/**
* Creates a list of TIFF image files from an image file. It basically converts images of other
* formats to TIFF format, or a multi-page TIFF image to multiple TIFF image files.
*
* @param imageFile input image file
* @param index an index of the page; -1 means all pages, as in a multi-page TIFF image
* @return a list of TIFF image files
* @throws Exception
*/
public static List<File> createTiffFiles(File imageFile, int index) throws IOException {
List<File> tiffFiles = new ArrayList<File>();
String imageFileName = imageFile.getName();
String imageFormat = imageFileName.substring(imageFileName.lastIndexOf('.') + 1);
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(imageFormat);
ImageReader reader = readers.next();
if (reader == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
ImageInputStream iis = ImageIO.createImageInputStream(imageFile);
reader.setInput(iis);
// Read the stream metadata
// IIOMetadata streamMetadata = reader.getStreamMetadata();
// Set up the writeParam
TIFFImageWriteParam tiffWriteParam = new TIFFImageWriteParam(Locale.US);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// Get tif writer and set output to file
Iterator<ImageWriter> writers = ImageIO.getImageWritersByFormatName(TIFF_FORMAT);
ImageWriter writer = writers.next();
// Read the stream metadata
IIOMetadata streamMetadata = writer.getDefaultStreamMetadata(tiffWriteParam);
int imageTotal = reader.getNumImages(true);
for (int i = 0; i < imageTotal; i++) {
// all if index == -1; otherwise, only index-th
if (index == -1 || i == index) {
// BufferedImage bi = reader.read(i);
// IIOImage oimage = new IIOImage(bi, null, reader.getImageMetadata(i));
IIOImage oimage = reader.readAll(i, reader.getDefaultReadParam());
File tiffFile = File.createTempFile(OUTPUT_FILE_NAME, TIFF_EXT);
ImageOutputStream ios = ImageIO.createImageOutputStream(tiffFile);
writer.setOutput(ios);
writer.write(streamMetadata, oimage, tiffWriteParam);
ios.close();
tiffFiles.add(tiffFile);
}
}
writer.dispose();
reader.dispose();
return tiffFiles;
}
public void saveView(String filename) {
BoundingSphere bs = _ipg.getBoundingSphere(true);
Vector3 tvec = _view.getTranslate();
try {
FileWriter fw = new FileWriter(filename);
PrintWriter out = new PrintWriter(fw);
out.println(bs.getRadius());
Point3 center = bs.getCenter();
out.printf("%f %f %f \n", center.x, center.y, center.z);
out.println(_view.getAzimuth());
out.println(_view.getElevation());
out.println(_view.getScale());
out.printf("%f %f %f \n", tvec.x, tvec.y, tvec.z);
Iterator<ImagePanel> itr = _ipg.getImagePanels();
while (itr.hasNext()) {
ImagePanel ip = itr.next();
AxisAlignedFrame aaf = ip.getFrame();
Point3 min = aaf.getCornerMin();
Point3 max = aaf.getCornerMax();
out.printf("%f %f %f %f %f %f\n", min.x, min.y, min.z, max.x, max.y, max.z);
}
out.println(_pmax);
out.println(_color.getCode());
out.close();
} catch (Exception e) {
System.out.println(e);
}
}
/**
* Gets pixel data of an <code>IIOImage</code> object.
*
* @param image an <code>IIOImage</code> object
* @return a byte buffer of pixel data
* @throws Exception
*/
public static ByteBuffer getImageByteBuffer(IIOImage image) throws IOException {
// Set up the writeParam
TIFFImageWriteParam tiffWriteParam = new TIFFImageWriteParam(Locale.US);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// Get tif writer and set output to file
Iterator<ImageWriter> writers = ImageIO.getImageWritersByFormatName(TIFF_FORMAT);
ImageWriter writer = writers.next();
if (writer == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
// Get the stream metadata
IIOMetadata streamMetadata = writer.getDefaultStreamMetadata(tiffWriteParam);
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(outputStream);
writer.setOutput(ios);
writer.write(
streamMetadata, new IIOImage(image.getRenderedImage(), null, null), tiffWriteParam);
// writer.write(image.getRenderedImage());
writer.dispose();
// ImageIO.write(image.getRenderedImage(), "tiff", ios); // this can be used in lieu of
// writer
ios.seek(0);
BufferedImage bi = ImageIO.read(ios);
return convertImageData(bi);
}
/**
* Gets a list of <code>IIOImage</code> objects for an image file.
