/*
* Prints the probe with the specified name. There
* are certain conditions that this method wont print
* anything:
*
* 1) No such probe exists.
* 2) The probe has not been closed.
*/
void printProbe(string s)
{
TimeProbe* tp;
if (probes[s] == 0)
return;
tp = probes[s];
if (tp->getStatus() != TimeProbe::CLOSED)
return;
timeval* t1 = tp->getStart();
timeval* t2 = tp->getEnd();
if (t1->tv_usec > t2->tv_usec)
{
t2->tv_usec += 1000000;
t2->tv_sec--;
}
timeval lapsed;
lapsed.tv_usec = t2->tv_usec - t1->tv_usec;
lapsed.tv_sec = (int) (t2->tv_sec - t1->tv_sec);
cout << s << ": ";
printf("Time elapsed: %d.%06dsec\n", (int) lapsed.tv_sec,(int) lapsed.tv_usec);
}
/**
* Open the probe with the specified name and measures
* the time value at that point in the program's path
* of execution.
*
* If a probe for that name already exists, this method
* does nothing.
*/
void openProbe(string s)
{
TimeProbe* tp;
if (probes[s] == 0)
{
tp = new TimeProbe();
probes[s] = tp;
}
else
{
tp = probes[s];
}
if (tp->getStatus() != TimeProbe::INACTIVE)
return;
tp->setStatus(TimeProbe::OPEN);
timeval* tv = new timeval();
struct timezone tz;
gettimeofday(tv, &tz);
tp->setStart(tv);
}
void QueryResult::init(const FieldSelector& selector,
const IndexReaderPtr& pIndexReader,
const QueryHits& hits)
{
StoredFieldsReaderPtr pStoredFieldsReader = pIndexReader->createStoredFieldsReader();
if (pStoredFieldsReader.isNull())
{
return;
}
TimeProbe probe;
probe.start();
m_docs.reserve(hits.size());
setTracer(hits.getTracer());
setTotalHits(hits.getTotalHits());
QueryHits::Iterator it = hits.iterator();
while (it.hasNext())
{
const QueryHits::HitDoc& hitDoc = it.next();
ResultDocPtr pResDoc(new ResultDoc(hitDoc.getDocId(),
hitDoc.getScore(), selector.size()));
addDoc(pResDoc);
pStoredFieldsReader->getDocument(selector, *pResDoc);
}
probe.stop();
FX_QUERY_TRACE(INFO, getTracer(), "fetch field time [%d] ms",
(int32_t)probe.elapsed() / 1000);
}
void IndexBuilderAppRunner::buildIndex()
{
try
{
cout << _T("Begin build index, config file: ") << m_sConfFile << endl;
TimeProbe p;
p.start();
ProgressObserverPtr pOb(new ConsoleProgressObserver(1000));
FX_NS(collection)::Collection::buildIndex(m_sConfFile, pOb);
p.stop();
cout << _T("Build index success! finished in ") << p.elapsedSeconds()
<< _T(" s.") << endl;
}
catch(const FirteXException& fe)
{
cout << _T("Build index FAILED: ") << fe.what() << endl;
}
}
/**
* Closes the probe for the given name. If the probe
* is not open or if the probe is already closed this
* method does nothing.
*/
void closeProbe(string s)
{
TimeProbe* tp;
if (probes[s] == 0)
return;
tp = probes[s];
if (tp->getStatus() != TimeProbe::OPEN)
return;
timeval* tv = new timeval();
struct timezone tz;
gettimeofday(tv, NULL);
tp->setEnd(tv);
tp->setStatus(TimeProbe::CLOSED);
}
void LexiconBuilderAppRunner::buildLexicon()
{
try
{
cout << "Begin build lexicon, source file: " << m_sSourceFile << endl
<< ", target file: " << m_sTargetFile << endl;
TimeProbe p;
DoubleArrayTrie trie(100000);
trie.buildFromFile(m_sSourceFile);
trie.save(m_sTargetFile);
cout << _T("Build lexicon success! finished in ") << p.elapsedSeconds()
<< _T(" s.") << endl;
}
catch(const FirteXException& fe)
{
cout << _T("Build lexicon FAILED: ") << fe.what() << endl;
}
}
void GibbsTrackingFilter< ItkQBallImageType >::GenerateData()
