/** Creates the images composing the grid when the color model is <code>GreyScale</code>. */
private void createGridImagesForGreyScale() {
int maxC = parent.getMaxC();
List l = parent.getActiveChannelsInGrid();
int n = l.size();
clearList(gridImages);
if (combinedImage != null) combinedImage.flush();
switch (n) {
case 0:
for (int i = 0; i < maxC; i++) gridImages.add(null);
combinedImage = null;
break;
case 1:
case 2:
case 3:
if (isImageMappedRGB(l)) {
BufferedImage image = parent.getCombinedGridImage();
if (image == null) {
for (int i = 0; i < maxC; i++) gridImages.add(null);
break;
}
combinedImage = Factory.magnifyImage(gridRatio, image);
int w = combinedImage.getWidth();
int h = combinedImage.getHeight();
DataBuffer buf = combinedImage.getRaster().getDataBuffer();
List<ChannelData> list = parent.getSortedChannelData();
Iterator<ChannelData> i = list.iterator();
int index;
while (i.hasNext()) {
index = i.next().getIndex();
if (l.contains(index)) {
if (parent.isChannelRed(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.RED_MASK, Factory.RED_MASK, Factory.RED_MASK));
} else if (parent.isChannelGreen(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.GREEN_MASK, Factory.GREEN_MASK, Factory.GREEN_MASK));
} else if (parent.isChannelBlue(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.BLUE_MASK, Factory.BLUE_MASK, Factory.BLUE_MASK));
}
} else {
gridImages.add(null);
}
}
} else {
retrieveGridImagesForGreyScale(l);
}
break;
default:
retrieveGridImagesForGreyScale(l);
}
}
/** Creates the images composing the grid. */
private void createGridImages() {
// if (combinedImage == null) return;
if (originalGridImages == null) originalGridImages = new ArrayList<BufferedImage>();
clearList(gridImages);
if (ImViewer.GREY_SCALE_MODEL.equals(parent.getColorModel())) {
createGridImagesForGreyScale();
return;
}
List l = parent.getActiveChannels();
int maxC = parent.getMaxC();
switch (l.size()) {
case 0:
for (int i = 0; i < maxC; i++) gridImages.add(null);
break;
case 1:
case 2:
case 3:
if (isImageMappedRGB(l) && !parent.isCompressed()) {
combinedImage = null;
combinedImage = Factory.magnifyImage(gridRatio, renderedImage);
int w = combinedImage.getWidth();
int h = combinedImage.getHeight();
DataBuffer buf = combinedImage.getRaster().getDataBuffer();
List<ChannelData> list = parent.getSortedChannelData();
Iterator<ChannelData> i = list.iterator();
int index;
while (i.hasNext()) {
index = i.next().getIndex();
if (parent.isChannelActive(index)) {
if (parent.isChannelRed(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.RED_MASK, Factory.BLANK_MASK, Factory.BLANK_MASK));
} else if (parent.isChannelGreen(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.BLANK_MASK, Factory.GREEN_MASK, Factory.BLANK_MASK));
} else if (parent.isChannelBlue(index)) {
gridImages.add(
Factory.createBandImage(
buf, w, h, Factory.BLANK_MASK, Factory.BLANK_MASK, Factory.BLUE_MASK));
}
} else {
gridImages.add(null);
}
}
} else {
retrieveGridImages();
}
break;
default:
retrieveGridImages();
}
}
/**
* Retrieves the images composing the grid when the color model is <code>RBG</code> and when the
* channels are not mapped to red, green or blue i.e. a channel mapped to yellow.
*/
private void retrieveGridImages() {
List<BufferedImage> images = parent.getGridImages();
if (images != null) {
Iterator<BufferedImage> i = images.iterator();
boolean b = originalGridImages.size() == 0;
BufferedImage img;
while (i.hasNext()) {
img = i.next();
gridImages.add(Factory.magnifyImage(img, gridRatio, 0));
if (b) originalGridImages.add(img);
}
combinedImage = Factory.magnifyImage(renderedImage, gridRatio, 0);
}
}
/**
* Sets the ratio of the grid image.
