-
-When you have done 1 slice,
-* add your name or github handle to our BRAINMAPPERS.md file
-* add the slice number where you have been working (currently, 111 & 112 are done, you could continue with 113++)
-* add "length:..." and
-* "volume:..." from the upper left corner of the BrainBox viewer into the file (just for the fun!! :D)
-* and make a pull request!
-
-The best devices for drawing over the brain are tablets with pens. With a computer mouse or trackpad it is a bit more tedious but works very fine as well 😃 Looking forward to seeing you!
-
-Just say hi in the BrainBox chat and we will guide you to the view where we are currently working.
-
-We will work in an axial slice (113++) and erase all the parts of the mask that cover the sulci of the brain. You see the impressively folded structure of the dolphin brain. The sulci, which are the valleys of the folds, appear darker. We erase them from the mask to being able to reconstruct the 3D surface preserving the folding.
-**It's fun! Join us! :)** Careful! It's addictive! <3 😄
-
-
-
diff --git a/BRAINMAPPERS.md b/BRAINMAPPERS.md
deleted file mode 100644
index 36f21c1d..00000000
--- a/BRAINMAPPERS.md
+++ /dev/null
@@ -1,23 +0,0 @@
-We are the brain mappers! \ö/
-
-Here, we are segmenting an amazingly folded [**dolphin brain**](http://brainbox.pasteur.fr/mri?url=http://braincatalogue.org/data/Bottlenose_dolphin/MRI-n4.nii.gz). Once you clicked the link, you will find our work in 'Cerebrum' annotation layer from the Braincatalogue project. You can **join our segmentation sprint any time!** You can also choose a different species to work on, if you prefer! Any contributions are featured below.
-
-"; - } - text.html(str); - - str=""; - if(me.User.measureLength) { - var W=parseFloat($('#atlasMaker canvas').css('width')); - var w=parseFloat($('#atlasMaker canvas').attr('width')); - var zx=W/w,zy=zx*me.brain_Hdim/me.brain_Wdim,p=me.User.measureLength,str1; - var W=parseFloat($('#atlasMaker canvas').css('width')); - var w=parseFloat($('#atlasMaker canvas').attr('width')); - str1="M"+zx*p[0].x+","+zy*p[0].y; - for(i=1;i
"; + } + text.html(str); + + str=""; + if(me.User.measureLength) { + var W=parseFloat($('#atlasMaker canvas').css('width')); + var w=parseFloat($('#atlasMaker canvas').attr('width')); + var zx=W/w,zy=zx*me.brain_Hdim/me.brain_Wdim,p=me.User.measureLength,str1; + var W=parseFloat($('#atlasMaker canvas').css('width')); + var w=parseFloat($('#atlasMaker canvas').attr('width')); + str1="M"+zx*p[0].x+","+zy*p[0].y; + for(i=1;i
");
- black.css({position:'fixed',top:0,left:0,width:'100%',height:'100%','z-index':5,'background-color':'#222'});
- $('body').append(black);
-
- // configure display mode
- // $("#atlasMaker").removeClass('display-mode');
- $("body").addClass('atlasMaker-fullscreen');
- $("#atlasMaker").detach().appendTo('body');
-
- // me.editMode=1;
- me.resizeWindow();
-
- // configure toolbar for edit mode
- //$("#log").outerHeight($("#tools-side").outerHeight()-$("#log").offset().top-$("#msg").closest("tr").outerHeight());
- me.fullscreen=true;
- } else {
+ if(me.fullscreen==false) {
+ // Enter fullscreen
+ //-----------------
+
+ // add black overlay
+ var black=$("Math.abs(mi.v)) mi={i:n,v:o}});
var mj={i:0,v:0};j.map(function(o,n){if(Math.abs(o)>Math.abs(mj.v)) mj={i:n,v:o}});
var mk={i:0,v:0};k.map(function(o,n){if(Math.abs(o)>Math.abs(mk.v)) mk={i:n,v:o}});
- mri.s2v = {
- // old s2v fields
- s2w: me.invMat(w2s),
- sdim: [],
- sori: [-wmin[0]/Math.abs(wpixdim[0]),-wmin[1]/Math.abs(wpixdim[1]),-wmin[2]/Math.abs(wpixdim[2])],
- wpixdim: [],
- w2v: me.invMat(v2w),
+ mri.s2v = {
+ // old s2v fields
+ s2w: me.invMat(w2s),
+ sdim: [],
+ sori: [-wmin[0]/Math.abs(wpixdim[0]),-wmin[1]/Math.abs(wpixdim[1]),-wmin[2]/Math.abs(wpixdim[2])],
+ wpixdim: [],
+ w2v: me.invMat(v2w),
wori: wori,
// new s2v transformation
@@ -317,7 +317,7 @@ var AtlasMakerIO = {
X: (mi.v>0)?0:(mri.dim[0]-1), // starting value for space coordinate x when voxel coordinate i starts
Y: (mj.v>0)?0:(mri.dim[1]-1), // same for y
Z: (mk.v>0)?0:(mri.dim[2]-1) // same for z
- };
+ };
mri.v2w=v2w;
mri.wori=wori;
mri.s2v.sdim[mi.i] = mri.dim[0];
@@ -326,119 +326,119 @@ var AtlasMakerIO = {
mri.s2v.wpixdim[mi.i] = mri.pixdim[0];
mri.s2v.wpixdim[mj.i] = mri.pixdim[1];
mri.s2v.wpixdim[mk.i] = mri.pixdim[2];
- },
+ },
/**
* @function testS2VTransformation
*/
- testS2VTransformation: function testS2VTransformation() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(testS2VTransformation);if(l)console.log.apply(undefined,l);
-
- /*
- check the S2V transformation to see if it looks correct.
- If it does not, reset it
- */
- var mri=me.User; // this line is different from server
- var doReset=false;
-
- // console.log("Transformation TEST:");
- // console.log(" 1. transformation volume");
-
- var vv=mri.dim[0]*mri.dim[1]*mri.dim[2];
- var vs=mri.s2v.sdim[0]*mri.s2v.sdim[1]*mri.s2v.sdim[2];
- var diff=(vs-vv)/vv;
- if(Math.abs(diff)>0.001) {
- console.log(" ERROR: Difference is too large");
- console.log(" original volume:",vv);
- console.log(" rotated volume:",vs);
- console.log(" % difference:",diff*100);
- doReset=true;
- } else {
- // console.log(" ok.");
- }
-
- // console.log(" 2. transformation origin");
- if( mri.s2v.sori[0]<0||mri.s2v.sori[0]>mri.s2v.sdim[0] ||
- mri.s2v.sori[1]<0||mri.s2v.sori[1]>mri.s2v.sdim[1] ||
- mri.s2v.sori[2]<0||mri.s2v.sori[2]>mri.s2v.sdim[2]) {
- // console.log(" Origin point is outside the dimensions of the data");
- doReset=true;
- } else {
- // console.log(" ok.");
- }
+ testS2VTransformation: function testS2VTransformation() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(testS2VTransformation);if(l)console.log.apply(undefined,l);
+
+ /*
+ check the S2V transformation to see if it looks correct.
+ If it does not, reset it
+ */
+ var mri=me.User; // this line is different from server
+ var doReset=false;
+
+ // console.log("Transformation TEST:");
+ // console.log(" 1. transformation volume");
+
+ var vv=mri.dim[0]*mri.dim[1]*mri.dim[2];
+ var vs=mri.s2v.sdim[0]*mri.s2v.sdim[1]*mri.s2v.sdim[2];
+ var diff=(vs-vv)/vv;
+ if(Math.abs(diff)>0.001) {
+ console.log(" ERROR: Difference is too large");
+ console.log(" original volume:",vv);
+ console.log(" rotated volume:",vs);
+ console.log(" % difference:",diff*100);
+ doReset=true;
+ } else {
+ // console.log(" ok.");
+ }
+
+ // console.log(" 2. transformation origin");
+ if( mri.s2v.sori[0]<0||mri.s2v.sori[0]>mri.s2v.sdim[0] ||
+ mri.s2v.sori[1]<0||mri.s2v.sori[1]>mri.s2v.sdim[1] ||
+ mri.s2v.sori[2]<0||mri.s2v.sori[2]>mri.s2v.sdim[2]) {
+ // console.log(" Origin point is outside the dimensions of the data");
+ doReset=true;
+ } else {
+ // console.log(" ok.");
+ }
- if(doReset) {
- // console.log("THE TRANSFORMATION WILL BE RESET");
- mri.v2w=[[mri.pixdim[0],0,0],[0,-mri.pixdim[1],0],[0,0,-mri.pixdim[2]]];
- mri.wori=[0,mri.dim[1]-1,mri.dim[2]-1];
+ if(doReset) {
+ // console.log("THE TRANSFORMATION WILL BE RESET");
+ mri.v2w=[[mri.pixdim[0],0,0],[0,-mri.pixdim[1],0],[0,0,-mri.pixdim[2]]];
+ mri.wori=[0,mri.dim[1]-1,mri.dim[2]-1];
- // re-compute the transformation from voxel space to screen space
- me.computeS2VTransformation(); // this line is different from server
- /*
- console.log(mri.dir);
- console.log(mri.ori);
- console.log(mri.s2v);
- */
- }
- },
+ // re-compute the transformation from voxel space to screen space
+ me.computeS2VTransformation(); // this line is different from server
+ /*
+ console.log(mri.dir);
+ console.log(mri.ori);
+ console.log(mri.s2v);
+ */
+ }
+ },
/**
* @function S2I
*/
- S2I: function S2I(s,mri) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(S2I,3);if(l)console.log.apply(undefined,l);
-
+ S2I: function S2I(s,mri) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(S2I,3);if(l)console.log.apply(undefined,l);
+
var s2v = mri.s2v;
var v = [s2v.X+s2v.dx*s[s2v.x],s2v.Y+s2v.dy*s[s2v.y],s2v.Z+s2v.dz*s[s2v.z]];
index = v[0] + v[1]*mri.dim[0] + v[2]*mri.dim[0]*mri.dim[1];
return index;
- },
+ },
/**
* @function mulMatVec
*/
- mulMatVec: function mulMatVec(m,v) {
- return [
- m[0][0]*v[0]+m[0][1]*v[1]+m[0][2]*v[2],
- m[1][0]*v[0]+m[1][1]*v[1]+m[1][2]*v[2],
- m[2][0]*v[0]+m[2][1]*v[1]+m[2][2]*v[2]
- ];
- },
+ mulMatVec: function mulMatVec(m,v) {
+ return [
+ m[0][0]*v[0]+m[0][1]*v[1]+m[0][2]*v[2],
+ m[1][0]*v[0]+m[1][1]*v[1]+m[1][2]*v[2],
+ m[2][0]*v[0]+m[2][1]*v[1]+m[2][2]*v[2]
+ ];
+ },
/**
* @function invMat
*/
- invMat: function invMat(m) {
- var det;
- var w=[[],[],[]];
+ invMat: function invMat(m) {
+ var det;
+ var w=[[],[],[]];
- det=m[0][1]*m[1][2]*m[2][0] + m[0][2]*m[1][0]*m[2][1] + m[0][0]*m[1][1]*m[2][2] - m[0][2]*m[1][1]*m[2][0] - m[0][0]*m[1][2]*m[2][1] - m[0][1]*m[1][0]*m[2][2];
-
- w[0][0]=(m[1][1]*m[2][2] - m[1][2]*m[2][1])/det;
- w[0][1]=(m[0][2]*m[2][1] - m[0][1]*m[2][2])/det;
- w[0][2]=(m[0][1]*m[1][2] - m[0][2]*m[1][1])/det;
-
- w[1][0]=(m[1][2]*m[2][0] - m[1][0]*m[2][2])/det;
- w[1][1]=(m[0][0]*m[2][2] - m[0][2]*m[2][0])/det;
- w[1][2]=(m[0][2]*m[1][0] - m[0][0]*m[1][2])/det;
-
- w[2][0]=(m[1][0]*m[2][1] - m[1][1]*m[2][0])/det;
- w[2][1]=(m[0][1]*m[2][0] - m[0][0]*m[2][1])/det;
- w[2][2]=(m[0][0]*m[1][1] - m[0][1]*m[1][0])/det;
-
- return w;
- },
+ det=m[0][1]*m[1][2]*m[2][0] + m[0][2]*m[1][0]*m[2][1] + m[0][0]*m[1][1]*m[2][2] - m[0][2]*m[1][1]*m[2][0] - m[0][0]*m[1][2]*m[2][1] - m[0][1]*m[1][0]*m[2][2];
+
+ w[0][0]=(m[1][1]*m[2][2] - m[1][2]*m[2][1])/det;
+ w[0][1]=(m[0][2]*m[2][1] - m[0][1]*m[2][2])/det;
+ w[0][2]=(m[0][1]*m[1][2] - m[0][2]*m[1][1])/det;
+
+ w[1][0]=(m[1][2]*m[2][0] - m[1][0]*m[2][2])/det;
+ w[1][1]=(m[0][0]*m[2][2] - m[0][2]*m[2][0])/det;
+ w[1][2]=(m[0][2]*m[1][0] - m[0][0]*m[1][2])/det;
+
+ w[2][0]=(m[1][0]*m[2][1] - m[1][1]*m[2][0])/det;
+ w[2][1]=(m[0][1]*m[2][0] - m[0][0]*m[2][1])/det;
+ w[2][2]=(m[0][0]*m[1][1] - m[0][1]*m[1][0])/det;
+
+ return w;
+ },
/**
* @function subVecVec
*/
- subVecVec: function subVecVec(a,b) {
- return [a[0]-b[0],a[1]-b[1],a[2]-b[2]];
- },
+ subVecVec: function subVecVec(a,b) {
+ return [a[0]-b[0],a[1]-b[1],a[2]-b[2]];
+ },
/**
* @function addVecVec
*/
- addVecVec: function addVecVec(a,b) {
- return [a[0]+b[0],a[1]+b[1],a[2]+b[2]];
- },
- /*
- Linear Algebra}
- */
+ addVecVec: function addVecVec(a,b) {
+ return [a[0]+b[0],a[1]+b[1],a[2]+b[2]];
+ },
+ /*
+ Linear Algebra}
+ */
};
\ No newline at end of file
diff --git a/public/js/atlasMaker-paint.js b/public/js/atlasMaker-paint.js
index a8eb34b6..b19ae2af 100644
--- a/public/js/atlasMaker-paint.js
+++ b/public/js/atlasMaker-paint.js
@@ -2,41 +2,41 @@
* @page AtlasMaker: Painting commands
*/
var AtlasMakerPaint = {
- //====================================================================================
- // Paint functions
- //====================================================================================
- showxy: function showxy(u,c,x,y,usr) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(showxy,1,"#0c0");if(l)console.log.apply(undefined,l);
-
- // u: user number
- // c: command
- // x, y: coordinates
- msg={c: c, x: x, y: y};
- if(u==-1 && JSON.stringify(msg)!=JSON.stringify(me.msg0)) {
- me.sendShowMessage(msg);
- me.msg0=msg;
- }
- if(u!=-1) {
- switch(c) {
- case 'u':
- if(usr.pointer) {
+ //====================================================================================
+ // Paint functions
+ //====================================================================================
+ showxy: function showxy(u,c,x,y,usr) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(showxy,1,"#0c0");if(l)console.log.apply(undefined,l);
+
+ // u: user number
+ // c: command
+ // x, y: coordinates
+ msg={c: c, x: x, y: y};
+ if(u==-1 && JSON.stringify(msg)!=JSON.stringify(me.msg0)) {
+ me.sendShowMessage(msg);
+ me.msg0=msg;
+ }
+ if(u!=-1) {
+ switch(c) {
+ case 'u':
+ if(usr.pointer) {
usr.pointer.remove();
delete usr.pointer;
}
- break;
- case 'm':
+ break;
+ case 'm':
if(!usr.pointer) {
usr.pointer = $('
'+((usr.username == 'Anonymous')?u:usr.username)+'');
$("#resizable").append(usr.pointer);
}
usr.pointer.css({left:x*$("#resizable").width()/me.brain_W,top:y*$("#resizable").height()/me.brain_H});
- break;
- }
- }
- usr.x0=x;
- usr.y0=y;
- },
+ break;
+ }
+ }
+ usr.x0=x;
+ usr.y0=y;
+ },
/**
* @function paintxy
* @desc Dispatches paint/erase commands to the annotation volume and to the server for broadcast
@@ -46,27 +46,27 @@ var AtlasMakerPaint = {
* @param {integer} y Y coordinate in slice space
* @param {Object} usr User object for the current user. Contains the painting value, view and slice
*/
- paintxy: function paintxy(u,c,x,y,usr) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(paintxy,1,"#0c0");if(l)console.log.apply(undefined,l);
-
- // u: user number
- // c: command
- // x, y: coordinates
- msg={c:c,x:x,y:y};
-
- if(u==-1 && JSON.stringify(msg)!=JSON.stringify(me.msg0)) {
- me.sendPaintMessage(msg);
- me.msg0=msg;
- }
-
- var dim=me.atlas.dim;
-
- var coord={x:x,y:y,z:usr.slice};
- if(usr.x0<0) {
- usr.x0=coord.x;
- usr.y0=coord.y;
- }
+ paintxy: function paintxy(u,c,x,y,usr) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(paintxy,1,"#0c0");if(l)console.log.apply(undefined,l);
+
+ // u: user number
+ // c: command
+ // x, y: coordinates
+ msg={c:c,x:x,y:y};
+
+ if(u==-1 && JSON.stringify(msg)!=JSON.stringify(me.msg0)) {
+ me.sendPaintMessage(msg);
+ me.msg0=msg;
+ }
+
+ var dim=me.atlas.dim;
+
+ var coord={x:x,y:y,z:usr.slice};
+ if(usr.x0<0) {
+ usr.x0=coord.x;
+ usr.y0=coord.y;
+ }
if(u!=-1) {
if(c === 'mu') {
@@ -98,30 +98,30 @@ var AtlasMakerPaint = {
break;
}
- usr.x0=coord.x;
- usr.y0=coord.y;
- },
+ usr.x0=coord.x;
+ usr.y0=coord.y;
+ },
/**
* @function paintvol
* @desc Paints a series of voxels as indicated in an array. This function is exclusively used for undoing
* @param {Array} voxels Array where each object contains a voxel index and a voxel value. The voxel index goes from 0 to dim[0]*dim[1]*dim[2]-1
*/
- paintvol: function paintvol(voxels) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(paintvol,0,"#0c0");if(l)console.log.apply(undefined,l);
-
- var i,
- ind, // voxel index
- val; // voxel delta-value, such that -=val undoes
- for(i=0;i0) {
- if(Q.length>max)
- max=Q.length;
- n=Q.shift();
- if(atlas.data[me.slice2index(n.x,n.y,z,myView)]!=bval)
- continue;
- left=n.x;
- right=n.x;
- y=n.y;
- while (left-1>=0 && atlas.data[me.slice2index(left-1,y,z,myView)]==bval) {
+ var Q=[],
+ left,
+ right,
+ n;
+ var i,max=0;
+ var bval=atlas.data[me.slice2index(x,y,z,myView)]; // background-value: value of the voxel where the click occurred
+
+ if(bval==val) // nothing to do
+ return;
+
+ Q.push({x:x,y:y});
+ while(Q.length>0) {
+ if(Q.length>max)
+ max=Q.length;
+ n=Q.shift();
+ if(atlas.data[me.slice2index(n.x,n.y,z,myView)]!=bval)
+ continue;
+ left=n.x;
+ right=n.x;
+ y=n.y;
+ while (left-1>=0 && atlas.data[me.slice2index(left-1,y,z,myView)]==bval) {
left--;
}
