Core classes

class `Branch`

class Branch
  : public neurostr::WithProperties

Summary

Members	Descriptions
`public Branch()`	Default constructor.
`public Branch(const id_type & id,int order)`	Creates a branch with given id and order.
`public Branch(const id_type & id,int order,constNode& root)`	Creates a branch with given id,order and root.
`public Branch(const id_type & id,int order,constNode& root,const std::vector<Node> & nodes)`	Creates a branch with given id,order, root and nodes.
`public template<typename Iter>` `inline Branch(const id_type & id,int order,constNode& root,const Iter & b,const Iter & e)`	Creates a branch with given id,order, root and nodes.
`public inline ~Branch()`	Empty destructor.
`public Branch(constBranch& b) = delete`	Copy constructor is not allowed.
`publicBranch& operator=(constBranch& b) = delete`	Copy assign is not allowed.
`public Branch(Branch&& b) = default`	Default move constructor.
`publicBranch& operator=(Branch&& b) = default`	Defaul move assign.
`public inline int order() const`	Centrifugal order accessor.
`public inline const id_type & id() const`	ID accessor.
`public std::string idString() const`	Returns Branch ID as a string.
`public inline bool valid_neurite() const`	Branch neurite reference validity check.
`public constNeurite& neurite() const`	Branch parent neurite.
`publicNeurite& neurite()`	Branch parent neurite.
`publicBranch& id(const id_type & id)`	Set branch id.
`publicBranch& order(int o)`	Set branch centrifugal order.
`publicBranch& neurite(Neurite* n)`	Set branch parent neurite.
`public inline void root(constNode& n)`	Copy a node as new root.
`public inline void remove_root()`	Removes the current root.
`public inline void root(Node&& n)`	Move a node as new root.
`public inline bool operator==(constBranch& b) const`	Compares two branches by their ID.
`public inline bool operator!=(constBranch& b) const`	Compares two branches by their ID.
`public inline size_type size() const`	Number of nodes in the b.
`public inline bool has_root() const`	Branch root validity check.
`public constNode& root() const`	Get root node reference.
`publicNode& root()`	Get root node reference.
`public constNode& first() const`	Returns branch first node.
`public constNode& last() const`	Returns branch last node.
`publicNode& first()`	Returns branch first node.
`publicNode& last()`	Returns branch last node.
`public point_type director_vector() const`	Returns vector from the first node of the branch to the last.
`public template<typename T>` `inline auto add_property(const std::string & key,T value,bool recursive)`	Adds a property to the branch and optionally to its nodes.
`public inline auto add_property(const std::string & key,bool recursive)`	Adds an empty property to the branch and optionally to its nodes.
`public inline iterator begin()`	Begin node iterator (indirect iterator)
`public inline iterator end()`	End node iterator (indirect iterator)
`public inline reverse_iterator rbegin()`	Reverse begin node iterator (indirect iterator)
`public inline reverse_iterator rend()`	Reverse end node iterator (indirect iterator)
`public inline const_iterator begin() const`	Begin node iterator (indirect iterator)
`public inline const_iterator end() const`	End node iterator (indirect iterator)
`public inline const_reverse_iterator rbegin() const`	Reverse begin node iterator (indirect iterator)
`public inline const_reverse_iterator rend() const`	Reverse end node iterator (indirect iterator)
`public inline const_iterator cbegin() const`	Begin const node iterator (indirect iterator)
`public inline const_iterator cend() const`	End const node iterator (indirect iterator)
`public void push_back(constNode& n)`	Copy a node to the end of the branch.
`public void push_back(Node&& n)`	Move a node to the end of the branch.
`public iterator insert(iterator pos,constNode& n)`	Copies the given node at the position.
`public template<typename Iter>` `inline void insert(iterator pos,Iter b,Iter e)`	Copies a range of nodes into the branch.
`public iterator erase(const iterator & pos)`	Deletes a node in the branch.
`public iterator erase(const iterator & first,const iterator & last)`	Deletes a range of nodes in the branch.
`public inline void clear()`	Deletes all nodes in the brnach.
`publicBranchsplit(const iterator & pos)`	Divides the branch at given position and creates a new branch.
`public void simplify(float eps)`	Applies RDF simplification to the branch nodes.
`public void scale(float r)`	Scales the branch wrt root by r (>1 bigger, <1 smaller)
`public void normalize()`	Scales the branch so its length is equal to 1.
`public void scale(float rx,float ry,float rz)`	Scales branch (including root)
`public float length() const`	Computes branch path length.
`public void traslate(const point_type & p)`	Moves the branch (root included) by the vector p.
`public void rotate(const Eigen::Quaternionf & q)`	Rotates the branch (Root included) aplying the quaternion q.
`public void remove_null_segments()`	Removes zero-length segments in the branch.
`public float discrete_frechet(constBranch& other) const`	Computes the frechet distance between two branche s.
`public float distance(constBranch& other,bool ignore_radius) const`	Computes the distance between both branches.
`public void set_nodes_branch()`	Updates branch memeber in all nodes.
`public box_type boundingBox() const`	Gets bounding box.

Members

`public Branch()`

Default constructor.

creates a branch with order -1 and empty id

Returns

Branch

`public Branch(const id_type & id,int order)`

Creates a branch with given id and order.

Parameters

id Branch id
order Branch order

Returns

Branch

`public Branch(const id_type & id,int order,constNode& root)`

Creates a branch with given id,order and root.

Parameters

id Branch id
order Centrifugal order
root Branch root node

Returns

Branch

`public Branch(const id_type & id,int order,constNode& root,const std::vector<Node> & nodes)`

Creates a branch with given id,order, root and nodes.

Parameters

id Branch id
order Centrifugal order
root Branch root node
nodes Branch nodes

Returns

Branch

`public template<typename Iter>`
`inline Branch(const id_type & id,int order,constNode& root,const Iter & b,const Iter & e)`

Creates a branch with given id,order, root and nodes.

Parameters

id Branch id
order Centrifugal order
root Branch root node
b Node begin iterator
e Node end iterator

Returns

Branch

`public inline ~Branch()`

Empty destructor.

`public Branch(constBranch& b) = delete`

Copy not allowed.

