Package net.preibisch.mvrecon.fiji.plugin.queryXML

Class GenericLoadParseQueryXML<AS extends mpicbg.spim.data.generic.AbstractSpimData<S>,S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V,D,L>,V extends mpicbg.spim.data.generic.sequence.BasicViewSetup,D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>,L extends mpicbg.spim.data.generic.sequence.BasicImgLoader,X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S,AS>>

java.lang.Object

net.preibisch.mvrecon.fiji.plugin.queryXML.GenericLoadParseQueryXML<AS,S,V,D,L,X>

Direct Known Subclasses:

LoadParseQueryXML

public abstract class GenericLoadParseQueryXML<AS extends mpicbg.spim.data.generic.AbstractSpimData<S>,S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V,D,L>,V extends mpicbg.spim.data.generic.sequence.BasicViewSetup,D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>,L extends mpicbg.spim.data.generic.sequence.BasicImgLoader,X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S,AS>>
extends Object

Interface for interactive parsing of spimdata XMLs

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields

Modifier and Type	Field	Description
protected HashMap<String,List<mpicbg.spim.data.generic.base.Entity>>	allAttributeInstances
protected HashMap<String,Integer>	attributeChoice
protected static String[]	attributeChoiceList
protected HashMap<String,List<mpicbg.spim.data.generic.base.Entity>>	attributeInstancesToProcess
protected ArrayList<String>	attributes
protected ArrayList<String>	buttonText
protected boolean	checkBoxResult
protected String	checkBoxText
protected Color	color
protected Comparator<String>	comparator
protected AS	data
static HashMap<String,Integer>	defaultAttributeChoice
static HashMap<String,Integer>	defaultAttributeEntityIndex
static HashMap<String,String>	defaultAttributePatternString
static HashMap<String,boolean[]>	defaultAttributeSelectedEntities
static String	defaultXMLURI
Button	defineNewDataset
protected static String	errorMsg1
protected ij.gui.GenericDialog	gd
protected static String	goodMsg1
protected X	io
protected ArrayList<ActionListener>	listener
protected String	message1
protected String	message2
protected static String	neutralMsg1a
protected static String	neutralMsg1b
protected static String	noMsg2
protected ArrayList<mpicbg.spim.data.sequence.TimePoint>	timepointsToProcess
protected static String	warningMsg1
protected String	xmlFileName

Constructor Summary

Constructors

Constructor	Description
GenericLoadParseQueryXML(X io)

Method Summary

Modifier and Type	Method	Description
void	addButton(String buttonText, ActionListener listener)
void	addCheckbox(String checkBoxText)	Add a checkbox to the XML-loading dialog.
protected void	addListeners(ij.gui.GenericDialog gd, TextField tf, Label label1, Label label2)
protected static String[]	buildEntityList(String attributeName, List<? extends mpicbg.spim.data.generic.base.Entity> entityList, boolean addTitle)
protected static String[]	buildTimepointList(List<mpicbg.spim.data.sequence.TimePoint> tpList, boolean addTitle)
protected final ArrayList<HashSet<Integer>>	entitiesPerAttribute()
static <AS extends mpicbg.spim.data.generic.AbstractSpimData<S>, S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V, D, L>, V extends mpicbg.spim.data.generic.sequence.BasicViewSetup, D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>, L extends mpicbg.spim.data.generic.sequence.BasicImgLoader, X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S, AS>> ArrayList<String>	getAttributes(AS data, Comparator<String> comparator)
Comparator<String>	getComparator()
AS	getData()
ij.gui.GenericDialog	getGenericDialog()
X	getIO()
static <AS extends mpicbg.spim.data.generic.AbstractSpimData<S>, S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V, D, L>, V extends mpicbg.spim.data.generic.sequence.BasicViewSetup, D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>, L extends mpicbg.spim.data.generic.sequence.BasicImgLoader, X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S, AS>> String	getSpimDataDescription(AS data, ArrayList<String> attributes, ArrayList<HashSet<Integer>> numEntitiesPerAttrib, int numAttributes)
List<mpicbg.spim.data.sequence.TimePoint>	getTimePointsToProcess()
ArrayList<V>	getViewSetupsToProcess()
String	getXMLFileName()
URI	getXMLURI()
boolean	isCheckBoxSelected()	Result of the checkbox added via addCheckbox(String); false if none was added.
protected static String[]	makeChoiceList(String attribute)
protected abstract AS	parseXML(URI xmlPath)
protected void	populateAttributesEntities(int numAttributes, ArrayList<HashSet<Integer>> numEntitiesPerAttrib)
protected <E extends mpicbg.spim.data.generic.base.Entity> boolean	query(int choice, String attribute, List<E> allEntities, List<E> entitiesToProcess)
protected boolean	queryDetails()
static int	queryIndividualEntry(String name, String[] list, int defaultSelection)	Querys a single element from the list
static boolean[]	queryMultipleEntries(String name, String[] list, boolean[] defaultSelection)	Querys a multiple element from the list
static boolean[]	queryPattern(String name, String[] list, String[] defaultSelectionArray)	Querys a pattern of element from the list
boolean	queryXML()
boolean	queryXML(String query)
boolean	queryXML(String additionalTitle, String query, List<String> specifyAttributes)
boolean	queryXML(String query, List<String> specifyAttributes)
boolean	queryXML(List<String> specifyAttributes)
void	setComparator(Comparator<String> comparator)
protected boolean	tryParsing(URI xmlURI, boolean parseAllTypes)

