public Zipper<Map<Integer, MZipper<RoiContainer>>> exec( Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) { JFileChooser fc = new JFileChooser(); int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas()); Map<Integer, MZipper<RoiContainer>> newRois; if (returnVal == JFileChooser.APPROVE_OPTION) { try { FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath()); MroiLisp parser = new MroiLisp(f); parser.ReInit(f); newRois = parser.roiFile(); // z.rights.clear(); // z.rights.add(newRois); // z = z.right(); // return z; return z.insertAndStep(newRois); } catch (IOException e) { IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage()); } catch (mroi.ParseException e) { IJ.error("Failed in parsing: " + e.getMessage()); } catch (Exception e) { IJ.error("Malformed input file: " + e.getMessage()); } } return z; }
public void drop(DropTargetDropEvent dtde) { dtde.acceptDrop(DnDConstants.ACTION_COPY); DataFlavor[] flavors = null; try { Transferable t = dtde.getTransferable(); iterator = null; flavors = t.getTransferDataFlavors(); if (IJ.debugMode) IJ.log("DragAndDrop.drop: " + flavors.length + " flavors"); for (int i = 0; i < flavors.length; i++) { if (IJ.debugMode) IJ.log(" flavor[" + i + "]: " + flavors[i].getMimeType()); if (flavors[i].isFlavorJavaFileListType()) { Object data = t.getTransferData(DataFlavor.javaFileListFlavor); iterator = ((List) data).iterator(); break; } else if (flavors[i].isFlavorTextType()) { Object ob = t.getTransferData(flavors[i]); if (!(ob instanceof String)) continue; String s = ob.toString().trim(); if (IJ.isLinux() && s.length() > 1 && (int) s.charAt(1) == 0) s = fixLinuxString(s); ArrayList list = new ArrayList(); if (s.indexOf("href=\"") != -1 || s.indexOf("src=\"") != -1) { s = parseHTML(s); if (IJ.debugMode) IJ.log(" url: " + s); list.add(s); this.iterator = list.iterator(); break; } BufferedReader br = new BufferedReader(new StringReader(s)); String tmp; while (null != (tmp = br.readLine())) { tmp = java.net.URLDecoder.decode(tmp.replaceAll("\\+", "%2b"), "UTF-8"); if (tmp.startsWith("file://")) tmp = tmp.substring(7); if (IJ.debugMode) IJ.log(" content: " + tmp); if (tmp.startsWith("http://")) list.add(s); else list.add(new File(tmp)); } this.iterator = list.iterator(); break; } } if (iterator != null) { Thread thread = new Thread(this, "DrawAndDrop"); thread.setPriority(Math.max(thread.getPriority() - 1, Thread.MIN_PRIORITY)); thread.start(); } } catch (Exception e) { dtde.dropComplete(false); return; } dtde.dropComplete(true); if (flavors == null || flavors.length == 0) { if (IJ.isMacOSX()) IJ.error( "First drag and drop ignored. Please try again. You can avoid this\n" + "problem by dragging to the toolbar instead of the status bar."); else IJ.error("Drag and drop failed"); } }
byte[] download(File f) { if (!f.exists()) { IJ.error("Plugin Installer", "File not found: " + f); return null; } byte[] data = null; try { int len = (int) f.length(); InputStream in = new BufferedInputStream(new FileInputStream(f)); DataInputStream dis = new DataInputStream(in); data = new byte[len]; dis.readFully(data); dis.close(); } catch (Exception e) { IJ.error("Plugin Installer", "" + e); data = null; } return data; }
boolean savePlugin(File f, byte[] data) { try { FileOutputStream out = new FileOutputStream(f); out.write(data, 0, data.length); out.close(); } catch (IOException e) { IJ.error("Plugin Installer", "" + e); return false; } return true; }
public void run(String arg) { OpenDialog od = new OpenDialog("Install Plugin, Macro or Script...", arg); String directory = od.getDirectory(); String name = od.getFileName(); if (name == null) return; if (!validExtension(name)) { IJ.error("Plugin Installer", errorMessage()); return; } String path = directory + name; install(path); }
String open(String path) { if (path == null) return null; try { StringBuffer sb = new StringBuffer(5000); BufferedReader r = new BufferedReader(new FileReader(path)); while (true) { String s = r.readLine(); if (s == null) break; else sb.append(s + "\n"); } r.close(); return new String(sb); } catch (Exception e) { IJ.error(e.getMessage()); return null; } }
