@ALDParametrizedClass public class SegResult_Particles extends Object implements SegResult_Interface
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.
Modifier and Type | Field and Description |
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protected double |
avgsize_particles
Average size of particles.
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protected MTBImageByte |
binMask
Binary segmentation mask.
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protected int |
image_channel
Channel of the image that was processed.
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protected String |
image_name
Name of the analyzed image.
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protected int |
number_particles
Count of detected particles.
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protected MTBRegion2DSet |
particleRegions
List of detected regions.
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protected HashMap<Integer,Double> |
perCellAvgSize
Average particle size per cell (optional).
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protected HashMap<Integer,Integer> |
perCellCount
Particle counts per cell (optional).
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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_Particles(String imgName,
int ch,
MTBRegion2DSet regions,
MTBImageByte mask,
int count,
double avgsize)
Default constructor.
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Modifier and Type | Method and Description |
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String |
getImageName()
Note: Returned string might be null if the result is associated with a
single cell rather than a complete image!
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MTBImageByte |
getMask()
Returns binary mask with segmentation result.
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SegResultEnums.MeasureUnit |
getMeasurementUnit()
Returns the unit of measurements.
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double |
getParticleAvgSize()
Returns average size of detected particles.
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int |
getParticleCount()
Returns number of detected particles.
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HashMap<Integer,Double> |
getPerCellAvgSize()
Returns detected particle average size per cell.
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HashMap<Integer,Integer> |
getPerCellCount()
Returns detected particles per cell.
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int |
getProcessedChannel()
Get the processed channel.
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void |
setPerCellAvgSize(HashMap<Integer,Double> map)
Sets particle average sizes per cell.
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void |
setPerCellCount(HashMap<Integer,Integer> map)
Sets particle counts per cell.
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@ALDClassParameter(label="Processed image", dataIOOrder=-10) protected String image_name
@ALDClassParameter(label="Analyzed channel", dataIOOrder=-9) protected int image_channel
@ALDClassParameter(label="Binary mask") protected MTBImageByte binMask
@ALDClassParameter(label="Set of regions", dataIOOrder=-8) protected MTBRegion2DSet particleRegions
@ALDClassParameter(label="Number of particles", dataIOOrder=-7) protected int number_particles
@ALDClassParameter(label="Average size", dataIOOrder=-6) protected double avgsize_particles
@ALDClassParameter(label="Measurement unit", dataIOOrder=-5) protected SegResultEnums.MeasureUnit units
@ALDClassParameter(label="Particle counts per cell", dataIOOrder=-4) protected HashMap<Integer,Integer> perCellCount
public SegResult_Particles(String imgName, int ch, MTBRegion2DSet regions, MTBImageByte mask, int count, double avgsize)
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.public String getImageName()
getImageName
in interface SegResult_Interface
public int getProcessedChannel()
public MTBImageByte getMask()
Note: Returned image might be null if the result is associated with a single cell rather than a complete image!
public int getParticleCount()
public double getParticleAvgSize()
public void setPerCellCount(HashMap<Integer,Integer> map)
map
- Map with index-count pairs.public HashMap<Integer,Integer> getPerCellCount()
public void setPerCellAvgSize(HashMap<Integer,Double> map)
map
- Map with index-size pairs.public HashMap<Integer,Double> getPerCellAvgSize()
public SegResultEnums.MeasureUnit getMeasurementUnit()
SegResult_Interface
getMeasurementUnit
in interface SegResult_Interface
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