{
TimeProbe preClock; preClock.Start();
// check if input is qball or tensor image and generate qball if necessary
if (m_QBallImage.IsNull() && m_TensorImage.IsNotNull())
{
TensorImageToQBallImageFilter<float,float>::Pointer filter = TensorImageToQBallImageFilter<float,float>::New();
filter->SetInput( m_TensorImage );
filter->Update();
m_QBallImage = filter->GetOutput();
}
else if (m_DuplicateImage) // generate local working copy of QBall image (if not disabled)
{
typedef itk::ImageDuplicator< ItkQBallImageType > DuplicateFilterType;
typename DuplicateFilterType::Pointer duplicator = DuplicateFilterType::New();
duplicator->SetInputImage( m_QBallImage );
duplicator->Update();
m_QBallImage = duplicator->GetOutput();
}
// perform mean subtraction on odfs
typedef ImageRegionIterator< ItkQBallImageType > InputIteratorType;
InputIteratorType it(m_QBallImage, m_QBallImage->GetLargestPossibleRegion() );
it.GoToBegin();
while (!it.IsAtEnd())
{
itk::OrientationDistributionFunction<float, QBALL_ODFSIZE> odf(it.Get().GetDataPointer());
float mean = odf.GetMeanValue();
odf -= mean;
it.Set(odf.GetDataPointer());
++it;
}
// check if mask image is given if it needs resampling
PrepareMaskImage();
// load parameter file
LoadParameters();
// prepare parameters
float minSpacing;
if(m_QBallImage->GetSpacing()[0]<m_QBallImage->GetSpacing()[1] && m_QBallImage->GetSpacing()[0]<m_QBallImage->GetSpacing()[2])
minSpacing = m_QBallImage->GetSpacing()[0];
else if (m_QBallImage->GetSpacing()[1] < m_QBallImage->GetSpacing()[2])
minSpacing = m_QBallImage->GetSpacing()[1];
else
minSpacing = m_QBallImage->GetSpacing()[2];
if(m_ParticleLength == 0)
m_ParticleLength = 1.5*minSpacing;
if(m_ParticleWidth == 0)
m_ParticleWidth = 0.5*minSpacing;
if(m_ParticleWeight == 0)
EstimateParticleWeight();
float alpha = log(m_EndTemperature/m_StartTemperature);
m_Steps = m_Iterations/10000;
if (m_Steps<10)
m_Steps = 10;
if (m_Steps>m_Iterations)
{
MITK_INFO << "GibbsTrackingFilter: not enough iterations!";
m_AbortTracking = true;
}
if (m_CurvatureThreshold < mitk::eps)
m_CurvatureThreshold = 0;
unsigned long singleIts = (unsigned long)((1.0*m_Iterations) / (1.0*m_Steps));
// seed random generators
Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New();
if (m_RandomSeed>-1)
randGen->SetSeed(m_RandomSeed);
else
randGen->SetSeed();
// load sphere interpolator to evaluate the ODFs
SphereInterpolator* interpolator = new SphereInterpolator(m_LutPath);
// handle lookup table not found cases
if( !interpolator->IsInValidState() )
{
m_IsInValidState = false;
m_AbortTracking = true;
m_BuildFibers = false;
mitkThrow() << "Unable to load lookup tables.";
}
// initialize the actual tracking components (ParticleGrid, Metropolis Hastings Sampler and Energy Computer)
ParticleGrid* particleGrid;
GibbsEnergyComputer* encomp;
MetropolisHastingsSampler* sampler;
try{
particleGrid = new ParticleGrid(m_MaskImage, m_ParticleLength, m_ParticleGridCellCapacity);
encomp = new GibbsEnergyComputer(m_QBallImage, m_MaskImage, particleGrid, interpolator, randGen);
encomp->SetParameters(m_ParticleWeight,m_ParticleWidth,m_ConnectionPotential*m_ParticleLength*m_ParticleLength,m_CurvatureThreshold,m_InexBalance,m_ParticlePotential);
sampler = new MetropolisHastingsSampler(particleGrid, encomp, randGen, m_CurvatureThreshold);
}
catch(...)
