ImageParser3D (Fiji Javadocs 0-SNAPSHOT API)

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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, Cancelable, Command, Contextual, 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_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 and Description

ImageParser3D(ij.ImagePlus imp)
Deprecated.

ImageParser3D(ij.ImagePlus imp, Context context)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected HashSet<ShollPoint>`	`getUnique3Dgroups(ArrayList<ShollPoint> points)`
`boolean`	`isSkipSingleVoxels()`
`void`	`parse()`
`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, getProfile, isRetrieveIntDensitiesSet, maxPossibleRadius, reset, run, setCenter, 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 Detail

ImageParser3D

@Deprecated
public ImageParser3D(ij.ImagePlus imp)

Deprecated.

ImageParser3D

public ImageParser3D(ij.ImagePlus imp,
                     Context context)

Method Detail

parse
```
public void parse()
```
Specified by:

parse in interface Parser

Overrides:

parse in class ImageParser

setPosition

public void setPosition(int channel,
                        int frame)

Overrides:: setPosition in class ImageParser

getUnique3Dgroups

protected HashSet<ShollPoint> getUnique3Dgroups(ArrayList<ShollPoint> points)

setSkipSingleVoxels

public void setSkipSingleVoxels(boolean skip)

isSkipSingleVoxels
```
public boolean isSkipSingleVoxels()
```

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