<br>
<span class="section">Views</span><br>
It is sometimes useful to view the segmentation results in different
-ways. The default selected view is the "Combined" view; it shows the
+ways. The default selected view is the "Segmented" view; it shows the
image, its highlighted segmentation, and any current foreground and background markup lines...all overlayed on
the same image. Using the drop-down menu, you can select a different
view:<br>
<ul>
-<li><span style="font-style: italic;">Combined</span>:
+<li><span style="font-style: italic;">Segmented</span>:
Shows the image with foreground areas brightened and background areas
darkened. Any current foreground and background annotation marks are overlayed.</li>
<li><span style="font-style: italic;">Original:</span>
status(AppStatus.Information, "Location [%4d,%4d] Color [%3d,%3d,%3d]",pt.x, pt.y, c.red, c.green, c.blue);
if(view.getContext().isEnabled())
{
- if(view.getContext().getEnabledMask().getImageData().getPixel(pt.x,pt.y) != 0 && (view.getPainter().getName().equals("Combined")) && SegmentationView.getLabelMode())
+ if(view.getContext().getEnabledMask().getImageData().getPixel(pt.x,pt.y) != 0 && (view.getPainter().getName().equals("Segmented")) && SegmentationView.getLabelMode())
{
String segmentName = view.getContext().getEnabledMask().ontologyTerm.getName();
view.getCanvas().setToolTipText(segmentName);
for (String s: Application.DEFAULT_PLUGIN_SEARCH_PATH) {
System.out.println(s);
}
-
+
Display.setAppName(Application.APP_NAME);
check();
loadPlugins();
private void init() {
- add(new CombinedPainter());
+ add(new SegmentPainter());
add(new OriginalPainter());
/*
- * Commented different views of segmentation. Currently original and combined painter are enabled
+ * Commented different views of segmentation. Currently original and Segment painter are enabled
*/
//add(new MarkupPainter());
//add(new MaskPainter());
*/
public void resetView() {
Tool.LabelMode.action.setChecked(false);
- resetViewSelectionToolbar(painters.get("Combined"));
-
+ resetViewSelectionToolbar(painters.get("Segmented"));
+ //panini
// clear metadata
comboLabel.removeAll();
comboLabel.setEnabled(false);
Assign the label to the segment on clicking assign button and update the image segment.
*/
private void assignLabel() {
- SegmentationPainter painter = painters.get("Combined");
+ SegmentationPainter painter = painters.get("Segmented");
+ //panini
setPainter(painter);
}
setLayout(new FillLayout());
view = new ImageControl(this, SWT.NONE);
listeners = new ArrayList<ContextChangeListener>(2);
- painter = new CombinedPainter();
+ painter = new SegmentPainter();
view.getCanvas().addMouseMoveListener(cursorChanger);
addDisposeListener(disposeListener);
}
import java.util.logging.Logger;
import java.util.zip.*;
-import javax.xml.bind.DatatypeConverter;
+//import javax.xml.bind.DatatypeConverter;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import org.eclipse.swt.widgets.Display;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
-import org.w3c.dom.Node;
+//import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
package ie.dcu.segment;
import ie.dcu.matrix.ByteMatrix;
-import ie.dcu.segment.annotate.Annotation;
+//import ie.dcu.segment.annotate.Annotation;
import ie.dcu.segment.annotate.AnnotationManager;
-import ie.dcu.segment.annotate.AnnotationType;
+//import ie.dcu.segment.annotate.AnnotationType;
import ie.dcu.apps.ist.labelling.OntologyTerm;
+++ /dev/null
-package ie.dcu.segment.painters;
-
-import ie.dcu.segment.*;
-import ie.dcu.swt.ObservableImage;
-
-import org.eclipse.swt.graphics.*;
-import org.eclipse.swt.widgets.*;
-
-/**
- * An overlaid view of the image, segmentation mask, and markup.
