TMUtils (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.util.TMUtils

```
public class TMUtils
extends Object
```
List of static utilities for TrackMate.

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static <T> boolean`	`checkMapKeys(Map<T,?> map, Collection<T> mandatoryKeys, Collection<T> optionalKeys, StringBuilder errorHolder)` Check that the given map has all some keys.
`static boolean`	`checkParameter(Map<String,Object> map, String key, Class<?> expectedClass, StringBuilder errorHolder)` Check the presence and the validity of a key in a map, and test it is of the desired class.
`static String`	`echoMap(Map<String,Object> map, int indent)` Generate a string representation of a map, typically a settings map.
`static <J,K> List<K>`	`getArrayFromMaping(Collection<J> keys, Map<J,K> mapping)` Returns the mapping in a map that is targeted by a list of keys, in the order given in the list.
`static Context`	`getContext()` Obtains the SciJava `Context` in use by ImageJ.
`static String`	`getCurrentTimeString()`
`static Interval`	`getInterval(ImgPlus<?> img, Settings settings)` Returns an interval object that in the specified `ImgPlus` slice in a single time frame.
`static Interval`	`getIntervalWithTime(ImgPlus<?> img, Settings settings)` Returns an interval object that slices in the specified `ImgPlus` in a single channel (the channel dimension is dropped).
`static int`	`getNBins(double[] values, int minBinNumber, int maxBinNumber)` Return the optimal bin number for a histogram of the data given in array, using the Freedman and Diaconis rule (bin_space = 2*IQR/n^(1/3)).
`static double`	`getPercentile(double[] values, double p)` Returns an estimate of the `p`th percentile of the values in the `values` array.
`static double[]`	`getSpatialCalibration(ij.ImagePlus imp)`
`static double[]`	`getSpatialCalibration(ImgPlusMetadata img)` Return the xyz calibration stored in an `ImgPlusMetadata` in a 3-elements double array.
`static String`	`getUnitsFor(Dimension dimension, String spaceUnits, String timeUnits)` Return a String unit for the given dimension.
`static <T extends Type<T>> ImgPlus<T>`	`hyperSlice(ImgPlus<T> img, long channel, long frame)`
`static void`	`localize(Spot spot, double[] coords)` Store the x, y, z coordinates of the specified spot in the first 3 elements of the specified double array.
`static double`	`otsuThreshold(double[] data)` Return a threshold for the given data, using an Otsu histogram thresholding method.
`static File`	`proposeTrackMateSaveFile(Settings settings, Logger logger)` Creates a default file path to save the TrackMate session to, based on the image TrackMate works on.
`static ImgPlus`	`rawWraps(ij.ImagePlus imp)` Wraps an IJ `ImagePlus` in an imglib2 `ImgPlus`, without parameterized types.
`static <K,V extends Comparable<? super V>> Map<K,V>`	`sortByValue(Map<K,V> map, Comparator<V> comparator)` Return a new map sorted by its values.
`static double`	`standardDeviation(double[] data)`
`static double`	`sum(double[] intensities)`
`static double`	`variance(double[] data)`

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

- Method Detail
  - sortByValue
```
public static <K,V extends Comparable<? super V>> Map<K,V> sortByValue(Map<K,V> map,
                                                                       Comparator<V> comparator)
```
    Return a new map sorted by its values. Adapted from http://stackoverflow.com /questions/109383/how-to-sort-a-mapkey-value-on-the-values-in-java
  - echoMap
```
public static final String echoMap(Map<String,Object> map,
                                   int indent)
```
    Generate a string representation of a map, typically a settings map.
  - rawWraps
```
public static final ImgPlus rawWraps(ij.ImagePlus imp)
```
    Wraps an IJ ImagePlus in an imglib2 ImgPlus, without parameterized types. The only way I have found to beat javac constraints on bounded multiple wildcard.
  - checkMapKeys
```
public static final <T> boolean checkMapKeys(Map<T,?> map,
                                             Collection<T> mandatoryKeys,
                                             Collection<T> optionalKeys,
                                             StringBuilder errorHolder)
```
    Check that the given map has all some keys. Two String collection allows specifying that some keys are mandatory, other are optional.
    
    Parameters:
    
    map - the map to inspect.
    
    mandatoryKeys - the collection of keys that are expected to be in the map. Can be null.
    
    optionalKeys - the collection of keys that can be - or not - in the map. Can be null.
    
    errorHolder - will be appended with an error message.
    
    Returns:
    
    if all mandatory keys are found in the map, and possibly some optional ones, but no others.
  - checkParameter
```
public static final boolean checkParameter(Map<String,Object> map,
                                           String key,
                                           Class<?> expectedClass,
                                           StringBuilder errorHolder)
```
    Check the presence and the validity of a key in a map, and test it is of the desired class.
    
