| Modifier and Type | Field and Description |
|---|---|
protected Model |
TrackMate.model
The model this trackmate will shape.
|
| Modifier and Type | Method and Description |
|---|---|
protected Model |
TrackMatePlugIn.createModel(ij.ImagePlus imp)
|
Model |
TrackMate.getModel() |
| Modifier and Type | Method and Description |
|---|---|
protected TrackMate |
TrackMatePlugIn.createTrackMate(Model model,
Settings settings)
Hook for subclassers:
Creates the TrackMate instance that will be controlled in the GUI. |
| Constructor and Description |
|---|
FeatureModel(Model model)
Instantiates a new feature model.
|
SelectionModel(Model parent) |
TrackMate(Model model,
Settings settings) |
| Modifier and Type | Method and Description |
|---|---|
static BranchTableView |
TrackBranchAnalysis.createBranchTable(Model model,
SelectionModel selectionModel) |
static ij.ImagePlus |
LabelImgExporter.createLabelImagePlus(Model model,
ij.ImagePlus imp,
boolean exportSpotsAsDots,
boolean exportTracksOnly)
Creates a new label
ImagePlus where the spots of the specified
model are painted as ellipsoids taken from their shape, with their track
ID as pixel value. |
static ij.ImagePlus |
LabelImgExporter.createLabelImagePlus(Model model,
ij.ImagePlus imp,
boolean exportSpotsAsDots,
boolean exportTracksOnly,
Logger logger)
Creates a new label
ImagePlus where the spots of the specified
model are painted as ellipsoids taken from their shape, with their track
ID as pixel value. |
static ij.ImagePlus |
LabelImgExporter.createLabelImagePlus(Model model,
int[] dimensions,
double[] calibration,
boolean exportSpotsAsDots,
boolean exportTracksOnly)
Creates a new label
ImagePlus where the spots of the specified
model are painted as ellipsoids taken from their shape, with their track
ID as pixel value. |
static ij.ImagePlus |
LabelImgExporter.createLabelImagePlus(Model model,
int[] dimensions,
double[] calibration,
boolean exportSpotsAsDots,
boolean exportTracksOnly,
Logger logger)
Creates a new label
ImagePlus where the spots of the specified
model are painted as ellipsoids taken from their shape, with their track
ID as pixel value. |
static Img<UnsignedShortType> |
LabelImgExporter.createLabelImg(Model model,
long[] dimensions,
double[] calibration,
boolean exportSpotsAsDots,
boolean exportTracksOnly)
Creates a new label
Img of UnsignedShortType where the
spots of the specified model are painted as ellipsoids taken from their
shape, with their track ID as pixel value. |
static Img<UnsignedShortType> |
LabelImgExporter.createLabelImg(Model model,
long[] dimensions,
double[] calibration,
boolean exportSpotsAsDots,
boolean exportTracksOnly,
Logger logger)
Creates a new label
Img of UnsignedShortType where the
spots of the specified model are painted as ellipsoids taken from their
shape, with their track ID as pixel value. |
static AllSpotsTableView |
ExportAllSpotsStatsAction.createSpotsTable(Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
static TrackTableView |
ExportStatsTablesAction.createTrackTables(Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
static void |
ExportTracksToXML.export(Model model,
Settings settings,
File file)
Static utility that silently exports tracks in a simplified xml format,
describe in this class.
|
static void |
ISBIChallengeExporter.exportToFile(Model model,
Settings settings,
File file) |
static void |
ISBIChallengeExporter.exportToFile(Model model,
Settings settings,
File file,
Logger logger) |
| Constructor and Description |
|---|
SpotGaussianFitter(Model model,
Settings settings,
Logger logger,
boolean fixRadius) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
ThresholdDetectorFactory.getDetectorConfigurationPanel(Settings lSettings,
Model model) |
ConfigurationPanel |
SpotDetectorFactoryBase.getDetectorConfigurationPanel(Settings settings,
Model model)
Returns a new GUI panel able to configure the settings suitable for this
specific detector factory.
|
ConfigurationPanel |
MaskDetectorFactory.getDetectorConfigurationPanel(Settings lSettings,
Model model) |
ConfigurationPanel |
ManualDetectorFactory.getDetectorConfigurationPanel(Settings settings,
Model model) |
ConfigurationPanel |
LogDetectorFactory.getDetectorConfigurationPanel(Settings lSettings,
Model model) |
ConfigurationPanel |
LabeImageDetectorFactory.getDetectorConfigurationPanel(Settings lSettings,
Model model) |
ConfigurationPanel |
DogDetectorFactory.getDetectorConfigurationPanel(Settings lSettings,
Model model) |
static void |
DetectionUtils.preview(Model model,
Settings settings,
SpotDetectorFactoryBase<?> detectorFactory,
Map<String,Object> detectorSettings,
int frame,
Logger logger,
Consumer<Boolean> buttonEnabler)
Preview a detection results.
