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The NetCDF-Java Library is a Java interface to NetCDF files,
as well as to many other types of scientific data formats.
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/*
* 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.
*
* Access and use of this software shall impose the following obligations
* and understandings on the user. The user is granted the right, without
* any fee or cost, to use, copy, modify, alter, enhance and distribute
* this software, and any derivative works thereof, and its supporting
* documentation for any purpose whatsoever, provided that this entire
* notice appears in all copies of the software, derivative works and
* supporting documentation. Further, UCAR requests that the user credit
* UCAR/Unidata in any publications that result from the use of this
* software or in any product that includes this software. The names UCAR
* and/or Unidata, however, may not be used in any advertising or publicity
* to endorse or promote any products or commercial entity unless specific
* written permission is obtained from UCAR/Unidata. The user also
* understands that UCAR/Unidata is not obligated to provide the user with
* any support, consulting, training or assistance of any kind with regard
* to the use, operation and performance of this software nor to provide
* the user with any updates, revisions, new versions or "bug fixes."
*
* THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
* INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
* FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
* NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
* WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
*/
package ucar.nc2.iosp.noaa;
import com.google.protobuf.InvalidProtocolBufferException;
import ucar.ma2.*;
import ucar.nc2.*;
import ucar.nc2.constants.AxisType;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.constants._Coordinate;
import ucar.nc2.iosp.AbstractIOServiceProvider;
import ucar.nc2.stream.NcStream;
import ucar.nc2.util.CancelTask;
import ucar.nc2.util.TableParser;
import ucar.unidata.io.RandomAccessFile;
import java.io.*;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* Nomads GLOBAL HISTORICAL CLIMATOLOGY NETWORK MONTHLY (GHCNM) v3 Beta.
* Ascii file. Write index into .ncsx using protobug (experimental)
* IOSP can then recognize the ncsx file, so it can be passed into NetdfFile.open() instead of the ascii file.
* Otherwise you have to explicitly specify the iosp, eg:
*
* Protobuf generation:
* cd c:/dev/tds4.2/thredds/cdm/src/main/java
* protoc --proto_path=. --java_out=. ucar/nc2/iosp/noaa/GhcnmIndex.proto
*
*
* @author caron
* @since Dec 8, 2010
*/
public class Ghcnm extends AbstractIOServiceProvider {
/*
ftp://ftp.ncdc.noaa.gov/pub/data/ghcn/v3/README
2.1 METADATA
The metadata has been carried over from GHCN-Monthly v2. This would
include basic geographical station information such as latitude,
longitude, elevation, station name, etc., and also extended metadata
information, such as surrounding vegetation, etc.
2.1.1 METADATA FORMAT
Variable Columns Type
-------- ------- ----
ID 1-11 Integer
LATITUDE 13-20 Real
LONGITUDE 22-30 Real
STNELEV 32-37 Real
NAME 39-68 Character
GRELEV 70-73 Integer
POPCLS 74-74 Character
POPSIZ 76-79 Integer
TOPO 80-81 Character
STVEG 82-83 Character
STLOC 84-85 Character
OCNDIS 86-87 Integer
AIRSTN 88-88 Character
TOWNDIS 89-90 Integer
GRVEG 91-106 Character
POPCSS 107-107 Character
Variable Definitions:
ID: 11 digit identifier, digits 1-3=Country Code, digits 4-8 represent
the WMO stnId if the station is a WMO station. It is a WMO station if
digits 9-11="000".
LATITUDE: latitude of station in decimal degrees
LONGITUDE: longitude of station in decimal degrees
STELEV: is the station elevation in meters. -999.0 = missing.
NAME: station name
GRELEV: station elevation in meters estimated from gridded digital
terrain data
POPCLS: population class
(U=Urban (>50,000 persons);
(S=Suburban (>=10,000 and <= 50,000 persons);
(R=Rural (<10,000 persons)
City and town boundaries are determined from location of station
on Operational Navigation Charts with a scale of 1 to 1,000,000.
For cities > 100,000 persons, population data were provided by
the United Nations Demographic Yearbook. For smaller cities and
towns several atlases were uses to determine population.
POPSIZ: the population of the city or town the station is location in
(expressed in thousands of persons).
TOPO: type of topography in the environment surrounding the station,
(Flat-FL,Hilly-HI,Mountain Top-MT,Mountainous Valley-MV).
STVEG: type of vegetation in environment of station if station is Rural
and when it is indicated on the Operational Navigation Chart
(Desert-DE,Forested-FO,Ice-IC,Marsh-MA).
STLOC: indicates whether station is near lake or ocean (<= 30 km of
ocean-CO, adjacent to a lake at least 25 square km-LA).
OCNDIS: distance to nearest ocean/lake from station (km).
AIRSTN: airport station indicator (A=station at an airport).
TOWNDIS: distance from airport to center of associated city or town (km).
