Making issue fmi-faim#13 pull request ready.

charismatic-claire · Mar 23, 2021 · 91bbc33 · 91bbc33
1 parent 6ab38db
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Showing 3 changed files with 51 additions and 24 deletions.
diff --git a/README.md b/README.md
@@ -20,15 +20,16 @@ If you want to install this plugin manually via the KNIME ImageJ2 integration, y
 
 | Project | Download `jar` from maven.imagej.net |
 | --- | --- |
-| [`AnalyzeSkeleton_`](https://github.com/fiji/AnalyzeSkeleton/) | [`AnalyzeSkeleton_-3.3.0.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/AnalyzeSkeleton_/3.3.0/AnalyzeSkeleton_-3.3.0.jar) |
-| [`Descriptor_based_registration`](https://github.com/fiji/Descriptor_based_registration) | [`Descriptor_based_registration-2.1.2.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/Descriptor_based_registration/2.1.2/Descriptor_based_registration-2.1.2.jar) |
+| [`AnalyzeSkeleton_`](https://github.com/fiji/AnalyzeSkeleton/) | [`AnalyzeSkeleton_-3.4.2.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/AnalyzeSkeleton_/3.4.2/AnalyzeSkeleton_-3.4.2.jar) |
+| [`Descriptor_based_registration`](https://github.com/fiji/Descriptor_based_registration) | [`Descriptor_based_registration-2.1.7.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/Descriptor_based_registration/2.1.7/Descriptor_based_registration-2.1.7.jar) |
 | [`Fiji_Plugins`](https://github.com/fiji/Fiji_Plugins) | [`Fiji_Plugins-3.1.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/Fiji_Plugins/3.1.1/Fiji_Plugins-3.1.1.jar) |
 | [`fmi-trackmate-addons`](https://github.com/fmi-faim/fmi-trackmate-addons) | [`fmi-trackmate-addons-0.1.2.jar`](http://maven.imagej.net/service/local/repositories/releases/content/ch/fmi/fmi-trackmate-addons/0.1.2/fmi-trackmate-addons-0.1.2.jar) |
 | [`guava`](https://github.com/google/guava) | [`guava-21.0.jar`](http://maven.imagej.net/service/local/repositories/central/content/com/google/guava/guava/21.0/guava-21.0.jar) |
 | `jdom2` | [`jdom2-2.0.6.jar`](http://maven.imagej.net/service/local/repositories/bedatadriven/content/org/jdom/jdom2/2.0.6/jdom2-2.0.6.jar) |
-| [`jgrapht-core`](https://github.com/jgrapht/jgrapht) | [`jgrapht-core-1.3.0.jar`](http://maven.imagej.net/service/local/repositories/central/content/org/jgrapht/jgrapht-core/1.3.0/jgrapht-core-1.3.0.jar) |
+| [`jgrapht-core`](https://github.com/jgrapht/jgrapht) | [`jgrapht-core-1.4.0.jar`](http://maven.imagej.net/service/local/repositories/central/content/org/jgrapht/jgrapht-core/1.4.0/jgrapht-core-1.4.0.jar) |
+| [`jts-core`](https://github.com/locationtech/jts) | [`jts-core-1.18.1.jar`](https://repo.maven.apache.org/maven2/org/locationtech/jts/jts-core/1.18.1/jts-core-1.18.1.jar) |
 | [`legacy-imglib1`](https://github.com/fiji/legacy-imglib1) | [`legacy-imglib1-1.1.9.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/legacy-imglib1/1.1.9/legacy-imglib1-1.1.9.jar) |
-| [`mpicbg`](https://github.com/axtimwalde/mpicbg/tree/master/mpicbg) | [`mpicbg-1.3.0.jar`](http://maven.imagej.net/service/local/repositories/releases/content/mpicbg/mpicbg/1.3.0/mpicbg-1.3.0.jar) |
-| [`SPIM_Registration`](https://github.com/fiji/SPIM_Registration) | [`SPIM_Registration-5.0.19.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/SPIM_Registration/5.0.19/SPIM_Registration-5.0.19.jar) |
-| [`TrackMate_`](https://github.com/fiji/TrackMate) | [`TrackMate_-4.0.0.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/TrackMate_/4.0.0/TrackMate_-4.0.0.jar) |
+| [`mpicbg`](https://github.com/axtimwalde/mpicbg/tree/master/mpicbg) | [`mpicbg-1.4.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/mpicbg/mpicbg/1.4.1/mpicbg-1.4.1.jar) |
+| [`SPIM_Registration`](https://github.com/fiji/SPIM_Registration) | [`SPIM_Registration-5.0.21.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/SPIM_Registration/5.0.21/SPIM_Registration-5.0.21.jar) |
+| [`TrackMate_`](https://github.com/fiji/TrackMate) | [`TrackMate_-6.0.1.jar`](http://maven.imagej.net/service/local/repositories/releases/content/sc/fiji/TrackMate_/6.0.1/TrackMate_-6.0.1.jar) |
 | [`TrackMate_extras`](https://github.com/tinevez/TrackMate-extras) | [`TrackMate_extras-0.0.4.jar`](http://maven.imagej.net/service/local/repositories/releases/content/org/scijava/TrackMate_extras/0.0.4/TrackMate_extras-0.0.4.jar) |
diff --git a/src/main/java/ch/fmi/ContourPolygonBitmaskToText.java b/src/main/java/ch/fmi/ContourPolygonBitmaskToText.java
@@ -1,6 +1,9 @@
 /*-
  * #%L
- * <MY TEXT HERE...>
+ * Plug-in to convert a 2D binary to a polygon geometry serialized to
+ * well-known text (wkt).
+ * %%
+ * @author Charismatic Claire
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as
@@ -26,6 +29,7 @@
 import net.imglib2.type.logic.BitType;
 import org.locationtech.jts.geom.Coordinate;
 import org.locationtech.jts.geom.GeometryFactory;
+import org.locationtech.jts.geom.Polygon;
 import org.scijava.ItemIO;
 import org.scijava.command.Command;
 import org.scijava.command.ContextCommand;
@@ -46,15 +50,20 @@ public class ContourPolygonBitmaskToText extends ContextCommand {
 