|
| Constructor and Description |
|---|
AbstractSemiAutoTracker(Model model,
SelectionModel selectionModel,
Logger logger) |
SemiAutoTracker(Model model,
SelectionModel selectionModel,
ij.ImagePlus imp,
Logger logger) |
| Modifier and Type | Field and Description |
|---|---|
static Model |
FeatureUtils.DUMMY_MODEL |
protected Model |
ModelDataset.model |
| Modifier and Type | Method and Description |
|---|---|
static double[] |
FeatureUtils.autoMinMax(Model model,
DisplaySettings.TrackMateObject type,
String feature) |
static Map<String,String> |
FeatureUtils.collectFeatureKeys(DisplaySettings.TrackMateObject target,
Model model,
Settings settings) |
static double[] |
FeatureUtils.collectFeatureValues(String featureKey,
DisplaySettings.TrackMateObject target,
Model model,
boolean visibleOnly)
Missing or undefined values are not included.
|
static FeatureColorGenerator<Spot> |
FeatureUtils.createSpotColorGenerator(Model model,
DisplaySettings displaySettings) |
static FeatureColorGenerator<org.jgrapht.graph.DefaultWeightedEdge> |
FeatureUtils.createTrackColorGenerator(Model model,
DisplaySettings displaySettings) |
static FeatureColorGenerator<Integer> |
FeatureUtils.createWholeTrackColorGenerator(Model model,
DisplaySettings displaySettings) |
static int |
FeatureUtils.nObjects(Model model,
DisplaySettings.TrackMateObject target,
boolean visibleOnly) |
| Constructor and Description |
|---|
EdgeCollectionDataset(Model model,
SelectionModel selectionModel,
DisplaySettings ds,
String xFeature,
List<String> yFeatures,
List<org.jgrapht.graph.DefaultWeightedEdge> edges) |
EdgeFeatureCalculator(Model model,
Settings settings) |
EdgeFeatureGrapher(List<org.jgrapht.graph.DefaultWeightedEdge> edges,
String xFeature,
List<String> yFeatures,
Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
ModelDataset(Model model,
SelectionModel selectionModel,
DisplaySettings ds,
String xFeature,
List<String> yFeatures) |
ModelFeatureUpdater(Model model,
Settings settings)
Constructs and activate a
ModelFeatureUpdater. |
SpotCollectionDataset(Model model,
SelectionModel selectionModel,
DisplaySettings ds,
String xFeature,
List<String> yFeatures,
List<Spot> spots) |
SpotFeatureCalculator(Model model,
Settings settings) |
SpotFeatureGrapher(List<Spot> spots,
String xFeature,
List<String> yFeatures,
Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
TrackCollectionDataset(Model model,
SelectionModel selectionModel,
DisplaySettings ds,
String xFeature,
List<String> yFeatures,
List<Integer> trackIDs) |
TrackFeatureCalculator(Model model,
Settings settings) |
TrackFeatureGrapher(List<Integer> trackIDs,
String xFeature,
List<String> yFeatures,
Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
EdgeTimeLocationAnalyzer.analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
Model model) |
protected void |
EdgeTargetAnalyzer.analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
Model model) |
protected void |
EdgeSpeedAnalyzer.analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
Model model) |
protected void |
DirectionalChangeAnalyzer.analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
Model model) |
protected abstract void |
AbstractEdgeAnalyzer.analyze(org.jgrapht.graph.DefaultWeightedEdge edge,
Model model) |
void |
EdgeAnalyzer.process(Collection<org.jgrapht.graph.DefaultWeightedEdge> edges,
Model model)
Scores a collection of link between two spots.