GRVEG: vegetation type at nearest 0.5 deg x 0.5 deg gridded data point of
vegetation dataset (44 total classifications).
BOGS, BOG WOODS
COASTAL EDGES
COLD IRRIGATED
COOL CONIFER
COOL CROPS
COOL DESERT
COOL FIELD/WOODS
COOL FOR./FIELD
COOL GRASS/SHRUB
COOL IRRIGATED
COOL MIXED
EQ. EVERGREEN
E. SOUTH. TAIGA
HEATHS, MOORS
HIGHLAND SHRUB
HOT DESERT
ICE
LOW SCRUB
MAIN TAIGA
MARSH, SWAMP
MED. GRAZING
NORTH. TAIGA
PADDYLANDS
POLAR DESERT
SAND DESERT
SEMIARID WOODS
SIBERIAN PARKS
SOUTH. TAIGA
SUCCULENT THORNS
TROPICAL DRY FOR
TROP. MONTANE
TROP. SAVANNA
TROP. SEASONAL
TUNDRA
WARM CONIFER
WARM CROPS
WARM DECIDUOUS
WARM FIELD WOODS
WARM FOR./FIELD
WARM GRASS/SHRUB
WARM IRRIGATED
WARM MIXED
WATER
WOODED TUNDRA
POPCSS: population class as determined by Satellite night lights
(C=Urban, B=Suburban, A=Rural)
2.2 DATA
The data within GHCNM v3 beta for the time being consist of monthly
average temperature, for the 7280 stations contained within GHCNM v2.
Several new sources have been added to v3 beta, and a new "3 flag"
format has been introduced, similar to that used within the Global
Historical Climatology Network-Daily (GHCND).
2.2.1 DATA FORMAT
Variable Columns Type
-------- ------- ----
ID 1-11 Integer
YEAR 12-15 Integer
ELEMENT 16-19 Character
VALUE1 20-24 Integer
DMFLAG1 25-25 Character
QCFLAG1 26-26 Character
DSFLAG1 27-27 Character
. . .
. . .
. . .
VALUE12 108-112 Integer
DMFLAG12 113-113 Character
QCFLAG12 114-114 Character
DSFLAG12 115-115 Character
Variable Definitions:
ID: 11 digit identifier, digits 1-3=Country Code, digits 4-8 represent
the WMO stnId if the station is a WMO station. It is a WMO station if
digits 9-11="000".
YEAR: 4 digit year of the station record.
ELEMENT: element type, currently just "TAVG".
VALUE: monthly value (MISSING=-9999)
DMFLAG: data measurement flag, nine possible values:
blank = no measurement information applicable
a-i = number of days missing in calculation of monthly mean
temperature (currently only applies to the 1218 USHCN
V2 stations included within GHCNM)
QCFLAG: quality control flag, seven possibilities within
quality controlled unadjusted (qcu) dataset, and 2
possibilities within the quality controlled adjusted (qca)
dataset.
Quality Controlled Unadjusted (QCU) QC Flags:
BLANK = no failure of quality control check or could not be
evaluated.
D = monthly value is part of an annual series of values that
are exactly the same (e.fldno. duplicated) within another
year in the station's record.
K = monthly value is part of a consecutive run (e.fldno. streak)
of values that are identical. The streak must be >= 4
months of the same value.
L = monthly value is isolated in time within the station
record, and this is defined by having no immediate non-
missing values 18 months on either side of the value.
O = monthly value that is >= 5 bi-weight standard deviations
from the bi-weight mean. Bi-weight statistics are
calculated from a series of all non-missing values in
the station's record for that particular month.
S = monthly value has failed spatial consistency check
(relative to their respective climatological means to
concurrent z-scores at the nearest 20 neighbors located
withing 500 km of the target; A temperature fails if
(i) its z-score differs from the regional (target and
neighbor) mean z-score by at least 3.5 standard
deviations and (ii) the target's temperature anomaly
differs by at least 2.5 deg C from all concurrent
temperature anomalies at the neighbors.
T = monthly value has failed temporal consistency check
(temperatures whose anomalies differ by more than
4 deg C from concurent anomalies at the five nearest
neighboring stations whose temperature anomalies are
well correlated with the target (correlation > 0.7 for
the corresponding calendar monthly).
W = monthly value is duplicated from the previous month,
based upon regional and spatial criteria and is only
applied from the year 2000 to the present.
Quality Controlled Adjusted (QCA) QC Flags:
M = values with a non-blank quality control flag in the "qcu"
dataset are set to missing the adjusted dataset and given
an "M" quality control flag.
X = pairwise algorithm removed the value because of too many
inhomogeneities.
DSFLAG: data source flag for monthly value, 18 possibilities:
C = Monthly Climatic Data of the World (MCDW) QC completed
but value is not yet published
G = GHCNM v2 station, that was not a v2 station that had multiple
time series (for the same element).
