de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Class SegResult_Nuclei

java.lang.Object
  extended by de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
All Implemented Interfaces:
SegResult_Interface

@ALDParametrizedClass
@ALDMetaInfo(export=ALLOWED)
public class SegResult_Nuclei
extends Object
implements SegResult_Interface

Nuclei segmentation result from a single image channel.

Author:
moeller

Field Summary
protected  double avgsize_nuclei
          Average size of nuclei.
protected  MTBImageByte binMask
          Binary segmentation mask.
protected  String image_name
          Name of the analyzed image.
protected  MTBImage labelImage
          Gray-scale label image of nuclei regions.
protected  MTBRegion2DSet nucleiRegions
          Set of detected regions.
protected  int nucleusChannelID
          Index of the nucleus channel, if -1 it is unknown or image has only one.
protected  int number_nuclei
          Count of detected nuclei.
protected  SegResultEnums.MeasureUnit units
          Unit in which measurements are provided.
 
Constructor Summary
SegResult_Nuclei(String imgName, int channel, MTBImageByte mask, MTBImage labels, MTBRegion2DSet regs, int count, double avgsize)
          Default constructor.
 
Method Summary
 String getImageName()
          Returns the name of the processed image.
 MTBImage getLabelImage()
          Returns label image of detected nuclei.
 MTBImageByte getMask()
          Returns binary mask with segmentation result.
 SegResultEnums.MeasureUnit getMeasurementUnit()
          Returns the unit of measurements.
 double getNucleiAvgSize()
          Returns average size of detected nuclei.
 int getNucleiCount()
          Returns number of detected nuclei.
 MTBRegion2DSet getNucleiRegions()
          Returns set of detected regions.
 void setLabelImage(MTBImage limg)
          Set label image of detected nuclei.
 void setMask(MTBImageByte m)
          Specify binary mask of nuclei.
 void setMeasurementUnit(SegResultEnums.MeasureUnit u)
          Specify unit for measurements.
 void setNucleiAvgSize(double avg)
          Specify average size of nuclei.
 void setNucleiCount(int c)
          Specify number of segmented nuclei regions.
 void setNucleiRegions(MTBRegion2DSet regs)
          Specify set of regions.
 void setNucleusChannel(int c)
          Specify image channel containing nuclei (just for reference).
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

image_name

@ALDClassParameter(label="Processed image",
                   dataIOOrder=-10)
protected String image_name
Name of the analyzed image.


binMask

@ALDClassParameter(label="Binary mask")
protected MTBImageByte binMask
Binary segmentation mask.


labelImage

@ALDClassParameter(label="Labeled nuclei regions")
protected MTBImage labelImage
Gray-scale label image of nuclei regions.


nucleiRegions

@ALDClassParameter(label="Set of nuclei regions",
                   dataIOOrder=-8)
protected MTBRegion2DSet nucleiRegions
Set of detected regions.


nucleusChannelID

@ALDClassParameter(label="Nucleus channel",
                   dataIOOrder=-9)
protected int nucleusChannelID
Index of the nucleus channel, if -1 it is unknown or image has only one.


number_nuclei

@ALDClassParameter(label="Number of nuclei",
                   dataIOOrder=-7)
protected int number_nuclei
Count of detected nuclei.


avgsize_nuclei

@ALDClassParameter(label="Average size",
                   dataIOOrder=-6)
protected double avgsize_nuclei
Average size of nuclei.


units

@ALDClassParameter(label="Measurement unit",
                   dataIOOrder=-5)
protected SegResultEnums.MeasureUnit units
Unit in which measurements are provided.

Constructor Detail

SegResult_Nuclei

public SegResult_Nuclei(String imgName,
                        int channel,
                        MTBImageByte mask,
                        MTBImage labels,
                        MTBRegion2DSet regs,
                        int count,
                        double avgsize)
Default constructor.

Parameters:
imgName - Name of processed image.
channel - Index of nucleus channel.
mask - Binary mask with segmentation result.
count - Number of detected nuclei.
avgsize - Average size of nuclei.
chan - Nucleus channel ID.
Method Detail

setNucleusChannel

public void setNucleusChannel(int c)
Specify image channel containing nuclei (just for reference).

Parameters:
c - Nucleus channel ID.

getImageName

public String getImageName()
Description copied from interface: SegResult_Interface
Returns the name of the processed image.

Specified by:
getImageName in interface SegResult_Interface

setMask

public void setMask(MTBImageByte m)
Specify binary mask of nuclei.

Parameters:
m - Binary mask of detected nuclei.

getMask

public MTBImageByte getMask()
Returns binary mask with segmentation result.

Returns:
Binary mask of segmented nuclei.

setLabelImage

public void setLabelImage(MTBImage limg)
Set label image of detected nuclei.

Parameters:
limg - Label image with detected nuclei.

getLabelImage

public MTBImage getLabelImage()
Returns label image of detected nuclei.

Returns:
Label image of segmentation result.

setNucleiRegions

public void setNucleiRegions(MTBRegion2DSet regs)
Specify set of regions.

Parameters:
Set - of detected nucleus regions.

getNucleiRegions

public MTBRegion2DSet getNucleiRegions()
Returns set of detected regions.

Returns:
Set of nucleus regions.

setNucleiCount

public void setNucleiCount(int c)
Specify number of segmented nuclei regions.

Parameters:
c - Number of detected nuclei.

getNucleiCount

public int getNucleiCount()
Returns number of detected nuclei.

Returns:
Count of detected nuclei.

setNucleiAvgSize

public void setNucleiAvgSize(double avg)
Specify average size of nuclei.

Parameters:
avg - Average size of detected nuclei.

getNucleiAvgSize

public double getNucleiAvgSize()
Returns average size of detected nuclei.

Returns:
Average size of detected nuclei.

getMeasurementUnit

public SegResultEnums.MeasureUnit getMeasurementUnit()
Description copied from interface: SegResult_Interface
Returns the unit of measurements.

Specified by:
getMeasurementUnit in interface SegResult_Interface

setMeasurementUnit

public void setMeasurementUnit(SegResultEnums.MeasureUnit u)
Specify unit for measurements.

Parameters:
u - Unit used for area and length measurements.


Copyright © 2010–2015 Martin Luther University Halle-Wittenberg. All rights reserved.