*
* @param gridRatio The value to set.
*/
void setGridRatio(double gridRatio) {
// if (ratio == 1) return; //We don't want to be too small.
double max = ZoomGridAction.MAX_ZOOM_FACTOR;
if (gridRatio > max) return;
this.gridRatio = gridRatio;
if (ImViewerAgent.hasOpenGLSupport()) return;
if (CollectionUtils.isEmpty(originalGridImages)) {
try {
createGridImages();
} catch (Exception e) {
handleGridImageCreationException(e);
}
return;
}
int n = originalGridImages.size();
clearList(gridImages);
int maxC = parent.getMaxC();
switch (n) {
case 0:
for (int i = 0; i < maxC; i++) gridImages.add(null);
break;
case 1:
case 2:
case 3:
// TODO: Review that code.
if (isImageMappedRGB(parent.getActiveChannels())) {
try {
createGridImages();
} catch (Exception e) {
handleGridImageCreationException(e);
}
} else {
combinedImage = null;
combinedImage = Factory.magnifyImage(gridRatio, renderedImage);
Iterator<BufferedImage> i = originalGridImages.iterator();
while (i.hasNext()) {
gridImages.add(Factory.magnifyImage(gridRatio, i.next()));
}
}
break;
default:
combinedImage = null;
combinedImage = Factory.magnifyImage(gridRatio, renderedImage);
Iterator<BufferedImage> i = originalGridImages.iterator();
while (i.hasNext()) {
gridImages.add(Factory.magnifyImage(gridRatio, i.next()));
}
}
}
/**
* Loads the thumbnails for the passed collection of files.
*
* @param files The collection of files to handle.
*/
private void loadFSThumbnails(List files) {
List result = new ArrayList();
try {
ExperimenterData exp = (ExperimenterData) context.lookup(LookupNames.CURRENT_USER_DETAILS);
long id = exp.getId();
Map<DataObject, BufferedImage> m = service.getFSThumbnailSet(ctx, files, maxLength, id);
Entry<DataObject, BufferedImage> entry;
Iterator<Entry<DataObject, BufferedImage>> i = m.entrySet().iterator();
BufferedImage thumb;
DataObject obj;
boolean valid = true;
FileData f;
while (i.hasNext()) {
entry = i.next();
obj = entry.getKey();
thumb = entry.getValue();
if (thumb == null) {
thumb = Factory.createDefaultImageThumbnail(Factory.IMAGE_ICON);
}
if (obj.getId() > 0) result.add(new ThumbnailData(obj.getId(), thumb, valid));
else result.add(new ThumbnailData(obj, thumb, valid));
}
currentThumbs = result;
} catch (Exception e) {
currentThumbs = result;
context.getLogger().error(this, "Cannot retrieve thumbnail: " + e.getMessage());
}
}
/**
* Creates a concrete loader.
*
* @see DataBrowserModel#createDataLoader(boolean, Collection)
*/
protected List<DataBrowserLoader> createDataLoader(boolean refresh, Collection ids) {
if (!withThumbnails) return null;
List<ImageDisplay> l = getNodes();
Iterator<ImageDisplay> i = l.iterator();
ImageSet node;
List<DataObject> images = new ArrayList<DataObject>();
ImageNode selected;
WellSampleData data;
Thumbnail thumb;
while (i.hasNext()) {
node = (ImageSet) i.next();
if (node instanceof WellImageSet) {
selected = ((WellImageSet) node).getSelectedWellSample();
data = (WellSampleData) selected.getHierarchyObject();
if (data.getId() < 0) {
thumb = selected.getThumbnail();
thumb.setValid(false);
thumb.setFullScaleThumb(
Factory.createDefaultImageThumbnail(wellDimension.width, wellDimension.height));
} else images.add(data.getImage());
}
}
if (images.size() == 0) return null;
return createThumbnailsLoader(sorter.sort(images));
}
/**
* Retrieves the images composing the grid when the color model is <code>GreyScale</code> and when
* the channels are not mapped to red, green or blue i.e. a channel mapped to yellow.