- *
- * @author Kevin McGuinness
- */
-public class CombinedPainter implements SegmentationPainter {
- public static final String NAME = "Combined";
-
- private ImageData maskBorderData;
- private Image maskBorderImage;
-
-
- public String getName() {
- return NAME;
- }
-
-
- public String getDescription() {
- return "An overlaid view of the image, segmentation mask, and markup";
- }
-
- public ImageData getMaskData(SegmentationContext ctx) {
- /*for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
- {
- if(segmentMask.enabled == true)
- {
- return segmentMask.getImageData();
- }
- }*/
- return maskBorderData;
- }
-
- public void paint(SegmentationContext ctx, ObservableImage im) {
-
- GC gc = im.beginPaint();
- // Paint image
- gc.drawImage(ctx.getImage(), 0, 0);
- int numberOfMaskObjects = ctx.getSegmentationMasks().size();
- // Paint all masks and its borders skipping the enabled mask.
- if(numberOfMaskObjects > 0)
- {
- // For drawing all the disabled masks.
- for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
- {
- if(segmentMask.enabled != true)
- {
- createVisibleMask(segmentMask,false);
- gc.drawImage(segmentMask.maskImage, 0, 0);
- createVisibleMaskBorder(segmentMask);
- gc.drawImage(maskBorderImage, 0, 0);
- }
- }
- // For drawing the enabled mask and its border..
- for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
- {
- // Blending of background pixel values while pasting the last mask only
- if(segmentMask.enabled == true)
- {
- createVisibleMask(segmentMask,true);
- gc.drawImage(segmentMask.maskImage, 0, 0);
- createVisibleMaskBorder(segmentMask);
- gc.drawImage(maskBorderImage, 0, 0);
- }
- }
- // Current mask which has not yet been made into an object
- createVisibleMask(ctx.getMask(),false);
- gc.drawImage(ctx.getMask().getImage(), 0, 0);
- createVisibleMaskBorder(ctx.getMask());
- gc.drawImage(maskBorderImage, 0, 0);
-
- }
- // Very initial mask, which has not yet been turned into an object.
- else
- {
- createVisibleMask(ctx.getMask(),true);
- gc.drawImage(ctx.getMask().getImage(), 0, 0);
- createVisibleMaskBorder(ctx.getMask());
- gc.drawImage(maskBorderImage, 0, 0);
- }
- // Paint all annotations
- ctx.getAnnotations().paint(im);
-
- // Commit changes
- im.endPaint();
- }
-
- /**
- *
- * @param mask
- * Mask object to be drawn.
- * @param isFirstObject
- * If set to <code>True</code> will blend the background and fore ground pixels.
- */
- private void createVisibleMask(SegmentationMask mask,boolean enabled) {
-
- dispose();
-
- if (isNewMaskDataRequired(mask)) {
- mask.maskImageData = createMaskData(mask.getBounds());
- }
- byte main_index = 9;
- // Blit in pixels
- for (int y = 0, i = 0; y < mask.height; y++) {
- int rowOffset = y * mask.maskImageData.bytesPerLine;
- for (int x = 0; x < mask.width; x++) {
- byte alpha, index;
- switch (mask.values[i]) {
- case SegmentationMask.BACKGROUND:
- alpha = enabled ? (byte) 128 : (byte) 0;
- index = 0;
- break;
- case SegmentationMask.FOREGROUND:
- alpha = (byte) 128;
- index = (byte) (mask.layerNumber%3+1);
- break;
- default:
- alpha = 0;
- index = 0;
- break;
- }
-
- // The SWT ImageData buffer doesn't usually have it's rows aligned
- // contiguously in memory (i.e. there are > width bytes per scan-line in
- // the buffer), so we can't directly copy in at the same index as the
- // mask.
