/** Quit using a separate thread, hopefully avoiding thread deadlocks. */ public void run() { quitting = true; boolean changes = false; int[] wList = WindowManager.getIDList(); if (wList != null) { for (int i = 0; i < wList.length; i++) { ImagePlus imp = WindowManager.getImage(wList[i]); if (imp != null && imp.changes == true) { changes = true; break; } } } Frame[] frames = WindowManager.getNonImageWindows(); if (frames != null) { for (int i = 0; i < frames.length; i++) { if (frames[i] != null && (frames[i] instanceof Editor)) { if (((Editor) frames[i]).fileChanged()) { changes = true; break; } } } } if (windowClosed && !changes && Menus.window.getItemCount() > Menus.WINDOW_MENU_ITEMS && !(IJ.macroRunning() && WindowManager.getImageCount() == 0)) { GenericDialog gd = new GenericDialog("ImageJ", this); gd.addMessage("Are you sure you want to quit ImageJ?"); gd.showDialog(); quitting = !gd.wasCanceled(); windowClosed = false; } if (!quitting) return; if (!WindowManager.closeAllWindows()) { quitting = false; return; } // IJ.log("savePreferences"); if (applet == null) { saveWindowLocations(); Prefs.savePreferences(); } IJ.cleanup(); // setVisible(false); // IJ.log("dispose"); dispose(); if (exitWhenQuitting) System.exit(0); }
/** Handles CheckboxMenuItem state changes. */ public void itemStateChanged(ItemEvent e) { MenuItem item = (MenuItem) e.getSource(); MenuComponent parent = (MenuComponent) item.getParent(); String cmd = e.getItem().toString(); if ((Menu) parent == Menus.window) WindowManager.activateWindow(cmd, item); else doCommand(cmd); }
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; }
private boolean showDialog() { String[] types = {"RAW", "JPEG", "ZLIB"}; GenericDialog gd = new GenericDialog("Generate Bricks"); gd.addChoice("FileType", types, filetype); gd.addNumericField("JPEG quality", jpeg_quality, 0); gd.addNumericField("Max file size (MB)", bdsizelimit, 0); int[] wlist = WindowManager.getIDList(); if (wlist == null) return false; String[] titles = new String[wlist.length]; for (int i = 0; i < wlist.length; i++) titles[i] = ""; int tnum = 0; for (int i = 0; i < wlist.length; i++) { ImagePlus imp = WindowManager.getImage(wlist[i]); if (imp != null) { titles[tnum] = imp.getTitle(); tnum++; } } gd.addChoice("Source image: ", titles, titles[0]); gd.showDialog(); if (gd.wasCanceled()) return false; filetype = types[gd.getNextChoiceIndex()]; jpeg_quality = (int) gd.getNextNumber(); if (jpeg_quality > 100) jpeg_quality = 100; if (jpeg_quality < 0) jpeg_quality = 0; bdsizelimit = (int) gd.getNextNumber(); int id = gd.getNextChoiceIndex(); lvImgTitle = new ArrayList<String>(); lvImgTitle.add(titles[id]); Prefs.set("filetype.string", filetype); Prefs.set("jpeg_quality.int", jpeg_quality); Prefs.set("bdsizelimit.int", bdsizelimit); return true; }
void saveWindowLocations() { Frame frame = WindowManager.getFrame("B&C"); if (frame != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, frame.getLocation()); frame = WindowManager.getFrame("Threshold"); if (frame != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, frame.getLocation()); frame = WindowManager.getFrame("Results"); if (frame != null) { Prefs.saveLocation(TextWindow.LOC_KEY, frame.getLocation()); Dimension d = frame.getSize(); Prefs.set(TextWindow.WIDTH_KEY, d.width); Prefs.set(TextWindow.HEIGHT_KEY, d.height); } frame = WindowManager.getFrame("Log"); if (frame != null) { Prefs.saveLocation(TextWindow.LOG_LOC_KEY, frame.getLocation()); Dimension d = frame.getSize(); Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width); Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height); } }
private boolean ignoreArrowKeys(ImagePlus imp) { Frame frame = WindowManager.getFrontWindow(); String title = frame.getTitle(); if (title != null && title.equals("ROI Manager")) return true; // Control Panel? if (frame != null && frame instanceof javax.swing.JFrame) return true; ImageWindow win = imp.getWindow(); // LOCI Data Browser window? if (imp.getStackSize() > 1 && win != null && win.getClass().getName().startsWith("loci")) return true; return false; }
