Threejs merge with multiple materials applies only one material - three.js

Question

I have searched on this and found several examples on stackoverflow, but the answers have not solved my problem.
What I have tried:
First I create the geometry bucket to be used for the group and an array to store my materials.
var totalGeom = new THREE.Geometry();
var materials = [];
I then run through my data (strData) with a for loop and call addMapMarker3d.
for(var i=0; i<strData.length;i++){
addMapMarker3d([strData[i].lat,strData[i].lon], strData[i].time, measureColors[i]);
}
The addMapMarker3d function is as follows:
addMapMarker3d = function(latLng, height, color){
var max = 600;
var dist = 25;
var opacity = (height/max);
var geometry = new THREE.BoxGeometry( Math.floor(dist), height, Math.floor(dist));
//create the material and add it to the materials array
var material = new THREE.MeshBasicMaterial({ transparent:true, color: Number(color), opacity:opacity});
this.materials.push(material);
//create a mesh from the geometry and material.
var cube = new THREE.Mesh( geometry, material);
//leaf is a simple lat/lng to pixel position converter
var actualMarkerPos = leaf.getPoint(latLng);
//apply the position on a 5000x5000 cartesian plane
var extent = 5000;
cube.position.setZ((actualMarkerPos[1] * extent) - extent/2);
cube.position.setX(-((actualMarkerPos[0] * extent) - extent/2));
cube.position.setY(height/2);
//update the matrix and add the cube to the totalGeom bucket
cube.updateMatrix();
totalGeom.merge( cube.geometry, cube.matrix);
}
After the for loop runs and all the cubes are created:
var mats = new THREE.MeshFaceMaterial(materials)
var total = new THREE.Mesh(totalGeom, mats);
world.scene.add(total);
The question
While the geometry merge functions, and my view port is running at a much improved FPS, all the cubes have exactly the same color and opacity. It appears the merge is using a single material of the 10k I supplied. Is there some way to ensure that the geometry uses the material supplied in the array? Am I doing something incorrect?
If I try this in addMapMarker3d:
totalGeom.merge( cube.geometry, cube.matrix, materials.length-1);
I get "Uncaught TypeError: Cannot read property 'transparent' of undefined" and nothing renders, which I don't understand, because by the examples, each geometry should index to a material in the materials array.
three.js r.70

Answer 1

The following technique uses just one material, but allows you to retain the individual color of each merged object. I don't know if it's possible to retain the individual alpha of each merged object.
http://jsfiddle.net/looshi/nsknn53p/61/
For each mesh, set each of its geometry.faces color :
function makeCube(size, color) {
var geom = new THREE.BoxGeometry(size, size, size);
for (var i = 0; i < geom.faces.length; i++) {
face = geom.faces[i];
face.color.setHex(color);
}
var cube = new THREE.Mesh(geom);
return cube;
}
Then, in the parent geometry you are going to mesh into, set its material vertexColors property.
var parentGeometry = new THREE.Geometry();
var parentMatrial = new THREE.MeshLambertMaterial({
color: 0xffffff,
shading: THREE.SmoothShading,
vertexColors: THREE.VertexColors
});
// in a loop you could create many objects and merge them
for (var i = 0; i < 1000; i++) {
cube = makeCube(size, color);
cube.position.set(x, y, z);
cube.rotation.set(rotation,rotation,rotation);
cube.updateMatrix()
parentGeometry.merge(cube.geometry, cube.matrix);
}
// after you're done creating objects and merging them, add the parent to the scene
parentMesh = new THREE.Mesh(parentGeometry, parentMatrial);
scene.add(parentMesh);

Answer 2

My original question was not answered: Is there some way to ensure that the geometry uses the material supplied in the array?
The answer is yes. Multiple materials can be applied to a single mesh during merge. After pushing the material to the materials array, the merge will utilize the geometry face material index. The merge will apply multiple materials when an array is supplied to new THREE.MeshFaceMaterial([materialsArray]) as the total mesh is created. This solves the mystery of the syntax. Just because you supply an array of materials does not mean that the merge will use each material in an iterative fashion as the objects are merged as of r71. The faces must inform the merge which material in the material array to use.
I am using this for a non rendered scene, and the final obj is exported. If you need render performance, see one of the other answers for some options.
A simple for loop on the face array on the geometry informs the merge which material to apply:
addMapMarker3d = function(latLng, height, color){
var max = 600;
var dist = 25;
var opacity = (height/max);
var geometry = new THREE.BoxGeometry( Math.floor(dist), height, Math.floor(dist));
//create the material and add it to the materials array
var material = new THREE.MeshBasicMaterial({ transparent:true, color: Number(color), opacity:opacity});
this.materials.push(material);
//set the material index of each face so a merge knows which material to apply
for ( var i = 0; i < geometry.faces.length; i ++ ) {
geometry.faces[i].materialIndex = this.materials.length-1;
}
//create a mesh from the geometry and material.
var cube = new THREE.Mesh( geometry, material);
//leaf is a simple lat/lng to pixel position converter
var actualMarkerPos = leaf.getPoint(latLng);
//apply the position on a 5000x5000 cartesian plane
var extent = 5000;
cube.position.setZ((actualMarkerPos[1] * extent) - extent/2);
cube.position.setX(-((actualMarkerPos[0] * extent) - extent/2));
cube.position.setY(height/2);
//update the matrix and add the cube to the totalGeom bucket
cube.updateMatrix();
totalGeom.merge( cube.geometry, cube.matrix);
}

Answer 3

The only reason you are seeing improved performance is because, after the merge, there is only one material. If you want your scene to have multiple materials you should not merge.
Adding to the same group:
var group = new THREE.Object3D();
group.add (object1);
group.add (object2);
group.add (object3);