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
@ALDMetaInfo(export=ALLOWED)
public class SegResult_Complete
extends 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  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  HashMap<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(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.
 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

image_name

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


number_channels

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


segMode

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


nucleusResult

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


cellsResult

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


particleResults

@ALDClassParameter(label="Particle segmentation results",
                   dataIOOrder=-15)
protected HashMap<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.


units

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

Constructor Detail

SegResult_Complete

public SegResult_Complete(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

getImageName

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

Specified by:
getImageName in interface SegResult_Interface

getNumberChannels

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


getCytoplasmResult

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


setNucleiResult

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


getNucleiResult

public SegResult_Nuclei getNucleiResult()
Returns 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.


getParticleResult

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


setResultImageStack

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


getResultImageStack

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


getSegmentationMode

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


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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