- mask.maskImageData.data[x + rowOffset] = index;
-
- // However, the alpha data is always aligned correctly
- mask.maskImageData.alphaData[i] = alpha;
-
- // Next location in the mask
- i++;
- main_index = index;
- }
- }
- // Create new mask
- mask.maskImage = new Image(Display.getCurrent(), mask.maskImageData);
- }
-
- private void createVisibleMaskBorder(SegmentationMask mask) {
- dispose();
-
- if (isNewMaskBorderDataRequired(mask.getBounds())) {
- maskBorderData = createMaskBorderData(mask.getBounds());
- }
-
- // Set pixels
- byte[] buff = new byte[maskBorderData.width];
- for (int y = 0, i = 0; y < mask.height-1; y++) {
- for (int x = 0; x < mask.width-1; x++) {
- // Make transparent
- buff[x] = 0;
-
- // Current pixel
- byte pix1 = mask.values[i];
-
- // Neighbor to right & neighbor below
- byte pix2 = mask.values[i+1];
- byte pix3 = mask.values[i+mask.width];
-
- // Set pixel if either neighbor is different
- if (pix1 != pix2 || pix1 != pix3) {
- buff[x] = 1;
- }
-
- // Next pixel
- i++;
- }
-
- if (mask.width != 0) {
- // Last pixel in row
- byte pix1 = mask.values[i];
- byte pix2 = mask.values[i+mask.width];
- buff[mask.width-1] = (pix1 != pix2) ? (byte) 1 : 0;
-
- // Next row
- i++;
- }
-
- // Blit pixels
- maskBorderData.setPixels(0, y, buff.length, buff, 0);
- }
-
- // Last row
- if (mask.height != 0) {
- int yoff = (mask.height - 1) * mask.width;
- for (int x = 0; x < mask.width-1; x++) {
- byte pix1 = mask.values[x+yoff];
- byte pix2 = mask.values[x+yoff+1];
- buff[x] = (pix1 != pix2) ? (byte) 1 : 0;
- }
-
- // Blit
- maskBorderData.setPixels(0, mask.height-1, buff.length, buff, 0);
- }
-
- // Create new maskBorder
- maskBorderImage = new Image(Display.getCurrent(), maskBorderData);
- }
-
- private boolean isNewMaskDataRequired(SegmentationMask mask) {
- if (mask.getImageData() == null) {
- return true;
- } else {
- return mask.getImageData().width != mask.getBounds().width || mask.getImageData().height != mask.getBounds().height;
- }
- }
-
- private boolean isNewMaskBorderDataRequired(Rectangle bounds) {
- if (maskBorderData == null) {
- return true;
- } else {
- return maskBorderData.width != bounds.width || maskBorderData.height != bounds.height;
- }
- }
-
- private static ImageData createMaskData(Rectangle bounds) {
- RGB[] colors = new RGB[] {
- new RGB(0, 0, 0),
- new RGB(255,180,180),
- new RGB(180,255,180),
- new RGB(180,180,255)
- };
-
- // Create 3 color indexed palette
- PaletteData palette = new PaletteData(colors);
-
- // Create 8 bit indexed image
- ImageData data = new ImageData(bounds.width, bounds.height, 8, palette);
-
- // Create alpha mask
- data.alphaData = new byte[bounds.width*bounds.height];
-
- // Create and return the image
- return data;
- }
-
- private static ImageData createMaskBorderData(Rectangle bounds) {
- RGB[] colors = new RGB[] {
- new RGB(255,255,255),
- new RGB(255,140,0)
- };
-
- // Create binary indexed palette
- PaletteData palette = new PaletteData(colors);
-
- // Create 1 bit indexed image
- ImageData data = new ImageData(
- bounds.width, bounds.height, 1, palette);
-
- // Set transparent pixel
- data.transparentPixel = 0;
-
- // Create and return the image
- return data;
- }
-
- public void dispose() {
-/* // Dispose mask
- if (maskImage != null) {
- if (!maskImage.isDisposed()) {
- maskImage.dispose();
- }
- maskImage = null;
- }
- if (maskBorderImage != null) {
- if (!maskBorderImage.isDisposed()) {
- maskBorderImage.dispose();
- }
- maskBorderImage = null;
- }*/
- }
-}
--- /dev/null
+package ie.dcu.segment.painters;
+
+import ie.dcu.segment.*;
+import ie.dcu.swt.ObservableImage;
+
+import org.eclipse.swt.graphics.*;
+import org.eclipse.swt.widgets.*;
+
+/**
+ * An overlaid view of the image, segmentation mask, and markup.
