public static boolean isMine(NetcdfFile ncfile) {
if (!ncfile.getFileTypeId().equals("HDF5")) return false;
Group loc = ncfile.findGroup("VHRR/Geo-Location");
if (null == loc) return false;
if (null == loc.findVariable("Latitude")) return false;
if (null == loc.findVariable("Longitude")) return false;
if (null == ncfile.findGroup("VHRR/Image Data")) return false;
return true;
}
private static String getStructMetadata(Group eosGroup) throws IOException {
StringBuilder sbuff = null;
String structMetadata = null;
int n = 0;
while (true) {
Variable structMetadataVar = eosGroup.findVariable("StructMetadata." + n);
if (structMetadataVar == null) break;
if ((structMetadata != null) && (sbuff == null)) { // more than 1 StructMetadata
sbuff = new StringBuilder(64000);
sbuff.append(structMetadata);
}
// read and parse the ODL
Array A = structMetadataVar.read();
if (A instanceof ArrayChar.D1) {
ArrayChar ca = (ArrayChar) A;
structMetadata = ca.getString(); // common case only StructMetadata.0, avoid extra copy
} else if (A instanceof ArrayObject.D0) {
ArrayObject ao = (ArrayObject) A;
structMetadata = (String) ao.getObject(0);
} else {
log.error("Unsupported array type {} for StructMetadata", A.getElementType());
}
if (sbuff != null) sbuff.append(structMetadata);
n++;
}
return (sbuff != null) ? sbuff.toString() : structMetadata;
}
private boolean compareGroups(Group org, Group copy) {
if (showCompare) f.format("compare Group %s to %s %n", org.getName(), copy.getName());
boolean ok = true;
if (!org.getName().equals(copy.getName())) {
f.format(" ** names are different %s != %s %n", org.getName(), copy.getName());
ok = false;
}
// dimensions
ok &= checkAll(org.getDimensions(), copy.getDimensions(), null);
// attributes
ok &= checkAll(org.getAttributes(), copy.getAttributes(), null);
// variables
// cant use object equality, just match on short name
for (Variable orgV : org.getVariables()) {
Variable copyVar = copy.findVariable(orgV.getShortName());
if (copyVar == null) {
f.format(" ** cant find variable %s in 2nd file%n", orgV.getFullName());
ok = false;
} else {
ok &= compareVariables(orgV, copyVar, compareData, true);
}
}
for (Variable copyV : copy.getVariables()) {
Variable orgV = org.findVariable(copyV.getShortName());
if (orgV == null) {
f.format(" ** cant find variable %s in 1st file%n", copyV.getFullName());
ok = false;
}
}
// nested groups
List groups = new ArrayList();
ok &= checkAll(org.getGroups(), copy.getGroups(), groups);
for (int i = 0; i < groups.size(); i += 2) {
Group orgGroup = (Group) groups.get(i);
Group ncmlGroup = (Group) groups.get(i + 1);
ok &= compareGroups(orgGroup, ncmlGroup);
}
return ok;
}
@Test
public void testForStructMetadata() throws IOException {
System.out.printf("TestH4eosReadAll %s%n", filename);
try (NetcdfFile ncfile = NetcdfFile.open(filename)) {
Group root = ncfile.getRootGroup();
Group g = root.findGroup("HDFEOS INFORMATION");
if (g == null) g = ncfile.getRootGroup();
Variable dset = g.findVariable("StructMetadata.0");
assert (dset != null);
}
}
/* (non-Javadoc)
* @see loci.formats.NetCDFService#getVariableAttributes(java.lang.String)
*/
public Hashtable<String, Object> getVariableAttributes(String name) {
String groupName = getDirectory(name);
String variableName = getName(name);
Group group = getGroup(groupName);
Variable variable = group.findVariable(variableName);
List<Attribute> attributes = variable.getAttributes();
Hashtable<String, Object> toReturn = new Hashtable<String, Object>();
for (Attribute attribute : attributes) {
toReturn.put(attribute.getName(), arrayToString(attribute.getValues()));
}
return toReturn;
}
/* (non-Javadoc)
* @see loci.formats.NetCDFService#getArray(java.lang.String, int[], int[])
*/
public Object getArray(String path, int[] origin, int[] shape) throws ServiceException {
String groupName = getDirectory(path);
