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

Class ImageParser3D

java.lang.Object

org.scijava.AbstractContextual

org.scijava.command.ContextCommand

sc.fiji.snt.analysis.sholl.parsers.ImageParser

sc.fiji.snt.analysis.sholl.parsers.ImageParser3D

All Implemented Interfaces:

Runnable, org.scijava.Cancelable, org.scijava.command.Command, org.scijava.Contextual, org.scijava.plugin.SciJavaPlugin, Parser, ProfileProperties

public class ImageParser3D
extends ImageParser

Parser for 3D images

Author:

Tiago Ferreira

Field Summary

Fields inherited from class sc.fiji.snt.analysis.sholl.parsers.ImageParser

cal, center, channel, frame, imp, lowerT, maxX, maxY, maxZ, minX, minY, minZ, profile, properties, radii, running, start, statusService, upperT, voxelSize, xc, yc, zc

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

Constructor Summary

Constructors

Constructor	Description
ImageParser3D(ij.ImagePlus imp)
ImageParser3D(ij.ImagePlus imp, org.scijava.Context context)

Method Summary

Modifier and Type	Method	Description
Profile	getProfile()	Gets the Sholl profile generated by the parsing operation.
boolean	isSkipSingleVoxels()
void	parse()	Performs the parsing operation to extract the Sholl profile.
void	setPosition(int channel, int frame)
void	setSkipSingleVoxels(boolean skip)

Methods inherited from class sc.fiji.snt.analysis.sholl.parsers.ImageParser

checkUnsetFields, checkUnsetFields, clearStatus, getCircumferencePoints, getIsotropicVoxelSize, getMask, getMaskProcessor, isRetrieveIntDensitiesSet, maxPossibleRadius, reset, run, setCenter, setCenterFromROI, setCenterFromROI, setCenterPx, setHemiShells, setRadii, setRadii, setRetrieveIntDensities, setThreshold, successful, terminate, withinBounds, withinThreshold, withinXYbounds, withinZbounds

Methods inherited from class org.scijava.command.ContextCommand

cancel, getCancelReason, isCanceled

Methods inherited from class org.scijava.AbstractContextual

context, getContext

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.scijava.Contextual

setContext

Constructor Details

ImageParser3D

public ImageParser3D(ij.ImagePlus imp)

ImageParser3D

public ImageParser3D(ij.ImagePlus imp,
 org.scijava.Context context)

Method Details

getProfile

public Profile getProfile()

Description copied from interface: Parser

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 Parser.parse() and verifying success with Parser.successful().

Specified by:

getProfile in interface Parser

Overrides:

getProfile in class ImageParser

Returns:

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

parse

public void parse()

Description copied from interface: Parser

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 Parser.getProfile().

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

Specified by:

parse in interface Parser

Overrides:

parse in class ImageParser

setPosition

public void setPosition(int channel,
 int frame)

Overrides:

setPosition in class ImageParser

setSkipSingleVoxels

public void setSkipSingleVoxels(boolean skip)

isSkipSingleVoxels

public boolean isSkipSingleVoxels()