K = received by the UK Met Office
M = Final (Published) Monthly Climatic Data of the World
(MCDW)
N = Netherlands, KNMI (Royal Netherlans Meteorological
Institute)
P = CLIMAT (Data transmitted over the GTS, not yet fully
processed for the MCDW)
U = USHCN v2
W = World Weather Records (WWR), 9th series 1991 through 2000
0 to 9 = For any station originating from GHCNM v2 that had
multiple time series for the same element, this flag
represents the 12th digit in the ID from GHCNM v2.
See section 2.2.2 for additional information.
2.2.2 STATIONS WITH MULTIPLE TIME SERIES
The GHCNM v2 contained several thousand stations that had multiple
time series of monthly mean temperature data. The 12th digit of
each data record, indicated the time series number, and thus there
was a potential maximum of 10 time series (e.fldno. 0 through 9). These
same stations in v3 beta have undergone a merge process, to reduce
the station time series to one single series, based upon these
original and at most 10 time series.
A simple algorithm was applied to perform the merge. The algorithm
consisted of first finding the length (based upon number of non
missing observations) for each of the time series and then
combining all of the series into one based upon a priority scheme
that would "write" data to the series for the longest series last.
Therefore, if station A, had 3 time series of TAVG data, as follows:
1900 to 1978 (79 years of data) [series 1]
1950 to 1985 (36 years of data) [series 2]
1990 to 2007 (18 years of data) [series 3]
The final series would consist of:
1900 to 1978 [series 1]
1979 to 1985 [series 2]
1990 to 2007 [series 3]
The original series number in GHCNM v2, is retained in the GHCNM v3
beta data source flag.
One caveat to this merge process, is that in the final GHCNM v3 beta
processing there is still a master level construction process
performed daily, where the entire dataset is construction according
to a source order overwrite hiearchy (section 2.3), and it is
possible that higher order data sources may be interspersed within
the 3 series listed above.
2.3 DATA SOURCE HIERARCHY
The GHCNM v3 beta is reprocessed on a daily basis, which means as a
part of that reprocessing, the dataset is reconstructed from all
original sources. The advantage to this process is when source
datasets are corrected and/or updated the inclusion into GHCNM v3
beta is seemless. The following sources (more fully described in
section 2.2.1) have the following overwrite precedance within the
daily reprocessing of GHCNM v3 (e.fldno. source K overwrites source P)
P,K,G,U,0-9,C,N,M,W
*/
/*
data
1 2 3 4 5 6 7 8 9 10 11 12
0123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
101603550001878TAVG 890 1 950 1 1110 1 1610 1 1980 1 2240 1 2490 1 2680 1 2320 1 2057E 1370 1 1150 1
101603550001932TAVG 1010 1 980 1-9999 1420 1 1840 1-9999 2290 1-9999 2440 1-9999 -9999 -9999
matches = true
group 1 == 101603550001932
group 2 == 1010
group 3 == 1
group 4 == 980
group 5 == 1
group 6 == -9999
group 7 ==
group 8 == 1420
group 9 == 1
group 10 == 1840
group 11 == 1
group 12 == -9999
group 13 ==
group 14 == 2290
group 15 == 1
group 16 == -9999
group 17 ==
group 18 == 2440
group 19 == 1
group 20 == -9999
group 21 ==
group 22 == -9999
group 23 ==
group 24 == -9999
group 25 == null
see testRegexp.testGhcnm()
*/
private static final String p = "(\\d{11})(\\d{4})TAVG([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)([ \\-\\d]{5})(...)?.*";
private static final Pattern dataPattern = Pattern.compile(p);
private static final String RECORD = "all_data";
private static final String DIM_NAME = "month";
private static final String STNID = "stnid";
private static final String TIME = "time";
private static final String YEAR = "year";
private static final String VALUE = "value";
private static final String DMFLAG = "dm";
private static final String QCFLAG = "qc";
private static final String DSFLAG = "ds";
private static final String STNS = "station";
private static final String LAT = "lat";
private static final String LON = "lon";
private static final String STELEV = "elevation";
private static final String NAME = "name";
private static final String GRELEV = "grelev";
private static final String POPCLS = "popClass";
private static final String POPSIZ = "popSize";
private static final String TOPO = "topoType";
private static final String STVEG = "vegType";
private static final String STLOC = "ocean";
private static final String OCNDIS = "oceanDist";
private static final String AIRSTN = "airportId";
private static final String TOWNDIS = "townDist";
private static final String GRVEG = "vegType";
private static final String POPCSS = "popClassFromLights";
private static final String WMO = "wmoId";
private static final String STN_DATA = "stn_data";
private NetcdfFile ncfile;
private RandomAccessFile stnRaf;
public boolean isValidFile(RandomAccessFile raf) throws IOException {
String dataFile = raf.getLocation();
int pos = dataFile.lastIndexOf(".");
if (pos <= 0) return false;
String base = dataFile.substring(0, pos);
String ext = dataFile.substring(pos);
// must be data file or index file
if (!ext.equals(DAT_EXT) && !ext.equals(IDX_EXT))
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 = new File(base + STN_EXT);
if (!stnFile.exists())
return false;
raf.seek(0);
byte[] b = new byte[MAGIC_START.length()];
raf.readFully(b);
String test = new String(b, CDM.utf8Charset);
return test.equals(MAGIC_START);
} else {
// stn files must be in the same directory
File stnFile = new File(base + STN_EXT);
return (stnFile.exists()); // LOOK BAD!! NOT GOOD ENOUGH
}
}
@Override
public void close() throws java.io.IOException {
if (raf != null)
raf.close();
if (stnRaf != null)
stnRaf.close();
raf = null;
stnRaf = null;
}
@Override
public void open(RandomAccessFile raf, NetcdfFile ncfile, CancelTask cancelTask) throws IOException {
this.ncfile = ncfile;
String dataFile = raf.getLocation();
int pos = dataFile.lastIndexOf(".");
String base = dataFile.substring(0, pos);
String ext = dataFile.substring(pos);
// did the index file get passed in ?