    Parameters:
    
    map - the map to inspect.
    
    key - the key to find.
    
    expectedClass - the expected class of the target value .
    
    errorHolder - will be appended with an error message.
    
    Returns:
    
    true if the key is found in the map, and map a value of the desired class.
  - getArrayFromMaping
```
public static final <J,K> List<K> getArrayFromMaping(Collection<J> keys,
                                                     Map<J,K> mapping)
```
    Returns the mapping in a map that is targeted by a list of keys, in the order given in the list.
  - getSpatialCalibration
```
public static final double[] getSpatialCalibration(ImgPlusMetadata img)
```
    Return the xyz calibration stored in an ImgPlusMetadata in a 3-elements double array. Calibration is ordered as X, Y, Z. If one axis is not found, then the calibration for this axis takes the value of 1.
  - getSpatialCalibration
```
public static double[] getSpatialCalibration(ij.ImagePlus imp)
```
  - getPercentile
```
public static final double getPercentile(double[] values,
                                         double p)
```
    Returns an estimate of the pth percentile of the values in the values array. Taken from commons-math.
  - localize
```
public static final void localize(Spot spot,
                                  double[] coords)
```
    Store the x, y, z coordinates of the specified spot in the first 3 elements of the specified double array.
  - getNBins
```
public static final int getNBins(double[] values,
                                 int minBinNumber,
                                 int maxBinNumber)
```
    Return the optimal bin number for a histogram of the data given in array, using the Freedman and Diaconis rule (bin_space = 2*IQR/n^(1/3)). It is ensured that the bin number returned is not smaller and no bigger than the bounds given in argument.
  - otsuThreshold
```
public static final double otsuThreshold(double[] data)
```
    Return a threshold for the given data, using an Otsu histogram thresholding method.
  - getUnitsFor
```
public static final String getUnitsFor(Dimension dimension,
                                       String spaceUnits,
                                       String timeUnits)
```
    Return a String unit for the given dimension. When suitable, the unit is taken from the settings field, which contains the spatial and time units. Otherwise, default units are used.
  - getCurrentTimeString
```
public static final String getCurrentTimeString()
```
  - hyperSlice
```
public static <T extends Type<T>> ImgPlus<T> hyperSlice(ImgPlus<T> img,
                                                        long channel,
                                                        long frame)
```
  - getIntervalWithTime
```
public static final Interval getIntervalWithTime(ImgPlus<?> img,
                                                 Settings settings)
```
    Returns an interval object that slices in the specified ImgPlus in a single channel (the channel dimension is dropped).
    The specified Settings object is used to determine a crop-cube that will determine the X,Y,Z size of the interval. The channel dimension will be dropped.
    If the specified ImgPlus has a time axis, it will be included, using the Settings.tstart and Settings.tend as bounds. If it is a singleton dimension (1 time-point) it won't be dropped.
    
    Parameters:
    
    img - the source image into which the interval is to be defined.
    
    settings - the settings object that will determine the interval size.
    
    Returns:
    
    a new interval.
  - getInterval
```
public static final Interval getInterval(ImgPlus<?> img,
                                         Settings settings)
```
    Returns an interval object that in the specified ImgPlus slice in a single time frame.
    The specified Settings object is used to determine a crop-cube that will determine the X,Y,Z size of the interval. A single channel will be taken in the case of a multi-channel image. If the detector set in the settings object has a parameter for the target channel DetectorKeys.KEY_TARGET_CHANNEL, it will be used; otherwise the first channel will be taken.
    If the specified ImgPlus has a time axis, it will be dropped and the returned interval will have one dimension less.
    
    Parameters:
    
    img - the source image into which the interval is to be defined.
    
    settings - the settings object that will determine the interval size.
    
    Returns:
    
    a new interval.
  - getContext
```
public static Context getContext()
```
    Obtains the SciJava Context in use by ImageJ.
  - proposeTrackMateSaveFile
```
public static File proposeTrackMateSaveFile(Settings settings,
                                            Logger logger)
```
    Creates a default file path to save the TrackMate session to, based on the image TrackMate works on.
    
    Parameters:
    
    settings - the settings object from which to read the image, its folder, etc.
    
    logger - a logger instance in which to echo problems if any.
    
    Returns:
    
    a new file.
  - variance
```
public static final double variance(double[] data)
```
  - standardDeviation
```
public static final double standardDeviation(double[] data)
```
  - sum
```
public static double sum(double[] intensities)
```

Class TMUtils

Method Summary

Methods inherited from class java.lang.Object

Method Detail

sortByValue

echoMap

rawWraps

checkMapKeys

checkParameter

getArrayFromMaping

getSpatialCalibration

getSpatialCalibration

getPercentile

localize

getNBins

otsuThreshold

getUnitsFor

getCurrentTimeString

hyperSlice

getIntervalWithTime

getInterval

getContext

proposeTrackMateSaveFile

variance

standardDeviation

sum