TmXmlReader (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- fiji.plugin.trackmate.io.TmXmlReader

```
public class TmXmlReader
extends Object
```

Field Summary

Fields
Modifier and Type	Field and Description
`protected ConcurrentHashMap<Integer,Spot>`	`cache` A map of all spots loaded.
`protected static boolean`	`DEBUG`
`protected org.jdom2.Document`	`document`
`protected File`	`file`
`protected Logger.StringBuilderLogger`	`logger`
`protected boolean`	`ok` If `false`, an error occurred during reading.
`protected org.jdom2.Element`	`root`

Constructor Summary

Constructors
Constructor and Description

TmXmlReader(File file)
Initialize this reader to read the file given in argument.

Constructors
Constructor and Description
`TmXmlReader(File file)` Initialize this reader to read the file given in argument.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`protected Model`	`createModel()` Hook for subclassers: Creates the instance of `Model` that will be built upon loading with this reader.
`protected void`	`getDetectorSettings(org.jdom2.Element settingsElement, Settings settings, DetectorProvider provider)` Update the given `Settings` object with the `SpotDetectorFactory` and settings map fields named `Settings.detectorFactory` and `Settings.detectorSettings` read within the XML file this reader is initialized with.
`DisplaySettings`	`getDisplaySettings()`
`String`	`getErrorMessage()` Returns an explanatory message about the last unsuccessful read attempt.
`String`	`getGUIState()` Returns the GUI state saved in the file.
`protected FeatureFilter`	`getInitialFilter(org.jdom2.Element settingsElement)` Return the initial filter value on quality stored in this file.
`String`	`getLog()` Returns the log text saved in the file, or `null` if log text was not saved.
`Model`	`getModel()` Returns the model saved in the file, or `null` if a saved model cannot be found in the xml file.
`protected List<FeatureFilter>`	`getSpotFeatureFilters(org.jdom2.Element settingsElement)` Return the list of `FeatureFilter` for spots stored in this file.
`protected void`	`getTrackerSettings(org.jdom2.Element settingsElement, Settings settings, TrackerProvider provider)` Update the given `Settings` object with `SpotTracker` proper settings map fields named `Settings.trackerSettings` and `Settings.trackerFactory` read within the XML file this reader is initialized with.
`protected List<FeatureFilter>`	`getTrackFeatureFilters(org.jdom2.Element settingsElement)` Returns the list of `FeatureFilter` for tracks stored in this file.
`String`	`getVersion()` Returns the version string stored in the file.
`Collection<TrackMateModelView>`	`getViews(ViewProvider provider, Model model, Settings settings, SelectionModel selectionModel, DisplaySettings displaySettings)` Returns the collection of views that were saved in this file.
`boolean`	`isReadingOk()` Returns `true` if the last reading method call happened without any warning or error, `false` otherwise.
`ij.ImagePlus`	`readImage()`
`Settings`	`readSettings(ij.ImagePlus imp)`
`Settings`	`readSettings(ij.ImagePlus imp, DetectorProvider detectorProvider, TrackerProvider trackerProvider, SpotAnalyzerProvider spotAnalyzerProvider, EdgeAnalyzerProvider edgeAnalyzerProvider, TrackAnalyzerProvider trackAnalyzerProvider, SpotMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider)` Reads the settings element of the file, and sets the fields of the specified `Settings` object according to the xml file content.
`protected boolean`	`readTracks(org.jdom2.Element modelElement, Model model)` Load the tracks, the track features and the ID of the filtered tracks into the model specified.
`protected static void`	`removeAttributeFromName(List<org.jdom2.Attribute> attributes, String attributeNameToRemove)`

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

- Field Detail
  - DEBUG
```
protected static final boolean DEBUG
```
    See Also:
    
    Constant Field Values
  - document
```
protected org.jdom2.Document document
```
  - file
```
protected final File file
```
  - cache
```
protected ConcurrentHashMap<Integer,Spot> cache
```
    A map of all spots loaded. We need this for performance, since we need to recreate both the filtered spot collection and the tracks graph from the same spot objects that the main spot collection.. In the file, they are referenced by their Spot.ID(), and parsing them all to retrieve the one with the right ID is a drag. We made this cache a ConcurrentHashMap because we hope to load large data in a multi-threaded way.
  - logger
```
protected Logger.StringBuilderLogger logger
```
  - root
```
protected final org.jdom2.Element root
```
  - ok
```
protected boolean ok
```
    If false, an error occurred during reading.
    
    See Also:
    
    getErrorMessage()
- Constructor Detail
  - TmXmlReader
```
public TmXmlReader(File file)
```
    Initialize this reader to read the file given in argument.
- Method Detail
  - getLog
```
public String getLog()
```
    Returns the log text saved in the file, or null if log text was not saved.
  - getGUIState
```
public String getGUIState()
```
    Returns the GUI state saved in the file.
    
    Returns:
    
    the saved GUI state, as a string.
  - getDisplaySettings
```
public DisplaySettings getDisplaySettings()
```
  - getViews
```
public Collection<TrackMateModelView> getViews(ViewProvider provider,
                                               Model model,
                                               Settings settings,
                                               SelectionModel selectionModel,
                                               DisplaySettings displaySettings)
```
    Returns the collection of views that were saved in this file. The views returned are not rendered yet.
    
    Parameters:
    
    provider - the ViewProvider to instantiate the view. Each saved view must be known by the specified provider.
    
    model - the model to display in the views.
    
    settings - the settings to build the views.
    
    selectionModel - the SelectionModel model that will be shared with the new views.
    
    displaySettings - the display settings to pass to the view.
    
