Skip to content

Commit

Permalink
Separated object orientation as a measurement during tracking
Browse files Browse the repository at this point in the history
  • Loading branch information
@sjcross
sjcross committed May 8, 2024
1 parent 7cc1241 commit 6685859
Show file tree
Hide file tree
Showing 3 changed files with 84 additions and 25 deletions.
103 changes: 79 additions & 24 deletions ...main/java/io/github/mianalysis/mia/module/objects/measure/spatial/MeasureTrackMotion.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
import org.scijava.Priority;
import org.scijava.plugin.Plugin;

import io.github.mianalysis.mia.MIA;
import io.github.mianalysis.mia.module.Categories;
import io.github.mianalysis.mia.module.Category;
import io.github.mianalysis.mia.module.Module;
Expand Down Expand Up @@ -95,6 +96,8 @@ public class MeasureTrackMotion extends Module implements MeasurementPositionPro
*/
public static final String SUBTRACT_AVERAGE_MOTION = "Subtract average motion";

public static final String CALCULATE_ORIENTATION = "Calculate orientation";

/**
* When selected, the "leading point" of each object in the track will be
* determined and stored as X,Y,Z coordinate measurements associated with the
Expand Down Expand Up @@ -161,7 +164,7 @@ public interface Measurements {
String ANGULAR_PERSISTENCE = "ANGULAR_PERSISTENCE";
String DETECTION_FRACTION = "DETECTION_FRACTION";
String RELATIVE_FRAME = "RELATIVE_FRAME";
String ORIENTATION = "ORIENTATION";
String ORIENTATION = "ORIENTATION_(DEGS)";
String LEADING_X_PX = "LEADING_POINT_X_(PX)";
String LEADING_Y_PX = "LEADING_POINT_Y_(PX)";
String LEADING_Z_PX = "LEADING_POINT_Z_(PX)";
Expand Down Expand Up @@ -298,9 +301,12 @@ public static void calculateVelocity(Obj trackObject, Track track, boolean avera
double distPerPxXY = trackObject.getDppXY();
double distPerPxZ = trackObject.getDppZ();

TreeMap<Integer, Double> xVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getX());
TreeMap<Integer, Double> yVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getY());
TreeMap<Integer, Double> zVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getZ());
TreeMap<Integer, Double> xVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getX());
TreeMap<Integer, Double> yVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getY());
TreeMap<Integer, Double> zVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getZ());
TreeMap<Integer, Double> speed = new InstantaneousSpeedCalculator().calculate(track);

CumStat cumStatX = new CumStat();
Expand Down Expand Up @@ -386,16 +392,17 @@ public static void calculateSpatialMeasurements(Obj trackObject, Track track, bo
name = getFullName(Measurements.TOTAL_PATH_LENGTH_CAL, averageSubtracted);
trackObject.addMeasurement(new Measurement(name, totalPathLength * distPerPxXY));
name = getFullName(Measurements.DIRECTIONALITY_RATIO, averageSubtracted);
trackObject.addMeasurement(new Measurement(name, euclideanDistance/totalPathLength));
trackObject.addMeasurement(new Measurement(name, euclideanDistance / totalPathLength));

}
}

public double getTotalPathLength(Track track) {
TreeMap<Integer,Double> steps = new InstantaneousStepSizeCalculator().calculate(track);
TreeMap<Integer, Double> steps = new InstantaneousStepSizeCalculator().calculate(track);

double totalPathLength = 0;
for (double value:steps.values()) totalPathLength += value;
for (double value : steps.values())
totalPathLength += value;

return totalPathLength;

Expand All @@ -406,9 +413,12 @@ public static void calculateInstantaneousVelocity(Obj trackObject, Track track,
double distPerPxXY = trackObject.getDppXY();
double distPerPxZ = trackObject.getDppZ();

TreeMap<Integer, Double> xVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getX());
TreeMap<Integer, Double> yVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getY());
TreeMap<Integer, Double> zVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),track.getZ());
TreeMap<Integer, Double> xVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getX());
TreeMap<Integer, Double> yVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getY());
TreeMap<Integer, Double> zVelocity = new InstantaneousVelocityCalculator().calculate(track.getF(),
track.getZ());
TreeMap<Integer, Double> speed = new InstantaneousSpeedCalculator().calculate(track);

