gik cell orientation worked out

js/cam/assemblers/Assembler.js

@@ -339,10 +339,10 @@ define(['underscore', 'appState', 'lattice', 'stlLoader', 'threeModel', 'cam', '
             if (totalThreads > 0) return;
             callback();
         }
-        var startingPos = {x:this.components.xAxis.getPosition().x, y:this.components.yAxis.getPosition().y, z:this.components.zAxis.getPosition().z};
+        var startingPos = {x:this.components.yAxis.getPosition().x, y:this.components.xAxis.getPosition().y, z:this.components.zAxis.getPosition().z};
         speed = this._normalizeSpeed(startingPos, position, new THREE.Vector3(speed, speed, speed));
-        this.components.xAxis.moveTo(this._makeAxisVector(position, "x"), speed.x, sketchyCallback);
-        this.components.yAxis.moveTo(this._makeAxisVector(position, "y"), speed.y, sketchyCallback);
+        this.components.yAxis.moveTo(this._makeAxisVector(position, "x"), speed.x, sketchyCallback);
+        this.components.xAxis.moveTo(this._makeAxisVector(position, "y"), speed.y, sketchyCallback);
         this.components.zAxis.moveTo(this._makeAxisVector(position, "z"), speed.z, sketchyCallback);
     };
     

js/highlighter/SuperCellHighlighter.js

@@ -43,7 +43,6 @@ define(['underscore', 'backbone', 'threeModel', 'appState', 'lattice', 'cell', '
                 if (!this.highlightedObject) return;
                 var index = this.highlightedObject.getAbsoluteIndex();
                 if (Math.abs(direction.z) > 0.9) index.z+=1;
-                else if (Math.abs(direction.z) < 0.1) index.z -=1;
                 if (appState._drawingWithCompositeMaterialType()) this.mesh.rotation.set(0,0, lattice._zIndexRotationSuperCell(index));
                 else this.mesh.rotation.set(0,0, lattice._zIndexRotation(index));
             }
@@ -69,7 +68,6 @@ define(['underscore', 'backbone', 'threeModel', 'appState', 'lattice', 'cell', '
             var offset = appState.get("superCellIndex").clone();
             offset.applyQuaternion(this.mesh.quaternion).round();
             newIndex.sub(offset);
-            console.log(newIndex.clone());
             return newIndex;
         }
     });

js/lattice/Lattice.js

@@ -143,7 +143,6 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
             var min = this.get("cellsMin").sub(bounds.min);
             var overlap = false;
             var forCAM = appState.get("currentNav") == "navAssemble";
-            console.log(forCAM);
             this._loopCells(this.sparseCells, function(cell){
                 if (!cell) return;
                 overlap |= cell.addToDenseArray(cells, min, forCAM);

js/lattice/LatticeBase.js

@@ -205,7 +205,7 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
                 if (cell){
                     var material = cell.getMaterial();
                     var dimensions = material.dimensions;
-                    if (dimensions) dimensions.clone();
+                    if (dimensions) dimensions = dimensions.clone();
                     else dimensions = new THREE.Vector3(cell.length, 1, 1);
                     dimensions.sub(new THREE.Vector3(1,1,1));
                     var subCellRange = (new THREE.Vector3(x, y, z)).add(cell.applyRotation(dimensions).round().add(new THREE.Vector3(1,1,1)));

js/lattice/latticeSubclasses/GIKLattice.js

@@ -49,7 +49,7 @@ define(['underscore', 'backbone', 'appState', 'globals', 'plist', 'three', 'thre
         },
 
         _zIndexRotationSuperCell: function(index){
-            if (index.z%2 != 0) return Math.PI/2;//this never changes
+            if (index.z%2 != 0) return -Math.PI/2;//this never changes
             return 0;
         },