// -----------------------------------------------------------------------------
// Sort the entries of filtMagUpdateMap and set the threshold to be ? percentile
// -----------------------------------------------------------------------------
Real_t BFReconstructionEngine::SetNonHomThreshold(RealImageType::Pointer magUpdateMap)
{
size_t dims[1] =
{ m_Geometry->N_z* m_Geometry->N_x};
RealArrayType::Pointer TempMagMap = RealArrayType::New(dims, "TempMagMap");
uint32_t ArrLength = m_Geometry->N_z * m_Geometry->N_x;
Real_t threshold;
//Copy into a new list for sorting
Real_t* src = magUpdateMap->getPointer();
Real_t* dest = TempMagMap->getPointer();
::memcpy(dest, src, ArrLength * sizeof(Real_t));
#ifdef DEBUG
Real_t TempSum = 0;
for(uint32_t i = 0; i < ArrLength; i++)
{ TempSum += TempMagMap->d[i]; }
if(getVerbose()) { std::cout << "Temp mag map average= " << TempSum / ArrLength << std::endl; }
#endif //DEBUG
/* for (uint32_t i = 0; i < m_Geometry->N_z; i++)
for (uint32_t j = 0; j < m_Geometry->N_x; j++)
{
//TempMagMap->d[i*geometry->N_x+j]=i*geometry->N_x+j;
TempMagMap->d[i * (uint32_t)m_Geometry->N_x + j] = magUpdateMap->getValue(i, j);
} */
uint32_t percentile_index = ArrLength / MBIR::Constants::k_NumNonHomogeniousIter;
if(getVerbose()) { std::cout << "Percentile to select= " << percentile_index << std::endl; }
//Partial selection sort
/*Real_t max;
uint32_t max_index;
for (uint32_t i = 0; i <= percentile_index; i++)
{
max = TempMagMap->d[i];
max_index = i;
for (uint32_t j = i + 1; j < ArrLength; j++)
{
if(TempMagMap->d[j] > max)
{
max = TempMagMap->d[j];
max_index = j;
}
}
Real_t temp = TempMagMap->d[i];
TempMagMap->d[i] = TempMagMap->d[max_index];
TempMagMap->d[max_index] = temp;
}
threshold = TempMagMap->d[percentile_index];*/
threshold = RandomizedSelect(TempMagMap, 0, ArrLength - 1, ArrLength - percentile_index);
return threshold;
}
uint8_t BFReconstructionEngine::stopCriteria(RealImageType::Pointer magUpdateMap, UInt8Image_t::Pointer magUpdateMask, Real_t PrevMagSum, uint32_t EffIterCount)
{
uint8_t exit_status = 1;
if(getVeryVerbose())
{
Real_t TempSum = 0;
for (int32_t j = 0; j < m_Geometry->N_z; j++)
{
for (int32_t k = 0; k < m_Geometry->N_x; k++)
{
TempSum += magUpdateMap->getValue(j, k);
}
}
std::cout << "**********************************************" << std::endl;
std::cout << "Average mag after voxel update" << TempSum / (m_Geometry->N_z * m_Geometry->N_x) << std::endl;
std::cout << "**********************************************" << std::endl;
}
#ifdef NHICD
//In non homogenous mode check stopping criteria only after a full equit = equivalet iteration
if(EffIterCount % MBIR::Constants::k_NumNonHomogeniousIter == 0 && EffIterCount > 0 && PrevMagSum > 0)
#else
if(EffIterCount > 0 && PrevMagSum > 0)
#endif //NHICD
{
Real_t TempSum = 0;
uint32_t counter = 0;
for (int32_t j = 0; j < m_Geometry->N_z; j++)
for (int32_t k = 0; k < m_Geometry->N_x; k++)
if(magUpdateMask->getValue(j, k) == 1)
{
TempSum += magUpdateMap->getValue(j, k);
counter++;
}
if(getVeryVerbose()) {std::cout << "Number of elements in the ROI after an equit= " << counter << std::endl;}
if(getVerbose())
{
std::cout << "************************************************" << std::endl;
std::cout << EffIterCount + 1 << " " << (fabs(TempSum) / fabs(PrevMagSum)) << std::endl;
std::cout << "************************************************" << std::endl;
}
if( (fabs(TempSum) / fabs(PrevMagSum)) < m_TomoInputs->StopThreshold && EffIterCount > 0)
{
if(getVerbose()) { std::cout << "This is the terminating point " << EffIterCount << std::endl; }
m_TomoInputs->StopThreshold *= m_AdvParams->THRESHOLD_REDUCTION_FACTOR; //Reducing the thresold for subsequent iterations
if(getVerbose()) { std::cout << "New threshold" << m_TomoInputs->StopThreshold << std::endl; }
exit_status = 0;
}
}
return exit_status;
}
// -----------------------------------------------------------------------------
//Function to generate a randomized list from a given input list
// -----------------------------------------------------------------------------
VoxelUpdateList::Pointer BFReconstructionEngine::GenRandList(VoxelUpdateList::Pointer InpList)
{
VoxelUpdateList::Pointer OpList;
const uint32_t rangeMin = 0;
const uint32_t rangeMax = std::numeric_limits<uint32_t>::max();
typedef boost::uniform_int<uint32_t> NumberDistribution;
typedef boost::mt19937 RandomNumberGenerator;
typedef boost::variate_generator<RandomNumberGenerator&, NumberDistribution> Generator;
NumberDistribution distribution(rangeMin, rangeMax);
RandomNumberGenerator generator;
Generator numberGenerator(generator, distribution);
boost::uint32_t arg = static_cast<boost::uint32_t>(EIMTOMO_getMilliSeconds());
generator.seed(arg); // seed with the current time
int32_t ArraySize = InpList.NumElts;
OpList.NumElts = ArraySize;
OpList.Array = (struct ImgIdx*)(malloc(ArraySize * sizeof(struct ImgIdx)));
size_t dims[3] =
{ ArraySize, 0, 0};
Int32ArrayType::Pointer Counter = Int32ArrayType::New(dims, "Counter");
for (int32_t j_new = 0; j_new < ArraySize; j_new++)
{
Counter->d[j_new] = j_new;
}
for(int32_t test_iter = 0; test_iter < InpList.NumElts; test_iter++)
{
int32_t Index = numberGenerator() % ArraySize;
OpList.Array[test_iter] = InpList.Array[Counter->d[Index]];
Counter->d[Index] = Counter->d[ArraySize - 1];
ArraySize--;
}
#ifdef DEBUG
if(getVerbose()) { std::cout << "Input" << std::endl; }
maxList(InpList);
if(getVerbose()) { std::cout << "Output" << std::endl; }
maxList(OpList);
#endif //Debug
return OpList;
}
IoContext IoWorker::doMap() const
{
const TraceSet &set = getTraceSet();
TraceSet::Iterator iter = set.between(getBeginPos(), getEndPos());
TraceSet::Iterator endIter = set.end();
IoContext data;
// Get event ids
std::set<event_id_t> readEventIds {};
for (const std::string &eventName : readSyscalls) {
event_id_t id = getEventId(set, eventName);
readEventIds.insert(id);
}
std::set<event_id_t> writeEventIds {};
for (const std::string &eventName : writeSyscalls) {
event_id_t id = getEventId(set, eventName);
writeEventIds.insert(id);
}
std::set<event_id_t> readWriteEventIds {};
for (const std::string &eventName : readWriteSyscalls) {
event_id_t id = getEventId(set, eventName);
readWriteEventIds.insert(id);
}
std::set<event_id_t> exitEventIds {};
for (const std::string &eventName : exitSyscalls) {
event_id_t id = getEventId(set, eventName);
exitEventIds.insert(id);
}
// Iterate through events
uint64_t count = 0;
for ((void)iter; iter != endIter; ++iter) {
count++;
const auto &event = *iter;
event_id_t id = event.getId();
if (readEventIds.find(id) != readEventIds.end()) {
data.handleSysRead(event);
} else if (writeEventIds.find(id) != writeEventIds.end()) {
data.handleSysWrite(event);
} else if (readWriteEventIds.find(id) != readWriteEventIds.end()) {
data.handleSysReadWrite(event);
} else if (exitEventIds.find(id) != exitEventIds.end()) {
data.handleExitSyscall(event);
}
}
if (getVerbose()) {
const timestamp_t *begin = getBeginPos();
const timestamp_t *end = getEndPos();
std::string beginString = begin ? std::to_string(*begin) : "START";
std::string endString = end ? std::to_string(*end) : "END";
std::cout << "Worker " << getId() << " processed " << count << " events between timestamps "
<< beginString << " and " << endString << std::endl;
}
data.handleEnd();
return data;
}
void _LogWrite(char *file, int line, const char *format, ...)
