/**
* @return the clipboard content as a String (DataFlavor.stringFlavor) Code snippet adapted from
* jEdit (Registers.java), http://www.jedit.org. Returns null if clipboard is empty.
*/
public static String getClipboardStringContent(Clipboard clipboard) {
// Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
try {
String selection =
(String) (clipboard.getContents(null).getTransferData(DataFlavor.stringFlavor));
if (selection == null) return null;
boolean trailingEOL =
(selection.endsWith("\n") || selection.endsWith(System.getProperty("line.separator")));
// Some Java versions return the clipboard contents using the native line separator,
// so have to convert it here , see jEdit's "registers.java"
BufferedReader in = new BufferedReader(new StringReader(selection));
StringBuffer buf = new StringBuffer();
String line;
while ((line = in.readLine()) != null) {
buf.append(line);
buf.append('\n');
}
// remove trailing \n
if (!trailingEOL) buf.setLength(buf.length() - 1);
return buf.toString();
} catch (Exception e) {
e.printStackTrace();
return null;
}
}
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");
}
}
/** Execute the system command 'cmd' and fill an ArrayList with the results. */
public static ArrayList<String> executeSystemCommand(String cmd) {
if (debug) System.out.println("cmd: " + cmd);
ArrayList<String> list = new ArrayList<>();
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec(/*comSpec +*/ cmd).getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
if (debug) System.out.println(line);
list.add(line);
}
} catch (IOException e) {
e.printStackTrace();
}
return list;
}
public static String ping(String address) {
String reply = "Request timed out";
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec("ping " + address).getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
if (line.trim().startsWith("Reply ")) {
reply = line;
break;
}
}
} catch (IOException e) {
e.printStackTrace();
}
return reply;
}
// =========================================================
public String recieve() throws IOException // RECIEVE METHOD
{
String recievedString;
recievedString = buffRdr.readLine();
System.out.println("RECD<<<< " + id + ": " + recievedString);
return recievedString;
}
public static Properties getEnvironmentVariables() {
synchronized (cygstartPath) {
if (envVars != null) return envVars;
envVars = new Properties();
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(RUNTIME.exec(comSpec + "env").getInputStream()))) {
for (String line = null; (line = br.readLine()) != null; ) {
// if (debug) System.out.println("getEnvironmentVariables(): line=" + line);
int idx = line.indexOf('=');
if (idx > 0) envVars.put(line.substring(0, idx), line.substring(idx + 1));
}
} catch (IOException e) {
e.printStackTrace();
}
return envVars;
}
}
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();
}
/**
* Paste the contents of the clipboard into the console buffer
*
* @return true if clipboard contents pasted
*/
public boolean paste() throws IOException {
Clipboard clipboard;
try { // May throw ugly exception on system without X
clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
} catch (Exception e) {
return false;
}
if (clipboard == null) {
return false;
}
Transferable transferable = clipboard.getContents(null);
if (transferable == null) {
return false;
}
try {
Object content = transferable.getTransferData(DataFlavor.plainTextFlavor);
/*
* This fix was suggested in bug #1060649 at
* http://sourceforge.net/tracker/index.php?func=detail&aid=1060649&group_id=64033&atid=506056
* to get around the deprecated DataFlavor.plainTextFlavor, but it
* raises a UnsupportedFlavorException on Mac OS X
*/
if (content == null) {
try {
content = new DataFlavor().getReaderForText(transferable);
} catch (Exception e) {
}
}
if (content == null) {
return false;
}
String value;
if (content instanceof Reader) {
// TODO: we might want instead connect to the input stream
// so we can interpret individual lines
value = "";
String line = null;
for (BufferedReader read = new BufferedReader((Reader) content);
(line = read.readLine()) != null; ) {
if (value.length() > 0) {
value += "\n";
}
value += line;
}
} else {
value = content.toString();
}
if (value == null) {
return true;
}
putString(value);
return true;
} catch (UnsupportedFlavorException ufe) {
if (debugger != null) debug(ufe + "");
return false;
}
}
/**
* Try to determine whether this application is running under Windows or some other platform by
* examining the "os.name" property.
*/
static {
String os = System.getProperty("os.name");
// String version = System.getProperty("os.version"); // for Win7, reports "6.0" on JDK7, should
// be "6.1"; for Win8, reports "6.2" as of JDK7u17
if (SystemUtils.startsWithIgnoreCase(os, "windows 7"))
isWin7 = true; // reports "Windows Vista" on JDK7
else if (SystemUtils.startsWithIgnoreCase(os, "windows 8"))
isWin7 = true; // reports "Windows 8" as of JDK7u17
else if (SystemUtils.startsWithIgnoreCase(os, "windows vista")) isVista = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows xp")) isWinXP = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows 2000")) isWin2k = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows nt")) isWinNT = true;
else if (SystemUtils.startsWithIgnoreCase(os, "windows"))
isWin9X = true; // win95 or win98 (what about WinME?)
else if (SystemUtils.startsWithIgnoreCase(os, "mac")) isMac = true;
else if (SystemUtils.startsWithIgnoreCase(os, "so")) isSolaris = true; // sunos or solaris
else if (os.equalsIgnoreCase("linux")) isLinux = true;
else isUnix = true; // assume UNIX, e.g. AIX, HP-UX, IRIX
String osarch = System.getProperty("os.arch");
String arch = (osarch != null && osarch.contains("64")) ? "_x64" /* eg. 'amd64' */ : "_x32";
String syslib = SYSLIB + arch;
try { // loading a native lib in a static initializer ensures that it is available before any
// method in this class is called:
System.loadLibrary(syslib);
System.out.println(
"Done loading '" + System.mapLibraryName(syslib) + "', PID=" + getProcessID());
} catch (Error e) {
System.err.println(
"Native library '"
+ System.mapLibraryName(syslib)
+ "' not found in 'java.library.path': "
+ System.getProperty("java.library.path"));
throw e; // re-throw
}
if (isWinPlatform()) {
System.setProperty(
"line.separator", "\n"); // so we won't have to mess with DOS line endings ever again
comSpec =
getEnv(
"comSpec"); // use native method here since getEnvironmentVariable() needs to know
// comSpec
comSpec = (comSpec != null) ? comSpec + " /c " : "";
try (BufferedReader br =
new BufferedReader(
new InputStreamReader(
RUNTIME.exec(comSpec + "ver").getInputStream()))) { // fix for Win7,8
for (String line = null; (line = br.readLine()) != null; ) {
if (isVista && (line.contains("6.1" /*Win7*/) || line.contains("6.2" /*Win8*/))) {
isVista = false;
isWin7 = true;
}
}
} catch (IOException e) {
e.printStackTrace();
}
String cygdir = getEnv("cygdir"); // this is set during CygWin install to "?:/cygwin/bin"
isCygWin = (cygdir != null && !cygdir.equals("%cygdir%"));
cygstartPath = cygdir + "/cygstart.exe"; // path to CygWin's cygutils' "cygstart" binary
if (getDebug() && Desktop.isDesktopSupported()) {
Desktop desktop = Desktop.getDesktop();
for (Desktop.Action action : Desktop.Action.values())
System.out.println(
"Desktop action " + action + " supported? " + desktop.isSupported(action));
}
}
}
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();
}
}