Fix Clientside viewer

butterfly/restapi.py

@@ -54,6 +54,9 @@ def initialize(self, core):
         '''
         self.core = core
 
+        self.set_header("Access-Control-Allow-Origin", "*")
+        self.set_header('Access-Control-Allow-Methods', 'GET')
+
     def get(self, command):
         '''Handle an HTTP GET request'''
 

butterfly/static/index/setup.js

@@ -1,4 +1,4 @@
-log = console.log.bind(window.console);
+//log = console.log.bind(window.console);
 //-----------------------------------
 //
 // DOJO.Setup: request data from server
@@ -20,7 +20,6 @@ DOJO.Setup.prototype = {
     'dataset','channel',
     'channel_metadata'
   ],
-  output: [],
   start: function(old){
     return this.loader(['root'],{old:old},0);
   },
@@ -65,9 +64,17 @@ DOJO.Setup.prototype = {
     return this.write.main(terms);
   },
   draw: function(parent, depth, result) {
+    var constant = {
+      old: result.old,
+      depth: depth
+    }
+    var target = {
+      self: parent.concat(0),
+      parent: parent,
+      target: 'body'
+    }
     var loader = this.loader.bind(this);
-    var build = this.build.bind(this,{old: result.old, depth: depth});
-    var target = {self:parent.concat(0), parent:parent, target:'body'};
+    var build = this.build.bind(this,constant);
     if (result.out instanceof Array){
       var promises = result.out.map(function(name,i){
         target.target = 'head';

butterfly/static/index/write.js

@@ -12,10 +12,6 @@ DOJO.Write.prototype = {
   copy: function(id,i){
     return document.getElementById(id).children[i].cloneNode(1);
   },
-  chan: [
-    new RegExp('(seg|id).*', 'i'),
-    new RegExp('(syn).*', 'i')
-  ],
   grandparent: function(el){
     return el.parentElement.parentElement;
   },
@@ -48,11 +44,10 @@ DOJO.Write.prototype = {
     var uncle = this.grandkid(ancestor,[1,1]);
     var size = source.dimensions;
     var dtype = source['data-type'];
-    var withGL = Number(dtype!='uint8');
-    var [w,h,d] = [size.x,size.y,size.z];
-    var channel = withGL + source.channel;
-    var path = 'viz.html?depth='+d+'&width='+w+'&height='+h;
+    var channel = Number(!dtype.match(/float|uint8/)) + source.channel;
     var old = source.old.replace(/&channel=([^&]+)/,'&channel='+channel);;
+    var [w,h,d] = [Math.max(size.x,512),Math.max(size.y,512),size.z];
+    var path = 'viz.html?depth='+d+'&width='+w+'&height='+h;
     cousin.children[0].href = path + '&' + old;
     if (uncle.children[0].href) {
       uncle.children[0].href += ',' + channel;

butterfly/static/viz/realtime.js

@@ -10,95 +10,95 @@
 
 
 DOJO.RealTime = function(scope) {
-    this.stack = scope.stack;
-    this.seaGL = new openSeadragonGL(scope.openSD);
-    this.seaGL.vShader = './shaders/vertex/rect.glsl';
-    this.seaGL.fShader = './shaders/fragment/rect.glsl';
+  this.stack = scope.stack;
+  this.seaGL = new openSeadragonGL(scope.openSD);
+  this.seaGL.vShader = './shaders/vertex/rect.glsl';
+  this.seaGL.fShader = './shaders/fragment/rect.glsl';
 }
 
