public void parse(File hdf5File) throws Hdf5Exception, EndOfSequenceException {
H5File h5File = Hdf5Utils.openForRead(hdf5File);
Group root = Hdf5Utils.getRootGroup(h5File);
parseGroup(root);
Hdf5Utils.close(h5File);
}
public void startGroup(Group g) throws Hdf5Exception {
logger.logComment("----- Going into a group: " + g.getFullName());
ArrayList<Attribute> attrs = Hdf5Utils.parseGroupForAttributes(g);
for (Attribute attribute : attrs) {
// attribute.
logger.logComment(
"Group: "
+ g.getName()
+ " has attribute: "
+ attribute.getName()
+ " = "
+ Hdf5Utils.getFirstStringValAttr(attrs, attribute.getName()));
}
if (g.getName().equals(NetworkMLConstants.ROOT_ELEMENT)) {
logger.logComment("Found the main group");
String simConfigName =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.NC_SIM_CONFIG);
if (simConfigName != null) this.foundSimConfig = simConfigName;
String randomSeed =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.NC_NETWORK_GEN_RAND_SEED);
if (randomSeed != null) this.foundRandomSeed = Long.parseLong(randomSeed);
} else if (g.getName().equals(NetworkMLConstants.POPULATIONS_ELEMENT)) {
logger.logComment("Found the pops group");
inPopulations = true;
} else if (g.getName().startsWith(NetworkMLConstants.POPULATION_ELEMENT) && inPopulations) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.POP_NAME_ATTR);
logger.logComment("Found a population: " + name);
currentCellGroup = name;
} else if (g.getName().equals(NetworkMLConstants.PROJECTIONS_ELEMENT)) {
logger.logComment("Found the projections group");
inProjections = true;
String units = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.UNITS_ATTR);
projUnitSystem = UnitConverter.getUnitSystemIndex(units);
} else if (g.getName().startsWith(NetworkMLConstants.PROJECTION_ELEMENT) && inProjections) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PROJ_NAME_ATTR);
String source = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.SOURCE_ATTR);
String target = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.TARGET_ATTR);
logger.logComment("Found a projection: " + name + " from " + source + " to " + target);
if (!project.morphNetworkConnectionsInfo.isValidSimpleNetConn(name)
&& !project.volBasedConnsInfo.isValidVolBasedConn(name)) {
throw new Hdf5Exception(
"Error: there is a network connection with name: "
+ name
+ " specified in "
+ "that file, but no such NetConn exists in the project. Add one to allow import of this file");
}
/* TODO: Add checks on source & target!!
*/
if (project.morphNetworkConnectionsInfo.isValidSimpleNetConn(name)) {
// if (project.morphNetworkConnectionsInfo)
}
currentNetConn = name;
} else if (g.getName().startsWith(NetworkMLConstants.SYN_PROPS_ELEMENT + "_")
&& inProjections) {
String name = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.SYN_TYPE_ATTR);
ConnSpecificProps cp = new ConnSpecificProps(name);
String internalDelay =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INTERNAL_DELAY_ATTR);
if (internalDelay != null)
cp.internalDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(internalDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
// Lump them in to the internal delay...
String preDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PRE_DELAY_ATTR);
if (preDelay != null)
cp.internalDelay =
cp.internalDelay
+ (float)
UnitConverter.getTime(
Float.parseFloat(preDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
String postDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.POST_DELAY_ATTR);
if (postDelay != null)
cp.internalDelay =
cp.internalDelay
+ (float)
UnitConverter.getTime(
Float.parseFloat(postDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
cp.weight =
Float.parseFloat(Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.WEIGHT_ATTR));
String propDelay = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.PROP_DELAY_ATTR);
if (propDelay != null)
globAPDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(propDelay),
projUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
logger.logComment("Found: " + cp);
globConnProps.add(cp);
} else if (g.getName().equals(NetworkMLConstants.INPUTS_ELEMENT)) {
logger.logComment("Found the Inputs group");
inInputs = true;
String units = Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.UNITS_ATTR);
inputUnitSystem = UnitConverter.getUnitSystemIndex(units);
} else if (g.getName().startsWith(NetworkMLConstants.INPUT_ELEMENT) && inInputs) {
// The table of input sites is within the input group so get sites from here
String inputName = g.getName().substring(6);
// String inputName = Hdf5Utils.getFirstStringValAttr(attrs,
// NetworkMLConstants.INPUT_ELEMENT);
logger.logComment("Found an Input: " + inputName);
// inInput = true;
if (project.elecInputInfo.getStim(inputName) == null) {
throw new Hdf5Exception(
"Error: there is an electrical input with name: "
+ inputName
+ " specified in "
+ "that file, but no such electrical input exists in the project. Add one to allow import of this file");
}
// Get the atributes of the Input and compare them with the attributes within the project
// Test to find out what type of input this is
} else if (g.getName().startsWith("IClamp") && inInputs) {
String inputName = g.getParent().getName().substring(6);
// Get the input sites from the table
String cellGroup =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR);
if (cellGroup == null) {
cellGroup =
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.INPUT_TARGET_CELLGROUP_OLD_ATTR); // check old name
}
float readDelay =
(float)
UnitConverter.getTime(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_DELAY_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
float readDuration =
(float)
UnitConverter.getTime(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_DUR_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
float readAmp =
(float)
UnitConverter.getCurrent(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_AMP_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
StimulationSettings nextStim = project.elecInputInfo.getStim(inputName);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
IClamp ic = (IClamp) myElectricalInput;
logger.logComment("Found an IClamp Input");
float currDelay = -1, currDur = -1, currAmp = -1;
/*
try
{
ic.getDelay().reset();
currDelay = ic.getDelay().getNumber();
ic.getDuration().reset();
currDur = ic.getDuration().getNumber();
ic.getAmplitude().reset();
currAmp = ic.getAmplitude().getNumber();
}
catch (Exception ex)
{
logger.logError("Legacy error getting iclamp params!!");
}*/
currDelay = ic.getDel().getNominalNumber();
currDur = ic.getDur().getNominalNumber();
currAmp = ic.getAmp().getNominalNumber();
if ((!project.elecInputInfo.getStim(inputName).getCellGroup().equals(cellGroup))
|| (readDelay != currDelay)
|| (readDuration != currDur)
|| (readAmp != currAmp)) {
throw new Hdf5Exception(
"Error: the input properties of the file do not match those in the project for input "
+ inputName
+ ""
+ "\nreadDelay: "
+ readDelay
+ ", currDelay: "
+ currDelay
+ "\nreadDuration: "
+ readDuration
+ ", currDur: "
+ currDur
+ "\nreadAmp: "
+ readAmp
+ ", currAmp: "
+ currAmp
+ ", str: "
+ Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_AMP_ATTR));
}
currentInput = inputName;
} else if (g.getName().startsWith("RandomSpikeTrain") && inInputs) {
String inputName = g.getParent().getName().substring(6);
// Get the input sites from the table
String cellGroup =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.INPUT_TARGET_POPULATION_ATTR);
if (cellGroup == null) {
cellGroup =
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.INPUT_TARGET_CELLGROUP_OLD_ATTR); // check old name
}
float frequency =
(float)
UnitConverter.getRate(
Float.parseFloat(
Hdf5Utils.getFirstStringValAttr(
attrs, NetworkMLConstants.RND_STIM_FREQ_ATTR)),
inputUnitSystem,
UnitConverter.NEUROCONSTRUCT_UNITS);
String mechanism =
Hdf5Utils.getFirstStringValAttr(attrs, NetworkMLConstants.RND_STIM_MECH_ATTR);
StimulationSettings nextStim = project.elecInputInfo.getStim(inputName);
ElectricalInput myElectricalInput = nextStim.getElectricalInput();
RandomSpikeTrain rs = (RandomSpikeTrain) myElectricalInput;
logger.logComment("Found an Random Spike Train Input");
if ((!project.elecInputInfo.getStim(inputName).getCellGroup().equals(cellGroup))
|| frequency != rs.getRate().getFixedNum()
|| !rs.getSynapseType().equals(mechanism)) {
throw new Hdf5Exception(
"Error: the input properties of the file do not match those in the project for input "
+ inputName);
}
currentInput = inputName;
}
}
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);
}
}
}