Do not privilege the TARGET_CHANNEL setting

Before this commit, the target channel was set in the main window
of the GUI, and used for all detectors and trackers. But some
detectors do not need it, or specify it another way. It makes no
sense to separate it from the other parameters. It adds clutter
and confusion.

Now the modules that require the TARGET_CHANNEL must specify it
as a parameter, that can be sweeped upon as well.

Author: tinevez

src/main/java/fiji/plugin/trackmate/helper/HelperRunner.java

@@ -8,12 +8,12 @@
  * it under the terms of the GNU General Public License as
  * published by the Free Software Foundation, either version 3 of the
  * License, or (at your option) any later version.
- * 
+ *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- * 
+ *
  * You should have received a copy of the GNU General Public
  * License along with this program.  If not, see
  * <http://www.gnu.org/licenses/gpl-3.0.html>.
@@ -74,8 +74,6 @@ public class HelperRunner implements Runnable, Cancelable
 
 	private final ParameterSweepModel model;
 
-	private int targetChannel;
-
 	private final String savePath;
 
 	private Logger batchLogger;
@@ -98,7 +96,6 @@ private HelperRunner(
 			final ImagePlus imp,
 			final ParameterSweepModel model,
 			final String modelPath,
-			final int targetChannel,
 			final String savePath,
 			final Logger batchLogger,
 			final Logger trackmateLogger,
@@ -109,7 +106,6 @@ private HelperRunner(
 		this.imp = imp;
 		this.model = model;
 		this.modelPath = modelPath;
-		this.targetChannel = targetChannel;
 		this.savePath = savePath;
 		this.batchLogger = batchLogger;
 		this.trackmateLogger = trackmateLogger;
@@ -133,7 +129,7 @@ private HelperRunner(
 	/**
 	 * Exposes the crawler of this runner that monitors result files appearing
 	 * in the save folder.
-	 * 
+	 *
 	 * @return the {@link ResultsCrawler}.
 	 */
 	public ResultsCrawler getCrawler()
@@ -143,7 +139,7 @@ public ResultsCrawler getCrawler()
 
 	/**
 	 * Exposes the settings model that will be used by this runner.
-	 * 
+	 *
 	 * @return the {@link ParameterSweepModel}.
 	 */
 	public ParameterSweepModel getModel()
@@ -155,7 +151,7 @@ public ParameterSweepModel getModel()
 	 * Returns the path to the file that stores the settings model that will be
 	 * used by this runner. This path is used to save the model to a file when
 	 * modified.
-	 * 
+	 *
 	 * @return the path to the settings model.
 	 */
 	public String getModelPath()
@@ -165,7 +161,7 @@ public String getModelPath()
 
 	/**
 	 * Exposes the input image this runner is configured to run on.
-	 * 
+	 *
 	 * @return the image.
 	 */
 	public ImagePlus getImage()
@@ -176,7 +172,7 @@ public ImagePlus getImage()
 	/**
 	 * Returns the path to the ground-truth file or folder this runner is
 	 * configured to use.
-	 * 
+	 *
 	 * @return the path to the ground-truth.
 	 */
 	public String getGroundTruthPath()
@@ -186,7 +182,7 @@ public String getGroundTruthPath()
 
 	/**
 	 * Returns the type of tracking metrics this runner is configured to use.
-	 * 
+	 *
 	 * @return the tracking metrics type.
 	 */
 	public TrackingMetricsType getType()
@@ -196,7 +192,7 @@ public TrackingMetricsType getType()
 
 	/**
 	 * Sets the logger to use to log progress of the run.
-	 * 
+	 *
 	 * @param batchLogger
 	 *            a {@link Logger} instance.
 	 */
@@ -208,7 +204,7 @@ public void setBatchLogger( final Logger batchLogger )
 	/**
 	 * Sets the logger to use to log individual tracking tests. This is only
 	 * useful for debugging.
-	 * 
+	 *
 	 * @param trackmateLogger
 	 *            a {@link Logger} instance.
 	 */
@@ -217,24 +213,11 @@ public void setTrackmateLogger( final Logger trackmateLogger )
 		this.trackmateLogger = trackmateLogger;
 	}
 
