/*
* Copyright 2010-2012 University Corporation for Atmospheric Research/Unidata
*
* Portions of this software were developed by the Unidata Program at the
* University Corporation for Atmospheric Research.
*
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* any fee or cost, to use, copy, modify, alter, enhance and distribute
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*/
package ucar.nc2.iosp.noaa;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.iosp.AbstractIOServiceProvider;
import ucar.nc2.ncml.NcmlConstructor;
import ucar.nc2.util.CancelTask;
import ucar.unidata.io.RandomAccessFile;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Nomads IGRA files.
* Can open all data by opening "igra-stations.txt", with data files in subdir "igra-por".
* Can open single station data by opening <stationId>.dat with igra-stations.txt in same or parent directory.
* - IGRA - Integrated Global Radiosonde Archive
* LOOK probably file leaks
* @author caron
* @see "http://www.ncdc.noaa.gov/oa/climate/igra/"
* @see "ftp://ftp.ncdc.noaa.gov/pub/data/igra"
* @since 3/3/11
*/
public class IgraPor extends AbstractIOServiceProvider {
private static final String dataPatternRegexp =
"(\\d{2})([ \\-\\d]{6})(.)([ \\-\\d]{5})(.)([ \\-\\d]{5})(.)([ \\-\\d]{5})([ \\-\\d]{5})([ \\-\\d]{5})$";
private static final String dataHeaderPatternRegexp =
"#(\\d{5})(\\d{4})(\\d{2})(\\d{2})(\\d{2})(\\d{4})([ \\d]{4})$";
private static final String stnPatternRegexp =
"([A-Z]{2}) (\\d{5}) (.{35}) ([ \\.\\-\\d]{6}) ([ \\.\\-\\d]{7}) ([ \\-\\d]{4}) (.)(.)(.) ([ \\d]{4}) ([ \\d]{4})$";
private static final Pattern dataPattern = Pattern.compile(dataPatternRegexp);
private static final Pattern dataHeaderPattern = Pattern.compile(dataHeaderPatternRegexp);
private static final Pattern stnPattern = Pattern.compile(stnPatternRegexp);
private static final String STNID = "stnid";
private static final String STN_FILE = "igra-stations.txt";
private static final String DAT_EXT = ".dat";
private static final String DAT_DIR = "igra-por";
private static final String IDX_EXT = ".ncx";
private static final String MAGIC_START_IDX = "IgraPorIndex";
private static final int version = 1;
@Override
public boolean isValidFile(RandomAccessFile raf) throws IOException {
String location = raf.getLocation();
File file = new File(location);
int pos = location.lastIndexOf(".");
if (pos <= 0) return false;
String base = location.substring(0, pos);
String ext = location.substring(pos);
// must be data file or station file or index file
if (!ext.equals(DAT_EXT) && !ext.equals(IDX_EXT) && !file.getName().equals(STN_FILE))
return false;
if (ext.equals(IDX_EXT)) {
// data, stn files must be in the same directory
File datFile = new File(base + DAT_EXT);
if (!datFile.exists())
return false;
File stnFile = getStnFile(location);
if (stnFile == null || !stnFile.exists())
return false;
raf.seek(0);
String test = raf.readString(MAGIC_START_IDX.length());
return test.equals(MAGIC_START_IDX);
} else if (ext.equals(DAT_EXT)) {
File stnFile = getStnFile(location);
return stnFile != null && isValidFile(raf, dataHeaderPattern);
} else {
// data directory must exist
File dataDir = new File(file.getParentFile(), DAT_DIR);
return dataDir.exists() && dataDir.isDirectory() && isValidFile(raf, stnPattern);
}
}
// stn file must be in the same directory or one up
private File getStnFile(String location) {
File file = new File(location);
File stnFile = new File(file.getParentFile(), STN_FILE);
if (!stnFile.exists()) {
if (file.getParentFile() == null) return null;
stnFile = new File(file.getParentFile().getParentFile(), STN_FILE);
if (!stnFile.exists()) return null;
}
return stnFile;
}
