@ALDParametrizedClass public class SegResult_Complete extends Object implements SegResult_Interface
This data structure subsumes cell boundary, nuclei and structure (particles, granules, etc.) segmentation results.
Modifier and Type | Class and Description |
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static class |
SegResult_Complete.SegmentationMode
Indicator for segmentation mode.
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Modifier and Type | Field and Description |
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protected SegResult_Cytoplasm |
cellsResult
Result for cell/cytoplasm channel.
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protected String |
image_name
Name of the image.
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protected SegResult_Nuclei |
nucleusResult
Result for nucleus channel.
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protected int |
number_channels
Number of channels in the image.
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protected HashMap<Integer,SegResult_Particles> |
particleResults
Detection results for particles.
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protected MTBImageRGB |
resultImageStack
(Optional) stack of result images with segmentation masks/overlays.
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protected SegResult_Complete.SegmentationMode |
segMode
Mode how the channel of the image was treated during segmentation.
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protected SegResultEnums.MeasureUnit |
units
Unit in which measurements are provided.
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Constructor and Description |
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SegResult_Complete(String iname,
int channels,
SegResult_Complete.SegmentationMode smode,
SegResult_Cytoplasm cells)
Default constructor.
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Modifier and Type | Method and Description |
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SegResult_Cytoplasm |
getCytoplasmResult()
Returns reference to cytoplasm/cell boundary detection result.
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String |
getImageName()
Returns the name of the processed image.
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SegResultEnums.MeasureUnit |
getMeasurementUnit()
Returns the unit of measurements.
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SegResult_Nuclei |
getNucleiResult()
Returns nuclei detection result.
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int |
getNumberChannels()
Returns the number of image channels available.
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SegResult_Particles |
getParticleResult(int channel)
Returns number of detected particles per channel.
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MTBImageRGB |
getResultImageStack()
Returns stack with result segmentation images.
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SegResult_Complete.SegmentationMode |
getSegmentationMode()
Returns mode activated during segmentation.
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void |
setNucleiResult(SegResult_Nuclei nr)
Set nuclei detection result.
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void |
setParticleResult(SegResult_Particles res,
int channel)
Set particle counts per channel.
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void |
setResultImageStack(MTBImageRGB stack)
Set stack with result segmentation images.
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@ALDClassParameter(label="Processed image", dataIOOrder=-20) protected String image_name
@ALDClassParameter(label="Number of channels in image", dataIOOrder=-19) protected int number_channels
@ALDClassParameter(label="Segmentation mode", dataIOOrder=-18) protected SegResult_Complete.SegmentationMode segMode
@ALDClassParameter(label="Nuclei segmentation result", dataIOOrder=-17) protected SegResult_Nuclei nucleusResult
@ALDClassParameter(label="Cytoplasm segmentation result", dataIOOrder=-16) protected SegResult_Cytoplasm cellsResult
@ALDClassParameter(label="Particle segmentation results", dataIOOrder=-15) protected HashMap<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="Measurement units", dataIOOrder=-10) protected SegResultEnums.MeasureUnit units
public SegResult_Complete(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.public String getImageName()
SegResult_Interface
getImageName
in interface SegResult_Interface
public int getNumberChannels()
public SegResult_Cytoplasm getCytoplasmResult()
public void setNucleiResult(SegResult_Nuclei nr)
public SegResult_Nuclei getNucleiResult()
public void setParticleResult(SegResult_Particles res, int channel)
Note that channel IDs start with 0! Prior results are replaced.
public SegResult_Particles getParticleResult(int channel)
public void setResultImageStack(MTBImageRGB stack)
public MTBImageRGB getResultImageStack()
public SegResult_Complete.SegmentationMode getSegmentationMode()
public SegResultEnums.MeasureUnit getMeasurementUnit()
SegResult_Interface
getMeasurementUnit
in interface SegResult_Interface
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