DELETED

`publicBranch& operator=(constBranch& b) = delete`

Copy not allowed.

DELETED

`public Branch(Branch&& b) = default`

Default move constructor.

`publicBranch& operator=(Branch&& b) = default`

Defaul move assign.

`public inline int order() const`

Centrifugal order accessor.

Returns

Centrifugal order

`public inline const id_type & id() const`

Returns the Branch ID as a vector of integers.

Returns

Branch Id

`public std::string idString() const`

Returns Branch ID as a string.

Returns

ID as string

`public inline bool valid_neurite() const`

Branch neurite reference validity check.

Returns

True if the Neurite reference is valid

`public constNeurite& neurite() const`

Branch parent neurite.

Returns

Parent Neurite reference

`publicNeurite& neurite()`

Branch parent neurite.

Returns

Parent neurite reference

`publicBranch& id(const id_type & id)`

Set branch id.

Parameters

id new id

Returns

Updated branch reference

`publicBranch& order(int o)`

Set branch centrifugal order.

Parameters

o new centrifugal order

Returns

Update branch reference

`publicBranch& neurite(Neurite* n)`

Set branch parent neurite.

Parameters

n Neurite pointer

Returns

Update branch reference

`public inline void root(constNode& n)`

Copy a node as new root.

Parameters

n node to copy

`public inline void remove_root()`

Removes the current root.

`public inline void root(Node&& n)`

Move a node as new root.

Parameters

n node to move

`public inline bool operator==(constBranch& b) const`

Compares two branches by their ID.

Parameters

b Branch

Returns

True if two ids are equal

`public inline bool operator!=(constBranch& b) const`

Compares two branches by their ID.

Parameters

b Branch

Returns

True if two ids are NOT equal

`public inline size_type size() const`

Number of nodes in the b.

Returns

Branch size

`public inline bool has_root() const`

Branch root validity check.

Returns

True/False

`public constNode& root() const`

Get root node reference.

Throws

runtime_error Attempt to access nullptr reference

Returns

Root node reference

`publicNode& root()`

Get root node reference.

Throws

runtime_error Attempt to access nullptr reference

Returns

Root node reference

`public constNode& first() const`

Returns branch first node.

Throws

runtime_error Attempt to access empty branch

Returns

Node reference

`public constNode& last() const`

Returns branch last node.

Throws

runtime_error Attempt to access empty branch

Returns

Node reference

`publicNode& first()`

Returns branch first node.

Throws

runtime_error Attempt to access empty branch

Returns

Node reference

`publicNode& last()`

Returns branch last node.

Throws

runtime_error Attempt to access empty branch

Returns

Node reference

`public point_type director_vector() const`

Returns vector from the first node of the branch to the last.

Returns

Vector

`public template<typename T>`
`inline auto add_property(const std::string & key,T value,bool recursive)`

Adds a property to the branch and optionally to its nodes.

Parameters

key Property name
value Property value
recursive If true, property is also added to branch nodes

Returns

Iterator to added property

`public inline auto add_property(const std::string & key,bool recursive)`

Adds an empty property to the branch and optionally to its nodes.

Parameters

key Property name
recursive If true, property is also added to branch nodes

Returns

Iterator to added property

`public inline iterator begin()`

Begin node iterator (indirect iterator)

Returns

Indirect iterator

`public inline iterator end()`

End node iterator (indirect iterator)

Returns

Indirect iterator

`public inline reverse_iterator rbegin()`

Reverse begin node iterator (indirect iterator)

Returns

Indirect iterator

`public inline reverse_iterator rend()`

Reverse end node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_iterator begin() const`

Begin node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_iterator end() const`

End node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_reverse_iterator rbegin() const`

Reverse begin node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_reverse_iterator rend() const`

Reverse end node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_iterator cbegin() const`

Begin const node iterator (indirect iterator)

Returns

Indirect iterator

`public inline const_iterator cend() const`

End const node iterator (indirect iterator)

Returns

Indirect iterator

`public void push_back(constNode& n)`

Copy a node to the end of the branch.

Parameters

n Node to copy

`public void push_back(Node&& n)`

Move a node to the end of the branch.

Parameters

n Node to move

`public iterator insert(iterator pos,constNode& n)`

Copies the given node at the position.

Parameters

pos Position to insert
n Node

Returns

Updated iterator

`public template<typename Iter>`
`inline void insert(iterator pos,Iter b,Iter e)`

Copies a range of nodes into the branch.

Parameters

pos Insert position
b Range begin iterator
e Range end iterator

`public iterator erase(const iterator & pos)`

Deletes a node in the branch.

Parameters

pos Position to delete

Returns

Updated iterator

`public iterator erase(const iterator & first,const iterator & last)`

Deletes a range of nodes in the branch.

Parameters

first first position to delete
last last position to delete

Returns

Updated iterator

`public inline void clear()`

Deletes all nodes in the branch.

`publicBranchsplit(const iterator & pos)`

Divides the branch at given position and creates a new branch.

Parameters

pos Split position

Returns

Split branch

`public void simplify(float eps)`

Applies RDF simplification to the branch nodes.

Root and last are always keeped

Parameters

eps RDF algorithm epsilon parameter (tolerance). If eps is <0 is used as a relative tolerance to the node radius

`public void scale(float r)`

Scales the branch wrt root by r (>1 bigger, <1 smaller)

Parameters

r Scale rate

`public void normalize()`

Scales the branch so its length is equal to 1.

`public void scale(float rx,float ry,float rz)`

Scales branch (including root)

Parameters

rx x-axis scale
ry y-axis scale
rz z-axis scale

`public float length() const`

Computes branch path length.

Returns

branch length

`public void traslate(const point_type & p)`

Moves the branch (root included) by the vector p.

Parameters

p Translation vector

`public void rotate(const Eigen::Quaternionf & q)`

Rotates the branch (Root included) aplying the quaternion q.

Parameters

q rotation quaternion

`public void remove_null_segments()`

Removes zero-length segments in the branch.

`public float discrete_frechet(constBranch& other) const`

Computes the Discrete Frechet distance between two branches.

Parameters

other Branch

Returns

Discrete frechet distance

`public float distance(constBranch& other,bool ignore_radius) const`

Computes the distance between both branches.