private boolean isValidFile(RandomAccessFile raf, Pattern p) throws IOException {
raf.seek(0);
String line;
while (true) {
line = raf.readLine();
if (line == null) break;
if (line.trim().length() == 0) continue;
Matcher matcher = p.matcher(line);
return matcher.matches();
}
return false;
}
@Override
public String getFileTypeId() {
return "IGRA-POR";
}
@Override
public String getFileTypeDescription() {
return "Integrated Global Radiosonde Archive";
}
@Override
public String getFileTypeVersion() {
return Integer.toString(version);
}
/////////////////////////////////////////////////////////////////////////
private RandomAccessFile stnRaf, dataRaf;
private File dataDir;
//private HashMap<Long, StationIndex> map = new HashMap<Long, StationIndex>(10000);
private int stn_fldno;
private StructureDataRegexp.Vinfo stnVinfo, seriesVinfo, profileVinfo;
private String stationId; // if a DAT file
@Override
public void open(RandomAccessFile raff, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
super.open(raff, ncfile, cancelTask);
int pos = location.lastIndexOf(".");
String ext = location.substring(pos);
File file = new File(location);
File stnFile = getStnFile(location);
if (stnFile == null)
throw new FileNotFoundException("Station File does not exist="+location);
if (ext.equals(IDX_EXT)) {
stnRaf = RandomAccessFile.acquire(stnFile.getPath());
} else if (ext.equals(DAT_EXT)) {
stnRaf = RandomAccessFile.acquire(stnFile.getPath());
dataRaf = raff;
//extract the station id
String name = file.getName();
stationId = name.substring(0, name.length() - DAT_EXT.length());
} else { // pointed to the station file
stnRaf = raff;
dataDir = new File(file.getParentFile(), DAT_DIR);
}
NcmlConstructor ncmlc = new NcmlConstructor();
if (!ncmlc.populateFromResource("resources/nj22/iosp/igra-por.ncml", ncfile)) {
throw new IllegalStateException(ncmlc.getErrlog().toString());
}
ncfile.finish();
//dataVinfo = setVinfo(dataRaf, ncfile, dataPattern, "all_data");
stnVinfo = setVinfo(stnRaf, ncfile, stnPattern, "station");
seriesVinfo = setVinfo(stnRaf, ncfile, dataHeaderPattern, "station.time_series");
profileVinfo = setVinfo(stnRaf, ncfile, dataPattern, "station.time_series.levels");
StructureMembers.Member m = stnVinfo.sm.findMember(STNID);
StructureDataRegexp.VinfoField f = (StructureDataRegexp.VinfoField) m.getDataObject();
stn_fldno = f.fldno;
/* make index file if needed
File idxFile = new File(base + IDX_EXT);
if (!idxFile.exists())
makeIndex(stnVinfo, dataVinfo, idxFile);
else
readIndex(idxFile.getPath()); */
}
private StructureDataRegexp.Vinfo setVinfo(RandomAccessFile raff, NetcdfFile ncfile, Pattern p, String seqName) {
Sequence seq = (Sequence) ncfile.findVariable(seqName);
StructureMembers sm = seq.makeStructureMembers();
StructureDataRegexp.Vinfo result = new StructureDataRegexp.Vinfo(raff, sm, p);
seq.setSPobject(result);
int fldno = 1;
for (StructureMembers.Member m : sm.getMembers()) {
StructureDataRegexp.VinfoField vf = new StructureDataRegexp.VinfoField(fldno++);
Variable v = seq.findVariable(m.getName());
Attribute att = v.findAttribute("iosp_scale");
if (att != null) {
vf.hasScale = true;
vf.scale = att.getNumericValue().floatValue();
//v.remove(att);
}
m.setDataObject(vf);
}
return result;
}
public void close() throws java.io.IOException {
if (stnRaf != null) stnRaf.close();
if (dataRaf != null) dataRaf.close();
stnRaf = null;
dataRaf = null;
}
////////////////////////////////////////////////////////////////////
@Override
public Array readData(Variable v2, Section section) throws IOException, InvalidRangeException {
StructureDataRegexp.Vinfo vinfo = (StructureDataRegexp.Vinfo) v2.getSPobject();
if (stationId != null)
