diff --git a/pom.xml b/pom.xml index 661d9bc..86ff253 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ de.csbdresden StarDist_ - 0.1.1 + 0.2.0 StarDist StarDist - Object Detection with Star-convex Shapes @@ -69,6 +69,16 @@ https://github.com/frauzufall reviewer + + Olivier Burri + https://github.com/lacan + developer + + + Romain Guiet + https://github.com/romainGuiet + developer + @@ -79,14 +89,14 @@ - scm:git:git://github.com/uschmidt83/stardist-imagej - scm:git:git://github.com/uschmidt83/stardist-imagej + scm:git:git://github.com/mpicbg-csbd/stardist-imagej + scm:git:git://github.com/mpicbg-csbd/stardist-imagej HEAD - https://github.com/uschmidt83/stardist-imagej + https://github.com/mpicbg-csbd/stardist-imagej GitHub Issues - https://github.com/uschmidt83/stardist-imagej/issues + https://github.com/mpicbg-csbd/stardist-imagej/issues None diff --git a/src/main/java/de/csbdresden/stardist/Candidates.java b/src/main/java/de/csbdresden/stardist/Candidates.java index 11ead20..951656c 100644 --- a/src/main/java/de/csbdresden/stardist/Candidates.java +++ b/src/main/java/de/csbdresden/stardist/Candidates.java @@ -32,7 +32,9 @@ public class Candidates { private final boolean[] suppressed; private final boolean verbose; private final LogService log; - public static final long S = 100; + + // scale all coordinates by this value and divide later to get subpixel resolution + private static final long S = 100; public Candidates(RandomAccessibleInterval prob, RandomAccessibleInterval dist) { this(prob, dist, 0.4); diff --git a/src/main/java/de/csbdresden/stardist/StarDist2D.java b/src/main/java/de/csbdresden/stardist/StarDist2D.java index 53cef9b..5c6fd11 100644 --- a/src/main/java/de/csbdresden/stardist/StarDist2D.java +++ b/src/main/java/de/csbdresden/stardist/StarDist2D.java @@ -210,7 +210,7 @@ public void run() { checkForCSBDeep(); if (!checkInputs()) return; - if (roiPosition == Opt.ROI_POSITION_AUTO) + if (roiPosition.equals(Opt.ROI_POSITION_AUTO)) roiPositionActive = input.numDimensions() > 3 ? Opt.ROI_POSITION_HYPERSTACK : Opt.ROI_POSITION_STACK; else roiPositionActive = roiPosition; diff --git a/src/main/java/de/csbdresden/stardist/StarDist2DBase.java b/src/main/java/de/csbdresden/stardist/StarDist2DBase.java index 57e270d..7f97d5e 100644 --- a/src/main/java/de/csbdresden/stardist/StarDist2DBase.java +++ b/src/main/java/de/csbdresden/stardist/StarDist2DBase.java @@ -98,16 +98,16 @@ protected void exportROIs(Candidates polygons, int framePosition, long numFrames for (final int i : polygons.getWinner()) { final PolygonRoi polyRoi = polygons.getPolygonRoi(i); if (framePosition > 0) setRoiPosition(polyRoi, framePosition, roiPosition); - roiManager.addRoi(polyRoi); + roiManager.add(polyRoi, -1); if (exportPointRois) { final PointRoi pointRoi = polygons.getOriginRoi(i); if (framePosition > 0) setRoiPosition(pointRoi, framePosition, roiPosition); - roiManager.addRoi(pointRoi); + roiManager.add(pointRoi, -1); } if (exportBboxRois) { final Roi bboxRoi = polygons.getBboxRoi(i); if (framePosition > 0) setRoiPosition(bboxRoi, framePosition, roiPosition); - roiManager.addRoi(bboxRoi); + roiManager.add(bboxRoi, -1); } }