public static byte[] download(String urlString, String name) { int maxLength = 52428800; // 50MB URL url = null; boolean unknownLength = false; byte[] data = null; ; int n = 0; try { url = new URL(urlString); if (IJ.debugMode) IJ.log("PluginInstaller: " + urlString + " " + url); if (url == null) return null; URLConnection uc = url.openConnection(); int len = uc.getContentLength(); unknownLength = len < 0; if (unknownLength) len = maxLength; if (name != null) IJ.showStatus("Downloading " + url.getFile()); InputStream in = uc.getInputStream(); data = new byte[len]; int lenk = len / 1024; while (n < len) { int count = in.read(data, n, len - n); if (count < 0) break; n += count; if (name != null) IJ.showStatus("Downloading " + name + " (" + (n / 1024) + "/" + lenk + "k)"); IJ.showProgress(n, len); } in.close(); } catch (Exception e) { String msg = "" + e; if (!msg.contains("://")) msg += "\n " + urlString; IJ.error("Plugin Installer", msg); return null; } finally { IJ.showProgress(1.0); } if (name != null) IJ.showStatus(""); if (unknownLength) { byte[] data2 = data; data = new byte[n]; for (int i = 0; i < n; i++) data[i] = data2[i]; } return data; }
static void error(String msg, FileInfo fi, long offset, long length) { IJ.error( "FileOpener", "FileInfo parameter error. \n" + msg + "\n \n" + " Width: " + fi.width + "\n" + " Height: " + fi.height + "\n" + " Offset: " + offset + "\n" + " Bytes/pixel: " + fi.getBytesPerPixel() + "\n" + (length > 0 ? " File length: " + length + "\n" : "")); }
void error(String msg) { IJ.error("ImageJ Updater", msg); }
/** * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ. */ public ImageJ(java.applet.Applet applet, int mode) { super("ImageJ"); if ((mode & DEBUG) != 0) IJ.setDebugMode(true); mode = mode & 255; if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: " + mode); embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW); this.applet = applet; String err1 = Prefs.load(this, applet); setBackground(backgroundColor); Menus m = new Menus(this, applet); String err2 = m.addMenuBar(); m.installPopupMenu(this); setLayout(new BorderLayout()); // Tool bar toolbar = new Toolbar(); toolbar.addKeyListener(this); add("Center", toolbar); // Status bar statusBar = new Panel(); statusBar.setLayout(new BorderLayout()); statusBar.setForeground(Color.black); statusBar.setBackground(backgroundColor); statusLine = new JLabel(); statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13)); statusLine.addKeyListener(this); statusLine.addMouseListener(this); statusBar.add("Center", statusLine); progressBar = new ProgressBar(120, 20); progressBar.addKeyListener(this); progressBar.addMouseListener(this); statusBar.add("East", progressBar); add("South", statusBar); IJ.init(this, applet); addKeyListener(this); addWindowListener(this); setFocusTraversalKeysEnabled(false); m.installStartupMacroSet(); // add custom tools runStartupMacro(); Point loc = getPreferredLocation(); Dimension tbSize = toolbar.getPreferredSize(); setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug if (mode != NO_SHOW) { if (IJ.isWindows()) try { setIcon(); } catch (Exception e) { } setLocation(loc.x, loc.y); setResizable(!IJ.isMacOSX()); pack(); setVisible(true); } if (err1 != null) IJ.error(err1); if (err2 != null) { IJ.error(err2); IJ.runPlugIn("ij.plugin.ClassChecker", ""); } if (IJ.isMacintosh() && applet == null) { Object qh = null; qh = IJ.runPlugIn("MacAdapter", ""); if (qh == null) IJ.runPlugIn("QuitHandler", ""); } if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", ""); String str = m.getMacroCount() == 1 ? " macro" : " macros"; IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str); configureProxy(); if (applet == null) loadCursors(); }