+ *
+ * @author Kevin McGuinness
+ */
+public class SegmentPainter implements SegmentationPainter {
+ public static final String NAME = "Segmented";
+ //here it applies
+ private ImageData maskBorderData;
+ private Image maskBorderImage;
+
+
+ public String getName() {
+ return NAME;
+ }
+
+
+ public String getDescription() {
+ return "An overlaid view of the image, segmentation mask, and markup";
+ }
+
+ public ImageData getMaskData(SegmentationContext ctx) {
+ /*for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
+ {
+ if(segmentMask.enabled == true)
+ {
+ return segmentMask.getImageData();
+ }
+ }*/
+ return maskBorderData;
+ }
+
+ public void paint(SegmentationContext ctx, ObservableImage im) {
+
+ GC gc = im.beginPaint();
+ // Paint image
+ gc.drawImage(ctx.getImage(), 0, 0);
+ int numberOfMaskObjects = ctx.getSegmentationMasks().size();
+ // Paint all masks and its borders skipping the enabled mask.
+ if(numberOfMaskObjects > 0)
+ {
+ // For drawing all the disabled masks.
+ for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
+ {
+ if(segmentMask.enabled != true)
+ {
+ createVisibleMask(segmentMask,false);
+ gc.drawImage(segmentMask.maskImage, 0, 0);
+ createVisibleMaskBorder(segmentMask);
+ gc.drawImage(maskBorderImage, 0, 0);
+ }
+ }
+ // For drawing the enabled mask and its border..
+ for(SegmentationMask segmentMask : ctx.getSegmentationMasks())
+ {
+ // Blending of background pixel values while pasting the last mask only
+ if(segmentMask.enabled == true)
+ {
+ createVisibleMask(segmentMask,true);
+ gc.drawImage(segmentMask.maskImage, 0, 0);
+ createVisibleMaskBorder(segmentMask);
+ gc.drawImage(maskBorderImage, 0, 0);
+ }
+ }
+ // Current mask which has not yet been made into an object
+ createVisibleMask(ctx.getMask(),false);
+ gc.drawImage(ctx.getMask().getImage(), 0, 0);
+ createVisibleMaskBorder(ctx.getMask());
+ gc.drawImage(maskBorderImage, 0, 0);
+
+ }
+ // Very initial mask, which has not yet been turned into an object.
+ else
+ {
+ createVisibleMask(ctx.getMask(),true);
+ gc.drawImage(ctx.getMask().getImage(), 0, 0);
+ createVisibleMaskBorder(ctx.getMask());
+ gc.drawImage(maskBorderImage, 0, 0);
+ }
+ // Paint all annotations
+ ctx.getAnnotations().paint(im);
+
+ // Commit changes
+ im.endPaint();
+ }
+
+ /**
+ *
+ * @param mask
+ * Mask object to be drawn.
+ * @param isFirstObject
+ * If set to <code>True</code> will blend the background and fore ground pixels.
+ */
+ private void createVisibleMask(SegmentationMask mask,boolean enabled) {
+
+ dispose();
+
+ if (isNewMaskDataRequired(mask)) {
+ mask.maskImageData = createMaskData(mask.getBounds());
+ }
+ //byte main_index;
+ // Blit in pixels
+ for (int y = 0, i = 0; y < mask.height; y++) {
+ int rowOffset = y * mask.maskImageData.bytesPerLine;
+ for (int x = 0; x < mask.width; x++) {
+ byte alpha, index;
+ switch (mask.values[i]) {
+ case SegmentationMask.BACKGROUND:
+ alpha = enabled ? (byte) 128 : (byte) 0;
+ index = 0;
+ break;
+ case SegmentationMask.FOREGROUND:
+ alpha = (byte) 128;
+ index = (byte) (mask.layerNumber%3+1);
+ break;
+ default:
+ alpha = 0;
+ index = 0;
+ break;
+ }
+
+ // The SWT ImageData buffer doesn't usually have it's rows aligned
+ // contiguously in memory (i.e. there are > width bytes per scan-line in
+ // the buffer), so we can't directly copy in at the same index as the
+ // mask.