Ignores nodes shared by both branches

Parameters

other

Returns

euclidean distance

`public void set_nodes_branch()`

Updates branch memeber in all nodes.

`public box_type boundingBox() const`

Gets bounding box.

class `Neurite`

class Neurite
  : public neurostr::WithProperties

Summary

Members	Descriptions
`classconst_node_iterator`
`classnode_iterator`
`classstem_iterator`
`public Neurite()`	Empty neurite constructor.
`public Neurite(int id)`	Create a neurite with given id and type undefined.
`public Neurite(int id,constNeuriteType& t)`	Create a neurite with given id and type.
`public Neurite(constNeurite& n) = default`	Default copy constructor.
`public Neurite(Neurite&& n) = default`	Default move constructor.
`publicNeurite& operator=(constNeurite& n) = default`	Default copy assign.
`publicNeurite& operator=(Neurite&& n) = default`	Default move assign.
`public inline ~Neurite()`	Empty destructor (Default)
`public inline bool operator==(constNeurite& n) const`	Compares two neurites by ID.
`public inline bool operator!=(constNeurite& n) const`	Compares two neurites by ID.
`public inline constNeuriteType& type() const`	Return neurite type.
`public inline const int id() const`	Returns neurite id.
`public inline bool root_is_soma() const`	Checks if root is soma.
`public inlineNeuron& neuron() const`	Return neurite parent neuron reference.
`public inline void type(constNeuriteType& t)`	Set neurite type.
`public inline void id(int id)`	Set neurite ID.
`public inline void neuron(Neuron*const n)`	Set neurite parent neuron pointer.
`public inline bool has_root() const`	Checks if the root branch of the neurite has root.
`public inline constNode& root() const`	Get root reference.
`public void set_root()`	Sets an empt branch as the root branch without root node.
`public void set_root(constNode& node)`	Creates an empty branch with node as root as root branch.
`public int max_centrifugal_order() const`	Get neurite max c.order.
`public inline int size() const`	Neurite size (branch count)
`public int node_count() const`	Neurite node count.
`public template<typename T>` `inline auto add_property(const std::string & key,T v,bool recursive)`	Adds a property to the neurite and optionally to its branches.
`public inline auto add_property(const std::string & key,bool recursive)`	Adds an empty property to the neurite and optionally to its branches.
`public inline branch_iterator begin_branch() const`	Begin DFS branch iterator.
`public inline branch_iterator end_branch() const`	End DFS branch iterator.
`public inline branch_iterator begin_branch_subtree(const typename tree_type::iterator_base & other) const`	Creates a branch DFS iterator over the subtree of the branch pointed by €{other}.
`public branch_iterator end_branch_subtree(const typename tree_type::iterator_base & other) const`	Creates a branch DFS iterator over the subtree of the branch pointed by €{other}.

Members

`public Neurite()`

Empty neurite constructor.

Id -1 and type undefined

Returns

Neurite

`public Neurite(int id)`

Create a neurite with given id and type undefined.

Parameters

id Neurite id

Returns

Neurite

`public Neurite(int id,constNeuriteType& t)`

Create a neurite with given id and type.

Parameters

id Neurite id
t Neurite type

Returns

Neurite

`public Neurite(constNeurite& n) = default`

Default copy constructor.

`public Neurite(Neurite&& n) = default`

Default move constructor.

`publicNeurite& operator=(constNeurite& n) = default`

Default copy assign.

`publicNeurite& operator=(Neurite&& n) = default`

Default move assign.

`public inline ~Neurite()`

Empty destructor (Default)

`public inline bool operator==(constNeurite& n) const`

Compares two neurites by ID.

Parameters

n Other neurite

Returns

True if ids match

`public inline bool operator!=(constNeurite& n) const`

Compares two neurites by ID.

Parameters

n Other neurite

Returns

True if ids dont match

`public inline constNeuriteType& type() const`

Return neurite type.

Returns

NeuriteType

`public inline const int id() const`

Returns neurite id.

Returns

Neurite ID

`public inline bool root_is_soma() const`

Checks if root is soma.

Returns

True if neurite root is soma

`public inlineNeuron& neuron() const`

Return neurite parent neuron reference.

Returns

Neuron reference

`public inline void type(constNeuriteType& t)`

Set neurite type.

Parameters

t New neurite type

`public inline void id(int id)`

Set neurite ID.

Parameters

id New neurite ID

`public inline void neuron(Neuron*const n)`

Set neurite parent neuron pointer.

Parameters

n Nueron pointer

`public inline bool has_root() const`

Checks if the root branch of the neurite has root.

Returns

True if the neurite is rooted (i.e. attached to soma)

`public inline constNode& root() const`

Get root reference.

Returns

Root reference

`public void set_root()`

Sets an empt branch as the root branch without root node.

`public void set_root(constNode& node)`

Creates an empty branch with node as root as root branch.

Parameters

node Root node

`public int max_centrifugal_order() const`

Get neurite max c.order.

Returns

Centrifugal order

`public inline int size() const`

Neurite size (branch count)

Returns

Number of branches in the neurite

`public int node_count() const`

Neurite node count.

Returns

Number of distinct node ins the neurite (roots excluded)

`public template<typename T>`
`inline auto add_property(const std::string & key,T v,bool recursive)`

Adds a property to the neurite and optionally to its branches.

Parameters

key Property key
v Property value
recursive If true, property is also added to braches and nodes

`public inline auto add_property(const std::string & key,bool recursive)`

Adds an empty property to the neurite and optionally to its branches.

Parameters

key Property key
recursive If true, property is also added to braches and nodes

`public inline branch_iterator begin_branch() const`

Begin DFS branch iterator.

Returns

branch_iterator

`public inline branch_iterator end_branch() const`

End DFS branch iterator.

Returns

branch_iterator

`public inline branch_iterator begin_branch_subtree(const typename tree_type::iterator_base & other) const`

Creates a branch DFS iterator over the subtree of the branch pointed by €{other}.

Parameters

other Branch iterator

Returns

DFS branch iterator

`public branch_iterator end_branch_subtree(const typename tree_type::iterator_base & other) const`

Creates a branch DFS iterator over the subtree of the branch pointed by €{other}.