{
va_list arg;
time_t t = time(NULL);
struct tm tm = *localtime(&t);
char timeStr[32];
sprintf(timeStr,"%4d-%.2d-%.2d %.2d:%.2d:%.2d",
1900+tm.tm_year,
tm.tm_mon+1,
tm.tm_mday,
tm.tm_hour,
tm.tm_min,
tm.tm_sec);
if ( getVerbose() )
{
fprintf(stdout, "%s %s:%d:", timeStr, file, line);
va_start(arg, format);
vfprintf(stdout, format, arg);
va_end(arg);
}
if ( getDaemonize() )
{
FILE *logFile;
logFile = fopen((const char *)getLogFile(), "a");
if ( ! logFile )
{
fprintf(stderr, "Error: Unable to open log file for writing!\n");
fprintf(stderr, "%s %s:%d:",timeStr, file, line);
va_start(arg, format);
vfprintf(stderr, format, arg);
va_end(arg);
return;
}
fprintf(logFile, "%s %s:%d:",timeStr, file, line);
va_start(arg, format);
vfprintf(logFile, format, arg);
va_end(arg);
fclose(logFile);
}
}
bool IApplication::start()
{
if(getVerbose())
{
Options::instance()->setOption<bool>(Options::log_options::enable, true);
Options::instance()->setOption<uint32>(Options::log_options::level, logLevelDebug);
Options::instance()->setOption<bool>(Options::log_options::serialize, true);
}
OS_ASSERT(Engine::exists() == false);
if(Engine::create()->start(getRecoveryMode()) == false)
return false;
// N.B.: è necessario avviare il thread di listener dopo aver avviato l'engine in modo da evitare di processare comandi prima che quest'ultimo sia stato inizializzato
if(m_notifyListener != nullptr)
m_notifyListener->start();
return true;
}
// -----------------------------------------------------------------------------
// Read the Input data from the supplied data file
// -----------------------------------------------------------------------------
int BFReconstructionEngine::readInputData()
{
TomoFilter::Pointer dataReader = TomoFilter::NullPointer();
std::string extension = MXAFileInfo::extension(m_TomoInputs->sinoFile);
if(extension.compare("bin") == 0)
{
dataReader = RawSinogramInitializer::NewTomoFilter();
}
else
// if(extension.compare("mrc") == 0 || extension.compare("ali") == 0)
{
// We are going to assume that the user has selected a valid MRC file to get this far so we are just going to try
// to read the file as an MRC file which may really cause issues but there does not seem to be any standard file
// extensions for MRC files.
dataReader = MRCSinogramInitializer::NewTomoFilter();
}
// {
// setErrorCondition(-1);
// notify("A supported file reader for the input file was not found.", 100, Observable::UpdateErrorMessage);
// return -1;
// }
dataReader->setTomoInputs(m_TomoInputs);
dataReader->setSinogram(m_Sinogram);
dataReader->setAdvParams(m_AdvParams);
dataReader->setObservers(getObservers());
dataReader->setVerbose(getVerbose());
dataReader->setVeryVerbose(getVeryVerbose());
dataReader->execute();
if(dataReader->getErrorCondition() < 0)
{
std::stringstream ss;
ss << "Error reading the input file: '" << m_TomoInputs->sinoFile << "'. MBIR currently considers .bin as a raw binary file "
<< "and any other file as an MRC input file. If this is NOT the case for your data consider contacting the developers "
<< " of this software.";
notify(ss.str(), 100, Observable::UpdateErrorMessage);
setErrorCondition(dataReader->getErrorCondition());
return -1;
}
return 0;
}
// insert start and goal nodes into the abstract graph before running
// any search.
node*
DefaultInsertionPolicy::insert(node* n)
throw(std::invalid_argument)
{
node* retVal = 0;
resetMetrics();
//assert(insertedStartNode == 0 && insertedGoalNode == 0);
if(n->getLabelL(kParent) == -1)
{
ClusterNode* target = dynamic_cast<ClusterNode*>(n);
AbstractCluster* cluster = map->getCluster(
target->getParentClusterId());
if(getVerbose())
{
const int x = target->getLabelL(kFirstData);
const int y = target->getLabelL(kFirstData+1);
std::cout << "inserting node ("<<x<<", "<<y<<") "
"into abstract graph"<<std::endl;
}
cluster->addParent(target);
graph* absg = map->getAbstractGraph(1);
retVal = absg->getNode(target->getLabelL(kParent));
addNode(retVal);
//assert(retVal);
searchTime = cluster->getSearchTime();
nodesExpanded = cluster->getNodesExpanded();
nodesGenerated = cluster->getNodesGenerated();
nodesTouched = cluster->getNodesTouched();
}
else
{
retVal = map->getAbstractGraph(1)->getNode(
n->getLabelL(kParent));
}
return retVal;
}
// -----------------------------------------------------------------------------
// Initialize the Geometry data from a rough reconstruction
// -----------------------------------------------------------------------------
int BFReconstructionEngine::initializeRoughReconstructionData()
{
InitialReconstructionInitializer::Pointer geomInitializer = InitialReconstructionInitializer::NullPointer();
std::string extension = MXAFileInfo::extension(m_TomoInputs->initialReconFile);
if (m_TomoInputs->initialReconFile.empty() == true)
{
// This will just initialize all the values to Zero (0) or a DefaultValue Set by user
geomInitializer = InitialReconstructionInitializer::New();
}
else if (extension.compare("bin") == 0 )
{
// This will read the values from a binary file
geomInitializer = InitialReconstructionBinReader::NewInitialReconstructionInitializer();
}
else if (extension.compare("mrc") == 0)
{
notify("We are not dealing with mrc volume files.", 0, Observable::UpdateErrorMessage);
return -1;
}
else
{
notify("Could not find a compatible reader for the initial reconstruction data file. The program will now end.", 0, Observable::UpdateErrorMessage);
return -1;
}
geomInitializer->setSinogram(m_Sinogram);
geomInitializer->setTomoInputs(m_TomoInputs);
geomInitializer->setGeometry(m_Geometry);
geomInitializer->setAdvParams(m_AdvParams);
geomInitializer->setObservers(getObservers());
geomInitializer->setVerbose(getVerbose());
geomInitializer->setVeryVerbose(getVeryVerbose());
geomInitializer->execute();
if(geomInitializer->getErrorCondition() < 0)
{
notify("Error reading Initial Reconstruction Data from File", 100, Observable::UpdateProgressValueAndMessage);
setErrorCondition(geomInitializer->getErrorCondition());
return -1;
}
return 0;
}
// addParent is responsible for adding new abstract nodes to the cluster and
// creating intra-edges that connect the new node to existing abstract nodes.