/** * If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is * ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ. */ public ImageJ(java.applet.Applet applet, int mode) { super("ImageJ"); embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW); this.applet = applet; String err1 = Prefs.load(this, applet); if (IJ.isLinux()) { backgroundColor = new Color(240, 240, 240); setBackground(backgroundColor); } Menus m = new Menus(this, applet); String err2 = m.addMenuBar(); m.installPopupMenu(this); setLayout(new GridLayout(2, 1)); // Tool bar toolbar = new Toolbar(); toolbar.addKeyListener(this); add(toolbar); // Status bar statusBar = new Panel(); statusBar.setLayout(new BorderLayout()); statusBar.setForeground(Color.black); statusBar.setBackground(backgroundColor); statusLine = new Label(); statusLine.setFont(SansSerif12); statusLine.addKeyListener(this); statusLine.addMouseListener(this); statusBar.add("Center", statusLine); progressBar = new ProgressBar(120, 20); progressBar.addKeyListener(this); progressBar.addMouseListener(this); statusBar.add("East", progressBar); statusBar.setSize(toolbar.getPreferredSize()); add(statusBar); IJ.init(this, applet); addKeyListener(this); addWindowListener(this); setFocusTraversalKeysEnabled(false); Point loc = getPreferredLocation(); Dimension tbSize = toolbar.getPreferredSize(); int ijWidth = tbSize.width + 10; int ijHeight = 100; setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug if (mode != NO_SHOW) { if (IJ.isWindows()) try { setIcon(); } catch (Exception e) { } setBounds(loc.x, loc.y, ijWidth, ijHeight); // needed for pack to work setLocation(loc.x, loc.y); pack(); setResizable(!(IJ.isMacintosh() || IJ.isWindows())); // make resizable on Linux show(); } if (err1 != null) IJ.error(err1); if (err2 != null) { IJ.error(err2); IJ.runPlugIn("ij.plugin.ClassChecker", ""); } m.installStartupMacroSet(); if (IJ.isMacintosh() && applet == null) { Object qh = null; qh = IJ.runPlugIn("MacAdapter", ""); if (qh == null) IJ.runPlugIn("QuitHandler", ""); } if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", ""); String str = m.getMacroCount() == 1 ? " macro" : " macros"; IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str); // if (applet==null && !embedded && Prefs.runSocketListener) // new SocketListener(); configureProxy(); if (applet == null) loadCursors(); }
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(); } }
public void run(String arg) { Frame[] niframes = WindowManager.getNonImageWindows(); String[] titles = new String[niframes.length + 1]; for (int i = 0; i < niframes.length; i++) { titles[i] = niframes[i].getTitle(); } titles[niframes.length] = "Clipboard"; GenericDialog gd = new GenericDialog("Windows"); boolean importfile = false; gd.addCheckbox("Import from file?", importfile); gd.addChoice("Windows", titles, titles[0]); boolean hasxvals = false; gd.addCheckbox("X Vals Column?", hasxvals); boolean multix = false; gd.addCheckbox("Multi_X_Columns?", multix); boolean skipendzeros = false; gd.addCheckbox("Skip_end_zeros?", skipendzeros); String[] delimiters = {"Tab", "Comma", "Space"}; gd.addChoice("Delimiter", delimiters, delimiters[0]); gd.showDialog(); if (gd.wasCanceled()) { return; } importfile = gd.getNextBoolean(); int index = gd.getNextChoiceIndex(); hasxvals = gd.getNextBoolean(); multix = gd.getNextBoolean(); skipendzeros = gd.getNextBoolean(); int delimindex = gd.getNextChoiceIndex(); if (multix) hasxvals = true; String textdata = ""; if (importfile) { OpenDialog od = new OpenDialog("Open File", "", ".txt"); String directory = od.getDirectory(); String name = od.getFileName(); if (name == null) { return; } try { File infile = new File(directory + name); BufferedReader b = new BufferedReader(new FileReader(infile)); textdata = (new jdataio()).readstringfile(b); b.close(); } catch (IOException e) { return; } } else { if (index == niframes.length) { // here we get the data from the clipboard Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null); try { if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) { textdata = (String) t.getTransferData(DataFlavor.stringFlavor); } } catch (UnsupportedFlavorException e) { } catch (IOException e) { } if (textdata.equals("")) { IJ.error("Error copying from clipboard."); return; } } else { if (niframes[index] instanceof Editor) { Editor tw = (Editor) niframes[index]; textdata = tw.getText(); } else { if (niframes[index] instanceof TextWindow) { TextWindow tw = (TextWindow) niframes[index]; textdata = tw.getTextPanel().getText(); } else { IJ.showMessage("Not a valid text window"); return; } } } } if (textdata == null) { IJ.showMessage("Error in Obtaining String"); return; } if (textdata.indexOf("\r") >= 