Methods inherited from class java.lang.Object

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

Field Details

defaultXMLURI

public static String defaultXMLURI

goodMsg1

protected static String goodMsg1

warningMsg1

protected static String warningMsg1

errorMsg1

protected static String errorMsg1

neutralMsg1a

protected static String neutralMsg1a

neutralMsg1b

protected static String neutralMsg1b

noMsg2

protected static String noMsg2

attributeChoiceList

protected static String[] attributeChoiceList

defaultAttributeChoice

public static HashMap<String,Integer> defaultAttributeChoice

defaultAttributeEntityIndex

public static HashMap<String,Integer> defaultAttributeEntityIndex

defaultAttributePatternString

public static HashMap<String,String> defaultAttributePatternString

defaultAttributeSelectedEntities

public static HashMap<String,boolean[]> defaultAttributeSelectedEntities

attributeChoice

protected HashMap<String,Integer> attributeChoice

io

protected X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S,AS> io

comparator

protected Comparator<String> comparator

message1

protected String message1

message2

protected String message2

color

protected Color color

data

protected AS extends mpicbg.spim.data.generic.AbstractSpimData<S> data

xmlFileName

protected String xmlFileName

timepointsToProcess

protected ArrayList<mpicbg.spim.data.sequence.TimePoint> timepointsToProcess

attributes

protected ArrayList<String> attributes

allAttributeInstances

protected HashMap<String,List<mpicbg.spim.data.generic.base.Entity>> allAttributeInstances

attributeInstancesToProcess

protected HashMap<String,List<mpicbg.spim.data.generic.base.Entity>> attributeInstancesToProcess

buttonText

protected ArrayList<String> buttonText

listener

protected ArrayList<ActionListener> listener

checkBoxText

protected String checkBoxText

checkBoxResult

protected boolean checkBoxResult

gd

protected ij.gui.GenericDialog gd

defineNewDataset

public Button defineNewDataset

Constructor Details

GenericLoadParseQueryXML

public GenericLoadParseQueryXML(X io)

Method Details

getIO

public X getIO()

Returns:

the i/o object used to parse the XML

getData

public AS getData()

Returns:

the SpimData object parsed from the xml

getXMLURI

public URI getXMLURI()

Returns:

The location of the xml file

getXMLFileName

public String getXMLFileName()

Returns:

ONLY the filename, without any path

getTimePointsToProcess

public List<mpicbg.spim.data.sequence.TimePoint> getTimePointsToProcess()

Returns:

All timepoints that should be processed

getViewSetupsToProcess

public ArrayList<V> getViewSetupsToProcess()

Returns:

