Package net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping

Class Group<V>

java.lang.Object

net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group<V>

All Implemented Interfaces:

Serializable, Iterable<V>

Direct Known Subclasses:

Subset

public class Group<V>
extends Object
implements Iterable<V>, Serializable

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected HashSet<V>	views

Constructor Summary

Constructors

Constructor	Description
Group()
Group(Collection<V> views)
Group(V view)

Method Summary

Modifier and Type	Method	Description
static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> List<Group<V>>	combineBy(List<V> vds, Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors)	Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3]
static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> List<Group<V>>	combineOrSplitBy(List<V> vds, Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors, boolean combine)	Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) Split means the opposite in some way, make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3] split by channel: [v1 v2], [v3]
boolean	contains(V view)
static <V> boolean	containsBoth(V viewIdA, V viewIdB, Collection<? extends Group<V>> groupCollection)
boolean	equals(Object obj)
void	filterMissingViews(Set<? extends V> missingViews)
static <V> void	filterMissingViews(Group<V> group, Set<? extends V> missingViews)
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<Group<V>>	getGroupsSorted(Collection<Group<V>> groups)
Set<V>	getViews()
static <V extends mpicbg.spim.data.sequence.ViewId> List<V>	getViewsSorted(Collection<V> views)
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<Group<V>>	groupByChannel(List<V> viewIds, mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>,?> sd)
static String	gvids(Collection<?> group)
static String	gvids(Group<?> group)
int	hashCode()
static <V> Group<V>	isContained(V view, Collection<? extends Group<V>> groupCollection)
Iterator<V>	iterator()
static void	main(String[] args)
static <V> ArrayList<Group<V>>	memberOf(V view, Set<Group<V>> groups)	Identifies all groups that a certain view is a member of
static <V> Group<V>	merge(Group<V> groupA, Group<V> groupB)	Merges two Groups of views
static <V> ArrayList<Group<V>>	mergeAllOverlappingGroups(Collection<Group<V>> groups)	Merges all overlapping groups into a new List, the input remains unchanged
static <V> Group<V>	mergeOverlapping(Group<V> groupA, Group<V> groupB)	Merges two Groups of views
static <V> net.imglib2.util.Pair<Integer,Integer>	nextOverlappingGroup(List<Group<V>> groups)	Identify the indices of the next overlapping groups ordered by size, or return null if none are overlapping
static <V> ArrayList<net.imglib2.util.Pair<Group<V>,Group<V>>>	overlappingGroups(Collection<Group<V>> groups)	Identify all pairs of overlapping groups
static <V> boolean	overlaps(Group<V> groupA, Group<V> groupB)	Test if there is any overlap between two groups (at least one view part of both)
static String	pvid(mpicbg.spim.data.sequence.ViewId viewId)
static String	pvids(mpicbg.spim.data.sequence.ViewId viewId)
static <V> void	removeEmptyGroups(List<Group<V>> groups)
int	size()
static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>> List<Group<V>>	splitBy(List<V> vds, Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors)	Split means to make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 split by channel: [v1 v2], [v3]
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<Group<V>>	toGroup(Collection<V> views)
static <V extends mpicbg.spim.data.sequence.ViewId> ArrayList<Group<V>>	toGroups(Collection<V> views)
String	toString()
static ArrayList<Group<mpicbg.spim.data.sequence.ViewId>>	toViewIdGroup(Collection<? extends mpicbg.spim.data.sequence.ViewId> views)
static ArrayList<Group<mpicbg.spim.data.sequence.ViewId>>	toViewIdGroups(Collection<? extends mpicbg.spim.data.sequence.ViewId> views)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Details

views

protected HashSet<V> views

Constructor Details

Group

public Group(Collection<V> views)

Group

public Group(V view)

Group

public Group()

Method Details

getViews

public Set<V> getViews()

size

public int size()

contains

public boolean contains(V view)

iterator

public Iterator<V> iterator()

Specified by:

iterator in interface Iterable<V>

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

filterMissingViews

public void filterMissingViews(Set<? extends V> missingViews)

filterMissingViews

public static <V> void filterMissingViews(Group<V> group,
 Set<? extends V> missingViews)

getViewsSorted

public static <V extends mpicbg.spim.data.sequence.ViewId>
List<V> getViewsSorted(Collection<V> views)

getGroupsSorted

public static <V extends mpicbg.spim.data.sequence.ViewId>
ArrayList<Group<V>> getGroupsSorted(Collection<Group<V>> groups)

combineBy

public static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>>
List<Group<V>> combineBy(List<V> vds,
 Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors)

Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3]

Type Parameters:

V - - something that extends BasicViewDescription

Parameters:

vds - - the ViewDescriptions to process

groupingFactors - - by which attribute(s)

Returns:

- list of groups

splitBy

public static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>>
List<Group<V>> splitBy(List<V> vds,
 Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors)

