de.unihalle.informatik.MiToBo.io.importer.rsml

Class MTBRSMLProjectImporter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.io.importer.rsml.MTBRSMLProjectImporter

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL)
public class MTBRSMLProjectImporter
extends MTBOperator

Reads the contents of the RSML project files in the given directory.

The importer assumes that all files belong to a single project or time-series.

Author:

Birgit Moeller, Stefan Posch

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 boolean	allUnified Flag indicating if identifiers in a time-series are unified.
private static byte	default_statuslabel Default status label for segments.
private static Double	EPSILON Maximal distance allowed for parent nodes to deviate from precise location.
private static String	FUNCTION_NAME_DIAMETER
private static String	FUNCTION_NAME_STATUSLABEL
private static String	opIdentifier Operator identifier.
private static String	PROPERTY_NAME_PARENTNODE
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	rsmlDir Directory of RSML files.
protected MTBRSMLProjectInfo	rsmlProjectInfo Resulting info object containing all information parsed from input files.
static int	STATUS_CONNECTOR Segments of a connector treeline.
static int	STATUS_UNDEFINED Undefined status.
static int	STATUS_VIRTUAL to represent (virtual) segments to connect branches (polylines) of a root to form one (connected) treeline used to represent genuine rizoTrak virtual segments
static int	STATUS_VIRTUAL_RSML to represent (virtual) segments created on import from RSML to connect all branches (polylines) of a root to form one (connected) treeline * used to represent virtual segments create for/from RSML

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MTBRSMLProjectImporter() Default constructor.

Method Summary

Modifier and Type	Method and Description
private MTBRootTree	createTreeForRoot(RootType root) Create a root tree from the given root object.
private void	fillTreeFromRoot(RootType root, MTBRootTree tree, HashMap<Integer,MTBTreeNode> parentTreelineNodes) Recursively parses all polylines belonging to the given root.
private RootType.Functions.Function	getFunctionByName(RootType root, String name) Get RSML function by name.
private int	getParentNodeIndex(RootType root) Parse the parent node or parent node attribute from the root.
private float	getRadiusFromRsml(RootType.Functions.Function diameters, int pointIndex) Get the radius for index pointIndex from the function diameters.
MTBRSMLProjectInfo	getRSMLProjectInfo() Get resulting info object.
private BigDecimal	getSampleValue(Element element) Get the value of a sample element in a function.
private byte	getStatuslabelFromRsml(RootType.Functions.Function statuslabels, int pointIndex) Get status label for index pointIndex from the function statuslabels.
private HashMap<Integer,String>	getStatusLabelMappingFromScene(Rsml rsml) Parse the status label mapping from given RSML file.
private boolean	isStatuslabelFromRsmlDefined(RootType.Functions.Function statuslabels, int pointIndex)
protected void	operate()
private MTBRSMLFileInfo	parseRsmlFile(Rsml rsml) Parse the given RSML file.
void	setInputDirectory(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString dir) Specify input directory.

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

FUNCTION_NAME_DIAMETER

private static final String FUNCTION_NAME_DIAMETER

See Also:

Constant Field Values

FUNCTION_NAME_STATUSLABEL

private static final String FUNCTION_NAME_STATUSLABEL

See Also:

Constant Field Values

PROPERTY_NAME_PARENTNODE

private static final String PROPERTY_NAME_PARENTNODE

See Also:

Constant Field Values

STATUS_UNDEFINED

public static final int STATUS_UNDEFINED

Undefined status.

See Also:

Constant Field Values

STATUS_CONNECTOR

public static final int STATUS_CONNECTOR

Segments of a connector treeline.

See Also:

Constant Field Values

STATUS_VIRTUAL

public static final int STATUS_VIRTUAL

to represent (virtual) segments to connect branches (polylines) of a root to form one (connected) treeline
used to represent genuine rizoTrak virtual segments

See Also:

Constant Field Values

STATUS_VIRTUAL_RSML

public static final int STATUS_VIRTUAL_RSML

to represent (virtual) segments created on import from RSML to connect all branches (polylines) of a root to form one (connected) treeline *
used to represent virtual segments create for/from RSML

See Also:

Constant Field Values

default_statuslabel

private static byte default_statuslabel

Default status label for segments.