return new ArraySequence(vinfo.sm, new SingleStationSeqIter(vinfo), vinfo.nelems);
else
return new ArraySequence(vinfo.sm, new StationSeqIter(vinfo), vinfo.nelems);
}
@Override
public StructureDataIterator getStructureIterator(Structure s, int bufferSize) throws java.io.IOException {
StructureDataRegexp.Vinfo vinfo = (StructureDataRegexp.Vinfo) s.getSPobject();
if (stationId != null)
return new SingleStationSeqIter(vinfo);
else
return new StationSeqIter(vinfo);
}
// when theres only one station
private class SingleStationSeqIter implements StructureDataIterator {
private StructureDataRegexp.Vinfo vinfo;
private int recno = 0;
SingleStationSeqIter(StructureDataRegexp.Vinfo vinfo) throws IOException {
this.vinfo = vinfo;
vinfo.rafile.seek(0);
}
@Override
public StructureDataIterator reset() {
recno = 0;
return this;
}
@Override
public boolean hasNext() throws IOException {
return recno == 0;
}
@Override
public StructureData next() throws IOException {
Matcher matcher;
while (true) {
String line = vinfo.rafile.readLine();
if (line == null) return null;
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
//System.out.printf("line %s%n", line);
matcher = vinfo.p.matcher(line);
if (matcher.matches()) {
String stnid = matcher.group(stn_fldno).trim();
if (stnid.equals(stationId)) break;
}
}
recno++;
return new StationData(vinfo.sm, matcher);
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return recno - 1;
}
@Override
public void finish() {
// ignored
}
}
// sequence of stations
private class StationSeqIter implements StructureDataIterator {
private StructureDataRegexp.Vinfo vinfo;
private long totalBytes;
private int recno;
private StructureData curr;
StationSeqIter(StructureDataRegexp.Vinfo vinfo) throws IOException {
this.vinfo = vinfo;
totalBytes = (int) vinfo.rafile.length();
vinfo.rafile.seek(0);
}
@Override
public StructureDataIterator reset() {
recno = 0;
try {
vinfo.rafile.seek(0);
} catch (IOException e) {
throw new RuntimeException(e);
}
return this;
}
@Override
public boolean hasNext() throws IOException {
boolean more = (vinfo.rafile.getFilePointer() < totalBytes); // && (recno < 10);
if (!more) {
vinfo.nelems = recno;
//System.out.printf("nelems=%d%n", recno);
return false;
}
curr = reallyNext();
more = (curr != null);
if (!more) {
vinfo.nelems = recno;
//System.out.printf("nelems=%d%n", recno);
return false;
}
return more;
}
@Override
public StructureData next() throws IOException {
return curr;
}
private StructureData reallyNext() throws IOException {
Matcher matcher;
while (true) {
String line = vinfo.rafile.readLine();
if (line == null) return null;
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
//System.out.printf("line %s%n", line);
matcher = vinfo.p.matcher(line);
if (matcher.matches())
break;
System.out.printf("FAIL %s%n", line);
}
recno++;
return new StationData(vinfo.sm, matcher);
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return recno - 1;
}
@Override
public void finish() {
// ignored
}
}
private class StationData extends StructureDataRegexp {
StationData(StructureMembers members, Matcher matcher) {
super(members, matcher);
}
@Override
// nested array sequence must be the stn_data
public ArraySequence getArraySequence(StructureMembers.Member m) {
String stnid = matcher.group(stn_fldno).trim();
return new ArraySequence(seriesVinfo.sm, new TimeSeriesIter(stnid), -1);
}
}
//////////////////////////////////////////////////////
// sequence of time series for one station
private class TimeSeriesIter implements StructureDataIterator {
private int countRead = 0;
private long totalBytes;
private File file;
private RandomAccessFile timeSeriesRaf = null;
private boolean exists;
TimeSeriesIter(String stnid) {
