ImageParser (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.scijava.AbstractContextual
- - org.scijava.command.ContextCommand
  - - sc.fiji.snt.analysis.sholl.parsers.ImageParser

All Implemented Interfaces:

Runnable, Cancelable, Command, Contextual, SciJavaPlugin, Parser, ProfileProperties

Direct Known Subclasses:

ImageParser2D, ImageParser3D
```
public class ImageParser
extends ContextCommand
implements Parser
```
Author:

Tiago Ferreira

Field Summary

Fields
Modifier and Type	Field and Description
`protected ij.measure.Calibration`	`cal`
`protected ShollPoint`	`center`
`protected int`	`channel`
`protected int`	`frame`
`protected ij.ImagePlus`	`imp`
`protected double`	`lowerT`
`protected int`	`maxX`
`protected int`	`maxY`
`protected int`	`maxZ`
`protected int`	`minX`
`protected int`	`minY`
`protected int`	`minZ`
`protected Profile`	`profile`
`protected Properties`	`properties`
`protected ArrayList<Double>`	`radii`
`protected boolean`	`running`
`protected long`	`start`
`protected StatusService`	`statusService`
`protected double`	`upperT`
`protected double`	`voxelSize`
`protected int`	`xc`
`protected int`	`yc`
`protected int`	`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
Modifier Constructor and Description

protected ImageParser(ij.ImagePlus imp)
Deprecated.

protected ImageParser(ij.ImagePlus imp, Context context)

Constructors
Modifier	Constructor and Description
`protected`	`ImageParser(ij.ImagePlus imp)` Deprecated.
`protected`	`ImageParser(ij.ImagePlus imp, Context context)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected void`	`checkUnsetFields()`
`protected void`	`checkUnsetFields(boolean includeThreshold)`
`protected void`	`clearStatus()`
`int[][]`	`getCircumferencePoints(int cx, int cy, int radius)`
`double`	`getIsotropicVoxelSize()`
`ij.ImagePlus`	`getMask()`
`ij.process.ImageProcessor`	`getMaskProcessor(boolean floatProcessor, double[] maskValues)` Creates a 2D 'Sholl heatmap' by applying measured values to the foreground pixels of a copy of the analyzed image.
`Profile`	`getProfile()`
`boolean`	`isRetrieveIntDensitiesSet()`
`double`	`maxPossibleRadius()`
`void`	`parse()`
`void`	`reset()`
`void`	`run()`
`void`	`setCenter(double x, double y, double z)`
`void`	`setCenterFromROI()`
`void`	`setCenterPx(int x, int y, int z)`
`void`	`setHemiShells(String flag)`
`protected void`	`setPosition(int channel, int frame)`
`void`	`setRadii(double[] radiiArray)`
`void`	`setRadii(double startRadius, double step, double endRadius)`
`void`	`setRetrieveIntDensities(boolean retrieveIntDensities)`
`void`	`setThreshold(double lower, double upper)`
`boolean`	`successful()`
`void`	`terminate()`
`protected boolean`	`withinBounds(int x, int y, int z)`
`protected boolean`	`withinThreshold(double value)`
`protected boolean`	`withinXYbounds(int x, int y)`
`protected boolean`	`withinZbounds(int z)`

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

Field Detail

statusService
```
protected StatusService statusService
```

profile
```
protected Profile profile
```

properties
```
protected Properties properties
```

center
```
protected ShollPoint center
```

radii
```
protected ArrayList<Double> radii
```

imp
```
protected final ij.ImagePlus imp
```

cal

protected final ij.measure.Calibration cal

voxelSize
```
protected final double voxelSize
```

lowerT
```
protected double lowerT
```

upperT
```
protected double upperT
```

channel
```
protected int channel
```

frame
```
protected int frame
```

minX
```
protected int minX
```

maxX
```
protected int maxX
```

minY
```
protected int minY
```

maxY
```
protected int maxY
```

minZ
```
protected int minZ
```

maxZ
```
protected int maxZ
```

xc
```
protected int xc
```

yc
```
protected int yc
```

zc
```
protected int zc
```

start
```
protected long start
```

running
```
protected volatile boolean running
```

Constructor Detail

ImageParser

@Deprecated
protected ImageParser(ij.ImagePlus imp)

Deprecated.

ImageParser

protected ImageParser(ij.ImagePlus imp,
                      Context context)

Method Detail

getIsotropicVoxelSize
```
public double getIsotropicVoxelSize()
```

setCenterFromROI
```
public void setCenterFromROI()
```

setCenterPx

public void setCenterPx(int x,
                        int y,
                        int z)

setCenter

public void setCenter(double x,
                      double y,
                      double z)

setThreshold

public void setThreshold(double lower,
                         double upper)

setRadii

public void setRadii(double[] radiiArray)

setRadii

public void setRadii(double startRadius,
                     double step,
                     double endRadius)

maxPossibleRadius
```
public double maxPossibleRadius()
```

setRetrieveIntDensities

public void setRetrieveIntDensities(boolean retrieveIntDensities)

isRetrieveIntDensitiesSet

public boolean isRetrieveIntDensitiesSet()

checkUnsetFields

protected void checkUnsetFields(boolean includeThreshold)

checkUnsetFields
```
protected void checkUnsetFields()
```

setHemiShells

public void setHemiShells(String flag)

getCircumferencePoints

public int[][] getCircumferencePoints(int cx,
                                      int cy,
                                      int radius)

getMask
```
public ij.ImagePlus getMask()
```

getMaskProcessor
```
public ij.process.ImageProcessor getMaskProcessor(boolean floatProcessor,
                                                  double[] maskValues)
```
Creates a 2D 'Sholl heatmap' by applying measured values to the foreground pixels of a copy of the analyzed image.

Parameters:

floatProcessor - if true, a FloatProcessor is returned, if false, a ShortProcessor is returned

maskValues - the mask values

Returns:

the processor containing the heatmap

setPosition

protected void setPosition(int channel,
                           int frame)

withinThreshold

protected boolean withinThreshold(double value)

withinXYbounds

protected boolean withinXYbounds(int x,
                                 int y)

withinZbounds

protected boolean withinZbounds(int z)

withinBounds

protected boolean withinBounds(int x,
                               int y,
                               int z)

clearStatus
```
protected void clearStatus()
```

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

parse in interface Parser

getProfile
```
public Profile getProfile()
```
Specified by:

getProfile in interface Parser

successful
```
public boolean successful()
```
Specified by:

successful in interface Parser

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

terminate in interface Parser

reset
```
public void reset()
```

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

run in interface Runnable

Class ImageParser

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class org.scijava.command.ContextCommand

Methods inherited from class org.scijava.AbstractContextual

Methods inherited from class java.lang.Object

Methods inherited from interface org.scijava.Contextual

Field Detail

statusService

profile

properties

center

radii

imp

cal

voxelSize

lowerT

upperT

channel

frame

minX

maxX

minY

maxY

minZ

maxZ

xc

yc

zc

start

running

Constructor Detail

ImageParser

ImageParser

Method Detail

getIsotropicVoxelSize

setCenterFromROI

setCenterPx

setCenter

setThreshold

setRadii

setRadii

maxPossibleRadius

setRetrieveIntDensities

isRetrieveIntDensitiesSet

checkUnsetFields

checkUnsetFields

setHemiShells

getCircumferencePoints

getMask

getMaskProcessor

setPosition

withinThreshold

withinXYbounds

withinZbounds

withinBounds

clearStatus

parse

getProfile

successful

terminate

reset

run