 DOJO.RealTime.prototype = {
-    init: function(input){
-        var seaGL = this.seaGL;
-        var stack = this.stack;
-        var fun = function(){ };
-        var found = input.findings;
-        var rgb2id = function(rgb){
-          return rgb[0] + 256*rgb[1] + 65536*rgb[2];
-        }
-        var isTarget = fun.call.bind(function(){
-          return this.source && this.source.gl;
-        });
-        var isDojo = fun.call.bind(function(){
-          return this.source && this.source.dojo;
-        });
-        var nearTile = function(tile){
-          var where = new OpenSeadragon.Point(tile.x,tile.y);
-          return this.level == tile.level && this.xy.equals(where);
-        }
-        var isTile = function(tile){
-          var here = this.bounds.getTopLeft();
-          var where = tile.bounds.getTopLeft();
-          return this.level == tile.level && here.equals(where);
-        }
-        var contextualize = function(tile){
-          return tile.cacheImageRecord.getRenderedContext();
-        }
-        var pointColor = function(point,tile) {
-            var shape = tile.bounds.getSize();
-            var space = tile.bounds.getTopLeft();
-            var inImg = contextualize(tile);
-            var inCanv = inImg.canvas;
-            var d = point.minus(space);
-            var tmp = [d.x/shape.x, d.y/shape.y];
-            var xy = [inCanv.width*tmp[0], inCanv.height*tmp[1]].map(Math.ceil);
-            return inImg.getImageData(xy[0], xy[1], 1, 1).data;
-        }
-        var click = function(callback,e){
-          var point = stack.vp.viewerElementToViewportCoordinates(e.position);
-          var allItems = stack.findLayer(0).reverse();
-          var targets = allItems.filter(isTarget)[0];
-          var dojo = stack.getDojo();
-          if(dojo && targets && targets.lastDrawn.length){
-            var here = {level: targets.lastDrawn[0].level};
-            here.xy = dojo.source.getTileAtPoint(here.level,point);
-            var hereTile = targets.lastDrawn.filter(nearTile.bind(here))[0];
-            if(hereTile){
-              this.viaGL.clickID = pointColor(point,hereTile);
-              found[1].childNodes[1].innerHTML = rgb2id(this.viaGL.clickID);
-              this.openSD.forceRedraw();
-            }
-          }
-        }
-        var draw = function(callback,e){
-          var allItems = stack.findLayer(0);
-          var dojo = e.tiledImage.source.dojo;
-          if (!dojo){
-             return;
-          }
-          var targets = allItems.filter(isTarget)[0];
-          if(targets && targets.lastDrawn.length){
-            var fromTile = targets.lastDrawn.filter(isTile.bind(e.tile))[0];
-            if(fromTile){
-              e.output = contextualize(e.tile);
-              e.rendered = contextualize(fromTile);
-              callback(e);
-            }
-          }
-        }
-        // Load for glsl
-        var GLloaded = function(program) {
-          this.clicker = this.gl.getUniformLocation(program, 'u_click_id');
+  init: function(input){
+    var seaGL = this.seaGL;
+    var stack = this.stack;
+    var fun = function(){ };
+    var found = input.findings;
+    var rgb2id = function(rgb){
+      return rgb[0] + 256*rgb[1] + 65536*rgb[2];
+    }
+    var isTarget = fun.call.bind(function(){
+      return this.source && this.source.target;
+    });
+    var isDojo = fun.call.bind(function(){
+      return this.source && this.source.dojo;
+    });
+    var nearTile = function(tile){
+      var where = new OpenSeadragon.Point(tile.x,tile.y);
+      return this.level == tile.level && this.xy.equals(where);
+    }
+    var isTile = function(tile){
+      var here = this.bounds.getTopLeft();
+      var where = tile.bounds.getTopLeft();
+      return this.level == tile.level && here.equals(where);
+    }
+    var contextualize = function(tile){
+      return tile.cacheImageRecord.getRenderedContext();
+    }
+    var pointColor = function(point,tile) {
+      var shape = tile.bounds.getSize();
+      var space = tile.bounds.getTopLeft();
+      var inImg = contextualize(tile);
+      var inCanv = inImg.canvas;
+      var d = point.minus(space);
+      var tmp = [d.x/shape.x, d.y/shape.y];
+      var xy = [inCanv.width*tmp[0], inCanv.height*tmp[1]].map(Math.ceil);
+      return inImg.getImageData(xy[0], xy[1], 1, 1).data;
+    }
+    var click = function(callback,e){
+      var point = stack.vp.viewerElementToViewportCoordinates(e.position);
+      var allItems = stack.findLayer(0).reverse();
+      var targets = allItems.filter(isTarget)[0];
+      var dojo = stack.getDojo();
+      if(dojo && targets && targets.lastDrawn.length){
+        var here = {level: targets.lastDrawn[0].level};
+        here.xy = dojo.source.getTileAtPoint(here.level,point);
+        var hereTile = targets.lastDrawn.filter(nearTile.bind(here))[0];
+        if(hereTile){
+          this.viaGL.clickID = pointColor(point,hereTile);
+          found[1].childNodes[1].innerHTML = rgb2id(this.viaGL.clickID);
+          this.openSD.forceRedraw();
         }
-        // Draw for glsl
-        var GLdrawing = function() {
-          var clickID = this.clickID || [-1,-1,-1,-1];
-          this.gl.uniform4f(this.clicker, clickID[0], clickID[1], clickID[2], clickID[3]);
+      }
+    }
+    var draw = function(callback,e){
+      var allItems = stack.findLayer(0);
+      var dojo = e.tiledImage.source.dojo;
+      if (!dojo){
+         return;
+      }
+      var targets = allItems.filter(isTarget)[0];
+      if(targets && targets.lastDrawn.length){
+        var fromTile = targets.lastDrawn.filter(isTile.bind(e.tile))[0];
+        if(fromTile){
+          e.output = contextualize(e.tile);
+          e.rendered = contextualize(fromTile);
+          callback(e);
         }
-        found[1].childNodes[1].innerHTML = 0;
-        seaGL.addHandler('gl-drawing',GLdrawing);
-        seaGL.addHandler('gl-loaded',GLloaded);
-        seaGL.addHandler('canvas-click',click);
-        seaGL.addHandler('tile-drawing',draw);
-        return seaGL.init();
+      }
+    }
+    // Load for glsl
+    var GLloaded = function(program) {
+      this.clicker = this.gl.getUniformLocation(program, 'u_click_id');
     }
-}
+    // Draw for glsl
+    var GLdrawing = function() {
+      var clickID = this.clickID || [-1,-1,-1,-1];
+      this.gl.uniform4f(this.clicker, clickID[0], clickID[1], clickID[2], clickID[3]);
+    }
+    found[1].childNodes[1].innerHTML = 0;
+    seaGL.addHandler('gl-drawing',GLdrawing);
+    seaGL.addHandler('gl-loaded',GLloaded);
+    seaGL.addHandler('canvas-click',click);
+    seaGL.addHandler('tile-drawing',draw);
+    return seaGL.init();
+  }
+}

