de.unihalle.informatik.MiToBo.apps.cellMorphology

Class PaCeQuant

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.apps.cellMorphology.PaCeQuant

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              allowBatchMode=false)
public class PaCeQuant
extends MTBOperator

Operator for segmenting and analyzing pavement cell shape.

The operator first applies several preprocessing steps to a given input image, e.g., noise reduction by filtering, binarization, and several morphological operations. The outcome of this first stage are binary regions corresponding to the cells in the image. Note that the input image can either be given by an 8-bit grayscale image or an already presegmented binary image. Select the input mode accordingly.

Subsequently, the cell regions are filtered according to area, i.e. too small regions are removed. In addition we seek to exclude regions from further processing which originate from more than one physical cell and have accidentally been merged into a single region during preprocessing and segmentation.

The final stage comprises the calculation of a set of features for each region suitable to characterize the region morphology. In this stage we use the MorphologyAnalyzer2D operator.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PaCeQuant.BorderBackgroundContrast Border color.
static class	PaCeQuant.GapCloseMode Heuristic for closing border gaps.
static class	PaCeQuant.ImageType Image type.
static class	PaCeQuant.LobeTypes Different types of lobes.
static class	PaCeQuant.MeasurementUnits Unit for measurements.
static class	PaCeQuant.OperationMode Operation mode of the operator.
static class	PaCeQuant.OperatorPhasesToRun Phases to run.
static class	PaCeQuant.PixelCalibration Mode of calibrating pixel size.
static class	PaCeQuant.SegmentationInputFormat Formats for input of external segmentation results.
private class	PaCeQuant.SegmentationResult Internal class for representing the result data of segmenting an image.
private class	PaCeQuant.SkeletonPostprocessor Helper operator to post-process border skeletons.

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private Vector<MTBImageRGB>	addResultImages Vector of additional result images.
PaCeQuant.BorderBackgroundContrast	borderContrast Border to background relation.
private boolean	classifyLobes Flag to classify lobes into different type classes.
private boolean	drawRegionIDsToOutputImages Flag to enable/disable drawing region IDs.
private static HashMap<String,String>	featureNameMapper
private static String[]	featureParameters List of parameters relevant for feature extraction phase.
private PaCeQuant.GapCloseMode	gapMode Mode for closing gaps.
private MTBImage	gaussFilterImg Gauss filtered input image (for internal use only).
private int	height Height of the input image.
PaCeQuant.ImageType	imType Image type.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	inDir Input directory where to find the images to process.
private MTBImageByte	inImg Input image to process.
private MTBRegion2DSet	inRegions Input image to process.
private double	maximalCellSize Threshold for the maximal admissible cell size.
private double	minimalCellSize Threshold for the minimal admissible cell size.
private MorphologyAnalyzer2D	morphFeatureOp Operator to analyze morphology of cells.
private int	naiveGapThreshold Maximal distance of gaps in naive mode to be closed.
double	niblackVarianceThresh Niblack threshold.
private static String	operatorID Identifier string for this operator class.
PaCeQuant.OperationMode	opMode Mode of operation of the operator.
private String	phaseAInfo Info string for segmentation phase configuration parameters.
private String	phaseBInfo Info string for segmentation phase configuration parameters.
private PaCeQuant.OperatorPhasesToRun	phasesToRun Select with phases to run.
private PaCeQuant.PixelCalibration	pixCalibMode Mode for calibrating physical pixel size.
private double	pixelLengthXY Physical size of a pixel.
private double	pixelLengthXYinternal Pixel length only used internally.
private String	pixelUnitString Unit for pixel length.
private MTBImageRGB	resultAdditionalImages Additional result images condensed into a single stack (only available if showAdditionalResultImages is true).
private MTBImageShort	resultCellLabelImg Label image of detected cell regions.
private MTBImageRGB	resultCellOverlayImg Overlay of input image with pseudo-colored cell regions.
private MTBRegion2DSet	resultCellRegions Set of detected cell regions.
private MTBImageRGB	resultFeatureStack Stack of individual feature images as heat maps (only available if showResultFeatureStack is true).
private MTBTableModel	resultFeatureTable Table with region features.
private String	resultInfo Info string for segmentation phase configuration parameters.
private Vector<MTBTableModel>	resultLobeFeatureTables (Optional) set of tables with type information and features per lobe.
private MTBImageRGB	resultLobeTypeImage Image showing lobe classification.
private double	resultMaxRegionSizeThreshold Used threshold for maximal size of valid regions.
private double	resultMinRegionSizeThreshold Used threshold for minimal size of valid regions.
private PaCeQuant.SegmentationInputFormat	segmentationInputFormat Format of external segmentation input.
private static String[]	segmentationParameters List of parameters relevant for segmentation phase.
private boolean	showAdditionalResultImages Flag to enable/disable showing additional and intermediate result images.
private boolean	showResultFeatureStack Flag to enable/disable showing feature visualization stack.
private PaCeQuant.MeasurementUnits	thresholdUnits Units for size thresholds.
private PaCeQuant.MeasurementUnits	unitXY Physical pixel size units.
private MTBImage	vesselImg Result of vesselness detection (for internal use only).
private int	width Width of the input image.

