/**
* Returns the array that contins the max dimension sizes of the dataset.
*
* @return the max dimension sizes of the dataset.
*/
public final long[] getMaxDims() {
if (rank < 0) init();
if (maxDims == null) return dims;
return maxDims;
}
/**
* Returns the dimension size of the vertical axis.
*
* <p>This function is used by GUI applications such as HDFView. GUI applications display a
* dataset in a 2D table or 2D image. The display order is specified by the index array of
* selectedIndex as follow:
*
* <dl>
* <dt>selectedIndex[0] -- height
* <dd>The vertical axis
* <dt>selectedIndex[1] -- width
* <dd>The horizontal axis
* <dt>selectedIndex[2] -- depth
* <dd>The depth axis is used for 3 or more dimensional datasets.
* </dl>
*
* Applications can use getSelectedIndex() to access and change the display order. For example, in
* a 2D dataset of 200x50 (dim0=200, dim1=50), the following code will set the height=200 and
* width=50.
*
* <pre>
* long[] selectedIndex = dataset.getSelectedIndex();
* selectedIndex[0] = 0;
* selectedIndex[1] = 1;
* </pre>
*
* @see #getSelectedIndex()
* @see #getWidth()
* @return the size of dimension of the vertical axis.
*/
public final int getHeight() {
if (rank < 0) init();
if ((selectedDims == null) || (selectedIndex == null)) {
return 0;
}
return (int) selectedDims[selectedIndex[0]];
}
/**
* Returns the size of dimension of the horizontal axis.
*
* <p>This function is used by GUI applications such as HDFView. GUI applications display dataset
* a 2D Table or 2D Image. The display order is specified by the index array of selectedIndex as
* follow:
*
* <dl>
* <dt>selectedIndex[0] -- height
* <dd>The vertical axis
* <dt>selectedIndex[1] -- width
* <dd>The horizontal axis
* <dt>selectedIndex[2] -- depth
* <dd>The depth axis, which is used for 3 or more dimension datasets.
* </dl>
*
* Applications can use getSelectedIndex() to access and change the display order. For example, in
* a 2D dataset of 200x50 (dim0=200, dim1=50), the following code will set the height=200 and
* width=100.
*
* <pre>
* long[] selectedIndex = dataset.getSelectedIndex();
* selectedIndex[0] = 0;
* selectedIndex[1] = 1;
* </pre>
*
* @see #getSelectedIndex()
* @see #getHeight()
* @return the size of dimension of the horizontal axis.
*/
public final int getWidth() {
if (rank < 0) init();
if ((selectedDims == null) || (selectedIndex == null)) {
return 0;
}
if ((selectedDims.length < 2) || (selectedIndex.length < 2)) {
return 1;
}
return (int) selectedDims[selectedIndex[1]];
}
/**
* Returns the selectedStride of the selected dataset.
*
* <p>Applications can use this array to change how many elements to move in each dimension.
*
* <p>Combined with the starting position and selected sizes, the subset of a rectangle selection
* is defined.
*
* <p>For example, a 4 X 5 dataset
*
* <pre>
* 0, 1, 2, 3, 4
* 10, 11, 12, 13, 14
* 20, 21, 22, 23, 24
* 30, 31, 32, 33, 34
* long[] dims = {4, 5};
* long[] startDims = {0, 0};
* long[] selectedDims = {2, 2};
* long[] selectedStride = {2, 3};
* then the following subset is selected by the startDims and selectedDims
* 0, 3
* 20, 23
* </pre>
*/
public final long[] getStride() {
if (rank < 0) init();
if (rank <= 0) {
return null;
}
if (selectedStride == null) {
selectedStride = new long[rank];
for (int i = 0; i < rank; i++) {
selectedStride[i] = 1;
}
}
return selectedStride;
}
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;
}
/**
* Returns the array that contains the dimension sizes of the chunk of the dataset. Returns null
* if the dataset is not chunked.
*
* @return the array of chunk sizes or returns null if the dataset is not chunked.
*/
public final long[] getChunkSize() {
if (rank < 0) init();
return chunkSize;
}
/**
* Returns the string representation of compression information.
