List<GeoPointCarbon> occurrencesToList(Document document, Region region) {
String DATASETNAME_LAT = "RetrievalGeometry/retrieval_latitude";
String DATASETNAME_LONG = "RetrievalGeometry/retrieval_longitude";
String DATASETNAME_XCO2 = "RetrievalResults/xco2";
String DATASETNAME_XCO2_INTERF = "RetrievalResults/xco2_uncert_interf";
String DATASETNAME_XCO2_NOISE = "RetrievalResults/xco2_uncert_noise";
String DATASETNAME_DATE = "Metadata/OrbitStartDate";
H5File file = null;
Dataset latitude = null;
Dataset longitude = null;
Dataset xco2 = null;
Dataset xco2_interf = null;
Dataset xco2_noise = null;
H5ScalarDS orbitStartDate = null;
int latitude_dataspace_id = -1;
int longitude_dataspace_id = -1;
int xco2_dataspace_id = -1;
int xco2_interf_dataspace_id = -1;
int xco2_noise_dataspace_id = -1;
int latitude_dataset_id = -1;
int longitude_dataset_id = -1;
int xco2_dataset_id = -1;
int xco2_interf_dataset_id = -1;
int xco2_noise_dataset_id = -1;
long[] latitude_dims = {1};
long[] longitude_dims = {1};
long[] xco2_dims = {1};
long[] xco2_interf_dims = {1};
long[] xco2_noise_dims = {1};
float[] latitude_data;
float[] longitude_data;
float[] xco2_data;
float[] xco2_interf_data;
float[] xco2_noise_data;
String[] date_data = {""};
List<GeoPointCarbon> listOfPoints = new ArrayList<>();
try {
// Open an existing file in the folder it is located.
file = new H5File(document.getFileName(), FileFormat.READ);
file.open();
// Open latitude dataset.
latitude = (Dataset) file.get(DATASETNAME_LAT);
latitude_dataset_id = latitude.open();
// Open longitude dataset.
longitude = (Dataset) file.get(DATASETNAME_LONG);
longitude_dataset_id = longitude.open();
// Open xco2 dataset.
xco2 = (Dataset) file.get(DATASETNAME_XCO2);
xco2_dataset_id = xco2.open();
// Get orbitStartDate dataset.
orbitStartDate = (H5ScalarDS) file.get(DATASETNAME_DATE);
// Get latitude dataspace and allocate memory for the read buffer.
if (latitude_dataset_id >= 0) latitude_dataspace_id = H5.H5Dget_space(latitude_dataset_id);
if (latitude_dataspace_id >= 0)
H5.H5Sget_simple_extent_dims(latitude_dataspace_id, latitude_dims, null);
// Get longitude dataspace and allocate memory for the read buffer.
if (longitude_dataset_id >= 0) longitude_dataspace_id = H5.H5Dget_space(longitude_dataset_id);
if (longitude_dataset_id >= 0)
H5.H5Sget_simple_extent_dims(longitude_dataspace_id, longitude_dims, null);
// Get xco2 dataspace and allocate memory for the read buffer.
if (xco2_dataset_id >= 0) xco2_dataspace_id = H5.H5Dget_space(xco2_dataset_id);
if (xco2_dataset_id >= 0) H5.H5Sget_simple_extent_dims(xco2_dataspace_id, xco2_dims, null);
// Allocate array of pointers to rows.
latitude_data = new float[(int) latitude_dims[0]];
longitude_data = new float[(int) longitude_dims[0]];
xco2_data = new float[(int) xco2_dims[0]];
// Read the data using the default properties.
latitude.init();
latitude_data = (float[]) latitude.getData();
longitude.init();
longitude_data = (float[]) longitude.getData();
xco2.init();
xco2_data = (float[]) xco2.getData();
date_data = (String[]) orbitStartDate.read();
// Process data
for (int i = 0; i < latitude_data.length; i++) {
if (region.inRegion(latitude_data[i], longitude_data[i])) {
listOfPoints.add(
new GeoPointCarbon(
latitude_data[i],
longitude_data[i],
date_data[0],
(float) (xco2_data[i] * Math.pow(10, 6))));
}
}
// End access to the latitude dataset and release resources used by it.
if (latitude_dataset_id >= 0) latitude.close(latitude_dataset_id);
if (latitude_dataspace_id >= 0) H5.H5Sclose(latitude_dataspace_id);
// End access to the longitude dataset and release resources used by it.
if (longitude_dataset_id >= 0) longitude.close(longitude_dataset_id);
if (longitude_dataspace_id >= 0) H5.H5Sclose(longitude_dataspace_id);
// End access to the xco2 dataset and release resources used by it.
if (xco2_dataset_id >= 0) xco2.close(xco2_dataset_id);
if (xco2_dataspace_id >= 0) H5.H5Sclose(xco2_dataspace_id);
// Close the file.
file.close();
} catch (Exception e) {
e.printStackTrace();
}
return listOfPoints;
}
