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Example 1 with Polygon

use of ome.xml.model.Polygon in project bioformats by openmicroscopy.

the class PrintROIs method printShape.

/**
 * Print the given shape.
 */
public static void printShape(Shape shapeObject) {
    if (shapeObject instanceof Ellipse) {
        Ellipse ellipse = (Ellipse) shapeObject;
        System.out.println("    Ellipse:");
        System.out.println("      Text = " + ellipse.getText());
        System.out.println("      X = " + ellipse.getX());
        System.out.println("      Y = " + ellipse.getY());
        System.out.println("      Radius (X) = " + ellipse.getRadiusX());
        System.out.println("      Radius (Y) = " + ellipse.getRadiusY());
    } else if (shapeObject instanceof Line) {
        Line line = (Line) shapeObject;
        System.out.println("    Line:");
        System.out.println("      Text = " + line.getText());
        System.out.println("      X1 = " + line.getX1());
        System.out.println("      Y1 = " + line.getY1());
        System.out.println("      X2 = " + line.getX2());
        System.out.println("      Y2 = " + line.getY2());
    } else if (shapeObject instanceof Point) {
        Point point = (Point) shapeObject;
        System.out.println("    Point:");
        System.out.println("      Text = " + point.getText());
        System.out.println("      X = " + point.getX());
        System.out.println("      Y = " + point.getY());
    } else if (shapeObject instanceof Polyline) {
        Polyline polyline = (Polyline) shapeObject;
        System.out.println("    Polyline:");
        System.out.println("      Text = " + polyline.getText());
        System.out.println("      Points = " + polyline.getPoints());
    } else if (shapeObject instanceof Polygon) {
        Polygon polygon = (Polygon) shapeObject;
        System.out.println("    Polygon:");
        System.out.println("      Text = " + polygon.getText());
        System.out.println("      Points = " + polygon.getPoints());
    } else if (shapeObject instanceof Rectangle) {
        Rectangle rectangle = (Rectangle) shapeObject;
        System.out.println("    Rectangle:");
        System.out.println("      Text = " + rectangle.getText());
    } else if (shapeObject instanceof Mask) {
        Mask mask = (Mask) shapeObject;
        System.out.println("    Mask:");
        System.out.println("      Text = " + mask.getText());
        System.out.println("      X = " + mask.getX());
        System.out.println("      Y = " + mask.getY());
        System.out.println("      Width = " + mask.getWidth());
        System.out.println("      Height = " + mask.getHeight());
    } else if (shapeObject instanceof Label) {
        Label text = (Label) shapeObject;
        System.out.println("    Label:");
        System.out.println("      Text = " + text.getText());
        System.out.println("      X = " + text.getX());
        System.out.println("      Y = " + text.getY());
    }
}
Also used : Line(ome.xml.model.Line) Ellipse(ome.xml.model.Ellipse) Polyline(ome.xml.model.Polyline) Rectangle(ome.xml.model.Rectangle) Mask(ome.xml.model.Mask) Label(ome.xml.model.Label) Point(ome.xml.model.Point) Polygon(ome.xml.model.Polygon)

Example 2 with Polygon

use of ome.xml.model.Polygon in project bioformats by openmicroscopy.

the class Schema2011_06_File_Upgrade_Test method testShape4.

@Test(groups = { "11-06-u-roi" }, dependsOnMethods = { "testROI2AndUnion" })
public void testShape4() {
    Assert.assertNotNull(union2);
    shape4 = union2.getShape(4);
    Assert.assertEquals(Polygon.class.getName(), shape4.getClass().getName());
    Polygon polygon4 = (Polygon) shape4;
    Assert.assertEquals(ref.ROI2Shape4Stroke, polygon4.getStrokeColor());
    Assert.assertEquals(ref.ROI2Shape4StrokeWidth, polygon4.getStrokeWidth());
    Assert.assertEquals(ref.ROI2Shape4PolylinePoints, polygon4.getPoints());
}
Also used : Polygon(ome.xml.model.Polygon) Test(org.testng.annotations.Test)

Example 3 with Polygon

use of ome.xml.model.Polygon in project bioformats by openmicroscopy.

the class ROIHandler method openROIs.