Parameters

other Branch iterator

Returns

DFS branch iterator

class `node_iterator`

class node_iterator
  : public boost::iterator_facade< node_iterator< iter >, Node, std::iterator_traits< iter >::iterator_category >

Template iterator that references directly to the nodes in the tree. The template parameter Iter, a branch iterator, determines tree-visitor strategy.

Summary

Members	Descriptions
`public node_iterator()`	Empty constructor.
`public node_iterator(const iter & b,const iter & e)`	Creates a node iterator that starts at the first node of b and ends at the first node of e.
`public node_iterator(const iter & b,const iter & e,const iter & c)`	Creates a node iterator that starts at the first node of b and ends at the first node of e.
`public node_iterator(const iter & b,const iter & e,const iter & c,const typename Branch::iterator & nodeit)`	Creates a node iterator that starts at the first node of b and ends at the first node of e.
`public node_iterator(constnode_iterator< iter > &) = default`	Default copy constructor.
`publicnode_iterator& operator=(constnode_iterator< iter > &) = default`	Default copy assign.
`public node_iterator(node_iterator< iter > &&) = default`	Default move constructor.
`publicnode_iterator& operator=(node_iterator< iter > &&) = default`	Default move assign.
`public iter begin() const`	Get iterator first branch.
`public iter end() const`	Get iterator last branch.
`public iter current() const`	Get iterator current branch.
`public iter branch() const`	Get iterator current branch.
`public Branch::iterator node() const`	Get iterator current noe.
`publicNeurite& neurite() const`	Get current branch neurite.
`publicNeuron& neuron() const`	Get current branch neuron.
`publicnode_iterator< iter > last() const`	Get an iterator to the end node.
`publicnode_iterator< iter > first() const`	Get an iterator to the first node.

Members

`public node_iterator()`

Empty constructor.

Returns

Node iterator

`public node_iterator(const iter & b,const iter & e)`

Creates a node iterator that starts at the first node of b and ends at the first node of e.

Parameters

b First branch
e Last branch

Returns

Node iterator

`public node_iterator(const iter & b,const iter & e,const iter & c)`

Creates a node iterator that starts at the first node of b and ends at the first node of e.

Current node is the first node of c.

Parameters

b First branch
e Last branch
c Current branch

Returns

Node iterator

`public node_iterator(const iter & b,const iter & e,const iter & c,const typename Branch::iterator & nodeit)`

Creates a node iterator that starts at the first node of b and ends at the first node of e.

Current node is the nodeit node of c.

Parameters

b First branch
e Last branch
c Current branch
nodeit Current node

Returns

Node iterator

`public node_iterator(constnode_iterator< iter > &) = default`

Default copy constructor.

`publicnode_iterator& operator=(constnode_iterator< iter > &) = default`

Default copy assign.

`public node_iterator(node_iterator< iter > &&) = default`

Default move constructor.

`publicnode_iterator& operator=(node_iterator< iter > &&) = default`

Default move assign.

`public iter begin() const`

Get iterator first branch.

Returns

First branch

`public iter end() const`

Get iterator last branch.

Returns

Last branch

`public iter current() const`

Get iterator current branch.

Returns

Current branch

`public iter branch() const`

Get iterator current branch.

Returns

Current branch

`public Branch::iterator node() const`

Get iterator current noe.

Returns

Current node

`publicNeurite& neurite() const`

Get current branch neurite.

Returns

Neurite reference

`publicNeuron& neuron() const`

Get current branch neuron.

Returns

Neuron reference

`publicnode_iterator< iter > last() const`

Get an iterator to the end node.

Returns

End node iterator

`publicnode_iterator< iter > first() const`

Get an iterator to the first node.

Returns

First node iterator

class `stem_iterator`

class stem_iterator
  : public iterator_base

Tree iterator (Actually a forward iterator) that ascends from the given tree node to the root.

Summary

Members	Descriptions
`public stem_iterator()`	Empty constructor.
`public stem_iterator(tree_node * tn)`	Creates an stem iterator that points to tn.
`public stem_iterator(const typename tree_type::iterator_base & other)`	Copies the given iterator as stem iterator.
`public bool operator==(conststem_iterator& other) const`	Equality operator (compares two iterators)
`public bool operator!=(conststem_iterator& other) const`	Inequality operator (compares two iterators)
`publicstem_iterator& operator++()`	Stem iterator single step - ascend one branch.
`publicstem_iteratoroperator++(int)`	Stem iterator single step - ascend one branch.
`publicstem_iterator& operator+=(unsigned int num)`	Stem iterator multi step - ascend num branches.

Members

`public stem_iterator()`

Empty constructor.

Returns

Default iterator (actually, useless)

`public stem_iterator(tree_node * tn)`

Creates an stem iterator that points to tn.

Parameters

tn Tree node pointer

Returns

Stem iterator

`public stem_iterator(const typename tree_type::iterator_base & other)`

Copies the given iterator as stem iterator.

Parameters

other Iterator

Returns

Copied stem iterator

`public bool operator==(conststem_iterator& other) const`

Equality operator (compares two iterators)

Parameters

other The other stem iterator

Returns

True if they both point to the same node

`public bool operator!=(conststem_iterator& other) const`

Inequality operator (compares two iterators)

Parameters

other The other stem iterator

Returns

True if they both dont point to the same node

`publicstem_iterator& operator++()`

Stem iterator single step - ascend one branch.

Returns

Updated iterator

`publicstem_iteratoroperator++(int)`

Stem iterator single step - ascend one branch.

Returns

new updated iterator

`publicstem_iterator& operator+=(unsigned int num)`

Stem iterator multi step - ascend num branches.

