/** Creates the images composing the grid. */
private void createGridImagesAsTextures() {
if (parent.getColorModel().equals(ImViewer.GREY_SCALE_MODEL)) {
if (!hasGridImagesAsTexture()) {
clearTextureMap(gridImagesAsTextures);
gridImagesAsTextures = parent.getGridImagesAsTexture();
}
} else {
clearTextureMap(gridImagesAsTextures);
gridImagesAsTextures = parent.getGridImagesAsTexture();
}
}
/** 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();
}
}
/**
* 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()));
}
}
}
/**
* Returns the number of row for the grid.
*
* @return See above.
*/
int getGridRow() {
int n = parent.getMaxC();
if (n == 1) return 1;
if (n == 2 || n == 3) return 2;
int row = n / 2;
if (n % 2 != 0) row += 1;
return row;
}
/** 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);
}
}
/**
* 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);
}
}
/**
* Returns the list of grid images for openGL.
*
* @return See above.
*/
List<GridImage> getGridImages() {
List<GridImage> list = new ArrayList<GridImage>();
List<ChannelData> l = parent.getSortedChannelData();
Iterator<ChannelData> i = l.iterator();
int index;
GridImage image;
// boolean[] rgb;
ChannelData data;
String label;
boolean b = isRenderedImageRGB();
if (!isModelRGB()) b = false;
while (i.hasNext()) {
data = i.next();
index = data.getIndex();
label = data.getChannelLabeling();
// rgb = new boolean[3];
if (parent.isChannelActive(index)) {
/*
if (b) {
rgb[0] = !parent.isChannelRed(index);
rgb[1] = !parent.isChannelGreen(index);
rgb[2] = !parent.isChannelBlue(index);
image = new GridImage(index, true, label, rgb);
} else {
image = new GridImage(index, true, label);
image.setTextureData(gridImagesAsTextures.get(index));
}
*/
image = new GridImage(index, true, label);
image.setTextureData(gridImagesAsTextures.get(index));
} else {
image = new GridImage(index, false, label);
}
list.add(image);
}
return list;
}
/**
* Creates a single image.
*
* @param image The image to create.
* @param constraint The constraint indicating to add the scale bar.
* @param name The name of the image.
* @throws EncoderException
* @throws IOException
*/
private void writeSingleImage(BufferedImage image, boolean constraint, String name)
throws EncoderException, IOException {
int width = image.getWidth();
int h = image.getHeight();
String v = getUnitBarValue();
int s = (int) model.getUnitBarSize();
BufferedImage newImage = new BufferedImage(width, h, BufferedImage.TYPE_INT_RGB);
Graphics2D g2 = (Graphics2D) newImage.getGraphics();
ImagePaintingFactory.setGraphicRenderingSettings(g2);
// Paint the original image.
g2.drawImage(image, null, 0, 0);
if (constraint) ImagePaintingFactory.paintScaleBar(g2, width - s - 10, h - 10, s, v);
writeImage(newImage, name);
}
/**
* 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);
}
}
}
/**
* Returns the size of the grid.
*
* @return See above.
*/
Dimension getGridSize() {
int w = (int) (getMaxX() * gridRatio);
int h = (int) (getMaxY() * gridRatio);
int n = parent.getMaxC();
int row = 0;
int col = 0;
if (n == 1) {
row = 1;
col = 2;
} else if (n == 2 || n == 3) {
row = 2;
col = 2;
} else {
col = 3;
row = n / 2;
if (n % 2 != 0) row += 1;
}
return new Dimension(col * w + (col - 1) * GAP, row * h + (row - 1) * GAP);
}
/**
* Returns a collection of images composing the grid.
*
* @return See above.
*/
List<SplitImage> getSplitImages() {
if (splitImages == null) splitImages = new ArrayList<SplitImage>();
else splitImages.clear();
String n;
splitImages = new ArrayList<SplitImage>();
List<ChannelData> list = parent.getSortedChannelData();
Iterator<ChannelData> i = list.iterator();
ChannelData channel;
int j = 0;
int size = gridImages.size();
while (i.hasNext()) {
channel = i.next();
n = PREFIX + channel.getChannelLabeling();
if (j >= size) splitImages.add(new SplitImage(null, n));
else splitImages.add(new SplitImage(gridImages.get(j), n));
j++;
}
splitImages.add(new SplitImage(combinedImage, COMBINED));
return splitImages;
}
/**
* Sets the selected XY-plane. A new plane is then rendered.