/**
 * Opens the rois and converts them into ImageJ Rois.
 *
 * @param retrieve The OMEXML store.
 * @param images The imageJ object.
 * @param isOMERO <code>true</code> if data stored in OMERO,
 *        <code>false</code> otherwise.
 * @param roisMode Determines whether to import Rois to overlay or RoiManager
 */
public static void openROIs(IMetadata retrieve, ImagePlus[] images, boolean isOMERO, String roisMode) {
    if (!(retrieve instanceof OMEXMLMetadata))
        return;
    int nextRoi = 0;
    RoiManager manager = RoiManager.getInstance();
    OME root = (OME) retrieve.getRoot();
    Roi roi;
    Float sw;
    Color sc;
    Color fc;
    int imageCount = images.length;
    for (int imageNum = 0; imageNum < imageCount; imageNum++) {
        int roiCount = root.sizeOfROIList();
        if (roiCount > 0 && manager == null && roisMode.equals(ImporterOptions.ROIS_MODE_MANAGER)) {
            manager = new RoiManager();
        }
        for (int roiNum = 0; roiNum < roiCount; roiNum++) {
            Union shapeSet = root.getROI(roiNum).getUnion();
            int shapeCount = shapeSet.sizeOfShapeList();
            for (int shape = 0; shape < shapeCount; shape++) {
                Shape shapeObject = shapeSet.getShape(shape);
                roi = null;
                sw = null;
                sc = null;
                fc = null;
                int c = 0;
                int z = 0;
                int t = 0;
                if (shapeObject instanceof Ellipse) {
                    Ellipse ellipse = (Ellipse) shapeObject;
                    int cx = ellipse.getX().intValue();
                    int cy = ellipse.getY().intValue();
                    int rx = ellipse.getRadiusX().intValue();
                    int ry = ellipse.getRadiusY().intValue();
                    roi = new OvalRoi(cx - rx, cy - ry, rx * 2, ry * 2);
                    if (ellipse.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = ellipse.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (ellipse.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = ellipse.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (ellipse.getStrokeWidth() != null) {
                        sw = ellipse.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof ome.xml.model.Line) {
                    ome.xml.model.Line line = (ome.xml.model.Line) shapeObject;
                    int x1 = line.getX1().intValue();
                    int x2 = line.getX2().intValue();
                    int y1 = line.getY1().intValue();
                    int y2 = line.getY2().intValue();
                    roi = new Line(x1, y1, x2, y2);
                    if (line.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = line.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (line.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = line.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (line.getStrokeWidth() != null) {
                        sw = line.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof Point) {
                    Point point = (Point) shapeObject;
                    int x = point.getX().intValue();
                    int y = point.getY().intValue();
                    roi = new PointRoi(x, y);
                    if (point.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = point.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (point.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = point.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (point.getStrokeWidth() != null) {
                        sw = point.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof Polyline) {
                    Polyline polyline = (Polyline) shapeObject;
                    String points = polyline.getPoints();
                    int[][] coordinates = parsePoints(points);
                    roi = new PolygonRoi(coordinates[0], coordinates[1], coordinates[0].length, Roi.POLYLINE);
                    if (polyline.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = polyline.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (polyline.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = polyline.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (polyline.getStrokeWidth() != null) {
                        sw = polyline.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof Polygon) {
                    Polygon polygon = (Polygon) shapeObject;
                    String points = polygon.getPoints();
                    int[][] coordinates = parsePoints(points);
                    roi = new PolygonRoi(coordinates[0], coordinates[1], coordinates[0].length, Roi.POLYGON);
                    if (polygon.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = polygon.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (polygon.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = polygon.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (polygon.getStrokeWidth() != null) {
                        sw = polygon.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof ome.xml.model.Label) {
                    // add support for TextROI's
                    ome.xml.model.Label label = (ome.xml.model.Label) shapeObject;
                    double x = label.getX().doubleValue();
                    double y = label.getY().doubleValue();
                    String labelText = label.getText();
                    int size = label.getFontSize().value().intValue();
                    Font font = new Font(labelText, Font.PLAIN, size);
                    roi = new TextRoi((int) x, (int) y, labelText, font);
                    if (label.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = label.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (label.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = label.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (label.getStrokeWidth() != null) {
                        sw = label.getStrokeWidth().value().floatValue();
                    }
                } else if (shapeObject instanceof ome.xml.model.Rectangle) {
                    ome.xml.model.Rectangle rectangle = (ome.xml.model.Rectangle) shapeObject;