void
AbstractCluster::addParent(node* _p) throw(std::invalid_argument)
{
Timer t;
t.startTimer();
ClusterNode* p = dynamic_cast<ClusterNode*>(_p);
if(p == 0)
throw std::invalid_argument(
"AbstractCluster::addParent: arg not of type AbstractClusterNode");
if(p->getParentClusterId() != this->getId())
throw std::invalid_argument(
"AbstractCluster::addParent: arg not assigned to this cluster");
if(parents.find(p->getUniqueID()) != parents.end())
return; // node already in parents collection
if(p->getLabelL(kAbstractionLevel) == 0)
{
ClusterNode* p2 = dynamic_cast<ClusterNode*>(
map->getNodeFactory()->newNode(p));
p2->setLabelL(kAbstractionLevel, 1);
p2->setLabelL(kParent, -1);
map->getAbstractGraph(1)->addNode(p2);
p->setLabelL(kParent, p2->getNum());
p = p2;
}
if(getVerbose())
{
std::cout << "AbstractCluster::addParent ";
p->Print(std::cout);
std::cout << std::endl;
}
p->setParentClusterId(this->getId());
parents.insert(std::pair<int, node*>(p->getUniqueID(), p));
connectParent(p);
searchTime = t.endTimer();
}
// -----------------------------------------------------------------------------
// Updates the voxels specified in the list for homogenous update. For non homgenous
// update computes the list. Calls the parallel update of voxels routine
// -----------------------------------------------------------------------------
uint8_t BFReconstructionEngine::updateVoxels(int16_t OuterIter,
int16_t Iter,
std::vector<AMatrixCol::Pointer>& TempCol,
RealVolumeType::Pointer ErrorSino,
std::vector<AMatrixCol::Pointer>& VoxelLineResponse,
CostData::Pointer cost,
QGGMRF::QGGMRF_Values* BFQGGMRF_values,
RealImageType::Pointer magUpdateMap,
RealImageType::Pointer filtMagUpdateMap,
UInt8Image_t::Pointer magUpdateMask,
UInt8Image_t::Pointer m_VisitCount,
Real_t PrevMagSum,
uint32_t EffIterCount)
{
#if ROI
//variables used to stop the process
Real_t AverageUpdate = 0;
Real_t AverageMagnitudeOfRecon = 0;
#endif
unsigned int updateType = MBIR::VoxelUpdateType::RegularRandomOrderUpdate;
VoxelUpdateList::Pointer NHList;//non homogenous list of voxels to update
#ifdef NHICD
if(0 == EffIterCount % 2)
{
updateType = MBIR::VoxelUpdateType::HomogeniousUpdate;
}
else
{
updateType = MBIR::VoxelUpdateType::NonHomogeniousUpdate;
}
#endif//NHICD end if
#if defined (OpenMBIR_USE_PARALLEL_ALGORITHMS)
tbb::task_scheduler_init init;
int m_NumThreads = init.default_num_threads();
#else
int m_NumThreads = 1;
#endif //Parallel algorithms
std::stringstream ss;
uint8_t exit_status = 1; //Indicates normal exit ; else indicates to stop inner iterations
uint16_t subIterations = 1;
std::string indent(" ");
uint8_t err = 0;
if(updateType == MBIR::VoxelUpdateType::RegularRandomOrderUpdate)
{
ss << indent << "Regular Random Order update of Voxels" << std::endl;
}
else if(updateType == MBIR::VoxelUpdateType::HomogeniousUpdate)
{
ss << indent << "Homogenous update of voxels" << std::endl;
}
else if(updateType == MBIR::VoxelUpdateType::NonHomogeniousUpdate)
{
ss << indent << "Non Homogenous update of voxels" << std::endl;
subIterations = SUB_ITER;
}
else
{
ss << indent << "Unknown Voxel Update Type. Returning Now" << std::endl;
notify(ss.str(), 0, Observable::UpdateErrorMessage);
return exit_status;
}
if(getVerbose())
{
std::cout << ss.str() << std::endl;
}
Real_t NH_Threshold = 0.0;
int totalLoops = m_TomoInputs->NumOuterIter * m_TomoInputs->NumIter;
#ifdef DEBUG
if (getVeryVerbose())
{
std::cout << "Max of list in ReconEngineExtra = " << std::endl;
m_VoxelIdxList->printMaxList(std::cout);
}
#endif //DEBUG
for (uint16_t NH_Iter = 0; NH_Iter < subIterations; ++NH_Iter) //This can be varied
//so each iterations of the voxels has multiple passes over the voxels
//but generally its set to 1
{
ss.str(" ");
ss << "Outer Iteration: " << OuterIter << " of " << m_TomoInputs->NumOuterIter;
ss << " Inner Iteration: " << Iter << " of " << m_TomoInputs->NumIter;
ss << " SubLoop: " << NH_Iter << " of " << subIterations;
float currentLoop = static_cast<float>(OuterIter * m_TomoInputs->NumIter + Iter);
notify(ss.str(), currentLoop / totalLoops * 100.0f, Observable::UpdateProgressValueAndMessage);
if(updateType == MBIR::VoxelUpdateType::NonHomogeniousUpdate)
{
#ifdef DEBUG
Real_t TempSum = 0;
for (int32_t j = 0; j < m_Geometry->N_z; j++)
{
for (int32_t k = 0; k < m_Geometry->N_x; k++)
{
TempSum += magUpdateMap->getValue(j, k);
}
}
if (getVeryVerbose())
{
std::cout << "**********************************************" << std::endl;
std::cout << "Average mag Prior to VSC" << TempSum / (m_Geometry->N_z * m_Geometry->N_x) << std::endl;
std::cout << "**********************************************" << std::endl;
}
#endif //debug
//Compute a filtered version of the magnitude update map
ComputeVSC(magUpdateMap, filtMagUpdateMap);
#ifdef DEBUG
TempSum = 0;
for (int32_t j = 0; j < m_Geometry->N_z; j++)
{
for (int32_t k = 0; k < m_Geometry->N_x; k++)
{
TempSum += magUpdateMap->getValue(j, k);
}
}
if (getVeryVerbose())
{
std::cout << "**********************************************" << std::endl;
std::cout << "Average mag Prior to NH Thresh" << TempSum / (m_Geometry->N_z * m_Geometry->N_x) << std::endl;
std::cout << "**********************************************" << std::endl;
}
#endif //debug
START_TIMER;
NH_Threshold = SetNonHomThreshold(filtMagUpdateMap);
STOP_TIMER;
PRINT_TIME(" SetNonHomThreshold");
if(getVerbose()) { std::cout << indent << "NHICD Threshold: " << NH_Threshold << std::endl; }
//Generate a new List based on the NH_threshold
m_VoxelIdxList = GenNonHomList(NH_Threshold, filtMagUpdateMap);
}
START_TIMER;
#if defined (OpenMBIR_USE_PARALLEL_ALGORITHMS)
std::vector<int> yCount(m_NumThreads, 0);
int t = 0;
for (int y = 0; y < m_Geometry->N_y; ++y)
{
yCount[t]++;
++t;
if(t == m_NumThreads)
{
t = 0;
}
}
//Checking which voxels are going to be visited and setting their magnitude value to zero
for(int32_t tmpiter = 0; tmpiter < m_VoxelIdxList->numElements(); tmpiter++)
{
// m_VisitCount->setValue(1, m_VoxelIdxList.Array[tmpiter].zidx, m_VoxelIdxList.Array[tmpiter].xidx);
m_VisitCount->setValue(1, m_VoxelIdxList->zIdx(tmpiter), m_VoxelIdxList->xIdx(tmpiter));
// magUpdateMap->setValue(0, m_VoxelIdxList.Array[tmpiter].zidx, m_VoxelIdxList.Array[tmpiter].xidx);
magUpdateMap->setValue(0, m_VoxelIdxList->zIdx(tmpiter), m_VoxelIdxList->xIdx(tmpiter));
}
uint16_t yStart = 0;
uint16_t yStop = 0;
tbb::task_list taskList;
//Variables to maintain stopping criteria for regular type ICD
boost::shared_array<Real_t> averageUpdate(new Real_t[m_NumThreads]);
::memset(averageUpdate.get(), 0, sizeof(Real_t) * m_NumThreads);
boost::shared_array<Real_t> averageMagnitudeOfRecon(new Real_t[m_NumThreads]);