EPSILON

private static final Double EPSILON

Maximal distance allowed for parent nodes to deviate from precise location.

opIdentifier

private static String opIdentifier

Operator identifier.

allUnified

private boolean allUnified

Flag indicating if identifiers in a time-series are unified.

rsmlDir

@Parameter(label="RSML Directory",
           required=true,
           direction=IN,
           dataIOOrder=0,
           mode=STANDARD,
           description="RSML input directory.")
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString rsmlDir

Directory of RSML files.

rsmlProjectInfo

@Parameter(label="Result RSML Info Object",
           direction=OUT,
           dataIOOrder=0,
           description="RSML info object.")
protected MTBRSMLProjectInfo rsmlProjectInfo

Resulting info object containing all information parsed from input files.

Constructor Detail

MTBRSMLProjectImporter

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

Default constructor.

Throws:

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

Method Detail

setInputDirectory

public void setInputDirectory(de.unihalle.informatik.Alida.datatypes.ALDDirectoryString dir)

Specify input directory.

Parameters:

dir - Input directory where to find the RSML files.

getRSMLProjectInfo

public MTBRSMLProjectInfo getRSMLProjectInfo()

Get resulting info object.

Returns:

Info object with all RSML data.

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

getStatusLabelMappingFromScene

private HashMap<Integer,String> getStatusLabelMappingFromScene(Rsml rsml)

Parse the status label mapping from given RSML file.

Parameters:

rsml - RSML file.

Returns:

Map of the status label mappings or null if none is defined in the RSML file.

parseRsmlFile

private MTBRSMLFileInfo parseRsmlFile(Rsml rsml)

Parse the given RSML file.

Parameters:

rsml - RSML data structure read from file.

Returns:

Info object with data from file.

createTreeForRoot

private MTBRootTree createTreeForRoot(RootType root)

Create a root tree from the given root object.

Parameters:

root - Root object to convert to MTBRootTree.

Returns:

Resulting root tree.

fillTreeFromRoot

private void fillTreeFromRoot(RootType root,
                              MTBRootTree tree,
                              HashMap<Integer,MTBTreeNode> parentTreelineNodes)

Recursively parses all polylines belonging to the given root.

Parameters:

root - Root object to be parsed.

tree - Target root tree.

parentTreelineNodes - Map of root tree nodes indexed by IDs from RSML.

getParentNodeIndex

private int getParentNodeIndex(RootType root)

Parse the parent node or parent node attribute from the root.

Parameters:

root - Root to analyze.

Returns:

Parent node index (starting with 1 by RSML convetions) or -1 if not found.

getStatuslabelFromRsml

private byte getStatuslabelFromRsml(RootType.Functions.Function statuslabels,
                                    int pointIndex)

Get status label for index pointIndex from the function statuslabels.

Parameters:

statuslabels - RSML function.

pointIndex - Index of point for which to get the status label.

Returns:

Status label or default_statuslabel if function is null or index out of range.

isStatuslabelFromRsmlDefined

private boolean isStatuslabelFromRsmlDefined(RootType.Functions.Function statuslabels,
                                             int pointIndex)

getFunctionByName

private RootType.Functions.Function getFunctionByName(RootType root,
                                                      String name)

Get RSML function by name.

Parameters:

root - Root object.

name - Function name.

Returns:

First function with name name, null if none exists.

getRadiusFromRsml

private float getRadiusFromRsml(RootType.Functions.Function diameters,
                                int pointIndex)

Get the radius for index pointIndex from the function diameters.

Parameters:

diameters - Function.

pointIndex - Index of point for which to get the diameter.

Returns:

Radius or null if diameters is null or index out of range.

getSampleValue

private BigDecimal getSampleValue(Element element)

Get the value of a sample element in a function.

Parameters:

element - Element to process.

Returns:

Value, otherwise null if neither value attribute nor the text content is defined.