Returns

Updated iterator

class `Contour`

Summary

Members	Descriptions
`public Contour()`	Contour empty constructor.
`public Contour(const std::vector< point_type > & v)`	Creates a contour from a point vector.
`public Contour(constContour&) = default`	Copy constructor.
`publicContour& operator=(constContour&) = default`	Copy assign.
`public Contour(Contour&&) = default`	Move constructor.
`publicContour& operator=(Contour&&) = default`	Move assign.
`public iterator begin()`	Returns an iterator to the first point in the contour.
`public const_iterator begin() const`	Returns an iterator to the first point in the contour.
`public iterator end()`	Returns an iterator to the next position after the last point in the contour.
`public const_iterator end() const`	Returns an iterator to the next position after the last point in the contour.
`public std::size_t size() const`	Contour size.
`public float length() const`	Computes the length of the contour.
`public float area(int component) const`	Contour planar area as 2D projection in the given component.
`public const std::string & name() const`	Returns contour name.
`public void name(const std::string & n)`	Set contour name.
`public const std::string & face_color() const`	Returns contour face color.
`public const std::string & back_color() const`	Returns contour back color.
`public void face_color(const std::string & s)`	Set contour face color.
`public void back_color(const std::string & s)`	Set contour back color.
`public float fill_density() const`	Return contour fill density (alpha channel)
`public void fill_density(float f)`	Set fill density value.
`public float resolution() const`	Contour resolution (im not sure what this actually is..like a ratio?)
`public void resolution(float f)`	Set resolution value.
`public bool is_closed() const`	True if the contour is defined as closed.
`public void properties_from_map(constPropertyMap& p)`	Set all contour properties getting them from a p.
`public float closing_gap() const`	Distance between the last and the first point in the contour.
`public void close()`	Mark the contour as closed (add a segment bw the last and the first)
`public int planar_axis() const`	Cehcks if the contour is planar for some axis.
`public std::pair< float, float > range(int component) const`	Computes min and max values for the given component (0,1,2 x,y,z)
`public std::vector<geometry::planar_point> planar_projection(int component) const`	Returns the contour points removing the ith component.
`public bool clockwise_oriented(int i) const`	Checks if the contour points are clockwise ordered (shoelace formula applied)
`public void reverse()`	Reverses the contour point order.
`public void rotate(iterator new_first)`	Rotates the contour (if it is closed) so the point pointed by new_first becomes the new first point.
`public point_type barycenter() const`	Computes contour barycenter.

Members

`public Contour()`

Contour empty constructor.

Initializes all members to its default value and leaves the contour as empty

`public Contour(const std::vector< point_type > & v)`

Creates a contour from a point vector.

Parameters

v Contour point vector

`public Contour(constContour&) = default`

Copy constructor.

`publicContour& operator=(constContour&) = default`

Copy assign.

`public Contour(Contour&&) = default`

Move constructor.

`publicContour& operator=(Contour&&) = default`

Move assign.

`public iterator begin()`

Returns an iterator to the first point in the contour.

Returns

point iterator

`public const_iterator begin() const`

Returns an iterator to the first point in the contour.

Returns

const point iterator

`public iterator end()`

Returns an iterator to the next position after the last point in the contour.

Returns

point iterator

`public const_iterator end() const`

Returns an iterator to the next position after the last point in the contour.

Returns

const point iterator

`public std::size_t size() const`

Contour size.

Returns

number of points that describe the contour

`public float length() const`

Computes the length of the contour.

Returns

Contour length

`public float area(int component) const`

Contour planar area as 2D projection in the given component.

Parameters

component Component that is ignored to compute the area

Returns

Contour planar area

`public const std::string & name() const`

Returns contour name.

Returns

Contour name as string

`public void name(const std::string & n)`

Set contour name.

Parameters

n The new contour name

`public const std::string & face_color() const`

Returns contour face color.

Returns

Color as hex string #RRGGBB

`public const std::string & back_color() const`

Returns contour back color.

Returns

Color as hex string #RRGGBB

`public void face_color(const std::string & s)`

Set contour face color.

Parameters

s Hex-string color. e.g. #FFFFFF

`public void back_color(const std::string & s)`

Set contour back color.

Parameters

s Hex-string color. e.g. #FFFFFF

`public float fill_density() const`

Return contour fill density (alpha channel)

Returns

Alpha (opacity) value

`public void fill_density(float f)`

Set fill density value.

Parameters

f Contour fill opacity. Between 0 and 1.

`public float resolution() const`

Contour resolution (im not sure what this actually is..like a ratio?)

Returns

Resolution as float

`public void resolution(float f)`

Set resolution value.

Parameters

f resolution value. Actual meaning is unknown.

`public bool is_closed() const`

True if the contour is defined as closed.

Returns

boolean flag

`public void properties_from_map(constPropertyMap& p)`

Set all contour properties getting them from a p.

map

Parameters

p input Property map

`public float closing_gap() const`

Distance between the last and the first point in the contour.

Returns

Closing gap distance

`public void close()`

Mark the contour as closed (add a segment bw the last and the first)

`public int planar_axis() const`

Cehcks if the contour is planar for some axis.

Returns

-1 is not planar, 0,1,2 x,y,z are constant respectively

`public std::pair< float, float > range(int component) const`

Computes min and max values for the given component (0,1,2 x,y,z)

Parameters

component Contour component index (0,1,2 <-> x,y,z)

Returns

Pair (min,max)

`public std::vector<geometry::planar_point> planar_projection(int component) const`

Returns the contour points removing the ith component.

Parameters

component Index of component to remove

Returns

Planar points

`public bool clockwise_oriented(int i) const`

Checks if the contour points are clockwise ordered (shoelace formula applied)

Parameters

i component index (0,1,2 <-> x,y,z) that is ignored to compute the orientation

Returns

True if clockwise ordered

`public void reverse()`

Reverses the contour point order.

`public void rotate(iterator new_first)`

Rotates the contour (if it is closed) so the point pointed by new_first becomes the new first point.

Parameters

new_first Point to become the first point

`public point_type barycenter() const`

Computes contour barycenter.

