public void parseGroup(Group g) throws Hdf5Exception, EndOfSequenceException {
startGroup(g);
java.util.List members = g.getMemberList();
// NOTE: parsing contents twice to ensure subgroups are handled before datasets
// This is mainly because synapse_props groups will need to be parsed before dataset of
// connections
for (int j = 0; j < members.size(); j++) {
HObject obj = (HObject) members.get(j);
if (obj instanceof Group) {
Group subGroup = (Group) obj;
logger.logComment("--------- Found a sub group: " + subGroup.getName());
parseGroup(subGroup);
}
}
for (int j = 0; j < members.size(); j++) {
HObject obj = (HObject) members.get(j);
if (obj instanceof Dataset) {
Dataset ds = (Dataset) obj;
logger.logComment("Found a dataset: " + ds.getName());
dataSet(ds);
}
}
endGroup(g);
}
/*
* (non-Javadoc)
*
* @see org.geppetto.core.model.state.visitors.DefaultStateVisitor#visitSimpleStateNode(org.geppetto.core.model.state.SimpleStateNode)
*/
@Override
public boolean visitVariableNode(VariableNode node) {
String variable = node.getInstancePath();
H5File file = _recording.getHDF5();
String variablePath = "/" + variable.replace(".", "/");
Dataset v = (Dataset) FileFormat.findObject(file, variablePath);
if (v != null) {
Object dataRead;
try {
dataRead = v.read();
Quantity quantity = new Quantity();
AValue readValue = null;
if (dataRead instanceof double[]) {
double[] dr = (double[]) dataRead;
readValue = ValuesFactory.getDoubleValue(dr[_currentIndex]);
} else if (dataRead instanceof float[]) {
float[] fr = (float[]) dataRead;
readValue = ValuesFactory.getFloatValue(fr[_currentIndex]);
} else if (dataRead instanceof int[]) {
int[] ir = (int[]) dataRead;
readValue = ValuesFactory.getIntValue(ir[_currentIndex]);
}
quantity.setValue(readValue);
node.addQuantity(quantity);
} catch (ArrayIndexOutOfBoundsException e) {
_endOfSteps = e.getMessage();
} catch (Exception | OutOfMemoryError e) {
_errorMessage = e.getMessage();
}
}
return super.visitVariableNode(node);
}
/*
* (non-Javadoc)
*
* @see org.geppetto.core.model.state.visitors.DefaultStateVisitor#visitSimpleStateNode(org.geppetto.core.model.state.SimpleStateNode)
*/
@Override
public boolean visitSkeletonAnimationNode(SkeletonAnimationNode node) {
String variable = node.getInstancePath();
H5File file = _recording.getHDF5();
String variablePath = "/" + variable.replace(".", "/");
Dataset v = (Dataset) FileFormat.findObject(file, variablePath);
if (v != null) {
Object dataRead;
try {
dataRead = v.read();
// get metadata from recording node
List<Attribute> attributes = v.getMetadata();
String meta = "";
for (Attribute a : attributes) {
if (a.getName().equals("custom_metadata")) meta = ((String[]) a.getValue())[0];
}
// split into key value pair
Map<String, String> metaMap = StringSplitter.keyValueSplit(meta, ";");
double[] flatMatrices = null;
if (dataRead instanceof double[]) {
double[] dr = (double[]) dataRead;
// get items of interest based on matrix dimension and items per step
int itemsPerStep = Integer.parseInt(metaMap.get("items_per_step"));
int startIndex = _currentIndex * itemsPerStep;
int endIndex = startIndex + (itemsPerStep);
if (endIndex <= dr.length) {
flatMatrices = Arrays.copyOfRange(dr, startIndex, endIndex);
} else {
throw new ArrayIndexOutOfBoundsException("ArrayIndexOutOfBounds");
}
}
// set matrices on skeleton animation node
node.addSkeletonTransformation(Arrays.asList(ArrayUtils.toObject(flatMatrices)));
} catch (ArrayIndexOutOfBoundsException e) {
_endOfSteps = e.getMessage();
} catch (Exception | OutOfMemoryError e) {
_errorMessage = e.getMessage();
}
}
return super.visitSkeletonAnimationNode(node);
}
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;
}
/**
* @deprecated Not for public use in the future. <br>
* Using {@link #convertToUnsignedC(Object, Object)}
*/
@Deprecated
public static Object convertToUnsignedC(Object data_in) {
return Dataset.convertToUnsignedC(data_in, null);
}
public void dataSet(Dataset d) throws Hdf5Exception {
logger.logComment("----- Looking through dataset: " + d);
ArrayList<Attribute> attrs = Hdf5Utils.parseDatasetForAttributes(d);
for (Attribute attribute : attrs) {
logger.logComment(
"Dataset: "
+ d.getName()
+ " has attribute: "
+ attribute.getName()
+ " = "
+ Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName()));
}
float[][] data = Hdf5Utils.parse2Ddataset(d);
logger.logComment("Data has size: (" + data.length + ", " + data[0].length + ")");
if (inPopulations && currentCellGroup != null) {
for (int i = 0; i < data.length; i++) {
int id = (int) data[i][0];
float x = data[i][1];
float y = data[i][2];
float z = data[i][3];
PositionRecord posRec = new PositionRecord(id, x, y, z);
if (data[0].length == 5) {
posRec.setNodeId((int) data[i][4]);
}
this.project.generatedCellPositions.addPosition(currentCellGroup, posRec);
}
}
if (inProjections && currentNetConn != null) {