+ mask.maskImageData.data[x + rowOffset] = index;
+
+ // However, the alpha data is always aligned correctly
+ mask.maskImageData.alphaData[i] = alpha;
+
+ // Next location in the mask
+ i++;
+ //main_index = index;
+ }
+ }
+ // Create new mask
+ mask.maskImage = new Image(Display.getCurrent(), mask.maskImageData);
+ }
+
+ private void createVisibleMaskBorder(SegmentationMask mask) {
+ dispose();
+
+ if (isNewMaskBorderDataRequired(mask.getBounds())) {
+ maskBorderData = createMaskBorderData(mask.getBounds());
+ }
+
+ // Set pixels
+ byte[] buff = new byte[maskBorderData.width];
+ for (int y = 0, i = 0; y < mask.height-1; y++) {
+ for (int x = 0; x < mask.width-1; x++) {
+ // Make transparent
+ buff[x] = 0;
+
+ // Current pixel
+ byte pix1 = mask.values[i];
+
+ // Neighbor to right & neighbor below
+ byte pix2 = mask.values[i+1];
+ byte pix3 = mask.values[i+mask.width];
+
+ // Set pixel if either neighbor is different
+ if (pix1 != pix2 || pix1 != pix3) {
+ buff[x] = 1;
+ }
+
+ // Next pixel
+ i++;
+ }
+
+ if (mask.width != 0) {
+ // Last pixel in row
+ byte pix1 = mask.values[i];
+ byte pix2 = mask.values[i+mask.width];
+ buff[mask.width-1] = (pix1 != pix2) ? (byte) 1 : 0;
+
+ // Next row
+ i++;
+ }
+
+ // Blit pixels
+ maskBorderData.setPixels(0, y, buff.length, buff, 0);
+ }
+
+ // Last row
+ if (mask.height != 0) {
+ int yoff = (mask.height - 1) * mask.width;
+ for (int x = 0; x < mask.width-1; x++) {
+ byte pix1 = mask.values[x+yoff];
+ byte pix2 = mask.values[x+yoff+1];
+ buff[x] = (pix1 != pix2) ? (byte) 1 : 0;
+ }
+
+ // Blit
+ maskBorderData.setPixels(0, mask.height-1, buff.length, buff, 0);
+ }
+
+ // Create new maskBorder
+ maskBorderImage = new Image(Display.getCurrent(), maskBorderData);
+ }
+
+ private boolean isNewMaskDataRequired(SegmentationMask mask) {
+ if (mask.getImageData() == null) {
+ return true;
+ } else {
+ return mask.getImageData().width != mask.getBounds().width || mask.getImageData().height != mask.getBounds().height;
+ }
+ }
+
+ private boolean isNewMaskBorderDataRequired(Rectangle bounds) {
+ if (maskBorderData == null) {
+ return true;
+ } else {
+ return maskBorderData.width != bounds.width || maskBorderData.height != bounds.height;
+ }
+ }
+
+ private static ImageData createMaskData(Rectangle bounds) {
+ RGB[] colors = new RGB[] {
+ new RGB(0, 0, 0),
+ new RGB(255,180,180),
+ new RGB(180,255,180),
+ new RGB(180,180,255)
+ };
+
+ // Create 3 color indexed palette
+ PaletteData palette = new PaletteData(colors);
+
+ // Create 8 bit indexed image
+ ImageData data = new ImageData(bounds.width, bounds.height, 8, palette);
+
+ // Create alpha mask
+ data.alphaData = new byte[bounds.width*bounds.height];
+
+ // Create and return the image
+ return data;
+ }
+
+ private static ImageData createMaskBorderData(Rectangle bounds) {
+ RGB[] colors = new RGB[] {
+ new RGB(255,255,255),
+ new RGB(255,140,0)
+ };
+
+ // Create binary indexed palette
+ PaletteData palette = new PaletteData(colors);
+
+ // Create 1 bit indexed image
+ ImageData data = new ImageData(
+ bounds.width, bounds.height, 1, palette);
+
+ // Set transparent pixel
+ data.transparentPixel = 0;
+
+ // Create and return the image
+ return data;
+ }
+
+ public void dispose() {
+/* // Dispose mask
+ if (maskImage != null) {
+ if (!maskImage.isDisposed()) {
+ maskImage.dispose();
+ }
+ maskImage = null;
+ }
+ if (maskBorderImage != null) {
+ if (!maskBorderImage.isDisposed()) {
+ maskBorderImage.dispose();
+ }
+ maskBorderImage = null;
+ }*/
+ }
+}
projects / old-jaiswallab-svn / .git / commitdiff