de.unihalle.informatik.MiToBo.core.imageJ

Class RoiWriter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.core.imageJ.RoiWriter

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=NONE,
              level=STANDARD,
              allowBatchMode=false)
public class RoiWriter
extends MTBOperator

Operator to save data objects to native ImageJ ROIs.

Note that only objects can be saved which implement the interface MTBDataExportableToImageJROI. Since the MiToBo data types are converted to ImageJ data types it is not guaranteed that all properties are preserved, but some information might get lost. However, objects saved with this writer can be opened in any ImageJ installation without requiring MiToBo to be installed.

Author:

moeller

Nested Class Summary

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 MTBDataExportableToImageJROI	data Data to save to file.
static String	operatorID Identifier string for this operator.
private de.unihalle.informatik.Alida.datatypes.ALDFileString	outFile Output file name.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
RoiWriter() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	operate()
private void	savePolygon(ij.gui.PolygonRoi pr) Saves the given polygon to the specified output file.
private void	savePolygonSet(ij.gui.PolygonRoi[] prs) Saves the set of polygons to the specified output file.
void	setData(MTBDataExportableToImageJROI d) Specify the data to save.
void	setOutputFile(String file) Specify the file where to save the data.

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

operatorID

public static final String operatorID

Identifier string for this operator.

See Also:

Constant Field Values

data

@Parameter(label="Data to save",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="Data.")
private MTBDataExportableToImageJROI data

Data to save to file.

outFile

@Parameter(label="Output file",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Output ROI file.")
private de.unihalle.informatik.Alida.datatypes.ALDFileString outFile

Output file name.

Constructor Detail

RoiWriter

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

Default constructor.

Throws:

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

Method Detail

setOutputFile

public void setOutputFile(String file)

Specify the file where to save the data.

Note that the name might be modified to meet ImageJ conventions, i.e., an ending '.roi' or '.zip' might be added.

Parameters:

file - Filename where to save the data.

setData

public void setData(MTBDataExportableToImageJROI d)

Specify the data to save.

Parameters:

d - Data object.

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

savePolygon

private void savePolygon(ij.gui.PolygonRoi pr)

Saves the given polygon to the specified output file.

The output file written by this method contains a single polygon.

The code of this method in parts origins from the ImageJ source code, for details see the method save() in https://imagej.nih.gov/ij/developer/source/ij/plugin/frame/RoiManager.java.html

Parameters:

pr - Polygon to save.

savePolygonSet

private void savePolygonSet(ij.gui.PolygonRoi[] prs)

Saves the set of polygons to the specified output file.

The output file is a zip archive containing a set of ROIs.

The code of this method in parts origins from the ImageJ source code, for details see the method save() in https://imagej.nih.gov/ij/developer/source/ij/plugin/frame/RoiManager.java.html

Parameters:

prs - Set of polygons to save.