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make type generic
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@kapoorlab
kapoorlab committed Apr 13, 2024
1 parent 7dca1cd commit d218c0f
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Showing 3 changed files with 36 additions and 31 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@

<groupId>sc.fiji</groupId>
<artifactId>TrackMate-Oneat</artifactId>
<version>3.2.4-SNAPSHOT</version>
<version>3.2.5-SNAPSHOT</version>


<name>TrackMate-Oneat</name>
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9 changes: 6 additions & 3 deletions src/main/java/fiji/plugin/trackmate/action/oneat/OneatCorrector.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,12 @@
import fiji.plugin.trackmate.visualization.hyperstack.TrackOverlay;
import ij.ImagePlus;
import net.imagej.ImgPlus;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.Pair;

public class OneatCorrector implements TrackCorrector {
public class OneatCorrector <T extends NativeType<T>> implements TrackCorrector {

private final File oneatdivision;

Expand All @@ -70,7 +71,7 @@ public class OneatCorrector implements TrackCorrector {

private HashMap<Integer, Pair<Spot, Spot>> Apoptosisspots;

private final ImgPlus<FloatType> img;
private final ImgPlus<T> img;

private final Map<String, Object> settings;

Expand All @@ -90,7 +91,7 @@ public class OneatCorrector implements TrackCorrector {

private static final String BASE_ERROR_MESSAGE = "[OneatTrackCorrector] ";

public OneatCorrector(final File oneatdivision, final File oneatapoptosis, final ImgPlus<FloatType> intimg,
public OneatCorrector(final File oneatdivision, final File oneatapoptosis, final ImgPlus<T> intimg,
final Model model, final TrackMate trackmate, final Settings modelsettings,
final DisplaySettings displaySettings, double[] calibration, Map<String, Object> settings,
final Logger logger, final Boolean addDisplay) {
Expand Down Expand Up @@ -118,6 +119,8 @@ public OneatCorrector(final File oneatdivision, final File oneatapoptosis, final
setNumThreads();

}



@Override
public SimpleWeightedGraph<Spot, DefaultWeightedEdge> getResult() {
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56 changes: 29 additions & 27 deletions src/main/java/fiji/plugin/trackmate/action/oneat/TrackCorrectorRunner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,7 @@
import net.imglib2.img.display.imagej.ImgPlusViews;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
import net.imglib2.util.LinAlgHelpers;
import net.imglib2.util.Pair;
Expand Down Expand Up @@ -231,11 +232,11 @@ private static Set<Spot> connectedSetOf(SimpleWeightedGraph<Spot, DefaultWeighte
return connectedSet;
}

public static List<Future<Graphobject>> LinkCreator(final Model model, final TrackMate trackmate,
public static <T extends NativeType<T>> List<Future<Graphobject>> LinkCreator(final Model model, final TrackMate trackmate,
HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID,
Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots,
HashMap<Integer, Pair<Spot, ArrayList<Spot>>> Mitosisspots, Map<String, Object> settings, final int ndim,
final Logger logger, final ImgPlus<FloatType> img, HashMap<Integer, ArrayList<Spot>> framespots,
final Logger logger, final ImgPlus<T> img, HashMap<Integer, ArrayList<Spot>> framespots,
int numThreads, double[] calibration, boolean addDisplay) {

// Get the trackmodel and spots in the default tracking result and start to
Expand Down Expand Up @@ -533,6 +534,7 @@ public Graphobject call() throws Exception {

/**
*
* @param <T>
* @param model The TrackMate model
* @param trackmate The TrackMate object
* @param uniquelabelID HashMap of (label, frame) with value being
Expand All @@ -558,12 +560,12 @@ public Graphobject call() throws Exception {
* @throws InterruptedException
*/

public static SimpleWeightedGraph<Spot, DefaultWeightedEdge> getCorrectedTracks(final Model model,
public static <T extends NativeType<T>> SimpleWeightedGraph<Spot, DefaultWeightedEdge> getCorrectedTracks(final Model model,
final TrackMate trackmate, HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID,
Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots,
HashMap<Integer, Pair<Spot, ArrayList<Spot>>> Mitosisspots,
HashMap<Integer, Pair<Spot, Spot>> Apoptosisspots, Map<String, Object> settings, final int ndim,
final Logger logger, final ImgPlus<FloatType> img, HashMap<Integer, ArrayList<Spot>> framespots,
final Logger logger, final ImgPlus<T> img, HashMap<Integer, ArrayList<Spot>> framespots,
int numThreads, double[] calibration, boolean addDisplay) throws InterruptedException, ExecutionException {