0) { textdata = textdata.replace('\r', '\n'); } char[] delims = {'\t', ',', ' '}; delimit_string ds = new delimit_string(delims[delimindex]); String[] rows = ds.getrows(textdata); int lines = rows.length; int columns = ds.getnumcolumns(rows[0]); int ycolumns = columns; if (hasxvals) { if (multix) { ycolumns /= 2; } else { ycolumns--; } } if (multix) { float[][] ydata = new float[ycolumns][lines]; float[][] xdata = new float[ycolumns][lines]; for (int i = 0; i < lines; i++) { float[] temp = ds.delim2float(rows[i], columns); for (int j = 0; j < ycolumns; j++) { ydata[j][i] = temp[2 * j + 1]; xdata[j][i] = temp[2 * j]; } } int[] npts = new int[ycolumns]; for (int i = 0; i < ycolumns; i++) { npts[i] = lines; } if (skipendzeros) { for (int i = 0; i < ycolumns; i++) { int counter = lines - 1; while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) { xdata[i][counter] = 0.0f; ydata[i][counter] = 0.0f; npts[i]--; counter--; } } } (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw(); } else { float[][] tempydata = new float[ycolumns][lines]; float[] tempxdata = new float[lines]; float[][] xdata = null; float[][] ydata = null; int startcolumn = 0; if (hasxvals) startcolumn = 1; for (int i = 0; i < lines; i++) { float[] temp = ds.delim2float(rows[i], columns); if (hasxvals) { tempxdata[i] = temp[0]; } else { tempxdata[i] = (float) (i + 1); } for (int j = 0; j < ycolumns; j++) { tempydata[j][i] = temp[j + startcolumn]; } } int[] npts = new int[ycolumns]; npts[0] = lines; if (skipendzeros) { int maxpts = 0; for (int i = 0; i < ycolumns; i++) { int counter = lines - 1; npts[i] = lines; while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter])) && counter > 0) { npts[i]--; counter--; } if (npts[i] > maxpts) maxpts = npts[i]; IJ.log("" + npts[i]); } ydata = new float[ycolumns][maxpts]; xdata = new float[ycolumns][maxpts]; for (int i = 0; i < ycolumns; i++) { // npts[i]=npts[0]; System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]); System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]); } } else { ydata = tempydata; xdata = new float[ycolumns][]; for (int i = 0; i < ycolumns; i++) { npts[i] = npts[0]; xdata[i] = tempxdata.clone(); } } (new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw(); } }
public boolean install(String path) { boolean isURL = path.contains("://"); String lcPath = path.toLowerCase(); if (isURL) path = Opener.updateUrl(path); boolean isTool = lcPath.endsWith("tool.ijm") || lcPath.endsWith("tool.txt") || lcPath.endsWith("tool.class") || lcPath.endsWith("tool.jar"); boolean isMacro = lcPath.endsWith(".txt") || lcPath.endsWith(".ijm"); byte[] data = null; String name = path; if (isURL) { int index = path.lastIndexOf("/"); if (index != -1 && index <= path.length() - 1) name = path.substring(index + 1); data = download(path, name); } else { File f = new File(path); name = f.getName(); data = download(f); } if (data == null) return false; if (name.endsWith(".txt") && !name.contains("_")) name = name.substring(0, name.length() - 4) + ".ijm"; if (name.endsWith(".zip")) { if (!name.contains("_")) { IJ.error("Plugin Installer", "No underscore in file name:\n \n " + name); return false; } name = name.substring(0, name.length() - 4) + ".jar"; } String dir = null; boolean isLibrary = name.endsWith(".jar") && !name.contains("_"); if (isLibrary) { dir = Menus.getPlugInsPath() + "jars"; File f = new File(dir); if (!f.exists()) { boolean ok = f.mkdir(); if (!ok) dir = Menus.getPlugInsPath(); } } if (isTool) { dir = Menus.getPlugInsPath() + "Tools" + File.separator; File f = new File(dir); if (!f.exists()) { boolean ok = f.mkdir(); if (!ok) dir = null; } if (dir != null && isMacro) { String name2 = getToolName(data); if (name2 != null) name = name2; } } if (dir == null) { SaveDialog sd = new SaveDialog("Save Plugin, Macro or Script...", Menus.getPlugInsPath(), name, null); String name2 = sd.getFileName(); if (name2 == null) return false; dir = sd.getDirectory(); } // IJ.log(dir+" "+Menus.getPlugInsPath()); if (!savePlugin(new File(dir, name), data)) return false; if (name.endsWith(".java")) IJ.runPlugIn("ij.plugin.Compiler", dir + name); Menus.updateImageJMenus(); if (isTool) { if (isMacro) IJ.runPlugIn("ij.plugin.Macro_Runner", "Tools/" + name); else if (name.endsWith(".class")) { name = name.replaceAll("_", " "); name = name.substring(0, name.length() - 6); IJ.run(name); } } return true; }