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
PaCeQuant() Default constructor.

Method Summary

Modifier and Type	Method and Description
private MTBTableModel	calculateRegionFeatures(MTBRegion2DSet regions, MTBImage labelImg) Extracts features for all detected and valid cell regions.
private MTBImageByte	closeGapsNativeLinks(MTBImageByte skelImg) Method to close gaps by linking adjacent endpoints.
private MTBImageByte	closeGapsWatershed(MTBImageByte skelImg) Method to close gaps by watershed transformation.
protected static void	drawStringToImage(MTBImageRGB img, String s, int r, int g, int b, int xPos, int yPos) Draws string at given position into image.
protected static void	drawStringToImage(MTBImageShort img, String s, int g, int xPos, int yPos) Draws string at given position into image.
private MTBRegion2DSet	filterValidCellRegions(MTBImageByte image) Postprocesses cell regions and applies some filtering.
protected void	operate()
protected void	prepareAdditionalResultDataStack(String title)
protected void	reinitOperator() Re-initialize the operator just in case it was already run before.
protected MTBTableModel	runFeatureExtractionPhase(MTBImage img, MTBRegion2DSet validRegions, MTBImage labelImg) Extracts features from given set of regions and corresponding images
protected PaCeQuant.SegmentationResult	runSegmentationPhase(MTBImage img) Method that processes a single image.
protected void	saveRegionData(String resultDir, String fileRoot, MTBRegion2DSet regions) Save region set to output file.
private MTBImageByte	segmentInputImage(MTBImage img) Preprocessing and segmentation of input image.
private void	switchGapCloseMode() Callback routine called if gap closing mode parameter changes.
private void	switchOpModeParameters() Callback routine to change operator mode parameters.
private void	switchPhaseConfigParameters() Callback routine to change phase parameters.
private void	switchPixelCalibParameters() Callback routine called if pixel calibration mode parameter changes.
private void	switchSegmentationFormatParameter() Callback routine called if format parameter changes.
void	validateCustom()

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

operatorID

private static final String operatorID

Identifier string for this operator class.