if (ext.equals(IDX_EXT)) {
// must be in the same directory
File datFile = new File(base + DAT_EXT);
if (!datFile.exists())
throw new FileNotFoundException(datFile.getPath() + " must exist");
File stnFile = new File(base + STN_EXT);
if (!stnFile.exists())
throw new FileNotFoundException(stnFile.getPath() + " must exist");
this.raf = new RandomAccessFile(base + DAT_EXT, "r");
this.stnRaf = new RandomAccessFile(base + STN_EXT, "r");
readIndex(raf.getLocation());
raf.close();
} else { // must be the data file, we will write an index if needed below
this.raf = raf;
if (!(ext.equals(DAT_EXT)))
throw new FileNotFoundException("Ghcnm: file must end with " + DAT_EXT);
File stnFile = new File(base + STN_EXT);
if (!stnFile.exists())
throw new FileNotFoundException(stnFile.getPath() + " must exist");
this.stnRaf = new RandomAccessFile(base + STN_EXT, "r");
}
//////////////////////////////////////////////////
// LOOK - can we externalize config ??
/*
ID 1-11 Integer
YEAR 12-15 Integer
ELEMENT 16-19 Character
VALUE1 20-24 Integer
DMFLAG1 25-25 Character
QCFLAG1 26-26 Character
DSFLAG1 27-27 Character
ID: 11 digit identifier, digits 1-3=Country Code, digits 4-8 represent
the WMO stnId if the station is a WMO station. It is a WMO station if
digits 9-11="000".
*/
TableParser dataParser = new TableParser("11L,15i,19,24i,25,26,27");
Structure dataSeq = new Sequence(ncfile, null, null, RECORD);
ncfile.addVariable(null, dataSeq);
ncfile.addDimension(null, new Dimension(DIM_NAME, 12));
Variable v;
makeMember(dataSeq, STNID, DataType.LONG, null, "station stnId", null, null, null);
makeMember(dataSeq, YEAR, DataType.INT, null, "year of the station record", null, null, null);
v = makeMember(dataSeq, VALUE, DataType.FLOAT, DIM_NAME, "monthly mean temperature", "Celsius", null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9999));
dataParser.getField(3).setScale(.01f);
makeMember(dataSeq, DMFLAG, DataType.CHAR, DIM_NAME, "data management flag", null, null, null);
makeMember(dataSeq, QCFLAG, DataType.CHAR, DIM_NAME, "quality control flag", null, null, null);
makeMember(dataSeq, DSFLAG, DataType.CHAR, DIM_NAME, "data source flag", null, null, null);
// synthetic time variable
v = makeMember(dataSeq, TIME, DataType.STRING, null, "starting time of the record", null, null, AxisType.Time);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, "missing"));
StructureMembers dataSm = dataSeq.makeStructureMembers();
dataSm.findMember(STNID).setDataObject(dataParser.getField(0));
dataSm.findMember(YEAR).setDataObject(dataParser.getField(1));
dataSm.findMember(VALUE).setDataObject(dataParser.getField(3));
dataSm.findMember(DMFLAG).setDataObject(dataParser.getField(4));
dataSm.findMember(QCFLAG).setDataObject(dataParser.getField(5));
dataSm.findMember(DSFLAG).setDataObject(dataParser.getField(6));
dataSeq.setSPobject(new Vinfo(this.raf, dataSm));
stnIdFromData = dataParser.getField(0);
// synthetic time variable
TableParser.Field org = dataParser.getField(1); // YEAR
TableParser.Field derived = dataParser.addDerivedField(org, new TableParser.Transform() {
public Object derive(Object org) {
int year = (Integer) org;
return year + "-01-01T00:00:00Z";
}
}, String.class);
dataSm.findMember(TIME).setDataObject(derived);
/*
ID 1-11 Integer
LATITUDE 13-20 Real
LONGITUDE 22-30 Real
STNELEV 32-37 Real
NAME 39-68 Character
GRELEV 70-73 Integer
POPCLS 74-74 Character
POPSIZ 76-79 Integer
TOPO 80-81 Character
STVEG 82-83 Character
STLOC 84-85 Character
OCNDIS 86-87 Integer
AIRSTN 88-88 Character
TOWNDIS 89-90 Integer
GRVEG 91-106 Character
POPCSS 107-107 Character
*/
TableParser stnParser = new TableParser("11L,20d,30d,37d,68,73i,74,79i,81,83,85,87i,88,90i,106,107");
Structure stnSeq = new Sequence(ncfile, null, null, STNS);
ncfile.addVariable(null, stnSeq);
v = makeMember(stnSeq, STNID, DataType.LONG, null, "station id", null, null, null);
v.addAttribute(new Attribute(CF.CF_ROLE, CF.TIMESERIES_ID));
makeMember(stnSeq, LAT, DataType.FLOAT, null, "latitude", CDM.LAT_UNITS, null, null);
makeMember(stnSeq, LON, DataType.FLOAT, null, "longitude", CDM.LON_UNITS, null, null);
makeMember(stnSeq, STELEV, DataType.FLOAT, null, "elevation", "m", null, null);
