Package net.preibisch.mvrecon.fiji.plugin

Class Interest_Point_Registration

java.lang.Object

net.preibisch.mvrecon.fiji.plugin.Interest_Point_Registration

All Implemented Interfaces:

ij.plugin.PlugIn

public class Interest_Point_Registration
extends Object
implements ij.plugin.PlugIn

Author:

Stephan Preibisch (stephan.preibisch@gmx.de)

Field Summary

Fields

Modifier and Type	Field	Description
static int	defaultAlgorithm
static boolean[]	defaultFixedViews
static int	defaultFixViews
static boolean	defaultGroupChannels
static boolean	defaultGroupIllums
static boolean	defaultGroupTiles
static boolean	defaultGroupTimePoints
static int	defaultInterestpointOverlapType
static double	defaultIPDistance
static int	defaultIPGrouping
static int	defaultLabel
static boolean[]	defaultLabelChoice
static double[]	defaultLabelWeights
static int	defaultMapBack
static boolean	defaultMatchAcrossLabels
static int	defaultOverlapType
static int	defaultRange
static int	defaultReferenceTimepointIndex
static int	defaultReferenceView
static int	defaultRegistrationType
static boolean	defaultSameFixedViews
static boolean	defaultSameReferenceView
static boolean	defaultShowStatistics
static ArrayList<PairwiseGUI>	staticPairwiseAlgorithms

Constructor Summary

Constructors

Constructor	Description
Interest_Point_Registration()

Method Summary

Modifier and Type	Method	Description
AdvancedRegistrationParameters	advancedRegistrationParameters(BasicRegistrationParameters brp, List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess, SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
protected boolean	askForFixedViews(Subset<mpicbg.spim.data.sequence.ViewId> subset, Set<mpicbg.spim.data.sequence.ViewId> fixedViews, String title)
protected mpicbg.spim.data.sequence.ViewId	askForReferenceView(Subset<mpicbg.spim.data.sequence.ViewId> subset, String title)
protected static String[]	assembleTimepoints(mpicbg.spim.data.sequence.TimePoints timepoints)
BasicRegistrationParameters	basicRegistrationParameters(List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess, int nAllTimepoints, SpimData2 data, List<mpicbg.spim.data.sequence.ViewId> viewIds)
List<mpicbg.spim.data.sequence.ViewId>	filterRemainingViewIdsAndLabels(List<mpicbg.spim.data.sequence.ViewId> viewIds, Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Double>> labelMap, Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> interestpointLists)
FixMapBackParameters	fixMapBackParameters(mpicbg.spim.data.sequence.SequenceDescription sd, PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup, int fixViewsIndex, int mapBackIndex, BasicRegistrationParameters.RegistrationType type)
protected ArrayList<Integer>	getListOfViewSetupIdsPresentInAllSubsets(List<Subset<mpicbg.spim.data.sequence.ViewId>> subsets)
List<net.imglib2.util.Pair<net.imglib2.util.Pair<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewId>,? extends PairwiseResult<?>>>	getStatistics()
GroupParameters	groupingParameters(Collection<Subset<mpicbg.spim.data.sequence.ViewId>> subsets)
static boolean	hasGroups(Collection<? extends Subset<?>> subsets)
void	identifySubsets(PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup, OverlapDetection<mpicbg.spim.data.sequence.ViewId> overlapDetection)
static ArrayList<String>	multipleInterestPointsGUI(String[] labels)
<M extends mpicbg.models.AbstractModel<M> & mpicbg.models.Affine3D<M>> boolean	processRegistration(PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup, Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> viewSetups, PairwiseGUI pairwiseMatching, GroupParameters.InterestpointGroupingType groupingType, BasicRegistrationParameters.InterestPointOverlapType interestPointOverlapType, double interestPointMergeDistance, Set<mpicbg.spim.data.sequence.ViewId> viewsToFix, mpicbg.models.Model<?> mapBackModel, Map<Subset<mpicbg.spim.data.sequence.ViewId>,net.imglib2.util.Pair<mpicbg.spim.data.sequence.ViewId,net.imglib2.Dimensions>> mapBackViews, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations, Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions, Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> interestpointLists, Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Double>> labelMap, GlobalOptimizationParameters globalOptParameters, boolean matchAcrossLabels, boolean collectStatistics)
boolean	register(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)
boolean	register(SpimData2 data, Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection, String xmlFileName, boolean saveXML)
void	run(String arg)

