TrackerKeys.java

/*-
 * #%L
 * TrackMate: your buddy for everyday tracking.
 * %%
 * Copyright (C) 2010 - 2024 TrackMate developers.
 * %%
 * This program is free software: you can redistribute it and/or modify
 * 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>.
 * #L%
 */
package fiji.plugin.trackmate.tracking;

import java.util.HashMap;
import java.util.Map;

public class TrackerKeys
{

	/*
	 * MARSHALLING CONSTANTS
	 */

	public static final String TRACKER_SETTINGS_ALLOW_EVENT_ATTNAME = "allowed";

	// Alternative costs & blocking
	public static final String TRACKER_SETTINGS_ALTERNATE_COST_FACTOR_ATTNAME = "alternatecostfactor";

	public static final String TRACKER_SETTINGS_CUTOFF_PERCENTILE_ATTNAME = "cutoffpercentile";

	public static final String TRACKER_SETTINGS_BLOCKING_VALUE_ATTNAME = "blockingvalue";

	// Cutoff elements
	public static final String TRACKER_SETTINGS_TIME_CUTOFF_ELEMENT = "TimeCutoff";

	public static final String TRACKER_SETTINGS_TIME_CUTOFF_ATTNAME = "value";

	public static final String TRACKER_SETTINGS_DISTANCE_CUTOFF_ELEMENT = "DistanceCutoff";

	public static final String TRACKER_SETTINGS_DISTANCE_CUTOFF_ATTNAME = "value";

	public static final String TRACKER_SETTINGS_FEATURE_ELEMENT = "FeatureCondition";

	public static final String TRACKER_SETTINGS_LINKING_ELEMENT = "LinkingCondition";

	public static final String TRACKER_SETTINGS_GAP_CLOSING_ELEMENT = "GapClosingCondition";

	public static final String TRACKER_SETTINGS_MERGING_ELEMENT = "MergingCondition";

	public static final String TRACKER_SETTINGS_SPLITTING_ELEMENT = "SplittingCondition";

	/*
	 *
	 */

	/**
	 * The attribute name for the {@link SpotTracker} key when marshalling to or
	 * unmarhsalling from XML.
	 */
	public static final String XML_ATTRIBUTE_TRACKER_NAME = "TRACKER_NAME";

	/**
	 * Key for the parameter specifying the maximal linking distance. The
	 * expected value must be a Double and should be expressed in physical
	 * units.
	 */
	public static final String KEY_LINKING_MAX_DISTANCE = "LINKING_MAX_DISTANCE";

	/** A default value for the {@value #KEY_LINKING_MAX_DISTANCE} parameter. */
	public static final double DEFAULT_LINKING_MAX_DISTANCE = 15.0;

	/**
	 * Key for the parameter specifying the feature penalties when linking
	 * particles. Expected values should be a
	 * <code>Map&lt;String, Double&gt;</code> where the map keys are spot
	 * feature names.
	 * 
	 * @see fiji.plugin.trackmate.Spot#getFeature(String)
	 */
	public static final String KEY_LINKING_FEATURE_PENALTIES = "LINKING_FEATURE_PENALTIES";

	/**
	 * A default value for the {@value #KEY_LINKING_FEATURE_PENALTIES}
	 * parameter.
	 */
	public static final Map< String, Double > DEFAULT_LINKING_FEATURE_PENALTIES = new HashMap<>();

	/** Search radius for the Kalman tracker. */
	public static final String KEY_KALMAN_SEARCH_RADIUS = "KALMAN_SEARCH_RADIUS";

	/** A default value for the {@value #KEY_KALMAN_SEARCH_RADIUS} parameter. */
	public static final double DEFAULT_KALMAN_SEARCH_RADIUS = 20.0;

	/**
	 * Key for the parameter specifying whether we allow the detection of
	 * gap-closing events. Expected values are {@link Boolean}s.
	 */
	public static final String KEY_ALLOW_GAP_CLOSING = "ALLOW_GAP_CLOSING";

	/** A default value for the {@value #KEY_ALLOW_GAP_CLOSING} parameter. */
	public static final boolean DEFAULT_ALLOW_GAP_CLOSING = true;