void saveWindowLocations() { Window win = WindowManager.getWindow("B&C"); if (win != null) Prefs.saveLocation(ContrastAdjuster.LOC_KEY, win.getLocation()); win = WindowManager.getWindow("Threshold"); if (win != null) Prefs.saveLocation(ThresholdAdjuster.LOC_KEY, win.getLocation()); win = WindowManager.getWindow("Results"); if (win != null) { Prefs.saveLocation(TextWindow.LOC_KEY, win.getLocation()); Dimension d = win.getSize(); Prefs.set(TextWindow.WIDTH_KEY, d.width); Prefs.set(TextWindow.HEIGHT_KEY, d.height); } win = WindowManager.getWindow("Log"); if (win != null) { Prefs.saveLocation(TextWindow.LOG_LOC_KEY, win.getLocation()); Dimension d = win.getSize(); Prefs.set(TextWindow.LOG_WIDTH_KEY, d.width); Prefs.set(TextWindow.LOG_HEIGHT_KEY, d.height); } win = WindowManager.getWindow("ROI Manager"); if (win != null) Prefs.saveLocation(RoiManager.LOC_KEY, win.getLocation()); }
/** @param context */ public static void showDiagnosticInfo(final Context context) { try { DBG.m(" Build.VERSION.SDK_INT: " + Build.VERSION.SDK_INT); DBG.m(" Build.VERSION.CODENAME: " + Build.VERSION.CODENAME); DBG.m(" Build.DEVICE: " + android.os.Build.DEVICE); DBG.m(" Build.MODEL: " + android.os.Build.MODEL); DBG.m(" Build.PRODUCT: " + android.os.Build.PRODUCT); final DisplayMetrics displaymetrics = new DisplayMetrics(); final WindowManager windowmanager = (WindowManager) context.getSystemService(Context.WINDOW_SERVICE); windowmanager.getDefaultDisplay().getMetrics(displaymetrics); DBG.m(" DisplayMetrics.density: " + displaymetrics.density); DBG.m(" DisplayMetrics.densityDpi: " + displaymetrics.densityDpi); DBG.m(" DisplayMetrics.heightPixels: " + displaymetrics.heightPixels); DBG.m(" DisplayMetrics.widthPixels: " + displaymetrics.widthPixels); DBG.m(" DisplayMetrics.scaledDensity: " + displaymetrics.scaledDensity); DBG.m(" DisplayMetrics.xdpi: " + displaymetrics.xdpi); DBG.m(" DisplayMetrics.ydpi: " + displaymetrics.ydpi); } catch (Exception x) { DBG.m(x); } }
protected void registerActiveImage() { ImagePlus activeImage = WindowManager.getCurrentImage(); if (activeImage != null && activeImage.getProcessor() != null) { // && activeImage.getImageStackSize() > 1 if (currentImage != null && currentImage.getWindow() != null && currentImage != activeImage) { // System.out.println("remove listener:"+currentImage.getTitle()); ImageUtils.removeScrollListener(currentImage, this, this); currentImage.killRoi(); currentImage.updateAndDraw(); currentImage = null; } if (currentImage != activeImage) { // System.out.println("add listener:"+activeImage.getTitle()); ImageUtils.addScrollListener(activeImage, this, this); this.currentImage = activeImage; } } }
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) { Calibration gcal = imp.getGlobalCalibration(); if (gcal == null || !showConflictMessage || IJ.isMacro()) return; if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return; GenericDialog gd = new GenericDialog(imp.getTitle()); gd.addMessage("The calibration of this image conflicts\nwith the current global calibration."); gd.addCheckbox("Disable_Global Calibration", true); gd.addCheckbox("Disable_these Messages", false); gd.showDialog(); if (gd.wasCanceled()) return; boolean disable = gd.getNextBoolean(); if (disable) { imp.setGlobalCalibration(null); imp.setCalibration(cal); WindowManager.repaintImageWindows(); } boolean dontShow = gd.getNextBoolean(); if (dontShow) showConflictMessage = false; }
public EventGenerator(Simulator sim, RoadMap map, TimeHorizon T, int probPeople, int probParcel) { this.map = map; this.T = T; R = new Random(); r_id = 0; this.probPeople = probPeople; this.probParcel = probParcel; this.sim = sim; used = new HashMap<Integer, Boolean>(); for (int i = 0; i < sim.lstDepots.size(); i++) { int v = sim.lstDepots.get(i); used.put(v, true); } for (int i = 0; i < sim.lstParkings.size(); i++) { Parking p = sim.lstParkings.get(i); used.put(p.locationID, true); } WM = new WindowManager(map); WM.generateWindows(5, 5); }