*
* @param z The selected z-section.
* @param t The selected timepoint.
*/
void setSelectedXYPlane(int z, int t) {
parent.setSelectedXYPlane(z, t);
}
/**
* Returns <code>true</code> if the textual information is painted on top of the grid image,
* <code>false</code> otherwise.
*
* @return See above.
*/
boolean isTextVisible() {
return parent.isTextVisible();
}
/**
* Returns the index of the selected pane.
*
* @return See above.
*/
int getSelectedIndex() {
return parent.getSelectedIndex();
}
/**
* Returns the size of the tiled image along the Y-axis i.e. the size of a tile along the Y-axis
* multiplied by the number of rows.
*
* @return See above.
*/
int getTiledImageSizeY() {
return parent.getTiledImageSizeY();
}
/**
* Loads the tiles.
*
* @param r The selected rectangle.
*/
void loadTiles(Rectangle r) {
parent.loadTiles(r);
}
/**
* Returns the size of the unit bar.
*
* @return See above.
*/
double getUnitBarSize() {
return model.getUnitBarSize();
}
/**
* Returns <code>true</code> if the unit bar is painted on top of the displayed image, <code>false
* </code> otherwise.
*
* @return See above.
*/
boolean isUnitBar() {
return model.isUnitBar();
}
/**
* Returns the name of the image.
*
* @return See above.
*/
String getPartialImageName() {
return UIUtilities.removeFileExtension(model.getImageName());
}
/**
* Sets the value of the flag controlling if the unit bar is painted or not.
*
* @param unitBar Pass <code>true</code> to paint the unit bar, <code>false</code> otherwise.
*/
void setUnitBar(boolean unitBar) {
double v = EditorUtil.transformSize(parent.getPixelsSizeX()).getValue();
if (v == 0 || v == 1) unitBar = false;
this.unitBar = unitBar;
}
/**
* Returns the number of timepoints.
*
* @return See above.
*/
int getMaxT() {
return parent.getRealT();
}
/**
* Returns <code>true</code> if the active channels are mapped to <code>Red</code>, <code>Green
* </code> or <code>Blue</code>, <code>false</code> only and exclusively, if the number of active
* channels is 0 or greater than 3.
*
* @param channels The collection of channels to handle.
* @return See above.
*/
private boolean isImageMappedRGB(List channels) {
return parent.isMappedImageRGB(channels);
}
/**
* Displays the preview dialog with images depending on the saving type.
*
* @param savingType The type of saving.
*/
private void createImages(int savingType) {
boolean b = uiDelegate.includeROI();
switch (savingType) {
default:
case ImgSaverUI.IMAGE:
imageType = ImgSaverUI.IMAGE;
mainImage = model.getDisplayedImage(b);
imageComponents = null;
break;
case ImgSaverUI.GRID_IMAGE:
imageType = ImgSaverUI.GRID_IMAGE;
mainImage = model.getGridImage();
imageComponents = null;
break;
case ImgSaverUI.PROJECTED_IMAGE:
imageType = ImgSaverUI.PROJECTED_IMAGE;
mainImage = model.getDisplayedProjectedImage();
imageComponents = null;
break;
case ImgSaverUI.IMAGE_AND_COMPONENTS:
imageType = ImgSaverUI.IMAGE_AND_COMPONENTS;
mainImage = model.getDisplayedImage(b);
imageComponents = model.getImageComponents(ImViewer.RGB_MODEL, b);
break;
case ImgSaverUI.IMAGE_AND_COMPONENTS_GREY:
imageType = ImgSaverUI.IMAGE_AND_COMPONENTS;
mainImage = model.getDisplayedImage(b);
imageComponents = model.getImageComponents(ImViewer.GREY_SCALE_MODEL, b);
break;
case ImgSaverUI.LENS_IMAGE:
imageType = ImgSaverUI.LENS_IMAGE;
mainImage = model.getZoomedLensImage();
imageComponents = null;
break;
case ImgSaverUI.LENS_IMAGE_AND_COMPONENTS:
imageType = ImgSaverUI.LENS_IMAGE_AND_COMPONENTS;
mainImage = model.getZoomedLensImage();
imageComponents = model.getLensImageComponents(ImViewer.RGB_MODEL);
break;
case ImgSaverUI.LENS_IMAGE_AND_COMPONENTS_GREY:
imageType = ImgSaverUI.LENS_IMAGE_AND_COMPONENTS;
mainImage = model.getZoomedLensImage();
imageComponents = model.getLensImageComponents(ImViewer.GREY_SCALE_MODEL);
}
}
/**
* Returns the real timepoint.