::memset(averageMagnitudeOfRecon.get(), 0, sizeof(Real_t) * m_NumThreads);
size_t dims[3];
//Initialize individual magnitude maps for the separate threads
dims[0] = m_Geometry->N_z; //height
dims[1] = m_Geometry->N_x; //width
std::vector<RealImageType::Pointer> magUpdateMaps;
std::vector<VoxelUpdateList::Pointer> NewList(m_NumThreads);
int16_t EffCoresUsed = 0;
if(getVerbose()) { std::cout << " Starting multicore allocation with " << m_NumThreads << " threads.." << std::endl; }
for (int t = 0; t < m_NumThreads; ++t)
{
yStart = yStop;
yStop = yStart + yCount[t];
if (getVeryVerbose())
{
std::cout << "Thread :" << t << "(" << yStart << "," << yStop << ")" << std::endl;
}
if(yStart == yStop)
{
continue;
} // Processor has NO tasks to run because we have less Y's than cores
else
{
EffCoresUsed++;
}
RealImageType::Pointer _magUpdateMap = RealImageType::New(dims, "Mag Update Map");
_magUpdateMap->initializeWithZeros();
magUpdateMaps.push_back(_magUpdateMap);
//NewList[t] = m_VoxelIdxList;
NewList[t] = VoxelUpdateList::GenRandList(m_VoxelIdxList);
BFUpdateYSlice& a =
*new (tbb::task::allocate_root()) BFUpdateYSlice(yStart, yStop, m_Geometry, OuterIter, Iter,
m_Sinogram, TempCol, ErrorSino,
VoxelLineResponse, m_ForwardModel.get(),
magUpdateMask,
_magUpdateMap,
magUpdateMask, updateType,
averageUpdate.get() + t,
averageMagnitudeOfRecon.get() + t,
m_AdvParams->ZERO_SKIPPING,
BFQGGMRF_values, NewList[t] );
taskList.push_back(a);
}
tbb::task::spawn_root_and_wait(taskList);
if(getVerbose())
{
std::cout << " Voxel update complete using " << EffCoresUsed << " threads" << std::endl;
}
// Now sum up magnitude update map values
//TODO: replace by a TBB reduce operation
for (int t = 0; t < m_NumThreads; ++t)
{
#ifdef DEBUG
if(getVeryVerbose()) //TODO: Change variable name averageUpdate to totalUpdate
{
std::cout << "Total Update for thread " << t << ":" << averageUpdate[t] << std::endl;
std::cout << "Total Magnitude for thread " << t << ":" << averageMagnitudeOfRecon[t] << std::endl;
}
#endif //Debug
AverageUpdate += averageUpdate[t];
AverageMagnitudeOfRecon += averageMagnitudeOfRecon[t];
}
averageUpdate.reset(); // We are forcing the array to be deallocated, we could wait till the current scope terminates then the arrays would be automatically cleaned up
averageMagnitudeOfRecon.reset(); // We are forcing the array to be deallocated, we could wait till the current scope terminates then the arrays would be automatically cleaned up
NewList.resize(0); // Frees all the pointers
//From individual threads update the magnitude map
if(getVerbose()) { std::cout << " Magnitude Map Update.." << std::endl; }
RealImageType::Pointer TempPointer;
for(int32_t tmpiter = 0; tmpiter < m_VoxelIdxList->numElements(); tmpiter++)
{
Real_t TempSum = 0;
for (uint16_t t = 0; t < magUpdateMaps.size(); ++t)
{
TempPointer = magUpdateMaps[t];
TempSum += TempPointer->getValue(m_VoxelIdxList->zIdx(tmpiter), m_VoxelIdxList->xIdx(tmpiter));
}
//Set the overall magnitude update map
magUpdateMap->setValue(TempSum, m_VoxelIdxList->zIdx(tmpiter), m_VoxelIdxList->xIdx(tmpiter));
}
#else //TODO modify the single thread code to handle the list based iterations
uint16_t yStop = m_Geometry->N_y;
uint16_t yStart = 0;
boost::shared_array<Real_t> averageUpdate(new Real_t[m_NumThreads]);
::memset(averageUpdate.get(), 0, sizeof(Real_t) * m_NumThreads);
boost::shared_array<Real_t> averageMagnitudeOfRecon(new Real_t[m_NumThreads]);
::memset(averageMagnitudeOfRecon.get(), 0, sizeof(Real_t) * m_NumThreads);
size_t dims[3];
//Initialize individual magnitude maps for the separate threads
dims[0] = m_Geometry->N_z; //height
dims[1] = m_Geometry->N_x; //width
RealImageType::Pointer _magUpdateMap = RealImageType::New(dims, "Mag Update Map");
_magUpdateMap->initializeWithZeros();
struct List NewList = m_VoxelIdxList;
NewList = GenRandList(NewList);
BFUpdateYSlice yVoxelUpdate = BFUpdateYSlice(yStart, yStop, m_Geometry, OuterIter, Iter,
m_Sinogram, TempCol, ErrorSino,
VoxelLineResponse, m_ForwardModel.get(),
magUpdateMask,
_magUpdateMap,
magUpdateMask, updateType,
averageUpdate,
averageMagnitudeOfRecon,
m_AdvParams->ZERO_SKIPPING,
BFQGGMRF_values, NewList);
/*BFUpdateYSlice(yStart, yStop, m_Geometry, OuterIter, Iter,
m_Sinogram, TempCol, ErrorSino,
VoxelLineResponse, m_ForwardModel.get(), mask,
magUpdateMap,
magUpdateMask, updateType,
NH_Threshold,
averageUpdate,
averageMagnitudeOfRecon ,
m_AdvParams->ZERO_SKIPPING,
BFQGGMRF_values, m_VoxelIdxList);*/
yVoxelUpdate.execute();
// AverageUpdate += averageUpdate[0];
// AverageMagnitudeOfRecon += averageMagnitudeOfRecon[0];
averageUpdate.reset(); // We are forcing the array to be deallocated, we could wait till the current scope terminates then the arrays would be automatically cleaned up
averageMagnitudeOfRecon.reset(); // We are forcing the array to be deallocated, we could wait till the current scope terminates then the arrays would be automatically cleaned up
#endif //Parallel algorithms
/* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% */STOP_TIMER;
ss.str("");
ss << "Inner Iter: " << Iter << " Voxel Update";
PRINT_TIME(ss.str());
if(getVerbose())
{
std::cout << "Total Update " << AverageUpdate << std::endl;
std::cout << "Total Mag " << AverageMagnitudeOfRecon << std::endl;
}
if(getCancel() == true)
{
setErrorCondition(err);
return exit_status;
}
}
//Stopping criteria code
exit_status = stopCriteria(magUpdateMap, magUpdateMask, PrevMagSum, EffIterCount);
#ifdef WRITE_INTERMEDIATE_RESULTS
if(Iter == NumOfWrites * WriteCount)
{
WriteCount++;
sprintf(buffer, "%d", Iter);
sprintf(Filename, "ReconstructedObjectAfterIter");
strcat(Filename, buffer);
strcat(Filename, ".bin");
Fp3 = fopen(Filename, "w");
TempPointer = geometry->Object;
NumOfBytesWritten = fwrite(&(geometry->Object->d[0][0][0]), sizeof(Real_t), geometry->N_x * geometry->N_y * geometry->N_z, Fp3);
printf("%d\n", NumOfBytesWritten);
fclose(Fp3);
}
#endif //write Intermediate results
#ifdef NHICD
/* NHList will go out of scope at the end of this function which will cause its destructor to be called and the memory automatically cleaned up */
// if(updateType == MBIR::VoxelUpdateType::NonHomogeniousUpdate && NHList.Array != NULL)
// {
// free(NHList.Array);
// std::cout<<"Freeing memory allocated to non-homogenous List"<<std::endl;
// }
#endif //NHICD
if(getVerbose()) { std::cout << "exiting voxel update routine" << std::endl; }
return exit_status;
}
// a transition point connects two nodes on the map. usually the nodes are on the
// border of two adjacent clusters (in which case the transition results in an
// inter-edge being created) but this is not necessary.