if (dataRaf != null)
exists = true;
else {
this.file = new File(dataDir, stnid + DAT_EXT);
exists = file.exists();
}
}
private void init() {
if (!exists) return;
try {
if (dataRaf != null)
this.timeSeriesRaf = dataRaf; // single station case - data file already open
else
this.timeSeriesRaf = RandomAccessFile.acquire(file.getPath());
totalBytes = timeSeriesRaf.length();
timeSeriesRaf.seek(0);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
@Override
public StructureDataIterator reset() {
if (!exists) return this;
if (timeSeriesRaf == null) init();
countRead = 0;
try {
timeSeriesRaf.seek(0);
} catch (IOException e) {
throw new RuntimeException(e);
}
return this;
}
@Override
public boolean hasNext() throws IOException {
if (!exists) return false;
if (timeSeriesRaf == null) init();
return (timeSeriesRaf.getFilePointer() < totalBytes); // && (recno < 10); LOOK not perfect, eg trailing blanks
}
@Override
public StructureData next() throws IOException {
Matcher matcher;
String line;
while (true) {
line = timeSeriesRaf.readLine();
if (line == null) return null; // only on EOF
if (line.trim().length() == 0) continue;
matcher = seriesVinfo.p.matcher(line);
if (matcher.matches())
break;
System.out.printf("FAIL TimeSeriesIter <%s>%n", line);
}
countRead++;
return new TimeSeriesData(matcher);
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return countRead - 1;
}
@Override
public void finish() {
try {
if (this.timeSeriesRaf != null && this.timeSeriesRaf != dataRaf) {
timeSeriesRaf.close();
timeSeriesRaf = null;
}
} catch (IOException e) {
e.printStackTrace();
}
}
private class TimeSeriesData extends StructureDataRegexp {
// Matcher matcher; // matcher on the station ascii
List<String> lines = new ArrayList<>(30);
TimeSeriesData(Matcher matcher) throws IOException {
super(seriesVinfo.sm, matcher);
String line;
long pos;
while (true) {
pos = timeSeriesRaf.getFilePointer();
line = timeSeriesRaf.readLine();
if (line == null) break;
if (line.trim().length() == 0) continue;
matcher = profileVinfo.p.matcher(line);
if (matcher.matches())
lines.add(line);
else {
timeSeriesRaf.seek(pos); // put the line back
break;
}
}
}
@Override
// nested array sequence must be the stn_data
public ArraySequence getArraySequence(StructureMembers.Member m) {
return new ArraySequence(profileVinfo.sm, new ProfileIter(), -1);
}
//////////////////////////////////////////////////////
// sequence of levels for one profile = station-timeSeries
private class ProfileIter implements StructureDataIterator {
private int countRead;
ProfileIter() {
countRead = 0;
}
@Override
public StructureDataIterator reset() {
countRead = 0;
return this;
}
@Override
public boolean hasNext() throws IOException {
return countRead < lines.size();
}
@Override
public StructureData next() throws IOException {
if (!hasNext()) return null;
Matcher matcher = profileVinfo.p.matcher(lines.get(countRead));
StructureData sd;
if (matcher.matches())
sd = new StructureDataRegexp(profileVinfo.sm, matcher);
else
throw new IllegalStateException("line = " + lines.get(countRead) + "pattern = " + profileVinfo.p);
countRead++;
return sd;
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return countRead - 1;
}
@Override
public void finish() {
// ignored
}
}
}
}
///////////////////////////////////////////
/*
private void readIndex(String indexFilename) throws IOException {
FileInputStream fin = new FileInputStream(indexFilename);
if (!NcStream.readAndTest(fin, MAGIC_START_IDX.getBytes("UTF-8")))
throw new IllegalStateException("bad index file");
int version = fin.read();
if (version != 1)
throw new IllegalStateException("Bad version = " + version);
int count = NcStream.readVInt(fin);