     @Override
     public void run() {
-        Polygon2D polygon = (Polygon2D) opService.run(Ops.Geometric.Contour.class, input, true);
-        int numVertices = polygon.numVertices();
+        // get imglib2-roi polygon from input
+        Polygon2D polygon2d = (Polygon2D) opService.run(Ops.Geometric.Contour.class, input, true);
+        // get coordinates
+        int numVertices = polygon2d.numVertices();
         Coordinate[] coordinates = new Coordinate[numVertices + 1];
         for (int i = 0; i < numVertices + 1; i++) {
-            Double x = polygon.vertex(i % numVertices).getDoublePosition(0);
-            Double y = polygon.vertex(i % numVertices).getDoublePosition(1);
+            Double x = polygon2d.vertex(i % numVertices).getDoublePosition(0);
+            Double y = polygon2d.vertex(i % numVertices).getDoublePosition(1);
             coordinates[i] = new Coordinate(x, y);
         }
+        // create GIS polygon
         GeometryFactory factory = new GeometryFactory();
-        output = factory.createPolygon(coordinates).toText();
+        Polygon polygon = factory.createPolygon(coordinates);
+        // return result
+        output = polygon.toText();
     }
 }
diff --git a/src/main/java/ch/fmi/ContourPolygonTextToBitmask.java b/src/main/java/ch/fmi/ContourPolygonTextToBitmask.java
@@ -1,6 +1,9 @@
 /*-
  * #%L
- * <MY TEXT HERE...>
+ * Plug-in to convert a polygon geometry represented in well-known text
+ * (wkt) to a 2D binary mask.
+ * %%
+ * @author Charismatic Claire
  * %%
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU Lesser General Public License as
@@ -31,6 +34,8 @@
 import net.imglib2.type.logic.BoolType;
 import net.imglib2.view.IntervalView;
 import net.imglib2.view.Views;
+import org.locationtech.jts.geom.Coordinate;
+import org.locationtech.jts.geom.Geometry;
 import org.locationtech.jts.geom.GeometryFactory;
 import org.locationtech.jts.geom.Polygon;
 import org.locationtech.jts.io.ParseException;
@@ -52,34 +57,46 @@ public class ContourPolygonTextToBitmask extends ContextCommand {
     @Parameter
     private LogService logService;
 
-    @Parameter(label = "X Dimension")
-    private long xDim;
-
-    @Parameter(label = "Y Dimension")
-    private long yDim;
-
     @Parameter(label = "Well-Known Text Polygons")
     private String text;
 
     @Parameter(type = ItemIO.OUTPUT)
     private Img<BitType> output;
 
+    private FinalInterval envelopeToDims(Geometry envelope) throws Exception {
+        Coordinate boxMin, boxMax;
+        boxMin = envelope.getCoordinates()[0];
+        if(envelope.getDimension() == 2) boxMax = envelope.getCoordinates()[2];
+        else if(envelope.getDimension() == 1) boxMax = envelope.getCoordinates()[1];
+        else throw new Exception(
+                String.format("Your envelop <%s> stems from another world!", envelope.toText()));
+        long[] min = new long[] { (long) boxMin.getX(), (long) boxMin.getY() };
+        long[] max = new long[] { (long) boxMax.getX(), (long) boxMax.getY() };
+        return new FinalInterval(min, max);
+    }
+
     @Override
     public void run() {
         GeometryFactory factory = new GeometryFactory();
         WKTReader reader = new WKTReader(factory);
         try {
+            // get GIS polygon from input
             Polygon polygon = (Polygon) reader.read(text);
+            // construct bitmask
             List<RealLocalizable> points = Arrays.stream(polygon.getCoordinates())
                     .map(coordinate -> new RealPoint(coordinate.getX(), coordinate.getY()))
                     .collect(Collectors.toList());
-            Polygon2D polygon2d = GeomMasks.polygon2D(points);
-            RealRandomAccessibleRealInterval<BoolType> mask = Masks.toRealRandomAccessibleRealInterval(polygon2d);
-            FinalInterval dims = new FinalInterval(new long[] {0, 0}, new long[] {xDim - 1, yDim - 1});
-            IntervalView<BoolType> view = Views.interval(Views.raster(mask), dims);
+            Polygon2D polygon2d = GeomMasks.polygon2D(points);  // imglib2-roi polygon
+            RealRandomAccessibleRealInterval<BoolType> bitmask = Masks.toRealRandomAccessibleRealInterval(polygon2d);
+            // create view
+            FinalInterval dims = envelopeToDims(polygon.getEnvelope());
+            IntervalView<BoolType> view = Views.interval(Views.raster(bitmask), dims);
+            // create image
             RandomAccessibleInterval<BitType> interval = Converters.convert(
                     (RandomAccessibleInterval<BoolType>) view, (in, out) -> out.set(in.get()), new BitType());
-            output = new ImgView<>(interval, new ArrayImgFactory<>());
+            Img<BitType> image = new ImgView<>(interval, new ArrayImgFactory<>());
+            // return result
+            output =  image;
         } catch (ParseException e) {
             logService.warn(String.format("Could not create a polygon from input <{}>", text));
         } catch(Exception e) {