// Get the trackmodel and spots in the default tracking result and start to
Expand Down Expand Up @@ -717,7 +719,7 @@ private static void addOverlay(final Roi overlay, final ImagePlus imp, final Spo

}

private static SpotCollection regionspot(final ImgPlus<FloatType> img, final SpotCollection allspots,
private static <T extends NativeType<T>> SpotCollection regionspot(final ImgPlus<T> img, final SpotCollection allspots,
final Spot motherspot, final Logger logger, final double[] calibration, final int frame,
final double region, final double[] motherslope, final double mariangle, final boolean mariprinciple) {

Expand Down Expand Up @@ -800,7 +802,7 @@ private static Pair<double[], double[]> getEigen(final Ellipsoid ellipsoid, int

}

private static Ellipsoid getEllipsoid(Spot currentspot, ImgPlus<FloatType> img, double[] calibration) {
private static <T extends NativeType<T>> Ellipsoid getEllipsoid(Spot currentspot, ImgPlus<T> img, double[] calibration) {

int ndim = img.numDimensions();
Ellipsoid currentellipsoid = null;
Expand All @@ -809,25 +811,25 @@ private static Ellipsoid getEllipsoid(Spot currentspot, ImgPlus<FloatType> img,
center[d] = Math.round(currentspot.getFeature(Spot.POSITION_FEATURES[d]).doubleValue() / calibration[d]);
}

ImgPlus<FloatType> frameimg = ImgPlusViews.hyperSlice(img, ndim - 1,
ImgPlus<T> frameimg = ImgPlusViews.hyperSlice(img, ndim - 1,
(int) currentspot.getFeature(Spot.FRAME).intValue());

long[] location = new long[ndim - 1];
RandomAccess<FloatType> ranac = frameimg.randomAccess();
RandomAccess<T> ranac = frameimg.randomAccess();
for (int d = 0; d < ndim - 1; ++d) {
location[d] = (long) (currentspot.getDoublePosition(d) / calibration[d]);
ranac.setPosition(location[d], d);
}

int label = (int) ranac.get().get();
int label = (int) ( (UnsignedShortType) ranac.get()).get();

Cursor<FloatType> cur = frameimg.localizingCursor();
Cursor<T> cur = frameimg.localizingCursor();
ArrayList<Localizable> points = new ArrayList<Localizable>();
while (cur.hasNext()) {

cur.fwd();

if (cur.get().get() == label) {
if ((int) ( (UnsignedShortType) cur.get()).get() == label) {

long[] point = new long[center.length];
for (int d = 0; d < center.length; d++) {
Expand Down Expand Up @@ -934,12 +936,12 @@ private static double[] computeAxisAndRadiiFromCovariance(double[][] covariance,
* Spot, A second HashMap of trackID + starting spot and trackID +
* list of dividing spots for that track
*/
public static Pair<HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>>, Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>>> getFirstTrackMateobject(
final Model model, final ImgPlus<FloatType> img, final Logger logger, double[] calibration) {
public static <T extends NativeType<T>> Pair<HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>>, Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>>> getFirstTrackMateobject(
final Model model, final ImgPlus<T> img, final Logger logger, double[] calibration) {

Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots = getTMStartSplit(model);
int ndim = img.numDimensions() - 1;
RandomAccess<FloatType> ranac = img.randomAccess();
RandomAccess<T> ranac = img.randomAccess();
Set<Integer> AllTrackIds = model.getTrackModel().trackIDs(true);
HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID = new HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>>();

Expand All @@ -964,7 +966,7 @@ public static Pair<HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>>, Pair<Ha
}

ranac.setPosition(frame, ndim);
int label = (int) ranac.get().get();
int label = (int) ( (UnsignedShortType) ranac.get()).get();

uniquelabelID.put(new ValuePair<Integer, Integer>(label, frame),
new ValuePair<Spot, Integer>(spot, trackID));
Expand All @@ -978,18 +980,18 @@ public static Pair<HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>>, Pair<Ha

}

public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot, Spot>> getapoptosisTrackID(
public static <T extends NativeType<T>> HashMap<Integer, Pair<Spot, Spot>> getapoptosisTrackID(
HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID,
Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots, final Model model,
final ImgPlus<FloatType> img, HashMap<Integer, ArrayList<Spot>> framespots,
final ImgPlus<T> img, HashMap<Integer, ArrayList<Spot>> framespots,
final Map<String, Object> mapsettings, final Logger logger, final int numThreads, double[] calibration) {

