Continuous time stochastic model for neurite branching (van Elburg 2011)

 Download zip file 
Help downloading and running models
"In this paper we introduce a continuous time stochastic neurite branching model closely related to the discrete time stochastic BES-model. The discrete time BES-model is underlying current attempts to simulate cortical development, but is difficult to analyze. The new continuous time formulation facilitates analytical treatment thus allowing us to examine the structure of the model more closely. ..."
1 . van Elburg R (2011) Stochastic Continuous Time Neurite Branching Models with Tree and Segment Dependent Rates Journal of Theoretical Biology 276(1):159-173 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite;
Brain Region(s)/Organism:
Cell Type(s):
Gap Junctions:
Simulation Environment: C or C++ program; MATLAB;
Model Concept(s): Development;
Implementer(s): van Elburg, Ronald A.J. [R.van.Elburg at];
/* class ObjectHandle: a handle class for mex-functions
 * Notes:
 * 1. If passing an object to the first (pointer) constructor, be sure that
 * the object was allocated on the heap as the ObjectHandle takes ownership
 * of the objects and will eventually delete it. Be sure to not delete any aliases
 * to the passed object.
 * 2. The second (reference) constructor permits static objects to be passed via 
 * ObjectHandles by ensuring the ObjectHandle does not take ownership of
 * the object. 
 * Tim Bailey 2004. Adapted from a design by Mike Stevens.


#include <mex.h>
#include <typeinfo>
#include <list>

template<typename T> class Collector;

template <typename T>
class ObjectHandle {
	// Constructor for free-store allocated objects.
	// Handle takes ownership, and will delete object when it is destroyed.
	ObjectHandle(T*& ptr) : type(&typeid(T)), owns(true), t(ptr) { 
		signature = this; 
		ptr = 0;

	// Constructor for non-owned objects.
	// Object may be heap or statically allocated; the handle does NOT
	// take ownership, and the client is responsible for deleting it.
	ObjectHandle(T& obj) : type(&typeid(T)), owns(false), t(&obj) { 
		signature= this; 

	~ObjectHandle() { 
		if (owns) delete t; // destroy object
		signature= 0; // destroy signature

	// Convert ObjectHandle<T> to a mxArray handle (to pass back from mex-function).
	mxArray* to_mex_handle(); 

	// Convert mxArray (passed to mex-function) to an ObjectHandle<T>.
	static ObjectHandle* from_mex_handle( const mxArray* ma );

	// Get the actual object contained by handle
	T& get_object() const { return *t; }

	ObjectHandle* signature; // use 'this' as a unique object signature 
	const std::type_info* type; // type checking information
	bool owns; // marks whether handle owns pointed-to object
	T *t; // object pointer

	friend class Collector<T>; // allow Collector access to signature

// --------------------------------------------------------- 
// ------------------ Helper functions ---------------------
// --------------------------------------------------------- 
// These functions remove the need to deal with ObjectHandle<T>
// class directly for most common operations.

template <typename T>
mxArray *create_handle(T* t)
// Create mex handle to object t (where t is heap allocated). 
// Client no longer owns t, and so must not delete it.
	ObjectHandle<T>* handle= new ObjectHandle<T>(t);
	return handle->to_mex_handle();

template <typename T>
T& get_object(const mxArray *mxh)
// Obtain object represented by handle.
	ObjectHandle<T>* handle= ObjectHandle<T>::from_mex_handle(mxh);
	return handle->get_object();

template <typename T>
void destroy_object(const mxArray *mxh)
// If deleting object, rather than leaving it to garbage collection,
// must delete it via the handle; do not delete T* directly.
	ObjectHandle<T>* handle= ObjectHandle<T>::from_mex_handle(mxh);
	delete handle;

// --------------------------------------------------------- 
// ------------------ Garbage Collection -------------------
// --------------------------------------------------------- 

// Garbage collection singleton (one collector object for each type T).
// Ensures that registered handles are deleted when the dll is released (they
// may also be deleted previously without problem).
//    The Collector provides protection against resource leaks in the case
// where 'clear all' is called in MatLab. (This is because MatLab will call
// the destructors of statically allocated objects but not free-store allocated
// objects.)
template <typename T>
class Collector {
	std::list<ObjectHandle<T>*> objlist;
	~Collector() {
		typename std::list<ObjectHandle<T>*>::iterator i;
		typename std::list<ObjectHandle<T>*>::iterator end= objlist.end();
		for (i= objlist.begin(); i!=end; ++i) {
			if ((*i)->signature == *i) // check for valid signature
				delete *i;
       mexWarnMsgIdAndTxt("BESTree:ObjectHandle:Collector","Destructor activated");

	static void register_handle (ObjectHandle<T>* obj) {
		static Collector singleton;

private: // prevent construction
	Collector() {}
	Collector(const Collector&);

// --------------------------------------------------------- 
// ---------- Implementation of member functions ----------- 
// --------------------------------------------------------- 

// Import a handle from MatLab as a mxArray of UINT32. Check that
// it is actually a pointer to an ObjectHandle<T>.
template <typename T>
ObjectHandle<T>* ObjectHandle<T>::from_mex_handle(const mxArray* handle) 
	if (mxGetClassID(handle) != mxUINT32_CLASS 
		|| mxIsComplex(handle) || mxGetM(handle)!=1 || mxGetN(handle)!=1)
		mexErrMsgTxt("Parameter is not an ObjectHandle type.");

	// We *assume* we can store ObjectHandle<T> pointer in the mxUINT32 of handle
	ObjectHandle* obj = *reinterpret_cast<ObjectHandle<T>**>(mxGetPr(handle));

	if (!obj) // gross check to see we don't have an invalid pointer
		mexErrMsgTxt("Parameter is NULL. It does not represent an ObjectHandle object.");
// TODO: change this for max-min check for pointer values

	if (obj->signature != obj) // check memory has correct signature
		mexErrMsgTxt("Parameter does not represent an ObjectHandle object.");

	if (*(obj->type) != typeid(T)) { // check type 
		mexPrintf("Given: <%s>, Required: <%s>.\n", obj->type->name(), typeid(T).name());
		mexErrMsgTxt("Given ObjectHandle does not represent the correct type.");

	return obj;

// Create a numeric array as handle for an ObjectHandle.
// We ASSUME we can store object pointer in the mxUINT32 element of mxArray.
template <typename T>
mxArray* ObjectHandle<T>::to_mex_handle() 
	mxArray* handle  = mxCreateNumericMatrix(1, 1, mxUINT32_CLASS, mxREAL);
	*reinterpret_cast<ObjectHandle<T>**>(mxGetPr(handle)) = this;
	return handle;


Loading data, please wait...