v = makeMember(stnSeq, NAME, DataType.STRING, null, "station name", null, null, null);
v.addAttribute(new Attribute(CF.STANDARD_NAME, CF.STATION_DESC));
makeMember(stnSeq, GRELEV, DataType.INT, null, "elevation estimated from gridded digital terrain data", "m", null, null);
makeMember(stnSeq, POPCLS, DataType.CHAR, null, "population class", null, null, null);
v = makeMember(stnSeq, POPSIZ, DataType.INT, null, "population of the city or town the station is located in", "thousands of persons", null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9));
makeMember(stnSeq, TOPO, DataType.STRING, null, "type of topography in the environment surrounding the station", null, null, null);
makeMember(stnSeq, STVEG, DataType.STRING, null, "type of vegetation in environment of station", null, null, null);
makeMember(stnSeq, STLOC, DataType.STRING, null, "station is near lake or ocean", null, null, null);
v = makeMember(stnSeq, OCNDIS, DataType.INT, null, "distance to nearest ocean/lake", "km", null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9));
makeMember(stnSeq, AIRSTN, DataType.CHAR, null, "airport station indicator", null, null, null);
v = makeMember(stnSeq, TOWNDIS, DataType.INT, null, "distance from airport to center of associated city or town", "km", null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9));
makeMember(stnSeq, GRVEG, DataType.STRING, null, "vegetation type at nearest 0.5 deg x 0.5 deg gridded data point of vegetation dataset", null, null, null);
makeMember(stnSeq, POPCSS, DataType.CHAR, null, "population class as determined by satellite night lights", null, null, null);
// nested sequence - just the data for this station
Structure nestedSeq = new Sequence(ncfile, null, stnSeq, STN_DATA);
stnSeq.addMemberVariable(nestedSeq);
v = makeMember(nestedSeq, YEAR, DataType.INT, null, "year", null, null, null);
v.addAttribute(new Attribute(CDM.UNITS, "years since 0000-01-01T00:00"));
v = makeMember(nestedSeq, VALUE, DataType.FLOAT, DIM_NAME, "monthly mean temperature", "Celsius", null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9999));
dataParser.getField(3).setScale(.01f);
makeMember(nestedSeq, DMFLAG, DataType.CHAR, DIM_NAME, "data management flag", null, null, null);
makeMember(nestedSeq, QCFLAG, DataType.CHAR, DIM_NAME, "quality control flag", null, null, null);
makeMember(nestedSeq, DSFLAG, DataType.CHAR, DIM_NAME, "data source flag", null, null, null);
// synthetic time variable in nested seq
v = makeMember(nestedSeq, TIME, DataType.STRING, null, "starting time of the record", null, null, AxisType.Time);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, "missing"));
StructureMembers nestedSm = nestedSeq.makeStructureMembers();
nestedSm.findMember(YEAR).setDataObject(dataParser.getField(1));
nestedSm.findMember(VALUE).setDataObject(dataParser.getField(3));
nestedSm.findMember(DMFLAG).setDataObject(dataParser.getField(4));
nestedSm.findMember(QCFLAG).setDataObject(dataParser.getField(5));
nestedSm.findMember(DSFLAG).setDataObject(dataParser.getField(6));
nestedSeq.setSPobject(new Vinfo(this.raf, nestedSm));
stnDataMembers = nestedSm;
// synthetic time variable in nested seq
TableParser.Field org2 = dataParser.getField(1); // YEAR
TableParser.Field derived2 = dataParser.addDerivedField(org2, new TableParser.Transform() {
public Object derive(Object org) {
int year = (Integer) org;
return year + "-01-01T00:00:00Z";
}
}, String.class);
nestedSm.findMember(TIME).setDataObject(derived2);
//// finish the stn sequence
// synthetic wmo variable in station
v = makeMember(stnSeq, WMO, DataType.INT, null, "WMO station id", null, null, null);
v.addAttribute(new Attribute(CDM.MISSING_VALUE, -9999));
v.addAttribute(new Attribute(CF.STANDARD_NAME, CF.STATION_WMOID));
StructureMembers stnSm = stnSeq.makeStructureMembers();
int count = 0;
int n = stnParser.getNumberOfFields();
for (StructureMembers.Member m : stnSm.getMembers()) {
if (count < n)
m.setDataObject(stnParser.getField(count++));
}
stnSeq.setSPobject(new Vinfo(stnRaf, stnSm));
// synthetic wmo variable in station
/* ID: 11 digit identifier, digits 1-3=Country Code, digits 4-8 represent
the WMO id if the station is a WMO station. It is a WMO station if
digits 9-11="000". */
