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
public class SegResult_Particles
extends java.lang.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  java.lang.String image_name
          Name of the analyzed image.
protected  int number_particles
          Count of detected particles.
protected  MTBRegion2DSet particleRegions
          List of detected regions.
protected  java.util.HashMap<java.lang.Integer,java.lang.Double> perCellAvgSize
          Average particle size per cell (optional).
protected  java.util.HashMap<java.lang.Integer,java.lang.Integer> perCellCount
          Particle counts per cell (optional).
protected  SegResultEnums.MeasureUnit units
          Unit in which measurements are provided.
 
Constructor Summary
SegResult_Particles(java.lang.String imgName, int ch, MTBRegion2DSet regions, MTBImageByte mask, int count, double avgsize)
          Default constructor.
 
Method Summary
 java.lang.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.
 java.util.HashMap<java.lang.Integer,java.lang.Double> getPerCellAvgSize()
          Returns detected particle average size per cell.
 java.util.HashMap<java.lang.Integer,java.lang.Integer> getPerCellCount()
          Returns detected particles per cell.
 int getProcessedChannel()
          Get the processed channel.
 void setPerCellAvgSize(java.util.HashMap<java.lang.Integer,java.lang.Double> map)
          Sets particle average sizes per cell.
 void setPerCellCount(java.util.HashMap<java.lang.Integer,java.lang.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

avgsize_particles

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


binMask

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


image_channel

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


image_name

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


number_particles

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


particleRegions

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


perCellAvgSize

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


perCellCount

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


units

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

Constructor Detail

SegResult_Particles

public SegResult_Particles(java.lang.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 java.lang.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

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.

getMeasurementUnit

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

Specified by:
getMeasurementUnit in interface SegResult_Interface

getParticleAvgSize

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

Returns:
Average size of particles.

getParticleCount

public int getParticleCount()
Returns number of detected particles.

Returns:
Number of detected particles.

getPerCellAvgSize

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

Returns:
Map with index-size pairs.

getPerCellCount

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

Returns:
Map with index-count pairs.

getProcessedChannel

public int getProcessedChannel()
Get the processed channel.

Returns:
Channel index.

setPerCellAvgSize

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

Parameters:
map - Map with index-size pairs.

setPerCellCount

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

Parameters:
map - Map with index-count pairs.