CTF - MEG SAM Analysis

Script

import java.awt.CardLayout;
import java.awt.Image;
import java.awt.Toolkit;
import java.io.File;
import java.util.HashMap;
import java.util.Map;

import javax.swing.ImageIcon;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.filechooser.FileFilter;

class FileExtFilter extends FileFilter {

	public FileExtFilter(String ext, String label, boolean includeDir) {
		this.ext = ext;
		this.label = label;
		this.includeDir = includeDir;
	}

	public String getDescription() {
		return this.label;
	}

	public boolean accept(File file) {
		if (file.isDirectory() && includeDir) {
			return true;
		} else {
			return file.getName().endsWith(this.ext);
		}
	}

	String ext, label;

	boolean includeDir;
}

if (title == void) {
	title = null;
}

if ((fileExtensions == void) || (fileExtensions == null)) {
	fileExtensions = "";
}

if ((fileExtLabels == void) || (fileExtLabels == null)) {
	fileExtLabels = "";
}

JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle(title);

String[] fileTypeList = fileExtensions.split(",");
String[] filterLabelList = fileExtLabels.split(",");

if (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {
	throw new RuntimeException("The list of extensions and file filter labels must be the same length");
}

// create the file filters
for (int i = 0; i < fileTypeList.length; i++) {
	FileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);
	chooser.setFileFilter(filter);
}

// folders only mod
chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);

chooser.showOpenDialog(null);
File file = chooser.getSelectedFile();
selectedFile = file.getAbsolutePath();

Script

import java.awt.CardLayout;
import java.awt.Image;
import java.awt.Toolkit;
import java.io.File;
import java.util.HashMap;
import java.util.Map;

import javax.swing.ImageIcon;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.filechooser.FileFilter;

class FileExtFilter extends FileFilter {

	public FileExtFilter(String ext, String label, boolean includeDir) {
		this.ext = ext;
		this.label = label;
		this.includeDir = includeDir;
	}

	public String getDescription() {
		return this.label;
	}

	public boolean accept(File file) {
		if (file.isDirectory() && includeDir) {
			return true;
		} else {
			return file.getName().endsWith(this.ext);
		}
	}

	String ext, label;

	boolean includeDir;
}

if (title == void) {
	title = null;
}

if ((fileExtensions == void) || (fileExtensions == null)) {
	fileExtensions = "";
}

if ((fileExtLabels == void) || (fileExtLabels == null)) {
	fileExtLabels = "";
}

JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle(title);

String[] fileTypeList = fileExtensions.split(",");
String[] filterLabelList = fileExtLabels.split(",");

if (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {
	throw new RuntimeException("The list of extensions and file filter labels must be the same length");
}

// create the file filters
for (int i = 0; i < fileTypeList.length; i++) {
	FileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);
	chooser.setFileFilter(filter);
}

chooser.showOpenDialog(null);
File file = chooser.getSelectedFile();
selectedFile = file.getAbsolutePath();

Script

if (command == void || command.equals("")) {
	throw new RuntimeException("The 'command' port cannot be null.");
}

String cmd = ctf+command+" -d "+dataset+" -s "+shape+" -M -v";

Process proc = null;
Runtime rt = Runtime.getRuntime();

proc = rt.exec(cmd);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();
  

Value

Script

BufferedReader getReader (String fileUrl) throws IOException {
		InputStreamReader reader;
		try {
			reader = new FileReader(fileUrl);
		}
		catch (FileNotFoundException e) {
			// try a real URL instead
			URL url = new URL(fileUrl);
			reader = new InputStreamReader (url.openStream());
		}
		return new BufferedReader(reader);
	}



StringBuffer sb = new StringBuffer(4000);

BufferedReader in = getReader(fileurl);
String str;
String lineEnding = System.getProperty("line.separator");

while ((str = in.readLine()) != null) {
	sb.append(str);
	sb.append(lineEnding);
}
in.close();
filecontents = sb.toString();
  

Script

import java.awt.CardLayout;
import java.awt.Image;
import java.awt.Toolkit;
import java.io.File;
import java.util.HashMap;
import java.util.Map;

import javax.swing.ImageIcon;
import javax.swing.JEditorPane;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.filechooser.FileFilter;

class FileExtFilter extends FileFilter {

	public FileExtFilter(String ext, String label, boolean includeDir) {
		this.ext = ext;
		this.label = label;
		this.includeDir = includeDir;
	}

	public String getDescription() {
		return this.label;
	}

	public boolean accept(File file) {
		if (file.isDirectory() && includeDir) {
			return true;
		} else {
			return file.getName().endsWith(this.ext);
		}
	}