- while (right+1=0 && atlas.data[me.slice2index(x,y-1,z,myView)]==bval)
- Q.push({x:x,y:y-1});
- if(y+1=0 && atlas.data[me.slice2index(x,y-1,z,myView)]==bval)
+ Q.push({x:x,y:y-1});
+ if(y+1 -dy) {
- err -= dy;
- x1 += sx;
- }
- if (e2 < dx) {
- err += dx;
- y1 += sy;
- }
+ xyzi1=me.slice2xyzi(x1,y1,z,usr.view);
+ xyzi2=me.slice2xyzi(x2,y2,z,usr.view);
+ me.annotationLength+=Math.sqrt( Math.pow(me.brain_pixdim[0]*(xyzi1[0]-xyzi2[0]),2)+
+ Math.pow(me.brain_pixdim[1]*(xyzi1[1]-xyzi2[1]),2)+
+ Math.pow(me.brain_pixdim[2]*(xyzi1[2]-xyzi2[2]),2));
+
+ for(j=0;j -dy) {
+ err -= dy;
+ x1 += sx;
+ }
+ if (e2 < dx) {
+ err += dx;
+ y1 += sy;
+ }
for(j=0;j
MRI");
+ $("#chat").text("Chat (1 connected)");
+ me.flagConnected=1;
+ me.reconnectionTimeout = 5;
+ def.resolve();
+ };
+
+ me.receiveFunctions["saveMetadata"]=me.receiveMetadata;
+ me.receiveFunctions["userData"]=me.receiveUserDataMessage;
+ me.receiveFunctions["volInfo"]=function(data){console.log("volInfo",data)};
+ me.receiveFunctions["chat"]=me.receiveChatMessage;
+ me.receiveFunctions["show"]=me.receiveShowMessage;
+ me.receiveFunctions["paint"]=me.receivePaintMessage;
+ me.receiveFunctions["paintvol"]=me.receivePaintVolumeMessage;
+ me.receiveFunctions["disconnect"]=me.receiveDisconnectMessage;
+ me.receiveFunctions["serverMessage"]=me.receiveServerMessage;
+
+ me.receiveFunctions["requestSlice"]=function(data){console.log("requestSlice",data)};
+ me.receiveFunctions["requestSlice2"]=function(data){console.log("requestSlice2",data)};
+
+ me.socket.onmessage = me.receiveSocketMessage;
+
+ me.socket.onclose = function(msg) {
+ me.flagConnected=0;
+
+ // Try to reconnect
+ // wait a random initial time, to prevent an avalanche
+ // of reconnections in case of server crash
+ var rand = 1000+5000*Math.random();
+ console.log("Initial random time:",rand);
+ setTimeout(function() {
+ var timeout = me.reconnectionTimeout;
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
+ if(me.timer) {
+ clearInterval(me.timer);
+ }
+ me.timer = setInterval(function() {
+ if(timeout < 0) {
+ $("#chat").text("Reconnecting...");
+ me.socket = null;
clearInterval(me.timer);
+ setTimeout(function() {
+ me.reconnectionTimeout *= 2;
+ me.initSocketConnection()
+ .then(function() {
+ me.sendUserDataMessage("allUserData");
+ me.sendUserDataMessage("sendAtlas");
+ clearInterval(me.timer);
+ })
+ .catch(function() {
+ timeout=me.reconnectionTimeout;
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
+ });
+ }, 1000);
+ } else {
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
}
- me.timer = setInterval(function () {
- if (timeout < 0) {
- $("#chat").text("Reconnecting...");
- me.socket = null;
- clearInterval(me.timer);
- setTimeout(function () {
- me.reconnectionTimeout *= 2;
- me.initSocketConnection()
- .then(function () {
- me.sendUserDataMessage("allUserData");
- me.sendUserDataMessage("sendAtlas");
- clearInterval(me.timer);
- })
- .catch(function () {
- timeout = me.reconnectionTimeout;
- $("#chat").text("Disconnected. Try to reconnect in " + (timeout--) + " s...");
- });
- }, 1000);
- } else {
- $("#chat").text("Disconnected. Try to reconnect in " + (timeout--) + " s...");
- }
- }, 1000);
- }, rand);
- };
-
- window.onbeforeunload = function () {
- me.socket.onclose = function () { }; // disable onclose handler first
- me.socket.close()
- };
- }
- catch (ex) {
- $("#chat").text("Chat (not connected - connection error)");
- }
- })
- },
- /**
+ }, 1000);
+ }, rand);
+ };
+
+ window.onbeforeunload = function() {
+ me.socket.onclose = function () {}; // disable onclose handler first
+ me.socket.close()
+ };
+ }
+ catch (ex) {
+ $("#chat").text("Chat (not connected - connection error)");
+ }
+
+ return def.promise();
+ },
+ /**
* @function receiveSocketMessage
*/
- receiveSocketMessage: function receiveSocketMessage(msg) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveSocketMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
- // Message: atlas data initialisation
- if (msg.data instanceof Blob) {
- me.receiveBinaryMessage(msg.data);
- return;
- }
-
- // Message: interaction message
- var data = JSON.parse(msg.data);
- me.receiveFunctions[data.type](data);
- },
- /**
+ receiveSocketMessage: function receiveSocketMessage(msg) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(receiveSocketMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
+ // Message: atlas data initialisation
+ if(msg.data instanceof Blob) {
+ me.receiveBinaryMessage(msg.data);
+ return;
+ }
+
+ // Message: interaction message
+ var data=JSON.parse(msg.data);
+ me.receiveFunctions[data.type](data);
+ },
+ /**
* @function sendUserDataMessage
*/
- sendUserDataMessage: function sendUserDataMessage(description) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(sendUserDataMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
- if (me.flagConnected == 0)
- return;
-
- if (me.debug > 1) console.log("message: " + description);
-
- if (description === "allUserData")
- var msg = { "type": "userData", "user": me.User, "description": description };
- else
- var msg = { "type": "userData", "description": description };
- try {
- me.socket.send(JSON.stringify(msg));
- } catch (ex) {
- console.log("ERROR: Unable to sendUserDataMessage", ex);
- }
- },
- /**
+ sendUserDataMessage: function sendUserDataMessage(description) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(sendUserDataMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
+ if(me.flagConnected==0)
+ return;
+
+ if(me.debug>1) console.log("message: "+description);
+
+ if(description === "allUserData")
+ var msg={"type":"userData","user":me.User,"description":description};
+ else
+ var msg={"type":"userData","description":description};
+ try {
+ me.socket.send(JSON.stringify(msg));
+ } catch (ex) {
+ console.log("ERROR: Unable to sendUserDataMessage",ex);
+ }
+ },
+ /**
* @function receiveBinaryMessage
*/
- receiveBinaryMessage: function receiveBinaryMessage(msgData) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveBinaryMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
+ receiveBinaryMessage: function receiveBinaryMessage(msgData) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(receiveBinaryMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
var fileReader = new FileReader();
fileReader.onload = function from_receiveSocketMessage() {
- var data = new Uint8Array(this.result);
- var sz = data.length;
- var ext = String.fromCharCode(data[sz - 8], data[sz - 7], data[sz - 6]);
-
- if (me.debug > 1) console.log("type: " + ext);
+ var data=new Uint8Array(this.result);
+ var sz=data.length;
+ var ext=String.fromCharCode(data[sz-8],data[sz-7],data[sz-6]);
- switch (ext) {
+ if(me.debug>1) console.log("type: "+ext);
+
+ switch(ext) {
case 'nii': {
- var inflate = new pako.Inflate();
- inflate.push(data, true);
- var atlas = new Object();
- atlas.data = inflate.result;
- atlas.name = me.atlasFilename;
- atlas.dim = me.brain_dim;
-
- me.atlas = atlas;
+ var inflate=new pako.Inflate();
+ inflate.push(data,true);
+ var atlas=new Object();
+ atlas.data=inflate.result;
+ atlas.name=me.atlasFilename;
+ atlas.dim=me.brain_dim;
+
+ me.atlas=atlas;
me.configureBrainImage();
me.configureAtlasImage();
me.resizeWindow();
- me.brain_img.img = null;
+ me.brain_img.img=null;
me.drawImages();
-
+
// compute total segmented volume
- var vol = me.computeSegmentedVolume();
- me.info.volume = parseInt(vol) + " mm3";
+ var vol=me.computeSegmentedVolume();
+ me.info.volume=parseInt(vol)+" mm3";
// setup download link
- var link = me.container.find("span#download_atlas");
- link.html("" + atlas.name);
+ var link=me.container.find("span#download_atlas");
+ link.html(""+atlas.name);
break;
}
@@ -205,283 +207,283 @@ var AtlasMakerWS = {
var urlCreator = window.URL || window.webkitURL;
var imageUrl = urlCreator.createObjectURL(msgData);
var img = new Image();
-
- me.isMRILoaded = true; // receiving a jpg is proof of a loaded MRI
-
- img.onload = function from_initSocketConnection() {
- var flagFirstImage = (me.brain_img.img == null);
- me.brain_img.img = img;
- me.brain_img.view = me.flagLoadingImg.view;
- me.brain_img.slice = me.flagLoadingImg.slice;
+
+ me.isMRILoaded=true; // receiving a jpg is proof of a loaded MRI
+
+ img.onload=function from_initSocketConnection(){
+ var flagFirstImage=(me.brain_img.img==null);
+ me.brain_img.img=img;
+ me.brain_img.view=me.flagLoadingImg.view;
+ me.brain_img.slice=me.flagLoadingImg.slice;
me.drawImages();
+
+ me.flagLoadingImg.loading=false;
- me.flagLoadingImg.loading = false;
-
- if (flagFirstImage || me.flagLoadingImg.view != me.User.view || me.flagLoadingImg.slice != me.User.slice) {
+ if(flagFirstImage || me.flagLoadingImg.view!=me.User.view ||me.flagLoadingImg.slice!=me.User.slice) {
me.sendRequestSliceMessage();
}
-
+
// remove loading indicator
$("#loadingIndicator").hide();
}
- img.src = imageUrl;
+ img.src=imageUrl;
break;
}
}
};
fileReader.readAsArrayBuffer(msgData);
- },
- /**
+ },
+ /**
* @function receiveUserDataMessage
*/
- receiveUserDataMessage: function receiveUserDataMessage(data) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveUserDataMessage, 0, "#aca"); if (l) console.log.apply(undefined, l);
-
- if (me.debug > 1) console.log("description: " + data.description, data);
-
- var u = data.uid;
-
- // First time the user is observed
- if (me.Collab[u] === undefined) {
- try {
- //var msg=""+data.user.username+" entered atlas "+data.user.specimenName+"/"+data.user.atlasFilename+"
" - var msg; - if (data.user === undefined || data.user.username === "Anonymous") { - msg = "" + data.uid + " entered
"; - } else { - msg = "" + data.user.username + " entered
"; - } - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - } catch (e) { - console.log("data:", data); - console.log(e); - } - } - - if (data.description === "allUserData") - me.Collab[u] = data.user; - else { - try { + receiveUserDataMessage: function receiveUserDataMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveUserDataMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.debug>1) console.log("description: "+data.description,data); + + var u=data.uid; + + // First time the user is observed + if(me.Collab[u]===undefined) { + try { + //var msg=""+data.user.username+" entered atlas "+data.user.specimenName+"/"+data.user.atlasFilename+"
" + var msg; + if(data.user === undefined || data.user.username === "Anonymous") { + msg=""+data.uid+" entered
"; + } else { + msg=""+data.user.username+" entered
"; + } + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + } catch (e) { + console.log("data:",data); + console.log(e); + } + } + + if(data.description === "allUserData") + me.Collab[u]=data.user; + else { + try { var changes = JSON.parse(data.description); var i; - for (i in changes) + for(i in changes) me.Collab[u][i] = changes[i]; } catch (e) { console.log(e); } - } - - var v, nusers = 1; - for (v in me.Collab) - nusers++; - $("#chat").text("Chat (" + nusers + " connected)"); - }, - /** + } + + var v,nusers=1; + for(v in me.Collab) + nusers++; + $("#chat").text("Chat ("+nusers+" connected)"); + }, + /** * @function sendChatMessage */ - sendChatMessage: function sendChatMessage() { - var me = AtlasMakerWidget; - var l = me.traceLog(sendChatMessage, 0, "#aca"); if (l) console.log.apply(undefined, l); - - if (me.flagConnected == 0) - return; - var msg = DOMPurify.sanitize($('input#msg')[0].value); - try { - me.socket.send(JSON.stringify({ "type": "chat", "msg": msg, "username": me.User.username })); - var msg = "me: " + msg + "
"; - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - $('input#msg').val(""); - } catch (ex) { - console.log("ERROR: Unable to sendChatMessage", ex); - } - }, - /** + sendChatMessage: function sendChatMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendChatMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + var msg = DOMPurify.sanitize($('input#msg')[0].value); + try { + me.socket.send(JSON.stringify({"type":"chat","msg":msg,"username":me.User.username})); + var msg="me: "+msg+"
"; + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + $('input#msg').val(""); + } catch (ex) { + console.log("ERROR: Unable to sendChatMessage",ex); + } + }, + /** * @function receiveChatMessage */ - receiveChatMessage: function receiveChatMessage(data) { - var me = AtlasMakerWidget; - var l = me.traceLog(receiveChatMessage, 0, "#aca"); if (l) console.log.apply(undefined, l); - console.log(data); - - var theSource = me.Collab[data.uid].source; - var theView = me.Collab[data.uid].view; - var theSlice = me.Collab[data.uid].slice; - var link = "/mri?url=" + theSource + "&view=" + theView + "&slice=" + theSlice; - var theUsername = data.username; - var msg = ""+theUsername+": "+data.msg+"
" - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - }, - /** + receiveChatMessage: function receiveChatMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveChatMessage,0,"#aca");if(l)console.log.apply(undefined,l); + console.log(data); + + var theSource=me.Collab[data.uid].source; + var theView=me.Collab[data.uid].view; + var theSlice=me.Collab[data.uid].slice; + var link = "/mri?url="+theSource+"&view="+theView+"&slice="+theSlice; + var theUsername=data.username; + var msg=""+theUsername+": "+data.msg+"
" + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + }, + /** * @function sendPaintMessage * @desc On user painting, this function broadcasts the painting event to all other connected users * @param {Object} msg Painting event object: {"c":c,"x":x,"y":y}, where "c" is the command (l,e,lf,ef) and x and y are the coordinates in slice space */ - sendPaintMessage: function sendPaintMessage(msg) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendPaintMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"paint",data:msg})); - } catch (ex) { - console.log("ERROR: Unable to sendPaintMessage",ex); - } - }, - /** + sendPaintMessage: function sendPaintMessage(msg) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendPaintMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"paint",data:msg})); + } catch (ex) { + console.log("ERROR: Unable to sendPaintMessage",ex); + } + }, + /** * @function receivePaintMessage * @desc Receive paint events from other connected users */ - receivePaintMessage: function receivePaintMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receivePaintMessage,3,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.data; - var u=data.uid; // user - var c=msg.c; // command - var x=parseInt(msg.x); // x coordinate - var y=parseInt(msg.y); // y coordinate - - if(me.Collab[u]) - me.paintxy(u,c,x,y,me.Collab[u]); - }, - /** + receivePaintMessage: function receivePaintMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receivePaintMessage,3,"#aca");if(l)console.log.apply(undefined,l); + + var msg=data.data; + var u=data.uid; // user + var c=msg.c; // command + var x=parseInt(msg.x); // x coordinate + var y=parseInt(msg.y); // y coordinate + + if(me.Collab[u]) + me.paintxy(u,c,x,y,me.Collab[u]); + }, + /** * @function sendShowMessage * @desc On user showing, this function broadcasts the showing event to all other connected users * @param {Object} msg Showing event object: {"x":x,"y":y}, where x and y are the coordinates in slice space */ - sendShowMessage: function sendShowMessage(msg) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendShowMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"show",data:msg})); - } catch (ex) { - console.log("ERROR: Unable to sendShowMessage",ex); - } - }, - /** + sendShowMessage: function sendShowMessage(msg) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendShowMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"show",data:msg})); + } catch (ex) { + console.log("ERROR: Unable to sendShowMessage",ex); + } + }, + /** * @function receiveShowMessage * @desc Receive show events from other connected users */ - receiveShowMessage: function receiveShowMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveShowMessage,3,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.data; - var u=data.uid; // user - var c=msg.c; // command - var x=parseInt(msg.x); // x coordinate - var y=parseInt(msg.y); // y coordinate - - if(me.Collab[u]) - me.showxy(u,c,x,y,me.Collab[u]); - }, - /** + receiveShowMessage: function receiveShowMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveShowMessage,3,"#aca");if(l)console.log.apply(undefined,l); + + var msg=data.data; + var u=data.uid; // user + var c=msg.c; // command + var x=parseInt(msg.x); // x coordinate + var y=parseInt(msg.y); // y coordinate + + if(me.Collab[u]) + me.showxy(u,c,x,y,me.Collab[u]); + }, + /** * @function receivePaintVolumeMessage */ - receivePaintVolumeMessage: function receivePaintVolumeMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receivePaintVolumeMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var i,ind,val,voxels; - - voxels=data.data; - me.paintvol(voxels.data); - - /* - TEST - */ - me.sendRequestSliceMessage(); - }, - /** + receivePaintVolumeMessage: function receivePaintVolumeMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receivePaintVolumeMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + var i,ind,val,voxels; + + voxels=data.data; + me.paintvol(voxels.data); + + /* + TEST + */ + me.sendRequestSliceMessage(); + }, + /** * @function sendUndoMessage */ - sendUndoMessage: function sendUndoMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendUndoMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"paint",data:{c:"u"}})); - } catch (ex) { - console.log("ERROR: Unable to sendUndoMessage",ex); - } - }, - /** + sendUndoMessage: function sendUndoMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendUndoMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"paint",data:{c:"u"}})); + } catch (ex) { + console.log("ERROR: Unable to sendUndoMessage",ex); + } + }, + /** * @function sendSaveMessage */ - sendSaveMessage: function sendSaveMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendSaveMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"save"})); - } catch (ex) { - console.log("ERROR: Unable to sendSaveMessage",ex); - } - }, - /** + sendSaveMessage: function sendSaveMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendSaveMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"save"})); + } catch (ex) { + console.log("ERROR: Unable to sendSaveMessage",ex); + } + }, + /** * @function sendRequestMRIMessage */ - sendRequestMRIMessage: function sendRequestMRIMessage(source) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendRequestMRIMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - - try { - me.socket.send(JSON.stringify({ - type:"requestMRI", - source:"sendRequestMRIMessage" - })); - } catch (ex) { - console.log("ERROR: Unable to sendRequestMRIMessage",ex); - } - }, - /** + sendRequestMRIMessage: function sendRequestMRIMessage(source) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendRequestMRIMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + + try { + me.socket.send(JSON.stringify({ + type:"requestMRI", + source:"sendRequestMRIMessage" + })); + } catch (ex) { + console.log("ERROR: Unable to sendRequestMRIMessage",ex); + } + }, + /** * @function sendRequestSliceMessage */ - sendRequestSliceMessage: function sendRequestSliceMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendRequestSliceMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - if(me.flagLoadingImg.loading==true) - return; - try { - me.socket.send(JSON.stringify({ - - type:"requestSlice", - /* - TEST - */ - //type:"requestSlice2", - - view:me.User.view, - slice:me.User.slice - })); - me.flagLoadingImg.loading=true; - me.flagLoadingImg.view=me.User.view; - me.flagLoadingImg.slice=me.User.slice; - - } catch (ex) { - console.log("ERROR: Unable to sendRequestSliceMessage",ex); - } - }, + sendRequestSliceMessage: function sendRequestSliceMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendRequestSliceMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + if(me.flagLoadingImg.loading==true) + return; + try { + me.socket.send(JSON.stringify({ + + type:"requestSlice", + /* + TEST + */ + //type:"requestSlice2", + + view:me.User.view, + slice:me.User.slice + })); + me.flagLoadingImg.loading=true; + me.flagLoadingImg.view=me.User.view; + me.flagLoadingImg.slice=me.User.slice; + + } catch (ex) { + console.log("ERROR: Unable to sendRequestSliceMessage",ex); + } + }, /** * @todo This is really not the place for some of this code. The receiveMetadata * function is ok, but the direct references to projectInfo -- a structure @@ -489,136 +491,136 @@ var AtlasMakerWS = { * mechanism for uncoupling the 2 pieces of code is not clear. It could be * a subscription, for example. */ - receiveMetadata: function receiveMetadata(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveMetadata,1,"#aca");if(l)console.log.apply(undefined,l); + receiveMetadata: function receiveMetadata(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveMetadata,1,"#aca");if(l)console.log.apply(undefined,l); var projShortname = projectInfo.shortname; - for (var i in projectInfo.files.list) { - if (projectInfo.files.list[i].source == data.metadata.source) { - for (var key in projectInfo.files.list[i].mri.annotations[projShortname]) { - info_proxy["files.list." + i + ".mri.annotations." + projShortname + "." + key] = data.metadata.mri.annotations[projShortname][key]; - } - info_proxy["files.list." + i + ".name"] = data.metadata.name; - break; - } - } - }, - /** + for (var i in projectInfo.files.list) { + if (projectInfo.files.list[i].source == data.metadata.source) { + for (var key in projectInfo.files.list[i].mri.annotations[projShortname]) { + info_proxy["files.list." + i + ".mri.annotations." + projShortname + "." + key] = data.metadata.mri.annotations[projShortname][key]; + } + info_proxy["files.list." + i + ".name"] = data.metadata.name; + break; + } + } + }, + /** * @function sendSaveMetadataMessage */ - sendSaveMetadataMessage: function sendSaveMetadataMessage(info, method, patch) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendSaveMetadataMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - return new Promise(function(resolve, reject) { - if(me.flagConnected==0) { - console.log("WARNING: Not connected: will not save metadata"); - return reject(); + sendSaveMetadataMessage: function sendSaveMetadataMessage(info, method, patch) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendSaveMetadataMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + var def = $.Deferred(); + if(me.flagConnected==0) { + console.log("WARNING: Not connected: will not save metadata"); + return def.reject().promise(); + } + + try { + var rnd = Math.random().toString(36).slice(20); + var met = method || "append"; + if(method == "patch") { + me.socket.send(JSON.stringify({ + type:"saveMetadata", + metadata: info, + method: met, + patch: patch, + rnd: rnd + })); + } else { + me.socket.send(JSON.stringify({ + type:"saveMetadata", + metadata: info, + method: met, + rnd: rnd + })); } - - try { - var rnd = Math.random().toString(36).slice(20); - var met = method || "append"; - if(method == "patch") { - me.socket.send(JSON.stringify({ - type:"saveMetadata", - metadata: info, - method: met, - patch: patch, - rnd: rnd - })); - } else { - me.socket.send(JSON.stringify({ - type:"saveMetadata", - metadata: info, - method: met, - rnd: rnd - })); - } - if(me.debug>1) { - console.log(rnd); - console.log(info); - } - resolve(); - - } catch (ex) { - console.log("ERROR: Unable to sendSaveMetadataMessage",ex); - reject(); + if(me.debug>1) { + console.log(rnd); + console.log(info); } - }); - }, - /** + def.resolve(); + + } catch (ex) { + console.log("ERROR: Unable to sendSaveMetadataMessage",ex); + def.reject(); + } + return def.promise(); + }, + /** * @function receiveDisconnectMessage */ - receiveDisconnectMessage: function receiveDisconnectMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveDisconnectMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var u=data.uid; // user - if(me.Collab[u]) { - var msg; - if(me.Collab[u].username === undefined || me.Collab[u].username === "Anonymous") - msg = ""+me.Collab[u].uid+" left
"; - else + receiveDisconnectMessage: function receiveDisconnectMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveDisconnectMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + var u=data.uid; // user + if(me.Collab[u]) { + var msg; + if(me.Collab[u].username === undefined || me.Collab[u].username === "Anonymous") + msg = ""+me.Collab[u].uid+" left
"; + else msg = ""+me.Collab[u].username+" left
"; - } - else - var msg=""+u+" left
"; - delete me.Collab[u]; - var v,nusers=1; for(v in me.Collab) nusers++; - $("#chat").text("Chat ("+nusers+" connected)"); - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - }, - /** + } + else + var msg=""+u+" left
"; + delete me.Collab[u]; + var v,nusers=1; for(v in me.Collab) nusers++; + $("#chat").text("Chat ("+nusers+" connected)"); + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + }, + /** * @function receiveServerMessage */ - receiveServerMessage: function receiveServerMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveServerMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.msg; - var prevMsg=$("#chat").text(); - $("#chat").text(msg); - setTimeout(function(){$("#chat").text(prevMsg)},5000); - }, - /** - * @function replayWSTraffic - * @desc Replays websocket traffic recorded at the served. Used for debugging - * @param Array recorded An array of websocket messages recorded in the server - */ - replayWSTraffic: function replayWSTraffic(recorded) { - var me=AtlasMakerWidget; - var l=me.traceLog(replayWSTraffic,0,"#aca");if(l)console.log.apply(undefined,l); - var i; - for(i=0;il)) {
var str,arg=[];
// str="am> "+(f.name)+" "+(f.caller?(f.caller.name||"annonymous"):"root");
@@ -103,141 +103,142 @@ var AtlasMakerWidget = {
return arg;
}
*/
- },
+ },
/**
* @function quit
*/
- quit: function quit() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(quit,0,"#bbd");if(l)console.log.apply(undefined,l);
-
- me.log("","Goodbye!");
- me.socket.close();
- me.socket = null;
- },
-
- //====================================================================================
- // Configuration
- //====================================================================================
+ quit: function quit() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(quit,0,"#bbd");if(l)console.log.apply(undefined,l);
+
+ me.log("","Goodbye!");
+ me.socket.close();
+ me.socket = null;
+ },
+
+ //====================================================================================
+ // Configuration
+ //====================================================================================
/**
* @function initAtlasMaker
*/
- initAtlasMaker: function initAtlasMaker(elem) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(initAtlasMaker,0,"#bbd");if(l)console.log.apply(undefined,l);
-
- // check if user is loged in
- $.get("/loggedIn",function(res) {
- console.log(res);
- if(res.loggedIn)
- me.User.username=res.username
- else
- me.User.username='Anonymous';
- });
-
- // Create offscreen canvas for mri and atlas
- me.brain_offcn=document.createElement('canvas');
- me.brain_offtx=me.brain_offcn.getContext('2d');
- me.atlas_offcn=document.createElement('canvas');
- me.atlas_offtx=me.atlas_offcn.getContext('2d');
-
- // Set widget div (create one if none)
- if(elem==undefined) {
- me.container=$("');
- me.canvas = me.container.find('canvas')[0];
- me.context = me.canvas.getContext('2d');
-
- // Add div to display slice number
- me.container.find("#resizable").append("");
-
- // Add div to display slice number
- me.container.find("#resizable").append("");
-
- // Add cursor (a small div)
- me.container.find("#resizable").append("");
-
- $('body').attr('data-toolbarDisplay','right');
-
- // Add precise cursor
- var isTouchArr=[];//["iPad","iPod"];
- var curDevice=navigator.userAgent.split(/[(;]/)[1];
- if($.inArray(curDevice,isTouchArr)>=0) {
- me.flagUsePreciseCursor=true;
- me.initCursor();
- }
-
- // Configure mouse events for desktop computers
- me.canvas.onmousedown = me.mousedown;
- me.canvas.onmousemove = me.mousemove;
- me.canvas.onmouseup = me.mouseup;
-
- // Connect event to respond to window resizing
- $(window).resize(function() {
- me.resizeWindow();
- });
-
- // get pointer to progress div
- me.progress=$("a.download_MRI");
-
- // Init the toolbar: load template, wire actions
- return new Promise(function(resolve, reject) {
- $.get("/templates/tools.html",function from_initAtlasMaker(html) {
- me.container.append(html);
-
- // intercept keyboard events
- $(document).keydown(function(e){me.keyDown(e)});
-
- // configure annotation tools
- $("#tools-minimized").click(function(){me.changeToolbarDisplay("maximize")});
- me.push($(".push#display-minimize"),function(){me.changeToolbarDisplay("minimize")});
- me.push($(".push#display-left"),function(){me.changeToolbarDisplay("left")});
- me.push($(".push#display-right"),function(){me.changeToolbarDisplay("right")});
- me.slider($(".slider#slice"),function(x){me.changeSlice(Math.round(x))});
- me.chose($(".chose#plane"),me.changeView);
- me.chose($(".chose#paintTool"),me.changeTool);
- me.chose($(".chose#penSize"),me.changePenSize);
- me.toggle($(".toggle#precise"),me.togglePreciseCursor);
- me.toggle($(".toggle#fill"),me.toggleFill);
- me.toggle($(".toggle#fullscreen"),me.toggleFullscreen);
- me.toggle($(".toggle#bubble"),me.toggleChat);
- me.push($(".push#3drender"),me.render3D);
- me.push($(".push#link"),me.link);
- me.push($(".push#upload"),me.upload);
- me.push($(".push#download"),me.download);
- me.push($(".push#color"),me.color);
- me.push($(".push#undo"),me.sendUndoMessage);