void
AbstractCluster::addTransition(node* from_, node* to_, double edgeweight)
throw(std::invalid_argument)
{
if(edgeweight < 0)
throw std::invalid_argument(
"AbstractCluster::addTransition edge weight cannot be < 0");
ClusterNode* from = dynamic_cast<ClusterNode*>(from_);
ClusterNode* to = dynamic_cast<ClusterNode*>(to_);
assert(from && to);
graph *g = map->getAbstractGraph(1);
ClusterNode* absfrom =
dynamic_cast<ClusterNode*>(g->getNode(from->getLabelL(kParent)));
ClusterNode* absto =
dynamic_cast<ClusterNode*>(g->getNode(to->getLabelL(kParent)));
// Try to reuse existing nodes from the abstract graph, else create new.
if(absfrom == 0)
{
if(from->getLabelL(kFirstData) == 20 && from->getLabelL(kFirstData+1) == 0)
std::cout << "master\n";
AbstractCluster* parentCluster =
map->getCluster(from->getParentClusterId());
parentCluster->addParent(from); // also creates intra-edges
absfrom = dynamic_cast<ClusterNode*>(g->getNode(from->getLabelL(kParent)));
assert(absfrom);
}
if(absto == 0)
{
AbstractCluster* parentCluster =
map->getCluster(to->getParentClusterId());
parentCluster->addParent(to); // also creates intra-edges
absto = dynamic_cast<ClusterNode*>(g->getNode(to->getLabelL(kParent)));
assert(absto);
}
edge* e = g->findEdge(absfrom->getNum(), absto->getNum());
if(!e)
{
edge* e = map->getEdgeFactory()->newEdge(absfrom->getNum(),
absto->getNum(), edgeweight);
g->addEdge(e);
if(getVerbose())
{
std::cout << "AbstractCluster::addTransition between ";
from->Print(std::cout);
to->Print(std::cout);
std::cout << " cost: "<<edgeweight<<std::endl;
}
}
else
{
if(getVerbose())
{
std::cout << "AbstractCluster::addTransition edge already exists: ";
from->Print(std::cout);
to->Print(std::cout);
std::cout << " cost: "<<e->getWeight()<<std::endl;
}
}
}
// -----------------------------------------------------------------------------
// Main ICD reconstruction
// -----------------------------------------------------------------------------
void BFReconstructionEngine::execute()
{
uint64_t totalTime = EIMTOMO_getMilliSeconds();
int32_t err = 0;
std::stringstream ss;
// int16_t i,j,k,Idx;
size_t dims[3];
uint16_t maxNumberOfDetectorElts;
uint8_t status; //set to 1 if ICD has converged
Real_t checksum = 0, temp;
RealImageType::Pointer voxelProfile;
RealVolumeType::Pointer detectorResponse;
RealVolumeType::Pointer h_t;
RealVolumeType::Pointer y_Est; //Estimated Sinogram
RealVolumeType::Pointer finalSinogram; //To store and write the final sinogram resulting from our reconstruction
RealVolumeType::Pointer errorSino; //Error Sinogram
std::string indent("");
//#ifdef COST_CALCULATE //Commented out because if not the code fails to run.
std::string filepath(m_TomoInputs->tempDir);
filepath = filepath.append(MXADir::getSeparator()).append(MBIR::Defaults::CostFunctionFile);
CostData::Pointer cost = CostData::New();
cost->initOutputFile(filepath);
//#endif
#if OpenMBIR_USE_PARALLEL_ALGORITHMS
tbb::task_scheduler_init init;
#endif
// Initialize the Sinogram
if(m_TomoInputs == NULL)
{
setErrorCondition(-1);
notify("Error: The TomoInput Structure was NULL. The proper API is to supply this class with that structure,", 100, Observable::UpdateErrorMessage);
return;
}
//Based on the inputs , calculate the "other" variables in the structure definition
if(m_Sinogram == NULL)
{
setErrorCondition(-1);
notify("Error: The Sinogram Structure was NULL. The proper API is to supply this class with that structure,", 100, Observable::UpdateErrorMessage);
return;
}
if(m_Geometry == NULL)
{
setErrorCondition(-1);
notify("Error: The Geometry Structure was NULL. The proper API is to supply this class with that structure,", 100, Observable::UpdateErrorMessage);
return;
}
if (m_ForwardModel.get() == NULL)
{
setErrorCondition(-1);
notify("Error: The forward model was not set.", 100, Observable::UpdateErrorMessage);
return;
}
// Read the Input data from the supplied data file - reconstruction from previous resolution ?
err = readInputData();
if(err < 0)
{
return;
}
if (getCancel() == true) { setErrorCondition(-999); return; }
if (getCancel() == true) { setErrorCondition(-999); return; }
//Additional parameters associated with the system
err = m_ForwardModel->createNuisanceParameters(m_Sinogram);
if(err < 0)
{
return;
}
//Periodically checking if user has sent a cancel signal from the GUI
if (getCancel() == true) { setErrorCondition(-999); return; }
m_ForwardModel->printNuisanceParameters(m_Sinogram);
//Take log of the input data after subtracting offset
m_ForwardModel->processRawCounts(m_Sinogram);
// Initialize the Geometry data from a rough reconstruction
err = initializeRoughReconstructionData();
if(err < 0)
{
return;
}
if (getCancel() == true) { setErrorCondition(-999); return; }
// Get the actual boundaries in the X Direction since we "Extend Object" which makes
// the output mrc file much wider than they really need to be.