{
MITK_ERROR << "Particle grid allocation failed. Not enough memory? Try to increase the particle length.";
m_IsInValidState = false;
m_AbortTracking = true;
m_BuildFibers = false;
return;
}
MITK_INFO << "----------------------------------------";
MITK_INFO << "Iterations: " << m_Iterations;
MITK_INFO << "Steps: " << m_Steps;
MITK_INFO << "Particle length: " << m_ParticleLength;
MITK_INFO << "Particle width: " << m_ParticleWidth;
MITK_INFO << "Particle weight: " << m_ParticleWeight;
MITK_INFO << "Start temperature: " << m_StartTemperature;
MITK_INFO << "End temperature: " << m_EndTemperature;
MITK_INFO << "In/Ex balance: " << m_InexBalance;
MITK_INFO << "Min. fiber length: " << m_MinFiberLength;
MITK_INFO << "Curvature threshold: " << m_CurvatureThreshold;
MITK_INFO << "Random seed: " << m_RandomSeed;
MITK_INFO << "----------------------------------------";
// main loop
preClock.Stop();
TimeProbe clock; clock.Start();
m_NumAcceptedFibers = 0;
unsigned long counter = 1;
boost::progress_display disp(m_Steps*singleIts);
if (!m_AbortTracking)
for( m_CurrentStep = 1; m_CurrentStep <= m_Steps; m_CurrentStep++ )
{
// update temperatur for simulated annealing process
float temperature = m_StartTemperature * exp(alpha*(((1.0)*m_CurrentStep)/((1.0)*m_Steps)));
sampler->SetTemperature(temperature);
for (unsigned long i=0; i<singleIts; i++)
{
++disp;
if (m_AbortTracking)
break;
sampler->MakeProposal();
if (m_BuildFibers || (i==singleIts-1 && m_CurrentStep==m_Steps))
{
m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter;
m_NumParticles = particleGrid->m_NumParticles;
m_NumConnections = particleGrid->m_NumConnections;
FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
m_BuildFibers = false;
}
counter++;
}
m_ProposalAcceptance = (float)sampler->GetNumAcceptedProposals()/counter;
m_NumParticles = particleGrid->m_NumParticles;
m_NumConnections = particleGrid->m_NumConnections;
if (m_AbortTracking)
break;
}
if (m_AbortTracking)
{
FiberBuilder fiberBuilder(particleGrid, m_MaskImage);
m_FiberPolyData = fiberBuilder.iterate(m_MinFiberLength);
m_NumAcceptedFibers = m_FiberPolyData->GetNumberOfLines();
}
clock.Stop();
delete sampler;
delete encomp;
delete interpolator;
delete particleGrid;
m_AbortTracking = true;
m_BuildFibers = false;
int h = clock.GetTotal()/3600;
int m = ((int)clock.GetTotal()%3600)/60;
int s = (int)clock.GetTotal()%60;
MITK_INFO << "GibbsTrackingFilter: finished gibbs tracking in " << h << "h, " << m << "m and " << s << "s";
m = (int)preClock.GetTotal()/60;
s = (int)preClock.GetTotal()%60;
MITK_INFO << "GibbsTrackingFilter: preparation of the data took " << m << "m and " << s << "s";
MITK_INFO << "GibbsTrackingFilter: " << m_NumAcceptedFibers << " fibers accepted";
// sampler->PrintProposalTimes();
SaveParameters();
}
void HTTPSearchService::handleQuery(const Statement& state,
EvHttpRequestContext* pCtx) const
{
IndexReaderPtr pIndexReader = m_searchRes.getIndexReader();
FIRTEX_ASSERT2(pIndexReader.isNotNull());
try
{
TimeProbe probe;
probe.start();
QueryParser parser(pIndexReader->getAnalyzerMapper(),
m_searchRes.getDefaultField());
IndexSearcher searcher(pIndexReader);
QueryHitsPtr pHits = searcher.search(state, parser);
QueryResult result;
if (pHits.isNotNull())
{
FieldSelectClausePtr pFieldClause = state.getFieldSelectClause();
QueryClausePtr pQueryClause = state.getQueryClause();
if (pFieldClause.isNotNull() && pQueryClause.isNotNull())
{
QueryPtr pQuery = parser.parse(pQueryClause->getQueryString());
FIRTEX_ASSERT2(pQuery.isNotNull());
FieldSelector selector(pIndexReader->getDocSchema());
for (size_t i = 0; i < pFieldClause->getFieldCount(); ++i)
{
const FieldSelectClause::SnippetParam& param = pFieldClause->getField(i);
FieldFilterPtr pFieldFilter;
if (param.snippet)
{
SnippetGenerator* pSnippetGen = new SnippetGenerator();
pFieldFilter.reset(pSnippetGen);
if (!pSnippetGen->init(pQuery, parser.getAnalyzerMapper(), param.field,
param.preTag, param.postTag, param.separator))
{
FX_LOG(ERROR, "Init snippet generator for field: [%s] FAILED", param.field.c_str());
sendErrorMessage("Init snippet generator for field: " +
param.field + " FAILED", pCtx);
return;
}
}
if (!selector.addField(param.field, pFieldFilter))
{
FX_LOG(ERROR, "Invalid field: [%s]", param.field.c_str());
}
}
result.init(selector, pIndexReader, *pHits);
}
else
{
result.init(pIndexReader, *pHits);
}
}
probe.stop();
result.setTimeCost(probe.elapsed() / 1000);
FX_QUERY_TRACE(INFO, result.getTracer(), "search phase time [%d]",
(int32_t)result.getTimeCost());
stringstream ss;
XMLResultFormatter formatter;
formatter.format(result, ss);
sendResponse(ss.str(), pCtx);
}
catch(const FirteXException& e)
{
FX_LOG(ERROR, "Handle request FAILED: [%s], reason: [%s]",
pCtx->getQuery().c_str(), e.what().c_str());
sendErrorMessage("Handle request failed", pCtx);
}
}