TableParser.Field org3 = stnParser.getField(0); // STNID
TableParser.Field derived3 = stnParser.addDerivedField(org3, new TableParser.Transform() {
public Object derive(Object org) {
long stnid = (Long) org;
return (stnid % 1000 == 0) ? new Integer((int) (stnid / 1000) % 100000) : new Integer(-9999);
}
}, int.class);
stnSm.findMember(WMO).setDataObject(derived3);
//// global attribites
ncfile.addAttribute(null, new Attribute("title", "Version 3 of the GHCN-Monthly dataset of land surface mean temperatures"));
ncfile.addAttribute(null, new Attribute(CDM.CONVENTIONS, "CDM"));
ncfile.addAttribute(null, new Attribute("CF:featureType", "timeSeries"));
ncfile.addAttribute(null, new Attribute("see", "http://www.ncdc.noaa.gov/ghcnm, ftp://ftp.ncdc.noaa.gov/pub/data/ghcn/v3"));
ncfile.finish();
// make index file if needed
File idxFile = new File(base + IDX_EXT);
if (!idxFile.exists())
makeIndex(idxFile);
else
readIndex(idxFile.getPath());
}
private Variable makeMember(Structure s, String shortName, DataType dataType, String dims, String longName, String units, String cfName,
AxisType atype) {
Variable v = new Variable(ncfile, null, s, shortName, dataType, dims);
v.addAttribute(new Attribute(CDM.LONG_NAME, longName));
if (cfName != null)
v.addAttribute(new Attribute(CF.STANDARD_NAME, cfName));
if (units != null)
v.addAttribute(new Attribute(CDM.UNITS, units));
if (atype != null)
v.addAttribute(new Attribute(_Coordinate.AxisType, atype.toString()));
s.addMemberVariable(v);
return v;
}
private static class Vinfo {
RandomAccessFile raf;
StructureMembers sm;
int nelems = -1;
private Vinfo(RandomAccessFile raf, StructureMembers sm) {
this.sm = sm;
this.raf = raf;
}
}
////////////////////////////////////////////////////////////////////////////////////////////
private static final String STN_EXT = ".inv";
private static final String DAT_EXT = ".dat";
private static final String IDX_EXT = ".ncsx";
private static final String MAGIC_START = "GhncmIndex";
private static final int version = 1;
private HashMap map = new HashMap(10000);
private TableParser.Field stnIdFromData;
private StructureMembers stnDataMembers;
private void readIndex(String indexFilename) throws IOException {
try (FileInputStream fin = new FileInputStream(indexFilename)) {
if (!NcStream.readAndTest(fin, MAGIC_START.getBytes(CDM.utf8Charset)))
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);
}
}
System.out.println(" read index map size=" + map.values().size());
}
private void makeIndex(File indexFile) throws IOException {
// get map of Stations
Sequence stnSeq = (Sequence) ncfile.findVariable(STNS);
Vinfo stnInfo = (Vinfo) stnSeq.getSPobject();
StructureMembers.Member m = stnInfo.sm.findMember(STNID);
TableParser.Field f = (TableParser.Field) m.getDataObject();
int stnCount = 0;
// read through entire file
stnInfo.raf.seek(0);
while (true) {
long stnPos = stnInfo.raf.getFilePointer();
String line = stnInfo.raf.readLine();
if (line == null) break;
StationIndex s = new StationIndex();
Long id = (Long) f.parse(line);
map.put(id, s);
s.stnId = id;
s.stnPos = stnPos;
stnCount++;
}
// assumes that the stn data is in order by stnId
Sequence dataSeq = (Sequence) ncfile.findVariable(RECORD);
Vinfo dataInfo = (Vinfo) dataSeq.getSPobject();
m = dataInfo.sm.findMember(STNID);
f = (TableParser.Field) m.getDataObject();
StationIndex currStn = null;
int totalCount = 0;
// read through entire file
dataInfo.raf.seek(0);
while (true) {
long dataPos = dataInfo.raf.getFilePointer();
String line = dataInfo.raf.readLine();
if (line == null) break;
Long id = (Long) f.parse(line);
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;
}
if (currStn != null) currStn.dataCount++;
}
//System.out.printf("ok stns=%s data=%d%n", stnCount, totalCount);
//////////////////////////////
// write the index file
try (FileOutputStream fout = new FileOutputStream(indexFile)) { // LOOK need DiskCache for non-writeable directories
long size = 0;
//// header message
fout.write(MAGIC_START.getBytes(CDM.utf8Charset));
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);
}
}
//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 static 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();
}
}