- me.push($(".push#save"),me.sendSaveMessage);
- me.push($(".push#prev"),me.prevSlice);
- me.push($(".push#next"),me.nextSlice);
-
- // connect chat message input
- $("#msg").keypress(function keypress_fromInitAtlasMaker(e) {me.onkey(e)});
-
- $("#tools-minimized").hide();
- })
- .then(function from_initAtlasMaker() {
- // Init web socket connection
- return me.initSocketConnection();
- }).then(function() {
- resolve()
- });
- });
- },
+ initAtlasMaker: function initAtlasMaker(elem) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(initAtlasMaker,0,"#bbd");if(l)console.log.apply(undefined,l);
+
+ // check if user is loged in
+ $.get("/loggedIn",function(res) {
+ console.log(res);
+ if(res.loggedIn)
+ me.User.username=res.username
+ else
+ me.User.username='Anonymous';
+ });
+
+ // Create offscreen canvas for mri and atlas
+ me.brain_offcn=document.createElement('canvas');
+ me.brain_offtx=me.brain_offcn.getContext('2d');
+ me.atlas_offcn=document.createElement('canvas');
+ me.atlas_offtx=me.atlas_offcn.getContext('2d');
+
+ // Set widget div (create one if none)
+ if(elem==undefined) {
+ me.container=$("');
+ me.canvas = me.container.find('canvas')[0];
+ me.context = me.canvas.getContext('2d');
+
+ // Add div to display slice number
+ me.container.find("#resizable").append("");
+
+ // Add div to display slice number
+ me.container.find("#resizable").append("");
+
+ // Add cursor (a small div)
+ me.container.find("#resizable").append("");
+
+ $('body').attr('data-toolbarDisplay','right');
+
+ // Add precise cursor
+ var isTouchArr=[];//["iPad","iPod"];
+ var curDevice=navigator.userAgent.split(/[(;]/)[1];
+ if($.inArray(curDevice,isTouchArr)>=0) {
+ me.flagUsePreciseCursor=true;
+ me.initCursor();
+ }
+
+ // Configure mouse events for desktop computers
+ me.canvas.onmousedown = me.mousedown;
+ me.canvas.onmousemove = me.mousemove;
+ me.canvas.onmouseup = me.mouseup;
+
+ // Connect event to respond to window resizing
+ $(window).resize(function() {
+ me.resizeWindow();
+ });
+
+ // get pointer to progress div
+ me.progress=$("a.download_MRI");
+
+ // Init the toolbar: load template, wire actions
+ var def=$.Deferred();
+ $.get("/templates/tools.html",function from_initAtlasMaker(html) {
+ me.container.append(html);
+
+ // intercept keyboard events
+ $(document).keydown(function(e){me.keyDown(e)});
+
+ // configure annotation tools
+ $("#tools-minimized").click(function(){me.changeToolbarDisplay("maximize")});
+ me.push($(".push#display-minimize"),function(){me.changeToolbarDisplay("minimize")});
+ me.push($(".push#display-left"),function(){me.changeToolbarDisplay("left")});
+ me.push($(".push#display-right"),function(){me.changeToolbarDisplay("right")});
+ me.slider($(".slider#slice"),function(x){me.changeSlice(Math.round(x))});
+ me.chose($(".chose#plane"),me.changeView);
+ me.chose($(".chose#paintTool"),me.changeTool);
+ me.chose($(".chose#penSize"),me.changePenSize);
+ me.toggle($(".toggle#precise"),me.togglePreciseCursor);
+ me.toggle($(".toggle#fill"),me.toggleFill);
+ me.toggle($(".toggle#fullscreen"),me.toggleFullscreen);
+ me.toggle($(".toggle#bubble"),me.toggleChat);
+ me.push($(".push#3drender"),me.render3D);
+ me.push($(".push#link"),me.link);
+ me.push($(".push#upload"),me.upload);
+ me.push($(".push#download"),me.download);
+ me.push($(".push#color"),me.color);
+ me.push($(".push#undo"),me.sendUndoMessage);
+ me.push($(".push#save"),me.sendSaveMessage);
+ me.push($(".push#prev"),me.prevSlice);
+ me.push($(".push#next"),me.nextSlice);
+
+ // connect chat message input
+ $("#msg").keypress(function keypress_fromInitAtlasMaker(e) {me.onkey(e)});
+
+ $("#tools-minimized").hide();
+ })
+ .then(function from_initAtlasMaker() {
+ // Init web socket connection
+ return me.initSocketConnection();
+ }).then(function() {
+ def.resolve()
+ });
+
+ return def.promise();
+ },
/**
* @function configureAtlasMaker
*/
- configureAtlasMaker: function configureAtlasMaker(info,index) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(configureAtlasMaker,0,"#bbd");if(l)console.log.apply(undefined,l);
+ configureAtlasMaker: function configureAtlasMaker(info,index) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(configureAtlasMaker,0,"#bbd");if(l)console.log.apply(undefined,l);
var def=$.Deferred();
@@ -273,146 +274,151 @@ var AtlasMakerWidget = {
});
return def.promise();
- },
+ },
/**
* @function configureOntology
*/
- configureOntology: function configureOntology(json) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(configureOntology,0,"#bbd");if(l)console.log.apply(undefined,l);
-
- me.ontology=json
- me.ontology.valueToIndex=[];
- me.ontology.labels.forEach(function(o,i){me.ontology.valueToIndex[o.value]=i});
- // to clear the region name being displayed on the info text-layer when having used eyedrop
- delete me.info.region;
- },
+ configureOntology: function configureOntology(json) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(configureOntology,0,"#bbd");if(l)console.log.apply(undefined,l);
+
+ me.ontology=json
+ me.ontology.valueToIndex=[];
+ me.ontology.labels.forEach(function(o,i){me.ontology.valueToIndex[o.value]=i});
+ // to clear the region name being displayed on the info text-layer when having used eyedrop
+ delete me.info.region;
+ },
/**
* @function requestMRIInfo
* @desc Request to download an MRI, with polling to prevent hangouts on lengthy
* downloads
*/
- requestMRIInfo: function requestMRIInfo(source, def) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(requestMRIInfo,0,"#bbd");if(l)console.log.apply(undefined,l);
+ requestMRIInfo: function requestMRIInfo(source, def) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(requestMRIInfo,0,"#bbd");if(l)console.log.apply(undefined,l);
+
+ if(!def) {
+ var def=$.Deferred();
+ }
$.post("/mri/json",{url:source}, function(info) {
if(info.success == true) {
- return Promise.resolve(info);
+ def.resolve(info);
} else if(info.success == 'downloading') {
if(me.User.source != source)
return;
+ setTimeout(function(){me.requestMRIInfo(source,def)},2000);
$("#loadingIndicator p").text("Loading... "+parseInt(info.cur/info.len*100,10)+"%");
- return new Promise(function(resolve, reject) {
- setTimeout(function(){
- resolve(me.requestMRIInfo(source))
- }, 2000);
- })
} else {
console.log("ERROR: requestMRIInfo",info);
- return Promise.reject();
+ def.reject();
}
});
- },
+
+ return def.promise();
+ },
/**
* @function configureMRI
*/
- configureMRI: function configureMRI(info,index) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(configureMRI,0,"#bbd");if(l)console.log.apply(undefined,l);
-
- return new Promise(function(resolve, reject) {
- me.User.source=info.source;
- me.requestMRIInfo(info.source)
- .then( function(info2) {
-
- if(!info.dim) {
- // the mri object used to call this function does not have a 'dim'
- // property, indicating that it had not been downloaded at the time of the
- // call. Here we merge the fields from info2 that are initialised upon
- // download of the mri server-side. The mri field in the original 'info',
- // which contains the newly created text 'annotations', is conserved
- $.extend(true, info, info2);
- }
- info2=info;
-
- // Get data from AtlasMaker object
- me.name=info2.name||"Untitled";
- me.url=info2.url;
- me.atlasFilename=info2.mri.atlas[index].filename;
- me.atlasName=info2.mri.atlas[index].name;
-
- // get local file path from url
- me.User.dirname=me.url; // TEMPORARY
- me.User.mri=info2.mri.brain;
- me.User.specimenName=me.name;
- me.User.atlasFilename=info2.mri.atlas[index].filename;
- me.User.isMRILoaded=false;
-
- // TODO: it's silly to have to put vol dim twice...
- // (first here, once again further down)
- me.User.dim=info2.dim;
- me.User.pixdim=info2.pixdim;
-
- // compute space transformations
- me.User.v2w=info2.voxel2world;
- me.User.wori=info2.worldOrigin;
- me.computeS2VTransformation();
-
- //me.testS2VTransformation();
-
- me.flagLoadingImg={loading:false};
-
- me.brain_img.img=null;
-
- // get volume dimensions
- me.brain_dim=info2.dim;
- if(info2.pixdim)
- me.brain_pixdim=info2.pixdim;
- else
- me.brain_pixdim=[1,1,1];
-
- resolve(info2);
- })
- .catch(function(err) {
- console.log("ERROR: DOWNLOAD FAILED", err);
- reject(err);
- });
+ configureMRI: function configureMRI(info,index) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(configureMRI,0,"#bbd");if(l)console.log.apply(undefined,l);
+
+ var def=$.Deferred();
+
+ me.User.source=info.source;
+ me.requestMRIInfo(info.source)
+ .then(function(info2) {
+
+ if(!info.dim) {
+ // the mri object used to call this function does not have a 'dim'
+ // property, indicating that it had not been downloaded at the time of the
+ // call. Here we merge the fields from info2 that are initialised upon
+ // download of the mri server-side. The mri field in the original 'info',
+ // which contains the newly created text 'annotations', is conserved
+ $.extend(true, info, info2);
+ }
+ info2=info;
+
+ // Get data from AtlasMaker object
+ me.name=info2.name||"Untitled";
+ me.url=info2.url;
+ me.atlasFilename=info2.mri.atlas[index].filename;
+ me.atlasName=info2.mri.atlas[index].name;
+
+ // get local file path from url
+ me.User.dirname=me.url; // TEMPORARY
+ me.User.mri=info2.mri.brain;
+ me.User.specimenName=me.name;
+ me.User.atlasFilename=info2.mri.atlas[index].filename;
+ me.User.isMRILoaded=false;
+
+ // TODO: it's silly to have to put vol dim twice...
+ // (first here, once again further down)
+ me.User.dim=info2.dim;
+ me.User.pixdim=info2.pixdim;
+
+ // compute space transformations
+ me.User.v2w=info2.voxel2world;
+ me.User.wori=info2.worldOrigin;
+ me.computeS2VTransformation();
+
+ //me.testS2VTransformation();
+
+ me.flagLoadingImg={loading:false};
+
+ me.brain_img.img=null;
+
+ // get volume dimensions
+ me.brain_dim=info2.dim;
+ if(info2.pixdim)
+ me.brain_pixdim=info2.pixdim;
+ else
+ me.brain_pixdim=[1,1,1];
+
+ def.resolve(info2);
+ })
+ .catch(function(err) {
+ console.log("ERROR: DOWNLOAD FAILED", err);
+ def.reject(err);
});
- }
+
+
+ return def.promise();
+ }
};
/*
- 0 int sizeof_hdr; //!< MUST be 348 // // int sizeof_hdr; //
- 4 char data_type[10]; //!< ++UNUSED++ // // char data_type[10]; //
- 14 char db_name[18]; //!< ++UNUSED++ // // char db_name[18]; //
- 32 int extents; //!< ++UNUSED++ // // int extents; //
- 36 short session_error; //!< ++UNUSED++ // // short session_error; //
- 38 char regular; //!< ++UNUSED++ // // char regular; //
- 39 char dim_info; //!< MRI slice ordering. // // char hkey_un0; //
-
- //--- was image_dimension substruct ---//
- 40 short dim[8]; //!< Data array dimensions.// // short dim[8]; //
- 56 float intent_p1 ; //!< 1st intent parameter. // // short unused8; //
- // short unused9; //
- 60 float intent_p2 ; //!< 2nd intent parameter. // // short unused10; //
- // short unused11; //
- 64 float intent_p3 ; //!< 3rd intent parameter. // // short unused12; //
- // short unused13; //
- 68 short intent_code ; //!< NIFTI_INTENT_* code. // // short unused14; //
- 70 short datatype; //!< Defines data type! // // short datatype; //
- 72 short bitpix; //!< Number bits/voxel. // // short bitpix; //
- 74 short slice_start; //!< First slice index. // // short dim_un0; //
- 76 float pixdim[8]; //!< Grid spacings. // // float pixdim[8]; //
- 108 float vox_offset; //!< Offset into .nii file // // float vox_offset; //
- 112 float scl_slope ; //!< Data scaling: slope. // // float funused1; //
- 116 float scl_inter ; //!< Data scaling: offset. // // float funused2; //
- 120 short slice_end; //!< Last slice index. // // float funused3; //
- 122 char slice_code ; //!< Slice timing order. //
- 123 char xyzt_units ; //!< Units of pixdim[1..4] //
- 124 float cal_max; //!< Max display intensity // // float cal_max; //
- 128 float cal_min; //!< Min display intensity // // float cal_min; //
- 132 float slice_duration;//!< Time for 1 slice. // // float compressed; //
- 136 float toffset; //!< Time axis shift. // // float verified; //
- 140 int glmax; //!< ++UNUSED++ // // int glmax; //
- 144 int glmin; //!< ++UNUSED++ // // int glmin; //
+ 0 int sizeof_hdr; //!< MUST be 348 // // int sizeof_hdr; //
+ 4 char data_type[10]; //!< ++UNUSED++ // // char data_type[10]; //
+ 14 char db_name[18]; //!< ++UNUSED++ // // char db_name[18]; //
+ 32 int extents; //!< ++UNUSED++ // // int extents; //
+ 36 short session_error; //!< ++UNUSED++ // // short session_error; //
+ 38 char regular; //!< ++UNUSED++ // // char regular; //
+ 39 char dim_info; //!< MRI slice ordering. // // char hkey_un0; //
+
+ //--- was image_dimension substruct ---//
+ 40 short dim[8]; //!< Data array dimensions.// // short dim[8]; //
+ 56 float intent_p1 ; //!< 1st intent parameter. // // short unused8; //
+ // short unused9; //
+ 60 float intent_p2 ; //!< 2nd intent parameter. // // short unused10; //
+ // short unused11; //
+ 64 float intent_p3 ; //!< 3rd intent parameter. // // short unused12; //
+ // short unused13; //
+ 68 short intent_code ; //!< NIFTI_INTENT_* code. // // short unused14; //
+ 70 short datatype; //!< Defines data type! // // short datatype; //
+ 72 short bitpix; //!< Number bits/voxel. // // short bitpix; //
+ 74 short slice_start; //!< First slice index. // // short dim_un0; //
+ 76 float pixdim[8]; //!< Grid spacings. // // float pixdim[8]; //
+ 108 float vox_offset; //!< Offset into .nii file // // float vox_offset; //
+ 112 float scl_slope ; //!< Data scaling: slope. // // float funused1; //
+ 116 float scl_inter ; //!< Data scaling: offset. // // float funused2; //
+ 120 short slice_end; //!< Last slice index. // // float funused3; //
+ 122 char slice_code ; //!< Slice timing order. //
+ 123 char xyzt_units ; //!< Units of pixdim[1..4] //
+ 124 float cal_max; //!< Max display intensity // // float cal_max; //
+ 128 float cal_min; //!< Min display intensity // // float cal_min; //
+ 132 float slice_duration;//!< Time for 1 slice. // // float compressed; //
+ 136 float toffset; //!< Time axis shift. // // float verified; //
+ 140 int glmax; //!< ++UNUSED++ // // int glmax; //
+ 144 int glmin; //!< ++UNUSED++ // // int glmin; //
*/
diff --git a/public/js/brainbox-intro.js b/public/js/brainbox-intro.js
index 68f41a8c..1bdcd674 100644
--- a/public/js/brainbox-intro.js
+++ b/public/js/brainbox-intro.js
@@ -1,31 +1,31 @@
-function startIntro() {
- const intro = introJs();
+function startIntro(){
+ var intro = introJs();
intro.setOptions({
steps: [
{
- intro: 'Welcome to BrainBox.' +
- 'BrainBox allows you to visualise and segment collaboratively ' +
- 'any brain MRI dataset available online. Follow this tutorial ' +
- 'to learn how to enter data into BrainBox, view it, edit it, ' +
- 'and create collaborative segmentation projects. BrainBox is an ' +
- 'open project – you will learn how to help us improving it by ' +
- 'reporting bugs and suggestions to our GitHub repository'
+ intro: "Welcome to BrainBox."