See Also:

Constant Field Values

segmentationParameters

private static transient String[] segmentationParameters

List of parameters relevant for segmentation phase.

featureParameters

private static transient String[] featureParameters

List of parameters relevant for feature extraction phase.

phasesToRun

@Parameter(label="Select phases to run",
           required=true,
           direction=IN,
           dataIOOrder=-10,
           mode=STANDARD,
           callback="switchPhaseConfigParameters",
           paramModificationMode=MODIFIES_INTERFACE,
           description="Choose between segmentation and/or feature extraction.")
private PaCeQuant.OperatorPhasesToRun phasesToRun

Select with phases to run.

segmentationInputFormat

@Parameter(label="   Format of external segmentation data",
           required=true,
           direction=IN,
           dataIOOrder=-8,
           mode=STANDARD,
           callback="switchSegmentationFormatParameter",
           paramModificationMode=MODIFIES_INTERFACE,
           description="Segmentation data format.")
private PaCeQuant.SegmentationInputFormat segmentationInputFormat

Format of external segmentation input.

This parameter is only used if no segmentation is done by PaCeQuant.

opMode

@Parameter(label="Operation Mode",
           required=true,
           direction=IN,
           dataIOOrder=-5,
           description="Operation mode of the operator.",
           callback="switchOpModeParameters",
           paramModificationMode=MODIFIES_INTERFACE)
public PaCeQuant.OperationMode opMode

Mode of operation of the operator.

imType

public PaCeQuant.ImageType imType

Image type.

inDir

@Parameter(label="Input Directory",
           required=true,
           direction=IN,
           description="Input directory.",
           dataIOOrder=-3)
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString inDir

Input directory where to find the images to process.

Depending on the chosen input type the image can either be given by an 8-bit grayscale image or a binary image. In the first case the image is preprocessed and segmentation procedures are applied to identify individual cell regions. In the latter case it is assumend that the cells have already been segmented and each cell is represented by a connected component, i.e. the preprocessing and segmentation steps are skipped.

inImg

@Parameter(label="Input Image",
           required=true,
           direction=IN,
           description="Input image.",
           dataIOOrder=-3)
private transient MTBImageByte inImg

Input image to process.

Depending on the chosen input type the image can either be given by an 8-bit grayscale image or a binary image. In the first case the image is preprocessed and segmentation procedures are applied to identify individual cell regions. In the latter case it is assumend that the cells have already been segmented and each cell is represented by a connected component, i.e. the preprocessing and segmentation steps are skipped.

inRegions

@Parameter(label="Input Regions",
           required=true,
           direction=IN,
           description="Input image.",
           dataIOOrder=-3)
private transient MTBRegion2DSet inRegions

Input image to process.

Depending on the chosen input type the image can either be given by an 8-bit grayscale image or a binary image. In the first case the image is preprocessed and segmentation procedures are applied to identify individual cell regions. In the latter case it is assumend that the cells have already been segmented and each cell is represented by a connected component, i.e. the preprocessing and segmentation steps are skipped.

pixCalibMode

@Parameter(label="Pixel calibration mode",
           required=true,
           direction=IN,
           dataIOOrder=0,
           description="In AUTO mode data is extracted from input data.",
           callback="switchPixelCalibParameters",
           paramModificationMode=MODIFIES_INTERFACE)
private PaCeQuant.PixelCalibration pixCalibMode

Mode for calibrating physical pixel size.

pixelLengthXY

@Parameter(label="Pixel length",
           required=true,
           direction=IN,
           description="Pixel length, note that we assume square pixels!",
           dataIOOrder=1)
private double pixelLengthXY

Physical size of a pixel.

unitXY

@Parameter(label="Size unit x/y",
           required=true,
           direction=IN,
           description="Pixel units.",
           dataIOOrder=2)
private PaCeQuant.MeasurementUnits unitXY

Physical pixel size units.

phaseAInfo

@Parameter(label="Configure segmentation phase:",
           required=true,
           direction=IN,
           dataIOOrder=3,
           info=true,
           mode=STANDARD,
           description="Info string.")
private String phaseAInfo

Info string for segmentation phase configuration parameters.

borderContrast

@Parameter(label="Border Contrast",
           required=true,
           direction=IN,
           dataIOOrder=4,
           description="Border to background relation.")
public PaCeQuant.BorderBackgroundContrast borderContrast

Border to background relation.