/* private byte[] encodeStationListProto(Collection stns) {
GhcnmProto.StationIndexList.Builder listBuilder = GhcnmProto.StationIndexList.newBuilder();
for (StationIndex s : stns) {
GhcnmProto.StationIndex.Builder builder = GhcnmProto.StationIndex.newBuilder();
builder.setStnid(s.stnId);
builder.setStnPos(s.stnPos);
builder.setDataPos(s.dataPos);
builder.setDataCount(s.dataCount);
listBuilder.addList(builder);
}
return listBuilder.build().toByteArray();
} */
////////////////////////////////////////////////////////////////////////////////////////////
/**
* Get a unique stnId for this file type.
*
* @return registered stnId of the file type
* @see "http://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"
*/
public String getFileTypeId() {
return "GHCNM";
}
/**
* Get a human-readable description for this file type.
*
* @return description of the file type
* @see "http://www.unidata.ucar.edu/software/netcdf-java/formats/FileTypes.html"
*/
public String getFileTypeDescription() {
return "GLOBAL HISTORICAL CLIMATOLOGY NETWORK MONTHLY";
}
/**
* Returns an ArraySequence, no subsetting is allowed.
*
* @param v2 a top-level Variable
* @param section the section of data to read.
* There must be a Range for each Dimension in the variable, in order.
* Note: no nulls allowed. IOSP may not modify.
* @return ArraySequence
* @throws IOException
* @throws InvalidRangeException
*/
public Array readData(Variable v2, Section section) throws IOException, InvalidRangeException {
Vinfo vinfo = (Vinfo) v2.getSPobject();
return new ArraySequence(vinfo.sm, new SeqIter(vinfo), vinfo.nelems);
}
/**
* Get the structure iterator
*
* @param s the Structure
* @param bufferSize the buffersize
* @return the data iterator
* @throws java.io.IOException if problem reading data
*/
public StructureDataIterator getStructureIterator(Structure s, int bufferSize) throws java.io.IOException {
Vinfo vinfo = (Vinfo) s.getSPobject();
return new SeqIter(vinfo);
}
private class SeqIter implements StructureDataIterator {
private Vinfo vinfo;
private long bytesRead;
private long totalBytes;
private int recno;
private StructureData curr;
SeqIter(Vinfo vinfo) throws IOException {
this.vinfo = vinfo;
totalBytes = (int) raf.length();
vinfo.raf.seek(0);
}
@Override
public StructureDataIterator reset() {
bytesRead = 0;
recno = 0;
try {
vinfo.raf.seek(0);
} catch (IOException e) {
throw new RuntimeException(e);
}
return this;
}
@Override
public boolean hasNext() throws IOException {
boolean more = (bytesRead < 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 {
String line;
while (true) {
line = vinfo.raf.readLine();
if (line == null) return null;
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
break;
}
//System.out.printf("%s%n", line);
bytesRead = vinfo.raf.getFilePointer();
recno++;
return new StructureDataAsciiGhcnm(vinfo.sm, line);
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return recno - 1;
}
@Override
public void finish() {
// ignored
}
}
private class StnDataIter implements StructureDataIterator {
private StructureMembers sm;
private int countRead;
private StationIndex stationIndex;
StnDataIter(StructureMembers sm, StationIndex stationIndex) {
this.sm = sm;
this.stationIndex = stationIndex;
reset();
}
@Override
public StructureDataIterator reset() {
countRead = 0;
try {
raf.seek(stationIndex.dataPos);
} catch (IOException e) {
throw new RuntimeException(e);
}
return this;
}
@Override
public boolean hasNext() throws IOException {
return (countRead < stationIndex.dataCount);
}
@Override
public StructureData next() throws IOException {
String line;
while (true) {
line = raf.readLine();
if (line == null) return null;
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
break;
}
//System.out.printf("%s%n", line);
countRead++;
return new StructureDataAscii(sm, line);
}
@Override
public void setBufferSize(int bytes) {
}
@Override
public int getCurrentRecno() {
return countRead - 1;
}
@Override
public void finish() {
// ignored
}
}
private class StructureDataAsciiGhcnm extends StructureDataAscii {
StructureDataAsciiGhcnm(StructureMembers members, String line) {
super(members, line);
}
@Override
public ArraySequence getArraySequence(StructureMembers.Member m) {