|
void |
AbstractEdgeAnalyzer.process(Collection<org.jgrapht.graph.DefaultWeightedEdge> edges,
Model model) |
| Modifier and Type | Method and Description |
|---|---|
void |
ManualEdgeColorAnalyzer.process(Collection<org.jgrapht.graph.DefaultWeightedEdge> edges,
Model model) |
| Modifier and Type | Method and Description |
|---|---|
protected void |
TrackSpotQualityFeatureAnalyzer.analyze(Integer trackID,
Model model) |
protected void |
TrackSpeedStatisticsAnalyzer.analyze(Integer trackID,
Model model) |
protected void |
TrackLocationAnalyzer.analyze(Integer trackID,
Model model) |
protected void |
TrackDurationAnalyzer.analyze(Integer trackID,
Model model) |
protected void |
TrackBranchingAnalyzer.analyze(Integer trackID,
Model model) |
protected abstract void |
AbstractTrackAnalyzer.analyze(Integer trackID,
Model model) |
void |
TrackMotilityAnalyzer.process(Collection<Integer> trackIDs,
Model model) |
void |
TrackIndexAnalyzer.process(Collection<Integer> trackIDs,
Model model) |
void |
TrackAnalyzer.process(Collection<Integer> trackIDs,
Model model)
Compute the features of the track whose ID is given.
|
void |
AbstractTrackAnalyzer.process(Collection<Integer> trackIDs,
Model model) |
| Constructor and Description |
|---|
ConvexBranchesDecomposition(Model model)
Creates a new track splitter.
|
ConvexBranchesDecomposition(Model model,
boolean forbidMiddleLinks,
boolean forbidGaps)
Creates a new track splitter.
|
| Modifier and Type | Method and Description |
|---|---|
static CategoryJComboBox<DisplaySettings.TrackMateObject,String> |
FeatureDisplaySelector.createComboBoxSelector(Model model,
Settings settings)
Return a
CategoryJComboBox that lets a user select among all
available features in TrackMate. |
| Constructor and Description |
|---|
FeatureDisplaySelector(Model model,
Settings settings,
DisplaySettings displaySettings) |
FilterGuiPanel(Model model,
Settings settings,
DisplaySettings.TrackMateObject target,
List<FeatureFilter> filters,
String defaultFeature,
FeatureDisplaySelector featureSelector) |
| Constructor and Description |
|---|
DogDetectorConfigurationPanel(Settings settings,
Model model,
String infoText,
String detectorName) |
LabelImageDetectorConfigurationPanel(Settings settings,
Model model) |
LogDetectorConfigurationPanel(Settings settings,
Model model,
String infoText,
String detectorName)
Creates a new
LogDetectorConfigurationPanel, a GUI able to
configure settings suitable to LogDetectorFactory and derived
implementations. |
MaskDetectorConfigurationPanel(Settings settings,
Model model) |
ThresholdDetectorConfigurationPanel(Settings settings,
Model model) |
ThresholdDetectorConfigurationPanel(Settings settings,
Model model,
String infoText,
String detectorName)
Creates a new
ThresholdDetectorConfigurationPanel, a GUI able to
configure settings suitable to a LogDetectorFactory and derived
implementations. |
| Modifier and Type | Method and Description |
|---|---|
protected Model |
TmXmlReader.createModel()
Hook for subclassers:
Creates the instance of Model that will be built upon loading
with this reader. |
Model |
TmXmlReader.getModel()
Returns the model saved in the file, or
null if a saved
model cannot be found in the xml file. |
Model |
TGMMImporter.getResult() |
| Modifier and Type | Method and Description |
|---|---|
void |
TmXmlWriter.appendModel(Model model)
Appends the content of a
Model to the file generated by this
writer. |
Collection<TrackMateModelView> |
TmXmlReader.getViews(ViewProvider provider,
Model model,
Settings settings,
SelectionModel selectionModel,
DisplaySettings displaySettings)
Returns the collection of views that were saved in this file.
|
protected boolean |
TmXmlReader.readTracks(org.jdom2.Element modelElement,
Model model)
Load the tracks, the track features and the ID of the filtered tracks
into the model specified.
|
| Constructor and Description |
|---|
IcyTrackFormatWriter(File file,
Model model,
double[] calibration) |
IcyTrackFormatWriter(File file,
Model model,
double[] calibration,
String description) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
SpotTrackerFactory.getTrackerConfigurationPanel(Model model)
Returns a new GUI panel able to configure the settings suitable for the
target tracker identified by the key parameter.