                    int x = rectangle.getX().intValue();
                    int y = rectangle.getY().intValue();
                    int w = rectangle.getWidth().intValue();
                    int h = rectangle.getHeight().intValue();
                    roi = new Roi(x, y, w, h);
                    if (rectangle.getStrokeColor() != null) {
                        ome.xml.model.primitives.Color StrokeColor = rectangle.getStrokeColor();
                        sc = new Color(StrokeColor.getRed(), StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha());
                        if (isOMERO) {
                            sc = new Color(StrokeColor.getGreen(), StrokeColor.getBlue(), StrokeColor.getAlpha(), StrokeColor.getRed());
                        }
                    }
                    if (rectangle.getFillColor() != null) {
                        ome.xml.model.primitives.Color FillColor = rectangle.getFillColor();
                        fc = new Color(FillColor.getRed(), FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha());
                        if (isOMERO) {
                            fc = new Color(FillColor.getGreen(), FillColor.getBlue(), FillColor.getAlpha(), FillColor.getRed());
                        }
                    }
                    if (rectangle.getStrokeWidth() != null) {
                        sw = rectangle.getStrokeWidth().value().floatValue();
                    }
                }
                if (roi != null) {
                    String roiLabel = shapeObject.getText();
                    if (roiLabel == null) {
                        roiLabel = shapeObject.getID();
                    }
                    roi.setName(roiLabel);
                    if (Prefs.showAllSliceOnly) {
                        if (shapeObject.getTheC() != null) {
                            c = shapeObject.getTheC().getValue();
                        }
                        if (shapeObject.getTheZ() != null) {
                            z = shapeObject.getTheZ().getValue();
                        }
                        if (shapeObject.getTheT() != null) {
                            t = shapeObject.getTheT().getValue();
                        }
                        // ImageJ expects 1-based indexing, opposed to
                        // 0-based indexing in OME
                        // Roi positions differ between hyperstacks and normal stacks
                        ImagePlus imp = images[imageNum];
                        if (imp.getNChannels() > 1) {
                            c++;
                        }
                        if (imp.getNSlices() > 1) {
                            z++;
                        }
                        if (imp.getNFrames() > 1) {
                            t++;
                        }
                        if (c == 0)
                            c = 1;
                        if (t == 0)
                            t = 1;
                        if (z == 0)
                            z = 1;
                        if (imp.getNChannels() == 1 && imp.getNSlices() == 1) {
                            roi.setPosition(t);
                        } else if (imp.getNChannels() == 1 && imp.getNFrames() == 1) {
                            roi.setPosition(z);
                        } else if (imp.getNSlices() == 1 && imp.getNFrames() == 1) {
                            roi.setPosition(c);
                        } else if (imp.isHyperStack()) {
                            roi.setPosition(c, z, t);
                        }
                    }
                    if (sw == null) {
                        roi.setStrokeWidth((float) 1);
                    }
                    if (sw != null) {
                        if (sw == 0) {
                            sw = (float) 1;
                        }
                        roi.setStrokeWidth(sw);
                    }
                    if (sc != null) {
                        roi.setStrokeColor(sc);
                    }
                    if (roisMode.equals(ImporterOptions.ROIS_MODE_MANAGER)) {
                        manager.add(images[imageNum], roi, nextRoi++);
                    } else if (roisMode.equals(ImporterOptions.ROIS_MODE_OVERLAY)) {
                        Overlay overlay = images[imageNum].getOverlay();
                        if (overlay == null) {
                            overlay = new Overlay(roi);
                            images[imageNum].setOverlay(overlay);
                        } else {
                            overlay.add(roi);
                        }
                    }
                }
            }
        }
        if (roiCount > 0 && manager != null) {
            manager.setAlwaysOnTop(true);
            manager.runCommand("show all with labels");
        }
    }
}
Also used : Ellipse(ome.xml.model.Ellipse) Shape(ome.xml.model.Shape) Rectangle(java.awt.Rectangle) TextRoi(ij.gui.TextRoi) OvalRoi(ij.gui.OvalRoi) Union(ome.xml.model.Union) Font(java.awt.Font) PolygonRoi(ij.gui.PolygonRoi) Polygon(ome.xml.model.Polygon) Overlay(ij.gui.Overlay) PointRoi(ij.gui.PointRoi) OME(ome.xml.model.OME) Color(java.awt.Color) Point(ome.xml.model.Point) PolygonRoi(ij.gui.PolygonRoi) TextRoi(ij.gui.TextRoi) OvalRoi(ij.gui.OvalRoi) PointRoi(ij.gui.PointRoi) EllipseRoi(ij.gui.EllipseRoi) ShapeRoi(ij.gui.ShapeRoi) Roi(ij.gui.Roi) ImagePlus(ij.ImagePlus) Point(ome.xml.model.Point) RoiManager(ij.plugin.frame.RoiManager) Line(ij.gui.Line) OMEXMLMetadata(loci.formats.ome.OMEXMLMetadata) Polyline(ome.xml.model.Polyline)

Aggregations

Polygon (ome.xml.model.Polygon)3 Ellipse (ome.xml.model.Ellipse)2 Point (ome.xml.model.Point)2 Polyline (ome.xml.model.Polyline)2 ImagePlus (ij.ImagePlus)1 EllipseRoi (ij.gui.EllipseRoi)1 Line (ij.gui.Line)1 OvalRoi (ij.gui.OvalRoi)1 Overlay (ij.gui.Overlay)1 PointRoi (ij.gui.PointRoi)1 PolygonRoi (ij.gui.PolygonRoi)1 Roi (ij.gui.Roi)1 ShapeRoi (ij.gui.ShapeRoi)1 TextRoi (ij.gui.TextRoi)1 RoiManager (ij.plugin.frame.RoiManager)1 Color (java.awt.Color)1 Font (java.awt.Font)1 Rectangle (java.awt.Rectangle)1 OMEXMLMetadata (loci.formats.ome.OMEXMLMetadata)1 Label (ome.xml.model.Label)1