*
* @return See above.
*/
int getRealSelectedT() {
return parent.getRealSelectedT();
}
/**
* Saves the displayed images.
*
* @param init Pass <code>true</code> to initialize the images to save, <code>false</code>
* otherwise.
*/
void saveImage(boolean init) {
UserNotifier un = ImViewerAgent.getRegistry().getUserNotifier();
if (init) createImages(uiDelegate.getSavingType());
// Builds the image to display.
boolean unitBar = model.isUnitBar();
String v = getUnitBarValue();
int s = (int) getUnitBarSize();
boolean constrain;
try {
String name = uiDelegate.getSelectedFilePath();
// make sure the parent directory paths all exist
FileUtils.forceMkdir(new File(name).getParentFile());
if (imageComponents == null) {
constrain =
unitBar && v != null && s < mainImage.getWidth() && imageType == ImgSaverUI.IMAGE;
writeSingleImage(mainImage, constrain, name);
} else {
if (mainImage == null) return;
Iterator i;
int h, w;
BufferedImage newImage;
Graphics2D g2;
if (uiDelegate.isSaveImagesInSeparatedFiles()) {
constrain =
unitBar && v != null && s < mainImage.getWidth() && imageType == ImgSaverUI.IMAGE;
writeSingleImage(mainImage, constrain, name);
i = imageComponents.iterator();
int j = 0;
while (i.hasNext()) {
constrain = unitBar && v != null && imageType != ImgSaverUI.LENS_IMAGE_AND_COMPONENTS;
writeSingleImage((BufferedImage) i.next(), constrain, name + "_" + j);
j++;
}
} else {
int width = mainImage.getWidth();
h = mainImage.getHeight();
int n = imageComponents.size();
w = width * (n + 1) + ImgSaverPreviewer.SPACE * (n - 1);
newImage = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
g2 = (Graphics2D) newImage.getGraphics();
g2.setColor(Color.WHITE);
ImagePaintingFactory.setGraphicRenderingSettings(g2);
// Paint the original image.
i = imageComponents.iterator();
int x = 0;
while (i.hasNext()) {
g2.drawImage((BufferedImage) i.next(), null, x, 0);
if (unitBar && v != null && imageType != ImgSaverUI.LENS_IMAGE_AND_COMPONENTS)
ImagePaintingFactory.paintScaleBar(g2, x + width - s - 10, h - 10, s, v);
x += width;
g2.fillRect(x, 0, ImgSaverPreviewer.SPACE, h);
x += ImgSaverPreviewer.SPACE;
}
g2.drawImage(mainImage, null, x, 0);
if (unitBar
&& v != null
&& !(imageType == ImgSaverUI.LENS_IMAGE_AND_COMPONENTS
|| imageType == ImgSaverUI.LENS_IMAGE))
ImagePaintingFactory.paintScaleBar(g2, x + width - s - 10, h - 10, s, v);
writeImage(newImage, name);
}
}
} catch (Exception e) {
if (e instanceof IOException || e.getCause() instanceof IOException)
un.notifyInfo(
"Save Image failure",
"Could not access file "
+ uiDelegate.getSelectedFilePath()
+ "\nMake sure you have the necessary permissions to perform this action.");
else un.notifyError("Save Image failure", "An error occurred while saving the image.", e);
return;
}
notifySave(getExtendedName(uiDelegate.getSelectedFilePath(), format));
if (uiDelegate.isSetDefaultFolder())
UIUtilities.setDefaultFolder(uiDelegate.getCurrentDirectory());
}
/**
* Returns the default z-section.
*
* @return See above.
*/
int getDefaultZ() {
return parent.getDefaultZ();
}
/**
* Returns the value (with two decimals) of the unit bar or <code>null</code> if the actual value
* is <i>negative</i>.
*
* @return See above.
*/
String getUnitBarValue() {
return model.getUnitBarValue();
}
/**
* Returns the number of pixels along the Y-axis.
*
* @return See above.
*/
int getMaxY() {
return parent.getMaxY();
}
/**
* Returns the color of the unit bar.
*
* @return See above.
*/
Color getUnitBarColor() {
return model.getUnitBarColor();
}
/**
* Returns the size in microns of a pixel along the Y-axis.
*
* @return See above.
*/
double getPixelsSizeZ() {
return parent.getPixelsSizeZ();
}