List of usage examples for java.awt.geom Path2D contains
public static boolean contains(PathIterator pi, Rectangle2D r)
From source file:vteaexploration.plottools.panels.XYExplorationPanel.java
@Override public int getGatedSelected(ImagePlus ip) { ArrayList<MicroObject> ImageGatedObjects = new ArrayList<MicroObject>(); ArrayList<MicroObject> volumes = (ArrayList) plotvalues.get(1); try {/*from w w w . j a v a 2 s .co m*/ ListIterator<MicroObject> itr = volumes.listIterator(); while (itr.hasNext()) { MicroObject m = itr.next(); int[] c = new int[2]; c = m.getBoundsCenter(); if (ip.getRoi().contains(c[0], c[1])) { ImageGatedObjects.add(m); } } } catch (NullPointerException e) { return 0; } Gate gate; ListIterator<Gate> gate_itr = gates.listIterator(); ArrayList<MicroObject> result = new ArrayList<MicroObject>(); while (gate_itr.hasNext()) { gate = gate_itr.next(); if (gate.getSelected()) { Path2D path = gate.createPath2DInChartSpace(); MicroObjectModel volume; double xValue = 0; double yValue = 0; ListIterator<MicroObject> it = ImageGatedObjects.listIterator(); try { while (it.hasNext()) { volume = it.next(); if (volume != null) { xValue = ((Number) processPosition(currentX, (MicroObject) volume)).doubleValue(); yValue = ((Number) processPosition(currentY, (MicroObject) volume)).doubleValue(); if (path.contains(xValue, yValue)) { result.add((MicroObject) volume); } } } } catch (NullPointerException e) { return 0; } } } return result.size(); }
From source file:vteaexploration.plottools.panels.XYExplorationPanel.java
@Override public int getSelectedObjects() { Gate gate;//from w ww .j a va 2 s . c om ListIterator<Gate> gate_itr = gates.listIterator(); //.get int selected = 0; int gated = 0; int total = 0; ArrayList<MicroObject> result = new ArrayList<MicroObject>(); while (gate_itr.hasNext()) { gate = gate_itr.next(); if (gate.getSelected()) { Path2D path = gate.createPath2DInChartSpace(); ArrayList<MicroObject> volumes = (ArrayList) this.plotvalues.get(1); MicroObjectModel volume; double xValue = 0; double yValue = 0; ListIterator<MicroObject> it = volumes.listIterator(); try { while (it.hasNext()) { volume = it.next(); if (volume != null) { xValue = ((Number) processPosition(currentX, (MicroObject) volume)).doubleValue(); yValue = ((Number) processPosition(currentY, (MicroObject) volume)).doubleValue(); if (path.contains(xValue, yValue)) { result.add((MicroObject) volume); } } } } catch (NullPointerException e) { return 0; } } } //System.out.println("RESULT: total gates " + gates.size() + ": " + this.getTitle() + ", Gated: " + selected + ", Total: " + total + ", for: " + 100 * (new Double(selected).doubleValue() / (new Double(total)).doubleValue()) + "%"); return result.size(); }
From source file:vteaexploration.plottools.panels.XYExplorationPanel.java
public void makeOverlayImage(ArrayList gates, int x, int y, int xAxis, int yAxis) { //convert gate to chart x,y path Gate gate;//from w w w . ja va2 s . c o m ListIterator<Gate> gate_itr = gates.listIterator(); //.get int total = 0; int gated = 0; int selected = 0; int gatedSelected = 0; int gatecount = gates.size(); while (gate_itr.hasNext()) { gate = gate_itr.next(); if (gate.getSelected()) { Path2D path = gate.createPath2DInChartSpace(); ArrayList<MicroObject> result = new ArrayList<MicroObject>(); ArrayList<MicroObject> volumes = (ArrayList) this.plotvalues.get(1); MicroObjectModel volume; double xValue = 0; double yValue = 0; ListIterator<MicroObject> it = volumes.listIterator(); try { while (it.hasNext()) { volume = it.next(); if (volume != null) { xValue = ((Number) processPosition(xAxis, (MicroObject) volume)).doubleValue(); yValue = ((Number) processPosition(yAxis, (MicroObject) volume)).doubleValue(); if (path.contains(xValue, yValue)) { result.add((MicroObject) volume); } } } } catch (NullPointerException e) { } ; Overlay overlay = new Overlay(); int count = 0; BufferedImage placeholder = new BufferedImage(impoverlay.getWidth(), impoverlay.getHeight(), BufferedImage.TYPE_INT_ARGB); ImageStack gateOverlay = new ImageStack(impoverlay.getWidth(), impoverlay.getHeight()); selected = getSelectedObjects(); total = volumes.size(); gated = getGatedObjects(impoverlay); gatedSelected = getGatedSelected(impoverlay); for (int i = 0; i <= impoverlay.getNSlices(); i++) { BufferedImage selections = new BufferedImage(impoverlay.getWidth(), impoverlay.getHeight(), BufferedImage.TYPE_INT_ARGB); Graphics2D g2 = selections.createGraphics(); ImageRoi ir = new ImageRoi(0, 0, placeholder); ListIterator<MicroObject> vitr = result.listIterator(); while (vitr.hasNext()) { try { MicroObject vol = (MicroObject) vitr.next(); int[] x_pixels = vol.getXPixelsInRegion(i); int[] y_pixels = vol.getYPixelsInRegion(i); for (int c = 0; c < x_pixels.length; c++) { g2.setColor(gate.getColor()); g2.drawRect(x_pixels[c], y_pixels[c], 1, 1); } ir = new ImageRoi(0, 0, selections); count++; } catch (NullPointerException e) { } } ir.setPosition(i); ir.setOpacity(0.4); overlay.add(ir); gateOverlay.addSlice(ir.getProcessor()); java.awt.Font f = new Font("Arial", Font.BOLD, 12); BigDecimal percentage = new BigDecimal(selected); BigDecimal totalBD = new BigDecimal(total); percentage = percentage.divide(totalBD, 4, BigDecimal.ROUND_UP); BigDecimal percentageGated = new BigDecimal(gated); BigDecimal totalGatedBD = new BigDecimal(total); percentageGated = percentageGated.divide(totalGatedBD, 4, BigDecimal.ROUND_UP); BigDecimal percentageGatedSelected = new BigDecimal(gatedSelected); BigDecimal totalGatedSelectedBD = new BigDecimal(total); percentageGatedSelected = percentageGatedSelected.divide(totalGatedSelectedBD, 4, BigDecimal.ROUND_UP); // System.out.println("PROFILING: gate fraction: " + percentage.toString()); if (impoverlay.getWidth() > 256) { TextRoi textTotal = new TextRoi(5, 10, selected + "/" + total + " gated (" + 100 * percentage.doubleValue() + "%)"); if (gated > 0) { textTotal = new TextRoi(5, 10, selected + "/" + total + " total (" + 100 * percentage.doubleValue() + "%)" + "; " + gated + "/" + total + " roi (" + 100 * percentageGated.doubleValue() + "%)" + "; " + gatedSelected + "/" + total + " overlap (" + 100 * percentageGatedSelected.doubleValue() + "%)", f); } //TextRoi textImageGated = new TextRoi(5, 18, selected + "/" + total + " gated objects (" + 100 * percentage.doubleValue() + "%)", f); textTotal.setPosition(i); //textImageGated.setPosition(i); overlay.add(textTotal); } else { f = new Font("Arial", Font.PLAIN, 10); TextRoi line1 = new TextRoi(5, 5, selected + "/" + total + " gated" + "(" + 100 * percentage.doubleValue() + "%)", f); overlay.add(line1); if (gated > 0) { f = new Font("Arial", Font.PLAIN, 10); TextRoi line2 = new TextRoi(5, 18, gated + "/" + total + " roi (" + 100 * percentageGated.doubleValue() + "%)", f); overlay.add(line2); TextRoi line3 = new TextRoi(5, 31, gatedSelected + "/" + total + " overlap (" + 100 * percentageGatedSelected.doubleValue() + "%)", f); overlay.add(line3); } line1.setPosition(i); } } impoverlay.setOverlay(overlay); //ImagePlus gateMaskImage = new ImagePlus("gates", gateOverlay); //gateMaskImage.show(); gate.setGateOverlayStack(gateOverlay); } impoverlay.draw(); impoverlay.setTitle(this.getTitle()); if (impoverlay.getDisplayMode() != IJ.COMPOSITE) { impoverlay.setDisplayMode(IJ.COMPOSITE); } if (impoverlay.getSlice() == 1) { impoverlay.setZ(Math.round(impoverlay.getNSlices() / 2)); } else { impoverlay.setSlice(impoverlay.getSlice()); } impoverlay.show(); } }