use of org.geotoolkit.observation.model.GeoSpatialBound in project geotoolkit by Geomatys.
the class NetCDFExtractor method parseDataBlockTS.
private static ExtractionResult parseDataBlockTS(final NCFieldAnalyze analyze, final String procedureID, final List<String> acceptedSensorID, Set<org.opengis.observation.Phenomenon> phenomenons) throws NetCDFParsingException {
final ExtractionResult results = new ExtractionResult();
if (analyze.mainField == null) {
LOGGER.warning("No main field found");
return results;
}
LOGGER.info("parsing netCDF TS");
try {
final List<String> separators = parseSeparatorValues(analyze);
final boolean single = separators.isEmpty();
Array latArray = null;
Array lonArray = null;
if (analyze.hasSpatial()) {
latArray = analyze.getArrayFromField(analyze.latField);
lonArray = analyze.getArrayFromField(analyze.lonField);
}
final Variable timeVar = analyze.vars.get(analyze.mainField.name);
final String timeUnits = analyze.mainField.uom;
final Array timeArray = analyze.file.readArrays(Arrays.asList(timeVar)).get(0);
final boolean constantT = analyze.mainField.dimension == 1;
final boolean timeFirst = analyze.mainField.mainVariableFirst;
final Map<String, Array> phenArrays = analyze.getPhenomenonArrayMap();
results.fields.addAll(phenArrays.keySet());
final AbstractDataRecord datarecord = OMUtils.getDataRecordTimeSeries("2.0.0", analyze.phenfields);
final Phenomenon phenomenon = OMUtils.getPhenomenon("2.0.0", analyze.phenfields, phenomenons);
results.phenomenons.add(phenomenon);
if (single) {
if (acceptedSensorID == null || acceptedSensorID.contains(procedureID)) {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree compo = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "Component", "timeseries");
results.procedures.add(compo);
final MeasureStringBuilder sb = new MeasureStringBuilder();
final int count = timeVar.getDimension(0).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
final String identifier = UUID.randomUUID().toString();
// read geometry (assume point)
SamplingFeature sp = null;
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
results.addFeatureOfInterest(sp);
gb.addXYCoordinate(longitude, latitude);
gb.addGeometry((AbstractGeometry) sp.getGeometry());
}
}
// iterating over time
for (int i = 0; i < count; i++) {
final long millis = getTimeValue(timeUnits, timeArray, i);
if (millis == 0 || millis == LIMIT) {
continue;
}
gb.addDate(millis);
sb.appendDate(millis);
for (NCField field : analyze.phenfields) {
final Array phenArray = phenArrays.get(field.name);
final Double value = getDoubleValue(phenArray, i, field.fillValue);
sb.appendValue(value);
}
sb.closeBlock();
}
results.observations.add(// id
OMUtils.buildObservation(// id
identifier, // foi
sp, // phenomenon
phenomenon, // procedure
proc, // result
count, // result
datarecord, // result
sb, // time
gb.getTimeObject("2.0.0")));
results.spatialBound.merge(gb);
compo.spatialBound.merge(gb);
}
} else {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree system = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "System", "timeseries");
results.procedures.add(system);
for (int j = 0; j < separators.size(); j++) {
final String identifier = separators.get(j);
final MeasureStringBuilder sb = new MeasureStringBuilder();
final int count = getGoodTimeDimension(timeVar, analyze.dimensionSeparator).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
final String currentProcID = procedureID + '-' + identifier;
final Process currentProc = (Process) OMUtils.buildProcess(currentProcID);
final ProcedureTree compo = new ProcedureTree(currentProc.getHref(), currentProc.getName(), currentProc.getDescription(), "Component", "timeseries");
if (acceptedSensorID == null || acceptedSensorID.contains(currentProcID)) {
// read geometry (assume point)
SamplingFeature sp = null;
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, j, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, j, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
results.addFeatureOfInterest(sp);
gb.addXYCoordinate(longitude, latitude);
gb.addGeometry((AbstractGeometry) sp.getGeometry());
}
}
for (int i = 0; i < count; i++) {
final long millis = getTimeValue(timeUnits, timeFirst, constantT, timeArray, i, j);
if (millis == 0 || millis == LIMIT) {
continue;
}
gb.addDate(millis);
sb.appendDate(millis);
for (NCField field : analyze.phenfields) {
final Array phenArray = phenArrays.get(field.name);
final boolean mainFirst = field.mainVariableFirst;
final Double value = getDoubleValue(mainFirst, phenArray, i, j, field.fillValue);
sb.appendValue(value);
}
// remove the last token separator
sb.closeBlock();
}
compo.spatialBound.merge(gb);
system.children.add(compo);
final String obsid = UUID.randomUUID().toString();
results.observations.add(// id
OMUtils.buildObservation(// id
obsid, // foi
sp, // phenomenon
phenomenon, // procedure
currentProc, // result
count, // result
datarecord, // result
sb, // time
gb.getTimeObject("2.0.0")));
results.spatialBound.merge(gb);
}
}
}
} catch (IOException | IllegalArgumentException ex) {
throw new NetCDFParsingException("error while parsing netcdf timeserie", ex);
}
LOGGER.info("datablock parsed");
return results;
}
use of org.geotoolkit.observation.model.GeoSpatialBound in project geotoolkit by Geomatys.