gapMode

@Parameter(label="Heuristic for Gap Closing",
           required=true,
           direction=IN,
           dataIOOrder=6,
           description="Choose mode for closing gaps.",
           callback="switchGapCloseMode",
           paramModificationMode=MODIFIES_INTERFACE)
private PaCeQuant.GapCloseMode gapMode

Mode for closing gaps.

naiveGapThreshold

@Parameter(label="  End-point distance for naive heuristic",
           required=true,
           direction=IN,
           dataIOOrder=7,
           description="Maximal distance of end-points to be linked.")
private int naiveGapThreshold

Maximal distance of gaps in naive mode to be closed.

thresholdUnits

@Parameter(label="Unit for Size Thresholds",
           required=true,
           direction=IN,
           dataIOOrder=8,
           description="Unit of specified size thresholds.")
private PaCeQuant.MeasurementUnits thresholdUnits

Units for size thresholds.

minimalCellSize

@Parameter(label="Minimal Size of Cells",
           required=true,
           direction=IN,
           dataIOOrder=8,
           description="Cells smaller than this threshold are discarded.")
private double minimalCellSize

Threshold for the minimal admissible cell size.

Cell regions falling below this threshold are ignored.

maximalCellSize

@Parameter(label="Maximal Size of Cells",
           required=true,
           direction=IN,
           dataIOOrder=9,
           description="Cells larger than this threshold are discarded.")
private double maximalCellSize

Threshold for the maximal admissible cell size.

Cell regions lying above this threshold are ignored.

phaseBInfo

@Parameter(label="Configure feature extraction phase:",
           required=true,
           direction=IN,
           dataIOOrder=10,
           info=true,
           mode=STANDARD,
           description="Info string.")
private String phaseBInfo

Info string for segmentation phase configuration parameters.

morphFeatureOp

@Parameter(label="Feature Extraction",
           required=true,
           direction=IN,
           dataIOOrder=11,
           mode=STANDARD,
           description="Feature extraction operator.")
private MorphologyAnalyzer2D morphFeatureOp

Operator to analyze morphology of cells.

classifyLobes

@Parameter(label="Analyze lobe types?",
           required=true,
           direction=IN,
           dataIOOrder=12,
           mode=STANDARD,
           description="Enable/disable lobe types.")
private boolean classifyLobes

Flag to classify lobes into different type classes.

niblackVarianceThresh

@Parameter(label="Niblack threshold",
           required=false,
           direction=IN,
           dataIOOrder=-5,
           mode=ADVANCED,
           description="Threshold for variance check in Niblack binarization.")
public double niblackVarianceThresh

Niblack threshold.

resultInfo

@Parameter(label="Configure result data:",
           required=false,
           direction=IN,
           dataIOOrder=0,
           info=true,
           mode=STANDARD,
           description="Info string.")
private String resultInfo

Info string for segmentation phase configuration parameters.

drawRegionIDsToOutputImages

@Parameter(label="Draw region IDs to output images?",
           required=false,
           direction=IN,
           dataIOOrder=10,
           mode=STANDARD,
           description="Enable/disable drawing of region IDs.")
private boolean drawRegionIDsToOutputImages

Flag to enable/disable drawing region IDs.

showAdditionalResultImages

@Parameter(label="Show/save additional results?",
           required=false,
           supplemental=true,
           direction=IN,
           dataIOOrder=1,
           mode=STANDARD,
           description="Enable/disable showing additional results.")
private boolean showAdditionalResultImages

Flag to enable/disable showing additional and intermediate result images.

showResultFeatureStack

@Parameter(label="Show/save feature stack? (takes some time...)",
           required=false,
           supplemental=true,
           direction=IN,
           dataIOOrder=2,
           mode=STANDARD,
           description="Enable/disable showing feature stack.")
private boolean showResultFeatureStack

Flag to enable/disable showing feature visualization stack.

