de.unihalle.informatik.MiToBo.core.imageJ

Class RoiManagerAdapter.RoiReader

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader

All Implemented Interfaces:

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

Enclosing class:

RoiManagerAdapter

private static class RoiManagerAdapter.RoiReader
extends MTBOperator

Class for parsing ImageJ roi files and zip archives.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RoiManagerAdapter.RoiReader.TargetFormat Format into which the ROIs should be converted.

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 double	domainXmax Maximal x coordinate of user-specified domain.
private double	domainXmin Minimal x coordinate of user-specified domain.
private double	domainYmax Maximal y coordinate of user-specified domain.
private double	domainYmin Minimal y coordinate of user-specified domain.
private RoiManagerAdapter.RoiReader.TargetFormat	format Target format.
private MTBStringData	inFile Input file name.
private MTBPolygon2DSet	polys Result polygon set, if target format are polygons or snakes.
private MTBRegion2DSet	regions Result region set, if target format are regions.
private Hashtable<String,ij.gui.Roi>	roitable Helper hash table.
private boolean	useSpecifiedDomain Flag for using user-specified domain information.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
RoiReader(String infile, RoiManagerAdapter.RoiReader.TargetFormat tFormat) Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	doUseSpecifiedDomain(boolean b) Enable/disable use of domain specified by the user.
MTBPolygon2DSet	getPolySet() Get the polygon set.
MTBRegion2DSet	getRegionSet() Get the region set.
private String	getUniqueName(String ename) Generates a unique name for a new roi in the manager.
private void	openRoiManagerFile(String path) Opens a zip file with ImageJ ROIs.
protected void	operate()
void	setDomainXMax(double xm) Set maximal x value of user-specified domain.
protected void	setDomainXMin(double xm) Set minimal x value of user-specified domain.
void	setDomainYMax(double ym) Set maximal y value of user-specified domain.
void	setDomainYMin(double ym) Set minimal y value of user-specified domain.

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

inFile

@Parameter(label="Input file",
           required=true,
           dataIOOrder=0,
           direction=IN,
           supplemental=false,
           description="Input ROI file.")
private MTBStringData inFile

Input file name.

format

@Parameter(label="Target format",
           required=true,
           dataIOOrder=1,
           direction=IN,
           supplemental=false,
           description="Target format.")
private RoiManagerAdapter.RoiReader.TargetFormat format

Target format.

useSpecifiedDomain

@Parameter(label="Use user-specified domain?",
           required=true,
           direction=IN,
           supplemental=false,
           dataIOOrder=10,
           mode=ADVANCED,
           description="Flag for using user-specified domain.")
private boolean useSpecifiedDomain

Flag for using user-specified domain information.

domainXmin

@Parameter(label="Minimal x",
           required=true,
           direction=IN,
           supplemental=false,
           dataIOOrder=11,
           mode=ADVANCED,
           description="Minimal value in x of user-specified domain.")
private double domainXmin

Minimal x coordinate of user-specified domain.

domainXmax

@Parameter(label="Maximal x",
           required=true,
           direction=IN,
           supplemental=false,
           dataIOOrder=12,
           mode=ADVANCED,
           description="Maximal value in x of user-specified domain.")
private double domainXmax

Maximal x coordinate of user-specified domain.

domainYmin

@Parameter(label="Minimal y",
           required=true,
           direction=IN,
           supplemental=false,
           dataIOOrder=13,
           mode=ADVANCED,
           description="Minimal value in y of user-specified domain.")
private double domainYmin

Minimal y coordinate of user-specified domain.

domainYmax

@Parameter(label="Maximal y",
           required=true,
           direction=IN,
           supplemental=false,
           dataIOOrder=14,
           mode=ADVANCED,
           description="Maximal value in y of user-specified domain.")
private double domainYmax

Maximal y coordinate of user-specified domain.

polys

@Parameter(label="Polygon set",
           supplemental=false,
           direction=OUT,
           description="Output set of polygons.")
private MTBPolygon2DSet polys

Result polygon set, if target format are polygons or snakes.

regions

@Parameter(label="Region set",
           supplemental=false,
           direction=OUT,
           description="Output set of regions.")
private MTBRegion2DSet regions

Result region set, if target format are regions.

roitable

private Hashtable<String,ij.gui.Roi> roitable

Helper hash table.

Constructor Detail

RoiReader

public RoiReader(String infile,
                 RoiManagerAdapter.RoiReader.TargetFormat tFormat)
          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

infile - Input filename.

tFormat - Target format to return.

Throws:

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

Method Detail

doUseSpecifiedDomain

protected void doUseSpecifiedDomain(boolean b)

Enable/disable use of domain specified by the user.

Parameters:

b - If true, domain usage is enabled, otherwise disabled.

setDomainXMin

protected void setDomainXMin(double xm)

Set minimal x value of user-specified domain.

Parameters:

xm - Minimal x value.

setDomainXMax

public void setDomainXMax(double xm)

Set maximal x value of user-specified domain.

Parameters:

xm - Maximal x value.

setDomainYMin

public void setDomainYMin(double ym)

Set minimal y value of user-specified domain.

Parameters:

ym - Minimal y value.

setDomainYMax

public void setDomainYMax(double ym)

Set maximal y value of user-specified domain.

Parameters:

ym - Maximal y value.

getPolySet

public MTBPolygon2DSet getPolySet()

Get the polygon set.

Returns:

Polygon set read from file.

getRegionSet

public MTBRegion2DSet getRegionSet()

Get the region set.

Returns:

Region set read from file.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

openRoiManagerFile

private void openRoiManagerFile(String path)

Opens a zip file with ImageJ ROIs.

Parameters:

path - Path to file that should be opened.

getUniqueName

private String getUniqueName(String ename)

Generates a unique name for a new roi in the manager.

Parameters:

ename - Roi to rename for uniqueness.

Returns:

Unique name of roi under consideration.