uint16_t cropStart = 0;
uint16_t cropEnd = m_Geometry->N_x;
computeOriginalXDims(cropStart, cropEnd);
// std::cout << "Crop Start: " << cropStart << std::endl;
// std::cout << "Crop End: " << cropEnd << std::endl;
m_ForwardModel->allocateNuisanceParameters(m_Sinogram);
//#ifdef COST_CALCULATE
// dims[0] = (m_TomoInputs->NumIter+1)*m_TomoInputs->NumOuterIter*3;
//#endif
dims[0] = m_Sinogram->N_theta;
dims[1] = m_Sinogram->N_r;
dims[2] = m_Sinogram->N_t;
y_Est = RealVolumeType::New(dims, "y_Est");//y_Est = A*x_{initial}
errorSino = RealVolumeType::New(dims, "ErrorSino");// y - y_est
m_ForwardModel->weightInitialization(dims); //Initialize the \lambda matrix
finalSinogram = RealVolumeType::New(dims, "Final Sinogram"); //Debug variable to store the final A*x_{Final}
/*************** Computation of partial Amatrix *************/
//calculate the trapezoidal voxel profile for each angle.Also the angles in the Sinogram
// Structure are converted to radians
voxelProfile = calculateVoxelProfile(); //This is used for computation of the partial A matrix
//Pre compute sine and cos theta to speed up computations
DetectorParameters::Pointer haadfParameters = DetectorParameters::New();
haadfParameters->setOffsetR ( ((m_TomoInputs->delta_xz / sqrt(3.0)) + m_Sinogram->delta_r / 2) / m_AdvParams->DETECTOR_RESPONSE_BINS);
haadfParameters->setOffsetT ( ((m_TomoInputs->delta_xz / 2) + m_Sinogram->delta_t / 2) / m_AdvParams->DETECTOR_RESPONSE_BINS);
haadfParameters->setBeamWidth(m_Sinogram->delta_r);
haadfParameters->calculateSinCos(m_Sinogram);
//Initialize the e-beam
haadfParameters->initializeBeamProfile(m_Sinogram, m_AdvParams); //The shape of the averaging kernel for the detector
if (getCancel() == true) { setErrorCondition(-999); return; }
//calculate sine and cosine of all angles and store in the global arrays sine and cosine
DetectorResponse::Pointer dResponseFilter = DetectorResponse::New();
dResponseFilter->setTomoInputs(m_TomoInputs);
dResponseFilter->setSinogram(m_Sinogram);
dResponseFilter->setAdvParams(m_AdvParams);
dResponseFilter->setDetectorParameters(haadfParameters);
dResponseFilter->setVoxelProfile(voxelProfile);
dResponseFilter->setObservers(getObservers());
dResponseFilter->setVerbose(getVerbose());
dResponseFilter->setVeryVerbose(getVeryVerbose());
dResponseFilter->execute();
if(dResponseFilter->getErrorCondition() < 0)
{
ss.str("");
ss << "Error Calling function detectorResponse in file " << __FILE__ << "(" << __LINE__ << ")" << std::endl;
setErrorCondition(-2);
notify(ss.str(), 100, Observable::UpdateErrorMessage);
return;
}
detectorResponse = dResponseFilter->getResponse();
// Writer the Detector Response to an output file
DetectorResponseWriter::Pointer responseWriter = DetectorResponseWriter::New();
responseWriter->setTomoInputs(m_TomoInputs);
responseWriter->setSinogram(m_Sinogram);
responseWriter->setAdvParams(m_AdvParams);
responseWriter->setObservers(getObservers());
responseWriter->setResponse(detectorResponse);
responseWriter->setVerbose(getVerbose());
responseWriter->setVeryVerbose(getVeryVerbose());
responseWriter->execute();
if(responseWriter->getErrorCondition() < 0)
{
ss.str("");
ss << __FILE__ << "(" << __LINE__ << ") " << "Error writing detector response to file." << std::endl;
setErrorCondition(-3);
notify(ss.str(), 100, Observable::UpdateErrorMessage);
return;
}
if (getCancel() == true) { setErrorCondition(-999); return; }
// Initialize H_t volume
dims[0] = 1;
dims[1] = m_Sinogram->N_theta;
dims[2] = m_AdvParams->DETECTOR_RESPONSE_BINS;
h_t = RealVolumeType::New(dims, "h_t");
initializeHt(h_t, haadfParameters->getOffsetT() );
checksum = 0;
ss.str("");
ss << "Calculating A Matrix....";
notify(ss.str(), 0, Observable::UpdateProgressMessage);
std::vector<AMatrixCol::Pointer> voxelLineResponse(m_Geometry->N_y);
maxNumberOfDetectorElts = (uint16_t)((m_TomoInputs->delta_xy / m_Sinogram->delta_t) + 2);
dims[0] = maxNumberOfDetectorElts;
for (uint16_t i = 0; i < m_Geometry->N_y; i++)
{
AMatrixCol::Pointer vlr = AMatrixCol::New(dims, 0);
voxelLineResponse[i] = vlr;
}
//Calculating A-Matrix one column at a time
//For each entry the idea is to initially allocate space for Sinogram.N_theta * Sinogram.N_x
// And then store only the non zero entries by allocating a new array of the desired size
std::vector<AMatrixCol::Pointer> tempCol(m_Geometry->N_x * m_Geometry->N_z);
checksum = 0;
temp = 0;
uint32_t voxel_count = 0;
for (uint16_t z = 0; z < m_Geometry->N_z; z++)
{
for (uint16_t x = 0; x < m_Geometry->N_x; x++)
{
tempCol[voxel_count] = AMatrixCol::calculateAMatrixColumnPartial(m_Sinogram, m_Geometry, m_TomoInputs, m_AdvParams,
z, x, 0, detectorResponse, haadfParameters);
temp += tempCol[voxel_count]->count;
if(0 == tempCol[voxel_count]->count )
{
//If this line is never hit and the Object is badly initialized
//set it to zero
for (uint16_t y = 0; y < m_Geometry->N_y; y++)
{
m_Geometry->Object->setValue(0.0, z, x, y);
}
}
voxel_count++;
}
}
storeVoxelResponse(h_t, voxelLineResponse, haadfParameters);
if (getCancel() == true) { setErrorCondition(-999); return; }
if(getVerbose())
{
printf("Number of non zero entries of the forward projector is %lf\n", temp);
printf("Geometry-Z %d\n", m_Geometry->N_z);
}
/************ End of A matrix partial computations **********************/
//Gain and Offset Parameters Initialization of the forward model
m_ForwardModel->gainAndOffsetInitialization(m_Sinogram->N_theta);
initializeVolume(y_Est, 0.0);
if (getCancel() == true) { setErrorCondition(-999); return; }
//Forward Project Geometry->Object one slice at a time and compute the Sinogram for each slice
// Forward Project using the Forward Model
err = m_ForwardModel->forwardProject(m_Sinogram, m_Geometry, tempCol, voxelLineResponse, y_Est , errorSino);
if (err < 0)
{
return;
}
if (getCancel() == true) { setErrorCondition(-999); return; }
#ifdef FORWARD_PROJECT_MODE
return 0; //exit the program once we finish forward projecting the object
#endif//Forward Project mode
// Initialize the Prior Model parameters - here we are using a QGGMRF Prior Model
QGGMRF::QGGMRF_Values QGGMRF_values;
QGGMRF::initializePriorModel(m_TomoInputs, &QGGMRF_values, NULL);
#ifdef COST_CALCULATE
err = calculateCost(cost, m_Sinogram, m_Geometry, errorSino, &QGGMRF_values);
#endif //Cost calculation endif
Real_t TempBraggValue, DesBraggValue;
#ifdef BRAGG_CORRECTION
if(m_TomoInputs->NumIter > 1)
{
//Get the value of the Bragg threshold from the User Interface the first time
DesBraggValue = m_ForwardModel->getBraggThreshold();
if (getVeryVerbose()) {std::cout << "Desired Bragg threshold =" << DesBraggValue << std::endl;}
TempBraggValue = DefBraggThreshold;//m_ForwardModel->getBraggThreshold();
m_ForwardModel->setBraggThreshold(TempBraggValue); //setting the Threshold T of \beta_{T,\delta}
//the \delta value is set in BFMultiResolutionReconstruction.cpp
}
else
{
TempBraggValue = m_ForwardModel->getBraggThreshold();
m_ForwardModel->setBraggThreshold(TempBraggValue);
}
#endif //Bragg correction
if (getVeryVerbose()) {std::cout << "Bragg threshold =" << TempBraggValue << std::endl;}
