fiji.plugin.trackmate.action

Class CTCExporter

java.lang.Object

fiji.plugin.trackmate.action.CTCExporter

public class CTCExporter
extends Object

An exporter that saves the current TrackMate session as files following the Cell-Tracking-Challenge convention.

See http://celltrackingchallenge.net/

Author:

Jean-Yves Tinevez

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CTCExporter.ExportType

Constructor Summary

Constructors

Constructor and Description
CTCExporter()

Method Summary

Modifier and Type	Method and Description
static String	exportAll(String exportRootFolder, TrackMate trackmate, CTCExporter.ExportType exportType, Logger logger)
static void	exportOriginalImageData(String exportRootFolder, int saveId, ij.ImagePlus imp, Logger logger)
static void	exportOriginalImageData(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger)
static void	exportSegmentationData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger) Writes the segmentation ground-truth files.
static void	exportSettingsFile(String exportRootFolder, int saveId, TrackMate trackmate, Logger logger) Saves the settings part as XML for reference.
static String	exportTrackingData(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate, Logger logger)
static int	getAvailableDatasetID(String exportRootFolder) Returns a suitable dataset id to save in the specified folder.
static String	getExportTrackingDataPath(String exportRootFolder, int saveId, CTCExporter.ExportType exportType, TrackMate trackmate) Returns the folder in which the tracking data will be exported.

Methods inherited from class java.lang.Object

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

Constructor Detail

CTCExporter

public CTCExporter()

Method Detail

exportAll

public static String exportAll(String exportRootFolder,
                               TrackMate trackmate,
                               CTCExporter.ExportType exportType,
                               Logger logger)
                        throws IOException

Throws:

IOException

exportSettingsFile

public static void exportSettingsFile(String exportRootFolder,
                                      int saveId,
                                      TrackMate trackmate,
                                      Logger logger)
                               throws IOException

Saves the settings part as XML for reference.

Parameters:

exportRootFolder - the root folder for exporting.

saveId - the id of the save file (exportRootFolder/01, exportRootFolder/02, etc)

trackmate - the trackmate to export.

logger - a logger to report progress.

Throws:

IOException

getAvailableDatasetID

public static int getAvailableDatasetID(String exportRootFolder)

Returns a suitable dataset id to save in the specified folder.

For instance the first id return will be '1', which means that the original image data will be saved under the folder '01'. If '01' already exists, then this method will return 2, etc.

Parameters:

exportRootFolder - the root folder in which to export the data.

Returns:

an integer id that can be passed in the other method of this class.

exportOriginalImageData

public static void exportOriginalImageData(String exportRootFolder,
                                           int saveId,
                                           TrackMate trackmate,
                                           Logger logger)
                                    throws IOException

Throws:

IOException

exportOriginalImageData

public static void exportOriginalImageData(String exportRootFolder,
                                           int saveId,
                                           ij.ImagePlus imp,
                                           Logger logger)
                                    throws IOException

Throws:

IOException

exportSegmentationData

public static void exportSegmentationData(String exportRootFolder,
                                          int saveId,
                                          CTCExporter.ExportType exportType,
                                          TrackMate trackmate,
                                          Logger logger)
                                   throws IOException

Writes the segmentation ground-truth files.

Only exports the spots that have a ROI, and write only the frames that have at least one spot with a ROI.

Parameters:

exportRootFolder - the root of the export folder.

saveId - the id under which to save the data.

exportType - the export type. Must be CTCExporter.ExportType.GOLD_TRUTH or CTCExporter.ExportType.SILVER_TRUTH.

trackmate - the TrackMate object to export.

logger - a Logger instance to report progress.

Throws:

IOException - if a problem happens during writing.

exportTrackingData

public static String exportTrackingData(String exportRootFolder,
                                        int saveId,
                                        CTCExporter.ExportType exportType,
                                        TrackMate trackmate,
                                        Logger logger)
                                 throws FileNotFoundException,
                                        IOException

Throws:

FileNotFoundException

IOException

getExportTrackingDataPath

public static final String getExportTrackingDataPath(String exportRootFolder,
                                                     int saveId,
                                                     CTCExporter.ExportType exportType,
                                                     TrackMate trackmate)

Returns the folder in which the tracking data will be exported.

Parameters:

exportRootFolder - the root folder to export in.

saveId - the save id.

exportType - the export type.

trackmate - the TrackMate object to eport.

Returns:

a path as a string.

See Also:

exportTrackingData(String, int, ExportType, TrackMate, Logger)