*
* @param channels Collection of active channels in the grid.
*/
private void retrieveGridImagesForGreyScale(List channels) {
List<BufferedImage> images = parent.getGridImages();
if (images != null) {
int last = images.size() - 1;
combinedImage = Factory.magnifyImage(gridRatio, images.get(last));
images.remove(last);
Iterator<BufferedImage> i = images.iterator();
boolean b = originalGridImages.size() == 0 && !isImageMappedRGB(channels);
BufferedImage img;
while (i.hasNext()) {
img = i.next();
gridImages.add(Factory.magnifyImage(gridRatio, img));
if (b) originalGridImages.add(img);
}
}
}
/**
* Sets the image representing the file.
*
* @param path The path to the file.
*/
void setThumbnail(String path) {
if (path == null) return;
this.thumbnail =
Factory.createIcon(path, Factory.THUMB_DEFAULT_WIDTH / 2, Factory.THUMB_DEFAULT_HEIGHT / 2);
if (thumbnail != null) {
label.setText("");
label.setIcon(thumbnail);
label.repaint();
revalidate();
repaint();
}
}
/**
* Writes the image.
*
* @param image The image to write to the file.
* @param n The name of the image.
* @throws EncoderException
* @throws IOException
*/
private void writeImage(BufferedImage image, String n) throws EncoderException, IOException {
// n += "."+format;
String extendedName = getExtendedName(n, format);
File f = new File(extendedName);
if (TIFFFilter.TIF.equals(format)) {
Encoder encoder =
new TIFFEncoder(
Factory.createImage(image), new DataOutputStream(new FileOutputStream(f)));
WriterImage.saveImage(encoder);
} else WriterImage.saveImage(f, image, format);
close();
}
/**
* Creates the {@link #displayedImage}. The method should be invoked after the {@link
* #setRenderedImage(BufferedImage)} method.
*/
void createDisplayedProjectedImage() {
if (projectedImage == null) return;
if (displayedProjectedImage != null) displayedProjectedImage.flush();
if (zoomFactor != ZoomAction.DEFAULT_ZOOM_FACTOR) {
BufferedImage img = null;
try {
img = Factory.magnifyImage(projectedImage, zoomFactor, 0);
} catch (Throwable e) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
un.notifyInfo("Magnification", "An error occurred while magnifying the image.");
}
if (img != null) displayedProjectedImage = img;
} else displayedProjectedImage = projectedImage;
}
/**
* Creates a concrete loader.
*
* @param row The row identifying the well.
* @param column The column identifying the well.
* @return See above.
*/
DataBrowserLoader createFieldsLoader(int row, int column) {
List<ImageDisplay> l = getNodes();
Iterator<ImageDisplay> i = l.iterator();
ImageSet node;
List<DataObject> images = new ArrayList<DataObject>();
WellSampleData data;
Thumbnail thumb;
WellImageSet wis;
List<WellSampleNode> nodes;
Iterator<WellSampleNode> j;
WellSampleNode n;
if (selectedNodes != null) selectedNodes.clear();
while (i.hasNext()) {
node = (ImageSet) i.next();
if (node instanceof WellImageSet) {
wis = (WellImageSet) node;
if (wis.getRow() == row && wis.getColumn() == column) {
setSelectedWell(wis);
nodes = wis.getWellSamples();
j = nodes.iterator();
while (j.hasNext()) {
n = j.next();
data = (WellSampleData) n.getHierarchyObject();
if (data.getId() < 0) {
thumb = n.getThumbnail();
thumb.setValid(false);
thumb.setFullScaleThumb(
Factory.createDefaultImageThumbnail(wellDimension.width, wellDimension.height));
} else images.add(data.getImage());
}
}
}
}
if (images.size() == 0) return null;
return new ThumbnailFieldsLoader(component, ctx, images, row, column);
}
/**
* Sets the photo of the user.
*
* @param image The image to set.