butterfly/static/viz/stack.js

@@ -6,7 +6,7 @@
 // -- Made by main.js
 // -- Init by main.js
 //-----------------------------------
-log = console.log.bind(window.console);
+//log = console.log.bind(window.console);
 
 DOJO.Stack = function(src_terms){
 
@@ -161,25 +161,6 @@ DOJO.Stack.prototype = {
     }
     return newBuff;
   },
-  log: function(newBuff){
-    log('z:' + this.z);
-    log('buffer: [' + newBuff.down + ':' + newBuff.up+']');
-    for (var zb = -newBuff.down; zb <= newBuff.up; zb++){
-      var tab = '   ';
-      var star = zb===0? '*' : ' ';
-      var image = this.findLayer(zb).pop();
-      if (image) {
-        var zeta = image.source.z;
-        var alpha = image.getOpacity();
-        var preload = image.getPreload();
-      }
-      log(star+tab+'layer '+ zeta || 'null' );
-      log(tab+tab+'opacity:'+alpha || 'null');
-      log(tab+tab+'preload:'+preload || 'null');
-      log(tab+tab+'index: ['+this.findIndex(zb)+']');
-    };
-    log(' ');
-  },
   refresher: function(e){
     e.item.addHandler('fully-loaded-change',function(e){
       var image = e.eventSource;

butterfly/static/viz/tools/osd/zipjob.js

@@ -23,7 +23,8 @@ ZipJob.prototype = {
     },
 
     set: function(raw) {
-        var size = this.parse(this.src).size.split(",").slice(0,2).map(Number);
+        var src = this.parse(this.src);
+        var size = [src.width, src.height].map(Number);
         var output = this.viaGL.toCanvas(raw,size);
         this.image.onload = this.finish.bind(this);
         this.image.src = output.toDataURL();

butterfly/static/viz/tools/osd/ziploader.js

@@ -41,7 +41,7 @@ ZipLoader.prototype = {
                 abort: options.abort
             };
         // Cool Hack from 2016-09-26
-        if (options.src.slice(-3) == 'zip') {
+        if (options.src.indexOf('&format=zip') >= 0) {
             var newJob = new ZipJob( this.viaGL, jobOptions );
         }
         else {

butterfly/webserver.py

@@ -144,7 +144,7 @@ def handle(self, handler):
                     # Rotate out of numpy array
                     volume = volume.transpose(1, 0, 2)
                     zipped_data = zlib.compress(
-                        volume.astype(np.uint32).tostring('F'))
+                        volume.astype(out_dtype).tostring('F'))
 
                     output = StringIO.StringIO()
                     output.write(zipped_data)

requirements.txt

@@ -1,6 +1,7 @@
 tornado==4.3
 h5py==2.6.0
 scipy==0.16.0
+https://storage.googleapis.com/google-code-archive-source/v2/code.google.com/pyrtree/source-archive.zip
 https://github.com/Rhoana/rh_config/archive/1.0.0.tar.gz#egg=rh_config-1.0.0
 https://github.com/Rhoana/rh_logger/archive/2.0.0.tar.gz#egg=rh_logger-2.0.0
 https://github.com/Rhoana/dataspec/archive/1.1.1.tar.gz#egg=dataspec-1.1.1