//Generate a List
if (getVeryVerbose()) {std::cout << "Generating a list of voxels to update" << std::endl;}
//Takes all the voxels along x-z slice and forms a list
m_VoxelIdxList = VoxelUpdateList::GenRegularList(m_Geometry->N_z, m_Geometry->N_x);
//Randomize the list of voxels
m_VoxelIdxList = VoxelUpdateList::GenRandList(m_VoxelIdxList);
if(getVerbose())
{
std::cout << "Initial random order list .." << std::endl;
m_VoxelIdxList->printMaxList(std::cout);
}
// Create a copy of the Voxel Update List because we are going to adjust the VoxelUpdateList instance variable
// with values for the array pointer and number of elements based on the iteration
VoxelUpdateList::Pointer TempList = VoxelUpdateList::New(m_VoxelIdxList->numElements(), m_VoxelIdxList->getArray() );
uint32_t listselector = 0; //For the homogenous updates this cycles through the random list one sublist at a time
//Initialize the update magnitude arrays (for NHICD mainly) & stopping criteria
dims[0] = m_Geometry->N_z; //height
dims[1] = m_Geometry->N_x; //width
dims[2] = 0;
RealImageType::Pointer magUpdateMap = RealImageType::New(dims, "Update Map for voxel lines");
RealImageType::Pointer filtMagUpdateMap = RealImageType::New(dims, "Filter Update Map for voxel lines");
UInt8Image_t::Pointer magUpdateMask = UInt8Image_t::New(dims, "Update Mask for selecting voxel lines NHICD");//TODO: Remove this variable. Under the new formulation not needed
Real_t PrevMagSum = 0;
magUpdateMap->initializeWithZeros();
filtMagUpdateMap->initializeWithZeros();
#if ROI
//A mask to check the stopping criteria for the algorithm
initializeROIMask(magUpdateMask);
#endif
//Debugging variable to check if all voxels are visited
dims[0] = m_Geometry->N_z;
dims[1] = m_Geometry->N_x;
dims[2] = 0;
UInt8Image_t::Pointer m_VisitCount = UInt8Image_t::New(dims, "VisitCount");
uint32_t EffIterCount = 0; //Maintains number of calls to updatevoxelroutine
//Loop through every voxel updating it by solving a cost function
for (int16_t reconOuterIter = 0; reconOuterIter < m_TomoInputs->NumOuterIter; reconOuterIter++)
{
ss.str(""); // Clear the string stream
indent = "";
//The first time we may need to update voxels multiple times and then on
//just optimize over I,d,sigma,f once each outer loop;
//Each outer loop after the first outer iter updates a subset of the voxels
//followed by other parameters if needed
if(reconOuterIter > 0)
{
m_TomoInputs->NumIter = 1;//Inner iterations
m_ForwardModel->setBraggThreshold(TempBraggValue);
}
for (int16_t reconInnerIter = 0; reconInnerIter < m_TomoInputs->NumIter; reconInnerIter++)
{
// If at the inner most loops at the coarsest resolution donot apply Bragg
// Only at the coarsest scale the NumIter > 1
if(m_TomoInputs->NumIter > 1 && reconInnerIter == 0)
{
m_ForwardModel->setBraggThreshold(DefBraggThreshold);
}
#ifdef DEBUG
//Prints the ratio of the sinogram entries selected
m_ForwardModel->printRatioSelected(m_Sinogram);
#endif //DEBUG
ss.str("");
ss << "Outer Iterations: " << reconOuterIter << "/" << m_TomoInputs->NumOuterIter << " Inner Iterations: " << reconInnerIter << "/" << m_TomoInputs->NumIter << std::endl;
indent = " ";
#ifdef DEBUG
// This is all done PRIOR to calling what will become a method
if (getVeryVerbose()) {std::cout << "Bragg Threshold =" << m_ForwardModel->getBraggThreshold() << std::endl;}
#endif //DEBUG
// This could contain multiple Subloops also - voxel update
/* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% */
#ifdef NHICD //NHICD alternates between updating a fixed subset of voxels and a
//list created on the fly based on the previous iterations
// Creating a sublist of voxels for the Homogenous
// iterations - cycle through the partial sub lists
if(EffIterCount % 2 == 0) //Even iterations == Homogenous update
{
listselector %= MBIR::Constants::k_NumHomogeniousIter;// A variable to cycle through the randmoized list of voxels
int32_t nElements = floor((Real_t)TempList->numElements() / MBIR::Constants::k_NumHomogeniousIter);
//If the number of voxels is NOT exactly divisible by NUM_NON .. then compensate and make the last of the lists longer
if(listselector == MBIR::Constants::k_NumHomogeniousIter - 1)
{
nElements += (TempList->numElements() - nElements * MBIR::Constants::k_NumHomogeniousIter);
if(getVeryVerbose())
{
std::cout << "**********Adjusted number of voxel lines for last iter**************" << std::endl;
std::cout << nElements << std::endl;
std::cout << "**********************************" << std::endl;
}
}
//Set the list array for updating voxels
int32_t start = (uint32_t)(floor(((Real_t)TempList->numElements() / MBIR::Constants::k_NumHomogeniousIter)) * listselector);
m_VoxelIdxList = TempList->subList(nElements, start);
//m_VoxelIdxList.Array = &(TempList.Array[]);
if (getVeryVerbose())
{
std::cout << "Partial random order list for homogenous ICD .." << std::endl;
m_VoxelIdxList->printMaxList(std::cout);
}
listselector++;
//printList(m_VoxelIdxList);
}
#endif //NHICD
#ifdef DEBUG
Real_t TempSum = 0;
for (int32_t j = 0; j < m_Geometry->N_z; j++)
{
for (int32_t k = 0; k < m_Geometry->N_x; k++)
{
TempSum += magUpdateMap->getValue(j, k);
}
}
if (getVeryVerbose())
{
std::cout << "**********************************************" << std::endl;
std::cout << "Average mag prior to calling update voxel = " << TempSum / (m_Geometry->N_z * m_Geometry->N_x) << std::endl;
std::cout << "**********************************************" << std::endl;
}
#endif //debug
status = updateVoxels(reconOuterIter, reconInnerIter, tempCol,
errorSino, voxelLineResponse, cost, &QGGMRF_values,
magUpdateMap, filtMagUpdateMap, magUpdateMask, m_VisitCount,
PrevMagSum,
EffIterCount);
#ifdef NHICD
if(EffIterCount % MBIR::Constants::k_NumNonHomogeniousIter == 0) // At the end of half an
//equivalent iteration compute average Magnitude of recon to test
//stopping criteria
{
PrevMagSum = roiVolumeSum(magUpdateMask);
if (getVeryVerbose()) {std::cout << " Previous Magnitude of the Recon = " << PrevMagSum << std::endl;}
}
#else
PrevMagSum = roiVolumeSum(magUpdateMask);
std::cout << " Previous Magnitude of the Recon = " << PrevMagSum << std::endl;
#endif //NHICD
//Debugging information to test if every voxel is getting touched
#ifdef NHICD
//Debug every equivalent iteration
if(EffIterCount % (2 * MBIR::Constants::k_NumNonHomogeniousIter) == 0 && EffIterCount > 0)
#endif //NHICD
{
for (int16_t j = 0; j < m_Geometry->N_z; j++)
{
for (int16_t k = 0; k < m_Geometry->N_x; k++)
{
if(m_VisitCount->getValue(j, k) == 0)
{
printf("Pixel (%d %d) not visited\n", j, k);
}
}
}
//Reset the visit counter once we have cycled through
//all voxels once via the homogenous updates
for (int16_t j = 0; j < m_Geometry->N_z; j++)
{
for (int16_t k = 0; k < m_Geometry->N_x; k++)
{ m_VisitCount->setValue(0, j, k); }
}
}
//end of debug
EffIterCount++; //cycles between the two types of voxel updates
/* %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% */
if(status == 0)
{
break; //stop inner loop if we have hit the threshold value for x
}
// Check to see if we are canceled.
