Merge branch 'log_seg' of git-bioimage.coe.drexel.edu:bioimage/leverjs into log_seg

matlab/+Helpers/scaleBar.m

-function [nPixels,microns] = scaleBar(CONSTANTS,targetPixels)
+function [nPixels,microns] = scaleBar(CONSTANTS,targetPixels,szim)
 
 if ~exist('targetPixels','var')
     targetPixels = 100;
@@ -9,7 +9,10 @@ microns = targetPixels .* microns_per_pixel;
 microns = 5 * round(microns/5);
 nPixels = round(microns / microns_per_pixel);
 
-rectangle('Position',[2*size(im,2)-100,25,nPixels,10],'facecolor','w')
-text(2*size(im,2)-100+nPixels/2,25,'30um','color','w','HorizontalAlignment','center', ...
-    'VerticalAlignment','bottom')
+% rectangle('Position',[szim(2)-100,25,nPixels,10],'facecolor','w')
+% text(szim(2)-100+nPixels/2,25,'30um','color','w','HorizontalAlignment','center', ...
+%     'VerticalAlignment','bottom')
 
+rectangle('Position',[szim(2)-30-nPixels,40,nPixels,15],'FaceColor','w');
+% text(szim(2)-30-nPixels,15,[num2str(microns) '\mum'],'color','w','VerticalAlignment','top','fontsize',12)
+text(szim(2)-30-nPixels,5,[num2str(microns) '\mum'],'color','w','VerticalAlignment','top','fontsize',12)

matlab/+MovieMaker/goFigureAnimation.m

+% this code can be functionalized
+% can also add features:
+% periodicity toggle? if true remove final frame
+% changing number of inbetweens to speed up or slow down the animation
+
+fileName = 'ssfClustering';              % name of movie generated
+frameRate = 30;                          % desired frame rate
+duration = 30;                           % desired length of movie in seconds
+azimuthList = [-20,-110,-190,-290,-380]; % camera pan angle at key frames
+elevationList = [10,10,10,10,10];        % camera tilt angle at key frames
+
+v = VideoWriter(fileName,'MPEG-4');
+v.FrameRate = frameRate;
+open(v);
+
+% interpolate viewing angles between key frames to match the specified duration
+
+keyFrameList = [azimuthList;elevationList]';
+numFrames = round(duration * frameRate);
+intervalLength = (numFrames - 1) / (size(keyFrameList,1) - 1);
+
+% initialize the angleList
+angleList = zeros(numFrames,2);
+
+for numKeyFrame = 1:size(keyFrameList,1) - 1
+    
+    firstRow = round(intervalLength * (numKeyFrame - 1) + 1); % first row of the interval between key frames
+    lastRow = round(intervalLength * numKeyFrame + 1);        % last row of the interval between key frames
+    
+    a = keyFrameList(numKeyFrame,1);     % initial key frame azimuth angle
+    b = keyFrameList(numKeyFrame + 1,1); % ending key frame azimuth angle
+    
+    c = keyFrameList(numKeyFrame,2);     % initial key frame elevation angle
+    d = keyFrameList(numKeyFrame + 1,2); % ending key frame elevation angle
+    
+    n = round(intervalLength * numKeyFrame) - round(intervalLength * (numKeyFrame - 1)) + 1; % number of angles to add 
+    
+    angleList(firstRow:lastRow,:) = [linspace(a,b,n).' , linspace(c,d,n).'];
+    
+end
+
+% capture frames and write to the movie file
+for frame = 1:size(angleList,1)
+    view(angleList(frame,:));
+    drawnow;
+    writeVideo(v,getframe(gcf));
+end
+
+close(v);