protected void read(DataInputStream in) {
if (in == null) {
err("NO input stream!");
}
try {
signature = FileUtils.getUInt32(in);
if (getSignature() != DAT_HEADER_SIGNATURE) {
err(
"Signature must be "
+ Long.toHexString(DAT_HEADER_SIGNATURE)
+ ", but was "
+ Long.toHexString(getSignature()));
}
setVersion(FileUtils.getUInt32(in));
headerSize = FileUtils.getUInt32(in);
dataSize = FileUtils.getUInt32(in);
if (getVersion() == 4) {
header = new PGMAcquisitionRegionHeader();
} else if (getVersion() == 3) {
header = new PGMAcquisitionHeader();
} else {
err("Unknown header version: " + getVersion());
}
header.read(in);
// p("read header: "+toString());
} catch (IOException ex) {
err("Could not read header info of acquisition", ex);
}
}
public String createConversionObject(String raw_dir, String cache_dir) {
String d = raw_dir;
if ((FileUtils.isUrl(d) && !FileUtils.exists(d + "acq_0000.dat"))
|| (!FileUtils.isUrl(d) && !(new File(d).exists()))) {
return "I cannot access the raw directory " + raw_dir + ", please check the path<br>";
}
File dir = new File(cache_dir);
if (!dir.exists()) {
return "I cannot access the cache directory " + dir + ", please check the path<br>";
}
if (!dir.canWrite()) {
return "I don't have write permssion in the ache directory "
+ dir
+ ", please change the path<br>";
}
conv = new Conversion[RawType.values().length];
String msg = "";
for (int i = 0; i < RawType.values().length; i++) {
RawType rtype = RawType.values()[i];
Conversion con = new Conversion(rtype);
conv[i] = con;
int nrfiles = RasterIO.getNrFiles(rtype, raw_dir);
con.max = nrfiles;
// count nr of flows so far
RawDataFacade io = RawDataFacade.getFacade(raw_dir, cache_dir, rtype);
int nrflowsSoFar = io.getNrFlowsInCache();
if (nrflowsSoFar < 0) {
String raw = io.getRawFilePath(rtype, raw_dir, 0);
if (raw != null && FileUtils.exists(raw)) {
p("I could not find the raw file or url " + raw + " (Myabe it's an old experiment?)<br>");
}
// else p("Problem with accessing raw file in " + raw_dir + " for type " + rtype + "<br>");
}
con.start = nrflowsSoFar;
// the end is between start and nrfiles so far
}
if (msg != null && msg.length() > 0) {
JOptionPane.showMessageDialog(null, "<html>RawFileConverter<br>" + msg + "</html>");
conv = null;
return msg;
}
return null;
}
private void initUrl(URL url) {
// this.file = file;
in = FileUtils.openUrl(url);
if (in == null) {
err("Could not open url " + url);
}
readHeader();
}
