protected override List <SimulatorInitEvent> GetInitialEvents()
{
var pairs = new List <SimulatorInitEvent>();
var testTraceReader = new NSTraceReader(testTracePath, blockLength);
var header = testTraceReader.ReadHeader(); // bypass the header
// load and schedule all NS-generated events
while (!testTraceReader.Finished)
{
// group events of the block by their node IDs
var nodeEventBlocks = testTraceReader.ReadNextGroupBlock(e => e.NodeID);
// convert each event block to the corresponding signal and then
// schedule the ProcessSignal method of the corresponding node passing
// the signal as an EventArg
foreach (var nodeEventBlock in nodeEventBlocks)
{
var time = nodeEventBlock.Last().Time;
var signals = GetSignals(nodeEventBlock.ToNSEventBlock());
foreach (var signal in signals)
{
pairs.Add(new SimulatorInitEvent(time, signal, nodeEventBlock.Key));
}
}
if (Initializing != null)
{
Initializing(this, new ProgressEventArgs("Loading initial NS events...",
testTraceReader.Length, testTraceReader.Position));
}
}
testTraceReader.Close();
return(pairs);
}
protected override List <MolecularPattern> GetSelfPatterns()
{
// load self molecular patterns
var selfTraceReader = new NSTraceReader(selfTracePath, blockLength);
var header = selfTraceReader.ReadHeader();
var MPs = new List <MolecularPattern>();
while (!selfTraceReader.Finished)
{
// read a block of events
var eventBlock = selfTraceReader.ReadNextEventBlock();
// group events of the block by their node IDs
var sinkEventBlock = eventBlock.Where(e => e.NodeID < header.NumSinks);
// convert to molecular patterns
var peptide = GetAntigenPeptide(sinkEventBlock.ToNSEventBlock());
if (peptide != null)
{
MPs.Add(peptide);
}
/*foreach (var nodeEventBlock in nodeEventBlocks)
* {
* var peptide = GetAntigenPeptide(nodeEventBlock);
*
* //var sdamp = GetSdamp(nodeEventBlock.ToNSEventBlock());
* //var spamp = GetSpamp(nodeEventBlock.ToNSEventBlock());
*
* //if (spamp != null)
* //{
* // sw.WriteLine(spamp[0] + "," + spamp[1] + "," + spamp[2] + "," + nodeEventBlock.Key);
* //}
*
* if (peptide != null)
* {
* MPs.Add(peptide);
* }
* }*/
if (Initializing != null)
{
// update progress indicator
Initializing(this, new ProgressEventArgs("Loading self events... ",
selfTraceReader.Length, selfTraceReader.Position));
}
}
//sw.Close();
selfTraceReader.Close();
return(MPs);
}
public void InitFromTrace(string selfTracePath, string testTracePath, double blockLength,
int numBoneMarrows, int numThymuses, int numLymphNodes, int numAPCs, int numTCs, bool registerLogger)
{
this.selfTracePath = selfTracePath;
this.testTracePath = testTracePath;
this.blockLength = blockLength;
/*this.testTracePath = "spamp_ex1.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex1.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex2.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex2.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex3.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex3.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex4.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex4.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex5.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex5.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex6.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex6.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex7.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex7.tr";
* GetSelfPatterns();
*
* this.testTracePath = "spamp_ex8.csv";
* this.selfTracePath = "../../../NSTraces/Traces-2009-12-23/ntr_ex8.tr";
* GetSelfPatterns();*/
var tr = new NSTraceReader(testTracePath, blockLength);
var header = tr.ReadHeader();
tr.Close();
// TODO: Number of local tissues should be set to total number of nodes not number of sinks
var args = new SimulatorInitArgs(numBoneMarrows, numThymuses, numLymphNodes,
header.NumSinks, numAPCs, numTCs, PEPTIDE_LENGTH);
Init(args, registerLogger);
}
public void InitFromDump(string selfDump, string testTracePath, int blockLen, int numBoneMarrows, int numThymuses,
int numLymphNodes, int numAPCs, int numTCs, bool registerLogger)
{
this.testTracePath = testTracePath;
this.blockLength = blockLen;
var selfStream = File.Open(selfDump, FileMode.Open);
var tr = new NSTraceReader(testTracePath, blockLength);
var header = tr.ReadHeader();
tr.Close();
// TODO: Number of local tissues should be set to total number of nodes not number of sinks
var args = new SimulatorInitArgs(numBoneMarrows, numThymuses, numLymphNodes,
header.NumSinks, numAPCs, numTCs, PEPTIDE_LENGTH);
Init(selfStream, args, registerLogger);
}