de.unihalle.informatik.MiToBo.core.imageJ

Class RoiFileToCSVConverter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.core.imageJ.RoiFileToCSVConverter

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 RoiFileToCSVConverter
extends MTBOperator

Operator to convert contours of ImageJ ROIs to CSV format.

Each ROI in the provided input file is converted into a CSV output file. In detail, the CSV file will contain the coordinates of the contour points of the ROI in integer format. Each row contains a single point where x and y coordinates are separated by a comma.

For files with ending ".roi" containing a single ROI also a single csv file with the given output filename is written. In case of a ROI zip archive containing multiple ROIs for each ROI an individual csv file is written. The names of these files are generated by extracting the root of the given output file name, adding a unique number and finally appending ending ".csv" to the filename.

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 de.unihalle.informatik.Alida.datatypes.ALDFileString	csvFile Output file name.
private static String	operatorID Identifier string for this operator.
private de.unihalle.informatik.Alida.datatypes.ALDFileString	roiFile Input ROI file or zip archive with ROIs.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
RoiFileToCSVConverter() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	operate()
void	setCSVFile(String file) Specify the file where to save csv data.
void	setROIFile(String file) Specify the ROI file to process.
private boolean	writeRoiToFile(MTBRegion2D r, String file) Writes the given region to the specified file in csv format.

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

private static final String operatorID

Identifier string for this operator.

See Also:

Constant Field Values

roiFile

@Parameter(label="Input ROI file",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="ImageJ ROI file.")
private de.unihalle.informatik.Alida.datatypes.ALDFileString roiFile

Input ROI file or zip archive with ROIs.

csvFile

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

Output file name.

In case that the input file contains multiple ROIs, the output filename is extended by a unique number and ending "*.cvs". Note that if only a single ROI is to be written and there is no or a wrong ending given this won't be corrected here.

Constructor Detail

RoiFileToCSVConverter

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

Default constructor.

Throws:

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

Method Detail

setROIFile

public void setROIFile(String file)

Specify the ROI file to process.

Parameters:

file - ROI file to convert, needs to be either in roi or zip format.

setCSVFile

public void setCSVFile(String file)

Specify the file where to save csv data.

Parameters:

file - Filename where to save the data.

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

writeRoiToFile

private boolean writeRoiToFile(MTBRegion2D r,
                               String file)

Writes the given region to the specified file in csv format.

Parameters:

r - Region to write.

file - File to where the region is to be written.

Returns:

True in case of success, false in case of failure.