    Returns:
    
    the collection of views.
    
    See Also:
    
    TrackMateModelView.render()
  - getModel
```
public Model getModel()
```
    Returns the model saved in the file, or null if a saved model cannot be found in the xml file.
    
    Returns:
    
    a new Model.
  - createModel
```
protected Model createModel()
```
    Hook for subclassers:
    Creates the instance of Model that will be built upon loading with this reader.
    
    Returns:
    
    a new Model instance.
  - readImage
```
public ij.ImagePlus readImage()
```
  - readSettings
```
public Settings readSettings(ij.ImagePlus imp)
```
  - readSettings
```
public Settings readSettings(ij.ImagePlus imp,
                             DetectorProvider detectorProvider,
                             TrackerProvider trackerProvider,
                             SpotAnalyzerProvider spotAnalyzerProvider,
                             EdgeAnalyzerProvider edgeAnalyzerProvider,
                             TrackAnalyzerProvider trackAnalyzerProvider,
                             SpotMorphologyAnalyzerProvider spotMorphologyAnalyzerProvider)
```
    Reads the settings element of the file, and sets the fields of the specified Settings object according to the xml file content.
    
    Parameters:
    
    imp -
    
    detectorProvider - the detector provider, required to configure the settings with a correct SpotDetectorFactory. If null, will skip reading detector parameters.
    
    trackerProvider - the tracker provider, required to configure the settings with a correct SpotTracker. If null, will skip reading tracker parameters.
    
    spotAnalyzerProvider - the spot analyzer provider, required to instantiates the saved SpotAnalyzerFactorys. If null, will skip reading spot analyzers.
    
    edgeAnalyzerProvider - the edge analyzer provider, required to instantiates the saved EdgeAnalyzers. If null, will skip reading edge analyzers.
    
    trackAnalyzerProvider - the track analyzer provider, required to instantiates the saved TrackAnalyzers. If null, will skip reading track analyzers.
  - getVersion
```
public String getVersion()
```
    Returns the version string stored in the file.
  - getErrorMessage
```
public String getErrorMessage()
```
    Returns an explanatory message about the last unsuccessful read attempt.
    
    Returns:
    
    an error message.
    
    See Also:
    
    isReadingOk()
  - isReadingOk
```
public boolean isReadingOk()
```
    Returns true if the last reading method call happened without any warning or error, false otherwise.
    
    Returns:
    
    true if reading was ok.
    
    See Also:
    
    getErrorMessage()
  - getInitialFilter
```
protected FeatureFilter getInitialFilter(org.jdom2.Element settingsElement)
```
    Return the initial filter value on quality stored in this file. Return null if the initial threshold data cannot be found in the file.
    
    Parameters:
    
    settingsElement - the settings Element to read from.
    
    Returns:
    
    the initial filter, as a FeatureFilter.
  - getSpotFeatureFilters
```
protected List<FeatureFilter> getSpotFeatureFilters(org.jdom2.Element settingsElement)
```
    Return the list of FeatureFilter for spots stored in this file.
    
    Parameters:
    
    settingsElement - the settings Element to read from.
    
    Returns:
    
    a list of FeatureFilters.
  - getTrackFeatureFilters
```
protected List<FeatureFilter> getTrackFeatureFilters(org.jdom2.Element settingsElement)
```
    Returns the list of FeatureFilter for tracks stored in this file.
    
    Parameters:
    
    settingsElement - the settings Element to read from.
    
    Returns:
    
    a list of FeatureFilters.
  - getDetectorSettings
```
protected void getDetectorSettings(org.jdom2.Element settingsElement,
                                   Settings settings,
                                   DetectorProvider provider)
```
    Update the given Settings object with the SpotDetectorFactory and settings map fields named Settings.detectorFactory and Settings.detectorSettings read within the XML file this reader is initialized with.
    
    Parameters:
    
    settingsElement - the Element in which the Settings parameters are stored.
    
    settings - the base Settings object to update.
    
    provider - a DetectorProvider, required to read detector parameters.
  - getTrackerSettings
```
protected void getTrackerSettings(org.jdom2.Element settingsElement,
                                  Settings settings,
                                  TrackerProvider provider)
```
    Update the given Settings object with SpotTracker proper settings map fields named Settings.trackerSettings and Settings.trackerFactory read within the XML file this reader is initialized with.
    If the tracker settings or the tracker info can be read, but cannot be understood (most likely because the class the XML refers to is unknown) then a default object is substituted.
    
    Parameters:
    
    settingsElement - the Element in which the tracker parameters are stored.
    
    settings - the base Settings object to update.
    
    provider - the TrackerProvider, required to read the tracker parameters.
  - readTracks
```
protected boolean readTracks(org.jdom2.Element modelElement,
                             Model model)
```
    Load the tracks, the track features and the ID of the filtered tracks into the model specified. The track collection element is expected to be found as a child of the specified element.
    
    Returns:
    
    true if reading tracks was successful, false otherwise.
  - removeAttributeFromName
```
protected static final void removeAttributeFromName(List<org.jdom2.Attribute> attributes,
                                                    String attributeNameToRemove)
```

Class TmXmlReader

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEBUG

document

file

cache

logger

root

ok

Constructor Detail

TmXmlReader

Method Detail

getLog

getGUIState

getDisplaySettings

getViews

getModel

createModel

readImage

readSettings

readSettings

getVersion

getErrorMessage

isReadingOk

getInitialFilter

getSpotFeatureFilters

getTrackFeatureFilters

getDetectorSettings

getTrackerSettings

readTracks

removeAttributeFromName