Package net.preibisch.mvrecon.fiji.spimdata

Class SpimData2

java.lang.Object

mpicbg.spim.data.generic.AbstractSpimData<mpicbg.spim.data.sequence.SequenceDescription>

mpicbg.spim.data.SpimData

net.preibisch.mvrecon.fiji.spimdata.SpimData2

public class SpimData2
extends mpicbg.spim.data.SpimData

Extends the SpimData class; has additonally detections

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields

Modifier and Type	Field	Description
boolean	gridMoveRequested

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SpimData2()
	SpimData2(URI basePathUri, mpicbg.spim.data.sequence.SequenceDescription sequenceDescription, mpicbg.spim.data.registration.ViewRegistrations viewRegistrations, ViewInterestPoints viewsInterestPoints, BoundingBoxes boundingBoxes, PointSpreadFunctions pointSpreadFunctions, StitchingResults stitchingResults, IntensityAdjustments intensityAdjustments)

Method Summary

Modifier and Type	Method	Description
static SpimData2	convert(mpicbg.spim.data.SpimData data1)
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<Group<V>>	filterGroupsForMissingViews(mpicbg.spim.data.generic.AbstractSpimData<?> data, Collection<Group<V>> groupsIn)	Removes Views in Groups that are missing, and entire groups if no views are left
static <V extends mpicbg.spim.data.sequence.ViewId> List<V>	filterMissingViews(mpicbg.spim.data.generic.AbstractSpimData<?> data, Collection<V> viewIds)	Removes all missing views from the list, be careful, it modifies the collection!
static <V extends mpicbg.spim.data.sequence.ViewId> List<V>	filterMissingViews(mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> seq, Collection<V> viewIds)	Removes all missing views from the list, be careful, it modifies the collection!
static ArrayList<mpicbg.spim.data.sequence.Angle>	getAllAnglesForChannelTimepointSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, mpicbg.spim.data.sequence.Channel c, mpicbg.spim.data.sequence.TimePoint t)
static ArrayList<mpicbg.spim.data.sequence.Angle>	getAllAnglesSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<mpicbg.spim.data.sequence.Channel>	getAllChannelsSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<mpicbg.spim.data.sequence.Illumination>	getAllIlluminationsForChannelTimepointSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, mpicbg.spim.data.sequence.Channel c, mpicbg.spim.data.sequence.TimePoint t)
static ArrayList<mpicbg.spim.data.sequence.Illumination>	getAllIlluminationsSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static <E extends mpicbg.spim.data.generic.base.Entity> ArrayList<E>	getAllInstancesOfEntitySorted(mpicbg.spim.data.generic.AbstractSpimData<?> data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, Class<E> cl)
static ArrayList<mpicbg.spim.data.sequence.Tile>	getAllTilesSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<mpicbg.spim.data.sequence.TimePoint>	getAllTimePointsSorted(Collection<? extends mpicbg.spim.data.sequence.ViewDescription> vds)
static ArrayList<mpicbg.spim.data.sequence.TimePoint>	getAllTimePointsSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<Integer>	getAllTimePointsSortedUnchecked(Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<Integer>	getAllTimePointsSortedWithoutPresenceCheck(Collection<? extends mpicbg.spim.data.sequence.ViewId> vds)
static ArrayList<mpicbg.spim.data.sequence.ViewDescription>	getAllViewDescriptionsSorted(mpicbg.spim.data.SpimData data, List<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
static ArrayList<mpicbg.spim.data.sequence.ViewDescription>	getAllViewIdsForChannelSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, mpicbg.spim.data.sequence.Channel channel)
static ArrayList<mpicbg.spim.data.sequence.ViewDescription>	getAllViewIdsForChannelTimePointSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, mpicbg.spim.data.sequence.Channel channel, mpicbg.spim.data.sequence.TimePoint timePoint)
static ArrayList<mpicbg.spim.data.sequence.ViewDescription>	getAllViewIdsForTimePointSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds, mpicbg.spim.data.sequence.TimePoint timepoint)
static ArrayList<mpicbg.spim.data.sequence.ViewId>	getAllViewIdsSorted(mpicbg.spim.data.SpimData data, List<? extends mpicbg.spim.data.sequence.ViewSetup> setups, List<? extends mpicbg.spim.data.sequence.TimePoint> tps)
static ArrayList<mpicbg.spim.data.sequence.ViewSetup>	getAllViewSetups(Collection<? extends mpicbg.spim.data.sequence.ViewDescription> vds)
static ArrayList<mpicbg.spim.data.sequence.ViewSetup>	getAllViewSetupsSorted(mpicbg.spim.data.SpimData data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)
BoundingBoxes	getBoundingBoxes()
IntensityAdjustments	getIntensityAdjustments()
PointSpreadFunctions	getPointSpreadFunctions()
StitchingResults	getStitchingResults()
static mpicbg.spim.data.sequence.ViewId	getViewId(mpicbg.spim.data.sequence.SequenceDescription seqDesc, mpicbg.spim.data.sequence.TimePoint t, mpicbg.spim.data.sequence.Channel c, mpicbg.spim.data.sequence.Angle a, mpicbg.spim.data.sequence.Illumination i, mpicbg.spim.data.sequence.Tile x)
ViewInterestPoints	getViewInterestPoints()
static mpicbg.spim.data.sequence.ViewSetup	getViewSetup(List<? extends mpicbg.spim.data.sequence.ViewSetup> list, mpicbg.spim.data.sequence.Channel c, mpicbg.spim.data.sequence.Angle a, mpicbg.spim.data.sequence.Illumination i, mpicbg.spim.data.sequence.Tile x)
protected void	setBoundingBoxes(BoundingBoxes boundingBoxes)
protected void	setIntensityAdjustments(IntensityAdjustments intensityAdjustments)
protected void	setPointSpreadFunctions(PointSpreadFunctions pointSpreadFunctions)
protected void	setStitchingResults(StitchingResults sr)
protected void	setViewsInterestPoints(ViewInterestPoints viewsInterestPoints)

