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

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

@ALDParametrizedClass
public class SegResult_Complete
extends java.lang.Object
implements SegResult_Interface

Complete segmentation result from multi-channel image.

This data structure subsumes cell boundary, nuclei and structure (particles, granules, etc.) segmentation results.

Author:
moeller

Nested Class Summary
static class SegResult_Complete.SegmentationMode
          Indicator for segmentation mode.
 
Field Summary
protected  SegResult_Cytoplasm cellsResult
          Result for cell/cytoplasm channel.
protected  java.lang.String image_name
          Name of the image.
protected  SegResult_Nuclei nucleusResult
          Result for nucleus channel.
protected  int number_channels
          Number of channels in the image.
protected  java.util.HashMap<java.lang.Integer,SegResult_Particles> particleResults
          Detection results for particles.
protected  MTBImageRGB resultImageStack
          (Optional) stack of result images with segmentation masks/overlays.
protected  SegResult_Complete.SegmentationMode segMode
          Mode how the channel of the image was treated during segmentation.
protected  SegResultEnums.MeasureUnit units
          Unit in which measurements are provided.
 
Constructor Summary
SegResult_Complete(java.lang.String iname, int channels, SegResult_Complete.SegmentationMode smode, SegResult_Cytoplasm cells)
          Default constructor.
 
Method Summary
 SegResult_Cytoplasm getCytoplasmResult()
          Returns reference to cytoplasm/cell boundary detection result.
 java.lang.String getImageName()
          Returns the name of the processed image.
 SegResultEnums.MeasureUnit getMeasurementUnit()
          Returns the unit of measurements.
 SegResult_Nuclei getNucleiResult()
          Returns nuclei detection result.
 int getNumberChannels()
          Returns the number of image channels available.
 SegResult_Particles getParticleResult(int channel)
          Returns number of detected particles per channel.
 MTBImageRGB getResultImageStack()
          Returns stack with result segmentation images.
 SegResult_Complete.SegmentationMode getSegmentationMode()
          Returns mode activated during segmentation.
 void setNucleiResult(SegResult_Nuclei nr)
          Set nuclei detection result.
 void setParticleResult(SegResult_Particles res, int channel)
          Set particle counts per channel.
 void setResultImageStack(MTBImageRGB stack)
          Set stack with result segmentation images.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

cellsResult

@ALDClassParameter(label="Cytoplasm segmentation result",
                   dataIOOrder=-16)
protected SegResult_Cytoplasm cellsResult
Result for cell/cytoplasm channel.


image_name

@ALDClassParameter(label="Processed image",
                   dataIOOrder=-20)
protected java.lang.String image_name
Name of the image.


nucleusResult

@ALDClassParameter(label="Nuclei segmentation result",
                   dataIOOrder=-17)
protected SegResult_Nuclei nucleusResult
Result for nucleus channel.


number_channels

@ALDClassParameter(label="Number of channels in image",
                   dataIOOrder=-19)
protected int number_channels
Number of channels in the image.


particleResults

@ALDClassParameter(label="Particle segmentation results",
                   dataIOOrder=-15)
protected java.util.HashMap<java.lang.Integer,SegResult_Particles> particleResults
Detection results for particles.

The map size is equal to the number of channels the image has and is indexed with the channel ID starting with 0. The contents of the detection results depend on the mode: - IMAGE_COMPLETE: only global data - INDIVIDUAL_CELLS: in addition particles per cell statistics


resultImageStack

@ALDClassParameter(label="Result image stack")
protected MTBImageRGB resultImageStack
(Optional) stack of result images with segmentation masks/overlays.


segMode

@ALDClassParameter(label="Segmentation mode",
                   dataIOOrder=-18)
protected SegResult_Complete.SegmentationMode segMode
Mode how the channel of the image was treated during segmentation.


units

@ALDClassParameter(label="Measurement units",
                   dataIOOrder=-10)
protected SegResultEnums.MeasureUnit units
Unit in which measurements are provided.

Constructor Detail

SegResult_Complete

public SegResult_Complete(java.lang.String iname,
                          int channels,
                          SegResult_Complete.SegmentationMode smode,
                          SegResult_Cytoplasm cells)
Default constructor.

Parameters:
iname - Name of the corresponding image.
channels - Number of channels of the processed image.
smode - Segmentation mode.
cells - Cell contour segmentation result.
Method Detail

getCytoplasmResult

public SegResult_Cytoplasm getCytoplasmResult()
Returns reference to cytoplasm/cell boundary detection result.


getImageName

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

Specified by:
getImageName in interface SegResult_Interface

getMeasurementUnit

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

Specified by:
getMeasurementUnit in interface SegResult_Interface

getNucleiResult

public SegResult_Nuclei getNucleiResult()
Returns nuclei detection result.


getNumberChannels

public int getNumberChannels()
Returns the number of image channels available.


getParticleResult

public SegResult_Particles getParticleResult(int channel)
Returns number of detected particles per channel.


getResultImageStack

public MTBImageRGB getResultImageStack()
Returns stack with result segmentation images.


getSegmentationMode

public SegResult_Complete.SegmentationMode getSegmentationMode()
Returns mode activated during segmentation.


setNucleiResult

public void setNucleiResult(SegResult_Nuclei nr)
Set nuclei detection result.


setParticleResult

public void setParticleResult(SegResult_Particles res,
                              int channel)
Set particle counts per channel.

Note that channel IDs start with 0! Prior results are replaced.


setResultImageStack

public void setResultImageStack(MTBImageRGB stack)
Set stack with result segmentation images.