/// <summary>
/// Read a 1x1 degree square from the HDF5 file, preferentially using data from the high-resolution dataset if it exists, and filling
/// in any holes in the high-res data from the corresponding area of the low-resolution dataset
/// </summary>
/// <param name="highResGroup">Group ID of the high resolution group</param>
/// <param name="highResolution">Resolution of the high resolution group, in minutes per sample</param>
/// <param name="lowResGroup">Group ID of the low resolution group</param>
/// <param name="lowResolution">Resolution of the low resolution group, in minutes per sample</param>
/// <param name="desiredResolution">Desired resolution of the output data, in minutes per sample</param>
/// <param name="latitude">Latitude of the south-west corner of the 1x1 degree square to be extracted from the HDF5 file</param>
/// <param name="longitude">Longitude of the south-west corner of the 1x1 degree square to be extracted from the HDF5 file</param>
/// <returns></returns>
static IEnumerable<SedimentSample> ReadDataset(H5FileOrGroupId highResGroup, double highResolution, H5FileOrGroupId lowResGroup, double lowResolution, double desiredResolution, int latitude, int longitude)
{
short[,] result = null;
double resolutionStep;
double sampleStepSize;
if (highResGroup != null) result = ReadDataset(highResGroup, latitude, longitude);
if (result != null)
{
resolutionStep = highResolution / 60;
sampleStepSize = desiredResolution / highResolution;
}
else
{
if (lowResGroup != null) result = ReadDataset(lowResGroup, latitude, longitude);
//if (result == null) throw new KeyNotFoundException(string.Format("Unable to locate sediment data for lat: {0}, lon: {1}", latitude, longitude));
if (result == null) return null;
resolutionStep = lowResolution / 60.0;
sampleStepSize = desiredResolution / lowResolution;
}
var sedimentList = new HashedArrayList<SedimentSample>();
for (var i = 0.0; i < result.GetLength(0); i += sampleStepSize)
for (var j = 0.0; j < result.GetLength(1); j += sampleStepSize)
if (result[(int)i, (int)j] > 0) sedimentList.Add(new SedimentSample(latitude + (i * resolutionStep), longitude + (j * resolutionStep), new SedimentSampleBase { SampleValue = result[(int)i, (int)j] }));
return sedimentList;
}
protected override void WriteEpochGroupStart(string label,
string source,
string[] keywords,
IDictionary <string, object> properties,
Guid identifier,
DateTimeOffset startTime,
double timeZoneOffset)
{
H5FileOrGroupId parent = CurrentEpochGroupID == null ?
(H5FileOrGroupId)fileId : CurrentEpochGroupID.SubGroupsId;
var epochGroup = H5G.create((H5LocId)parent, label + "-" + identifier);
var subGroups = H5G.create((H5LocId)epochGroup, "epochGroups");
var epochs = H5G.create((H5LocId)epochGroup, "epochs");
WriteAttribute(epochGroup, "label", label);
WriteAttribute(epochGroup, "source", string.IsNullOrEmpty(source) ? "<none>" : source);
WriteDictionary(epochGroup, "properties", properties);
WriteAttribute(epochGroup, "symphony.uuid", identifier.ToString());
WriteKeywords(epochGroup, new HashSet <string>(keywords));
WriteAttribute(epochGroup, startTimeUtcName, startTime.Ticks);
WriteAttribute(epochGroup, startTimeOffsetName, timeZoneOffset);
//H5G.close(subGroups);
//H5G.close(epochs);
EpochGroupsIDs.Push(new EpochGroupIDs(epochGroup, subGroups, epochs));
}
public static void GetDataSet <T> (H5FileOrGroupId groupOrFileId, string name, out T[,,,] array, int width, int height, int depth, int number)
{
if (groupOrFileId is null)
{
throw new ArgumentNullException(nameof(groupOrFileId));
}
if (name is null)
{
throw new ArgumentNullException(nameof(name));
}
H5DataSetId h5DataSetId = H5D.open(groupOrFileId, name);
H5DataTypeId h5DataTypeId = H5D.getType(h5DataSetId);
array = new T[height, width, depth, number];
H5D.read(h5DataSetId, h5DataTypeId, new H5Array <T> (array));
H5T.close(h5DataTypeId);
H5D.close(h5DataSetId);
}
public static void GetDataSet <T> (H5FileOrGroupId groupOrFileId, string name, out T[] array, int length)
{
if (groupOrFileId is null)
{
throw new ArgumentNullException(nameof(groupOrFileId));
}
if (name is null)
{
throw new ArgumentNullException(nameof(name));
}
array = new T[length];
H5DataSetId h5DataSetId = H5D.open(groupOrFileId, name);