All ViewSetups that should be processed per timepoint (based on the selected attributes)

setComparator

public void setComparator(Comparator<String> comparator)

getComparator

public Comparator<String> getComparator()

queryXML

public boolean queryXML()

queryXML

public boolean queryXML(List<String> specifyAttributes)

queryXML

public boolean queryXML(String query)

queryXML

public boolean queryXML(String query,
 List<String> specifyAttributes)

addButton

public void addButton(String buttonText,
 ActionListener listener)

addCheckbox

public void addCheckbox(String checkBoxText)

Add a checkbox to the XML-loading dialog. Read the user's choice via isCheckBoxSelected() after queryXML() returns.

isCheckBoxSelected

public boolean isCheckBoxSelected()

Result of the checkbox added via addCheckbox(String); false if none was added.

getGenericDialog

public ij.gui.GenericDialog getGenericDialog()

queryXML

public boolean queryXML(String additionalTitle,
 String query,
 List<String> specifyAttributes)

queryIndividualEntry

public static int queryIndividualEntry(String name,
 String[] list,
 int defaultSelection)

Querys a single element from the list

Parameters:

name - - type of elements (e.g. "Timepoint")

list - - list of available elements

defaultSelection - - default selection

Returns:

the selection or -1 if cancelled

queryMultipleEntries

public static boolean[] queryMultipleEntries(String name,
 String[] list,
 boolean[] defaultSelection)

Querys a multiple element from the list

Parameters:

name - - type of elements (e.g. "Timepoints")

list - - list of available elements

defaultSelection - - default selection

Returns:

the selection or null if cancelled

queryPattern

public static boolean[] queryPattern(String name,
 String[] list,
 String[] defaultSelectionArray)

Querys a pattern of element from the list

Parameters:

name - - type of elements (e.g. "Timepoints")

list - - list of available elements

defaultSelectionArray - - default selection (array of size 1 to be able to return it)

Returns:

the selection or null if cancelled

query

protected <E extends mpicbg.spim.data.generic.base.Entity>
boolean query(int choice,
 String attribute,
 List<E> allEntities,
 List<E> entitiesToProcess)

queryDetails

protected boolean queryDetails()

buildTimepointList

protected static String[] buildTimepointList(List<mpicbg.spim.data.sequence.TimePoint> tpList,
 boolean addTitle)

buildEntityList

protected static String[] buildEntityList(String attributeName,
 List<? extends mpicbg.spim.data.generic.base.Entity> entityList,
 boolean addTitle)

makeChoiceList

protected static String[] makeChoiceList(String attribute)

tryParsing

protected boolean tryParsing(URI xmlURI,
 boolean parseAllTypes)

populateAttributesEntities

protected void populateAttributesEntities(int numAttributes,
 ArrayList<HashSet<Integer>> numEntitiesPerAttrib)

entitiesPerAttribute

protected final ArrayList<HashSet<Integer>> entitiesPerAttribute()

getAttributes

public static <AS extends mpicbg.spim.data.generic.AbstractSpimData<S>,
S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V,
D,
L>,
V extends mpicbg.spim.data.generic.sequence.BasicViewSetup,
D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>,
L extends mpicbg.spim.data.generic.sequence.BasicImgLoader,
X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S,
AS>>
ArrayList<String> getAttributes(AS data,
 Comparator<String> comparator)

getSpimDataDescription

public static <AS extends mpicbg.spim.data.generic.AbstractSpimData<S>,
S extends mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<V,
D,
L>,
V extends mpicbg.spim.data.generic.sequence.BasicViewSetup,
D extends mpicbg.spim.data.generic.sequence.BasicViewDescription<V>,
L extends mpicbg.spim.data.generic.sequence.BasicImgLoader,
X extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<S,
AS>>
String getSpimDataDescription(AS data,
 ArrayList<String> attributes,
 ArrayList<HashSet<Integer>> numEntitiesPerAttrib,
 int numAttributes)

parseXML

protected abstract AS parseXML(URI xmlPath)
                        throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException

addListeners

protected void addListeners(ij.gui.GenericDialog gd,
 TextField tf,
 Label label1,
 Label label2)