Returns

Barycenter

class `Neuron`

class Neuron
  : public neurostr::WithProperties

Summary

Members	Descriptions
`public Neuron()`	Empty constructor.
`public Neuron(const std::string & id)`	Create a neuron with given id, and no neurites nor soma.
`public Neuron(const std::string & id,const std::vector<Node> & soma)`	Creates a neuron with given id and soma nodes.
`public inline ~Neuron()`	Default destructor.
`public Neuron(constNeuron&) = delete`	Deleted.
`publicNeuron& operator=(constNeuron&) = delete`	Deleted.
`public Neuron(Neuron&&) = default`	Default implementation.
`publicNeuron& operator=(Neuron&&) = default`	Default implementation.
`public inline const std::string & id() const`	Get neuron id string.
`public inline const point_type & up() const`	Get neuron Up vector.
`public void up(const point_type & up)`	Set neuron up vector.
`public inline int size() const`	Count number of neurites.
`public int node_count() const`	Number of different nodes in the neuron.
`public neurite_iterator add_neurite(Neurite*const n)`	Add new neurite to the neuron.
`public void add_soma(const std::vector<Node> & v)`	Add node set to soma.
`public inline void add_soma(constNode& n)`	Add single node to soma.
`public template<typename T>` `inline auto add_property(const std::string & key,const T & v,bool recursive)`	Adds a proprety to the neuron and, optionally, to its neurites.
`public inline auto add_property(const std::string & key,bool recursive)`	Adds an empty proprety to the neuron and, optionally, to its neurites.
`public inline neurite_iterator begin_neurite()`	Creates neurite iterator.
`public inline neurite_iterator end_neurite()`	Creates neurite iterator.
`public inline const_neurite_iterator begin_neurite() const`	Creates neurite iterator.
`public inline const_neurite_iterator end_neurite() const`	Creates neurite iterator.
`public inline soma_iterator begin_soma()`	Iterator over soma nodes.
`public inline soma_iterator end_soma()`	Iterator over soma nodes.
`public inline const_soma_iterator begin_soma() const`	Iterator over soma nodes.
`public inline const_soma_iterator end_soma() const`	Iterator over soma nodes.
`public inline auto begin_axon()`	Iterator over axon.
`public inline auto end_axon()`	Iterator over axon.
`public inline auto begin_apical()`	Iterator over apical.
`public inline auto end_apical()`	Iterator over apical.
`public inline auto begin_dendrite()`	Iterator over basal dendrites.
`public inline auto end_dendrite()`	Iterator over basal dendrites.
`public inline auto begin_axon() const`	Iterator over axon.
`public inline auto end_axon() const`	Iterator over axon.
`public inline auto begin_apical() const`	Iterator over apical.
`public inline auto end_apical() const`	Iterator over apical.
`public inline auto begin_dendrites() const`	Iterator over basal dendrites.
`public inline auto end_dendrites() const`	Iterator over basal dendrites.
`public inline int axon_count() const`	Counts number of axon neuritesin the neuron.
`public inline int apical_count() const`	Counts number of apical neurites in the neuron.
`public inline int dendrite_count() const`	Counts number of basal dendrites in the neuron.
`public inline bool has_soma() const`	Checks if the neuron soma is not empty.
`publicNeurite::base_node_iteratorfind(constNode& n)`	Finds a node in the neuron.
`public inlineNeurite::base_node_iteratorfind(Node::id_type id)`	Finds a node in the neuron that matches the id.
`public soma_iterator find_soma(constNode& n)`	Finds a node in the soma.
`public inline soma_iterator find_soma(Node::id_type id)`	Finds a node in the soma by id.
`public bool point_in_soma(const point_type & p) const`	Checks if the given point is within the soma.
`public void correct()`	Correct function calls the correct function over each.
`public void remove_null_segments()`	Removes zero-length segements in all neurites.
`public point_type soma_barycenter() const`	Computes soma barycenter.
`public void scale(float r)`	Scales all nodes in the neuron by r.
`public void scale(float rx,float ry,float rz)`	Scales all nodes in the neuron by (rx,ry,rz)
`public void traslate(const point_type & p)`	Moves all nodes in the neuron by p.
`public void rotate(const Eigen::Quaternionf & q)`	rotates all nodes in the neuron
`public void center()`	Traslates the neuron so the soma barycenter lies at 0,0,0.
`public neurite_iterator erase(const neurite_iterator & n)`	Removes a neurite from the neuron.
`public void erase_axon()`	Removes all axon neurites from the neuron.
`public void erase_apical()`	Removes all apical dendrties from the neuron.
`public void erase_dendrites()`	Removes all non-apical dendrties from the neuron.
`public void set_apical_up()`	Rotates the neuron so the apical towards "up" direction.
`public void set_basal_roots_xz()`	Rotates the neuron so the basal plane is close to the z=0 plane.
`public box_type boundingBox()`	Computes the axis-aligned bounding box of the neuron.
`public float somaArea() const`	Computes soma area.
`public void order()`	Order all neurites.
`public void simplify(float eps)`	Applies RDP simplification to all branches in the neruon.

Members

`public Neuron()`

Empty constructor.

Create a neuron with no id, neurites nor soma. up vector is set to default value (0,0,1)

Returns

Neuron

`public Neuron(const std::string & id)`

Create a neuron with given id, and no neurites nor soma.

up vector is set to default value (0,0,1)

Parameters

id Neuron id

Returns

Neuron

`public Neuron(const std::string & id,const std::vector<Node> & soma)`

Creates a neuron with given id and soma nodes.

up vector is set to default value (0,0,1)

Parameters

id Neuron id
soma Soma nodes

Returns

Neuron

`public inline ~Neuron()`

Default destructor.

`public Neuron(constNeuron&) = delete`

DELETED

`publicNeuron& operator=(constNeuron&) = delete`

DELETED

`public Neuron(Neuron&&) = default`

Default implementation.

`publicNeuron& operator=(Neuron&&) = default`

Default implementation.

`public inline const std::string & id() const`

Get neuron id string.

Returns

Neuron id string

`public inline const point_type & up() const`

Get neuron Up vector.

Up vector allows us to orient angles in 3D space

Returns

Point

`public void up(const point_type & up)`

Set neuron up vector.

Given vector is normalized

Parameters

up New up vector

`public inline int size() const`

Count number of neurites.

Returns

Neurite count

`public int node_count() const`

Number of different nodes in the neuron.

Returns

Node count

`public neurite_iterator add_neurite(Neurite*const n)`

Add new neurite to the neuron.

Parameters

n Neurite pointer to be added

Returns

Insert point

`public void add_soma(const std::vector<Node> & v)`

Add node set to soma.

Parameters

v Vector of nodes to add to the soma

`public inline void add_soma(constNode& n)`

Add single node to soma.

