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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 1998-2014 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.dataset.conv;
import ucar.ma2.Array;
import ucar.ma2.DataType;
import ucar.nc2.*;
import ucar.nc2.constants.*;
import ucar.nc2.dataset.*;
import ucar.nc2.iosp.hdf4.HdfEos;
import ucar.nc2.time.CalendarDate;
import ucar.nc2.util.CancelTask;
import ucar.unidata.geoloc.projection.Sinusoidal;
import java.io.IOException;
/**
* HDF4-EOS TERRA MODIS
*
* @author caron
* @since 2/23/13
* @see "https://lpdaac.usgs.gov/products/modis_overview"
*/
public class HdfEosModisConvention extends ucar.nc2.dataset.CoordSysBuilder {
private static final String CRS = "Projection";
private static final String DATA_GROUP = "Data_Fields";
private static final String DIMX_NAME = "XDim";
private static final String DIMY_NAME = "YDim";
private static final String TIME_NAME = "time";
public static boolean isMine(NetcdfFile ncfile) {
if (!ncfile.getFileTypeId().equals("HDF4-EOS")) return false;
String typeName = ncfile.findAttValueIgnoreCase(null, CF.FEATURE_TYPE, null);
if (typeName == null) return false;
if (!typeName.equals(FeatureType.GRID.toString()) &&
!typeName.equals(FeatureType.SWATH.toString())) return false;
return checkGroup(ncfile.getRootGroup());
}
private static boolean checkGroup(Group g) {
Variable crs = g.findVariable(HdfEos.HDFEOS_CRS);
Group dataG = g.findGroup(DATA_GROUP);
if (crs != null && dataG != null) {
Attribute att = crs.findAttribute(HdfEos.HDFEOS_CRS_Projection);
if (att == null) return false;
if (!att.getStringValue().equals("GCTP_SNSOID") && !att.getStringValue().equals("GCTP_GEO")) return false;
return !(dataG.findDimensionLocal(DIMX_NAME) == null || dataG.findDimensionLocal(DIMY_NAME) == null);
}
for (Group ng : g.getGroups()) {
if (checkGroup(ng)) return true;
}
return false;
}
public HdfEosModisConvention() {
this.conventionName = "HDF4-EOS-MODIS";
}
/*
group: MODIS_Grid_16DAY_250m_500m_VI {
variables:
short _HDFEOS_CRS;
:Projection = "GCTP_SNSOID";
:UpperLeftPointMtrs = -2.0015109354E7, 1111950.519667; // double
:LowerRightMtrs = -1.8903158834333E7, 0.0; // double
:ProjParams = 6371007.181, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0; // double
:SphereCode = "-1";
group: Data_Fields {
dimensions:
YDim = 4800;
XDim = 4800;
variables:
short 250m_16_days_NDVI(YDim=4800, XDim=4800);
...
*/
private boolean addTimeCoord;
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
addTimeCoord = addTimeCoordinate(ds);
augmentGroup(ds, ds.getRootGroup());
ds.addAttribute(ds.getRootGroup(), new Attribute(CDM.CONVENTIONS, "CF-1.0"));
ds.finish();
}
private boolean addTimeCoordinate(NetcdfDataset ds) {
// add time coordinate
CalendarDate cd = parseFilenameForDate(ds.getLocation());
if (cd == null) return false;
ds.addAttribute(ds.getRootGroup(), new Attribute("_MODIS_Date", cd.toString()));
// add the time dimension
int nTimesDim = 1;
Dimension newDim = new Dimension(TIME_NAME, nTimesDim);
ds.addDimension( null, newDim);
// add the coordinate variable
String units = "seconds since "+cd.toString();
String desc = "time coordinate";
Array data = Array.makeArray(DataType.DOUBLE, 1, 0.0, 0.0) ;
CoordinateAxis1D timeCoord = new CoordinateAxis1D( ds, null, TIME_NAME, DataType.DOUBLE, "", units, desc);
timeCoord.setCachedData(data, true);
timeCoord.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Time.toString()));
ds.addCoordinateAxis(timeCoord);
return true;
}
private CalendarDate parseFilenameForDate(String filename) {
// filename MOD13Q1.A2000065.h11v04.005.2008238031620.hdf
String[] tokes = filename.split("\\.");
if (tokes.length < 2) return null;
if (tokes[1].length() < 8) return null;
String want = tokes[1];
String yearS = want.substring(1,5);
String jdayS = want.substring(5,8);
try {
int year = Integer.parseInt(yearS);
int jday = Integer.parseInt(jdayS);
return CalendarDate.withDoy(null, year, jday, 0,0,0);
} catch (Exception e) {
return null;
}
}
private void augmentGroup(NetcdfDataset ds, Group g) {
Variable crs = g.findVariable(HdfEos.HDFEOS_CRS);
if (crs != null) augmentGroupWithProjectionInfo(ds, g);
for (Group ng : g.getGroups())
augmentGroup(ds, ng);
}
private void augmentGroupWithProjectionInfo(NetcdfDataset ds, Group g) {
Dimension dimX = null, dimY = null;
Group dataG = g.findGroup(DATA_GROUP);
if (dataG != null) {
dimX = dataG.findDimensionLocal(DIMX_NAME);
dimY = dataG.findDimensionLocal(DIMY_NAME);
}
if (dimX == null || dimY == null) return;
Variable crs = g.findVariable(HdfEos.HDFEOS_CRS);
Attribute projAtt = crs.findAttribute(HdfEos.HDFEOS_CRS_Projection);
if (projAtt != null) {
Attribute upperLeft = crs.findAttribute(HdfEos.HDFEOS_CRS_UpperLeft);