*
* @param imageFile input image file. It can be any of the supported formats, including TIFF,
* JPEG, GIF, PNG, BMP, JPEG, and PDF if GPL Ghostscript is installed
* @return a list of <code>IIOImage</code> objects
* @throws Exception
*/
public static List<IIOImage> getIIOImageList(File imageFile) throws IOException {
File workingTiffFile = null;
ImageReader reader = null;
ImageInputStream iis = null;
try {
// convert PDF to TIFF
if (imageFile.getName().toLowerCase().endsWith(".pdf")) {
workingTiffFile = PdfUtilities.convertPdf2Tiff(imageFile);
imageFile = workingTiffFile;
}
List<IIOImage> iioImageList = new ArrayList<IIOImage>();
String imageFileName = imageFile.getName();
String imageFormat = imageFileName.substring(imageFileName.lastIndexOf('.') + 1);
if (imageFormat.matches("(pbm|pgm|ppm)")) {
imageFormat = "pnm";
} else if (imageFormat.equals("jp2")) {
imageFormat = "jpeg2000";
}
Iterator<ImageReader> readers = ImageIO.getImageReadersByFormatName(imageFormat);
reader = readers.next();
if (reader == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
iis = ImageIO.createImageInputStream(imageFile);
reader.setInput(iis);
int imageTotal = reader.getNumImages(true);
for (int i = 0; i < imageTotal; i++) {
// IIOImage oimage = new IIOImage(reader.read(i), null,
// reader.getImageMetadata(i));
IIOImage oimage = reader.readAll(i, reader.getDefaultReadParam());
iioImageList.add(oimage);
}
return iioImageList;
} finally {
try {
if (iis != null) {
iis.close();
}
if (reader != null) {
reader.dispose();
}
} catch (Exception e) {
// ignore
}
if (workingTiffFile != null && workingTiffFile.exists()) {
workingTiffFile.delete();
}
}
}
public Iterator getAttachments(Iterator iter) {
while (iter.hasNext()) {
Object obj = iter.next();
if (!(obj instanceof AttachmentPart)) {
return null;
}
}
return iter;
}
/** highlight a route (maybe to show it's in use...) */
public void highlightRoute(String src, String dst) {
Iterator i = rows.iterator();
while (i.hasNext()) {
Map temp = (Map) i.next();
if (temp.get("Address").equals(dst) && temp.get("Pivot").equals(src)) {
temp.put("Active", Boolean.TRUE);
}
}
}
public void loadView(String filename) {
Point3 point;
Vector3 tvec;
double radius;
double azimuth;
double elevation;
double scale;
double x, y, z;
double vx, vy, vz;
try {
if (_ipg == null) throw new Exception("Must load a cube first!");
Scanner s = new Scanner(new File(filename));
radius = s.nextDouble();
x = s.nextDouble();
y = s.nextDouble();
z = s.nextDouble();
point = new Point3(x, y, z);
azimuth = s.nextDouble();
elevation = s.nextDouble();
scale = s.nextDouble();
vx = s.nextDouble();
vy = s.nextDouble();
vz = s.nextDouble();
tvec = new Vector3(vx, vy, vz);
Iterator<ImagePanel> itr = _ipg.getImagePanels();
while (itr.hasNext()) {
ImagePanel ip = itr.next();
AxisAlignedFrame aaf = ip.getFrame();
double lx = s.nextDouble();
double ly = s.nextDouble();
double lz = s.nextDouble();
double mx = s.nextDouble();
double my = s.nextDouble();
double mz = s.nextDouble();
Point3 min = new Point3(lx, ly, lz);
Point3 max = new Point3(mx, my, mz);
aaf.setCorners(min, max);
}
_pmax = s.nextFloat();
int code = s.nextInt();
_color = ColorList.getMatch(code);
setColorMap();
_view.setWorldSphere(new BoundingSphere(point, radius));
_view.setTranslate(tvec);
_view.setAzimuth(azimuth);
_view.setElevation(elevation);
_view.setScale(scale);
_ipg.setPercentiles(_pmin, _pmax);
} catch (Exception e) {
System.out.println("Failed to load view point!");
System.out.println(e);
}
}
/** show the meterpreter routes . :) */
public void setRoutes(Route[] routes) {
Iterator i = rows.iterator();
while (i.hasNext()) {
Map temp = (Map) i.next();
for (int x = 0; x < routes.length; x++) {
Route r = routes[x];
if (r.shouldRoute(temp.get("Address") + "")) temp.put("Pivot", r.getGateway());
}
}
}
public void tabRemoveHighlight(int tabIndex) {