Split means to make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 split by channel: [v1 v2], [v3]

Type Parameters:

V - - something that extends BasicViewDescription

Parameters:

vds - - the ViewDescriptions to process

groupingFactors - - by which attribute(s)

Returns:

- list of groups

combineOrSplitBy

public static <V extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>>
List<Group<V>> combineOrSplitBy(List<V> vds,
 Set<Class<? extends mpicbg.spim.data.generic.base.Entity>> groupingFactors,
 boolean combine)

Combining means to combine all views that share everything except what they are grouped after, e.g. channel (for example used to group GFP, RFP, DAPI for a Tile) Split means the opposite in some way, make a group for every instance of an attribute, e.g. channel (for example group everthing that is GFP and everything that it RFP) v1: angle 0, channel 0 v2: angle 1, channel 0 v3: angle 1, channel 1 combine by channel: [v1], [v2 v3] split by channel: [v1 v2], [v3]

Type Parameters:

V - - something that extends BasicViewDescription

Parameters:

vds - - the ViewDescriptions to process

groupingFactors - - by which attribute(s)

combine - - combine or split

Returns:

- list of groups

toGroups

public static <V extends mpicbg.spim.data.sequence.ViewId>
ArrayList<Group<V>> toGroups(Collection<V> views)

toViewIdGroups

public static ArrayList<Group<mpicbg.spim.data.sequence.ViewId>> toViewIdGroups(Collection<? extends mpicbg.spim.data.sequence.ViewId> views)

toGroup

public static <V extends mpicbg.spim.data.sequence.ViewId>
ArrayList<Group<V>> toGroup(Collection<V> views)

toViewIdGroup

public static ArrayList<Group<mpicbg.spim.data.sequence.ViewId>> toViewIdGroup(Collection<? extends mpicbg.spim.data.sequence.ViewId> views)

groupByChannel

public static <V extends mpicbg.spim.data.sequence.ViewId>
ArrayList<Group<V>> groupByChannel(List<V> viewIds,
 mpicbg.spim.data.generic.sequence.AbstractSequenceDescription<?,? extends mpicbg.spim.data.generic.sequence.BasicViewDescription<?>,?> sd)

containsBoth

public static <V> boolean containsBoth(V viewIdA,
 V viewIdB,
 Collection<? extends Group<V>> groupCollection)

isContained

public static <V> Group<V> isContained(V view,
 Collection<? extends Group<V>> groupCollection)

overlaps

public static <V> boolean overlaps(Group<V> groupA,
 Group<V> groupB)

Test if there is any overlap between two groups (at least one view part of both)

Type Parameters:

V - - view id type

Parameters:

groupA - - first group

groupB - - second group

Returns:

whether there is overlap

memberOf

public static <V> ArrayList<Group<V>> memberOf(V view,
 Set<Group<V>> groups)

Identifies all groups that a certain view is a member of

Type Parameters:

V - - view id type

Parameters:

view - - a view

groups - - all views

Returns:

the groups that view is a member of

overlappingGroups

public static <V>
ArrayList<net.imglib2.util.Pair<Group<V>,Group<V>>> overlappingGroups(Collection<Group<V>> groups)

Identify all pairs of overlapping groups

Type Parameters:

V - - view id type

Parameters:

groups - the groups

Returns:

all overlapping group pairs

mergeAllOverlappingGroups

public static <V> ArrayList<Group<V>> mergeAllOverlappingGroups(Collection<Group<V>> groups)

Merges all overlapping groups into a new List, the input remains unchanged

Type Parameters:

V - - view id type

Parameters:

groups - the groups to merge

Returns:

merger Groups

nextOverlappingGroup

public static <V>
net.imglib2.util.Pair<Integer,Integer> nextOverlappingGroup(List<Group<V>> groups)

Identify the indices of the next overlapping groups ordered by size, or return null if none are overlapping

Type Parameters:

V - - view id type

Parameters:

groups - list of Groups

Returns:

index of first overlapping pair (Gi, Gj) in grops

merge

public static <V> Group<V> merge(Group<V> groupA,
 Group<V> groupB)

Merges two Groups of views

Type Parameters:

V - - view id type

Parameters:

groupA - first Group

groupB - second Group

Returns:

merged Group

mergeOverlapping

public static <V> Group<V> mergeOverlapping(Group<V> groupA,
 Group<V> groupB)

Merges two Groups of views

Type Parameters:

V - - view id type

Parameters:

groupA - first Group

groupB - second Group

Returns:

merged Group

removeEmptyGroups

public static <V> void removeEmptyGroups(List<Group<V>> groups)

pvid

public static String pvid(mpicbg.spim.data.sequence.ViewId viewId)

pvids

public static String pvids(mpicbg.spim.data.sequence.ViewId viewId)

gvids

public static String gvids(Collection<?> group)

gvids

public static String gvids(Group<?> group)

main

public static void main(String[] args)