Attribute lowerRight = crs.findAttribute(HdfEos.HDFEOS_CRS_LowerRight);
Attribute projParams = crs.findAttribute(HdfEos.HDFEOS_CRS_ProjParams);
double minX = upperLeft.getNumericValue(0).doubleValue();
double minY = upperLeft.getNumericValue(1).doubleValue();
double maxX = lowerRight.getNumericValue(0).doubleValue();
double maxY = lowerRight.getNumericValue(1).doubleValue();
boolean hasProjection = false;
String coordinates = null;
ProjectionCT ct;
if (projAtt.getStringValue().equals("GCTP_SNSOID")) {
hasProjection = true;
ct = makeSinusoidalProjection(CRS, projParams);
VariableDS crss = makeCoordinateTransformVariable(ds, ct);
crss.addAttribute(new Attribute(_Coordinate.AxisTypes, "GeoX GeoY"));
ds.addVariable(dataG, crss);
ds.addCoordinateAxis(makeCoordAxis(ds, dataG, DIMX_NAME, dimX.getLength(), minX, maxX, true));
ds.addCoordinateAxis(makeCoordAxis(ds, dataG, DIMY_NAME, dimY.getLength(), minY, maxY, false));
coordinates = addTimeCoord ? TIME_NAME+" "+DIMX_NAME + " " + DIMY_NAME : DIMX_NAME + " " + DIMY_NAME;
} else if (projAtt.getStringValue().equals("GCTP_GEO")) {
ds.addCoordinateAxis(makeLatLonCoordAxis(ds, dataG, dimX.getLength(), minX * 1e-6, maxX * 1e-6, true));
ds.addCoordinateAxis(makeLatLonCoordAxis(ds, dataG, dimY.getLength(), minY * 1e-6, maxY * 1e-6, false));
coordinates = addTimeCoord ? TIME_NAME+" Lat Lon" : "Lat Lon";
}
for (Variable v : dataG.getVariables()) {
if (v.getRank() != 2) continue;
if (!v.getDimension(0).equals(dimY)) continue;
if (!v.getDimension(1).equals(dimX)) continue;
if (coordinates != null)
v.addAttribute(new Attribute(CF.COORDINATES, coordinates));
if (hasProjection)
v.addAttribute(new Attribute(CF.GRID_MAPPING, CRS));
}
}
}
/*
The UpperLeftPointMtrs is in projection coordinates, and identifies the very upper left corner of the upper left pixel of the image data
• The LowerRightMtrs identifies the very lower right corner of the lower right pixel of the image data. These projection coordinates are the only metadata that accurately reflect the extreme corners of the gridded image
*/
private CoordinateAxis makeCoordAxis(NetcdfDataset ds, Group g, String name, int n, double start, double end, boolean isX) {
CoordinateAxis v = new CoordinateAxis1D(ds, g, name, DataType.DOUBLE, name, "km", isX ? "x coordinate" : "y coordinate");
double incr = (end - start) / n;
v.setValues(n, start * .001, incr * .001); // km
v.addAttribute(new Attribute(_Coordinate.AxisType, isX ? AxisType.GeoX.toString() : AxisType.GeoY.toString()));
return v;
}
/*
group: MOD_Grid_MOD17A3 {
variables:
short _HDFEOS_CRS;
:Projection = "GCTP_GEO";
:UpperLeftPointMtrs = -1.8E8, 9.0E7; // double
:LowerRightMtrs = 1.8E8, -9.0E7; // double
*/
private CoordinateAxis makeLatLonCoordAxis(NetcdfDataset ds, Group g, int n, double start, double end, boolean isLon) {
String name = isLon ? AxisType.Lon.toString() : AxisType.Lat.toString();
String dimName = isLon ? DIMX_NAME : DIMY_NAME;
CoordinateAxis v = new CoordinateAxis1D(ds, g, name, DataType.DOUBLE, dimName, isLon ? "degrees_east" : "degrees_north", null);
double incr = (end - start) / n;
v.setValues(n, start, incr);
v.addAttribute(new Attribute(_Coordinate.AxisType, name));
return v;
}
/*
1 5 7 8
16 PGSd_SNSOID Sphere CentMer FE FN
*/
private ProjectionCT makeSinusoidalProjection(String name, Attribute projParams) {
double radius = projParams.getNumericValue(0).doubleValue();
double centMer = projParams.getNumericValue(4).doubleValue();
double falseEast = projParams.getNumericValue(6).doubleValue();
double falseNorth = projParams.getNumericValue(7).doubleValue();
Sinusoidal proj = new Sinusoidal(centMer, falseEast * .001, falseNorth * .001, radius * .001);
return new ProjectionCT(name, "FGDC", proj);
}
}
/*
Can we extract projection info ??
// external xml
Terra
MODIS
MODIS
// ODL
UpperLeftPointMtrs=(-20015109.354000,1111950.519667)
LowerRightMtrs=(-18903158.834333,-0.000000)
Projection=GCTP_SNSOID
ProjParams=(6371007.181000,0,0,0,0,0,0,0,0,0,0,0,0)
SphereCode=-1
// from http://datamirror.csdb.cn/modis/resource/doc/HDFEOS5ref.pdf
1 5 7 8
16 PGSd_SNSOID Sphere CentMer FE FN
CentMer Longitude of the central meridian
OriginLat Latitude of the projection origin
FE False easting in the same units as the semi-major axis
FN False northing in the same units as the semi-major axis
according to snyder (p 243), sinusoidal projection parameterized only by CentMer and R
its a very simple form for sphere.
question as usual is what are the x,y coordinates? Assuming even spacing from the cornerss is the only thing you can do:
UpperLeftPointMtrs=(-20015109.354000, 1111950.519667)
LowerRightMtrs=(-18903158.834333,-0.000000)
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