Iterator<Integer> highlightedIter = highlightedTabs.iterator();
while (highlightedIter.hasNext()) {
if (highlightedIter.next().intValue() == tabIndex) {
highlightedIter.remove();
break;
}
}
}
public boolean compareImages(Image image1, Image image2, Rectangle rect, String attach) {
if (image1 == null || image2 == null) return false;
boolean matched = false;
Iterator iter1 = handlePixels(image1, rect);
Iterator iter2 = handlePixels(image2, rect);
while (iter1.hasNext() && iter2.hasNext()) {
Pixel pixel = (Pixel) iter1.next();
if (pixel.equals((Pixel) iter2.next())) {
matched = true;
} else {
matched = false;
}
}
if (matched) return true;
return false;
}
private void load_snap_from_xml(Element snap, StructureCollection structs, LinkedList tempList)
throws VisualizerLoadException {
Iterator iterator = snap.getChildren().iterator();
if (!iterator.hasNext()) throw new VisualizerLoadException("Ran out of elements");
structs.loadTitle((Element) (iterator.next()), tempList, this);
structs.calcDimsAndStartPts(tempList, this);
if (!iterator.hasNext()) return;
Element child = (Element) iterator.next();
if (child.getName().compareTo("doc_url") == 0) {
// load the doc_url
add_a_documentation_URL(child.getText().trim());
if (!iterator.hasNext()) return;
child = (Element) iterator.next();
}
if (child.getName().compareTo("pseudocode_url") == 0) {
// load the psuedocode_url
add_a_pseudocode_URL(child.getText().trim());
if (!iterator.hasNext()) return;
child = (Element) iterator.next();
}
if (child.getName().compareTo("audio_text") == 0) {
// load the psuedocode_url
add_audio_text(child.getText().trim());
if (!iterator.hasNext()) return;
child = (Element) iterator.next();
}
// create & load the individual structures, hooking them into the StructureCollection.
// linespernode : calculate it at end of loadStructure call
while (child.getName().compareTo("question_ref") != 0) {
StructureType child_struct = assignStructureType(child);
child_struct.loadStructure(child, tempList, this);
structs.addChild(child_struct);
if (!iterator.hasNext()) return;
child = (Element) iterator.next();
}
if (child.getName().compareTo("question_ref") == 0) {
// set up question ref
add_a_question_xml(child.getAttributeValue("ref"));
} else
// should never happen
throw new VisualizerLoadException(
"Expected question_ref element, but found " + child.getName());
if (iterator.hasNext()) {
child = (Element) iterator.next();
throw new VisualizerLoadException(
"Found " + child.getName() + " when expecting end of snap.");
}
} // load_snap_from_xml
@Override
public void actionPerformed(ActionEvent e) {
if (fc == null) {
fc = new IDEFileChooser();
fc.setFileView(new IDEFileView());
fc.setAcceptAllFileFilterUsed(false);
fc.setFileSelectionMode(JFileChooser.FILES_ONLY);
fc.setMultiSelectionEnabled(false);
fc.setDialogTitle(
messagesBundle.getString("ImageViewerPanelSaveAction.Choose_filename_to_save_4"));
//$NON-NLS-1$
// prepare file filters
IIORegistry theRegistry = IIORegistry.getDefaultInstance();
Iterator it = theRegistry.getServiceProviders(ImageWriterSpi.class, false);
while (it.hasNext()) {
ImageWriterSpi writer = (ImageWriterSpi) it.next();
if ((imageType == BufferedImage.TYPE_INT_ARGB
|| imageType == BufferedImage.TYPE_INT_ARGB_PRE)
&& "JPEG".equals(writer.getFormatNames()[0].toUpperCase())) continue;
ImageWriterSpiFileFilter ff = new ImageWriterSpiFileFilter(writer);
fc.addChoosableFileFilter(ff);
}
}
if (fc.showSaveDialog(viewerPanel) == JFileChooser.APPROVE_OPTION) {
File selectedFile = fc.getSelectedFile();
if (selectedFile != null) {
String fileName = selectedFile.getAbsolutePath();
ImageWriterSpiFileFilter ff = (ImageWriterSpiFileFilter) fc.getFileFilter();
if (!ff.hasCorrectSuffix(fileName)) fileName = ff.addSuffix(fileName);
selectedFile = new File(fileName);
if (selectedFile.exists()) {
String message =