Attention, stack is large, saving to disk takes some time!

resultCellRegions

@Parameter(label="Detected cell regions",
           supplemental=false,
           direction=OUT,
           dataIOOrder=0,
           description="Set of detected and filtered cell regions.")
private transient MTBRegion2DSet resultCellRegions

Set of detected cell regions.

resultFeatureTable

@Parameter(label="Result Table of Feature Value",
           dataIOOrder=1,
           direction=OUT,
           description="Result table of region features.")
private transient MTBTableModel resultFeatureTable

Table with region features.

Each row contains one region, each column corresponds to a feature.

resultCellOverlayImg

@Parameter(label="Detected Cell Regions Image",
           dataIOOrder=2,
           direction=OUT,
           description="Image of detected cell regions (overlay).")
private transient MTBImageRGB resultCellOverlayImg

Overlay of input image with pseudo-colored cell regions.

resultCellLabelImg

@Parameter(label="Label Image of Detected Cell Regions",
           dataIOOrder=3,
           direction=OUT,
           description="Label image of detected cell regions.")
private transient MTBImageShort resultCellLabelImg

Label image of detected cell regions.

resultMinRegionSizeThreshold

@Parameter(label="Minimal Size of Valid Regions",
           dataIOOrder=4,
           direction=OUT,
           description="Calculated threshold for filtering regions.")
private double resultMinRegionSizeThreshold

Used threshold for minimal size of valid regions.

resultMaxRegionSizeThreshold

@Parameter(label="Maximal Size of Valid Regions",
           dataIOOrder=5,
           direction=OUT,
           description="Calculated threshold for filtering regions.")
private double resultMaxRegionSizeThreshold

Used threshold for maximal size of valid regions.

resultLobeFeatureTables

@Parameter(label="Result Tables of Lobe Types and Features",
           dataIOOrder=6,
           direction=OUT,
           description="Result tables of lobe types and features.")
private transient Vector<MTBTableModel> resultLobeFeatureTables

(Optional) set of tables with type information and features per lobe.

These data are only available if classifyLobes is true.

resultLobeTypeImage

@Parameter(label="Result Image with Lobe Types",
           dataIOOrder=7,
           direction=OUT,
           description="Image displaying lobe types.")
private transient MTBImageRGB resultLobeTypeImage

Image showing lobe classification.

This result image is only available if classifyLobes is true.

resultAdditionalImages

@Parameter(label="Additonal Result Images",
           dataIOOrder=0,
           direction=OUT,
           supplemental=true,
           description="Additional result images (as stack).")
private transient MTBImageRGB resultAdditionalImages

Additional result images condensed into a single stack (only available if showAdditionalResultImages is true).

resultFeatureStack

@Parameter(label="Result Feature Stack",
           dataIOOrder=5,
           direction=OUT,
           supplemental=true,
           description="Result image stack with feature values.")
private transient MTBImageRGB resultFeatureStack

Stack of individual feature images as heat maps (only available if showResultFeatureStack is true).

width

private transient int width

Width of the input image.

height

private transient int height

Height of the input image.

pixelLengthXYinternal

private double pixelLengthXYinternal

Pixel length only used internally.

pixelUnitString

private String pixelUnitString

Unit for pixel length.

gaussFilterImg

private transient MTBImage gaussFilterImg

Gauss filtered input image (for internal use only).

vesselImg

private transient MTBImage vesselImg

Result of vesselness detection (for internal use only).

addResultImages

private transient Vector<MTBImageRGB> addResultImages

Vector of additional result images.

featureNameMapper

private static transient HashMap<String,String> featureNameMapper

Constructor Detail

PaCeQuant

public PaCeQuant()
          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown if construction fails.