Parameters

n Node to add

`public template<typename T>`
`inline auto add_property(const std::string & key,const T & v,bool recursive)`

Adds a proprety to the neuron and, optionally, to its neurites.

Parameters

key Property key
v Property value
recursive If true, property is also added to neuron neurites.

`public inline auto add_property(const std::string & key,bool recursive)`

Adds an empty proprety to the neuron and, optionally, to its neurites.

Parameters

key Property key
recursive If true, property is also added to neuron neurites.

`public inline neurite_iterator begin_neurite()`

Creates neurite iterator.

Returns

Begin neurite iterator

`public inline neurite_iterator end_neurite()`

Creates neurite iterator.

Returns

End neurite iterator

`public inline const_neurite_iterator begin_neurite() const`

Creates neurite iterator.

Returns

Begin neurite iterator

`public inline const_neurite_iterator end_neurite() const`

Creates neurite iterator.

Returns

End neurite iterator

`public inline soma_iterator begin_soma()`

Iterator over soma nodes.

Returns

Begin soma iterator

`public inline soma_iterator end_soma()`

Iterator over soma nodes.

Returns

End soma iterator

`public inline const_soma_iterator begin_soma() const`

Iterator over soma nodes.

Returns

Begin soma iterator

`public inline const_soma_iterator end_soma() const`

Iterator over soma nodes.

Returns

End soma iterator

`public inline auto begin_axon()`

Iterator over axon.

Axon is supposed to be unique...

Returns

Begin axon iterator

`public inline auto end_axon()`

Iterator over axon.

Axon is supposed to be unique...

Returns

End axon iterator

`public inline auto begin_apical()`

Iterator over apical.

Apical is supposed to be unique...

Returns

Begin apical iterator

`public inline auto end_apical()`

Iterator over apical.

Apical is supposed to be unique...

Returns

End apical iterator

`public inline auto begin_dendrite()`

Iterator over basal dendrites.

Returns

Begin basal dendrites iterator

`public inline auto end_dendrite()`

Iterator over basal dendrites.

Returns

End basal dendrites iterator

`public inline auto begin_axon() const`

Iterator over axon.

Axon is supposed to be unique...

Returns

Begin axon iterator

`public inline auto end_axon() const`

Iterator over axon.

Axon is supposed to be unique...

Returns

End axon iterator

`public inline auto begin_apical() const`

Iterator over apical.

Apical is supposed to be unique...

Returns

Begin apical iterator

`public inline auto end_apical() const`

Iterator over apical.

Apical is supposed to be unique...

Returns

End apical iterator

`public inline auto begin_dendrites() const`

Iterator over basal dendrites.

Returns

Begin basal dendrites iterator

`public inline auto end_dendrites() const`

Iterator over basal dendrites.

Returns

End basal dendrites iterator

`public inline int axon_count() const`

Counts number of axon neuritesin the neuron.

Returns

Number of axon

`public inline int apical_count() const`

Counts number of apical neurites in the neuron.

Returns

Number of apical

`public inline int dendrite_count() const`

Counts number of basal dendrites in the neuron.

Returns

Number of apical

`public inline bool has_soma() const`

Checks if the neuron soma is not empty.

Returns

True if soma is not empty

`publicNeurite::base_node_iteratorfind(constNode& n)`

Finds a node in the neuron.

doesnt search in soma nodes

Parameters

n Node to be found

Returns

Node iterator. IF node is not found returns the iterator created by the empty constructor

`public inlineNeurite::base_node_iteratorfind(Node::id_type id)`

Finds a node in the neuron that matches the id.

doesnt search in soma nodes

Parameters

id Node Id

Returns

Node iterator. IF node is not found returns the iterator created by the empty constructor

`public soma_iterator find_soma(constNode& n)`

Finds a node in the soma.

Parameters

n Node to be found

Returns

Iterator to the node. end_soma otherwise

`public inline soma_iterator find_soma(Node::id_type id)`

Finds a node in the soma by id.

Parameters

id ID of the node to be found

Returns

Iterator to the node. end_soma otherwise

`public bool point_in_soma(const point_type & p) const`

Checks if the given point is within the soma.

The condition is that the given point should be closer to the soma barycenter than at least one point in the soma

Parameters

p Point

Returns

True if point is considered to be in the soma

`public void correct()`

Correct function calls the correct function over each.

Additionaly checks if the neurite root is part of the soma and set is as such if necessary.

`public void remove_null_segments()`

Removes zero-length segements in all neurites.

`public point_type soma_barycenter() const`

Computes soma barycenter.

Returns

soma barycenter

`public void scale(float r)`

Scales all nodes in the neuron by r.

Parameters

r scale rate

`public void scale(float rx,float ry,float rz)`

Scales all nodes in the neuron by (rx,ry,rz)

Parameters

rx x-axis scale
ry y-axis scale
rz z-axis scale

`public void traslate(const point_type & p)`

Moves all nodes in the neuron by p.

Parameters

p Traslation vector

`public void rotate(const Eigen::Quaternionf & q)`

rotates all nodes in the neuron

Parameters

q rotation quaternion

`public void center()`

Traslates the neuron so the soma barycenter lies at 0,0,0.

`public neurite_iterator erase(const neurite_iterator & n)`

Removes a neurite from the neuron.

Parameters

n Neurite iterator

Returns

updated iterator

`public void erase_axon()`

Removes all axon neurites from the neuron.

`public void erase_apical()`

Removes all apical dendrties from the neuron.

`public void erase_dendrites()`

Removes all non-apical dendrties from the neuron.

`public void set_apical_up()`

Rotates the neuron so the apical towards "up" direction.

`public void set_basal_roots_xz()`

Rotates the neuron so the basal plane is close to the z=0 plane.

`public box_type boundingBox()`

Computes the axis-aligned bounding box of the neuron.

Returns

bounding box

`public float somaArea() const`

Computes soma area.

Returns

Soma area

`public void order()`

Order all neurites.

`public void simplify(float eps)`

Applies RDP simplification to all branches in the neruon.