MessageFormat.format(
messagesBundle.getString("ImageViewerPanelSaveAction.Overwrite_question_5"),
//$NON-NLS-1$
fileName);
if (JOptionPane.NO_OPTION
== JOptionPane.showConfirmDialog(
viewerPanel,
message,
messagesBundle.getString("ImageViewerPanelSaveAction.Warning_6"),
//$NON-NLS-1$
JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE)) return;
}
writeToFile(selectedFile, ff);
}
}
}
/** Print it! */
public String printClusters(Cluster clustering, float threshold, HTMLFile f) {
int maxSize = 0;
ArrayList<Cluster> clusters = getClusters(clustering, threshold);
for (Iterator<Cluster> i = clusters.iterator(); i.hasNext(); ) {
Cluster cluster = i.next();
if (cluster.size() > maxSize) maxSize = cluster.size();
}
TreeSet<Cluster> sorted = new TreeSet<Cluster>(clusters);
clusters = null;
// Now print them:
return outputClustering(f, sorted, maxSize);
}
public AttachmentPart getAttachment(java.net.URI ref, Iterator iter) {
if (iter == null || ref == null) {
System.err.println("getAttachment: null Iterator for AttachmentPart");
return null;
}
while (iter.hasNext()) {
AttachmentPart tempAttachment = (AttachmentPart) iter.next();
if (ref.isOpaque() && ref.getScheme().equals("cid")) {
String refId = ref.getSchemeSpecificPart();
String cId = tempAttachment.getContentId();
if (cId.equals("<" + refId + ">") || cId.equals(refId)) {
return tempAttachment;
}
}
}
return null;
}
public static byte[] getImageBytes(Image image, String type) throws IOException {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
BufferedImage bufImage = convertToBufferedImage(image);
ImageWriter writer = null;
Iterator i = ImageIO.getImageWritersByMIMEType(type);
if (i.hasNext()) {
writer = (ImageWriter) i.next();
}
if (writer != null) {
ImageOutputStream stream = null;
stream = ImageIO.createImageOutputStream(baos);
writer.setOutput(stream);
writer.write(bufImage);
stream.close();
return baos.toByteArray();
}
return null;
}
public static List<File> createTiffFiles(List<IIOImage> imageList, int index, int dpiX, int dpiY)
throws IOException {
List<File> tiffFiles = new ArrayList<File>();
// Set up the writeParam
TIFFImageWriteParam tiffWriteParam = new TIFFImageWriteParam(Locale.US);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// Get tif writer and set output to file
Iterator<ImageWriter> writers = ImageIO.getImageWritersByFormatName(TIFF_FORMAT);
ImageWriter writer = writers.next();
if (writer == null) {
throw new RuntimeException(
"Need to install JAI Image I/O package.\nhttps://jai-imageio.dev.java.net");
}
// Get the stream metadata
IIOMetadata streamMetadata = writer.getDefaultStreamMetadata(tiffWriteParam);
// all if index == -1; otherwise, only index-th
for (IIOImage oimage : (index == -1 ? imageList : imageList.subList(index, index + 1))) {
if (dpiX != 0 && dpiY != 0) {
// Get the default image metadata.
ImageTypeSpecifier imageType =
ImageTypeSpecifier.createFromRenderedImage(oimage.getRenderedImage());
IIOMetadata imageMetadata = writer.getDefaultImageMetadata(imageType, null);
imageMetadata = setDPIViaAPI(imageMetadata, dpiX, dpiY);
oimage.setMetadata(imageMetadata);
}
File tiffFile = File.createTempFile(OUTPUT_FILE_NAME, TIFF_EXT);
ImageOutputStream ios = ImageIO.createImageOutputStream(tiffFile);
writer.setOutput(ios);
writer.write(streamMetadata, oimage, tiffWriteParam);
ios.close();
tiffFiles.add(tiffFile);
}
writer.dispose();
return tiffFiles;
}
public void end() {
final int[] selected = table.getSelectedRows();
model.clear(rows.size());
Iterator i = rows.iterator();
while (i.hasNext()) {
model.addEntry((Map) i.next());
}
rows.clear();
if (SwingUtilities.isEventDispatchThread()) {
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
model.fireListeners();
fixSelection(selected);
}
});
} else {
model.fireListeners();
fixSelection(selected);
}
}
/**
* Merges multiple images into one TIFF image.