|
ConfigurationPanel |
ManualTrackerFactory.getTrackerConfigurationPanel(Model model) |
ConfigurationPanel |
LAPTrackerFactory.getTrackerConfigurationPanel(Model model) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
KalmanTrackerFactory.getTrackerConfigurationPanel(Model model) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
NearestNeighborTrackerFactory.getTrackerConfigurationPanel(Model model) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
OverlapTrackerFactory.getTrackerConfigurationPanel(Model model) |
| Modifier and Type | Method and Description |
|---|---|
ConfigurationPanel |
SimpleSparseLAPTrackerFactory.getTrackerConfigurationPanel(Model model) |
| Modifier and Type | Method and Description |
|---|---|
static void |
ModelTools.linkSpots(Model model,
SelectionModel selectionModel)
Links all the spots in the selection, in time-forward order.
|
| Constructor and Description |
|---|
TrackNavigator(Model model,
SelectionModel selectionModel) |
| Modifier and Type | Field and Description |
|---|---|
protected Model |
AbstractTrackMateModelView.model
The model displayed by this class.
|
| Modifier and Type | Method and Description |
|---|---|
Model |
TrackMateModelView.getModel()
Returns the model displayed in this view.
|
Model |
AbstractTrackMateModelView.getModel() |
| Modifier and Type | Method and Description |
|---|---|
TrackMateModelView |
ViewFactory.create(Model model,
Settings settings,
SelectionModel selectionModel,
DisplaySettings displaySettings)
Returns a new instance of the concrete view.
|
static ij.ImagePlus |
ViewUtils.makeEmpytImagePlus(Model model) |
| Constructor and Description |
|---|
AbstractTrackMateModelView(Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
ManualEdgeColorGenerator(Model model,
Color missingValueColor) |
ManualEdgePerSpotColorGenerator(Model model,
Color missingValueColor) |
ManualSpotPerEdgeColorGenerator(Model model,
Color missingValueColor) |
PerEdgeFeatureColorGenerator(Model model,
String edgeFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
PerSpotFeatureColorGenerator(Model model,
String spotFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
PerTrackFeatureColorGenerator(Model model,
String trackFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
SpotColorGeneratorPerEdgeFeature(Model model,
String edgeFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
SpotColorGeneratorPerTrackFeature(Model model,
String trackFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
WholeTrackFeatureColorGenerator(Model model,
String trackFeature,
Color missingValueColor,
Color undefinedValueColor,
Colormap colormap,
double min,
double max) |
| Modifier and Type | Field and Description |
|---|---|
protected Model |
TrackOverlay.model |
protected Model |
SpotOverlay.model |
| Modifier and Type | Method and Description |
|---|---|
TrackMateModelView |
HyperStackDisplayerFactory.create(Model model,
Settings settings,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
| Constructor and Description |
|---|
HyperStackDisplayer(Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
HyperStackDisplayer(Model model,
SelectionModel selectionModel,
ij.ImagePlus imp,
DisplaySettings displaySettings) |
SpotOverlay(Model model,
ij.ImagePlus imp,
DisplaySettings displaySettings) |
TrackOverlay(Model model,
ij.ImagePlus imp,
DisplaySettings displaySettings) |
| Modifier and Type | Method and Description |
|---|---|
Model |
TrackTableView.getModel() |
Model |
BranchTableView.getModel() |
Model |
AllSpotsTableView.getModel() |
| Modifier and Type | Method and Description |
|---|---|
static TablePanel<BranchTableView.Branch> |
BranchTableView.createBranchTable(Model model,
SelectionModel selectionModel) |
static TablePanel<Spot> |
AllSpotsTableView.createSpotTable(Model model,
DisplaySettings ds) |
| Constructor and Description |
|---|
AllSpotsTableView(Model model,
SelectionModel selectionModel,
DisplaySettings ds) |
BranchTableView(Model model,
SelectionModel selectionModel) |
TrackTableView(Model model,
SelectionModel selectionModel,
DisplaySettings ds) |
| Modifier and Type | Method and Description |
|---|---|
Model |
TrackScheme.getModel() |
| Modifier and Type | Method and Description |
|---|---|
TrackMateModelView |
TrackSchemeFactory.create(Model model,
Settings settings,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
| Constructor and Description |
|---|
InfoPane(Model model,
SelectionModel selectionModel)
Creates a new Info pane that displays information on the current spot
selection in a table.
|
JGraphXAdapter(Model tmm) |
TrackScheme(Model model,
SelectionModel selectionModel,
DisplaySettings displaySettings) |
TrackSchemeGraphLayout(JGraphXAdapter graph,
Model model,
TrackSchemeGraphComponent component) |
TrackSchemeStylist(Model model,
JGraphXAdapter graphx,
DisplaySettings displaySettings) |
| Constructor and Description |
|---|
SearchBar(Model model,
TrackMateModelView view)
Creates new form SearchBox
|
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