// Starting point of the tree + apoptotic spot in the trackID
HashMap<Integer, Pair<Spot, Spot>> Trackapoptosis = new HashMap<Integer, Pair<Spot, Spot>>();
// Spots from trackmate

int ndim = img.numDimensions() - 1;
RandomAccess<FloatType> ranac = img.randomAccess();
RandomAccess<T> ranac = img.randomAccess();

logger.log("Matching with oneat apoptosis spots.\n");
logger.setProgress(1.);
Expand All @@ -1013,7 +1015,7 @@ public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot
}
ranac.setPosition(frame, ndim);
ArrayList<Integer> Alllabels = new ArrayList<Integer>();
int labelID = (int) ranac.get().get();
int labelID = (int) ( (UnsignedShortType) ranac.get()).get();
if (labelID != 0)
Alllabels.add(labelID);

Expand Down Expand Up @@ -1050,10 +1052,10 @@ public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot
return Trackapoptosis;
}

public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot, ArrayList<Spot>>> getmitosisTrackID(
public static <T extends NativeType<T>> HashMap<Integer, Pair<Spot, ArrayList<Spot>>> getmitosisTrackID(
HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID,
Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots, final Model model,
final ImgPlus<FloatType> img, HashMap<Integer, ArrayList<Spot>> framespots,
final ImgPlus<T> img, HashMap<Integer, ArrayList<Spot>> framespots,
final Map<String, Object> mapsettings, final Logger logger, final int numThreads, double[] calibration) {

// Starting point of the tree + list of mitosis spots in the trackID
Expand All @@ -1062,7 +1064,7 @@ public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot

int ndim = img.numDimensions() - 1;
int tmoneatdeltat = (int) mapsettings.get(KEY_GAP_CLOSING_MAX_FRAME_GAP);
RandomAccess<FloatType> ranac = img.randomAccess();
RandomAccess<T> ranac = img.randomAccess();

logger.log("Matching with oneat mitosis spots.\n");
logger.setProgress(1.);
Expand All @@ -1087,7 +1089,7 @@ public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot
ranac.setPosition(frame, ndim);

ArrayList<Integer> Alllabels = new ArrayList<Integer>();
int labelID = (int) ranac.get().get();
int labelID = (int) ( (UnsignedShortType) ranac.get()).get();
if (labelID != 0)
Alllabels.add(labelID);

Expand Down Expand Up @@ -1149,10 +1151,10 @@ public static <T extends RealType<T> & NativeType<T>> HashMap<Integer, Pair<Spot
return Trackmitosis;
}

private static SimpleWeightedGraph<Spot, DefaultWeightedEdge> BreakLinksTrack(final Model model,
private static <T extends NativeType<T>> SimpleWeightedGraph<Spot, DefaultWeightedEdge> BreakLinksTrack(final Model model,
HashMap<Pair<Integer, Integer>, Pair<Spot, Integer>> uniquelabelID,
Pair<HashMap<Integer, Spot>, HashMap<Integer, ArrayList<Spot>>> DividingStartspots,
HashMap<Integer, ArrayList<Spot>> framespots, final ImgPlus<FloatType> img, final Logger logger,
HashMap<Integer, ArrayList<Spot>> framespots, final ImgPlus<T> img, final Logger logger,
final SimpleWeightedGraph<Spot, DefaultWeightedEdge> graph, double[] calibration, int N) {

int count = 0;
Expand All @@ -1163,7 +1165,7 @@ private static SimpleWeightedGraph<Spot, DefaultWeightedEdge> BreakLinksTrack(fi

Set<Integer> AllTrackIds = model.getTrackModel().trackIDs(true);

RandomAccess<FloatType> ranac = img.randomAccess();
RandomAccess<T> ranac = img.randomAccess();
ArrayList<Integer> DividingTrackids = new ArrayList<Integer>();
for (Map.Entry<Integer, ArrayList<Spot>> framemap : framespots.entrySet()) {

Expand All @@ -1184,7 +1186,7 @@ private static SimpleWeightedGraph<Spot, DefaultWeightedEdge> BreakLinksTrack(fi
}
ranac.setPosition(frame, ndim);
// Get the label ID of the current interesting spot
int labelID = (int) ranac.get().get();
int labelID = (int) ( (UnsignedShortType) ranac.get()).get();

if (uniquelabelID.containsKey(new ValuePair<Integer, Integer>(labelID, frame))) {
Pair<Spot, Integer> spotandtrackID = uniquelabelID
Expand Down

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