String variableName = getName(path);
Group group = getGroup(groupName);
Variable variable = group.findVariable(variableName);
try {
if (origin != null && shape != null) {
return variable.read(origin, shape).reduce().copyToNDJavaArray();
}
return variable.read().copyToNDJavaArray();
} catch (InvalidRangeException e) {
throw new ServiceException(e);
} catch (IOException e) {
throw new ServiceException(e);
}
}
private FeatureType amendGrid(
Element gridElem, NetcdfFile ncfile, Group parent, String location) {
List<Dimension> unknownDims = new ArrayList<>();
// always has x and y dimension
String xdimSizeS = gridElem.getChild("XDim").getText().trim();
String ydimSizeS = gridElem.getChild("YDim").getText().trim();
int xdimSize = Integer.parseInt(xdimSizeS);
int ydimSize = Integer.parseInt(ydimSizeS);
parent.addDimensionIfNotExists(new Dimension("XDim", xdimSize));
parent.addDimensionIfNotExists(new Dimension("YDim", ydimSize));
/* see HdfEosModisConvention
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
*/
Element proj = gridElem.getChild("Projection");
if (proj != null) {
Variable crs = new Variable(ncfile, parent, null, HDFEOS_CRS);
crs.setDataType(DataType.SHORT);
crs.setDimensions(""); // scalar
crs.setCachedData(Array.makeArray(DataType.SHORT, 1, 0, 0)); // fake data
parent.addVariable(crs);
addAttributeIfExists(gridElem, HDFEOS_CRS_Projection, crs, false);
addAttributeIfExists(gridElem, HDFEOS_CRS_UpperLeft, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_LowerRight, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_ProjParams, crs, true);
addAttributeIfExists(gridElem, HDFEOS_CRS_SphereCode, crs, false);
}
// global Dimensions
Element d = gridElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
Dimension old = parent.findDimension(name);
if ((old == null) || (old.getLength() != length)) {
if (length > 0) {
Dimension dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
} else {
log.warn("Dimension {} has size {} {} ", sizeS, name, location);
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Element floc = gridElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null)
dataG =
parent.findGroup(
DATA_FIELDS2); // eg C:\data\formats\hdf4\eos\mopitt\MOP03M-200501-L3V81.0.1.hdf
if (dataG != null) {
Element f = gridElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
String varname = elem.getChild("DataFieldName").getText().trim();
varname = NetcdfFile.makeValidCdmObjectName(varname);
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, location);
}
// get projection
String projS = null;
Element projElem = gridElem.getChild("Projection");
if (projElem != null) projS = projElem.getText().trim();
boolean isLatLon = "GCTP_GEO".equals(projS);
// look for XDim, YDim coordinate variables
if (isLatLon) {
for (Variable v : dataG.getVariables()) {
if (v.isCoordinateVariable()) {
if (v.getShortName().equals("YDim")) {
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
v.addAttribute(new Attribute(CDM.UNITS, CDM.LAT_UNITS));
}
if (v.getShortName().equals("XDim"))
v.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
}
}
}
}
return FeatureType.GRID;
}
private FeatureType amendSwath(NetcdfFile ncfile, Element swathElem, Group parent) {
FeatureType featureType = FeatureType.SWATH;
List<Dimension> unknownDims = new ArrayList<>();
// Dimensions
Element d = swathElem.getChild("Dimension");
List<Element> dims = d.getChildren();
for (Element elem : dims) {
String name = elem.getChild("DimensionName").getText().trim();
name = NetcdfFile.makeValidCdmObjectName(name);
if (name.equalsIgnoreCase("scalar")) continue;
String sizeS = elem.getChild("Size").getText().trim();
int length = Integer.parseInt(sizeS);
if (length > 0) {
Dimension dim = parent.findDimensionLocal(name);
if (dim != null) { // already added - may be dimension scale ?