-	/**
-	 * Sets the index of the channel in the input image to use for tracking.
-	 * Channels are here 1-numbered, meaning that "1" is the first available
-	 * channel.
-	 * 
-	 * @param targetChannel
-	 *            the channel index
-	 */
-	public void setTargetChannel( final int targetChannel )
-	{
-		this.targetChannel = targetChannel;
-	}
-
 	/**
 	 * Sets whether TrackMate results XML files will be saved for every test.
 	 * <p>
 	 * This can consume a lot off disk space if there are many tests to run.
-	 * 
+	 *
 	 * @param saveTrackMateFiles
 	 *            whether TrackMate XML files will be saved for every test.
 	 */
@@ -265,7 +248,7 @@ public void run()
 	/**
 	 * Iterates over possible several detector configurations, and adds them to
 	 * the specified base settings, then loop over spot filter configurations.
-	 * 
+	 *
 	 * @param base
 	 *            the {@link Settings} base. Must be fully configured except for
 	 *            detector settings, spot filters, tracker settings and track
@@ -284,7 +267,7 @@ private int loopDetectorSettings( final Settings base, final IterationData itera
 	{
 		MAIN_LOOP: for ( final DetectorSweepModel detectorModel : model.getActiveDetectors() )
 		{
-			final Iterator< Settings > detectorIterator = detectorModel.iterator( base, targetChannel );
+			final Iterator< Settings > detectorIterator = detectorModel.iterator( base );
 			while ( detectorIterator.hasNext() )
 			{
 				if ( isCanceled() )
@@ -307,7 +290,7 @@ private int loopDetectorSettings( final Settings base, final IterationData itera
 	/**
 	 * Iterates over possible several spot filter configurations, and adds them
 	 * to the specified base settings, then loop over tracker configurations.
-	 * 
+	 *
 	 * @param base
 	 *            the {@link Settings} base. Must be fully configured except for
 	 *            spot filters, tracker settings and track filters.
@@ -353,7 +336,7 @@ private int loopSpotFilterSettings( final Settings base, final IterationData ite
 	/**
 	 * Iterates over possible several tracker configurations, and adds them to
 	 * the specified base settings, then loop over track filters configurations.
-	 * 
+	 *
 	 * @param base
 	 *            the {@link Settings} base. Must be fully configured except for
 	 *            tracker settings and track filters.
@@ -372,7 +355,7 @@ private int loopTrackerSettings( final Settings base, final IterationData iterat
 	{
 		MAIN_LOOP: for ( final TrackerSweepModel trackerModel : model.getActiveTracker() )
 		{
-			final Iterator< Settings > trackerIterator = trackerModel.iterator( base, targetChannel );
+			final Iterator< Settings > trackerIterator = trackerModel.iterator( base );
 			while ( trackerIterator.hasNext() )
 			{
 				if ( isCanceled() )
@@ -394,7 +377,7 @@ private int loopTrackerSettings( final Settings base, final IterationData iterat
 	 * Iterates over possible several track filter configurations, and adds them
 	 * to the specified base settings, then execute the tracking and metrics
 	 * measurements.
-	 * 
+	 *
 	 * @param base
 	 *            the {@link Settings} base. Must be fully configured except for
 	 *            track filters.
@@ -444,7 +427,7 @@ private int loopTrackFilterSettings( final Settings base, final IterationData it
 	/**
 	 * Execute the full tracking process using the fully configured
 	 * {@link Settings}.
-	 * 
+	 *
 	 * @param settings
 	 *            the settings to use to run TrackMate.
 	 * @param iterationData
@@ -667,8 +650,6 @@ public static final class Builder
 
 		private String runSettingsPath;
 
-		private int targetChannel = 1;
-
 		private String savePath;
 
 		private Logger batchLogger = Logger.DEFAULT_LOGGER;
@@ -687,7 +668,7 @@ public static final class Builder
 
 		/**
 		 * Sets the tracking metrics type to use.
-		 * 
+		 *
 		 * @param type
 		 *            the tracking metrics type.
 		 * @return this builder.
@@ -704,7 +685,7 @@ public Builder trackingMetricsType( final TrackingMetricsType type )
 		 * Sets the tracking metrics type to use with a string. Currently
 		 * supported types are "CTC" (Cell-Tracking-Challenge) and "SPT"
 		 * (Single-Particle Tracking Challenge).
-		 * 
+		 *
 		 * @param type
 		 *            the tracking metrics type as a string.
 		 * @return this builder.
@@ -724,7 +705,7 @@ public Builder trackingMetricsType( final String type )
 		 * Sets the path to the ground-truth file or folder.
 		 * <p>
 		 * The files need to comply to the tracking metrics.
-		 * 
+		 *
 		 * @param groundTruth
 		 *            path to the ground-truth file or folder.
 		 * @return this builder.
@@ -745,7 +726,7 @@ public Builder groundTruth( final String groundTruth )
 		 * The config file is used to specify what parameters to test. It is a
 		 * JSon file named <code>helperrunnersettings.json</code>. Use the GUI
 		 * to set it.
-		 * 
+		 *
 		 * @param runSettings
 		 *            path to the helper runner configuration file.
 		 * @return this builder.
@@ -760,7 +741,7 @@ public Builder runSettings( final String runSettings )
 