Method Detail

switchOpModeParameters

private void switchOpModeParameters()

Callback routine to change operator mode parameters.

switchPixelCalibParameters

private void switchPixelCalibParameters()

Callback routine called if pixel calibration mode parameter changes.

switchSegmentationFormatParameter

private void switchSegmentationFormatParameter()

Callback routine called if format parameter changes.

switchPhaseConfigParameters

private void switchPhaseConfigParameters()

Callback routine to change phase parameters.

switchGapCloseMode

private void switchGapCloseMode()

Callback routine called if gap closing mode parameter changes.

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

reinitOperator

protected void reinitOperator()

Re-initialize the operator just in case it was already run before.

saveRegionData

protected void saveRegionData(String resultDir,
                              String fileRoot,
                              MTBRegion2DSet regions)
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Save region set to output file.

This method saves each region of the set to an individual output file and in addition all regions together to a common zip file.

Parameters:

resultDir - Directory where to save the files.

fileRoot - Common root of all file names.

regions - Set of regions to save.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

prepareAdditionalResultDataStack

protected void prepareAdditionalResultDataStack(String title)

runSegmentationPhase

protected PaCeQuant.SegmentationResult runSegmentationPhase(MTBImage img)
                                                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Method that processes a single image.

Parameters:

img - Image to process.

Returns:

Cell region segmentation result.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

runFeatureExtractionPhase

protected MTBTableModel runFeatureExtractionPhase(MTBImage img,
                                                  MTBRegion2DSet validRegions,
                                                  MTBImage labelImg)
                                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Extracts features from given set of regions and corresponding images

Parameters:

img - Input image to process.

validRegions - Corresponding set of regions.

labelImg - Corresponding label image.

Returns:

Feature table, for details see also MorphologyAnalyzer2D.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

segmentInputImage

private MTBImageByte segmentInputImage(MTBImage img)
                                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Preprocessing and segmentation of input image.

Parameters:

img - Image to process.

Returns:

Preprocessed image, i.e. binary image with cell regions.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of processing failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with processing history.

closeGapsWatershed

private MTBImageByte closeGapsWatershed(MTBImageByte skelImg)
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Method to close gaps by watershed transformation.

Parameters:

skelImg - Input skeleton image of cell borders.

Returns:

Post-processed skeleton image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of failure.

closeGapsNativeLinks

private MTBImageByte closeGapsNativeLinks(MTBImageByte skelImg)

Method to close gaps by linking adjacent endpoints.

Parameters:

skelImg - Input skeleton image of cell borders.

Returns:

Post-processed skeleton image.

filterValidCellRegions

private MTBRegion2DSet filterValidCellRegions(MTBImageByte image)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Postprocesses cell regions and applies some filtering.

The method mainly targets at discarding invalid regions, e.g., regions which are too small, touch the image border, or which most likely refer to more than one cell and have accidentally been merged.

Parameters:

image - Binary input image (regions white, background black).

Returns:

Set of valid cell regions.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of operation failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with the processing history.

calculateRegionFeatures

private MTBTableModel calculateRegionFeatures(MTBRegion2DSet regions,
                                              MTBImage labelImg)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Extracts features for all detected and valid cell regions.

Parameters:

regions - Set of valid regions.

labelImg - Corresponding label image of region set.

Returns:

Feature table.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with the processing history.

drawStringToImage

protected static void drawStringToImage(MTBImageRGB img,
                                        String s,
                                        int r,
                                        int g,
                                        int b,
                                        int xPos,
                                        int yPos)

Draws string at given position into image.

Parameters:

img - Image where to draw the string into.

s - String to draw.

r - Red color ratio.

g - Green color ratio.

b - Blue color ratio.

xPos - Position of string in x.

yPos - Position of string in y.

drawStringToImage

protected static void drawStringToImage(MTBImageShort img,
                                        String s,
                                        int g,
                                        int xPos,
                                        int yPos)

Draws string at given position into image.

Parameters:

img - Image where to draw the string into.

s - String to draw.

g - Grayscale value.

xPos - Position of string in x.

yPos - Position of string in y.