void install() { subMenus.clear(); if (text != null) { Tokenizer tok = new Tokenizer(); pgm = tok.tokenize(text); } if (macrosMenu != null) IJ.showStatus(""); int[] code = pgm.getCode(); Symbol[] symbolTable = pgm.getSymbolTable(); int count = 0, token, nextToken, address; String name; Symbol symbol; shortcutsInUse = null; inUseCount = 0; nShortcuts = 0; toolCount = 0; macroStarts = new int[MAX_MACROS]; macroNames = new String[MAX_MACROS]; boolean isPluginsMacrosMenu = false; if (macrosMenu != null) { int itemCount = macrosMenu.getItemCount(); isPluginsMacrosMenu = macrosMenu == Menus.getMacrosMenu(); int baseCount = isPluginsMacrosMenu ? MACROS_MENU_COMMANDS : Editor.MACROS_MENU_ITEMS; if (itemCount > baseCount) { for (int i = itemCount - 1; i >= baseCount; i--) macrosMenu.remove(i); } } if (pgm.hasVars() && pgm.macroCount() > 0 && pgm.getGlobals() == null) new Interpreter().saveGlobals(pgm); ArrayList tools = new ArrayList(); for (int i = 0; i < code.length; i++) { token = code[i] & TOK_MASK; if (token == MACRO) { nextToken = code[i + 1] & TOK_MASK; if (nextToken == STRING_CONSTANT) { if (count == MAX_MACROS) { if (isPluginsMacrosMenu) IJ.error("Macro Installer", "Macro sets are limited to " + MAX_MACROS + " macros."); break; } address = code[i + 1] >> TOK_SHIFT; symbol = symbolTable[address]; name = symbol.str; macroStarts[count] = i + 2; macroNames[count] = name; if (name.indexOf('-') != -1 && (name.indexOf("Tool") != -1 || name.indexOf("tool") != -1)) { tools.add(name); toolCount++; } else if (name.startsWith("AutoRun")) { if (autoRunCount == 0 && !openingStartupMacrosInEditor) { new MacroRunner(pgm, macroStarts[count], name, (String) null); if (name.equals("AutoRunAndHide")) autoRunAndHideCount++; } autoRunCount++; count--; } else if (name.equals("Popup Menu")) installPopupMenu(name, pgm); else if (!name.endsWith("Tool Selected")) { if (macrosMenu != null) { addShortcut(name); int pos = name.indexOf(">"); boolean inSubMenu = name.startsWith("<") && (pos > 1); if (inSubMenu) { Menu parent = macrosMenu; Menu subMenu = null; String parentStr = name.substring(1, pos).trim(); String childStr = name.substring(pos + 1).trim(); MenuItem mnuItem = new MenuItem(); mnuItem.setActionCommand(name); mnuItem.setLabel(childStr); for (int jj = 0; jj < subMenus.size(); jj++) { String aName = subMenus.get(jj).getName(); if (aName.equals(parentStr)) subMenu = subMenus.get(jj); } if (subMenu == null) { subMenu = new Menu(parentStr); subMenu.setName(parentStr); subMenu.addActionListener(this); subMenus.add(subMenu); parent.add(subMenu); } subMenu.add(mnuItem); } else macrosMenu.add(new MenuItem(name)); } } // IJ.log(count+" "+name+" "+macroStarts[count]); count++; } } else if (token == EOF) break; } nMacros = count; if (toolCount > 0 && (isPluginsMacrosMenu || macrosMenu == null) && installTools) { Toolbar tb = Toolbar.getInstance(); if (toolCount == 1) tb.addMacroTool((String) tools.get(0), this); else { for (int i = 0; i < tools.size(); i++) { String toolName = (String) tools.get(i); if (toolName.startsWith("Abort Macro or Plugin") && toolCount > 6) toolName = "Unused " + toolName; tb.addMacroTool(toolName, this, i); } } if (toolCount > 1 && Toolbar.getToolId() >= Toolbar.CUSTOM1) tb.setTool(Toolbar.RECTANGLE); tb.repaint(); } if (macrosMenu != null) this.instance = this; if (shortcutsInUse != null && text != null) IJ.showMessage( "Install Macros", (inUseCount == 1 ? "This keyboard shortcut is" : "These keyboard shortcuts are") + " already in use:" + shortcutsInUse); if (nMacros == 0 && fileName != null) { if (text == null || text.length() == 0) return; int dotIndex = fileName.lastIndexOf('.'); if (dotIndex > 0) anonymousName = fileName.substring(0, dotIndex); else anonymousName = fileName; if (macrosMenu != null) macrosMenu.add(new MenuItem(anonymousName)); macroNames[0] = anonymousName; nMacros = 1; } String word = nMacros == 1 ? " macro" : " macros"; if (isPluginsMacrosMenu) IJ.showStatus(nMacros + word + " installed"); }