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

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

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

Particle detection result for a single channel of an image.

Particles are defined as sub-cellular structures inside cells which are fluorescently labeled. The result of a particle detection comprises data like number and average size of particles, or the set of corresponding regions. In addition, binary masks of the particles are provided.

Author:
moeller

Field Summary
protected  double avgsize_particles
          Average size of particles.
protected  MTBImageByte binMask
          Binary segmentation mask.
protected  int image_channel
          Channel of the image that was processed.
protected  String image_name
          Name of the analyzed image.
protected  int number_particles
          Count of detected particles.
protected  MTBRegion2DSet particleRegions
          List of detected regions.
protected  HashMap<Integer,Double> perCellAvgSize
          Average particle size per cell (optional).
protected  HashMap<Integer,Integer> perCellCount
          Particle counts per cell (optional).
protected  SegResultEnums.MeasureUnit units
          Unit in which measurements are provided.
 
Constructor Summary
SegResult_Particles(String imgName, int ch, MTBRegion2DSet regions, MTBImageByte mask, int count, double avgsize)
          Default constructor.
 
Method Summary
 String getImageName()
          Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
 MTBImageByte getMask()
          Returns binary mask with segmentation result.
 SegResultEnums.MeasureUnit getMeasurementUnit()
          Returns the unit of measurements.
 double getParticleAvgSize()
          Returns average size of detected particles.
 int getParticleCount()
          Returns number of detected particles.
 HashMap<Integer,Double> getPerCellAvgSize()
          Returns detected particle average size per cell.
 HashMap<Integer,Integer> getPerCellCount()
          Returns detected particles per cell.
 int getProcessedChannel()
          Get the processed channel.
 void setPerCellAvgSize(HashMap<Integer,Double> map)
          Sets particle average sizes per cell.
 void setPerCellCount(HashMap<Integer,Integer> map)
          Sets particle counts per cell.
 
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.


image_channel

@ALDClassParameter(label="Analyzed channel",
                   dataIOOrder=-9)
protected int image_channel
Channel of the image that was processed.


binMask

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


particleRegions

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


number_particles

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


avgsize_particles

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


units

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


perCellCount

@ALDClassParameter(label="Particle counts per cell",
                   dataIOOrder=-4)
protected HashMap<Integer,Integer> perCellCount
Particle counts per cell (optional).


perCellAvgSize

@ALDClassParameter(label="Average particle size per cell",
                   dataIOOrder=-3)
protected HashMap<Integer,Double> perCellAvgSize
Average particle size per cell (optional).

Constructor Detail

SegResult_Particles

public SegResult_Particles(String imgName,
                           int ch,
                           MTBRegion2DSet regions,
                           MTBImageByte mask,
                           int count,
                           double avgsize)
Default constructor.

Parameters:
imgName - Name of analyzed image.
ch - Processed channel.
regions - Set of detected regions.
mask - Binary mask with segmentation result.
count - Number of detected particles.
avgsize - Average size of nuclei.
Method Detail

getImageName

public String getImageName()
Note: Returned string might be null if the result is associated with a single cell rather than a complete image!

Specified by:
getImageName in interface SegResult_Interface

getProcessedChannel

public int getProcessedChannel()
Get the processed channel.

Returns:
Channel index.

getMask

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

Note: Returned image might be null if the result is associated with a single cell rather than a complete image!

Returns:
Binary image.

getParticleCount

public int getParticleCount()
Returns number of detected particles.

Returns:
Number of detected particles.

getParticleAvgSize

public double getParticleAvgSize()
Returns average size of detected particles.

Returns:
Average size of particles.

setPerCellCount

public void setPerCellCount(HashMap<Integer,Integer> map)
Sets particle counts per cell.

Parameters:
map - Map with index-count pairs.

getPerCellCount

public HashMap<Integer,Integer> getPerCellCount()
Returns detected particles per cell.

Returns:
Map with index-count pairs.

setPerCellAvgSize

public void setPerCellAvgSize(HashMap<Integer,Double> map)
Sets particle average sizes per cell.

Parameters:
map - Map with index-size pairs.

getPerCellAvgSize

public HashMap<Integer,Double> getPerCellAvgSize()
Returns detected particle average size per cell.

Returns:
Map with index-size pairs.

getMeasurementUnit

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

Specified by:
getMeasurementUnit in interface SegResult_Interface


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