// Getting the first timepoint
Expand Down Expand Up @@ -494,6 +504,20 @@ public static void calculateInstantaneousSpatialMeasurements(Obj trackObject, Tr
}
}

public static void calculateOrientation(Objs objects, String orientationMode, boolean averageSubtracted) {
String name = getFullName(Measurements.ORIENTATION, averageSubtracted);

for (Obj obj : objects.values()) {
double angle = getInstantaneousOrientationRads(obj, objects, orientationMode);

if (Double.isNaN(angle))
obj.addMeasurement(new Measurement(name, Double.NaN));
else
obj.addMeasurement(new Measurement(name, Math.toDegrees(angle)));

}
}

public static double getInstantaneousOrientationRads(Obj object, Objs objects, String orientationMode) {
double prevAngle = Double.NaN;
double nextAngle = Double.NaN;
Expand Down Expand Up @@ -525,16 +549,25 @@ else if (!Double.isNaN(prevAngle) && !Double.isNaN(nextAngle))

}

public static void identifyLeading(Objs objects, String orientationMode) {
public static void identifyLeading(Objs objects, String orientationMode, boolean averageSubtracted) {
for (Obj obj : objects.values()) {
double angle = getInstantaneousOrientationRads(obj, objects, orientationMode);
// Get previously-calculated orientation
String name = getFullName(Measurements.ORIENTATION, averageSubtracted);
Measurement orientation = obj.getMeasurement(name);
double angle = Double.NaN;
if (orientation != null)
angle = orientation.getValue();

if (Double.isNaN(angle)) {
// Adding furthest point coordinates to measurements
obj.addMeasurement(new Measurement(Measurements.ORIENTATION, Double.NaN));
obj.addMeasurement(new Measurement(Measurements.LEADING_X_PX, Double.NaN));
obj.addMeasurement(new Measurement(Measurements.LEADING_Y_PX, Double.NaN));
obj.addMeasurement(new Measurement(Measurements.LEADING_Z_PX, Double.NaN));
name = getFullName(Measurements.LEADING_X_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, Double.NaN));

name = getFullName(Measurements.LEADING_Y_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, Double.NaN));

name = getFullName(Measurements.LEADING_Z_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, Double.NaN));

} else {
double xCent = obj.getXMean(true);
Expand Down Expand Up @@ -569,10 +602,14 @@ public static void identifyLeading(Objs objects, String orientationMode) {
}

// Adding furthest point coordinates to measurements
obj.addMeasurement(new Measurement(Measurements.ORIENTATION, Math.toDegrees(angle)));
obj.addMeasurement(new Measurement(Measurements.LEADING_X_PX, furthestPoint.getX()));
obj.addMeasurement(new Measurement(Measurements.LEADING_Y_PX, furthestPoint.getY()));
obj.addMeasurement(new Measurement(Measurements.LEADING_Z_PX, 0));
name = getFullName(Measurements.LEADING_X_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, furthestPoint.getX()));

name = getFullName(Measurements.LEADING_Y_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, furthestPoint.getY()));

name = getFullName(Measurements.LEADING_Z_PX, averageSubtracted);
obj.addMeasurement(new Measurement(name, 0));

}
}
Expand Down Expand Up @@ -603,9 +640,14 @@ public Status process(Workspace workspace) {
// Getting input spot objects
String inputSpotObjectsName = parameters.getValue(INPUT_SPOT_OBJECTS, workspace);
boolean subtractAverage = parameters.getValue(SUBTRACT_AVERAGE_MOTION, workspace);
boolean calculateOrientation = parameters.getValue(CALCULATE_ORIENTATION, workspace);
boolean identifyLeading = parameters.getValue(IDENTIFY_LEADING_POINT, workspace);
String orientationMode = parameters.getValue(ORIENTATION_MODE, workspace);

// Always need to calculate orientation if identifying the leading point
if (identifyLeading)
calculateOrientation = true;

// If necessary, creating the average track
Track averageTrack = null;
if (subtractAverage)
Expand All @@ -629,10 +671,16 @@ public Status process(Workspace workspace) {