*
* <p>For example, "SZIP: Pixels per block = 8: H5Z_FILTER_CONFIG_DECODE_ENABLED".
*
* @return the string representation of compression information.
*/
public final String getCompression() {
if (rank < 0) init();
return compression;
}
/**
* Returns the indices of display order.
*
* <p>selectedIndex[] is provided for two purpose:
*
* <OL>
* <LI>selectedIndex[] is used to indicate the order of dimensions for display. selectedIndex[0]
* is for the row, selectedIndex[1] is for the column and selectedIndex[2] for the depth.
* <p>For example, for a four dimesion dataset, if selectedIndex[] = {1, 2, 3}, then dim[1]
* is selected as row index, dim[2] is selected as column index and dim[3] is selected as
* depth index.
* <LI>selectedIndex[] is also used to select dimensions for display for datasets with three or
* more dimensions. We assume that applications such as HDFView can only display data values
* up to three dimension (2D spreadsheet/image with a third dimension which the 2D
* spreadsheet/image is selected from). For dataset with more than three dimensions, we need
* selectedIndex[] to tell applications which three dimensions are chosen for display. <br>
* For example, for a four dimesion dataset, if selectedIndex[] = {1, 2, 3}, then dim[1] is
* selected as row index, dim[2] is selected as column index and dim[3] is selected as depth
* index. dim[0] is not selected. Its location is fixed at 0 by default.
* </OL>
*
* @return the array of the indices of display order.
*/
public final int[] getSelectedIndex() {
if (rank < 0) init();
return selectedIndex;
}
/**
* Returns the starting position of a selected subset.
*
* <p>Applications can use this array to change the starting position of a selection. Combined
* with the selected dimensions, selected sizes and stride, the subset of a rectangle selection is
* fully defined.
*
* <p>For example, a 4 X 5 dataset
*
* <pre>
* 0, 1, 2, 3, 4
* 10, 11, 12, 13, 14
* 20, 21, 22, 23, 24
* 30, 31, 32, 33, 34
* long[] dims = {4, 5};
* long[] startDims = {1, 2};
* long[] selectedDims = {3, 3};
* long[] selectedStride = {1, 1};
* then the following subset is selected by the startDims and selectedDims
* 12, 13, 14
* 22, 23, 24
* 32, 33, 34
* </pre>
*
* @return the starting position of a selected subset.
*/
public final long[] getStartDims() {
if (rank < 0) init();
return startDims;
}
/**
* Returns the dimension sizes of the selected subset.
*
* <p>The SelectedDims is the number of data points of the selected subset. Applications can use
* this array to change the size of selected subset.
*
* <p>The select size must be less than or equal to the current dimension size. Combined with the
* starting position, selected sizes and stride, the subset of a rectangle selection is fully
* defined.
*
* <p>For example, a 4 X 5 dataset
*
* <pre>
* 0, 1, 2, 3, 4
* 10, 11, 12, 13, 14
* 20, 21, 22, 23, 24
* 30, 31, 32, 33, 34
* long[] dims = {4, 5};
* long[] startDims = {1, 2};
* long[] selectedDims = {3, 3};
* long[] selectedStride = {1, 1};
* then the following subset is selected by the startDims and selectedDims
* 12, 13, 14
* 22, 23, 24
* 32, 33, 34
* </pre>
*
* @return the dimension sizes of the selected subset.
*/
public final long[] getSelectedDims() {
if (rank < 0) init();
return selectedDims;
}
/**
* Returns the array that contins the dimension sizes of the dataset.
*
* @return the dimension sizes of the dataset.
*/
public final long[] getDims() {
if (rank < 0) init();
return dims;
}
/**
* Returns the rank (number of dimensions) of the dataset.
*
* @return the number of dimensions of the dataset.
*/
public final int getRank() {
if (rank < 0) init();
return rank;
}
/**
* Returns the array of strings that represent the dimension names. Returns null if there is no
* dimension name.
*
* <p>Some datasets have pre-defined names for each dimension such as "Latitude" and "Longitude".
* getDimNames() returns these pre-defined names.
*
* @return the names of dimensions, or null if there is no dimension name.
*/
public final String[] getDimNames() {
if (rank < 0) init();
return dimNames;
}