public void run(String arg) { GenericDialog gd = new GenericDialog("Options"); double sfreq = 20000.0; gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null); String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"}; gd.addChoice("PSF Type?", psfchoice, psfchoice[0]); String[] filetypechoice = { "Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File" }; gd.addChoice("File Type?", filetypechoice, filetypechoice[0]); boolean ch2green = true; gd.addCheckbox("Ch2 is green?", ch2green); gd.showDialog(); if (gd.wasCanceled()) { return; } sfreq = gd.getNextNumber(); int psfflag = gd.getNextChoiceIndex(); int fileflag = gd.getNextChoiceIndex(); ch2green = gd.getNextBoolean(); int nfiles = 0; Object[] histograms = null; int xmax = 0; int ymax = 0; String[] names = null; if (fileflag < 2) { jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length / 2; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = organize_c3_files(filearray); for (int i = 0; i < nfiles; i++) { try { int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0); int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0); int length3 = (int) (((double) filearray[2 * i].length()) / 2.0); int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0); InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i])); InputStream instream2 = new BufferedInputStream(new FileInputStream(filearray[2 * i + 1])); if (fileflag == 0) { int[] pmdata = new int[length1]; int[] pmdata2 = new int[length2]; if (!ioclass.skipstreambytes(instream, 128)) { showioerror(); instream.close(); return; } if (!ioclass.skipstreambytes(instream2, 128)) { showioerror(); instream2.close(); return; } if (!ioclass.readintelintfile(instream, length1, pmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelintfile(instream2, length2, pmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000); } else { histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000); } } else { float[] tmdata = new float[length3]; float[] tmdata2 = new float[length4]; if (!ioclass.readintelshortfile(instream, length3, tmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata); } else { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2); } } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } instream.close(); instream2.close(); } catch (IOException e) { showioerror(); return; } } } else { if (fileflag == 2) { ImageWindow iw = WindowManager.getCurrentWindow(); float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues"); float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues"); sfreq = 1.0 / ((double) tempxvals[0][1]); nfiles = trajectories.length / 2; if (nfiles > 25) { nfiles = 25; } names = new String[nfiles + 1]; names[nfiles] = "avg"; histograms = new Object[nfiles]; for (int i = 0; i < nfiles; i++) { names[i] = "trajectory " + (i + 1); if (ch2green) { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]); } else { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]); } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } else { // here we read tab delimited lines from files jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = new String[nfiles + 1]; names[nfiles] = "avg"; for (int i = 0; i < nfiles; i++) { try { names[i] = filearray[i].getName(); BufferedReader d = new BufferedReader(new FileReader(filearray[i])); String[] lines = new String[256]; int counter = 0; do { lines[counter] = d.readLine(); counter++; } while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256); int numcolumns = 0; for (int j = 0; j < counter - 1; j++) { int temp = getncolumns(lines[j]); if (temp > numcolumns) { numcolumns = temp; } } float[][] temphist2 = null; if (ch2green) { temphist2 = new float[numcolumns][counter - 1]; } else { temphist2 = new float[counter - 1][numcolumns]; } for (int k = 0; k < counter - 1; k++) { float[] temp = tab_delim2float(lines[k]); for (int j = 0; j < numcolumns; j++) { if (ch2green) { temphist2[j][k] = temp[j]; } else { temphist2[k][j] = temp[j]; } } } histograms[i] = temphist2; d.close(); } catch (IOException e) { showioerror(); return; } } for (int i = 0; i < nfiles; i++) { if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } } // note that here x is green and y is red float[][][] pch = new float[nfiles][xmax][ymax]; for (int i = 0; i < nfiles; i++) { for (int j = 0; j < ((float[][]) histograms[i]).length; j++) { for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) { pch[i][j][k] = ((float[][]) histograms[i])[j][k]; } } } final PCH2DFitWindow cw = new PCH2DFitWindow(); cw.init(names, pch, psfflag); final Frame f = new Frame("PCH 2D Analysis"); f.setLocation(10, 10); f.addWindowListener( new WindowAdapter() { public void windowClosing(WindowEvent e) { f.dispose(); } }); f.add(cw); f.pack(); f.setResizable(false); Insets ins = f.getInsets(); cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65; cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right; f.setSize(cw.totalSize); f.setVisible(true); cw.requestFocus(); }
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 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 keyPressed(KeyEvent e) { // if (e.isConsumed()) return; int keyCode = e.getKeyCode(); IJ.setKeyDown(keyCode); hotkey = false; if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return; char keyChar = e.getKeyChar(); int flags = e.getModifiers(); if (IJ.debugMode) IJ.log( "keyPressed: code=" + keyCode + " (" + KeyEvent.getKeyText(keyCode) + "), char=\"" + keyChar + "\" (" + (int) keyChar + "), flags=" + KeyEvent.getKeyModifiersText(flags)); boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0; boolean control = (flags & KeyEvent.CTRL_MASK) != 0; boolean alt = (flags & KeyEvent.ALT_MASK) != 0; boolean meta = (flags & KeyEvent.META_MASK) != 0; String cmd = null; ImagePlus imp = WindowManager.getCurrentImage(); boolean isStack = (imp != null) && (imp.getStackSize() > 1); if (imp != null && !control && ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) { Roi roi = imp.getRoi(); if (roi instanceof TextRoi) { if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return; if (alt) { switch (keyChar) { case 'u': case 'm': keyChar = IJ.micronSymbol; break; case 'A': keyChar = IJ.angstromSymbol; break; default: } } ((TextRoi) roi).addChar(keyChar); return; } } // Handle one character macro shortcuts if (!control && !meta) { Hashtable macroShortcuts = Menus.getMacroShortcuts(); if (macroShortcuts.size() > 0) { if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200)); else cmd = (String) macroShortcuts.get(new Integer(keyCode)); if (cmd != null) { // MacroInstaller.runMacroCommand(cmd); commandName = cmd; MacroInstaller.runMacroShortcut(cmd); return; } } } if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') { Hashtable shortcuts = Menus.getShortcuts(); if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200)); else cmd = (String) shortcuts.get(new Integer(keyCode)); } if (cmd == null) { switch (keyChar) { case '<': case ',': if (isStack) cmd = "Previous Slice [<]"; break; case '>': case '.': case ';': if (isStack) cmd = "Next Slice [>]"; break; case '+': case '=': cmd = "In [+]"; break; case '-': cmd = "Out [-]"; break; case '/': cmd = "Reslice [/]..."; break; default: } } if (cmd == null) { switch (keyCode) { case KeyEvent.VK_TAB: WindowManager.putBehind(); return; case KeyEvent.VK_BACK_SPACE: // delete if (deleteOverlayRoi(imp)) return; cmd = "Clear"; hotkey = true; break; // case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start // Animation"; break; case KeyEvent.VK_EQUALS: cmd = "In [+]"; break; case KeyEvent.VK_MINUS: cmd = "Out [-]"; break; case KeyEvent.VK_SLASH: case 0xbf: cmd = "Reslice [/]..."; break; case KeyEvent.VK_COMMA: case 0xbc: if (isStack) cmd = "Previous Slice [<]"; break; case KeyEvent.VK_PERIOD: case 0xbe: if (isStack) cmd = "Next Slice [>]"; break; case KeyEvent.VK_LEFT: case KeyEvent.VK_RIGHT: case KeyEvent.VK_UP: case KeyEvent.VK_DOWN: // arrow keys if (imp == null) return; Roi roi = imp.getRoi(); if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return; boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown()); boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown(); if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]"; else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]"; else