if (dim.getLength() != length) { // ok as long as it matches
log.error("Conflicting Dimensions = {} {}", dim, ncfile.getLocation());
throw new IllegalStateException("Conflicting Dimensions = " + name);
}
} else {
dim = new Dimension(name, length);
if (parent.addDimensionIfNotExists(dim) && showWork)
System.out.printf(" Add dimension %s %n", dim);
}
} else {
log.warn("Dimension " + name + " has size " + sizeS, ncfile.getLocation());
Dimension udim = new Dimension(name, 1);
udim.setGroup(parent);
unknownDims.add(udim);
if (showWork) System.out.printf(" Add dimension %s %n", udim);
}
}
// Dimension Maps
Element dmap = swathElem.getChild("DimensionMap");
List<Element> dimMaps = dmap.getChildren();
for (Element elem : dimMaps) {
String geoDimName = elem.getChild("GeoDimension").getText().trim();
geoDimName = NetcdfFile.makeValidCdmObjectName(geoDimName);
String dataDimName = elem.getChild("DataDimension").getText().trim();
dataDimName = NetcdfFile.makeValidCdmObjectName(dataDimName);
String offsetS = elem.getChild("Offset").getText().trim();
String incrS = elem.getChild("Increment").getText().trim();
int offset = Integer.parseInt(offsetS);
int incr = Integer.parseInt(incrS);
// make new variable for this dimension map
Variable v = new Variable(ncfile, parent, null, dataDimName);
v.setDimensions(geoDimName);
v.setDataType(DataType.INT);
int npts = (int) v.getSize();
Array data = Array.makeArray(v.getDataType(), npts, offset, incr);
v.setCachedData(data, true);
v.addAttribute(new Attribute("_DimensionMap", ""));
parent.addVariable(v);
if (showWork) System.out.printf(" Add dimensionMap %s %n", v);
}
// Geolocation Variables
Group geoFieldsG = parent.findGroup(GEOLOC_FIELDS);
if (geoFieldsG == null) geoFieldsG = parent.findGroup(GEOLOC_FIELDS2);
if (geoFieldsG != null) {
Variable latAxis = null, lonAxis = null;
Element floc = swathElem.getChild("GeoField");
List<Element> varsLoc = floc.getChildren();
for (Element elem : varsLoc) {
String varname = elem.getChild("GeoFieldName").getText().trim();
Variable v = geoFieldsG.findVariable(varname);
// if (v == null)
// v = geoFieldsG.findVariable( H4header.createValidObjectName(varname));
assert v != null : varname;
AxisType axis = addAxisType(ncfile, v);
if (axis == AxisType.Lat) latAxis = v;
if (axis == AxisType.Lon) lonAxis = v;
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
if (showWork) System.out.printf(" set coordinate %s %n", v);
}
if ((latAxis != null) && (lonAxis != null)) {
List<Dimension> xyDomain = CoordinateSystem.makeDomain(new Variable[] {latAxis, lonAxis});
if (xyDomain.size() < 2) featureType = FeatureType.PROFILE; // ??
}
}
// Data Variables
Group dataG = parent.findGroup(DATA_FIELDS);
if (dataG == null) dataG = parent.findGroup(DATA_FIELDS2);
if (dataG != null) {
Element f = swathElem.getChild("DataField");
List<Element> vars = f.getChildren();
for (Element elem : vars) {
Element dataFieldNameElem = elem.getChild("DataFieldName");
if (dataFieldNameElem == null) continue;
String varname = NetcdfFile.makeValidCdmObjectName(dataFieldNameElem.getText().trim());
Variable v = dataG.findVariable(varname);
// if (v == null)
// v = dataG.findVariable( H4header.createValidObjectName(varname));
if (v == null) {
log.error("Cant find variable {} {}", varname, ncfile.getLocation());
continue;
}
Element dimList = elem.getChild("DimList");
List<Element> values = dimList.getChildren("value");
setSharedDimensions(v, values, unknownDims, ncfile.getLocation());
}
}
return featureType;
}
/**
* Add this coord as a variable in the netCDF file
*
* @param ncfile netCDF file to add to
* @param g group in file
*/
void addToNetcdfFile(NetcdfFile ncfile, Group g) {
if (dontUseVertical) {
typicalRecord = null;
return;
}
if (g == null) {
g = ncfile.getRootGroup();
}
// coordinate axis
