LAPUtils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.tracking.LAPUtils

```
public class LAPUtils
extends Object
```

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`XML_ELEMENT_NAME_FEATURE_PENALTIES`
`static String`	`XML_ELEMENT_NAME_GAP_CLOSING`
`static String`	`XML_ELEMENT_NAME_LINKING`
`static String`	`XML_ELEMENT_NAME_MERGING`
`static String`	`XML_ELEMENT_NAME_SPLITTING`

Constructor Summary

Constructors
Constructor and Description

LAPUtils()

Constructors
Constructor and Description
`LAPUtils()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`addFeaturePenaltyToSettings(Map<?,?> motherMap, Object motherKey, Object childKey, Object childValue, StringBuilder errorHolder)` Utility method to put a value in a map, contained in a mother map.
`static boolean`	`checkFeatureMap(Map<String,Object> map, String featurePenaltiesKey, StringBuilder errorHolder)` Check the validity of a feature penalty map in a settings map.
`static boolean`	`checkSettingsValidity(Map<String,Object> settings, StringBuilder errorHolder)`
`static double`	`computeLinkingCostFor(Spot s0, Spot s1, double distanceCutOff, double blockingValue, Map<String,Double> featurePenalties)` Compute the cost to link two spots, in the default way for the TrackMate trackmate.
`static void`	`displayCostMatrix(double[][] costs, int nSegments, int nSpots, double blockingValue, int[][] solutions)` Display the cost matrix solved by the Hungarian algorithm in the LAP approach.
`static void`	`displayLAPresults(int[][] array)`
`static String`	`echoFeaturePenalties(Map<String,Double> featurePenalties)`
`static void`	`echoMatrix(double[][] m)`
`static void`	`echoSolutions(int[][] solutions)`
`static Map<String,Object>`	`getDefaultLAPSettingsMap()` Returns a new settings map filled with default values suitable for the LAP trackers.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - XML_ELEMENT_NAME_LINKING
```
public static final String XML_ELEMENT_NAME_LINKING
```
    See Also:
    
    Constant Field Values
  - XML_ELEMENT_NAME_GAP_CLOSING
```
public static final String XML_ELEMENT_NAME_GAP_CLOSING
```
    See Also:
    
    Constant Field Values
  - XML_ELEMENT_NAME_MERGING
```
public static final String XML_ELEMENT_NAME_MERGING
```
    See Also:
    
    Constant Field Values
  - XML_ELEMENT_NAME_SPLITTING
```
public static final String XML_ELEMENT_NAME_SPLITTING
```
    See Also:
    
    Constant Field Values
  - XML_ELEMENT_NAME_FEATURE_PENALTIES
```
public static final String XML_ELEMENT_NAME_FEATURE_PENALTIES
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - LAPUtils
```
public LAPUtils()
```
- Method Detail
  - addFeaturePenaltyToSettings
```
public static final boolean addFeaturePenaltyToSettings(Map<?,?> motherMap,
                                                        Object motherKey,
                                                        Object childKey,
                                                        Object childValue,
                                                        StringBuilder errorHolder)
```
    Utility method to put a value in a map, contained in a mother map. Here it is mainly use to feed feature penalties to LAP tracker settings map.
    
    Parameters:
    
    motherMap - the mother map
    
    motherKey - the key in the mother map that points to the child map
    
    childKey - the key in the child map to put
    
    childValue - the value in the child map to put
    
    errorHolder - an error holder that will be appended with an error message if modifying the child map is unsuccessful.
    
    Returns:
    
    true if the child map could be modified correctly.
  - getDefaultLAPSettingsMap
```
public static final Map<String,Object> getDefaultLAPSettingsMap()
```
    Returns a new settings map filled with default values suitable for the LAP trackers.
    
    Returns:
    
    a new map.
  - echoFeaturePenalties
```
public static String echoFeaturePenalties(Map<String,Double> featurePenalties)
```
  - computeLinkingCostFor
```
public static final double computeLinkingCostFor(Spot s0,
                                                 Spot s1,
                                                 double distanceCutOff,
                                                 double blockingValue,
                                                 Map<String,Double> featurePenalties)
```
    Compute the cost to link two spots, in the default way for the TrackMate trackmate.
    This cost is calculated as follow:
    - The distance between the two spots D is calculated
    - If the spots are separated by more than the distance cutoff, the cost is set to be the blocking value. If not,
    - For each feature in the map, a penalty p is calculated as p = 3 × α × |f1-f2| / (f1+f2), where α is the factor associated to the feature in the map. This expression is such that:
      
      there is no penalty if the 2 feature values f1 and f2 are the same;
      that, with a factor of 1, the penalty if 1 is one value is the double of the other;
      the penalty is 2 if one is 5 times the other one.
    - All penalties are summed, to form P = (1 + ∑ p )
    - The cost is set to the square of the product: C = ( D × P )²
    For instance: if 2 spots differ by twice the value in a feature which is in the penalty map with a factor of 1, they will look as if they were twice as far.
  - checkSettingsValidity
```
public static final boolean checkSettingsValidity(Map<String,Object> settings,
                                                  StringBuilder errorHolder)
```
    Parameters:
    
    settings - the map to test.
    
    errorHolder - a StringBuilder that will contain an error message if the check is not successful.
    
    Returns:
    
    true if the settings map can be used with the LAP trackers. We do not check that all the spot features used in penalties are indeed found in all spots, because if such a feature is absent from one spot, the LAP trackers simply ignores the penalty and does not generate an error.
  - checkFeatureMap
```
public static final boolean checkFeatureMap(Map<String,Object> map,
                                            String featurePenaltiesKey,
                                            StringBuilder errorHolder)
```
    Check the validity of a feature penalty map in a settings map.
    A feature penalty setting is valid if it is either null (not here, that is) or an actual Map<String, Double>. Then, all its keys must be Strings and all its values as well.
    
    Parameters:
    
    map - the map to inspect.
    
    featurePenaltiesKey - the key that should map to a feature penalty map.
    
    errorHolder - will be appended with an error message.
    
    Returns:
    
    true if the feature penalty map is valid.
  - echoMatrix
```
public static final void echoMatrix(double[][] m)
```
  - displayCostMatrix
```
public static final void displayCostMatrix(double[][] costs,
                                           int nSegments,
                                           int nSpots,
                                           double blockingValue,
                                           int[][] solutions)
```
    Display the cost matrix solved by the Hungarian algorithm in the LAP approach.
    
    Parameters:
    
    costs - the cost matrix
    
    nSegments - the number of track segments found in the first step of the LAP tracking
    
    nSpots - the number of middle spots to consider
    
    blockingValue - the blocking value for cost
    
    solutions - the Hungarian assignment couple
  - echoSolutions
```
public static void echoSolutions(int[][] solutions)
```
  - displayLAPresults
```
public static void displayLAPresults(int[][] array)
```

Class LAPUtils

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

XML_ELEMENT_NAME_LINKING

XML_ELEMENT_NAME_GAP_CLOSING

XML_ELEMENT_NAME_MERGING

XML_ELEMENT_NAME_SPLITTING

XML_ELEMENT_NAME_FEATURE_PENALTIES

Constructor Detail

LAPUtils

Method Detail

addFeaturePenaltyToSettings

getDefaultLAPSettingsMap

echoFeaturePenalties

computeLinkingCostFor

checkSettingsValidity

checkFeatureMap

echoMatrix

displayCostMatrix

echoSolutions

displayLAPresults