*
* @param inputImages an array of image files
* @param outputTiff the output TIFF file
* @throws Exception
*/
public static void mergeTiff(File[] inputImages, File outputTiff) throws IOException {
List<IIOImage> imageList = new ArrayList<IIOImage>();
for (int i = 0; i < inputImages.length; i++) {
imageList.addAll(getIIOImageList(inputImages[i]));
}
if (imageList.isEmpty()) {
// if no image
return;
}
Iterator<ImageWriter> writers = ImageIO.getImageWritersByFormatName(TIFF_FORMAT);
ImageWriter writer = writers.next();
// Set up the writeParam
TIFFImageWriteParam tiffWriteParam = new TIFFImageWriteParam(Locale.US);
tiffWriteParam.setCompressionMode(ImageWriteParam.MODE_DISABLED);
// Get the stream metadata
IIOMetadata streamMetadata = writer.getDefaultStreamMetadata(tiffWriteParam);
ImageOutputStream ios = ImageIO.createImageOutputStream(outputTiff);
writer.setOutput(ios);
IIOImage firstIioImage = imageList.remove(0);
writer.write(streamMetadata, firstIioImage, tiffWriteParam);
int i = 1;
for (IIOImage iioImage : imageList) {
writer.writeInsert(i++, iioImage, tiffWriteParam);
}
ios.close();
writer.dispose();
}
/** This method returns the distribution HTML code as a string */
private String outputClustering(HTMLFile f, Collection<Cluster> allClusters, int maxSize) {
int[] distribution = new int[maxSize + 1];
int max = 0;
for (int i = 0; i <= maxSize; i++) distribution[i] = 0;
// Now output the clustering:
f.println("<TABLE CELLPADDING=2 CELLSPACING=2>");
f.println(
"<TR><TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Cluster_number")
+ "<TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Size")
+ "<TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Threshold")
+ "<TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Cluster_members")
+ "<TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Most_frequent_words")
+ "</TR>");
Iterator<Cluster> clusterI = allClusters.iterator();
for (int i = 1; clusterI.hasNext(); i++) {
Cluster cluster = clusterI.next();
if (max < ++distribution[cluster.size()]) max = distribution[cluster.size()];
// no singleton clusters
if (cluster.size() == 1) continue;
f.print(
"<TR><TD ALIGN=center BGCOLOR=#8080ff>"
+ i
+ "<TD ALIGN=center BGCOLOR=#c0c0ff>"
+ cluster.size()
+ "<TD ALIGN=center BGCOLOR=#c0c0ff>"
+ cluster.getSimilarity()
+ "<TD ALIGN=left BGCOLOR=#c0c0ff>");
// sort names
TreeSet<Submission> sortedSubmissions = new TreeSet<Submission>();
for (int x = 0; x < cluster.size(); x++) {
sortedSubmissions.add(submissions.elementAt(cluster.getSubmissionAt(x)));
}
for (Iterator<Submission> iter = sortedSubmissions.iterator(); iter.hasNext(); ) {
Submission sub = iter.next();
int index = submissions.indexOf(sub);
f.print("<A HREF=\"submission" + index + ".html\">" + sub.name + "</A>");
if (iter.hasNext()) f.print(", ");
neededSubmissions.add(sub); // write files for these.
}
if (this.program.get_language() instanceof jplag.text.Language) {
f.println(
"<TD ALIGN=left BGCOLOR=#c0c0ff>"
+ ThemeGenerator.generateThemes(
sortedSubmissions, this.program.get_themewords(), true, this.program));
} else {
f.println("<TD ALIGN=left BGCOLOR=#c0c0ff>-");
}
f.println("</TR>");
}
f.println("</TABLE>\n<P>\n");
f.println("<H5>" + msg.getString("Clusters.Distribution_of_cluster_size") + ":</H5>");
String text;
text = "<TABLE CELLPADDING=1 CELLSPACING=1>\n";
text +=
"<TR><TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Cluster_size")
+ "<TH ALIGN=center BGCOLOR=#8080ff>"
+ msg.getString("Clusters.Number_of_clusters")
+ "<TH ALIGN=center BGCOLOR=#8080ff>.</TR>\n";
for (int i = 0; i <= maxSize; i++) {
if (distribution[i] == 0) continue;
text +=
"<TR><TD ALIGN=center BGCOLOR=#c0c0ff>"
+ i
+ "<TD ALIGN=right BGCOLOR=#c0c0ff>"
+ distribution[i]
+ "<TD BGCOLOR=#c0c0ff>\n";
for (int j = (distribution[i] * barLength / max); j > 0; j--) text += ("#");
if (distribution[i] * barLength / max == 0) {
if (distribution[i] == 0) text += (".");
else text += ("#");
}
text += ("</TR>\n");
}
text += ("</TABLE>\n");
f.print(text);
return text;
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}