if (zoomKey && keyCode == KeyEvent.VK_DOWN && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]"; else if (zoomKey && keyCode == KeyEvent.VK_UP && !ignoreArrowKeys(imp) && Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]"; else if (roi != null) { if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode); else roi.nudge(keyCode); return; } break; case KeyEvent.VK_ESCAPE: abortPluginOrMacro(imp); return; case KeyEvent.VK_ENTER: WindowManager.toFront(this); return; default: break; } } if (cmd != null && !cmd.equals("")) { commandName = cmd; if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true; if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd); else { doCommand(cmd); keyPressedTime = System.currentTimeMillis(); lastKeyCommand = cmd; } } }
public void mousePressed(MouseEvent e) { Undo.reset(); if (!Prefs.noClickToGC) System.gc(); IJ.showStatus(version() + IJ.freeMemory()); if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount()); }
public void onCreate() { int flags, screenLightVal = 1; Sensor mSensor; List<Sensor> sensors; if (scanData == null) return; // no ScanData, not possible to run correctly... PowerManager pm = (PowerManager) getSystemService(POWER_SERVICE); SP = PreferenceManager.getDefaultSharedPreferences(getBaseContext()); try { screenLightVal = Integer.parseInt(SP.getString("screenLight", "2")); } catch (NumberFormatException nfe) { } if (screenLightVal == 1) flags = PowerManager.PARTIAL_WAKE_LOCK; else if (screenLightVal == 3) flags = PowerManager.FULL_WAKE_LOCK; else flags = PowerManager.SCREEN_DIM_WAKE_LOCK; wl = pm.newWakeLock(flags, "OpenWLANMap"); wl.acquire(); while (myWLocate == null) { try { myWLocate = new MyWLocate(this); break; } catch (IllegalArgumentException iae) { myWLocate = null; } try { Thread.sleep(100); } catch (InterruptedException ie) { } } try { scanData.setUploadThres(Integer.parseInt(SP.getString("autoUpload", "0"))); } catch (NumberFormatException nfe) { } try { scanData.setNoGPSExitInterval( Integer.parseInt(SP.getString("noGPSExitInterval", "0")) * 60 * 1000); } catch (NumberFormatException nfe) { } Intent intent = new Intent(this, OWMapAtAndroid.class); intent.setFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP | Intent.FLAG_ACTIVITY_SINGLE_TOP); PendingIntent pendIntent = PendingIntent.getActivity(this, 0, intent, 0); notification = new NotificationCompat.Builder(this) .setSmallIcon(R.drawable.icon) .setContentTitle(getResources().getText(R.string.app_name)) .setContentText("") .setContentIntent(pendIntent) .build(); notification.flags |= Notification.FLAG_NO_CLEAR; notification.flags |= Notification.FLAG_ONGOING_EVENT; startForeground(1703, notification); getScanData().setService(this); getScanData().setmView(new HUDView(this)); getScanData().getmView().setValue(getScanData().incStoredValues()); WindowManager.LayoutParams params = new WindowManager.LayoutParams( WindowManager.LayoutParams.TYPE_SYSTEM_OVERLAY, WindowManager.LayoutParams.FLAG_NOT_TOUCHABLE | WindowManager.LayoutParams.FLAG_NOT_FOCUSABLE, PixelFormat.TRANSLUCENT); params.gravity = Gravity.LEFT | Gravity.BOTTOM; params.setTitle("Load Average"); WindowManager wm = (WindowManager) getSystemService(WINDOW_SERVICE); wm.addView(getScanData().getmView(), params); sensorManager = (SensorManager) getSystemService(SENSOR_SERVICE); sensorManager.registerListener( this, sensorManager.getDefaultSensor(Sensor.TYPE_ACCELEROMETER), SensorManager.SENSOR_DELAY_GAME); sensorManager.registerListener( this, sensorManager.getDefaultSensor(Sensor.TYPE_ORIENTATION), SensorManager.SENSOR_DELAY_GAME); sensors = sensorManager.getSensorList(Sensor.TYPE_ACCELEROMETER); mSensor = sensors.get(0); getScanData().getTelemetryData().setAccelMax(mSensor.getMaximumRange()); telemetryDir = Environment.getExternalStorageDirectory().getPath() + "/telemetry/"; File dir = new File(telemetryDir); dir.mkdir(); connManager = (ConnectivityManager) getSystemService(CONNECTIVITY_SERVICE); }