- Figures.cells.PostDrawHookOnce{end+1} = @(Ax) (plot(Ax, hull1.points(:,1), hull1.points(:,2), 'Color', [.2 .2 .2], 'LineStyle', '-', 'LineWidth', 1.5));
- Figures.cells.PostDrawHookOnce{end+1} = @(Ax) (plot(Ax, hull2.points(:,1), hull2.points(:,2), 'Color', [.8 .8 .8], 'LineStyle', '-', 'LineWidth', 1.5));
- end
-
- for i=1:length(likelyHulls)
- likelyHulls(i) = Hulls.GetTrackID(likelyHulls(i));
- end
-end
-
-% NLS - 6/8/2012 - Created
-function mitosisHandleDragging(mitosis)
-global Figures CellTracks;
-
- Y = get(Figures.tree.timeIndicatorLine, 'YData');
- Y = Y(2);
-
- mitosisHandle = get(mitosis,'UserData');
- %don't allow adjusting a mitosis through other mitoses
- minY = CellTracks(mitosisHandle.trackID).startTime + 1;
- if (Y <= minY)
- return;
- end
-
- children = CellTracks(mitosisHandle.trackID).childrenTracks;
- Figures.tree.movingMitosis = [children, FindLowestCostHulls(mitosisHandle.trackID, Y)];
-
- %determine how far up/down the user should be allowed to drag a mitosis
- if(isempty(CellTracks(children(1)).childrenTracks))
- if(isempty(CellTracks(children(2)).childrenTracks))
- maxY = Inf;
- else
- maxY = CellTracks(children(1)).endTime - 1;
- end
- elseif(isempty(CellTracks(children(2)).childrenTracks))
- maxY = CellTracks(children(2)).endTime - 1;
- else
- maxY = min(CellTracks(children(1)).endTime,CellTracks(children(2)).endTime) - 1;
- end
-
- if (Y >= maxY)
- return;
- end
-
- previousMitosisTime = get(mitosisHandle.hLine, 'YData');
- set(mitosisHandle.hLine, 'YData', [Y Y]);
-% set(mitosisHandle.diamondHandle, 'YData', Y+1);
-
- set(mitosisHandle.child1Handles(1), 'YData', Y+1);
- text1 = get(mitosisHandle.child1Handles(2), 'Position');
- text1(2) = Y+1;
- set(mitosisHandle.child1Handles(2), 'Position', text1);
-
- set(mitosisHandle.child2Handles(1), 'YData', Y+1);
- text2 = get(mitosisHandle.child2Handles(2), 'Position');
- text2(2) = Y+1;
- set(mitosisHandle.child2Handles(2), 'Position', text2);
-end
-
-function indicatorMouseUp(src,evt)
- global indicatorMotionListener indicatorMouseUpListener Figures CellTracks;
-
- delete(indicatorMotionListener);
- delete(indicatorMouseUpListener);
-
- if(~isempty(Figures.tree.dragging))
- Y = get(Figures.tree.timeIndicatorLine, 'YData');
- Y = Y(2);
-
- mitosis = Figures.tree.dragging;
- mitosisHandle = get(mitosis,'UserData');
- children = CellTracks(mitosisHandle.trackID).childrenTracks;
-
- Figures.tree.movingMitosis = [];
- %TODO: actually commit tree changes
- %GraphEditMoveMitosis(Y, children(1));
- %History('Push');
- %DrawTree(CellTracks(mitosisHandle.trackID).familyID);
- Figures.tree.dragging = [];
- end
-end
-
-function figureTreeMotion(src,evnt)
-global Figures
- moveLine();
- UI.DrawCells();
-end
-
-function moveLine()
-global Figures HashedCells
-time = get(Figures.tree.axesHandle,'CurrentPoint');
-time = round(time(3));
-
-if(strcmp(Figures.advanceTimerHandle.Running,'on'))
- UI.TogglePlay([],[]);
-end
-if(time < 1)
- Figures.time = 1;
-elseif(time > length(HashedCells))
- Figures.time = length(HashedCells);
-else
- Figures.time = time;
-end
-% DrawCells();
-UI.UpdateTimeIndicatorLine();
-end
-
-function figureTreeUp(src,evnt)
-global Figures
-if(strcmp(get(Figures.tree.handle,'SelectionType'),'normal'))
- UI.TimeChange(Figures.time);
-end
-end
-
-function deleteSelectedCells()
- global Figures CellFamilies
-
- bErr = Editor.ReplayableEditAction(@Editor.DeleteCells, Figures.cells.selectedHulls);
- if ( bErr )
- return;
- end
-
- UI.ClearCellSelection();
- Error.LogAction(['Removed selected cells [' num2str(Figures.cells.selectedHulls) ']'],Figures.cells.selectedHulls);
-
- %if the whole family disappears with this change, pick a diffrent family to display
- if(isempty(CellFamilies(Figures.tree.familyID).tracks))
- for i=1:length(CellFamilies)
- if(~isempty(CellFamilies(i).tracks))
- Figures.tree.familyID = i;
- break
- end
- end
- end
-
- UI.DrawTree(Figures.tree.familyID);
- UI.DrawCells();
-end
-
-function mergeSelectedCells()
- global Figures
-
- [bErr deletedCells replaceCell] = Editor.ReplayableEditAction(@Editor.MergeCells, Figures.cells.selectedHulls);
- if ( bErr )
- return;
- end
-