the class NetCDFExtractor method parseDataBlockXY.
private static ExtractionResult parseDataBlockXY(final NCFieldAnalyze analyze, final String procedureID, final List<String> acceptedSensorID, Set<org.opengis.observation.Phenomenon> phenomenons) throws NetCDFParsingException {
final ExtractionResult results = new ExtractionResult();
if (analyze.mainField == null) {
LOGGER.warning("No main field found");
return results;
}
LOGGER.info("parsing datablock XY");
try {
final List<String> separators = parseSeparatorValues(analyze);
final boolean single = separators.isEmpty();
Array latArray = null;
Array lonArray = null;
if (analyze.hasSpatial()) {
latArray = analyze.getArrayFromField(analyze.latField);
lonArray = analyze.getArrayFromField(analyze.lonField);
}
Array timeArray = null;
String timeUnits = null;
if (analyze.hasTime()) {
timeUnits = analyze.timeField.uom;
timeArray = analyze.getArrayFromField(analyze.timeField);
}
final Variable zVar = analyze.vars.get(analyze.mainField.name);
final Array zArray = analyze.file.readArrays(Arrays.asList(zVar)).get(0);
final boolean constantZ = analyze.mainField.dimension == 1;
final boolean Zfirst = analyze.mainField.mainVariableFirst;
final Map<String, Array> phenArrays = analyze.getPhenomenonArrayMap();
results.fields.addAll(phenArrays.keySet());
final AbstractDataRecord datarecord = OMUtils.getDataRecordProfile("2.0.0", analyze.phenfields);
final Phenomenon phenomenon = OMUtils.getPhenomenon("2.0.0", analyze.phenfields, phenomenons);
results.phenomenons.add(phenomenon);
if (single) {
if (acceptedSensorID == null || acceptedSensorID.contains(procedureID)) {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree compo = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "profile", "Component");
results.procedures.add(compo);
final MeasureStringBuilder sb = new MeasureStringBuilder();
final int count = zVar.getDimension(0).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
final String identifier = UUID.randomUUID().toString();
// read geometry (assume point)
SamplingFeature sp = null;
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, 0, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, 0, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
results.addFeatureOfInterest(sp);
gb.addXYCoordinate(longitude, latitude);
gb.addGeometry((AbstractGeometry) sp.getGeometry());
}
}
if (analyze.hasTime()) {
final long millis = getTimeValue(timeUnits, timeArray, 0);
if (millis != 0 && millis != LIMIT) {
gb.addDate(millis);
}
}
for (int zIndex = 0; zIndex < zVar.getDimension(0).getLength(); zIndex++) {
double zLevel = getDoubleValue(zArray, zIndex, analyze.mainField.fillValue);
if (zLevel == 0 || zLevel == FILL_VALUE) {
continue;
}
sb.appendValue(zLevel);
for (NCField field : analyze.phenfields) {
final Array phenArray = phenArrays.get(field.name);
final double value = getDoubleValue(phenArray, zIndex, field.fillValue);
sb.appendValue(value);
}
sb.closeBlock();
}
results.observations.add(// id
OMUtils.buildObservation(// id
identifier, // foi
sp, // phenomenon
phenomenon, // procedure
proc, // result
count, // result
datarecord, // result
sb, // time
gb.getTimeObject("2.0.0")));
results.spatialBound.merge(gb);
compo.spatialBound.merge(gb);
}
} else {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree system = new ProcedureTree(proc.getHref(), proc.getName(), proc.getDescription(), "profile", "System");
results.procedures.add(system);
for (int profileIndex = 0; profileIndex < separators.size(); profileIndex++) {
final String identifier = separators.get(profileIndex);
final int count = zVar.getDimension(0).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
final String currentProcID = procedureID + '-' + identifier;
final Process currentProc = (Process) OMUtils.buildProcess(currentProcID);
final ProcedureTree compo = new ProcedureTree(currentProc.getHref(), currentProc.getName(), currentProc.getDescription(), "profile", "Component");
if (acceptedSensorID == null || acceptedSensorID.contains(currentProcID)) {
// read geometry (assume point)
SamplingFeature sp = null;
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, 0, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, 0, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
sp = OMUtils.buildSamplingPoint(identifier, latitude, longitude);
results.addFeatureOfInterest(sp);
gb.addXYCoordinate(longitude, latitude);
gb.addGeometry((AbstractGeometry) sp.getGeometry());
}
}
if (analyze.hasTime()) {
final long millis = getTimeValue(timeUnits, timeArray, 0);
if (millis != 0 && millis != LIMIT) {
gb.addDate(millis);
}
}
final MeasureStringBuilder sb = new MeasureStringBuilder();
for (int zIndex = 0; zIndex < zVar.getDimension(0).getLength(); zIndex++) {
double zLevel = getZValue(Zfirst, constantZ, zArray, zIndex, profileIndex, analyze.mainField.fillValue);
if (zLevel == 0 || zLevel == FILL_VALUE) {
continue;
}
sb.appendValue(zLevel);
for (NCField field : analyze.phenfields) {
final Array phenArray = phenArrays.get(field.name);
final boolean mainFirst = field.mainVariableFirst;
final double value = getDoubleValue(mainFirst, phenArray, zIndex, profileIndex, field.fillValue);
sb.appendValue(value);
}
sb.closeBlock();
}
compo.spatialBound.merge(gb);
system.children.add(compo);
final String obsid = UUID.randomUUID().toString();
results.observations.add(// id
OMUtils.buildObservation(// id
obsid, // foi
sp, // phenomenon
phenomenon, // procedure
currentProc, // result
count, // result
datarecord, // result
sb, // time
gb.getTimeObject("2.0.0")));
results.spatialBound.merge(gb);
}
}
}
} catch (IOException | IllegalArgumentException ex) {
throw new NetCDFParsingException("error while parsing netcdf profile", ex);
}
LOGGER.info("datablock parsed");
return results;
}
use of org.geotoolkit.observation.model.GeoSpatialBound in project geotoolkit by Geomatys.
