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

elever/main.js

@@ -5,7 +5,6 @@ const app = electron.app
 
 // Module to create native browser window.
 const BrowserWindow = electron.BrowserWindow
-
 const path = require('path')
 const url = require('url')
 const {ipcMain} = require('electron');
@@ -24,7 +23,9 @@ function createWindow ()
   // Create the browser window.
   mainWindow = new BrowserWindow({width: 800, height: 600, icon:path.join(__dirname,'..','leverjs/leverjs.ico'), 
     webPreferences: {
-      nodeIntegration: true
+      nodeIntegration: true,
+      contextIsolation: false,
+      enableRemoteModule: true
     } 
   });
  

leverjs/ImageWindowBuilder.js

@@ -41,7 +41,8 @@ var miniMapmousedrag = false;
 // database is read only
 var gbReadOnlyDB=false;
 
-const IS_NODE = typeof module !== 'undefined' && module.exports;
+// const IS_NODE = typeof module !== 'undefined' && module.exports;
+var IS_NODE = navigator.userAgent.indexOf('Electron') >= 0
 
 // set to tell render.js (reDraw) not to kick off a multires if we're in the experiment window
 var gbExperimentRender=false;
@@ -171,7 +172,7 @@ window.onload = function () {
             ROOT=params[1].slice('ROOT='.length)
             title=params[2].slice('TITLE='.length)
             
-            console.log('lever figure window found :: port='+port+" :: root="+root)
+            console.log('lever figure window found :: port='+port+" :: root="+ROOT)
             uiServer.init(port,window)
             document.title='leversc '+title
             setLeverscUI()

leversc/src/MATLAB/@leversc/show.m

@@ -106,8 +106,18 @@ end
 
 function launch_electron_posix(port,fignum,workdir, leverpath,strDB)
 elec_cmd = 'leverjs';
+px = getenv('PATH');
 if ( ~isempty(leverpath) )
+        % first try NVM
+        nvm_path = getenv('NVM_DIR');
+        if ~isempty(nvm_path)
+            [ret,elec_path] = system('source ~/.nvm/nvm.sh;which electron');  
+            elec_path = replace(elec_path,newline,'');
+            nodePath = fileparts(elec_path);            
+            px = [px ':' nodePath];
+        else
             elec_path = fullfile(leverpath,'node_modules','.bin','electron');            
+        end
         elec_cmd = [elec_path ' ' fullfile(leverpath,'elever','main.js')];
 else
     [status,~] = system(['which ' elec_cmd]);
@@ -118,8 +128,8 @@ end
 if exist('strDB','var') && ~isempty(strDB)
     elec_cmd = [elec_cmd ' --leverFile=' strDB ' '];
 end
-cmd = [elec_cmd ' --port=' num2str(port) ' --title="figure ' num2str(fignum) '"' ' &'];
-system(cmd);
+cmd = [elec_cmd ' --port=' num2str(port) ' --title="figure ' num2str(fignum) '"' ' &']
+system(cmd,'PATH',px);
 end
 
 function launch_electron_windows(port,fignum,workdir, leverpath, strDB)

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);