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java.lang.Objectde.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
@ALDParametrizedClass public class SegResult_Complete
Complete segmentation result from multi-channel image.
This data structure subsumes cell boundary, nuclei and structure (particles, granules, etc.) segmentation results.
Nested Class Summary | |
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static class |
SegResult_Complete.SegmentationMode
Indicator for segmentation mode. |
Field Summary | |
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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 | |
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SegResult_Complete(java.lang.String iname,
int channels,
SegResult_Complete.SegmentationMode smode,
SegResult_Cytoplasm cells)
Default constructor. |
Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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@ALDClassParameter(label="Cytoplasm segmentation result", dataIOOrder=-16) protected SegResult_Cytoplasm cellsResult
@ALDClassParameter(label="Processed image", dataIOOrder=-20) protected java.lang.String image_name
@ALDClassParameter(label="Nuclei segmentation result", dataIOOrder=-17) protected SegResult_Nuclei nucleusResult
@ALDClassParameter(label="Number of channels in image", dataIOOrder=-19) protected int number_channels
@ALDClassParameter(label="Particle segmentation results", dataIOOrder=-15) protected java.util.HashMap<java.lang.Integer,SegResult_Particles> particleResults
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
@ALDClassParameter(label="Result image stack") protected MTBImageRGB resultImageStack
@ALDClassParameter(label="Segmentation mode", dataIOOrder=-18) protected SegResult_Complete.SegmentationMode segMode
@ALDClassParameter(label="Measurement units", dataIOOrder=-10) protected SegResultEnums.MeasureUnit units
Constructor Detail |
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public SegResult_Complete(java.lang.String iname, int channels, SegResult_Complete.SegmentationMode smode, SegResult_Cytoplasm cells)
iname
- Name of the corresponding image.channels
- Number of channels of the processed image.smode
- Segmentation mode.cells
- Cell contour segmentation result.Method Detail |
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public SegResult_Cytoplasm getCytoplasmResult()
public java.lang.String getImageName()
SegResult_Interface
getImageName
in interface SegResult_Interface
public SegResultEnums.MeasureUnit getMeasurementUnit()
SegResult_Interface
getMeasurementUnit
in interface SegResult_Interface
public SegResult_Nuclei getNucleiResult()
public int getNumberChannels()
public SegResult_Particles getParticleResult(int channel)
public MTBImageRGB getResultImageStack()
public SegResult_Complete.SegmentationMode getSegmentationMode()
public void setNucleiResult(SegResult_Nuclei nr)
public void setParticleResult(SegResult_Particles res, int channel)
Note that channel IDs start with 0! Prior results are replaced.
public void setResultImageStack(MTBImageRGB stack)
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