the class NetCDFExtractor method getProcedureTS.
private static List<ProcedureTree> getProcedureTS(final NCFieldAnalyze analyze, final String procedureID, final List<String> acceptedSensorID) throws NetCDFParsingException {
final List<ProcedureTree> results = new ArrayList<>();
if (analyze.mainField == null) {
LOGGER.warning("No main field found");
return results;
}
LOGGER.info("parsing netCDF TS");
try {
final List<String> separators = parseSeparatorValues(analyze);
final boolean single = separators.isEmpty();
Array latArray = null;
Array lonArray = null;
if (analyze.hasSpatial()) {
latArray = analyze.getArrayFromField(analyze.latField);
lonArray = analyze.getArrayFromField(analyze.lonField);
}
final Variable timeVar = analyze.vars.get(analyze.mainField.name);
final String timeUnits = analyze.mainField.uom;
final Array timeArray = analyze.file.readArrays(Arrays.asList(timeVar)).get(0);
final boolean constantT = analyze.mainField.dimension == 1;
final boolean timeFirst = analyze.mainField.mainVariableFirst;
final Set<String> fields = analyze.getPhenomenonArrayMap().keySet();
if (single) {
if (acceptedSensorID == null || acceptedSensorID.contains(procedureID)) {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree compo = new ProcedureTree(proc.getHref(), proc.getName(), proc.getHref(), "Component", "timeseries", fields);
results.add(compo);
final int count = timeVar.getDimension(0).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
gb.addXYCoordinate(longitude, latitude);
}
}
// iterating over time
for (int i = 0; i < count; i++) {
final long millis = getTimeValue(timeUnits, timeArray, i);
if (millis == 0 || millis == LIMIT) {
continue;
}
gb.addDate(millis);
}
compo.spatialBound.merge(gb);
}
} else {
final Process proc = (Process) OMUtils.buildProcess(procedureID);
final ProcedureTree system = new ProcedureTree(proc.getHref(), proc.getName(), proc.getHref(), "System", "timeseries", fields);
results.add(system);
for (int j = 0; j < separators.size(); j++) {
final String identifier = separators.get(j);
final int count = getGoodTimeDimension(timeVar, analyze.dimensionSeparator).getLength();
final GeoSpatialBound gb = new GeoSpatialBound();
final String currentProcID = procedureID + '-' + identifier;
final Process currentProc = (Process) OMUtils.buildProcess(currentProcID);
final ProcedureTree compo = new ProcedureTree(currentProc.getHref(), currentProc.getName(), currentProc.getDescription(), "Component", "timeseries", fields);
if (acceptedSensorID == null || acceptedSensorID.contains(currentProcID)) {
if (analyze.hasSpatial()) {
final double latitude = getDoubleValue(latArray, j, analyze.latField.fillValue);
final double longitude = Longitude.normalize(getDoubleValue(lonArray, j, analyze.lonField.fillValue));
if (!Double.isNaN(latitude) && !Double.isNaN(longitude)) {
gb.addXYCoordinate(longitude, latitude);
}
}
for (int i = 0; i < count; i++) {
final long millis = getTimeValue(timeUnits, timeFirst, constantT, timeArray, i, j);
if (millis == 0 || millis == LIMIT) {
continue;
}
gb.addDate(millis);
}
compo.spatialBound.merge(gb);
system.children.add(compo);
}
}
}
} catch (IOException | IllegalArgumentException ex) {
throw new NetCDFParsingException("error while parsing netcdf timeserie", ex);
}
LOGGER.info("datablock parsed");
return results;
}
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