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import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
import ij.plugin.frame.*;
import ij.plugin.filter.PlugInFilter;
import ij.*;
import ij.io.*;
import ij.plugin.*;
import ij.plugin.filter.*;
import java.awt.event.*;
import java.awt.geom.*;
import java.util.*;
import java.util.zip.*;
import java.io.*;
import javax.swing.*;
import javax.swing.event.*;
import java.lang.InterruptedException;
import java.lang.System;
import java.lang.Math.*;
class XYPair
{
public int x, y;
@Override
public boolean equals(Object o)
{
XYPair p = (XYPair)o;
return p.x == x && p.y == y;
}
int hash(int x)
{
x = ((x >> 16) ^ x) * 0x45d9f3b;
x = ((x >> 16) ^ x) * 0x45d9f3b;
x = ((x >> 16) ^ x);
return x;
}
@Override
public int hashCode()
{
int seed = hash(x);
seed ^= hash(y) + 0x9e3779b9 + (seed << 6) + (seed >> 2);
return seed;
}
};
///Plugin class to load up an old 3B run.
///
///@ingroup gPlugin
public class QuickPalmLoader implements PlugIn {
private void close(InputStream i)
{
//Not sure what to do here...
if(i != null)
{
try{
i.close();
}
catch(IOException ioe)
{
Toolkit.getDefaultToolkit().beep();
ij.IJ.showStatus("Error closing file: " + ioe.getMessage());
}
}
}
public void run(String arg) {
InputStream in = null;
String name;
double ini_FWHM=100., ini_reconstruction_pixel_size=10.;
boolean show_control_panel=true;
boolean do_filtering=true;
final double pixel_size_in_nm_ = 200; //Make a fake pixel size because we need one
try{
OpenDialog o = new OpenDialog("Open QuickPalm data...", null);
name = o.getFileName();
try{
in = new FileInputStream(o.getDirectory() + o.getFileName());
}
catch(java.io.FileNotFoundException ferr)
{
Toolkit.getDefaultToolkit().beep();
ij.IJ.showStatus("Error opening file: " + ferr.getMessage());
return;
}
GenericDialog g = new GenericDialog("Reconstruction Parameters");
g.addNumericField("FWHM (initial) ", ini_FWHM, 0, 5, "nm");
g.addNumericField("Reconstruction size (initial)", ini_reconstruction_pixel_size, 0, 5, "nm");
g.addCheckbox("Show control panel", show_control_panel);
((Checkbox)g.getCheckboxes().get(0)).hide();
g.showDialog();
ini_FWHM = g.getNextNumber();
ini_reconstruction_pixel_size=g.getNextNumber();
show_control_panel=g.getNextBoolean();
//Yay @ cargoculting
InputStreamReader d = new InputStreamReader(in);
BufferedReader r = new BufferedReader(d);
String line;
final ArrayList<Spot> spots = new ArrayList<Spot>();
int iterations=0;
Rectangle roi=null;
HashSet<XYPair> filter_sdddash = new HashSet<XYPair>();
int line_number=0;
int frames=0;
double max_val = 0; //Assume square image: almost all scientific imagers are close enough to square
for( ; (line = r.readLine()) != null; line_number++)
{
//discard the header
if(line_number == 0)
continue;
String tokens[] = line.split("\\p{Space}+");
//Tokens are:
//number intensity xpx ypx xnm ynm ...
if((tokens.length) < 15)
throw new IOException("corrupt file (short line)");
Spot s = new Spot();
try
{
s.x = Double.parseDouble(tokens[4]) / pixel_size_in_nm_;
s.y = Double.parseDouble(tokens[5]) / pixel_size_in_nm_;
//QuickPalm has the frame number as a double, but is always integral
int frame = (int)Double.parseDouble(tokens[14]);
if(frame > frames)
frames = frame;
if(s.x > max_val)
max_val = s.x;
if(s.y > max_val)
max_val = s.y;
}
catch(NumberFormatException nerr)
{
throw new IOException("corrupt file (bad spot position)");
}
spots.add(s);
}
roi = new Rectangle(0, 0, (int)Math.ceil(max_val), (int)Math.ceil(max_val));
if(show_control_panel)
{
final String fname = name;
final Rectangle roi_ = roi;
final int its = iterations;
final double ini_FWHM_ = ini_FWHM;
final double ini_reconstruction_pixel_size_ = ini_reconstruction_pixel_size;
final String msg = "Using " + fname + ": " + Integer.toString(frames) + " frames, " + Integer.toString(spots.size()) + " localisations .";
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
EControlPanel e = new EControlPanel(roi_, pixel_size_in_nm_, fname, null);
e.append(spots, 100000); // 100000 == frames, to stop "Export" button from being red as a warning. This qualifies as lolhax
e.send_update_canvas_event();
e.send_status_text_message(msg);
e.set_reconstructed_pixel_size(ini_reconstruction_pixel_size_);
e.set_reconstruction_blur_fwhm(ini_FWHM_);
e.send_update_canvas_event();
}
}
);
}
else
{
System.out.println("etf\n");
double zoom=pixel_size_in_nm_ / ini_reconstruction_pixel_size;
ImagePlus linear_reconstruction;
linear_reconstruction = new ImagePlus();
linear_reconstruction.setProcessor(Reconstruction.reconstruct(roi, zoom, ini_FWHM, pixel_size_in_nm_, spots));
linear_reconstruction.show();
}
}
catch(IOException another_ioe){
Toolkit.getDefaultToolkit().beep();
ij.IJ.showStatus("Error reading data: " + another_ioe.getMessage());
}
finally{
close(in);
}
}
}
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