	String ext, label;

	boolean includeDir;
}

if (title == void) {
	title = null;
}

if ((fileExtensions == void) || (fileExtensions == null)) {
	fileExtensions = "";
}

if ((fileExtLabels == void) || (fileExtLabels == null)) {
	fileExtLabels = "";
}

JFileChooser chooser = new JFileChooser();
chooser.setDialogTitle(title);

String[] fileTypeList = fileExtensions.split(",");
String[] filterLabelList = fileExtLabels.split(",");

if (fileTypeList != null && filterLabelList != null && fileTypeList.length != filterLabelList.length) {
	throw new RuntimeException("The list of extensions and file filter labels must be the same length");
}

// create the file filters
for (int i = 0; i < fileTypeList.length; i++) {
	FileExtFilter filter = new FileExtFilter(fileTypeList[i], filterLabelList[i], true);
	chooser.setFileFilter(filter);
}

chooser.showOpenDialog(null);
File file = chooser.getSelectedFile();
selectedFile = file.getAbsolutePath();

Script

// parse protocol file
// look for csv bands and piped triggers
String[] pFileLines = protocol.split("\\n");
String[] bands;

ArrayList windows = new ArrayList();
ArrayList windowFiles = new ArrayList();

for(int i=0;i1)
	{
		if(pFileLines[i].indexOf(",")>0)
		{ // freq bands
			bands = pFileLines[i].split(";");
		}

		if(pFileLines[i].indexOf("|")>0)
		{ // time window
			 windows.add(pFileLines[i]);
		}
	}	
}

String out0;

// create file for each window
for(int x=0;x

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Script

import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;

ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));

messagePanel.add(new JLabel((message == void ? null : message)));
		
JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
for (int i = 0; i < buttonArray.length; i++) {			
	buttonArray[i] = new JRadioButton(selectionValues.get(i));
	if (i==0) buttonArray[i].setSelected(true);
	group.add(buttonArray[i]);
	messagePanel.add(buttonArray[i]);
}				

JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
		JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
		
String answer="";
for (JRadioButton button : buttonArray) {
	if (button.isSelected()) {
		answer=button.getText();
	}
}

Value

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Script

if(choice!="Skip")
{

Process proc = null;
Runtime rt = Runtime.getRuntime();

String cmd = ctf+"SAMMenu "+ds;

proc = rt.exec(cmd);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();
}
  

Script

import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JRadioButton;

ButtonGroup group = new ButtonGroup();
JPanel messagePanel = new JPanel();
messagePanel.setLayout(new BoxLayout(messagePanel,BoxLayout.Y_AXIS));

messagePanel.add(new JLabel((message == void ? null : message)));
		
JRadioButton[] buttonArray = new JRadioButton[selectionValues.size()];
for (int i = 0; i < buttonArray.length; i++) {			
	buttonArray[i] = new JRadioButton(selectionValues.get(i));
	if (i==0) buttonArray[i].setSelected(true);
	group.add(buttonArray[i]);
	messagePanel.add(buttonArray[i]);
}				

JOptionPane.showOptionDialog(null, messagePanel, (title == void ? null : title),
		JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, new Object[]{"OK"}, null);
		
String answer="";
for (JRadioButton button : buttonArray) {
	if (button.isSelected()) {
		answer=button.getText();
	}
}

Value

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Script

if(choice!="Skip")
{
String cmd = ctf+"MRIViewer";

Process proc = null;
Runtime rt = Runtime.getRuntime();

proc = rt.exec(cmd);

// Get the input stream and read from it
InputStream in = proc.getInputStream();

int c;
StringBuffer sb = new StringBuffer();
while ((c = in.read()) != -1) {
	sb.append((char) c);
}
in.close();
result = sb.toString();

}
  

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Script

import javax.swing.JOptionPane;

JOptionPane.showMessageDialog(null, (message == void ? null : message), (title == void ? null : title),	JOptionPane.INFORMATION_MESSAGE);

answer = "answer";

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