de.unihalle.informatik.MiToBo.apps.cytoskeleton

Class CytoskeletonFeatureExtractor

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor

All Implemented Interfaces:

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

Direct Known Subclasses:

CytoskeletonFeatureExtractorEigenStructures, CytoskeletonFeatureExtractorTiles

public abstract class CytoskeletonFeatureExtractor
extends MTBOperator

Operator for extracting features for the ActinAnalyzer2D.

The features which are to be extracted by operators extending this class should be specifically dedicated to filament like structures, e.g., actin fiberes or microtubuli.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CytoskeletonFeatureExtractor.CellMaskFormat Format of cell segmentation data.

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 int	cytoChannel Channel of input image containing stained cytoskeleton.
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	imageDir Input image directory.
protected int	imageHeight Height of the images, taking first image as reference.
protected int	imageWidth Width of the images, taking first image as reference.
protected static ImageReaderMTB	iRead Operator for reading image files from disk.
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	maskDir Directory with (cell) masks.
protected CytoskeletonFeatureExtractor.CellMaskFormat	maskFormat Format of provided cell masks.
protected String	operatorID Identifier string for the operator class.
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	outDir Output and working directory.
protected int	tileShiftX Tile shift in x-direction.
protected int	tileShiftY Tile size in y-direction.
protected int	tileSizeX Tile size in x-direction.
protected int	tileSizeY Tile size in y-direction.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CytoskeletonFeatureExtractor() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected abstract void	calculateFeatures() Performs the feature calculation.
protected void	operate()
protected MTBImage	readInputImageMaxProjectChannel(String f) Read image from file, do optional max projection and extract selected cytoskeleton channel.
static MTBImage	readMaskImage(String maskDir, String basename, CytoskeletonFeatureExtractor.CellMaskFormat maskFormat, double xmin, double ymin, double xmax, double ymax, boolean verbose) Read mask data from disk if available.
void	setCytoskeletonChannel(int c) Specify channel with stained cytoskeleton.
void	setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir) Specify input image directory.
void	setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir) Specify input mask directory.
void	setMaskFormat(CytoskeletonFeatureExtractor.CellMaskFormat mFormat) Specify input mask format.
void	setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir) Specify output directory.
void	setTileShiftX(int tShiftX) Specify shift of tiles in x-direction.
void	setTileShiftY(int tShiftY) Specify shift of tiles in y-direction.
void	setTileSizeX(int tSizeX) Specify size of tiles in x-direction.
void	setTileSizeY(int tSizeY) Specify size of tiles in y-direction.

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, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

imageDir

@Parameter(label="Image directory",
           required=true,
           dataIOOrder=-11,
           direction=IN,
           description="Input image directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString imageDir

Input image directory.

All files in the directory and its sub-directories are considered. If a file cannot be opened (e.g. because it is not an image) it is skipped.

cytoChannel

@Parameter(label="Cytoskeleton Channel",
           required=true,
           direction=IN,
           dataIOOrder=-10,
           description="Cytoskeleton channel, e.g., 1, 2 and so on.")
private int cytoChannel

Channel of input image containing stained cytoskeleton.

maskDir

@Parameter(label="Mask directory",
           required=true,
           dataIOOrder=-9,
           direction=IN,
           description="Cell mask directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString maskDir

Directory with (cell) masks.

maskFormat

@Parameter(label="Mask format",
           required=true,
           dataIOOrder=-8,
           direction=IN,
           description="Format of cell masks.",
           mode=STANDARD)
protected CytoskeletonFeatureExtractor.CellMaskFormat maskFormat

Format of provided cell masks.

outDir

@Parameter(label="Output and working directory",
           required=true,
           dataIOOrder=-7,
           direction=IN,
           description="Output and working directory.",
           mode=STANDARD)
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString outDir

Output and working directory.

tileSizeX

@Parameter(label="Tile size x",
           required=true,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Tile size in x-direction.")
protected int tileSizeX

Tile size in x-direction.

tileSizeY

@Parameter(label="Tile size y",
           required=true,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="Tile size in y-direction.")
protected int tileSizeY

Tile size in y-direction.

