Package sc.fiji.snt.analysis.sholl.parsers

Interface Parser

All Superinterfaces:

ProfileProperties

All Known Implementing Classes:

ImageParser, ImageParser2D, ImageParser3D, TabularParser, TreeParser

public interface Parser
extends ProfileProperties

Interface for parsing data sources to extract Sholl analysis profiles.

A Parser is responsible for extracting intersection counts at various radial distances from a center point, which forms the basis of Sholl analysis. This interface defines the contract for parsers that can handle different data sources such as neuronal reconstructions (Trees), images, or tabular data.

The Parser extends ProfileProperties to provide metadata about the analysis, including source information, calibration details, and analysis parameters.

Author:

Tiago Ferreira

See Also:

• Profile
• ProfileProperties
• TreeParser
• ImageParser
• TabularParser

Field Summary

Fields inherited from interface sc.fiji.snt.analysis.sholl.ProfileProperties

HEMI_EAST, HEMI_NONE, HEMI_NORTH, HEMI_SOUTH, HEMI_WEST, INTG_MEAN, INTG_MEDIAN, INTG_MODE, KEY_2D3D, KEY_CALIBRATION, KEY_CENTER, KEY_CHANNEL_POS, KEY_EFFECTIVE_STEP_SIZE, KEY_EXTRA_MEASUREMENT, KEY_FRAME_POS, KEY_HEMISHELLS, KEY_ID, KEY_NSAMPLES, KEY_NSAMPLES_INTG, KEY_SLICE_POS, KEY_SOURCE, KEY_THRESHOLD_RANGE, SRC_IMG, SRC_TABLE, SRC_TRACES, UNSET

Method Summary

Modifier and Type	Method	Description
Profile	getProfile()	Gets the Sholl profile generated by the parsing operation.
void	parse()	Performs the parsing operation to extract the Sholl profile.
boolean	successful()	Checks if the parsing operation was successful.
void	terminate()	Terminates the parsing operation.

Method Details

successful

boolean successful()

Checks if the parsing operation was successful.

This method should be called after parse() to determine if the parsing completed without errors and produced a valid profile.

Returns:

true if parsing was successful, false otherwise

parse

void parse()

Performs the parsing operation to extract the Sholl profile.

This method analyzes the data source and computes intersection counts at various radial distances from the center point. The resulting profile can be retrieved using getProfile().

Implementations should handle any necessary preprocessing, validation, and error handling during the parsing process.

terminate

void terminate()

Terminates the parsing operation.

This method should be called to clean up resources and stop any ongoing parsing operations. It may be used to interrupt long-running analyses or to ensure proper cleanup when the parser is no longer needed.

getProfile

Profile getProfile()

Gets the Sholl profile generated by the parsing operation.

This method returns the profile containing intersection counts at various radial distances. The profile should only be retrieved after calling parse() and verifying success with successful().

Returns:

the Sholl profile, or null if parsing has not been performed or was unsuccessful