for (int i = 0; i < count; i++) {
int size = NcStream.readVInt(fin);
byte[] pb = new byte[size];
NcStream.readFully(fin, pb);
StationIndex si = decodeStationIndex(pb);
map.put(si.stnId, si);
}
fin.close();
System.out.println(" read index map size=" + map.values().size());
}
private void makeIndex(StructureDataRegexp.Vinfo stnInfo, StructureDataRegexp.Vinfo dataInfo, File indexFile) throws IOException {
// get map of Stations
StructureMembers.Member m = stnInfo.sm.findMember(STNID);
StructureDataRegexp.VinfoField f = (StructureDataRegexp.VinfoField) m.getDataObject();
int stnCount = 0;
// read through entire file LOOK: could use SeqIter
stnInfo.rafile.seek(0);
while (true) {
long stnPos = stnInfo.rafile.getFilePointer();
String line = stnInfo.rafile.readLine();
if (line == null) break;
Matcher matcher = stnInfo.p.matcher(line);
if (!matcher.matches()) {
System.out.printf("FAIL %s%n", line);
continue;
}
String svalue = matcher.group(f.fldno);
Long id = Long.parseLong(svalue.trim());
StationIndex s = new StationIndex();
s.stnId = id;
s.stnPos = stnPos;
map.put(id, s);
stnCount++;
}
// assumes that the stn data is in order by stnId
m = dataInfo.sm.findMember(STNID);
f = (StructureDataRegexp.VinfoField) m.getDataObject();
StationIndex currStn = null;
int totalCount = 0;
// read through entire data file
dataInfo.rafile.seek(0);
while (true) {
long dataPos = dataInfo.rafile.getFilePointer();
String line = dataInfo.rafile.readLine();
if (line == null) break;
Matcher matcher = dataInfo.p.matcher(line);
if (!matcher.matches()) {
System.out.printf("FAIL %s%n", line);
continue;
}
String svalue = matcher.group(f.fldno).trim();
Long id = Long.parseLong(svalue);
if ((currStn == null) || (currStn.stnId != id)) {
StationIndex s = map.get(id);
if (s == null)
System.out.printf("Cant find %d%n", id);
else if (s.dataCount != 0)
System.out.printf("Not in order %d at pos %d %n", id, dataPos);
else {
s.dataPos = dataPos;
totalCount++;
}
currStn = s;
}
currStn.dataCount++;
}
//System.out.printf("ok stns=%s data=%d%n", stnCount, totalCount);
//////////////////////////////
// write the index file
FileOutputStream fout = new FileOutputStream(indexFile); // LOOK need DiskCache for non-writeable directories
long size = 0;
//// header message
fout.write(MAGIC_START_IDX.getBytes("UTF-8"));
fout.write(version);
size += NcStream.writeVInt(fout, stnCount);
/* byte[] pb = encodeStationListProto( map.values());
size += NcStream.writeVInt(fout, pb.length);
size += pb.length;
fout.write(pb);
for (StationIndex s : map.values()) {
byte[] pb = s.encodeStationProto();
size += NcStream.writeVInt(fout, pb.length);
size += pb.length;
fout.write(pb);
}
fout.close();
//System.out.println(" index size=" + size);
}
private StationIndex decodeStationIndex(byte[] data) throws InvalidProtocolBufferException {
ucar.nc2.iosp.noaa.GhcnmProto.StationIndex proto = GhcnmProto.StationIndex.parseFrom(data);
return new StationIndex(proto);
}
private class StationIndex {
long stnId;
long stnPos; // file pos in inv file
long dataPos; // file pos of first data line in the data file
int dataCount; // number of data records
StationIndex() {
}
StationIndex(ucar.nc2.iosp.noaa.GhcnmProto.StationIndex proto) {
this.stnId = proto.getStnid();
this.stnPos = proto.getStnPos();
this.dataPos = proto.getDataPos();
this.dataCount = proto.getDataCount();
}
private byte[] encodeStationProto() {
GhcnmProto.StationIndex.Builder builder = GhcnmProto.StationIndex.newBuilder();
builder.setStnid(stnId);
builder.setStnPos(stnPos);
builder.setDataPos(dataPos);
builder.setDataCount(dataCount);
ucar.nc2.iosp.noaa.GhcnmProto.StationIndex proto = builder.build();
return proto.toByteArray();
}
} */
}