 		/**
 		 * Sets the path to the folder in which runner results will be saved.
-		 * 
+		 *
 		 * @param savePath
 		 *            path to the save folder.
 		 * @return this builder.
@@ -775,7 +756,7 @@ public Builder savePath( final String savePath )
 
 		/**
 		 * Sets the path to the image file to use as input.
-		 * 
+		 *
 		 * @param imagePath
 		 *            path to the image file to use as input.
 		 * @return this builder.
@@ -790,7 +771,7 @@ public Builder imagePath( final String imagePath )
 
 		/**
 		 * Sets the path to the image to use as input.
-		 * 
+		 *
 		 * @param image
 		 *            path to the image to use as input.
 		 * @return this builder.
@@ -803,26 +784,9 @@ public Builder image( final ImagePlus image )
 			return this;
 		}
 
-		/**
-		 * Sets the index of the channel in the input image to use for tracking.
-		 * Channels are here 1-numbered, meaning that "1" is the first available
-		 * channel.
-		 * 
-		 * @param targetChannel
-		 *            the channel index
-		 * @return this builder.
-		 */
-		public Builder targetChannel( final int targetChannel )
-		{
-			if ( this.targetChannel != targetChannel )
-				this.targetChannel = targetChannel;
-
-			return this;
-		}
-
 		/**
 		 * Sets the logger to use to log progress of the run.
-		 * 
+		 *
 		 * @param batchLogger
 		 *            a {@link Logger} instance.
 		 * @return this builder.
@@ -838,7 +802,7 @@ public Builder batchLogger( final Logger batchLogger )
 		/**
 		 * Sets the logger to use to log individual tracking tests. This is only
 		 * useful for debugging.
-		 * 
+		 *
 		 * @param trackmateLogger
 		 *            a {@link Logger} instance.
 		 * @return this builder.
@@ -856,7 +820,7 @@ public Builder trackmateLogger( final Logger trackmateLogger )
 		 * test.
 		 * <p>
 		 * This can consume a lot off disk space if there are many tests to run.
-		 * 
+		 *
 		 * @param saveTrackMateFiles
 		 *            whether TrackMate XML files will be saved for every test.
 		 * @return this builder
@@ -875,7 +839,7 @@ public Builder saveTrackMateFiles( final boolean saveTrackMateFiles )
 		 * <p>
 		 * Only affect the SPT metrics type, if it is specified via the string
 		 * method {@link #trackingMetricsType(String)} of this builder.
-		 * 
+		 *
 		 * @param maxDist
 		 *            the max pairing distance.
 		 * @return this builder.
@@ -1025,7 +989,6 @@ else if ( typeStr.equals( "SPT" ) )
 					imp,
 					model,
 					runSettingsPath,
-					targetChannel,
 					savePath,
 					batchLogger,
 					trackmateLogger,

src/main/java/fiji/plugin/trackmate/helper/model/AbstractSweepModelBase.java

@@ -48,7 +48,7 @@ protected AbstractSweepModelBase( final String name, final Map< String, Abstract
 		this.models = models;
 	}
 
-	public abstract Iterator< Settings > iterator( final Settings base, final int targetChannel );
+	public abstract Iterator< Settings > iterator( final Settings base );
 
 	public String getName()
 	{

src/main/java/fiji/plugin/trackmate/helper/model/ParameterSweepModel.java

@@ -206,12 +206,11 @@ public int count()
 	 */
 	public int countTrackerSettings()
 	{
-		final int targetChannel = 1;
 		final Settings base = new Settings( null );
 		int count = 0;
 		for ( final TrackerSweepModel trackerModel : getActiveTracker() )
 		{
-			final Iterator< Settings > tit = trackerModel.iterator( base, targetChannel );
+			final Iterator< Settings > tit = trackerModel.iterator( base );
 			while ( tit.hasNext() )
 			{
 				tit.next();
@@ -229,12 +228,11 @@ public int countTrackerSettings()
 	 */
 	public int countDetectorSettings()
 	{
-		final int targetChannel = 1;
 		final Settings base = new Settings( null );
 		int count = 0;
 		for ( final DetectorSweepModel detectorModel : getActiveDetectors() )
 		{
-			final Iterator< Settings > dit = detectorModel.iterator( base, targetChannel );
+			final Iterator< Settings > dit = detectorModel.iterator( base );
 			while ( dit.hasNext() )
 			{
 				dit.next();