+ + "BrainBox allows you to visualise and segment collaboratively "
+ + "any brain MRI dataset available online. Follow this tutorial "
+ + "to learn how to enter data into BrainBox, view it, edit it, "
+ + "and create collaborative segmentation projects. BrainBox is an "
+ + "open project – you will learn how to help us improving it by "
+ + "reporting bugs and suggestions to our GitHub repository"
},
{
- element: '#url',
- intro: 'This is BrainBox\'s URL field. You can paste here a link ' +
- 'to any MRI on the web. Currently, BrainBox supports Nifti ' +
- 'format (.nii.gz files) and MGH format (.mgz files). Any link ' +
- 'on the Web should work, from Zenodo, FigShare, DropBox, Amazon, ' +
- 'etc. If you want to try BrainBox but you don\'t have any link to ' +
- 'an MRI, you can select a brain from the "Take me to a brain" ' +
- 'list, or browse among the community created projects.',
+ element: "#url",
+ intro: "This is BrainBox's URL field. You can paste here a link "
+ + "to any MRI on the web. Currently, BrainBox supports Nifti "
+ + "format (.nii.gz files) and MGH format (.mgz files). Any link "
+ + "on the Web should work, from Zenodo, FigShare, DropBox, Amazon, "
+ + "etc. If you want to try BrainBox but you don't have any link to "
+ + "an MRI, you can select a brain from the \"Take me to a brain\" "
+ + "list, or browse among the community created projects.",
position: 'top'
},
{
element: '#go',
- intro: 'Once you have entered the link to an MRI in the URL field ' +
- 'click the Go button to go to BrainBox\'s viewer'
+ intro: "Once you have entered the link to an MRI in the URL field "
+ + "click the Go button to go to BrainBox's viewer"
}
]
});
diff --git a/public/js/brainbox.js b/public/js/brainbox.js
index 62e1b3c0..9acb02ff 100644
--- a/public/js/brainbox.js
+++ b/public/js/brainbox.js
@@ -9,50 +9,50 @@
*/
var BrainBox={
- version: 1,
- debug: 1,
- info:{},
- labelSets:null,
- annotationType:["volume","text"],
- accessLevels: ["none","view","edit","add","remove"],
+ version: 1,
+ debug: 1,
+ info:{},
+ labelSets:null,
+ annotationType:["volume","text"],
+ accessLevels: ["none","view","edit","add","remove"],
/**
* @function traceLog
*/
- traceLog: function traceLog(f,l) {
- /*
- if(BrainBox.debug && (l==undefined || BrainBox.debug>l))
- // return "bb> "+(f.name)+" "+(f.caller?(f.caller.name||"annonymous"):"root");
- return "bb> ";//+(f.name);
- */
- },
+ traceLog: function traceLog(f,l) {
+ /*
+ if(BrainBox.debug && (l==undefined || BrainBox.debug>l))
+ // return "bb> "+(f.name)+" "+(f.caller?(f.caller.name||"annonymous"):"root");
+ return "bb> ";//+(f.name);
+ */
+ },
- /*
- JavaScript implementation of Java's hashCode method from
- http://werxltd.com/wp/2010/05/13/javascript-implementation-of-javas-string-hashcode-method/
- */
- /**
+ /*
+ JavaScript implementation of Java's hashCode method from
+ http://werxltd.com/wp/2010/05/13/javascript-implementation-of-javas-string-hashcode-method/
+ */
+ /**
* @function hash
*/
- hash: function hash(str) {
- var l=BrainBox.traceLog(hash);if(l)console.log(l);
-
- var v0=0,v1,abc="0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ";
- for(i=0;i
');
- $("#atlasMaker").addClass('edit-mode');
-
- BrainBox.loadScript('/lib/jquery-ui.min.js', function(){return window.jQuery.ui != undefined})
- .then(function(){return BrainBox.loadScript('/lib/pako/pako.min.js', function(){return window.pako != undefined})})
- .then(function(){return BrainBox.loadScript('/lib/purify.min.js', function(){return window.DOMPurify != undefined})})
- .then(function(){return BrainBox.loadScript('/lib/json-patch-duplex.min.js', function(){return window.jsonpatch != undefined})})
- .then(function(){return BrainBox.loadScript('/lib/npm-bundle.js')})
- .then(function(){return BrainBox.loadScript('/js/twoWayBinding.js')})
- .then(function(){
- $.when(
- BrainBox.loadScript('/js/atlasMaker-draw.js'),
- BrainBox.loadScript('/js/atlasMaker-interaction.js'),
- BrainBox.loadScript('/js/atlasMaker-io.js'),
- BrainBox.loadScript('/js/atlasMaker-paint.js'),
- BrainBox.loadScript('/js/atlasMaker-ui.js'),
- BrainBox.loadScript('/js/atlasMaker-ws.js'),
- BrainBox.loadScript('/js/atlasMaker.js')
- ).then(function () {
- $.extend(AtlasMakerWidget,AtlasMakerDraw);
- $.extend(AtlasMakerWidget,AtlasMakerInteraction);
- $.extend(AtlasMakerWidget,AtlasMakerIO);
- $.extend(AtlasMakerWidget,AtlasMakerPaint);
- $.extend(AtlasMakerWidget,AtlasMakerUI);
- $.extend(AtlasMakerWidget,AtlasMakerWS);
- AtlasMakerWidget.initAtlasMaker($("#atlasMaker"))
- .then(function() {
- resolve();
- });
- })
- });
+ initBrainBox: function initBrainBox() {
+ var l=BrainBox.traceLog(initBrainBox);if(l)console.log(l);
+
+ var def=$.Deferred();
- // store state on exit
- $(window).on('unload',BrainBox.unload);
+ // Add AtlasMaker and friends
+ $("#stereotaxic").html('');
+ $("#atlasMaker").addClass('edit-mode');
+
+ BrainBox.loadScript('/lib/jquery-ui.min.js', function(){return window.jQuery.ui != undefined})
+ .then(function(){return BrainBox.loadScript('/lib/pako/pako.min.js', function(){return window.pako != undefined})})
+ .then(function(){return BrainBox.loadScript('/lib/purify.min.js', function(){return window.DOMPurify != undefined})})
+ .then(function(){return BrainBox.loadScript('/lib/json-patch-duplex.min.js', function(){return window.jsonpatch != undefined})})
+ .then(function(){return BrainBox.loadScript('/lib/npm-bundle.js')})
+ .then(function(){return BrainBox.loadScript('/js/twoWayBinding.js')})
+ .then(function(){
+ $.when(
+ BrainBox.loadScript('/js/atlasMaker-draw.js'),
+ BrainBox.loadScript('/js/atlasMaker-interaction.js'),
+ BrainBox.loadScript('/js/atlasMaker-io.js'),
+ BrainBox.loadScript('/js/atlasMaker-paint.js'),
+ BrainBox.loadScript('/js/atlasMaker-ui.js'),
+ BrainBox.loadScript('/js/atlasMaker-ws.js'),
+ BrainBox.loadScript('/js/atlasMaker.js')
+ ).then(function () {
+ $.extend(AtlasMakerWidget,AtlasMakerDraw);
+ $.extend(AtlasMakerWidget,AtlasMakerInteraction);
+ $.extend(AtlasMakerWidget,AtlasMakerIO);
+ $.extend(AtlasMakerWidget,AtlasMakerPaint);
+ $.extend(AtlasMakerWidget,AtlasMakerUI);
+ $.extend(AtlasMakerWidget,AtlasMakerWS);
+ AtlasMakerWidget.initAtlasMaker($("#atlasMaker"))
+ .then(function() {
+ def.resolve();
+ });
+ })
});
- },
- /**
+
+ // store state on exit
+ $(window).on('unload',BrainBox.unload);
+
+ return def.promise();
+ },
+ /**
* @function configureBrainBox
*/
- configureBrainBox: function configureBrainBox(param) {
- var l=BrainBox.traceLog(configureBrainBox);if(l)console.log(l);
-
- var def=new Promise(function(resolve, reject) {
- var date=new Date();
- var index=param.annotationItemIndex||0;
-
- // Copy MRI from source
- $("#msgLog").html("");
+ black.css({position:'fixed',top:0,left:0,width:'100%',height:'100%','z-index':5,'background-color':'#222'});
+ $('body').append(black);
+
+ // configure display mode
+ // $("#atlasMaker").removeClass('display-mode');
+ $("body").addClass('atlasMaker-fullscreen');
+ $("#atlasMaker").detach().appendTo('body');
+
+ // me.editMode=1;
+ me.resizeWindow();
+
+ // configure toolbar for edit mode
+ //$("#log").outerHeight($("#tools-side").outerHeight()-$("#log").offset().top-$("#msg").closest("tr").outerHeight());
+ me.fullscreen=true;
+ } else {
- // Exit fullscreen
- //----------------
-
- // remove black overlay
- $("#blackOverlay").remove();
-
- // go back to display mode
- $("body").removeClass('atlasMaker-fullscreen');
- // $("#atlasMaker").addClass('display-mode');
- $("#atlasMaker").detach().appendTo('#stereotaxic');
- // me.editMode=0;
- me.resizeWindow();
+ // Exit fullscreen
+ //----------------
+
+ // remove black overlay
+ $("#blackOverlay").remove();
+
+ // go back to display mode
+ $("body").removeClass('atlasMaker-fullscreen');
+ // $("#atlasMaker").addClass('display-mode');
+ $("#atlasMaker").detach().appendTo('#stereotaxic');
+ // me.editMode=0;
+ me.resizeWindow();
- me.fullscreen=false;
- }
- },
+ me.fullscreen=false;
+ }
+ },
/**
* @function render3D
*/
- render3D: function render3D() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(render3D,0,"#f00");if(l)console.log.apply(undefined,l);
-
- // puts a fresh version of the segmentation in localStorage
- localStorage.brainbox=URL.createObjectURL(new Blob([me.encodeNifti()]));
-
- // opens 3d render window
- window.open("/templates/surface.html?path="+me.User.dirname+me.User.atlasFilename,"_blank");
- },
+ render3D: function render3D() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(render3D,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ // puts a fresh version of the segmentation in localStorage
+ localStorage.brainbox=URL.createObjectURL(new Blob([me.encodeNifti()]));
+
+ // opens 3d render window
+ window.open("/templates/surface.html?path="+me.User.dirname+me.User.atlasFilename,"_blank");
+ },
/**
* @function link
*/
- link: function link() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(link,0,"#f00");if(l)console.log.apply(undefined,l);
- window.prompt("Copy to clipboard:", location.href+"&view="+AtlasMakerWidget.User.view+"&slice="+AtlasMakerWidget.User.slice);
- },
+ link: function link() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(link,0,"#f00");if(l)console.log.apply(undefined,l);
+ window.prompt("Copy to clipboard:", location.href+"&view="+AtlasMakerWidget.User.view+"&slice="+AtlasMakerWidget.User.slice);
+ },
/**
* @function upload
*/
- upload: function upload() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(upload,0,"#f00");if(l)console.log.apply(undefined,l);
-
- var inp=$("");
- inp.hide();
- $("body").append(inp);
- var input=inp.get(0);
- input.type="file";
- input.onchange=function from_upload(e){
- var name=this.files[0];
- var reader = new FileReader();
- reader.onload = function from_upload(e) {
- var result=e.target.result;
- var nii;
- if(name.name.split('.').pop()=="gz") {
- var inflate=new pako.Inflate();
- inflate.push(new Uint8Array(result),true);
- nii=inflate.result.buffer;
- }
- else
- nii=result;
- var mri=me.loadNifti(nii);
+ upload: function upload() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(upload,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ var inp=$("");
+ inp.hide();
+ $("body").append(inp);
+ var input=inp.get(0);
+ input.type="file";
+ input.onchange=function from_upload(e){
+ var name=this.files[0];
+ var reader = new FileReader();
+ reader.onload = function from_upload(e) {
+ var result=e.target.result;
+ var nii;
+ if(name.name.split('.').pop()=="gz") {
+ var inflate=new pako.Inflate();
+ inflate.push(new Uint8Array(result),true);
+ nii=inflate.result.buffer;
+ }
+ else
+ nii=result;
+ var mri=me.loadNifti(nii);
- if( mri.dim[0]!=me.User.dim[0] ||
- mri.dim[1]!=me.User.dim[1] ||
- mri.dim[2]!=me.User.dim[2]) {
- console.log("ERROR: Volume dimensions do not match");
- return;
- }
-
- // copy uploaded data to atlas data
- var i;
- for(i=0;i
");
- $("#finger").addClass("touchDevice");
+ var W=parseFloat($('#atlasMaker canvas').css('width'));
+ var H=parseFloat($('#atlasMaker canvas').css('height'));
+ var w=parseFloat($('#atlasMaker canvas').attr('width'));
+ var h=parseFloat($('#atlasMaker canvas').attr('height'));
+
+ me.Crsr.x=parseInt(w/2);
+ me.Crsr.y=parseInt(h/2);
+
+ me.Crsr.fx=parseInt(w/2)*(W/w);
+ me.Crsr.fy=parseInt(h/2)*(H/h);
+ $("#cursor").css({left:(me.Crsr.x*(W/w))+"px",top:(me.Crsr.y*(H/h))+"px",width:me.User.penSize*(W/w),height:me.User.penSize*(H/h)});
+
+ if(me.flagUsePreciseCursor) {
+ if($("#finger").length==0) {
+ me.container.append("");
+ $("#finger").addClass("touchDevice");
- // configure touch events for tablets
- $("#finger").on("touchstart",function(e){me.touchstart(e)});
- $("#finger").on("touchend",function(e){me.touchend(e)});
- $("#finger").on("touchmove",function(e){me.touchmove(e)});
-
- // turn off eventual touch events handled by canvas
- me.canvas.ontouchstart=null;
- me.canvas.ontouchmove=null;
- me.canvas.ontouchend=null;
- }
- me.updateCursor();
+ // configure touch events for tablets
+ $("#finger").on("touchstart",function(e){me.touchstart(e)});
+ $("#finger").on("touchend",function(e){me.touchend(e)});
+ $("#finger").on("touchmove",function(e){me.touchmove(e)});
+
+ // turn off eventual touch events handled by canvas
+ me.canvas.ontouchstart=null;
+ me.canvas.ontouchmove=null;
+ me.canvas.ontouchend=null;
+ }
+ me.updateCursor();
- $("#finger").css({left:me.Crsr.fx+"px",top:me.Crsr.fy+"px"});
- } else {
- // remove precise cursor
- $("#finger").remove();
+ $("#finger").css({left:me.Crsr.fx+"px",top:me.Crsr.fy+"px"});
+ } else {
+ // remove precise cursor
+ $("#finger").remove();
- // configure touch events for tablets
- me.canvas.ontouchstart=me.touchstart;
- me.canvas.ontouchmove=me.touchmove;
- me.canvas.ontouchend=me.touchend;
- }
- },
+ // configure touch events for tablets
+ me.canvas.ontouchstart=me.touchstart;
+ me.canvas.ontouchmove=me.touchmove;
+ me.canvas.ontouchend=me.touchend;
+ }
+ },
/**
* @function updateCursor
*/
- updateCursor: function updateCursor() {
- var me=AtlasMakerWidget;
- var l=me.traceLog(updateCursor,1,"#f00");if(l)console.log.apply(undefined,l);
+ updateCursor: function updateCursor() {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(updateCursor,1,"#f00");if(l)console.log.apply(undefined,l);
- $("#finger").removeClass("move draw configure");
- switch(me.Crsr.state) {
- case "move": $("#finger").addClass("move"); break;
- case "draw": $("#finger").addClass("draw"); break;
- case "configure": $("#finger").addClass("configure"); break;
- }
- },
+ $("#finger").removeClass("move draw configure");
+ switch(me.Crsr.state) {
+ case "move": $("#finger").addClass("move"); break;
+ case "draw": $("#finger").addClass("draw"); break;
+ case "configure": $("#finger").addClass("configure"); break;
+ }
+ },
/**
* @function mousedown
*/
- mousedown: function mousedown(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(mousedown,0,"#f00");if(l)console.log.apply(undefined,l);
-
- e.preventDefault();
+ mousedown: function mousedown(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(mousedown,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ e.preventDefault();
- var W=parseFloat($('#atlasMaker canvas').css('width'));
- var H=parseFloat($('#atlasMaker canvas').css('height'));
- var w=parseFloat($('#atlasMaker canvas').attr('width'));
- var h=parseFloat($('#atlasMaker canvas').attr('height'));
- var o=$('#atlasMaker canvas').offset();
- var x=parseInt((e.pageX-o.left)*(w/W));
- // i have to add here the compensation for rectangular pixels: f(brain_Wdim, brain_Hdim)
- var y=parseInt((e.pageY-o.top)*(h/H));
- me.down(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
- },
+ var W=parseFloat($('#atlasMaker canvas').css('width'));
+ var H=parseFloat($('#atlasMaker canvas').css('height'));
+ var w=parseFloat($('#atlasMaker canvas').attr('width'));
+ var h=parseFloat($('#atlasMaker canvas').attr('height'));
+ var o=$('#atlasMaker canvas').offset();
+ var x=parseInt((e.pageX-o.left)*(w/W));
+ // i have to add here the compensation for rectangular pixels: f(brain_Wdim, brain_Hdim)
+ var y=parseInt((e.pageY-o.top)*(h/H));
+ me.down(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
+ },
/**
* @function mousemove
* @desc Handles a mouse move event. The x and y slice screens are computed from the pageX and pageY screen coordinates and dispatched to the generic move handler. The position and size of the cursor are adjusted.