tileShiftX

@Parameter(label="Tile shift x",
           required=true,
           dataIOOrder=5,
           direction=IN,
           mode=ADVANCED,
           description="Tile shift in x-direction.")
protected int tileShiftX

Tile shift in x-direction.

tileShiftY

@Parameter(label="Tile shift y",
           required=true,
           dataIOOrder=6,
           direction=IN,
           mode=ADVANCED,
           description="Tile shift in y-direction.")
protected int tileShiftY

Tile size in y-direction.

operatorID

protected transient String operatorID

Identifier string for the operator class.

imageWidth

protected transient int imageWidth

Width of the images, taking first image as reference.

imageHeight

protected transient int imageHeight

Height of the images, taking first image as reference.

iRead

protected static ImageReaderMTB iRead

Operator for reading image files from disk.

Constructor Detail

CytoskeletonFeatureExtractor

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

Default constructor.

Throws:

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

Method Detail

setImageDir

public void setImageDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString iDir)

Specify input image directory.

Parameters:

iDir - Directory with images.

setCytoskeletonChannel

public void setCytoskeletonChannel(int c)

Specify channel with stained cytoskeleton.

Parameters:

c - ID of channel with stained cytoskeleton.

setMaskDir

public void setMaskDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString mDir)

Specify input mask directory.

Parameters:

mDir - Directory with masks.

setMaskFormat

public void setMaskFormat(CytoskeletonFeatureExtractor.CellMaskFormat mFormat)

Specify input mask format.

Parameters:

mFormat - Format of mask files, i.e. label images or ImageJ ROI files.

setOutputDir

public void setOutputDir(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString oDir)

Specify output directory.

Parameters:

oDir - Output directory for feature files.

setTileSizeX

public void setTileSizeX(int tSizeX)

Specify size of tiles in x-direction.

Parameters:

tSizeX - Tile size in x.

setTileSizeY

public void setTileSizeY(int tSizeY)

Specify size of tiles in y-direction.

Parameters:

tSizeY - Tile size in y.

setTileShiftX

public void setTileShiftX(int tShiftX)

Specify shift of tiles in x-direction.

Parameters:

tShiftX - Tile shift in x.

setTileShiftY

public void setTileShiftY(int tShiftY)

Specify shift of tiles in y-direction.

Parameters:

tShiftY - Tile shift in y.

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

calculateFeatures

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

Performs the feature calculation.

The features are saved to files in the given feature directory. If the directory is null, the output directory is to be used. Note that both directories can be the same.
For each image four files are to be saved:

• *-features.tif: stack with visualizations of individual features
• *-features.ald: history file corresponding to feature stack
• *-features.txt: features, each row refers to a specific tile, each column to an individual feature
• *-features-config.ald: history/configuration of the feature calculator

Throws:

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

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

readInputImageMaxProjectChannel

protected MTBImage readInputImageMaxProjectChannel(String f)
                                            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                   de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Read image from file, do optional max projection and extract selected cytoskeleton channel.

Parameters:

f - Name of image file to read.

Returns:

Channel of provided image file containing cytoskeleton.

Throws:

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

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

readMaskImage

public static MTBImage readMaskImage(String maskDir,
                                     String basename,
                                     CytoskeletonFeatureExtractor.CellMaskFormat maskFormat,
                                     double xmin,
                                     double ymin,
                                     double xmax,
                                     double ymax,
                                     boolean verbose)

Read mask data from disk if available.

The method reads segmentation data from file. It considers the specified mask format, i.e., if a label image is to be read or ImageJ 1.x ROIs. In the latter case it automatically differentiates between files ending with '.zip', i.e., containing more than one region, and files ending with '.roi' which contain exactly a single region.

Parameters:

maskDir - Directory where to search for the mask images.

basename - Basename of the corresponding image file.

maskFormat - Format of the mask data file.

xmin - Minimum x-value of input image domain.

ymin - Minimum y-value of input image domain.

xmax - Maximum x-value of input image domain, i.e. image width - 1.

ymax - Maximum y-value of input image domain, i.e. image height - 1.

verbose - If true, additional information is printed.

Returns:

Mask image, null if appropriate file could not be found.