	/**
	 * Key for the parameter that specify the maximal number of frames to bridge
	 * when detecting gap closing. Expected values are {@link Integer}s greater
	 * than 0. A value of 1 means that a detection might be missed in 1 frame,
	 * and the track will not be broken. And so on.
	 */
	public static final String KEY_GAP_CLOSING_MAX_FRAME_GAP = "MAX_FRAME_GAP";

	/**
	 * A default value for the {@value #KEY_GAP_CLOSING_MAX_FRAME_GAP}
	 * parameter.
	 */
	public static final int DEFAULT_GAP_CLOSING_MAX_FRAME_GAP = 2;

	/**
	 * Key for the parameter specifying the max gap-closing distance. Expected
	 * values are {@link Double}s and should be expressed in physical units. If
	 * two spots, candidate for a gap-closing event, are found separated by a
	 * distance larger than this parameter value, gap-closing will not occur.
	 */
	public static final String KEY_GAP_CLOSING_MAX_DISTANCE = "GAP_CLOSING_MAX_DISTANCE";

	/**
	 * A default value for the {@value #KEY_GAP_CLOSING_MAX_DISTANCE} parameter.
	 */
	public static final double DEFAULT_GAP_CLOSING_MAX_DISTANCE = 15.0;

	/**
	 * Key for the parameter specifying the feature penalties when detecting
	 * gap-closing events. Expected values should be a
	 * <code>Map&lt;String, Double&gt;</code> where the map keys are spot
	 * feature names.
	 * 
	 * @see fiji.plugin.trackmate.Spot#getFeature(String)
	 */
	public static final String KEY_GAP_CLOSING_FEATURE_PENALTIES = "GAP_CLOSING_FEATURE_PENALTIES";

	/**
	 * A default value for the {@value #KEY_GAP_CLOSING_FEATURE_PENALTIES}
	 * parameter.
	 */
	public static final Map< String, Double > DEFAULT_GAP_CLOSING_FEATURE_PENALTIES = new HashMap<>();

	/**
	 * Key for the parameter specifying whether we allow the detection of
	 * merging events. Expected values are {@link Boolean}s.
	 */
	public static final String KEY_ALLOW_TRACK_MERGING = "ALLOW_TRACK_MERGING";

	/** A default value for the {@value #KEY_ALLOW_TRACK_MERGING} parameter. */
	public static final boolean DEFAULT_ALLOW_TRACK_MERGING = false;

	/**
	 * Key for the parameter specifying the max merging distance. Expected
	 * values are {@link Double}s and should be expressed in physical units. If
	 * two spots, candidate for a merging event, are found separated by a
	 * distance larger than this parameter value, track merging will not occur.
	 */
	public static final String KEY_MERGING_MAX_DISTANCE = "MERGING_MAX_DISTANCE";

	/** A default value for the {@value #KEY_MERGING_MAX_DISTANCE} parameter. */
	public static final double DEFAULT_MERGING_MAX_DISTANCE = 15.0;

	/**
	 * Key for the parameter specifying the feature penalties when dealing with
	 * merging events. Expected values should be a
	 * <code>Map&lt;String, Double&gt;</code> where the map keys are spot
	 * feature names.
	 * 
	 * @see fiji.plugin.trackmate.Spot#getFeature(String)
	 */
	public static final String KEY_MERGING_FEATURE_PENALTIES = "MERGING_FEATURE_PENALTIES";

	/**
	 * A default value for the {@value #KEY_MERGING_FEATURE_PENALTIES}
	 * parameter.
	 */
	public static final Map< String, Double > DEFAULT_MERGING_FEATURE_PENALTIES = new HashMap<>();

	/**
	 * Key for the parameter specifying whether we allow the detection of
	 * splitting events. Expected values are {@link Boolean}s.
	 */
	public static final String KEY_ALLOW_TRACK_SPLITTING = "ALLOW_TRACK_SPLITTING";

	/**
	 * A default value for the {@value #KEY_ALLOW_TRACK_SPLITTING} parameter.
	 */
	public static final boolean DEFAULT_ALLOW_TRACK_SPLITTING = false;

	/**
	 * Key for the parameter specifying the max splitting distance. Expected
	 * values are {@link Double}s and should be expressed in physical units. If
	 * two spots, candidate for a merging event, are found separated by a
	 * distance larger than this parameter value, track splitting will not
	 * occur.
	 */
	public static final String KEY_SPLITTING_MAX_DISTANCE = "SPLITTING_MAX_DISTANCE";

