endrov.typeLineageAutoNucJH
Class AutolineageJHdic1.Algo

java.lang.Object
  endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo

All Implemented Interfaces:

LineagingAlgorithm

Enclosing class:

AutolineageJHdic1

public static class AutolineageJHdic1.Algo
extends java.lang.Object
implements LineagingAlgorithm

Instance of the algorithm

Nested Class Summary

class

AutolineageJHdic1.Algo.BeforeAfterPair Pairing of cell from last frame to candidates

Nested classes/interfaces inherited from interface endrov.windowAutoLineaging.LineagingAlgorithm

LineagingAlgorithm.LineageAlgorithmDef, LineagingAlgorithm.LineageSession

Constructor Summary

AutolineageJHdic1.Algo()

Method Summary

java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair>	chooseBeforeAfterGlobalMatch(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore, java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, EvDecimal frameBefore, Lineage lin, java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList) Fit together cell in last frame with cell in this frame.
java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair>	chooseBeforeAfterLocalMatch(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore, java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, EvDecimal frameBefore, Lineage lin, java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList) Fit together cell in last frame with cell in this frame.
java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair>	chooseBeforeAfterNoDiv(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore, java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, EvDecimal frameBefore, Lineage lin, java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList) Fit together cell in last frame with cell in this frame.
EvStack	convertDICtoHisFluo(ProgressHandle ph, EvStack stackDIC) To use the his-algorithm, emulate his image using transformed DIC
static void	createLinesFromCandDiv(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> pairs, EvContainer parentContainer, EvDecimal frame) Debugging: draw lines for candidate divisions
void	createNucFromBeforeAfter(java.util.Collection<AutolineageJHdic1.Algo.BeforeAfterPair> joiningNucBefore, Lineage lin, EvDecimal currentFrame) Create nuclei and add new coordinates for the next frame
void	dataChangedEvent()
void	estimateParameters(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist) Estimate parameters to be used for the next frame
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>	filterCandDivHeuristic(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> candlist) Filter candidate division pairs using heuristics
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>	filterCandDivWeightedOverlap(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> pairs) Filter candidate divisions such that a nucleus is assigned to exactly 0 or 1 other candidate nucleus.
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate>	filterCandidatesStrongestIntensityOverlap(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist) Filter candidate list by removing candidates overlapped by another candidate that has a stronger intensity.
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate>	filterCandidatesTake(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, int num) Take #num first entries in list.
java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair>	findBestMatchingBeforeAfter(java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> baPairs, java.util.Set<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> usedBefore, java.util.Set<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> usedAfter) Given a list of (candidate before) - (candidates after), find the optimal match.
java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate>	findCandidatesDoG(ProgressHandle ph, EvStack stackHis, Shell shell, double sigmaHis1) Find candidate nuclei.
java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair>	generateAllBeforeAfter(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore, java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, EvDecimal frame, Lineage lin) Generate complete list of candidate before-after matchings.
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>	generateCandDivAll(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist) Generate every possible candidate division pair (except not the symmetric pair)
java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>	generateCandDivVoronoi(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist) Generate candidate division pairs as the Delaunay edges.
javax.swing.JComponent	getComponent() Get custom GUI component
void	reassignID(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist) Redo all ID assignments
void	run(ProgressHandle ph, LineagingAlgorithm.LineageSession session) Lineage one frame
void	setStopping(boolean b) Set if to stop the algorithm prematurely
static void	sortBeforeAfter(java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> baList) Sort before-after list, best to worst
void	sortCandDiv(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divlist) Sort list of candidates best to worst
Tuple<java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>,java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate>>	takeBestDivCandidates(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist, java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList, int numTake) Take the numTake best candidate dividing nuclei.

Methods inherited from class java.lang.Object

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

Constructor Detail

AutolineageJHdic1.Algo

public AutolineageJHdic1.Algo()

Method Detail

setStopping

public void setStopping(boolean b)

Set if to stop the algorithm prematurely

Specified by:

setStopping in interface LineagingAlgorithm

getComponent

public javax.swing.JComponent getComponent()

Get custom GUI component

Specified by:

getComponent in interface LineagingAlgorithm

sortCandDiv

public void sortCandDiv(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divlist)

Sort list of candidates best to worst

generateCandDivVoronoi

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> generateCandDivVoronoi(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist)

Generate candidate division pairs as the Delaunay edges. Turns out to be hypersensitive to false positives.

generateCandDivAll

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> generateCandDivAll(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist)

Generate every possible candidate division pair (except not the symmetric pair)

filterCandDivHeuristic

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> filterCandDivHeuristic(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> candlist)