* @param {Event} e Event object
*/
- mousemove: function mousemove(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(mousemove,2,"#f00");if(l)console.log.apply(undefined,l);
-
- e.preventDefault();
- var W=parseFloat($('#atlasMaker canvas').css('width'));
- var H=parseFloat($('#atlasMaker canvas').css('height'));
- var w=parseFloat($('#atlasMaker canvas').attr('width'));
- var h=parseFloat($('#atlasMaker canvas').attr('height'));
- var o=$('#atlasMaker canvas').offset();
- var x=parseInt((e.pageX-o.left)*(w/W));
- var y=parseInt((e.pageY-o.top)*(h/H));
-
- $("#cursor").css({
- left:(x*(W/w))+'px',
- top:(y*(H/h))+'px',
- width:me.User.penSize*(W/w),
- height:me.User.penSize*(H/h)
- });
- me.move(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
- },
+ mousemove: function mousemove(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(mousemove,2,"#f00");if(l)console.log.apply(undefined,l);
+
+ e.preventDefault();
+ var W=parseFloat($('#atlasMaker canvas').css('width'));
+ var H=parseFloat($('#atlasMaker canvas').css('height'));
+ var w=parseFloat($('#atlasMaker canvas').attr('width'));
+ var h=parseFloat($('#atlasMaker canvas').attr('height'));
+ var o=$('#atlasMaker canvas').offset();
+ var x=parseInt((e.pageX-o.left)*(w/W));
+ var y=parseInt((e.pageY-o.top)*(h/H));
+
+ $("#cursor").css({
+ left:(x*(W/w))+'px',
+ top:(y*(H/h))+'px',
+ width:me.User.penSize*(W/w),
+ height:me.User.penSize*(H/h)
+ });
+ me.move(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
+ },
/**
* @function mouseup
*/
- mouseup: function mouseup(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(mouseup,0,"#f00");if(l)console.log.apply(undefined,l);
-
- me.up(e);
- },
+ mouseup: function mouseup(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(mouseup,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ me.up(e);
+ },
/**
* @function touchstart
*/
- touchstart: function touchstart(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(touchstart,0,"#f00");if(l)console.log.apply(undefined,l);
-
- e.preventDefault();
+ touchstart: function touchstart(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(touchstart,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ e.preventDefault();
- var W=parseFloat($('#atlasMaker canvas').css('width'));
- var H=parseFloat($('#atlasMaker canvas').css('height'));
- var w=parseFloat($('#atlasMaker canvas').attr('width'));
- var h=parseFloat($('#atlasMaker canvas').attr('height'));
- var o=$('#atlasMaker canvas').offset();
- var touchEvent;
- if(e.originalEvent)
- touchEvent=e.originalEvent.changedTouches[0];
- else
- touchEvent=e.changedTouches[0];
- var x=parseInt((touchEvent.pageX-o.left)*(w/W));
- var y=parseInt((touchEvent.pageY-o.top)*(h/H));
-
- if(me.flagUsePreciseCursor) {
- // Precision cursor
- me.Crsr.x0=x;
- me.Crsr.cachedX=x;
- me.Crsr.y0=y;
- me.Crsr.cachedY=y;
- me.Crsr.fx=$("#finger").offset().left;
- me.Crsr.fy=$("#finger").offset().top;
- me.Crsr.touchStarted=true;
- setTimeout(function() {
- if( me.Crsr.cachedX == me.Crsr.x0 && me.Crsr.cachedY==me.Crsr.y0 && !me.Crsr.touchStarted) {
- // short tap: change mode
- me.Crsr.state=(me.Crsr.state=="move")?"draw":"move";
- me.updateCursor();
- }
- },200);
- setTimeout(function() {
- if (me.Crsr.cachedX==me.Crsr.x0 && me.Crsr.cachedY==me.Crsr.y0 && me.Crsr.touchStarted) {
- // long tap: change to configure mode
- me.Crsr.prevState=me.Crsr.state;
- me.Crsr.state="configure";
- me.updateCursor();
- }
- },1000);
- me.down(me.Crsr.x,Math.round(me.Crsr.y*me.brain_Wdim/me.brain_Hdim));
- } else
- me.down(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
- },
+ var W=parseFloat($('#atlasMaker canvas').css('width'));
+ var H=parseFloat($('#atlasMaker canvas').css('height'));
+ var w=parseFloat($('#atlasMaker canvas').attr('width'));
+ var h=parseFloat($('#atlasMaker canvas').attr('height'));
+ var o=$('#atlasMaker canvas').offset();
+ var touchEvent;
+ if(e.originalEvent)
+ touchEvent=e.originalEvent.changedTouches[0];
+ else
+ touchEvent=e.changedTouches[0];
+ var x=parseInt((touchEvent.pageX-o.left)*(w/W));
+ var y=parseInt((touchEvent.pageY-o.top)*(h/H));
+
+ if(me.flagUsePreciseCursor) {
+ // Precision cursor
+ me.Crsr.x0=x;
+ me.Crsr.cachedX=x;
+ me.Crsr.y0=y;
+ me.Crsr.cachedY=y;
+ me.Crsr.fx=$("#finger").offset().left;
+ me.Crsr.fy=$("#finger").offset().top;
+ me.Crsr.touchStarted=true;
+ setTimeout(function() {
+ if( me.Crsr.cachedX == me.Crsr.x0 && me.Crsr.cachedY==me.Crsr.y0 && !me.Crsr.touchStarted) {
+ // short tap: change mode
+ me.Crsr.state=(me.Crsr.state=="move")?"draw":"move";
+ me.updateCursor();
+ }
+ },200);
+ setTimeout(function() {
+ if (me.Crsr.cachedX==me.Crsr.x0 && me.Crsr.cachedY==me.Crsr.y0 && me.Crsr.touchStarted) {
+ // long tap: change to configure mode
+ me.Crsr.prevState=me.Crsr.state;
+ me.Crsr.state="configure";
+ me.updateCursor();
+ }
+ },1000);
+ me.down(me.Crsr.x,Math.round(me.Crsr.y*me.brain_Wdim/me.brain_Hdim));
+ } else
+ me.down(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
+ },
/**
* @function touchmove
*/
- touchmove: function touchmove(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(touchmove,2,"#f00");if(l)console.log.apply(undefined,l);
-
- if(me.Crsr.touchStarted==false && me.debug) {
- console.log("WARNING: touch can move without having started");
- }
-
- e.preventDefault();
+ touchmove: function touchmove(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(touchmove,2,"#f00");if(l)console.log.apply(undefined,l);
+
+ if(me.Crsr.touchStarted==false && me.debug) {
+ console.log("WARNING: touch can move without having started");
+ }
+
+ e.preventDefault();
- var W=parseFloat($('#atlasMaker canvas').css('width'));
- var H=parseFloat($('#atlasMaker canvas').css('height'));
- var w=parseFloat($('#atlasMaker canvas').attr('width'));
- var h=parseFloat($('#atlasMaker canvas').attr('height'));
- var o=$('#atlasMaker canvas').offset();
- var touchEvent;
- if(e.originalEvent)
- touchEvent=e.originalEvent.changedTouches[0];
- else
- touchEvent=e.changedTouches[0];
- var x=parseInt((touchEvent.pageX-o.left)*(w/W));
- var y=parseInt((touchEvent.pageY-o.top)*(h/H));
-
- if(me.flagUsePreciseCursor) {
- // Precision cursor
- var dx=x-me.Crsr.x0;
- var dy=y-me.Crsr.y0;
- if(me.Crsr.state=="move"||me.Crsr.state=="draw") {
- me.Crsr.x+=dx;
- me.Crsr.y+=dy;
- $("#cursor").css({left:me.Crsr.x*(W/w),top:me.Crsr.y*(H/h),width:me.User.penSize*(W/w),height:me.User.penSize*(H/h)});
- if(me.Crsr.state=="draw")
- me.move(me.Crsr.x,Math.round(me.Crsr.y*me.brain_Wdim/me.brain_Hdim));
- }
- me.Crsr.fx+=dx*(W/w);
- me.Crsr.fy+=dy*(H/h);
- $("#finger").offset({left:me.Crsr.fx,top:me.Crsr.fy});
-
- me.Crsr.x0=x;
- me.Crsr.y0=y;
- } else {
- $("#cursor").css({
- left:(x*(W/w))+'px',
- top:(y*(H/h))+'px',
- width:me.User.penSize*(W/w),
- height:me.User.penSize*(H/h)
- });
- me.move(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
- }
- },
+ var W=parseFloat($('#atlasMaker canvas').css('width'));
+ var H=parseFloat($('#atlasMaker canvas').css('height'));
+ var w=parseFloat($('#atlasMaker canvas').attr('width'));
+ var h=parseFloat($('#atlasMaker canvas').attr('height'));
+ var o=$('#atlasMaker canvas').offset();
+ var touchEvent;
+ if(e.originalEvent)
+ touchEvent=e.originalEvent.changedTouches[0];
+ else
+ touchEvent=e.changedTouches[0];
+ var x=parseInt((touchEvent.pageX-o.left)*(w/W));
+ var y=parseInt((touchEvent.pageY-o.top)*(h/H));
+
+ if(me.flagUsePreciseCursor) {
+ // Precision cursor
+ var dx=x-me.Crsr.x0;
+ var dy=y-me.Crsr.y0;
+ if(me.Crsr.state=="move"||me.Crsr.state=="draw") {
+ me.Crsr.x+=dx;
+ me.Crsr.y+=dy;
+ $("#cursor").css({left:me.Crsr.x*(W/w),top:me.Crsr.y*(H/h),width:me.User.penSize*(W/w),height:me.User.penSize*(H/h)});
+ if(me.Crsr.state=="draw")
+ me.move(me.Crsr.x,Math.round(me.Crsr.y*me.brain_Wdim/me.brain_Hdim));
+ }
+ me.Crsr.fx+=dx*(W/w);
+ me.Crsr.fy+=dy*(H/h);
+ $("#finger").offset({left:me.Crsr.fx,top:me.Crsr.fy});
+
+ me.Crsr.x0=x;
+ me.Crsr.y0=y;
+ } else {
+ $("#cursor").css({
+ left:(x*(W/w))+'px',
+ top:(y*(H/h))+'px',
+ width:me.User.penSize*(W/w),
+ height:me.User.penSize*(H/h)
+ });
+ me.move(x,Math.round(y*me.brain_Wdim/me.brain_Hdim));
+ }
+ },
/**
* @function touchend
*/
- touchend: function touchend(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(touchend,0,"#f00");if(l)console.log.apply(undefined,l);
-
- e.preventDefault();
-
- if(me.flagUsePreciseCursor) {
- // Precision cursor
- me.Crsr.touchStarted=false;
- if(me.Crsr.state=="configure") {
- me.Crsr.state=me.Crsr.prevState;
- me.updateCursor();
- }
- }
- me.up(e);
- },
+ touchend: function touchend(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(touchend,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ e.preventDefault();
+
+ if(me.flagUsePreciseCursor) {
+ // Precision cursor
+ me.Crsr.touchStarted=false;
+ if(me.Crsr.state=="configure") {
+ me.Crsr.state=me.Crsr.prevState;
+ me.updateCursor();
+ }
+ }
+ me.up(e);
+ },
/**
* @function down
* @desc Generic pointer down event: Deals with down events generated by mouse clicks or touch events. The effect of the down event is determined by the current User.tool
* @param {integer} x X coordinate in slice space
* @param {integer} y Y coordinate in slice space
*/
- down: function down(x,y) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(down,0,"#f00");if(l)console.log.apply(undefined,l);
-
- var z=me.User.slice;
-
- switch(me.User.tool) {
- case 'show':
+ down: function down(x,y) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(down,0,"#f00");if(l)console.log.apply(undefined,l);
+
+ var z=me.User.slice;
+
+ switch(me.User.tool) {
+ case 'show':
me.User.mouseIsDown = true;
me.sendUserDataMessage(JSON.stringify({'mouseIsDown':true}));
me.showxy(-1,'m',x,y,me.User);
- break;
- case 'paint':
- // check for 'edit' access
- if(me.editMode == 0)
- return;
- // fill
- if(me.User.doFill)
- me.paintxy(-1,'f',x,y,me.User);
- //paint
- else {
- me.User.mouseIsDown = true;
- me.sendUserDataMessage(JSON.stringify({'mouseIsDown':true}));
- me.paintxy(-1,'mf',x,y,me.User);
- }
- break;
- case 'erase':
- // check for 'edit' access
- if(me.editMode == 0)
- return;
- // fill
- if(me.User.doFill)
- me.paintxy(-1,'e',x,y,me.User);
+ break;
+ case 'paint':
+ // check for 'edit' access
+ if(me.editMode == 0)
+ return;
+ // fill
+ if(me.User.doFill)
+ me.paintxy(-1,'f',x,y,me.User);
+ //paint
+ else {
+ me.User.mouseIsDown = true;
+ me.sendUserDataMessage(JSON.stringify({'mouseIsDown':true}));
+ me.paintxy(-1,'mf',x,y,me.User);
+ }
+ break;
+ case 'erase':
+ // check for 'edit' access
+ if(me.editMode == 0)
+ return;
+ // fill
+ if(me.User.doFill)
+ me.paintxy(-1,'e',x,y,me.User);
// erase
- else {
- me.User.mouseIsDown = true;
- me.sendUserDataMessage(JSON.stringify({'mouseIsDown':true}));
- me.paintxy(-1,'me',x,y,me.User);
- }
- break;
- case 'measure':
- if(me.User.measureLength==null)
- me.User.measureLength=[{x:x,y:y}];
- else
- me.User.measureLength.push({x:x,y:y});
- break;
- case 'adjust':
- me.User.mouseIsDown = true;
- me.info.x=x/me.brain_W;
- me.info.y=1-y/me.brain_H;
- break;
- case 'eyedrop':
- var value = me.eyedrop( x,y,me.User );
- var index = me.ontology.valueToIndex[ value ];
- var selRegionName = me.ontology.labels[ index ].name;
- me.info.region = selRegionName;
- me.changePenColor( index );
- var selRegionColor = me.ontology.labels[ index ].color;
- break;
- }
-
- // init annotation length counter
- me.annotationLength=0;
- },
+ else {
+ me.User.mouseIsDown = true;
+ me.sendUserDataMessage(JSON.stringify({'mouseIsDown':true}));
+ me.paintxy(-1,'me',x,y,me.User);
+ }
+ break;
+ case 'measure':
+ if(me.User.measureLength==null)
+ me.User.measureLength=[{x:x,y:y}];
+ else
+ me.User.measureLength.push({x:x,y:y});
+ break;
+ case 'adjust':
+ me.User.mouseIsDown = true;
+ me.info.x=x/me.brain_W;
+ me.info.y=1-y/me.brain_H;
+ break;
+ case 'eyedrop':
+ var value = me.eyedrop( x,y,me.User );
+ var index = me.ontology.valueToIndex[ value ];
+ var selRegionName = me.ontology.labels[ index ].name;
+ me.info.region = selRegionName;
+ me.changePenColor( index );
+ var selRegionColor = me.ontology.labels[ index ].color;
+ break;
+ }
+
+ // init annotation length counter
+ me.annotationLength=0;
+ },
/**
* @function move
* @desc Generic pointer move event: Deals with move events generated by mouse clicks or touch events. The effect of the move event is determined by the current User.tool
* @param {integer} x X coordinate in slice space
* @param {integer} y Y coordinate in slice space
*/
- move: function move(x,y) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(move,2,"#f00");if(l)console.log.apply(undefined,l);
-
- /*
- if(MyLoginWidget.loggedin==0 || me.editMode==0)
- return;
- */
+ move: function move(x,y) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(move,2,"#f00");if(l)console.log.apply(undefined,l);
+
+ /*
+ if(MyLoginWidget.loggedin==0 || me.editMode==0)
+ return;
+ */
- var z=me.User.slice;
+ var z=me.User.slice;
- if(!me.User.mouseIsDown)
- return;
-
- switch(me.User.tool) {
- case 'show':
- me.showxy(-1,'m',x,y,me.User);
- break;
- case 'paint':
- me.paintxy(-1,'lf',x,y,me.User);
- break;
- case 'erase':
- me.paintxy(-1,'le',x,y,me.User);
- break;
- case 'adjust':
- me.info.x=x/me.brain_W;
- me.info.y=1-y/me.brain_H;
- me.drawImages();
- break;
- }
- },
+ if(!me.User.mouseIsDown)
+ return;
+
+ switch(me.User.tool) {
+ case 'show':
+ me.showxy(-1,'m',x,y,me.User);
+ break;
+ case 'paint':
+ me.paintxy(-1,'lf',x,y,me.User);
+ break;
+ case 'erase':
+ me.paintxy(-1,'le',x,y,me.User);
+ break;
+ case 'adjust':
+ me.info.x=x/me.brain_W;
+ me.info.y=1-y/me.brain_H;
+ me.drawImages();
+ break;
+ }
+ },
/**
* @function up
* @desc Generic pointer up event: Deals with up events generated by mouse clicks or touch events.