- if ( isempty(replaceCell) )
- msgbox(['Unable to merge [' num2str(Figures.cells.selectedHulls) '] in this frame'],'Unable to Merge','help','modal');
- return;
- end
-
-
- UI.ClearCellSelection();
- Error.LogAction('Merged cells', [deletedCells replaceCell], replaceCell);
-
- UI.DrawTree(Figures.tree.familyID);
- UI.DrawCells();
-end
-
function learnFromEdits(src,evnt)
global CellFamilies CellTracks SegmentationEdits Figures
diff --git a/src/MATLAB/+UI/KeyStateRelease.m b/src/MATLAB/+UI/KeyStateRelease.m
new file mode 100644
index 0000000000000000000000000000000000000000..28c1e2c1cc143dde58cc3604f74e73dcebf9a177
--- /dev/null
+++ b/src/MATLAB/+UI/KeyStateRelease.m
@@ -0,0 +1,5 @@
+function KeyStateRelease(src,evnt)
+ global Figures
+
+ Figures.controlDown = false;
+end
diff --git a/src/MATLAB/+UI/MitosisEditInterface.m b/src/MATLAB/+UI/MitosisEditInterface.m
index 5b0b2bf933b85e6c5793339aa4bfaeed6dfbfc6c..fcd9914350cf9386def4b21eff90c71b509edca3 100644
--- a/src/MATLAB/+UI/MitosisEditInterface.m
+++ b/src/MATLAB/+UI/MitosisEditInterface.m
@@ -14,12 +14,12 @@ function MitosisEditInterface()
rootTrackID = CellFamilies(editTree).rootTrackID;
firstHull = CellTracks(rootTrackID).hulls(1);
- UI.MitosisSelectTrackingCell(rootTrackID,CellHulls(firstHull).time, true);
-
% Order matters here, we want the Init action to be part of the subtask
Editor.ReplayableEditAction(@Editor.StartReplayableSubtask, 'MitosisEditTask');
Editor.ReplayableEditAction(@Editor.MitosisEditInitializeAction, editTree, length(HashedCells));
+ UI.MitosisSelectTrackingCell(rootTrackID,CellHulls(firstHull).time, true);
+
hToolbar = addButtons();
end
diff --git a/src/MATLAB/+UI/MitosisSelectPhenotype.m b/src/MATLAB/+UI/MitosisSelectPhenotype.m
new file mode 100644
index 0000000000000000000000000000000000000000..4cea8c36dbce0ec34f21e548f54879b440ed28b2
--- /dev/null
+++ b/src/MATLAB/+UI/MitosisSelectPhenotype.m
@@ -0,0 +1,17 @@
+function [hullID trackID] = MitosisSelectPhenotype()
+ global Figures MitosisEditStruct
+
+ hullID = [];
+ trackID = [];
+ if ( isempty(MitosisEditStruct.selectedTrackID) )
+ msgbox('No cells selected for mitosis or phenotype identification','No Cell Selected','warn');
+ return;
+ end
+
+ trackID = MitosisEditStruct.selectedTrackID;
+
+ currentPoint = UI.GetClickedCellPoint();
+ [bErr hullID] = Editor.ReplayableEditAction(@Editor.MitosisHullPhenotypeAction, currentPoint, Figures.time, trackID);
+
+ trackID = Hulls.GetTrackID(hullID);
+end
diff --git a/src/MATLAB/+UI/MoveLine.m b/src/MATLAB/+UI/MoveLine.m
new file mode 100644
index 0000000000000000000000000000000000000000..f06beb1305770c099e118e6ce7a11f74d8675049
--- /dev/null
+++ b/src/MATLAB/+UI/MoveLine.m
@@ -0,0 +1,20 @@
+function MoveLine()
+ global Figures HashedCells
+
+ time = get(Figures.tree.axesHandle,'CurrentPoint');
+ time = round(time(3));
+
+ if(strcmp(Figures.advanceTimerHandle.Running,'on'))
+ UI.TogglePlay([],[]);
+ end
+
+ if(time < 1)
+ Figures.time = 1;
+ elseif(time > length(HashedCells))
+ Figures.time = length(HashedCells);
+ else
+ Figures.time = time;
+ end
+
+ UI.UpdateTimeIndicatorLine();
+end
diff --git a/src/MATLAB/+UI/Play.m b/src/MATLAB/+UI/Play.m
new file mode 100644
index 0000000000000000000000000000000000000000..706adb458b8a2be80d3cd92283103de6a7ca3a21
--- /dev/null
+++ b/src/MATLAB/+UI/Play.m
@@ -0,0 +1,11 @@
+function Play(src,evt)
+ global Figures HashedCells
+
+ time = Figures.time + 1;
+
+ if(time >= length(HashedCells))
+ time = 1;
+ end
+
+ UI.TimeChange(time);
+end
diff --git a/src/MATLAB/+UI/UpdatePhenotypeMenu.m b/src/MATLAB/+UI/UpdatePhenotypeMenu.m
index e52115d31de765050138361355183c673e80e688..ecbdfc19b756392f854207eadd48507e9c85dc61 100644
--- a/src/MATLAB/+UI/UpdatePhenotypeMenu.m
+++ b/src/MATLAB/+UI/UpdatePhenotypeMenu.m
@@ -45,9 +45,13 @@ end
function setPhenotype(src, evnt)
global Figures CellPhenotypes
- [hullID trackID] = UI.GetClosestCell(0);
- if(isempty(trackID))
- return
+ if ( strcmpi(Figures.cells.editMode, 'mitosis') )
+ [hullID trackID] = UI.MitosisSelectPhenotype();
+ else
+ [hullID trackID] = UI.GetClosestCell(0);
+ if(isempty(trackID))
+ return
+ end
end
clickPheno = get(src, 'UserData');