Filter candidate division pairs using heuristics

filterCandDivWeightedOverlap

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> filterCandDivWeightedOverlap(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> pairs)

Filter candidate divisions such that a nucleus is assigned to exactly 0 or 1 other candidate nucleus. It is done by finding (approximately) candidate pairs such that the sum of error is minimized. Also sort by error in fit.

createLinesFromCandDiv

public static void createLinesFromCandDiv(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> pairs,
                                          EvContainer parentContainer,
                                          EvDecimal frame)

Debugging: draw lines for candidate divisions

convertDICtoHisFluo

public EvStack convertDICtoHisFluo(ProgressHandle ph,
                                   EvStack stackDIC)

To use the his-algorithm, emulate his image using transformed DIC

findCandidatesDoG

public java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> findCandidatesDoG(ProgressHandle ph,
                                                                                                      EvStack stackHis,
                                                                                                      Shell shell,
                                                                                                      double sigmaHis1)

Find candidate nuclei. These are the only candidates considered, and the final selection is a filtered list. Candidates are found by looking for features at several frequencies using difference of gaussian (Rickert wavelet approximation). Candidates has to be within the shell.

filterCandidatesStrongestIntensityOverlap

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> filterCandidatesStrongestIntensityOverlap(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist)

Filter candidate list by removing candidates overlapped by another candidate that has a stronger intensity. This is an extremely efficient filter and doesn't seem to make any mistakes

filterCandidatesTake

public java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> filterCandidatesTake(java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                                               int num)

Take #num first entries in list. Assumes list is sorted best to worst

sortBeforeAfter

public static void sortBeforeAfter(java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> baList)

Sort before-after list, best to worst

generateAllBeforeAfter

public java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> generateAllBeforeAfter(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore,
                                                                                           java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                           EvDecimal frame,
                                                                                           Lineage lin)

Generate complete list of candidate before-after matchings.

findBestMatchingBeforeAfter

public java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> findBestMatchingBeforeAfter(java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> baPairs,
                                                                                                java.util.Set<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> usedBefore,
                                                                                                java.util.Set<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> usedAfter)

Given a list of (candidate before) - (candidates after), find the optimal match. Assumes list of pairs is sorted best to worst Return which candidates were used

takeBestDivCandidates

public Tuple<java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair>,java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate>> takeBestDivCandidates(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                                                                                                                                            java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList,
                                                                                                                                                                                                            int numTake)

Take the numTake best candidate dividing nuclei. Assumes divlist sorted best to worst

Returns:

Unused candidates and the best candidate divisions

chooseBeforeAfterNoDiv

public java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> chooseBeforeAfterNoDiv(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore,
                                                                                           java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                           EvDecimal frameBefore,
                                                                                           Lineage lin,
                                                                                           java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList)

Fit together cell in last frame with cell in this frame. Assume no divisions

chooseBeforeAfterGlobalMatch

public java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> chooseBeforeAfterGlobalMatch(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore,
                                                                                                 java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                                 EvDecimal frameBefore,
                                                                                                 Lineage lin,
                                                                                                 java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList)

Fit together cell in last frame with cell in this frame. Relies mainly on division candidate list to find matchings. Alternative not used strategy: virtual candidates, join 1-1. there will be tons of virtual cand, need to filter them aggressively. no guarantee that all nuclei are used; not very nice. if only 1 cell divides then hard to control aggression

chooseBeforeAfterLocalMatch

public java.util.LinkedList<AutolineageJHdic1.Algo.BeforeAfterPair> chooseBeforeAfterLocalMatch(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.NucBefore> joiningNucBefore,
                                                                                                java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist,
                                                                                                EvDecimal frameBefore,
                                                                                                Lineage lin,
                                                                                                java.util.LinkedList<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.CandDivPair> divList)

Fit together cell in last frame with cell in this frame. Relies mainly on distance before-after to find divisions.

createNucFromBeforeAfter

public void createNucFromBeforeAfter(java.util.Collection<AutolineageJHdic1.Algo.BeforeAfterPair> joiningNucBefore,
                                     Lineage lin,
                                     EvDecimal currentFrame)

Create nuclei and add new coordinates for the next frame

run

public void run(ProgressHandle ph,
                LineagingAlgorithm.LineageSession session)

Lineage one frame

Specified by:

run in interface LineagingAlgorithm

estimateParameters

public void estimateParameters(java.util.List<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist)

Estimate parameters to be used for the next frame

reassignID

public void reassignID(java.util.Collection<endrov.typeLineageAutoNucJH.AutolineageJHdic1.Algo.Candidate> candlist)

Redo all ID assignments

dataChangedEvent

public void dataChangedEvent()

Specified by:

dataChangedEvent in interface LineagingAlgorithm