Examples with RoiManager ij.plugin.frame.RoiManager used on opensource projects

Example 6 with RoiManager

use of ij.plugin.frame.RoiManager in project imagej1 by imagej.

the class OverlayCommands method fromRoiManager.

void fromRoiManager() {
    ImagePlus imp = IJ.getImage();
    RoiManager rm = RoiManager.getInstance2();
    if (rm == null) {
        IJ.error("ROI Manager is not open");
        return;
    }
    Roi[] rois = rm.getRoisAsArray();
    if (rois.length == 0) {
        IJ.error("ROI Manager is empty");
        return;
    }
    rm.moveRoisToOverlay(imp);
    imp.deleteRoi();
}

Example 7 with RoiManager

use of ij.plugin.frame.RoiManager 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");
        }
    }
}

Example 8 with RoiManager

use of ij.plugin.frame.RoiManager in project mcib3d-core by mcib3d.

the class ManualSpot method segmentSpots.

// End of variables declaration//GEN-END:variables
private void segmentSpots() {
    Roi roi;
    RoiManager manager = RoiManager.getInstance();
    Roi[] rois = manager.getRoisAsArray();
    if ((manager == null) || (rois.length == 0)) {
        IJ.showMessage("Put rois in the RoiManager");
        return;
    }
    if (objs == null) {
        objs = new Object3D[rois.length];
    }
    String text = "";
    for (int r = 0; r < rois.length; r++) {
        roi = rois[r];
        Rectangle rect = roi.getBounds();
        int x = rect.x;
        int y = rect.y;
        int z = manager.getSliceNumber(manager.getName(r));
        text = text.concat("\nx=" + x + " " + y + " " + z);
        jTextFieldLog.setText(text);
        Segment3DSpots segSpots = new Segment3DSpots(spot3DImage, null);
        segSpots.setLabelImage(labelImage);
        segSpots.show = true;
        // find local maximum
        Voxel3D v = segSpots.getLocalMaximum(x, y, z, 2, 2, 2);
        if (v != null) {
            text = text.concat("\nMax local " + v.getX() + " " + v.getY() + " " + v.getZ() + " " + v.getValue());
            jTextFieldLog.setText(text);
            x = v.getRoundX();
            y = v.getRoundY();
            z = v.getRoundZ();
        }
        // set parameter
        if (threshold_method == 0) {
            segSpots.setMethodLocal(Segment3DSpots.LOCAL_CONSTANT);
        } else if (threshold_method == 1) {
            segSpots.setMethodLocal(Segment3DSpots.LOCAL_MEAN);
        } else {
            segSpots.setMethodLocal(Segment3DSpots.LOCAL_GAUSS);
        }
        if (spot_method == 0) {
            segSpots.setMethodSeg(Segment3DSpots.SEG_CLASSICAL);
        } else if (spot_method == 0) {
            segSpots.setMethodSeg(Segment3DSpots.SEG_MAX);
        } else {
            segSpots.setMethodSeg(Segment3DSpots.SEG_BLOCK);
        }
        segSpots.setLocalThreshold(threshold_constant);
        segSpots.setGaussMaxr(rad_gauss);
        segSpots.setGaussPc(sd_gauss / 10.0);
        segSpots.setRadiusLocalMean(r0, r1, r2, weight);
        segSpots.setWatershed(false);
        // reset labelimage
        if (objs[r] != null) {
            objs[r].draw(labelImage, 0);
        // IJ.log("deleting old spot " + r);
        }
        // redraw population (in case spot has erased objects)
        popOrig.draw(labelImage);
        segSpots.setLabelImage(labelImage);
        ArrayList<Voxel3D> spot = segSpots.segmentOneSpot(x, y, z, col);
        // IJ.log("spot " + r + " at " + x + " " + y + " " + z + " : " + spot);
        if (spot != null) {
            // IJ.log("spot found, size " + spot.size());
            if (spot.size() > 0) {
                objs[r] = new Object3DVoxels(spot);
                objs[r].draw(labelImage, col);
            }
            if (plusres == null) {
                plusres = labelImage.getImagePlus();
                plusres.show();
                IJ.run(plusres, "3-3-2 RGB", "");
            }
            IJ.setMinAndMax(plusres, 0, col);
            plusres.setSlice((int) objs[r].getCenterZ() + 1);
            plusres.updateAndDraw();
        } else {
            jTextFieldLog.setText(jTextFieldLog.getText() + "\nno spot found !");
        }
    }
    labelImage.updateDisplay();
}

Example 9 with RoiManager

use of ij.plugin.frame.RoiManager in project mcib3d-core by mcib3d.

the class ManualSpot method initInterface.

private void initInterface() {
    // adjust slider threshold
    jSliderConstant.setMaximum((int) spot3DImage.getMax());
    jSliderConstant.setMinimum(0);
    ArrayUtil hist = new ArrayUtil(spot3DImage.getHistogram(new BlankMask(spot3DImage)));
    int pcHigh = hist.indexOfSumPercent(0.999);
    jSliderConstant.setValue(pcHigh);
    // set tool point and open RoiManager
    IJ.setTool(Toolbar.POINT);
    RoiManager manager = RoiManager.getInstance();
    if (manager == null) {
        manager = new RoiManager();
    }
}