H5DataTypeId h5DataTypeId = H5D.getType(h5DataSetId);
H5D.read(h5DataSetId, h5DataTypeId, new H5Array <T> (array));
H5T.close(h5DataTypeId);
H5D.close(h5DataSetId);
}
static short[,] ReadDataset(H5FileOrGroupId groupId, int latitude, int longitude)
{
if (groupId == null) return null;
try
{
var data = H5D.open(groupId, string.Format("{0}_{1}", latitude, longitude));
var sid = H5D.getSpace(data);
var dims = H5S.getSimpleExtentDims(sid);
var readBuf = new short[dims[0], dims[1]];
H5D.read(data, H5T.copy(H5T.H5Type.NATIVE_SHORT), new H5Array<short>(readBuf));
H5D.close(data);
return readBuf;
}
catch (HDFException)
{
return null;
}
}
static short[,] ReadDataset(H5FileOrGroupId groupId, double nativeResolution, double desiredResolution, int latitude, int longitude)
{
var decimationStepSize = desiredResolution / nativeResolution;
var rawData = ReadDataset(groupId, latitude, longitude);
if (rawData == null) return null;
var resampledData = new short[(int)((rawData.GetLength(0) - 1) / decimationStepSize), (int)((rawData.GetLength(1) - 1) / decimationStepSize)];
for (var i = 0; i < resampledData.GetLength(0); i++)
for (var j = 0; j < resampledData.GetLength(1); j++)
resampledData[i, j] = rawData[(int)(i * decimationStepSize), (int)(j * decimationStepSize)];
return resampledData;
}
/// <summary>
/// Read a 1x1 degree square from the HDF5 file, preferentially using data from the high-resolution dataset if it exists, and filling
/// in any holes in the high-res data from the corresponding area of the low-resolution dataset
/// </summary>
/// <param name="highResGroup">Group ID of the high resolution group</param>
/// <param name="highResolution">Resolution of the high resolution group, in minutes per sample</param>
/// <param name="lowResGroup">Group ID of the low resolution group</param>
/// <param name="lowResolution">Resolution of the low resolution group, in minutes per sample</param>
/// <param name="desiredResolution">Desired resolution of the output data, in minutes per sample</param>
/// <param name="latitude">Latitude of the south-west corner of the 1x1 degree square to be extracted from the HDF5 file</param>
/// <param name="longitude">Longitude of the south-west corner of the 1x1 degree square to be extracted from the HDF5 file</param>
/// <returns></returns>
static IEnumerable<SedimentSample> ReadDatasetHierarchical(H5FileOrGroupId highResGroup, double highResolution, H5FileOrGroupId lowResGroup, double lowResolution, double desiredResolution, int latitude, int longitude)
{
short[,] highResData = null;
short[,] lowResData = null;
if (highResGroup != null) highResData = ReadDataset(highResGroup, highResolution, desiredResolution, latitude, longitude);
if (lowResGroup != null) lowResData = ReadDataset(lowResGroup, lowResolution, desiredResolution, latitude, longitude);
if (highResData == null && lowResData == null)
throw new KeyNotFoundException(string.Format("Unable to locate sediment data for lat: {0}, lon: {1}", latitude, longitude));
var resolutionStepSize = desiredResolution / 60;
var resolutionStepCount = (int)(1.0 / resolutionStepSize);
if (highResData != null && (highResData.GetLength(0) != resolutionStepCount || highResData.GetLength(1) != resolutionStepCount)) throw new IndexOutOfRangeException("High resolution dataset is not the correct size");
if (lowResData != null && (lowResData.GetLength(0) != resolutionStepCount || lowResData.GetLength(1) != resolutionStepCount)) throw new IndexOutOfRangeException("Low resolution dataset is not the correct size");
Func<int, int, short> highResDataFunc = (i, j) => highResData[i, j] == NoData ? (short)0 : highResData[i, j];
Func<int, int, short> lowResDataFunc = (i, j) => lowResData[i, j] == NoData ? (short)0 : lowResData[i, j];
Func<int, int, short> dataFunc;
if (highResData != null && lowResData != null) dataFunc = (i, j) => highResDataFunc(i, j) == 0 ? lowResDataFunc(i, j) : highResDataFunc(i, j);
else
if (highResData != null) dataFunc = highResDataFunc;
else dataFunc = lowResDataFunc;
return BuildSedimentSampleList(desiredResolution, latitude, longitude, dataFunc);
}
internal HDF5Dataset(H5FileOrGroupId _parentObjectId, string _name)
{
m_ParentObjectID = _parentObjectId;
m_DatasetId = H5D.open(_parentObjectId, _name);
}
