namespace io

IO namespace contains write/read functionality for most common file formats.

Summary

Members	Descriptions
classASCParser
classDATParser
classJSONParser
classJSONWriter
classParser
classSWCParser
classSWCWriter
structcontour_info	Contour header in DAT files.
structmarker_type	Markerset structure for NL files.
structsubtree_info	SubTree header in DAT files.
structtree_info	Tree header in DAT files.

---

class ASCParser

class ASCParser
  : public neurostr::io::Parser

Summary

Members	Descriptions
public inline ASCParser(std::istream & stream)	Creates a ASC parser.
public inline ~ASCParser()	Default.
public virtual std::unique_ptr<Reconstruction> read(const std::string & name)	Reads a reconstruction from the stream.
protectedblock_typenext_block_type(bool in_block)	Deduces the type of the next block.
protected void process_(Reconstruction& r)	Process a single reconstruction.
protected PropertyMap::property_type process_property()	Process a property in the stream.
protectedNodeprocess_sample()	Process a sample (node) in the stream.
protected Neurite::branch_iterator process_container_(const Neurite::branch_iterator & pos)	Process a Tree (or contour) inserting the nodes in the container as children of the given parent.

Members

public inline ASCParser(std::istream & stream)

Creates a ASC parser.

Parameters

• s Input stream to read from

Returns

A ASC parser

---

public inline ~ASCParser()

Default.

---

public virtual std::unique_ptr<Reconstruction> read(const std::string & name)

Reads a reconstruction from the stream.

Parameters

• name Reconstruction ID

Returns

Unique ptr to the reconstruction (Ownership)

---

protectedblock_typenext_block_type(bool in_block)

Deduces the type of the next block.

Parameters

• in_block Flag: Called inside another block

Returns

block type

---

protected void process_(Reconstruction& r)

Process a single reconstruction.

Parameters

• r Reconstruction to be fill

---

protected PropertyMap::property_type process_property()

Process a property in the stream.

Returns

Extracted property

---

protectedNodeprocess_sample()

Process a sample (node) in the stream.

Returns

Node

---

protected Neurite::branch_iterator process_container_(const Neurite::branch_iterator & pos)

Process a Tree (or contour) inserting the nodes in the container as children of the given parent.

Parameters

• parent Point of insertion

Returns

Last point of insertion

---

class DATParser

class DATParser
  : public neurostr::io::Parser

Summary

Members	Descriptions
public inline DATParser(std::istream & stream)	Creates a DAT parser.
public inline ~DATParser()	Default.
public virtual std::unique_ptr<Reconstruction> read(const std::string &)	Reads a reconstruction from the stream.
protected bool valid_header()	Checks that the header is correct.
protected std::string process_string(std::size_t len)	Process binary string block.
protectedNodeprocess_sample()	Process binary sample block.
protected PropertyMap::property_type process_property()	Process binary property block.
protectedmarker_typeprocess_markerset()	Proces binary markeset block.
protected std::vector<Node> process_samplelist_()	Process sample list block.
protected std::vector< PropertyMap::property_type > process_proplist_()	Porcess list of properties.
protected std::vector<marker_type> process_markersetlist_()	Process list of markers.
protected std::size_t process_container_(const Neurite::branch_iterator & pos)	Process container block in buffer.
protected void process_block_(Reconstruction& r)	Process block in buffer.
protected void skip_block()	Skips current block in buffer.

Members

public inline DATParser(std::istream & stream)

Creates a DAT parser.

Parameters

• s Input stream to read from

Returns

A DAT parser

---

public inline ~DATParser()

Default.

---

public virtual std::unique_ptr<Reconstruction> read(const std::string &)

Reads a reconstruction from the stream.

Parameters

• name Reconstruction ID

Returns

Unique ptr to the reconstruction (Ownership)

---

protected bool valid_header()

Checks that the header is correct.

Returns

True if header is valid

---

protected std::string process_string(std::size_t len)

Process binary string block.

Parameters

• len String length

Returns

String

---

protectedNodeprocess_sample()

Process binary sample block.

Returns

Node

---

protected PropertyMap::property_type process_property()

Process binary property block.

Returns

Property

---

protectedmarker_typeprocess_markerset()

Proces binary markeset block.

Returns

Marker

---

protected std::vector<Node> process_samplelist_()

Process sample list block.

Returns

Node vector

---

protected std::vector< PropertyMap::property_type > process_proplist_()

Porcess list of properties.

Returns

Property vector

---

protected std::vector<marker_type> process_markersetlist_()

Process list of markers.

Returns

Vector of markers

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protected std::size_t process_container_(const Neurite::branch_iterator & pos)

Process container block in buffer.

Parameters

• pos Insertion position

Returns

Number of bytes extended

---

protected void process_block_(Reconstruction& r)

Process block in buffer.

Parameters

• r Reconstruction to fill

---

protected void skip_block()

Skips current block in buffer.