Parameters

eps Tolerance

class `Node`

class Node
  : public neurostr::WithProperties

Summary

Members	Descriptions
`public Node()`	Empty constructor, creates a node with ID -1 at 0,0,0 with radius 0.
`public Node(int id)`	Creates a node with ID id at 0,0,0 with radius 0.
`public Node(int id,const point_type & p,double r)`	Creates a node with ID id at position p with radius r.
`public Node(int id,double x,double y,double z,double r)`	Creates a node with ID id at position (x,y,z) with radius r
`public Node(constNode& n) = default`	Default.
`public Node(Node&& n) = default`	Default.
`publicNode& operator=(constNode& n) = default`	Default.
`publicNode& operator=(Node&& n) = default`	Default.
`public inline ~Node()`	Empty destructor.
`public inline bool operator==(constNode& n) const`	Compare two nodes by ID.
`public inline bool operator!=(constNode& n) const`	Compare two nodes by ID.
`public inline float radius() const`	Returns node radius.
`public inline const id_type id() const`	Returns node id.
`public inline const point_type & position() const`	Return node position.
`public inline float x() const`	Returns node X coordinate.
`public inline float y() const`	Returns node Y coordinate.
`public inline float z() const`	Returns node Z coordinate.
`public inline bool valid_branch() const`	Checks wether the parent branch referece is valid.
`publicBranch& branch()`	Returns parent branch.
`public constBranch& branch() const`	Returns parent branch.
`publicNode& position(const point_type & p)`	Changes node position for.

Members

`public Node()`

Empty constructor, creates a node with ID -1 at 0,0,0 with radius 0.

Returns

Node

`public Node(int id)`

Creates a node with ID id at 0,0,0 with radius 0

Parameters

id The Node ID

`public Node(int id,const point_type & p,double r)`

Creates a node with ID id at position p with radius r

Parameters

id The Node ID
p Node position (3D point)
r Node radius

`public Node(int id,double x,double y,double z,double r)`

Creates a node with ID id at position (x,y,z) with radius r

Parameters

id The Node ID
x Node x coord.
y Node y coord.
z Node z coord.
r Node radius

`public Node(constNode& n) = default`

Default.

`public Node(Node&& n) = default`

Default.

`publicNode& operator=(constNode& n) = default`

Default.

`publicNode& operator=(Node&& n) = default`

Default.

`public inline ~Node()`

Empty destructor.

Returns

`public inline bool operator==(constNode& n) const`

Compare two nodes by ID.

Parameters

n The other node

Returns

True if both ids are equal

`public inline bool operator!=(constNode& n) const`

Compare two nodes by ID.

Parameters

n The other node

Returns

True if both ids are different

`public inline float radius() const`

Returns node radius.

Returns

Radius

`public inline const id_type id() const`

Returns node id.

Returns

ID

`public inline const point_type & position() const`

Return node position.

Returns

Position

`public inline float x() const`

Returns node X coordinate.

Returns

X coord

`public inline float y() const`

Returns node Y coordinate.

Returns

Y coord

`public inline float z() const`

Returns node Z coordinate.

Returns

Z coordinate

`public inline bool valid_branch() const`

Checks whether the parent branch reference is valid.

Returns

True if the reference is valid

`publicBranch& branch()`

Returns parent branch.

Throws

runtime_exception If we attempt to access null branch

Returns

Parent branch reference

`public constBranch& branch() const`

Returns parent branch.

Parameters

runtime_exception If attempt to access null branch

Returns

Parent branch const reference

`publicNode& position(const point_type & p)`

Changes node position for.

Parameters

*

class `PropertyMap`

Summary

Members	Descriptions
`public PropertyMap()`	Initializes an empty property map.
`public template<typename Iter>` `inline PropertyMap(const Iter & begin,const Iter & end)`	Initializes a property map with the content in the range.
`public const_iterator find(const std::string & k) const`	Returns the property with key k.
`public PropertyMap(constPropertyMap&) = default`	Default.
`publicPropertyMap& operator=(constPropertyMap&) = default`	Default.
`public PropertyMap(PropertyMap&&) = default`	Default.
`publicPropertyMap& operator=(PropertyMap&&) = default`	Default.
`public template<typename T>` `inline T get(const std::string & k) const`	Returns the value of the poperty with key k.
`public std::pair< iterator, bool > set(const property_type & p)`	Adds a new property to the map.
`public std::pair< iterator, bool > set(const std::string & k)`	Adds an empty property to the map.
`public std::pair< iterator, bool > set(const std::string & k,int v)`	Adds a new int valued property to the map.
`public std::pair< iterator, bool > set(const std::string & k,bool v)`	Adds a new bool valued property to the map.
`public std::pair< iterator, bool > set(const std::string & k,float v)`	Adds a new float valued property to the map.
`public std::pair< iterator, bool > set(const std::string & k,const std::string v)`	Adds a new string valued property to the map.
`public std::pair< iterator, bool > set(const std::string & k,const point_type v)`	Adds a new point valued property to the map.
`public std::pair< iterator, bool > set(const std::string & k,boost::any v)`	Adds a property to the map.
`public bool exists(const std::string & k) const`	Property exists.
`public void remove(const std::string & k)`	Deletes a property.
`public void remove(const iterator & i)`	Deletes a property.
`public map_type::size_type size() const`	Property map size.
`public const_iterator begin() const`	Property begin iterator.
`public iterator begin()`	Property begin iterator.
`public const_iterator end() const`	Property end iterator.
`public iterator end()`	Property end iterator.

Members

`public PropertyMap()`

Initializes an empty property map.

`public template<typename Iter>`
`inline PropertyMap(const Iter & begin,const Iter & end)`

Initializes a property map with the content in the range.

Parameters

begin property begin iterator
end property end iterator

`public const_iterator find(const std::string & k) const`

Returns the property with key k.

Parameters

k Property key

Returns

Const iterator. End() if no property with key k exists

`public PropertyMap(constPropertyMap&) = default`

Default.

`publicPropertyMap& operator=(constPropertyMap&) = default`

Default.

`public PropertyMap(PropertyMap&&) = default`

Default.

`publicPropertyMap& operator=(PropertyMap&&) = default`

Default.

`public template<typename T>`
`inline T get(const std::string & k) const`

Returns the value of the poperty with key k.

Parameters

k Key

Returns

Property value

`public std::pair< iterator, bool > set(const property_type & p)`

Adds a new property to the map.