Commit 7aeefd78 authored by Andrew Cohen's avatar Andrew Cohen

license header

parent badf5d0d
......@@ -2,10 +2,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function helpStruct = FrameSegHelp(funcName)
helpStruct = [];
......
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function hashList = GetCoreHashList()
global CellHulls CellTracks CellFamilies HashedCells CellPhenotypes Costs GraphEdits
......
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function MakeSegHelp()
funcPrefix = {
'% helpStruct = CompiledSegHelp(funcName)'
......
% PrintIntegrityErrors(errs, filename)
% Prints integrity errors to filename (or stdout if no name specified)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function PrintIntegrityErrors(errs, fid)
if ( isempty(errs) )
......
% ReplayActionsFile(filename)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ReplayActionsFile(filename)
loadStruct = load(filename, 'ReplayEditActions');
......
......@@ -2,6 +2,30 @@
%
% ReplayEditAction attempts to replay an action from an editaction list.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [bErr chkHash varargout] = ReplayEditAction(actPtr, varargin)
varargout = cell(1,max(0,nargout-2));
......
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function WriteFrozenErrorCounts(rootDir)
flist = dir(fullfile(rootDir,'*.mat'));
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -5,6 +5,30 @@
% leftChild is non-empty also change its label to the parent track before
% adding the mitosis.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function historyAction = AddMitosisAction(parentTrack, leftChild, siblingTrack, time)
global CellTracks
......
......@@ -5,6 +5,30 @@
% find a segmentation result, add a singple point segmentation at
% clickPoint
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [historyAction newTrack] = AddNewCell(clickPoint, time)
newTrack = Segmentation.AddNewSegmentHull(clickPoint, time);
......
......@@ -5,6 +5,30 @@
% NOTE: this is one of the few edit actions that does not directly affect
% undo stack it will always be followed by a ContextSetPhenotype action.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [historyAction phenoID] = AddPhenotype(description)
global CellPhenotypes Colors
......
......@@ -3,6 +3,30 @@
%
% Changes trackID to newTrackID beginning at time.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function historyAction = ChangeLabelAction(trackID, newTrackID, time)
%TODO: This edit graph update may need to more complicated to truly
%capture user edit intentions.
......
......@@ -5,6 +5,30 @@
% Context Swap Labels
% Toggle lock on family ID
% Maria Enokian
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function historyAction = ChangeParent(familyID,trackID,newTrackID, time)
% Initialized variables
global CellFamilies CellTracks Figures
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
% ContextAddMitosis(trackID, siblingTrack, time)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ChangeLog:
% EW 6/8/12 created
function ContextAddMitosis(trackID, siblingTrack, time, localLabels, revLocalLabels)
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -5,10 +5,10 @@
% EW 6/8/12 reviewed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
% ContextChangeParent.m - Allows user to correct the parents during the
% mitosis stage, and fix the tree.
% Maria Enokian
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ContextChangeParent(familyID,time,trackID)
global CellTracks
global Figures
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -3,10 +3,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -5,10 +5,10 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011 Andrew Cohen, Eric Wait and Mark Winter
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% https://pantherfile.uwm.edu/cohena/www/LEVer.html for details
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
......
......@@ -4,6 +4,30 @@
% Sets or clears the phenotype specified for the given hull. If the
% phenotype is "dead" there is also some special handling to drop children.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function historyAction = ContextSetPhenotype(hullID, phenotype, bActive)
global CellPhenotypes
......
......@@ -3,6 +3,30 @@
%
% Swap tracking for tracks A and B beginning at specified time.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% LEVer is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with LEVer in file "gnu gpl v3.txt". If not, see
% <http://www.gnu.org/licenses/>.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function historyAction = ContextSwapLabels(trackA, trackB, time)
Tracker.GraphEditSetEdge(trackA, trackB, time);
......
......@@ -3,6 +3,30 @@
%
% Create user identified mitosis events and add to current tree.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Copyright 2011-2016 Andrew Cohen
%
% This file is part of LEVer - the tool for stem cell lineaging. See
% http://n2t.net/ark:/87918/d9rp4t for details
%
% LEVer is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or