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

getBasePath, getBasePathURI, getSequenceDescription, getViewRegistrations, setBasePath, setBasePathURI, setSequenceDescription, setViewRegistrations

Methods inherited from class java.lang.Object

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

Field Details

gridMoveRequested

public boolean gridMoveRequested

Constructor Details

SpimData2

public SpimData2(URI basePathUri,
 mpicbg.spim.data.sequence.SequenceDescription sequenceDescription,
 mpicbg.spim.data.registration.ViewRegistrations viewRegistrations,
 ViewInterestPoints viewsInterestPoints,
 BoundingBoxes boundingBoxes,
 PointSpreadFunctions pointSpreadFunctions,
 StitchingResults stitchingResults,
 IntensityAdjustments intensityAdjustments)

SpimData2

protected SpimData2()

Method Details

getViewInterestPoints

public ViewInterestPoints getViewInterestPoints()

getBoundingBoxes

public BoundingBoxes getBoundingBoxes()

getPointSpreadFunctions

public PointSpreadFunctions getPointSpreadFunctions()

getStitchingResults

public StitchingResults getStitchingResults()

getIntensityAdjustments

public IntensityAdjustments getIntensityAdjustments()

setViewsInterestPoints

protected void setViewsInterestPoints(ViewInterestPoints viewsInterestPoints)

setBoundingBoxes

protected void setBoundingBoxes(BoundingBoxes boundingBoxes)

setPointSpreadFunctions

protected void setPointSpreadFunctions(PointSpreadFunctions pointSpreadFunctions)

setStitchingResults

protected void setStitchingResults(StitchingResults sr)

setIntensityAdjustments

protected void setIntensityAdjustments(IntensityAdjustments intensityAdjustments)

getViewId

public static mpicbg.spim.data.sequence.ViewId getViewId(mpicbg.spim.data.sequence.SequenceDescription seqDesc,
 mpicbg.spim.data.sequence.TimePoint t,
 mpicbg.spim.data.sequence.Channel c,
 mpicbg.spim.data.sequence.Angle a,
 mpicbg.spim.data.sequence.Illumination i,
 mpicbg.spim.data.sequence.Tile x)

Parameters:

seqDesc - the sequence description

t - - the timepoint

c - - the channel

a - - the angle

i - - the illumination

x - - the tile

Returns:

