//
// ExtractSDTData.java
//
import java.io.*;
import loci.formats.in.SDTReader;
/**
* Reads SDT files and creates text files containing histogram data.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/utils/ExtractSDTData.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/utils/ExtractSDTData.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class ExtractSDTData {
public static void main(String[] args) throws Exception {
if (args.length < 1) {
System.out.println("Usage: java ExtractSDTData file.sdt");
System.exit(1);
}
String id = args[0];
String tid = id.substring(0, id.indexOf("."));
SDTReader r = new SDTReader();
r.setId(id);
int bins = r.getTimeBinCount();
int chan = r.getChannelCount();
int w = r.getSizeX();
int h = r.getSizeY();
System.out.println("Data is " + w + " x " + h +
", bins=" + bins + ", channels=" + chan);
byte[][] data = new byte[chan][h * w * bins * 2];
for (int c=0; c<chan; c++) {
System.out.println("Reading channel #" + c + "...");
r.openBytes(c, data[c]);
int i = 0;
for (int y=0; y<h; y++) {
for (int x=0; x<w; x++) {
String oid = tid + "-c" + c + "-row" + y + "-col" + x;
System.out.println(oid);
PrintWriter out = new PrintWriter(new FileWriter(oid));
for (int b=0; b<bins; b++) {
i += 2;
int v0 = data[c][i];
int v1 = data[c][i + 1];
int v = (v0 << 8) & v1;
out.println(b + " " + v);
}
out.close();
}
}
}
}
}