}

// Determining the orientation
if (calculateOrientation) {
Objs spotObjects = workspace.getObjects(inputSpotObjectsName);
calculateOrientation(spotObjects, orientationMode, subtractAverage);
}

// Determining the leading point in the object (to next object)
if (identifyLeading) {
Objs spotObjects = workspace.getObjects(inputSpotObjectsName);
identifyLeading(spotObjects, orientationMode);
identifyLeading(spotObjects, orientationMode, subtractAverage);
}

if (showOutput)
Expand All @@ -653,6 +701,7 @@ protected void initialiseParameters() {
parameters.add(new SeparatorP(MEASUREMENT_SEPARATOR, this));
parameters.addAll(initialisePositionParameters(this));
parameters.add(new BooleanP(SUBTRACT_AVERAGE_MOTION, this, false));
parameters.add(new BooleanP(CALCULATE_ORIENTATION, this, false));
parameters.add(new BooleanP(IDENTIFY_LEADING_POINT, this, false));
parameters.add(new ChoiceP(ORIENTATION_MODE, this, OrientationModes.RELATIVE_TO_BOTH, OrientationModes.ALL));

Expand All @@ -676,9 +725,11 @@ public Parameters updateAndGetParameters() {
returnedParameters.add(parameters.getParameter(MEASUREMENT_SEPARATOR));
returnedParameters.addAll(updateAndGetPositionParameters(spotObjectsName, parameters));
returnedParameters.add(parameters.getParameter(SUBTRACT_AVERAGE_MOTION));
returnedParameters.add(parameters.getParameter(IDENTIFY_LEADING_POINT));
if ((boolean) parameters.getValue(IDENTIFY_LEADING_POINT, workspace))
returnedParameters.add(parameters.getParameter(CALCULATE_ORIENTATION));
if ((boolean) parameters.getValue(IDENTIFY_LEADING_POINT, workspace)
|| (boolean) parameters.getValue(CALCULATE_ORIENTATION, workspace))
returnedParameters.add(parameters.getParameter(ORIENTATION_MODE));
returnedParameters.add(parameters.getParameter(IDENTIFY_LEADING_POINT));

return returnedParameters;

Expand Down Expand Up @@ -857,12 +908,16 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
reference.setObjectsName(inputSpotObjects);
returnedRefs.add(reference);

if ((boolean) parameters.getValue(IDENTIFY_LEADING_POINT, workspace)) {
if ((boolean) parameters.getValue(IDENTIFY_LEADING_POINT, workspace)
|| (boolean) parameters.getValue(CALCULATE_ORIENTATION, workspace)) {
name = getFullName(Measurements.ORIENTATION, subtractAverage);
reference = objectMeasurementRefs.getOrPut(name);
reference.setObjectsName(inputSpotObjects);
returnedRefs.add(reference);

}

if ((boolean) parameters.getValue(IDENTIFY_LEADING_POINT, workspace)) {
name = getFullName(Measurements.LEADING_X_PX, subtractAverage);
reference = objectMeasurementRefs.getOrPut(name);
reference.setObjectsName(inputSpotObjects);
Expand Down
4 changes: 4 additions & 0 deletions mia-modules/src/main/java/io/github/mianalysis/mia/module/objects/relate/TrackObjects.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,10 @@ public class TrackObjects extends Module {
*
*/
public static final String MEASUREMENT_SEPARATOR = "Measurement cost";

/**
*
*/
public static final String USE_MEASUREMENT = "Use measurement (minimise change)";

/**
Expand Down
2 changes: 1 addition & 1 deletion mia-modules/src/main/java/io/github/mianalysis/mia/module/visualise/overlays/AddArrows.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ public static void addOverlay(Obj object, ImagePlus ipl, Color colour, double li
double x2 = arrowLength * Math.cos(oriRads);
double y2 = arrowLength * Math.sin(oriRads);

Arrow arrow = new Arrow(xMean, yMean, xMean + x2, yMean + y2);
Arrow arrow = new Arrow(xMean, yMean, xMean - x2, yMean - y2);
arrow.setHeadSize(headSize);
arrow.setStrokeColor(colour);
arrow.setStrokeWidth(lineWidth);
Expand Down

0 comments on commit 6685859

Please sign in to comment.