*/
void setUserPhoto(BufferedImage image) {
if (image == null) return;
BufferedImage img = Factory.scaleBufferedImage(image, UserProfileCanvas.WIDTH);
userPicture.setImage(img);
}
/**
* Creates a default thumbnail for the passed pixels set.
*
* @param pxd The pixels set to handle.
* @return See above.
*/
private BufferedImage createDefaultImage(PixelsData pxd) {
if (pxd == null) return Factory.createDefaultImageThumbnail(-1);
Dimension d =
Factory.computeThumbnailSize(maxLength, maxLength, pxd.getSizeX(), pxd.getSizeY());
return Factory.createDefaultImageThumbnail(d.width, d.height);
}
/** Save the results to an Excel File. */
private void saveResults() {
channelsSelectionForm = new ChannelSelectionForm(channelName);
FileChooser chooser = view.createSaveToExcelChooser();
chooser.addComponentToControls(channelsSelectionForm);
int results = chooser.showDialog();
if (results != JFileChooser.APPROVE_OPTION) return;
File file = chooser.getFormattedSelectedFile();
// TODO: Modify that code when we have various writer.
if (!file.getAbsolutePath().endsWith(ExcelFilter.EXCEL)) {
String fileName = file.getAbsolutePath() + "." + ExcelFilter.EXCEL;
file = new File(fileName);
}
List<Integer> channels = channelsSelectionForm.getUserSelection();
if (channels == null || channels.size() == 0) {
UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier();
un.notifyInfo("Save Results", " Please select at least a channel.");
view.setStatus("No Channel selected to output.");
return;
}
try {
ExcelWriter writer = new ExcelWriter(file.getAbsolutePath());
writer.openFile();
writer.createSheet("Channel Summary");
Iterator<Coord3D> coordMapIterator = shapeMap.keySet().iterator();
Coord3D currentCoord;
int n = channels.size();
Integer channel;
if (channelSummarySelected(channels)) outputSummary(writer, shapeMap);
BufferedImage originalImage = model.getRenderedImage();
if (originalImage != null) {
BufferedImage image = Factory.copyBufferedImage(originalImage);
// Add the ROI for the current plane to the image.
// TODO: Need to check that.
model.setAttributes(MeasurementAttributes.SHOWID, true);
model.getDrawingView().print(image.getGraphics());
model.setAttributes(MeasurementAttributes.SHOWID, false);
try {
writer.addImageToWorkbook("ThumbnailImage", image);
} catch (Exception e) {
// TODO
}
int col = writer.getMaxColumn(0);
writer.writeImage(0, col + 1, 256, 256, "ThumbnailImage");
}
if (channelSummarySelected(channels) && channels.size() != 1)
while (coordMapIterator.hasNext()) {
currentCoord = coordMapIterator.next();
for (int i = 0; i < n; i++) {
channel = channels.get(i);
if (channel == ChannelSelectionForm.SUMMARYVALUE) continue;
if (!nameMap.containsKey(channelName.get(channel))) continue;
int rowIndex = 0;
writer.createSheet("Channel Number " + channelName.get(channel));
writeHeader(writer, rowIndex, currentCoord);
channel = nameMap.get(channelName.get(channel));
writeData(writer, rowIndex, currentCoord, channel.intValue());
}
}
writer.close();
} catch (Exception e) {
Logger logger = MeasurementAgent.getRegistry().getLogger();
logger.error(this, "Cannot save ROI results: " + e.toString());
UserNotifier un = MeasurementAgent.getRegistry().getUserNotifier();
String message = "An error occurred while trying to" + " save the data.\nPlease try again.";
if (e instanceof NumberFormatException) {
message =
"We only support the British/American style of "
+ "representing numbers,\nusing a decimal point rather "
+ "than a comma.";
}
un.notifyInfo("Save Results", message);
return;
}
Registry reg = MeasurementAgent.getRegistry();
UserNotifier un = reg.getUserNotifier();
un.notifyInfo("Save ROI results", "The ROI results have been " + "successfully saved.");
}