---

class JSONParser

class JSONParser
  : public neurostr::io::Parser

Summary

Members	Descriptions
public inline JSONParser(std::istream & stream)	Creates a JSON parser.
public inline ~JSONParser()	Default.
public virtual std::unique_ptr<Reconstruction> read(const std::string & name)	Reads a reconstruction from the stream.

Members

public inline JSONParser(std::istream & stream)

Creates a JSON parser.

Parameters

• s Input stream to read from

Returns

JSON parser

---

public inline ~JSONParser()

Default.

---

public virtual std::unique_ptr<Reconstruction> read(const std::string & name)

Reads a reconstruction from the stream.

Parameters

• name Reconstruction ID

Returns

Unique ptr to the reconstruction (Ownership)

---

class JSONWriter

Summary

Members	Descriptions
public JSONWriter(std::ostream & s,bool pretty)	Creates a writer over the given output stream.
public inline ~JSONWriter()	Default.
public void write(constneurostr::Reconstruction& r)	Writes a reconstruction.
public void writeNeuron(constneurostr::Neuron& n)	Writes a single neuron (wo rec.
protected void writePoint(const neurostr::point_type & point)	Writes a point object as {x,y,z}.
protected void writeProperty(const neurostr::PropertyMap::const_iterator & p)	Writes the given property as key:value.
protected void writeSoma(constneurostr::Neuron& n)	Writes the neuron soma as {nodes:[nodes]}.
protected void writeContour(constneurostr::Contour& c)	Writes the given contour as an object.
protected void writePropertyMap(constneurostr::PropertyMap& pm)	Writes the property map as an object {}.
protected void writeNeurite(constneurostr::Neurite& n)	Writes the neurite as an object { id:, type: , tree:}.
protected void writeBranch(const neurostr::Neurite::tree_type::iterator_base & b,constneurostr::Neurite& n)	Writes the given branch (member of n) as {root: node, properties: , nodes:[], children:[] }.
protected void writeNode(constneurostr::Node& n)	Writes a single node as {id,x,y,z,r,properties:{}}.

Members

public JSONWriter(std::ostream & s,bool pretty)

Creates a writer over the given output stream.

Parameters

• s Stream

• pretty If true, ouptut is prettyfied

---

public inline ~JSONWriter()

Default.

---

public void write(constneurostr::Reconstruction& r)

Writes a reconstruction.

Parameters

• r Reconstruction

---

public void writeNeuron(constneurostr::Neuron& n)

Writes a single neuron (wo rec.

contours)

Parameters

• n Neuron

---

protected void writePoint(const neurostr::point_type & point)

Writes a point object as {x,y,z}.

Parameters

• point 3D Point

---

protected void writeProperty(const neurostr::PropertyMap::const_iterator & p)

Writes the given property as key:value.

Parameters

• p Property iterator

---

protected void writeSoma(constneurostr::Neuron& n)

Writes the neuron soma as {nodes:[nodes]}.

Parameters

• n Neuron

---

protected void writeContour(constneurostr::Contour& c)

Writes the given contour as an object.

Contour points are in a array

Parameters

• c Contour

---

protected void writePropertyMap(constneurostr::PropertyMap& pm)

Writes the property map as an object {}.

Parameters

• pm Property map

---

protected void writeNeurite(constneurostr::Neurite& n)

Writes the neurite as an object { id:, type: , tree:}.

Parameters

• n Neurite

---

protected void writeBranch(const neurostr::Neurite::tree_type::iterator_base & b,constneurostr::Neurite& n)

Writes the given branch (member of n) as {root: node, properties: , nodes:[], children:[] }.

Parameters

• b Branch iterator

• n Neurite

---

protected void writeNode(constneurostr::Node& n)

Writes a single node as {id,x,y,z,r,properties:{}}.

Parameters

• n Node

---

class Parser

Summary

Members	Descriptions
public inline Parser(std::istream & s)	Constructs copy the istream reference.
public inline virtual ~Parser()
public Parser(constParser&) = delete	Deleted copy constructor.
publicParser& operator=(constParser&) = delete	Deleted copy operator.
public inline void reset_errors()	Set the error count to the default state.
public inline int error() const	Get number of errors.
public inline int warn() const	Get number of warnigs.
public inline bool critical() const	Critical error flag.
public std::unique_ptr<Reconstruction> read(const std::string & name)	Reads a reconstruction from the stream and returns a unique_ptr.
protected std::istream & stream_	Input stream variable.
protected int error_count	Error status.
protected int warn_count
protected bool critical_error
protected inline void process_error(const std::exception & e)	Processes the error, log it and increments the error count.

Members

public inline Parser(std::istream & s)

Constructs copy the istream reference.

Parameters

• s Input stream

---

public inline virtual ~Parser()

---

public Parser(constParser&) = delete

Deleted copy constructor.

---

publicParser& operator=(constParser&) = delete

Deleted copy operator.

---

public inline void reset_errors()

Set the error count to the default state.

