Package net.preibisch.mvrecon.fiji.spimdata

Class XmlIoSpimData2

java.lang.Object

mpicbg.spim.data.generic.base.XmlIoSingleton<SpimData2>

mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2

public class XmlIoSpimData2
extends mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

Field Summary

Fields

Modifier and Type	Field	Description
static boolean	initN5Writing
static int	numBackups

Fields inherited from class mpicbg.spim.data.generic.base.XmlIoSingleton

handledTags

Constructor Summary

Constructors

Constructor	Description
XmlIoSpimData2()

Method Summary

Modifier and Type	Method	Description
static List<InterestPointsN5.InterestPointData>	collectInterestPointData(SpimData2 spimData, boolean modifiedOnly)	Collect all modified interest points as serializable InterestPointData objects.
SpimData2	fromXml(org.jdom2.Element root, URI xmlFile)
URI	lastURI()
SpimData2	load(URI xmlURI)
void	save(SpimData2 spimData, String xmlPath)	Deprecated.
boolean	save(SpimData2 spimData, URI xmlURI)
static void	saveInterestPointsInParallel(SpimData2 spimData)	Save all interest points using a single shared N5Writer with parallel writes.
static void	savePSFsInParallel(SpimData2 spimData)
URI	saveWithFilename(SpimData2 data, String xmlFileName)	Saves a SpimData2 object using its own URI into a filename specified by xmlFilename
org.jdom2.Element	toXml(SpimData2 spimData, File xmlFileDirectory)
org.jdom2.Element	toXml(SpimData2 spimData, URI xmlFileDirectory)

Methods inherited from class mpicbg.spim.data.generic.XmlIoAbstractSpimData

fromXml, getVersion, load, load, loadBasePathURI, save

Methods inherited from class mpicbg.spim.data.generic.base.XmlIoSingleton

fromXml, getTag, toXml

Methods inherited from class java.lang.Object

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

Field Details

numBackups

public static int numBackups

initN5Writing

public static boolean initN5Writing

Constructor Details

XmlIoSpimData2

public XmlIoSpimData2()

Method Details

lastURI

public URI lastURI()

save

@Deprecated
public void save(SpimData2 spimData,
 String xmlPath)
          throws mpicbg.spim.data.SpimDataException

Deprecated.

Overrides:

save in class mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

Throws:

mpicbg.spim.data.SpimDataException

save

public boolean save(SpimData2 spimData,
 URI xmlURI)

saveWithFilename

public URI saveWithFilename(SpimData2 data,
 String xmlFileName)

Saves a SpimData2 object using its own URI into a filename specified by xmlFilename

Parameters:

data - - SpimData2 object (contains basePath)

xmlFileName - - the filename (e.g. dataset.xml)

Returns:

the assembled, full path it was saved as

load

public SpimData2 load(URI xmlURI)
               throws mpicbg.spim.data.SpimDataException

Throws:

mpicbg.spim.data.SpimDataException

fromXml

public SpimData2 fromXml(org.jdom2.Element root,
 URI xmlFile)
                  throws mpicbg.spim.data.SpimDataException

Overrides:

fromXml in class mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

Throws:

mpicbg.spim.data.SpimDataException

toXml

public org.jdom2.Element toXml(SpimData2 spimData,
 File xmlFileDirectory)
                        throws mpicbg.spim.data.SpimDataException

Overrides:

toXml in class mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

Throws:

mpicbg.spim.data.SpimDataException

toXml

public org.jdom2.Element toXml(SpimData2 spimData,
 URI xmlFileDirectory)
                        throws mpicbg.spim.data.SpimDataException

Overrides:

toXml in class mpicbg.spim.data.generic.XmlIoAbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription,SpimData2>

Throws:

mpicbg.spim.data.SpimDataException

savePSFsInParallel

public static void savePSFsInParallel(SpimData2 spimData)

saveInterestPointsInParallel

public static void saveInterestPointsInParallel(SpimData2 spimData)

Save all interest points using a single shared N5Writer with parallel writes. Opens the N5Writer once and reuses it across all views, avoiding per-view open/close overhead while preserving parallel write performance. Each view writes to an independent dataset path so concurrent writes are safe. Modified flags are cleared on each InterestPoints instance after a successful save, so subsequent XML serialization does not trigger a redundant second save.

Parameters:

spimData - the SpimData2 object whose interest points should be saved

collectInterestPointData

public static List<InterestPointsN5.InterestPointData> collectInterestPointData(SpimData2 spimData,
 boolean modifiedOnly)

Collect all modified interest points as serializable InterestPointData objects. This method is useful for Spark-based parallel saving.

Parameters:

spimData - The SpimData2

modifiedOnly - If true, only include interest points that have been modified

Returns:

List of InterestPointData suitable for Spark RDD operations