Long stnId = (Long) stnIdFromData.parse(line); // extract the station id
StationIndex si = map.get(stnId); // find its index
return new ArraySequence(stnDataMembers, new StnDataIter(stnDataMembers, si), -1);
}
}
/////////////////////////////////////////////////////////////////////////////////
// debug
static private NetcdfFile open(String filename) throws IOException {
Ghcnm iosp = new Ghcnm();
RandomAccessFile raf = new RandomAccessFile(filename, "r");
NetcdfFile ncfile = new NetcdfFileSubclass(iosp, filename);
iosp.open(raf, ncfile, null);
return ncfile;
}
static private void stnDuplicates(String filename, Set stns, boolean wantDups) throws IOException {
System.out.printf("%s%n", filename);
int count = 0;
int countDups = 0;
NetcdfFile ncfile = open(filename);
Sequence seq = (Sequence) ncfile.findVariable(STNS);
StructureDataIterator iter = seq.getStructureIterator(-1);
try {
while (iter.hasNext()) {
count++;
StructureData sdata = iter.next();
StructureMembers.Member m = sdata.findMember(STNID);
int stnid = sdata.getScalarInt(m);
if (stns.contains(stnid)) {
countDups++;
if (!wantDups) System.out.printf(" dup %d%n", stnid);
} else {
stns.add(stnid);
if (wantDups) System.out.printf(" dup %d%n", stnid);
}
}
} finally {
iter.finish();
}
System.out.printf(" counts=%d dups=%d%n", count, countDups);
}
static public void main2(String args[]) throws IOException {
Set stns = new HashSet(10 * 1000);
stnDuplicates("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qae.inv", stns, false);
stnDuplicates("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qca.inv", stns, true);
stnDuplicates("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qcu.inv", stns, true);
}
////////////////////////////////////
static private int parseLine(String line) throws IOException {
int balony = 0;
Matcher matcher = dataPattern.matcher(line);
if (matcher.matches()) {
for (int i = 1; i <= matcher.groupCount(); i++) {
String r = matcher.group(i);
if (r == null) continue;
int value = (int) Long.parseLong(r.trim());
balony += value;
}
} else {
System.out.printf("Fail on %s%n", line);
}
return balony;
}
static private void readDataRegexp(String filename) throws IOException {
int balony = 0;
long start = System.currentTimeMillis();
System.out.printf("regexp %s%n", filename);
try (RandomAccessFile raf = new RandomAccessFile(filename, "r")) {
String line;
while (true) {
line = raf.readLine();
if (line == null) break;
if (line.startsWith("#")) continue;
if (line.trim().length() == 0) continue;
balony += parseLine(line);
}
}
long took = System.currentTimeMillis() - start;
System.out.printf("DONE %d == %d msecs%n", balony, took);
}
static private void readData(String filename) throws IOException {
long start = System.currentTimeMillis();
System.out.printf("%s%n", filename);
int balony = 0;
try (NetcdfFile ncfile = open(filename)) {
Sequence seq = (Sequence) ncfile.findVariable(RECORD);
StructureDataIterator iter = seq.getStructureIterator(-1);
try {
while (iter.hasNext()) {
StructureData sdata = iter.next();
StructureMembers.Member m = sdata.findMember(YEAR);
balony += sdata.getScalarInt(m);
/* StructureMembers sm = sdata.getStructureMembers();
for (StructureMembers.Member m : sm.getMembers()) {
Array data = sdata.getArray(m);
balony += data.getSize();
} */
}
} finally {
iter.finish();
}
}
long took = System.currentTimeMillis() - start;
System.out.printf("DONE %d == %d msecs%n", balony, took);
}
static public void main(String args[]) throws IOException {
readData("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qcu.dat");
readDataRegexp("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qcu.dat");
}
}
/*
static public void main(String args[]) throws IOException {
//InputStream is = cl.getResourceAsStream("resources/nj22/tables/nexrad.tbl");
InputStream is = new FileInputStream("C:/data/ghcnm/ghcnm.v3.0.0-beta1.20101207.qae.inv");
List recs = TableParser.readTable(is, "11,20d,30d,37d,68,73i,74,79i,81,83,85,87i,88,90i,106,107", 10);
Formatter f = new Formatter(System.out);
//f.format("CNTRY WMO ID YEAR ELEM VAL DM QC DS%n");
for (TableParser.Record record : recs) {
record.toString(f);
}
}
*/
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