	/**
	 * A default value for the {@link #KEY_SPLITTING_MAX_DISTANCE} parameter.
	 */
	public static final double DEFAULT_SPLITTING_MAX_DISTANCE = 15.0;

	/**
	 * Key for the parameter specifying the feature penalties when dealing with
	 * splitting events. Expected values should be a
	 * <code>Map&lt;String, Double&gt;</code> where the map keys are spot
	 * feature names.
	 * 
	 * @see fiji.plugin.trackmate.Spot#getFeature(String)
	 */
	public static final String KEY_SPLITTING_FEATURE_PENALTIES = "SPLITTING_FEATURE_PENALTIES";

	/**
	 * A default value for the {@value #KEY_SPLITTING_FEATURE_PENALTIES}
	 * parameter.
	 */
	public static final Map< String, Double > DEFAULT_SPLITTING_FEATURE_PENALTIES = new HashMap<>();

	/**
	 * Key for the parameter specifying the factor used to compute alternative
	 * linking costs. Expected values are {@link Double}s.
	 */
	public static final String KEY_ALTERNATIVE_LINKING_COST_FACTOR = "ALTERNATIVE_LINKING_COST_FACTOR";

	/**
	 * A default value for the {@value #KEY_ALTERNATIVE_LINKING_COST_FACTOR}
	 * parameter.
	 */
	public static final double DEFAULT_ALTERNATIVE_LINKING_COST_FACTOR = 1.05d;

	/**
	 * Key for the cutoff percentile parameter. Expected values are
	 * {@link Double}s.
	 */
	public static final String KEY_CUTOFF_PERCENTILE = "CUTOFF_PERCENTILE";

	/** A default value for the {@value #KEY_CUTOFF_PERCENTILE} parameter. */
	public static final double DEFAULT_CUTOFF_PERCENTILE = 0.9d;

	/**
	 * Key for the parameter that stores the blocking value: cost for
	 * non-physical, forbidden links. Expected values are {@link Double}s, and
	 * are typically very large.
	 */
	public static final String KEY_BLOCKING_VALUE = "BLOCKING_VALUE";

	/** A default value for the {@value #KEY_BLOCKING_VALUE} parameter. */
	public static final double DEFAULT_BLOCKING_VALUE = Double.POSITIVE_INFINITY;

	/**
	 * Key for the parameter specifying the minimum linking IoU. The
	 * expected value must be a Double.
	 */
	public static final String KEY_LINKING_MIN_IOU = "LINKING_MIN_IOU";

	/** A default value for the {@value #KEY_LINKING_MIN_IOU} parameter. */
	public static final double DEFAULT_LINKING_MIN_IOU = 0.0;

	/**
	 * Key for the parameter specifying the min gap-closing IoU. Expected
	 * values are {@link Double}s. If two spots, candidate for a gap-closing 
	 * event, are found separated by a IoU smaller than this parameter value, 
	 * gap-closing will not occur.
	 */
	public static final String KEY_GAP_CLOSING_MIN_IOU = "GAP_CLOSING_MIN_IOU";

	/**
	 * A default value for the {@value #KEY_GAP_CLOSING_MIN_IOU} parameter.
	 */
	public static final double DEFAULT_GAP_CLOSING_MIN_IOU = 0.0;

	/**
	 * Key for the parameter specifying the min merging IoU. Expected
	 * values are {@link Double}s. If two spots, candidate for a merging 
	 * event, are found separated by an IoU smaller than this parameter 
	 * value, track merging will not occur.
	 */
	public static final String KEY_MERGING_MIN_IOU = "MERGING_MIN_IOU";

	/** A default value for the {@value #KEY_MERGING_MIN_IOU} parameter. */
	public static final double DEFAULT_MERGING_MIN_IOU = 0.0;

	/**
	 * Key for the parameter specifying the min splitting IoU. Expected
	 * values are {@link Double}s. If two spots, candidate for a merging event, 
	 * are found separated by an IoU smaller than this parameter value, 
	 * track splitting will not occur.
	 */
	public static final String KEY_SPLITTING_MIN_IOU = "SPLITTING_MIN_IOU";

	/**
	 * A default value for the {@link #KEY_SPLITTING_MIN_IOU} parameter.
	 */
	public static final double DEFAULT_SPLITTING_MIN_IOU = 0.0;

}