--- a
+++ b/Analysis/jPCA_ForDistribution/phaseMovie.m
@@ -0,0 +1,180 @@
+% For making rosette movies for the paper
+% useage:
+%
+%   phaseMovie(Projection, Summary);    Easiest usage.  Just plot in matlab. Use default params.
+%   phaseMovie(Projection, Summary, movieParams);   Can override one or more parameters
+%   MV = phaseMovie(Projection, Summary, movieParams);   if you need to save a movie
+%
+%   To save the movie use: movie2avi(MV, 'movieName', 'FPS', 12, 'compression', 'none');
+%
+%   'movieParams' can contain the following fields:
+%       .plane2plot   Default is 1.  Set to 2 to see the second plane (and so on)
+%       .rankType     Default is 'eig': the first plane is that associated with the largest eigenvalue.
+%                     Can also be 'varCapt'
+%       .times        Default is Projection(1).times.  Note that you can specify a subset of those
+%                     times or a superset.  If the latter, only those times that lie within
+%                     'allTimes' will be used.
+%       .conds2plot   Default is 'all'.  Can also be a scalar (to plot a single cond), or a vector of
+%                     conds (e.g., [1 5 12 27];
+%       .substRawPCs  Substitute raw PCs.
+%       .pixelsToGet  You may wish to customize these, esp. if the defaults don't work well on your
+%                     screen.  Co-ordinates are left then bottom, then width then height.
+%                     See getframe for more info.  
+%       .usePads      Default is 0.  If '1', stationary pads will be added to start and end of
+%                     movie.  This can be useful in some media players (though not keynote).
+%       .arrowGain    Controls how much the arrow grows with speed.  Default is 25;
+%       .tail         If specified and not empty, a tail of this length (in ms) will be produced, instead of the whole trajectory. 
+
+
+function MV = phaseMovie(Projection, Summary, movieParams)
+
+
+%% Set defaults and override if fields are set in 'movieParams'
+
+
+% PLANE
+% Plot the first plane (eigenvalue-wise) unless asked to do otherwise
+frameParams.planes2plot = 1;
+if exist('movieParams', 'var') && isfield(movieParams,'plane2plot')
+    frameParams.planes2plot = movieParams.plane2plot(1); % do what we are told, but we can only plot one plane
+end
+frameParams.rankType = 'eig';  % can also be 'varCapt'
+if exist('movieParams', 'var') && isfield(movieParams,'rankType')
+    frameParams.rankType = movieParams.rankType;
+end
+
+
+% TIMES
+times2plot = Projection(1).times;
+if exist('movieParams', 'var') && isfield(movieParams,'times')
+    times2plot = movieParams.times;
+    times2plot = times2plot(ismember(times2plot, Projection(1).allTimes));  % can only plot what we have access to 
+end
+
+% CONDS
+frameParams.conds2plot = 'all';
+if exist('movieParams', 'var') && isfield(movieParams,'conds2plot')
+    frameParams.conds2plot = movieParams.conds2plot;
+end
+
+% jPCs or raw PCs
+frameParams.substRawPCs = false;
+if exist('movieParams', 'var') && isfield(movieParams,'substRawPCs')
+    frameParams.substRawPCs = movieParams.substRawPCs;
+end
+
+% PIXELS
+pixelsToGet = [70 -90 600 590];
+if exist('movieParams', 'var') && isfield(movieParams,'pixelsToGet')
+    pixelsToGet = movieParams.pixelsToGet;
+end
+
+% Stationary Padding
+% Default is we do not add any stationary padding to start or end.  But we will if asked
+usePads = false;
+if exist('movieParams', 'var') && isfield(movieParams,'usePads')
+    usePads = movieParams.usePads;
+end
+% These are used only if the above flag is true
+stationaryPadStart = 18;  % extra frames at the beginning of stationary image.
+stationaryPadEnd = 24;  % extra frames at the end of stationary image.
+
+% Arrow size changes with speed
+frameParams.arrowGain = 25;  % controls how the arrow grows with speed
+if exist('movieParams', 'var') && isfield(movieParams,'arrowGain')
+    frameParams.arrowGain = movieParams.arrowGain;
+end
+
+% Tail
+tail = [];
+if exist('movieParams', 'var') && isfield(movieParams,'tail')
+    tail = movieParams.tail;
+end
+
+
+
+% These plotting parameters are currently hard coded (can't be changed by movieParams)
+% If needed, one can of course 
+frameParams.arrowSize = 3.3;  % will likely grow
+frameParams.planMarkerSize = 6.5;
+frameParams.lineWidth = 0.5;
+frameParams.useAxes = 0;
+frameParams.useLabel = 0;
+frameParams.plotPlanEllipse = 0;
+frameParams.reusePlot = 0;  % will change to one after first frame
+
+if ~isempty(tail)
+    frameParams.planMarkerSize = 0;  % not plan marker if we are using a non-infinite tail
+end
+    
+
+%% Done handling parameters and defaults
+% Print some things out to confirm to the user the choices being made
+fprintf('using plane %d (ordered by %s)\n',  frameParams.planes2plot, frameParams.rankType);
+fprintf('movie runs from time %d to %d\n',  times2plot([1,end]));
+fprintf('pixels: [%d %d %d %d]\n',  pixelsToGet);
+
+
+%% Now start plotting stuff
+
+fi = 1;  % frame index
+
+%% start pad
+if nargout > 0  && usePads == 1
+    % pad at start if we are making the  movie to export, rather than just view in matlab
+
+    for i = 1:stationaryPadStart
+        frameParams.times = times2plot(1):times2plot(2);
+
+        phaseSpace(Projection, Summary, frameParams);
+        drawnow;
+        frameParams.reusePlot = 1;  % after the first frame, always reuse
+
+        if nargout > 0
+            MV(fi) = getframe(gca, pixelsToGet);
+            fi=fi+1;
+        end
+    end
+end
+
+%% ** ACTUAL MOVIE **
+for ti = 2:length(times2plot)
+    frameParams.times = times2plot(1):times2plot(ti);  % only times that match one of these will be used
+    if ~isempty(tail)  && range(frameParams.times) > tail
+        frameParams.times = frameParams.times(frameParams.times > frameParams.times(end)-tail);
+    end
+        
+    phaseSpace(Projection, Summary, frameParams);
+    drawnow;
+    frameParams.reusePlot = 1;  % after the first frame, always reuse
+    
+    if nargout > 0
+        MV(fi) = getframe(gca, pixelsToGet);
+        fi=fi+1;
+    end
+end
+
+%% end pad
+if nargout > 0  && usePads == 1
+    % pad at start if we are making the  movie to export, rather than just view in matlab
+    for i = 1:stationaryPadEnd
+        frameParams.times = times2plot(1):times2plot(end);
+
+        phaseSpace(Projection, Summary, frameParams);
+        drawnow;
+        frameParams.reusePlot = 1;  % after the first frame, always reuse
+
+        if nargout > 0
+            MV(fi) = getframe(gca, pixelsToGet);
+            fi=fi+1;
+        end
+    end
+end
+
+
+if ~exist('MV', 'var')  % if we were not asked to make the movie structure
+    MV = [];
+end
+    
+
+