- the ViewId that fits to timepoint, angle, channel & illumination by ID (or null if it does not exist)

getViewSetup

public static mpicbg.spim.data.sequence.ViewSetup getViewSetup(List<? extends mpicbg.spim.data.sequence.ViewSetup> list,
 mpicbg.spim.data.sequence.Channel c,
 mpicbg.spim.data.sequence.Angle a,
 mpicbg.spim.data.sequence.Illumination i,
 mpicbg.spim.data.sequence.Tile x)

getAllViewSetupsSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewSetup> getAllViewSetupsSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllViewIdsSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewId> getAllViewIdsSorted(mpicbg.spim.data.SpimData data,
 List<? extends mpicbg.spim.data.sequence.ViewSetup> setups,
 List<? extends mpicbg.spim.data.sequence.TimePoint> tps)

getAllViewDescriptionsSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewDescription> getAllViewDescriptionsSorted(mpicbg.spim.data.SpimData data,
 List<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllAnglesForChannelTimepointSorted

public static ArrayList<mpicbg.spim.data.sequence.Angle> getAllAnglesForChannelTimepointSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 mpicbg.spim.data.sequence.Channel c,
 mpicbg.spim.data.sequence.TimePoint t)

getAllAnglesSorted

public static ArrayList<mpicbg.spim.data.sequence.Angle> getAllAnglesSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllTilesSorted

public static ArrayList<mpicbg.spim.data.sequence.Tile> getAllTilesSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllIlluminationsForChannelTimepointSorted

public static ArrayList<mpicbg.spim.data.sequence.Illumination> getAllIlluminationsForChannelTimepointSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 mpicbg.spim.data.sequence.Channel c,
 mpicbg.spim.data.sequence.TimePoint t)

getAllIlluminationsSorted

public static ArrayList<mpicbg.spim.data.sequence.Illumination> getAllIlluminationsSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllInstancesOfEntitySorted

public static <E extends mpicbg.spim.data.generic.base.Entity>
ArrayList<E> getAllInstancesOfEntitySorted(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 Class<E> cl)

getAllChannelsSorted

public static ArrayList<mpicbg.spim.data.sequence.Channel> getAllChannelsSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllViewIdsForChannelSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewDescription> getAllViewIdsForChannelSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 mpicbg.spim.data.sequence.Channel channel)

getAllViewIdsForChannelTimePointSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewDescription> getAllViewIdsForChannelTimePointSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 mpicbg.spim.data.sequence.Channel channel,
 mpicbg.spim.data.sequence.TimePoint timePoint)

getAllViewIdsForTimePointSorted

public static ArrayList<mpicbg.spim.data.sequence.ViewDescription> getAllViewIdsForTimePointSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds,
 mpicbg.spim.data.sequence.TimePoint timepoint)

getAllViewSetups

public static ArrayList<mpicbg.spim.data.sequence.ViewSetup> getAllViewSetups(Collection<? extends mpicbg.spim.data.sequence.ViewDescription> vds)

getAllTimePointsSortedUnchecked

public static ArrayList<Integer> getAllTimePointsSortedUnchecked(Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllTimePointsSorted

public static ArrayList<mpicbg.spim.data.sequence.TimePoint> getAllTimePointsSorted(mpicbg.spim.data.SpimData data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewIds)

getAllTimePointsSorted

public static ArrayList<mpicbg.spim.data.sequence.TimePoint> getAllTimePointsSorted(Collection<? extends mpicbg.spim.data.sequence.ViewDescription> vds)

getAllTimePointsSortedWithoutPresenceCheck

public static ArrayList<Integer> getAllTimePointsSortedWithoutPresenceCheck(Collection<? extends mpicbg.spim.data.sequence.ViewId> vds)

convert

public static SpimData2 convert(mpicbg.spim.data.SpimData data1)

filterMissingViews

public static <V extends mpicbg.spim.data.sequence.ViewId>
List<V> filterMissingViews(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 Collection<V> viewIds)

Removes all missing views from the list, be careful, it modifies the collection!

Type Parameters:

V - - something extending ViewId

Parameters:

data - - the spimdata object

viewIds - - the views

Returns:

those who were removed

filterMissingViews

public static <V extends mpicbg.spim.data.sequence.ViewId>
List<V> filterMissingViews(mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,?,?> seq,
 Collection<V> viewIds)

Removes all missing views from the list, be careful, it modifies the collection!

Type Parameters:

V - - something extending ViewId

Parameters:

seq - - the sequence description

viewIds - - the views

Returns:

those who were removed

filterGroupsForMissingViews

public static <V extends mpicbg.spim.data.sequence.ViewId>
ArrayList<Group<V>> filterGroupsForMissingViews(mpicbg.spim.data.generic.AbstractSpimData<?> data,
 Collection<Group<V>> groupsIn)

Removes Views in Groups that are missing, and entire groups if no views are left

Type Parameters:

V - - something extending ViewId

Parameters:

data - - the SpimData object

groupsIn - - a collection of groups consisting of views

Returns:

a filtered list, potentially of size 0