public void initialize(String dir) throws IOException {
// Set Time Zone to UTC
formatUTC.setTimeZone(TimeZone.getTimeZone("UTC"));
this.dir = dir;
File f = new File(dir);
// Ensure the path is a directory
if (!f.isDirectory()) {
throw new IllegalArgumentException(f.getName() + " is not a directory.");
}
// Filter the list of files
File[] fa = f.listFiles(new FilenamePatternFilter(".*_[uvw].*\\.nc"));
if (fa == null) {
throw new IOException("File list is empty.");
}
for (File fil : fa) {
String name = fil.getName();
NetcdfFile ncf = NetcdfFile.open(fil.getPath());
tVar = ncf.findVariable(tName);
if (tVar == null) {
System.out.println(
"WARNING: Time variable "
+ tVar
+ " was not found in "
+ fil.getPath()
+ " when initializing the VelocityReader. This file will be skipped.");
continue;
}
Array arr = tVar.read();
// Convert into a java array
double[] ja = (double[]) arr.copyTo1DJavaArray();
// Determine the minimum and maximum times
long[] minmax = new long[2];
minmax[0] = TimeConvert.HYCOMToMillis((long) ja[0]);
minmax[1] = TimeConvert.HYCOMToMillis((long) ja[ja.length - 1]);
// Put into an index linking start time with the associated file
if (name.lastIndexOf("_u") > 0) {
if (uFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ uFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
uFiles.put(minmax[0], ncf);
}
}
if (name.lastIndexOf("_v") > 0) {
if (vFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ vFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
vFiles.put(minmax[0], ncf);
}
}
if (name.lastIndexOf("_w") > 0) {
if (wFiles.containsKey(minmax[0])) {
System.out.print(
"WARNING: Velocity files have duplicate time keys. "
+ name
+ "/"
+ wFiles.get(minmax[0])
+ " at "
+ new Date(minmax[0]));
System.out.println(" Skipping latter file.");
} else {
wFiles.put(minmax[0], ncf);
}
}
}
// If there are no files in one of the index collections, then exit.
if (uFiles.size() == 0 || vFiles.size() == 0 || wFiles.size() == 0) {
System.out.println(
"Velocity directory is empty, or files/variables are not named properly."
+ "Files must be named as *_u*, *_v*, and *_w*.");
System.exit(0);
}
uKeys = new ArrayList<Long>(uFiles.keySet());
vKeys = new ArrayList<Long>(vFiles.keySet());
wKeys = new ArrayList<Long>(wFiles.keySet());
// Populate uFile, vFile and wFile with the first entry so that they
// are not null
uFile = uFiles.get(uKeys.get(0));
vFile = vFiles.get(vKeys.get(0));
wFile = wFiles.get(wKeys.get(0));
uVar = uFile.findVariable(uName);
vVar = vFile.findVariable(vName);
wVar = wFile.findVariable(wName);
// Latitude and depth are read here because they should not change
// and therefore can be input once only.
latVar = uFile.findVariable(latName);
lonVar = uFile.findVariable(lonName);
zVar = uFile.findVariable(zName);
setXLookup(lonName);
setYLookup(latName);
setZLookup(zName);
if (positiveDown) {
zloc.setNegate(true);
}
bounds[0][0] = uKeys.get(0);
NetcdfFile lastfile = uFiles.get(uKeys.get(uKeys.size() - 1));
Variable t = lastfile.findVariable(tName);
double last;
try {
last = t.read(new int[] {t.getShape(0) - 1}, new int[] {1}).getDouble(0);
bounds[0][1] = TimeConvert.HYCOMToMillis((long) last);
} catch (InvalidRangeException e) {
e.printStackTrace();
}
}