Variable v = new Variable(ncfile, g, null, getVariableName());
v.setDataType(DataType.DOUBLE);
String desc = lookup.getLevelDescription(typicalRecord);
if (lookup instanceof Grib2GridTableLookup && usesBounds) {
desc = "Layer between " + desc;
}
v.addAttribute(new Attribute("long_name", desc));
v.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
// positive attribute needed for CF-1 Height and Pressure
if (positive != null) {
v.addAttribute(new Attribute("positive", positive));
}
if (units != null) {
AxisType axisType;
if (SimpleUnit.isCompatible("millibar", units)) {
axisType = AxisType.Pressure;
} else if (SimpleUnit.isCompatible("m", units)) {
axisType = AxisType.Height;
} else {
axisType = AxisType.GeoZ;
}
if (lookup instanceof Grib2GridTableLookup || lookup instanceof Grib1GridTableLookup) {
v.addAttribute(
new Attribute("GRIB_level_type", Integer.toString(typicalRecord.getLevelType1())));
} else {
v.addAttribute(
new Attribute("level_type", Integer.toString(typicalRecord.getLevelType1())));
}
v.addAttribute(new Attribute(_Coordinate.AxisType, axisType.toString()));
}
if (coordValues == null) {
coordValues = new double[levels.size()];
for (int i = 0; i < levels.size(); i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
coordValues[i] = lc.mid;
}
}
Array dataArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length}, coordValues);
v.setDimensions(getVariableName());
v.setCachedData(dataArray, true);
ncfile.addVariable(g, v);
if (usesBounds) {
String boundsDimName = "bounds_dim";
if (g.findDimension(boundsDimName) == null) {
ncfile.addDimension(g, new Dimension(boundsDimName, 2, true));
}
String bname = getVariableName() + "_bounds";
v.addAttribute(new Attribute("bounds", bname));
v.addAttribute(new Attribute(_Coordinate.ZisLayer, "true"));
Variable b = new Variable(ncfile, g, null, bname);
b.setDataType(DataType.DOUBLE);
b.setDimensions(getVariableName() + " " + boundsDimName);
b.addAttribute(new Attribute("long_name", "bounds for " + v.getName()));
b.addAttribute(new Attribute("units", lookup.getLevelUnit(typicalRecord)));
Array boundsArray = Array.factory(DataType.DOUBLE, new int[] {coordValues.length, 2});
ucar.ma2.Index ima = boundsArray.getIndex();
for (int i = 0; i < coordValues.length; i++) {
LevelCoord lc = (LevelCoord) levels.get(i);
boundsArray.setDouble(ima.set(i, 0), lc.value1);
boundsArray.setDouble(ima.set(i, 1), lc.value2);
}
b.setCachedData(boundsArray, true);
ncfile.addVariable(g, b);
}
if (factors != null) {
// check if already created
if (g == null) {
g = ncfile.getRootGroup();
}
if (g.findVariable("hybrida") != null) return;
v.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate"));
v.addAttribute(new Attribute("formula_terms", "ap: hybrida b: hybridb ps: Pressure"));
// create hybrid factor variables
// add hybrida variable
Variable ha = new Variable(ncfile, g, null, "hybrida");
ha.setDataType(DataType.DOUBLE);
ha.addAttribute(new Attribute("long_name", "level_a_factor"));
ha.addAttribute(new Attribute("units", ""));
ha.setDimensions(getVariableName());
// add data
int middle = factors.length / 2;
double[] adata;
double[] bdata;
if (levels.size() < middle) { // only partial data wanted
adata = new double[levels.size()];
bdata = new double[levels.size()];
} else {
adata = new double[middle];
bdata = new double[middle];
}
for (int i = 0; i < middle && i < levels.size(); i++) adata[i] = factors[i];
Array haArray = Array.factory(DataType.DOUBLE, new int[] {adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor"));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
for (int i = 0; i < middle && i < levels.size(); i++) bdata[i] = factors[i + middle];
Array hbArray = Array.factory(DataType.DOUBLE, new int[] {bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
/* // TODO: delete next time modifying code