Methods inherited from class java.lang.Object

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

Field Details

staticPairwiseAlgorithms

public static ArrayList<PairwiseGUI> staticPairwiseAlgorithms

defaultAlgorithm

public static int defaultAlgorithm

defaultRegistrationType

public static int defaultRegistrationType

defaultOverlapType

public static int defaultOverlapType

defaultInterestpointOverlapType

public static int defaultInterestpointOverlapType

defaultLabel

public static int defaultLabel

defaultMatchAcrossLabels

public static boolean defaultMatchAcrossLabels

defaultGroupTiles

public static boolean defaultGroupTiles

defaultGroupIllums

public static boolean defaultGroupIllums

defaultGroupChannels

public static boolean defaultGroupChannels

defaultLabelChoice

public static boolean[] defaultLabelChoice

defaultLabelWeights

public static double[] defaultLabelWeights

defaultRange

public static int defaultRange

defaultReferenceTimepointIndex

public static int defaultReferenceTimepointIndex

defaultGroupTimePoints

public static boolean defaultGroupTimePoints

defaultFixViews

public static int defaultFixViews

defaultMapBack

public static int defaultMapBack

defaultShowStatistics

public static boolean defaultShowStatistics

defaultSameFixedViews

public static boolean defaultSameFixedViews

defaultSameReferenceView

public static boolean defaultSameReferenceView

defaultFixedViews

public static boolean[] defaultFixedViews

defaultReferenceView

public static int defaultReferenceView

defaultIPGrouping

public static int defaultIPGrouping

defaultIPDistance

public static double defaultIPDistance

Constructor Details

Interest_Point_Registration

public Interest_Point_Registration()

Method Details

run

public void run(String arg)

Specified by:

run in interface ij.plugin.PlugIn

register

public boolean register(SpimData2 data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection)

register

public boolean register(SpimData2 data,
 Collection<? extends mpicbg.spim.data.sequence.ViewId> viewCollection,
 String xmlFileName,
 boolean saveXML)

processRegistration

public <M extends mpicbg.models.AbstractModel<M> & mpicbg.models.Affine3D<M>>
boolean processRegistration(PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup,
 Map<Integer,? extends mpicbg.spim.data.generic.sequence.BasicViewSetup> viewSetups,
 PairwiseGUI pairwiseMatching,
 GroupParameters.InterestpointGroupingType groupingType,
 BasicRegistrationParameters.InterestPointOverlapType interestPointOverlapType,
 double interestPointMergeDistance,
 Set<mpicbg.spim.data.sequence.ViewId> viewsToFix,
 mpicbg.models.Model<?> mapBackModel,
 Map<Subset<mpicbg.spim.data.sequence.ViewId>,net.imglib2.util.Pair<mpicbg.spim.data.sequence.ViewId,net.imglib2.Dimensions>> mapBackViews,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.registration.ViewRegistration> registrations,
 Map<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewDescription> viewDescriptions,
 Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> interestpointLists,
 Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Double>> labelMap,
 GlobalOptimizationParameters globalOptParameters,
 boolean matchAcrossLabels,
 boolean collectStatistics)

filterRemainingViewIdsAndLabels

public List<mpicbg.spim.data.sequence.ViewId> filterRemainingViewIdsAndLabels(List<mpicbg.spim.data.sequence.ViewId> viewIds,
 Map<mpicbg.spim.data.sequence.ViewId,HashMap<String,Double>> labelMap,
 Map<mpicbg.spim.data.sequence.ViewId,ViewInterestPointLists> interestpointLists)

identifySubsets

public void identifySubsets(PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup,
 OverlapDetection<mpicbg.spim.data.sequence.ViewId> overlapDetection)

advancedRegistrationParameters

public AdvancedRegistrationParameters advancedRegistrationParameters(BasicRegistrationParameters brp,
 List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess,
 SpimData2 data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds)

basicRegistrationParameters

public BasicRegistrationParameters basicRegistrationParameters(List<mpicbg.spim.data.sequence.TimePoint> timepointToProcess,
 int nAllTimepoints,
 SpimData2 data,
 List<mpicbg.spim.data.sequence.ViewId> viewIds)

multipleInterestPointsGUI

public static ArrayList<String> multipleInterestPointsGUI(String[] labels)

groupingParameters

public GroupParameters groupingParameters(Collection<Subset<mpicbg.spim.data.sequence.ViewId>> subsets)

fixMapBackParameters

public FixMapBackParameters fixMapBackParameters(mpicbg.spim.data.sequence.SequenceDescription sd,
 PairwiseSetup<mpicbg.spim.data.sequence.ViewId> setup,
 int fixViewsIndex,
 int mapBackIndex,
 BasicRegistrationParameters.RegistrationType type)

hasGroups

public static boolean hasGroups(Collection<? extends Subset<?>> subsets)

getListOfViewSetupIdsPresentInAllSubsets

protected ArrayList<Integer> getListOfViewSetupIdsPresentInAllSubsets(List<Subset<mpicbg.spim.data.sequence.ViewId>> subsets)

askForFixedViews

protected boolean askForFixedViews(Subset<mpicbg.spim.data.sequence.ViewId> subset,
 Set<mpicbg.spim.data.sequence.ViewId> fixedViews,
 String title)

askForReferenceView

protected mpicbg.spim.data.sequence.ViewId askForReferenceView(Subset<mpicbg.spim.data.sequence.ViewId> subset,
 String title)

assembleTimepoints

protected static String[] assembleTimepoints(mpicbg.spim.data.sequence.TimePoints timepoints)

getStatistics

public List<net.imglib2.util.Pair<net.imglib2.util.Pair<mpicbg.spim.data.sequence.ViewId,mpicbg.spim.data.sequence.ViewId>,? extends PairwiseResult<?>>> getStatistics()