Resolves #103 with integration refactor

Allocate all voxels before integration and garbage once after

applications/reconstruct/include/ftl/voxel_scene.hpp

@@ -49,11 +49,11 @@ class SceneRep : public ftl::Configurable {
 	 * Note: lastRigidTransform appears to be the estimated camera pose.
 	 * Note: bitMask can be nullptr if not streaming out voxels from GPU
 	 */
-	void integrate(const Eigen::Matrix4f& lastRigidTransform, const DepthCameraData& depthCameraData, const DepthCameraParams& depthCameraParams, unsigned int* d_bitMask);
+	//void integrate(const Eigen::Matrix4f& lastRigidTransform, const DepthCameraData& depthCameraData, const DepthCameraParams& depthCameraParams, unsigned int* d_bitMask);
 
 	void setLastRigidTransform(const Eigen::Matrix4f& lastRigidTransform);
 
-	void setLastRigidTransformAndCompactify(const Eigen::Matrix4f& lastRigidTransform, const DepthCameraData& depthCameraData);
+	//void setLastRigidTransformAndCompactify(const Eigen::Matrix4f& lastRigidTransform, const DepthCameraData& depthCameraData);
 
 
 	const Eigen::Matrix4f getLastRigidTransform() const;
@@ -81,9 +81,10 @@ class SceneRep : public ftl::Configurable {
 	void _create(const HashParams& params);
 	void _destroy();
 	void _alloc(const DepthCameraData& depthCameraData, const DepthCameraParams& depthCameraParams, const unsigned int* d_bitMask);
-	void _compactifyHashEntries();
+	void _compactifyVisible();
+	void _compactifyAllocated();
 	void _integrateDepthMap(const DepthCameraData& depthCameraData, const DepthCameraParams& depthCameraParams);
-	void _garbageCollect(const DepthCameraData& depthCameraData);
+	void _garbageCollect();