double[] adata = new double[ middle ];
for( int i = 0; i < middle; i++ )
adata[ i ] = factors[ i ];
Array haArray = Array.factory(DataType.DOUBLE, new int[]{adata.length}, adata);
ha.setCachedData(haArray, true);
ncfile.addVariable(g, ha);
// add hybridb variable
Variable hb = new Variable(ncfile, g, null, "hybridb");
hb.setDataType(DataType.DOUBLE);
hb.addAttribute(new Attribute("long_name", "level_b_factor" ));
//hb.addAttribute(new Attribute("standard_name", "atmosphere_hybrid_sigma_pressure_coordinate" ));
hb.addAttribute(new Attribute("units", ""));
hb.setDimensions(getVariableName());
// add data
double[] bdata = new double[ middle ];
for( int i = 0; i < middle; i++ )
bdata[ i ] = factors[ i + middle ];
Array hbArray = Array.factory(DataType.DOUBLE, new int[]{bdata.length}, bdata);
hb.setCachedData(hbArray, true);
ncfile.addVariable(g, hb);
*/
}
}
public void augmentDataset(NetcdfDataset ds, CancelTask cancelTask) throws IOException {
ds.addAttribute(null, new Attribute("FeatureType", FeatureType.IMAGE.toString())); // LOOK
Group vhrr = ds.findGroup("VHRR");
Group loc = vhrr.findGroup("Geo-Location");
Variable lat = loc.findVariable("Latitude");
lat.addAttribute(new Attribute(CDM.UNITS, "degrees_north"));
lat.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lat.toString()));
Variable lon = loc.findVariable("Longitude");
lon.addAttribute(new Attribute(CDM.UNITS, "degrees_east"));
lon.addAttribute(new Attribute(_Coordinate.AxisType, AxisType.Lon.toString()));
int[] shape = lat.getShape();
assert shape.length == 2;
Dimension scan = new Dimension("scan", shape[0]);
Dimension xscan = new Dimension("xscan", shape[1]);
vhrr.addDimension(scan);
vhrr.addDimension(xscan);
lat.setDimensions("scan xscan");
lon.setDimensions("scan xscan");
Group data = vhrr.findGroup("Image Data");
for (Variable v : data.getVariables()) {
int[] vs = v.getShape();
if ((vs.length == 2) && (vs[0] == shape[0]) && (vs[1] == shape[1])) {
v.setDimensions("scan xscan");
v.addAttribute(new Attribute(_Coordinate.Axes, "lat lon time"));
}
}
/* Group PRODUCT_METADATA {
Group PRODUCT_DETAILS {
PRODUCT_DETAILS:UNIQUE_ID = "3AVHR_22NOV2007_0902";
PRODUCT_DETAILS:PRODUCT_TYPE = "STANDARD(FULL DISK) ";
PRODUCT_DETAILS:PROCESSING_SOFTWARE = "InPGS_XXXXXXXXXXXXXX";
PRODUCT_DETAILS:SPACECRAFT_ID = "INSAT-3A ";
PRODUCT_DETAILS:SENSOR_ID = "VHR";
PRODUCT_DETAILS:ACQUISITION_TYPE = "FULL FRAME ";
PRODUCT_DETAILS:ACQUISITION_DATE = "22NOV2007";
PRODUCT_DETAILS:ACQUISITION_TIME_IN_GMT = "0902";
PRODUCT_DETAILS:PRODUCT_NAME = " FULL DISK";
PRODUCT_DETAILS:PROCESSING_LEVEL = "L1B";
PRODUCT_DETAILS:BAND_COMBINATION = "Visible(VIS),Thermal Infrared(TIR),Water Vapour(WV)";
PRODUCT_DETAILS:PRODUCT_CODE = "ST00001HD";
} */
Group info = ds.findGroup("PRODUCT_METADATA/PRODUCT_DETAILS");
String dateS = info.findAttribute("ACQUISITION_DATE").getStringValue();
String timeS = info.findAttribute("ACQUISITION_TIME_IN_GMT").getStringValue();
SimpleDateFormat format = new SimpleDateFormat("ddMMMyyyyHHmm");
format.setTimeZone(java.util.TimeZone.getTimeZone("GMT"));
try {
Date d = format.parse(dateS + timeS);
VariableDS time =
new VariableDS(
ds,
vhrr,
null,
"time",
DataType.LONG,
"",
"seconds since 1970-01-01 00:00",
"time generated from PRODUCT_METADATA/PRODUCT_DETAILS");
time.addAttribute(
new Attribute(
_Coordinate.AxisType,
AxisType.Time.toString())); // // LOOK : cant handle scalar coordinates yet ??
time.addAttribute(new Attribute("IsoDate", new DateFormatter().toDateTimeStringISO(d)));
CoordinateAxis1D timeAxis = new CoordinateAxis1D(ds, time);
ds.addVariable(vhrr, timeAxis);
ArrayLong.D0 timeData = new ArrayLong.D0();
timeData.set(d.getTime() / 1000);
time.setCachedData(timeData, true);
} catch (ParseException e) {
e.printStackTrace();
throw new IOException(e.getMessage());
}
ds.finish();
}