logger.logComment("Adding info for NetConn: " + currentNetConn);
int id_col = -1;
int pre_cell_id_col = -1;
int pre_segment_id_col = -1;
int pre_fraction_along_col = -1;
int post_cell_id_col = -1;
int post_segment_id_col = -1;
int post_fraction_along_col = -1;
int prop_delay_col = -1;
for (Attribute attribute : attrs) {
String storedInColumn = Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName());
if (storedInColumn.equals(NetworkMLConstants.CONNECTION_ID_ATTR)) {
id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("id col: " + id_col);
} else if (storedInColumn.equals(NetworkMLConstants.PRE_CELL_ID_ATTR)) {
pre_cell_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.PRE_SEGMENT_ID_ATTR)) {
pre_segment_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("pre_segment_id_col: " + pre_segment_id_col);
} else if (storedInColumn.equals(NetworkMLConstants.PRE_FRACT_ALONG_ATTR)) {
pre_fraction_along_col =
Integer.parseInt(attribute.getName().substring("column_".length()));
logger.logComment("pre_fraction_along_col: " + pre_fraction_along_col);
} else if (storedInColumn.equals(NetworkMLConstants.POST_CELL_ID_ATTR)) {
post_cell_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.POST_SEGMENT_ID_ATTR)) {
post_segment_id_col = Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.equals(NetworkMLConstants.POST_FRACT_ALONG_ATTR)) {
post_fraction_along_col =
Integer.parseInt(attribute.getName().substring("column_".length()));
} else if (storedInColumn.startsWith(NetworkMLConstants.PROP_DELAY_ATTR)) {
prop_delay_col = Integer.parseInt(attribute.getName().substring("column_".length()));
}
for (String synType : getConnectionSynTypes()) {
if (storedInColumn.endsWith(synType)) {
ConnSpecificProps cp = null;
for (ConnSpecificProps currCp : localConnProps) {
if (currCp.synapseType.equals(synType)) cp = currCp;
}
if (cp == null) {
cp = new ConnSpecificProps(synType);
cp.internalDelay = -1;
cp.weight = -1;
localConnProps.add(cp);
}
if (storedInColumn.startsWith(NetworkMLConstants.INTERNAL_DELAY_ATTR)) {
cp.internalDelay =
Integer.parseInt(
attribute
.getName()
.substring("column_".length())); // store the col num temporarily..
}
if (storedInColumn.startsWith(NetworkMLConstants.WEIGHT_ATTR)) {
cp.weight =
Integer.parseInt(
attribute
.getName()
.substring("column_".length())); // store the col num temporarily..
}
}
}
}
for (int i = 0; i < data.length; i++) {
int pre_seg_id = 0;
float pre_fract_along = 0.5f;
int post_seg_id = 0;
float post_fract_along = 0.5f;
int id = (int) data[i][id_col];
int pre_cell_id = (int) data[i][pre_cell_id_col];
int post_cell_id = (int) data[i][post_cell_id_col];
float prop_delay = 0;
if (pre_segment_id_col >= 0) pre_seg_id = (int) data[i][pre_segment_id_col];
if (pre_fraction_along_col >= 0) pre_fract_along = data[i][pre_fraction_along_col];
if (post_segment_id_col >= 0) post_seg_id = (int) data[i][post_segment_id_col];
if (post_fraction_along_col >= 0) post_fract_along = data[i][post_fraction_along_col];
// (float)UnitConverter.getTime(XXXXXXXXX, UnitConverter.NEUROCONSTRUCT_UNITS,
// unitSystem)+"";
if (prop_delay_col >= 0)
prop_delay =
(float)
UnitConverter.getTime(
data[i][prop_delay_col], projUnitSystem, UnitConverter.NEUROCONSTRUCT_UNITS);
ArrayList<ConnSpecificProps> props = new ArrayList<ConnSpecificProps>();
if (localConnProps.size() > 0) {
for (ConnSpecificProps currCp : localConnProps) {
logger.logComment("Pre cp: " + currCp);
ConnSpecificProps cp2 = new ConnSpecificProps(currCp.synapseType);
if (currCp.internalDelay > 0) // index was stored in this val...
cp2.internalDelay =
(float)
UnitConverter.getTime(
data[i][(int) currCp.internalDelay],
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
if (currCp.weight > 0) // index was stored in this val...
cp2.weight = data[i][(int) currCp.weight];
logger.logComment("Filled cp: " + cp2);
props.add(cp2);
}
}
this.project.generatedNetworkConnections.addSynapticConnection(
currentNetConn,
GeneratedNetworkConnections.MORPH_NETWORK_CONNECTION,
pre_cell_id,
pre_seg_id,
pre_fract_along,
post_cell_id,
post_seg_id,
post_fract_along,
prop_delay,
props);
}
}
if (inInputs && currentInput != null) {
logger.logComment("Adding info for: " + currentInput);
StimulationSettings nextStim = project.elecInputInfo.getStim(currentInput);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
String electricalInputType = myElectricalInput.getType();
String cellGroup = nextStim.getCellGroup();
for (int i = 0; i < data.length; i++) {
Float fileCellId = data[i][0];
Float fileSegmentId = data[i][1];
Float fractionAlong = data[i][2];
int cellId = fileCellId.intValue();
int segmentId = fileSegmentId.intValue();
SingleElectricalInput singleElectricalInputFromFile =
new SingleElectricalInput(
electricalInputType, cellGroup, cellId, segmentId, fractionAlong, null);
this.project.generatedElecInputs.addSingleInput(
currentInput, singleElectricalInputFromFile);
}
}
}