Struct SwcNeuron

pub struct SwcNeuron<S: StructureIdentifier, H: Header> {
    pub samples: Vec<SwcSample<S>>,
    pub header: Option<H>,
}

Struct representing a neuron skeleton as a tree of SwcSamples.

Fields

samples: Vec<SwcSample<S>>

Samples present in the SWC file.

header: Option<H>

Header of the SWC file

Implementations

impl<S: StructureIdentifier, H: Header> SwcNeuron<S, H>

pub fn len(&self) -> usize

Number of samples in the neuron.

pub fn is_empty(&self) -> bool

Whether there are any samples in the neuron.

pub fn sort_index(self) -> Self

Sort the neuron’s samples by their index.

pub fn reindex(self) -> Result<Self, MissingSampleError>

Re-index the neuron’s samples in order of occurrence, starting at 1. Returns error if the SWC is missing a parent sample

pub fn sort_topo(self, reindex: bool) -> Result<Self, InconsistentNeuronError>

Re-order its samples in pre-order depth first search. Children are visited in the order of their original sample number.

Returns an error if the neuron is not a self-consistent tree.

pub fn validate( &self, validate_order: bool, ) -> Result<(), InconsistentNeuronError>

Ensure that SwcNeuron is a self-consistent tree.

If validate_order is false, samples may be defined earlier in the file than their parents.

pub fn from_reader<R: BufRead>(reader: R) -> Result<Self, SwcParseError>

Parse a SwcNeuron from a [Read]er.

Does not check the neuron for consistency, but does check for valid structures.

pub fn to_writer<W: Write>(&self, writer: &mut W) -> Result<(), Error>

Dump this SwcNeuron to a Writer.

These writes are quite small: consider wrapping it in a [BufWriter].

pub fn replace_header(&mut self, header: Option<H>) -> Option<H>

Replace the existing header with a new one, returning the existing.

pub fn map_header<H2: Header, F: Fn(&Self) -> Option<H2>>( self, f: F, ) -> SwcNeuron<S, H2>

Create a new header by applying a function to this SwcNeuron, then create a new neuron with that header.

Trait Implementations

impl<S: Clone + StructureIdentifier, H: Clone + Header> Clone for SwcNeuron<S, H>

fn clone(&self) -> SwcNeuron<S, H>

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<S: Debug + StructureIdentifier, H: Debug + Header> Debug for SwcNeuron<S, H>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<S: StructureIdentifier, H: Header> FromIterator<SwcSample<S>> for SwcNeuron<S, H>

fn from_iter<I: IntoIterator<Item = SwcSample<S>>>(iter: I) -> Self

Creates a value from an iterator.

impl<S: StructureIdentifier, H: Header, R: BufRead> TryFrom<SwcLines<S, R>> for SwcNeuron<S, H>

type Error = SwcParseError

The type returned in the event of a conversion error.

fn try_from(lines: SwcLines<S, R>) -> Result<Self, Self::Error>

Performs the conversion.