---

public inline int error() const

Get number of errors.

Returns

Error count

---

public inline int warn() const

Get number of warnigs.

Returns

Warning count

---

public inline bool critical() const

Critical error flag.

Returns

True if a critical error has happened.

---

public std::unique_ptr<Reconstruction> read(const std::string & name)

Reads a reconstruction from the stream and returns a unique_ptr.

Parameters

• name Reconstruction ID

Returns

Unique ptr to the reconstruction (Ownership)

---

protected std::istream & stream_

Input stream variable.

---

protected int error_count

Error status.

---

protected int warn_count

---

protected bool critical_error

---

protected inline void process_error(const std::exception & e)

Processes the error, log it and increments the error count.

Parameters

• e Error

---

class SWCParser

class SWCParser
  : public neurostr::io::Parser

luis

28/10/16

Summary

Members	Descriptions
public const char comment_char
public const size_t field_count
public SWCParser(std::istream & s)	Creates a SWC parser with default separators (space)
public SWCParser(std::istream & s,const std::string & sep)	Creates a SWC parser with given separators.
public ~SWCParser()	Default.
public virtual std::unique_ptr<Reconstruction> read(const std::string & name)	Reads a reconstruction from the stream.
public bool is_key(const std::string & s) const	Checks if the given string is a known property name.
public void add_property_key(const std::string &)	Adds a string to the set of recognized property keys.
public void remove_property_key(const std::string &)	Removes a string of the set of recognized property keys.
public const std::set< std::string > & get_property_keys() const	Retrieves the set of recognized property keys.
protected separator sep_
protectedNeuron* neuron_
protected std::set< std::string > property_keys_

Members

public const char comment_char

---

public const size_t field_count

---

public SWCParser(std::istream & s)

Creates a SWC parser with default separators (space)

Parameters

• s Input stream to read from

Returns

A SWC parser

---

public SWCParser(std::istream & s,const std::string & sep)

Creates a SWC parser with given separators.

Parameters

• s Input stream

• sep String of separator characters

Returns

A SWC parser

---

public ~SWCParser()

Default.

---

public virtual std::unique_ptr<Reconstruction> read(const std::string & name)

Reads a reconstruction from the stream.

For SWC files the return will always consist of a reconstruction with exactly one neuron and no contour

Parameters

• name Reconstruction ID

Returns

Unique ptr to the reconstruction (Ownership)

---

public bool is_key(const std::string & s) const

Checks if the given string is a known property name.

Parameters

• s String to check

Returns

True if the string is in the property key set

---

public void add_property_key(const std::string &)

Adds a string to the set of recognized property keys.

Parameters

• s String to add

---

public void remove_property_key(const std::string &)

Removes a string of the set of recognized property keys.

Parameters

• s String to add

---

public const std::set< std::string > & get_property_keys() const

Retrieves the set of recognized property keys.

Returns

Set of strings

---

protected separator sep_

---

protectedNeuron* neuron_

---

protected std::set< std::string > property_keys_

---

class SWCWriter

Summary

Members	Descriptions
public const char comment_char
public const int no_parent_id
public SWCWriter(std::ostream &)	Creates a writer over the given stream.
public ~SWCWriter()
public std::ostream & write(Neuron&) const	Writes the given neuron in SWC format.
protected void writeHeader(Neuron&) const	Writes document header.
protected void writeData(Neuron&) const	Writes Neuron node positions (SWC DATA)

Members

public const char comment_char

---

public const int no_parent_id

---

public SWCWriter(std::ostream &)

Creates a writer over the given stream.

Returns

SWCWriter

---

public ~SWCWriter()

---

public std::ostream & write(Neuron&) const

Writes the given neuron in SWC format.

Returns

Output stream reference

---

protected void writeHeader(Neuron&) const

Writes document header.

Static header + properties as comments

---

protected void writeData(Neuron&) const

Writes Neuron node positions (SWC DATA)

---

struct contour_info

Contour header in DAT files.

Summary

Members	Descriptions
public std::uint16_t closed
public std::uint8_t face_color
public std::uint8_t back_color

Members

public std::uint16_t closed

---

public std::uint8_t face_color

---

public std::uint8_t back_color

---

struct marker_type

Markerset structure for NL files.

Summary

Members	Descriptions
public std::string name
public std::uint8_t color
public std::vector< property_type > properties
public std::vector<Node> samples

Members

public std::string name

---

public std::uint8_t color

---

public std::vector< property_type > properties

---

public std::vector<Node> samples

---

struct subtree_info

SubTree header in DAT files.

Summary

Members	Descriptions
public uint16_t value1
public uint16_t value2

Members

public uint16_t value1

---

public uint16_t value2

---

struct tree_info

Tree header in DAT files.

Summary

Members	Descriptions
publictree_type_cdtype
public uint8_t face_color
public uint8_t back_color

Members

publictree_type_cdtype

---

public uint8_t face_color

---

public uint8_t back_color