* @param {integer} x X coordinate in slice space
* @param {integer} y Y coordinate in slice space
*/
- up: function up(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(up,0,"#f00");if(l)console.log.apply(undefined,l);
+ up: function up(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(up,0,"#f00");if(l)console.log.apply(undefined,l);
- /*
- if(MyLoginWidget.loggedin==0 || me.editMode==0)
- return;
- */
+ /*
+ if(MyLoginWidget.loggedin==0 || me.editMode==0)
+ return;
+ */
- // Send mouse up (touch ended) message
- me.User.mouseIsDown = false;
- me.User.x0=-1;
+ // Send mouse up (touch ended) message
+ me.User.mouseIsDown = false;
+ me.User.x0=-1;
me.sendUserDataMessage(JSON.stringify({'mouseIsDown':false}));
-
- var msg;
-
- switch(me.User.tool) {
- case 'show':
+
+ var msg;
+ switch(me.User.tool) {
+ case 'show':
var msg={"c":"u"};
me.sendShowMessage(msg);
break;
@@ -761,7 +760,7 @@ var AtlasMakerInteraction = {
case 'erase':
var msg={c:"mu"};
me.sendPaintMessage(msg);
-
+
// add annotated length to User.annotation length and post to DB
me.logToDatabase("annotationLength",{
source:me.User.source,
@@ -773,78 +772,72 @@ var AtlasMakerInteraction = {
me.info.length = length+" mm";
me.displayInformation();
});
-
+
me.annotationLength=0;
-
+
// compute total segmented volume
var vol=me.computeSegmentedVolume();
me.info.volume=parseInt(vol)+" mm3";
break;
- case 'eyedrop':
- me.displayInformation();
-
- var msg={"c":"mu"};
- me.sendPaintMessage(msg);
- break;
default:
var msg={"c":"mu"};
me.sendPaintMessage(msg);
}
-
- /*
- TEST
- */
- //me.sendRequestSliceMessage();
- },
+
+ /*
+ TEST
+ */
+ //me.sendRequestSliceMessage();
+ },
/**
* @function keyDown
*/
- keyDown: function keyDown(e) {
- var me=AtlasMakerWidget;
- var l=me.traceLog(keyDown,2,"#f00");if(l)console.log.apply(undefined,l);
-
- // console.log("key:",e.which);
-
- if(e.which==13 && $(e.target).attr('contenteditable')) {
+ keyDown: function keyDown(e) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(keyDown,2,"#f00");if(l)console.log.apply(undefined,l);
+
+ // console.log("key:",e.which);
+
+ if(e.which==13 && $(e.target).attr('contenteditable')) {
e.preventDefault();
return;
}
-
- if(e.target.tagName!="BODY")
- return;
-
- switch(e.which) {
- case 13: // return
- if(me.User.measureLength) {
- var length=0;
- var p=me.User.measureLength;
- var wdim=me.brain_Wdim,hdim=me.brain_Hdim;
- var i;
- for(i=1;i'+((usr.username == 'Anonymous')?u:usr.username)+'MRI");
+ $("#chat").text("Chat (1 connected)");
+ me.flagConnected=1;
+ me.reconnectionTimeout = 5;
+ def.resolve();
+ };
+
+ me.receiveFunctions["saveMetadata"]=me.receiveMetadata;
+ me.receiveFunctions["userData"]=me.receiveUserDataMessage;
+ me.receiveFunctions["volInfo"]=function(data){console.log("volInfo",data)};
+ me.receiveFunctions["chat"]=me.receiveChatMessage;
+ me.receiveFunctions["show"]=me.receiveShowMessage;
+ me.receiveFunctions["paint"]=me.receivePaintMessage;
+ me.receiveFunctions["paintvol"]=me.receivePaintVolumeMessage;
+ me.receiveFunctions["disconnect"]=me.receiveDisconnectMessage;
+ me.receiveFunctions["serverMessage"]=me.receiveServerMessage;
+
+ me.receiveFunctions["requestSlice"]=function(data){console.log("requestSlice",data)};
+ me.receiveFunctions["requestSlice2"]=function(data){console.log("requestSlice2",data)};
+
+ me.socket.onmessage = me.receiveSocketMessage;
+
+ me.socket.onclose = function(msg) {
+ me.flagConnected=0;
+
+ // Try to reconnect
+ // wait a random initial time, to prevent an avalanche
+ // of reconnections in case of server crash
+ var rand = 1000+5000*Math.random();
+ console.log("Initial random time:",rand);
+ setTimeout(function() {
+ var timeout = me.reconnectionTimeout;
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
+ if(me.timer) {
+ clearInterval(me.timer);
+ }
+ me.timer = setInterval(function() {
+ if(timeout < 0) {
+ $("#chat").text("Reconnecting...");
+ me.socket = null;
clearInterval(me.timer);
+ setTimeout(function() {
+ me.reconnectionTimeout *= 2;
+ me.initSocketConnection()
+ .then(function() {
+ me.sendUserDataMessage("allUserData");
+ me.sendUserDataMessage("sendAtlas");
+ clearInterval(me.timer);
+ })
+ .catch(function() {
+ timeout=me.reconnectionTimeout;
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
+ });
+ }, 1000);
+ } else {
+ $("#chat").text("Disconnected. Try to reconnect in "+(timeout--)+" s...");
}
- me.timer = setInterval(function () {
- if (timeout < 0) {
- $("#chat").text("Reconnecting...");
- me.socket = null;
- clearInterval(me.timer);
- setTimeout(function () {
- me.reconnectionTimeout *= 2;
- me.initSocketConnection()
- .then(function () {
- me.sendUserDataMessage("allUserData");
- me.sendUserDataMessage("sendAtlas");
- clearInterval(me.timer);
- })
- .catch(function () {
- timeout = me.reconnectionTimeout;
- $("#chat").text("Disconnected. Try to reconnect in " + (timeout--) + " s...");
- });
- }, 1000);
- } else {
- $("#chat").text("Disconnected. Try to reconnect in " + (timeout--) + " s...");
- }
- }, 1000);
- }, rand);
- };
-
- window.onbeforeunload = function () {
- me.socket.onclose = function () { }; // disable onclose handler first
- me.socket.close()
- };
- }
- catch (ex) {
- $("#chat").text("Chat (not connected - connection error)");
- }
- })
- },
- /**
+ }, 1000);
+ }, rand);
+ };
+
+ window.onbeforeunload = function() {
+ me.socket.onclose = function () {}; // disable onclose handler first
+ me.socket.close()
+ };
+ }
+ catch (ex) {
+ $("#chat").text("Chat (not connected - connection error)");
+ }
+
+ return def.promise();
+ },
+ /**
* @function receiveSocketMessage
*/
- receiveSocketMessage: function receiveSocketMessage(msg) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveSocketMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
- // Message: atlas data initialisation
- if (msg.data instanceof Blob) {
- me.receiveBinaryMessage(msg.data);
- return;
- }
-
- // Message: interaction message
- var data = JSON.parse(msg.data);
- me.receiveFunctions[data.type](data);
- },
- /**
+ receiveSocketMessage: function receiveSocketMessage(msg) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(receiveSocketMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
+ // Message: atlas data initialisation
+ if(msg.data instanceof Blob) {
+ me.receiveBinaryMessage(msg.data);
+ return;
+ }
+
+ // Message: interaction message
+ var data=JSON.parse(msg.data);
+ me.receiveFunctions[data.type](data);
+ },
+ /**
* @function sendUserDataMessage
*/
- sendUserDataMessage: function sendUserDataMessage(description) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(sendUserDataMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
- if (me.flagConnected == 0)
- return;
-
- if (me.debug > 1) console.log("message: " + description);
-
- if (description === "allUserData")
- var msg = { "type": "userData", "user": me.User, "description": description };
- else
- var msg = { "type": "userData", "description": description };
- try {
- me.socket.send(JSON.stringify(msg));
- } catch (ex) {
- console.log("ERROR: Unable to sendUserDataMessage", ex);
- }
- },
- /**
+ sendUserDataMessage: function sendUserDataMessage(description) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(sendUserDataMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
+ if(me.flagConnected==0)
+ return;
+
+ if(me.debug>1) console.log("message: "+description);
+
+ if(description === "allUserData")
+ var msg={"type":"userData","user":me.User,"description":description};
+ else
+ var msg={"type":"userData","description":description};
+ try {
+ me.socket.send(JSON.stringify(msg));
+ } catch (ex) {
+ console.log("ERROR: Unable to sendUserDataMessage",ex);
+ }
+ },
+ /**
* @function receiveBinaryMessage
*/
- receiveBinaryMessage: function receiveBinaryMessage(msgData) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveBinaryMessage, 1, "#aca"); if (l) console.log.apply(undefined, l);
-
+ receiveBinaryMessage: function receiveBinaryMessage(msgData) {
+ var me=AtlasMakerWidget;
+ var l=me.traceLog(receiveBinaryMessage,1,"#aca");if(l)console.log.apply(undefined,l);
+
var fileReader = new FileReader();
fileReader.onload = function from_receiveSocketMessage() {
- var data = new Uint8Array(this.result);
- var sz = data.length;
- var ext = String.fromCharCode(data[sz - 8], data[sz - 7], data[sz - 6]);
-
- if (me.debug > 1) console.log("type: " + ext);
+ var data=new Uint8Array(this.result);
+ var sz=data.length;
+ var ext=String.fromCharCode(data[sz-8],data[sz-7],data[sz-6]);
- switch (ext) {
+ if(me.debug>1) console.log("type: "+ext);
+
+ switch(ext) {
case 'nii': {
- var inflate = new pako.Inflate();
- inflate.push(data, true);
- var atlas = new Object();
- atlas.data = inflate.result;
- atlas.name = me.atlasFilename;
- atlas.dim = me.brain_dim;
-
- me.atlas = atlas;
+ var inflate=new pako.Inflate();
+ inflate.push(data,true);
+ var atlas=new Object();
+ atlas.data=inflate.result;
+ atlas.name=me.atlasFilename;
+ atlas.dim=me.brain_dim;
+
+ me.atlas=atlas;
me.configureBrainImage();
me.configureAtlasImage();
me.resizeWindow();
- me.brain_img.img = null;
+ me.brain_img.img=null;
me.drawImages();
-
+
// compute total segmented volume
- var vol = me.computeSegmentedVolume();
- me.info.volume = parseInt(vol) + " mm3";
+ var vol=me.computeSegmentedVolume();
+ me.info.volume=parseInt(vol)+" mm3";
// setup download link
- var link = me.container.find("span#download_atlas");
- link.html("" + atlas.name);
+ var link=me.container.find("span#download_atlas");
+ link.html(""+atlas.name);
break;
}
@@ -205,283 +207,283 @@ var AtlasMakerWS = {
var urlCreator = window.URL || window.webkitURL;
var imageUrl = urlCreator.createObjectURL(msgData);
var img = new Image();
-
- me.isMRILoaded = true; // receiving a jpg is proof of a loaded MRI
-
- img.onload = function from_initSocketConnection() {
- var flagFirstImage = (me.brain_img.img == null);
- me.brain_img.img = img;
- me.brain_img.view = me.flagLoadingImg.view;
- me.brain_img.slice = me.flagLoadingImg.slice;
+
+ me.isMRILoaded=true; // receiving a jpg is proof of a loaded MRI
+
+ img.onload=function from_initSocketConnection(){
+ var flagFirstImage=(me.brain_img.img==null);
+ me.brain_img.img=img;
+ me.brain_img.view=me.flagLoadingImg.view;
+ me.brain_img.slice=me.flagLoadingImg.slice;
me.drawImages();
+
+ me.flagLoadingImg.loading=false;
- me.flagLoadingImg.loading = false;
-
- if (flagFirstImage || me.flagLoadingImg.view != me.User.view || me.flagLoadingImg.slice != me.User.slice) {
+ if(flagFirstImage || me.flagLoadingImg.view!=me.User.view ||me.flagLoadingImg.slice!=me.User.slice) {
me.sendRequestSliceMessage();
}
-
+
// remove loading indicator
$("#loadingIndicator").hide();
}
- img.src = imageUrl;
+ img.src=imageUrl;
break;
}
}
};
fileReader.readAsArrayBuffer(msgData);
- },
- /**
+ },
+ /**
* @function receiveUserDataMessage
*/
- receiveUserDataMessage: function receiveUserDataMessage(data) {
- var me = AtlasMakerWidget;
- var l = me.traceLog(receiveUserDataMessage, 0, "#aca"); if (l) console.log.apply(undefined, l);
-
- if (me.debug > 1) console.log("description: " + data.description, data);
-
- var u = data.uid;
-
- // First time the user is observed
- if (me.Collab[u] === undefined) {
- try {
- //var msg=""+data.user.username+" entered atlas "+data.user.specimenName+"/"+data.user.atlasFilename+"" - var msg; - if (data.user === undefined || data.user.username === "Anonymous") { - msg = "" + data.uid + " entered
"; - } else { - msg = "" + data.user.username + " entered
"; - } - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - } catch (e) { - console.log("data:", data); - console.log(e); - } - } - - if (data.description === "allUserData") - me.Collab[u] = data.user; - else { - try { + receiveUserDataMessage: function receiveUserDataMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveUserDataMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.debug>1) console.log("description: "+data.description,data); + + var u=data.uid; + + // First time the user is observed + if(me.Collab[u]===undefined) { + try { + //var msg=""+data.user.username+" entered atlas "+data.user.specimenName+"/"+data.user.atlasFilename+"
" + var msg; + if(data.user === undefined || data.user.username === "Anonymous") { + msg=""+data.uid+" entered
"; + } else { + msg=""+data.user.username+" entered
"; + } + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + } catch (e) { + console.log("data:",data); + console.log(e); + } + } + + if(data.description === "allUserData") + me.Collab[u]=data.user; + else { + try { var changes = JSON.parse(data.description); var i; - for (i in changes) + for(i in changes) me.Collab[u][i] = changes[i]; } catch (e) { console.log(e); } - } - - var v, nusers = 1; - for (v in me.Collab) - nusers++; - $("#chat").text("Chat (" + nusers + " connected)"); - }, - /** + } + + var v,nusers=1; + for(v in me.Collab) + nusers++; + $("#chat").text("Chat ("+nusers+" connected)"); + }, + /** * @function sendChatMessage */ - sendChatMessage: function sendChatMessage() { - var me = AtlasMakerWidget; - var l = me.traceLog(sendChatMessage, 0, "#aca"); if (l) console.log.apply(undefined, l); - - if (me.flagConnected == 0) - return; - var msg = DOMPurify.sanitize($('input#msg')[0].value); - try { - me.socket.send(JSON.stringify({ "type": "chat", "msg": msg, "username": me.User.username })); - var msg = "me: " + msg + "
"; - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - $('input#msg').val(""); - } catch (ex) { - console.log("ERROR: Unable to sendChatMessage", ex); - } - }, - /** + sendChatMessage: function sendChatMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendChatMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + var msg = DOMPurify.sanitize($('input#msg')[0].value); + try { + me.socket.send(JSON.stringify({"type":"chat","msg":msg,"username":me.User.username})); + var msg="me: "+msg+"
"; + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + $('input#msg').val(""); + } catch (ex) { + console.log("ERROR: Unable to sendChatMessage",ex); + } + }, + /** * @function receiveChatMessage */ - receiveChatMessage: function receiveChatMessage(data) { - var me = AtlasMakerWidget; - var l = me.traceLog(receiveChatMessage, 0, "#aca"); if (l) console.log.apply(undefined, l); - console.log(data); - - var theSource = me.Collab[data.uid].source; - var theView = me.Collab[data.uid].view; - var theSlice = me.Collab[data.uid].slice; - var link = "/mri?url=" + theSource + "&view=" + theView + "&slice=" + theSlice; - var theUsername = data.username; - var msg = ""+theUsername+": "+data.msg+"
" - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - }, - /** + receiveChatMessage: function receiveChatMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveChatMessage,0,"#aca");if(l)console.log.apply(undefined,l); + console.log(data); + + var theSource=me.Collab[data.uid].source; + var theView=me.Collab[data.uid].view; + var theSlice=me.Collab[data.uid].slice; + var link = "/mri?url="+theSource+"&view="+theView+"&slice="+theSlice; + var theUsername=data.username; + var msg=""+theUsername+": "+data.msg+"
" + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + }, + /** * @function sendPaintMessage * @desc On user painting, this function broadcasts the painting event to all other connected users * @param {Object} msg Painting event object: {"c":c,"x":x,"y":y}, where "c" is the command (l,e,lf,ef) and x and y are the coordinates in slice space */ - sendPaintMessage: function sendPaintMessage(msg) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendPaintMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"paint",data:msg})); - } catch (ex) { - console.log("ERROR: Unable to sendPaintMessage",ex); - } - }, - /** + sendPaintMessage: function sendPaintMessage(msg) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendPaintMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"paint",data:msg})); + } catch (ex) { + console.log("ERROR: Unable to sendPaintMessage",ex); + } + }, + /** * @function receivePaintMessage * @desc Receive paint events from other connected users */ - receivePaintMessage: function receivePaintMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receivePaintMessage,3,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.data; - var u=data.uid; // user - var c=msg.c; // command - var x=parseInt(msg.x); // x coordinate - var y=parseInt(msg.y); // y coordinate - - if(me.Collab[u]) - me.paintxy(u,c,x,y,me.Collab[u]); - }, - /** + receivePaintMessage: function receivePaintMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receivePaintMessage,3,"#aca");if(l)console.log.apply(undefined,l); + + var msg=data.data; + var u=data.uid; // user + var c=msg.c; // command + var x=parseInt(msg.x); // x coordinate + var y=parseInt(msg.y); // y coordinate + + if(me.Collab[u]) + me.paintxy(u,c,x,y,me.Collab[u]); + }, + /** * @function sendShowMessage * @desc On user showing, this function broadcasts the showing event to all other connected users * @param {Object} msg Showing event object: {"x":x,"y":y}, where x and y are the coordinates in slice space */ - sendShowMessage: function sendShowMessage(msg) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendShowMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"show",data:msg})); - } catch (ex) { - console.log("ERROR: Unable to sendShowMessage",ex); - } - }, - /** + sendShowMessage: function sendShowMessage(msg) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendShowMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"show",data:msg})); + } catch (ex) { + console.log("ERROR: Unable to sendShowMessage",ex); + } + }, + /** * @function receiveShowMessage * @desc Receive show events from other connected users */ - receiveShowMessage: function receiveShowMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveShowMessage,3,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.data; - var u=data.uid; // user - var c=msg.c; // command - var x=parseInt(msg.x); // x coordinate - var y=parseInt(msg.y); // y coordinate - - if(me.Collab[u]) - me.showxy(u,c,x,y,me.Collab[u]); - }, - /** + receiveShowMessage: function receiveShowMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveShowMessage,3,"#aca");if(l)console.log.apply(undefined,l); + + var msg=data.data; + var u=data.uid; // user + var c=msg.c; // command + var x=parseInt(msg.x); // x coordinate + var y=parseInt(msg.y); // y coordinate + + if(me.Collab[u]) + me.showxy(u,c,x,y,me.Collab[u]); + }, + /** * @function receivePaintVolumeMessage */ - receivePaintVolumeMessage: function receivePaintVolumeMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receivePaintVolumeMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var i,ind,val,voxels; - - voxels=data.data; - me.paintvol(voxels.data); - - /* - TEST - */ - me.sendRequestSliceMessage(); - }, - /** + receivePaintVolumeMessage: function receivePaintVolumeMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receivePaintVolumeMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + var i,ind,val,voxels; + + voxels=data.data; + me.paintvol(voxels.data); + + /* + TEST + */ + me.sendRequestSliceMessage(); + }, + /** * @function sendUndoMessage */ - sendUndoMessage: function sendUndoMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendUndoMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"paint",data:{c:"u"}})); - } catch (ex) { - console.log("ERROR: Unable to sendUndoMessage",ex); - } - }, - /** + sendUndoMessage: function sendUndoMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendUndoMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"paint",data:{c:"u"}})); + } catch (ex) { + console.log("ERROR: Unable to sendUndoMessage",ex); + } + }, + /** * @function sendSaveMessage */ - sendSaveMessage: function sendSaveMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendSaveMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - try { - me.socket.send(JSON.stringify({type:"save"})); - } catch (ex) { - console.log("ERROR: Unable to sendSaveMessage",ex); - } - }, - /** + sendSaveMessage: function sendSaveMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendSaveMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + try { + me.socket.send(JSON.stringify({type:"save"})); + } catch (ex) { + console.log("ERROR: Unable to sendSaveMessage",ex); + } + }, + /** * @function sendRequestMRIMessage */ - sendRequestMRIMessage: function sendRequestMRIMessage(source) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendRequestMRIMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - - try { - me.socket.send(JSON.stringify({ - type:"requestMRI", - source:"sendRequestMRIMessage" - })); - } catch (ex) { - console.log("ERROR: Unable to sendRequestMRIMessage",ex); - } - }, - /** + sendRequestMRIMessage: function sendRequestMRIMessage(source) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendRequestMRIMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + + try { + me.socket.send(JSON.stringify({ + type:"requestMRI", + source:"sendRequestMRIMessage" + })); + } catch (ex) { + console.log("ERROR: Unable to sendRequestMRIMessage",ex); + } + }, + /** * @function sendRequestSliceMessage */ - sendRequestSliceMessage: function sendRequestSliceMessage() { - var me=AtlasMakerWidget; - var l=me.traceLog(sendRequestSliceMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - if(me.flagConnected==0) - return; - if(me.flagLoadingImg.loading==true) - return; - try { - me.socket.send(JSON.stringify({ - - type:"requestSlice", - /* - TEST - */ - //type:"requestSlice2", - - view:me.User.view, - slice:me.User.slice - })); - me.flagLoadingImg.loading=true; - me.flagLoadingImg.view=me.User.view; - me.flagLoadingImg.slice=me.User.slice; - - } catch (ex) { - console.log("ERROR: Unable to sendRequestSliceMessage",ex); - } - }, + sendRequestSliceMessage: function sendRequestSliceMessage() { + var me=AtlasMakerWidget; + var l=me.traceLog(sendRequestSliceMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + if(me.flagConnected==0) + return; + if(me.flagLoadingImg.loading==true) + return; + try { + me.socket.send(JSON.stringify({ + + type:"requestSlice", + /* + TEST + */ + //type:"requestSlice2", + + view:me.User.view, + slice:me.User.slice + })); + me.flagLoadingImg.loading=true; + me.flagLoadingImg.view=me.User.view; + me.flagLoadingImg.slice=me.User.slice; + + } catch (ex) { + console.log("ERROR: Unable to sendRequestSliceMessage",ex); + } + }, /** * @todo This is really not the place for some of this code. The receiveMetadata * function is ok, but the direct references to projectInfo -- a structure @@ -489,136 +491,136 @@ var AtlasMakerWS = { * mechanism for uncoupling the 2 pieces of code is not clear. It could be * a subscription, for example. */ - receiveMetadata: function receiveMetadata(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveMetadata,1,"#aca");if(l)console.log.apply(undefined,l); + receiveMetadata: function receiveMetadata(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveMetadata,1,"#aca");if(l)console.log.apply(undefined,l); var projShortname = projectInfo.shortname; - for (var i in projectInfo.files.list) { - if (projectInfo.files.list[i].source == data.metadata.source) { - for (var key in projectInfo.files.list[i].mri.annotations[projShortname]) { - info_proxy["files.list." + i + ".mri.annotations." + projShortname + "." + key] = data.metadata.mri.annotations[projShortname][key]; - } - info_proxy["files.list." + i + ".name"] = data.metadata.name; - break; - } - } - }, - /** + for (var i in projectInfo.files.list) { + if (projectInfo.files.list[i].source == data.metadata.source) { + for (var key in projectInfo.files.list[i].mri.annotations[projShortname]) { + info_proxy["files.list." + i + ".mri.annotations." + projShortname + "." + key] = data.metadata.mri.annotations[projShortname][key]; + } + info_proxy["files.list." + i + ".name"] = data.metadata.name; + break; + } + } + }, + /** * @function sendSaveMetadataMessage */ - sendSaveMetadataMessage: function sendSaveMetadataMessage(info, method, patch) { - var me=AtlasMakerWidget; - var l=me.traceLog(sendSaveMetadataMessage,1,"#aca");if(l)console.log.apply(undefined,l); - - return new Promise(function(resolve, reject) { - if(me.flagConnected==0) { - console.log("WARNING: Not connected: will not save metadata"); - return reject(); + sendSaveMetadataMessage: function sendSaveMetadataMessage(info, method, patch) { + var me=AtlasMakerWidget; + var l=me.traceLog(sendSaveMetadataMessage,1,"#aca");if(l)console.log.apply(undefined,l); + + var def = $.Deferred(); + if(me.flagConnected==0) { + console.log("WARNING: Not connected: will not save metadata"); + return def.reject().promise(); + } + + try { + var rnd = Math.random().toString(36).slice(20); + var met = method || "append"; + if(method == "patch") { + me.socket.send(JSON.stringify({ + type:"saveMetadata", + metadata: info, + method: met, + patch: patch, + rnd: rnd + })); + } else { + me.socket.send(JSON.stringify({ + type:"saveMetadata", + metadata: info, + method: met, + rnd: rnd + })); } - - try { - var rnd = Math.random().toString(36).slice(20); - var met = method || "append"; - if(method == "patch") { - me.socket.send(JSON.stringify({ - type:"saveMetadata", - metadata: info, - method: met, - patch: patch, - rnd: rnd - })); - } else { - me.socket.send(JSON.stringify({ - type:"saveMetadata", - metadata: info, - method: met, - rnd: rnd - })); - } - if(me.debug>1) { - console.log(rnd); - console.log(info); - } - resolve(); - - } catch (ex) { - console.log("ERROR: Unable to sendSaveMetadataMessage",ex); - reject(); + if(me.debug>1) { + console.log(rnd); + console.log(info); } - }); - }, - /** + def.resolve(); + + } catch (ex) { + console.log("ERROR: Unable to sendSaveMetadataMessage",ex); + def.reject(); + } + return def.promise(); + }, + /** * @function receiveDisconnectMessage */ - receiveDisconnectMessage: function receiveDisconnectMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveDisconnectMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var u=data.uid; // user - if(me.Collab[u]) { - var msg; - if(me.Collab[u].username === undefined || me.Collab[u].username === "Anonymous") - msg = ""+me.Collab[u].uid+" left
"; - else + receiveDisconnectMessage: function receiveDisconnectMessage(data) { + var me=AtlasMakerWidget; + var l=me.traceLog(receiveDisconnectMessage,0,"#aca");if(l)console.log.apply(undefined,l); + + var u=data.uid; // user + if(me.Collab[u]) { + var msg; + if(me.Collab[u].username === undefined || me.Collab[u].username === "Anonymous") + msg = ""+me.Collab[u].uid+" left
"; + else msg = ""+me.Collab[u].username+" left
"; - } - else - var msg=""+u+" left
"; - delete me.Collab[u]; - var v,nusers=1; for(v in me.Collab) nusers++; - $("#chat").text("Chat ("+nusers+" connected)"); - $("#log").append(msg); - $("#log").scrollTop($("#log")[0].scrollHeight); - }, - /** + } + else + var msg=""+u+" left
"; + delete me.Collab[u]; + var v,nusers=1; for(v in me.Collab) nusers++; + $("#chat").text("Chat ("+nusers+" connected)"); + $("#log").append(msg); + $("#log").scrollTop($("#log")[0].scrollHeight); + }, + /** * @function receiveServerMessage */ - receiveServerMessage: function receiveServerMessage(data) { - var me=AtlasMakerWidget; - var l=me.traceLog(receiveServerMessage,0,"#aca");if(l)console.log.apply(undefined,l); - - var msg=data.msg; - var prevMsg=$("#chat").text(); - $("#chat").text(msg); - setTimeout(function(){$("#chat").text(prevMsg)},5000); - }, - /** - * @function replayWSTraffic - * @desc Replays websocket traffic recorded at the served. Used for debugging - * @param Array recorded An array of websocket messages recorded in the server - */ - replayWSTraffic: function replayWSTraffic(recorded) { - var me=AtlasMakerWidget; - var l=me.traceLog(replayWSTraffic,0,"#aca");if(l)console.log.apply(undefined,l); - var i; - for(i=0;i
Downloading from source to server..."); - - // Configure MRI into atlasMaker - if(param.info.success===false) { - date=new Date(); - $("#msgLog").append("
ERROR: "+param.info.message+"."); - console.log("
ERROR: "+param.info.message+"."); - return reject(); - } - BrainBox.info=param.info; + configureBrainBox: function configureBrainBox(param) { + var l=BrainBox.traceLog(configureBrainBox);if(l)console.log(l); + + var def=$.Deferred(); + var date=new Date(); + var index=param.annotationItemIndex||0; + + // Copy MRI from source + $("#msgLog").html("
Downloading from source to server..."); - var arr=param.url.split("/"); - var name=arr[arr.length-1]; - date=new Date(); - $("#msgLog").append("
Downloading from server...");
-
- /**
- * @todo Check it these two lines are of any use...
- */
- param.dim=BrainBox.info.dim; // this allows to keep dim and pixdim through annotation changes
- param.pixdim=BrainBox.info.pixdim;
-
- // re-instance stored configuration
- var stored=localStorage.AtlasMaker;
- if(stored) {
- var stored=JSON.parse(stored);
- if(stored.version && stored.version==BrainBox.version) {
- for(var i=0;i ERROR: "+param.info.message+".");
+ return def.promise().reject();
+ }
+ BrainBox.info=param.info;
- // enact configuration in param, eventually overriding the stored one
- if(param.view) {
- AtlasMakerWidget.User.view=param.view;
- AtlasMakerWidget.User.slice=null; // this will set the slider to the middle slice in case no slice were specified
- }
- if(param.slice)
- AtlasMakerWidget.User.slice=param.slice;
+ var arr=param.url.split("/");
+ var name=arr[arr.length-1];
+ date=new Date();
+ $("#msgLog").append(" Downloading from server...");
- if(param.fullscreen)
- AtlasMakerWidget.fullscreen=param.fullscreen;
- else
- AtlasMakerWidget.fullscreen=false;
+ /**
+ * @todo Check it these two lines are of any use...
+ */
+ param.dim=BrainBox.info.dim; // this allows to keep dim and pixdim through annotation changes
+ param.pixdim=BrainBox.info.pixdim;
- AtlasMakerWidget.configureAtlasMaker(BrainBox.info,index)
- .then(function(info2) {
- BrainBox.info = info2;
+ // re-instance stored configuration
+ var stored=localStorage.AtlasMaker;
+ if(stored) {
+ var stored=JSON.parse(stored);
+ if(stored.version && stored.version==BrainBox.version) {
+ for(var i=0;i
- 
- 
- 
- 
- 
+
+
+
+
+
{{{login}}}
diff --git a/views/index.mustache b/views/index.mustache
index 70e40b7e..96548afc 100644
--- a/views/index.mustache
+++ b/views/index.mustache
@@ -15,24 +15,19 @@
-
-
-
-
-
-
-
+
@@ -221,25 +216,25 @@ function goToURL(e) {
* @function testWebSockets
*/
function testWebSockets() {
- return new Promise(function(resolve, reject) {
- var host = "ws://ws.websocketstest.com:8080/service";
- var ws;
-
- if (window.WebSocket) {
- ws=new WebSocket(host);
- } else if (window.MozWebSocket) {
- ws=new MozWebSocket(host);
- } else {
- reject("BrainBox requires access to WebSockets, but this web browser does not support them. Try Firefox, Chrome or Safari.");
- }
- ws.onopen = function(e) {
- ws.close();
- resolve("Connection ok");
- };
- ws.onerror = function(e) {
- reject("BrainBox requires access to WebSockets, but your connection does not allow it. Ask your provider to allow WebSockets on port 8080");
- };
- });
+ var def = $.Deferred();
+ var host = "ws://ws.websocketstest.com:8080/service";
+ var ws;
+
+ if (window.WebSocket) {
+ ws=new WebSocket(host);
+ } else if (window.MozWebSocket) {
+ ws=new MozWebSocket(host);
+ } else {
+ def.reject("BrainBox requires access to WebSockets, but this web browser does not support them. Try Firefox, Chrome or Safari.");
+ }
+ ws.onopen = function(e) {
+ ws.close();
+ def.resolve("Connection ok");
+ };
+ ws.onerror = function(e) {
+ def.reject("BrainBox requires access to WebSockets, but your connection does not allow it. Ask your provider to allow WebSockets on port 8080");
+ };
+ return def;
}
diff --git a/views/mri.mustache b/views/mri.mustache
index c88bcbb5..3270f87d 100644
--- a/views/mri.mustache
+++ b/views/mri.mustache
@@ -24,11 +24,11 @@
-
-
-
-
-
+
-
+
+
+
+
+
+
{{{login}}}
-
-
-
-
-
+
+
+
+
+
{{{login}}}
diff --git a/views/project.mustache b/views/project.mustache
index 71817da2..efa796ab 100644
--- a/views/project.mustache
+++ b/views/project.mustache
@@ -23,12 +23,12 @@
-
- 
-
-
-
-
+
+
+
+
+
+
{{{login}}}
@@ -446,110 +446,112 @@ function appendFilesToProject(list) {
* @desc load a new mri from the project list
*/
function loadProjectFile(index) {
- return new Promise(function(resolve, reject) {
- var url=projectInfo.files.list[index].source;
- var params={url:url,view:"cor",slice:180,fullscreen:false};
- $("#loadingIndicator p").text("Loading...");
- $("#loadingIndicator").show();
-
- /**
- * @todo The mri entry may correspond to a file that has not been downloaded yet!
- */
- var info = projectInfo.files.list[index];
-
- if($.isEmptyObject(info) === false) {
- // check if the mri contains the required annotations
- var irow; // index of the table row
- var iarr; // index of the object in the data array
- for(irow=0;irow", // volume name
- " ", // volume label set
- ""],function(o){return o}).join(),
- objTemplate: [
- { typeOfBinding:1,
- path:"mri.atlas.#.name"
- },
- { typeOfBinding:1,
- path:"mri.atlas.#.labels"
- }
- ]
+ // if it doesn't, create them
+ if(found == false) {
+ // add annotation
+ var date=new Date();
+ // add data to annotations array
+ var atlas = {
+ name: annotations.volume[irow].name,
+ project: projectInfo.shortname,
+ created: date.toJSON(),
+ modified: date.toJSON(),
+ modifiedBy: AtlasMakerWidget.User.username,
+ filename: Math.random().toString(36).slice(2)+".nii.gz", // automatically generated filename
+ labels: annotations.volume[irow].values,
+ owner: AtlasMakerWidget.User.username,
+ type: "volume"
};
-
- // add and bind new table row
- for(irow=0;irow ",
+ " "],function(o){return o}).join(),
+ objTemplate: [
+ { typeOfBinding:1,
+ path:"mri.atlas.#.name"
+ },
+ { typeOfBinding:1,
+ path:"mri.atlas.#.labels"
+ }
+ ]
+ };
+
+ // add and bind new table row
+ for(irow=0;irow", // volume name
+ " ", // volume label set
+ "
-
-
-
-
-
+
+
+
+
+
{{{login}}}
diff --git a/views/projectSettings.mustache b/views/projectSettings.mustache
index 68e5edc2..53114dfe 100644
--- a/views/projectSettings.mustache
+++ b/views/projectSettings.mustache
@@ -24,11 +24,11 @@
-
-
-
-
-
+
+
+
+
+
{{{login}}}
diff --git a/views/user.mustache b/views/user.mustache
index 306c7ecf..6952fbe7 100644
--- a/views/user.mustache
+++ b/views/user.mustache
@@ -7,7 +7,6 @@
-
-
-
-
-
+
+
+
+
+
{{{login}}}