if (getCancel() == true)
{
setErrorCondition(-999);
return;
}
// Write out the MRC File ; If NHICD only after half an equit do a write
#ifdef NHICD
if(EffIterCount % (MBIR::Constants::k_NumNonHomogeniousIter) == 0)
#endif //NHICD
{
ss.str("");
ss << m_TomoInputs->tempDir << MXADir::getSeparator() << reconOuterIter << "_" << reconInnerIter << "_" << MBIR::Defaults::ReconstructedMrcFile;
writeMRCFile(ss.str(), cropStart, cropEnd);
notify(ss.str(), 0, Observable::UpdateIntermediateImage);
m_TomoInputs->tempFiles.push_back(ss.str());
}
#ifdef COST_CALCULATE //typically run only for debugging
/*********************Cost Calculation*************************************/
int16_t err = calculateCost(cost, m_Sinogram, m_Geometry, errorSino, &QGGMRF_values);
if(err < 0)
{
std::cout << "Cost went up after voxel update" << std::endl;
return;
// break;
}
/**************************************************************************/
#endif //Cost calculation endif
#ifdef BRAGG_CORRECTION
//If at the last iteration of the inner loops at coarsest resolution adjust parameters
if(reconInnerIter == m_TomoInputs->NumIter - 1 && reconInnerIter != 0)
{
//The first time at the coarsest resolution at the end of
// inner iterations set the Bragg Threshold
TempBraggValue = DesBraggValue;//threshold;
m_ForwardModel->setBraggThreshold(TempBraggValue);
}
#endif //Bragg correction
} /* ++++++++++ END Inner Iteration Loop +++++++++++++++ */
if(0 == status && reconOuterIter >= 1) //if stopping criteria is met and
//number of iterations is greater than 1
{
if (getVeryVerbose()) {std::cout << "Exiting the code because status =0" << std::endl;}
break;
}
if(getVeryVerbose())
{ std::cout << " Starting nuisance parameter estimation" << std::endl; }
if(m_TomoInputs->NumOuterIter > 1) //Dont update any parameters if we just have one outer iteration
{
if(m_AdvParams->JOINT_ESTIMATION)
{
m_ForwardModel->jointEstimation(m_Sinogram, errorSino, y_Est, cost);
m_ForwardModel->updateSelector(m_Sinogram, errorSino);
#ifdef COST_CALCULATE //Debug info
int16_t err = calculateCost(cost, m_Sinogram, m_Geometry, errorSino, &QGGMRF_values);
if(err < 0)
{
std::cout << "Cost went up after offset update" << std::endl;
break;
}
#endif//cost
} //Joint estimation endif
if(m_AdvParams->NOISE_ESTIMATION)
{
m_ForwardModel->updateWeights(m_Sinogram, errorSino);
m_ForwardModel->updateSelector(m_Sinogram, errorSino);
#ifdef COST_CALCULATE
//err = calculateCost(cost, Weight, errorSino);
err = calculateCost(cost, m_Sinogram, m_Geometry, errorSino, &QGGMRF_values);
if (err < 0 && reconOuterIter > 1)
{
std::cout << "Cost went up after variance update" << std::endl;
std::cout << "Effective iterations =" << EffIterCount << std::endl;
return;
//break;
}
#endif//cost
}
if(getVeryVerbose())
{ std::cout << " Ending nuisance parameter estimation" << std::endl; }
}
}/* ++++++++++ END Outer Iteration Loop +++++++++++++++ */
indent = "";
#if DEBUG_COSTS
cost->printCosts(std::cout);
#endif
#ifdef FORWARD_PROJECT_MODE
int fileError = 0;
FILE* Fp6;
MAKE_OUTPUT_FILE(Fp6, fileError, m_TomoInputs->tempDir, MBIR::Defaults::BFForwardProjectedObjectFile);
if (fileError == 1)
{
}
#endif
if (getCancel() == true) { setErrorCondition(-999); return; }
/* Write the Gains,Offsets and variance to an output file */
m_ForwardModel->writeNuisanceParameters(m_Sinogram);
//Compute final value of Ax_{final}
Real_t temp_final = 0.0;
for (uint16_t i_theta = 0; i_theta < m_Sinogram->N_theta; i_theta++)
{
for (uint16_t i_r = 0; i_r < m_Sinogram->N_r; i_r++)
{
for (uint16_t i_t = 0; i_t < m_Sinogram->N_t; i_t++)
{
temp_final = m_Sinogram->counts->getValue(i_theta, i_r, i_t) - errorSino->getValue(i_theta, i_r, i_t);
finalSinogram->setValue(temp_final, i_theta, i_r, i_t);
}
}
}
// This is writing the "ReconstructedSinogram.bin" file
m_ForwardModel->writeSinogramFile(m_Sinogram, finalSinogram); // Writes the sinogram to a file
if (getCancel() == true) { setErrorCondition(-999); return; }
// Writes ReconstructedObject.bin file for next resolution
{
std::stringstream ss;
ss << m_TomoInputs->tempDir << MXADir::getSeparator() << MBIR::Defaults::ReconstructedObjectFile;
writeReconstructionFile(ss.str());
}
// Write out the VTK file
if (m_TomoInputs->vtkOutputFile.empty() == false)
{
writeVtkFile(m_TomoInputs->vtkOutputFile, cropStart, cropEnd);
}
// Write out the MRC File
if (m_TomoInputs->mrcOutputFile.empty() == false)
{
writeMRCFile(m_TomoInputs->mrcOutputFile, cropStart, cropEnd);
}
//Write out avizo fire file
if (m_TomoInputs->avizoOutputFile.empty() == false)
{
writeAvizoFile(m_TomoInputs->avizoOutputFile, cropStart, cropEnd);
}
//Debug : Writing out the selector array as an MRC file
m_ForwardModel->writeSelectorMrc(m_TomoInputs->braggSelectorFile, m_Sinogram, m_Geometry, errorSino);
if (getVerbose())
{
std::cout << "Final Dimensions of Object: " << std::endl;
std::cout << " Nx = " << m_Geometry->N_x << std::endl;
std::cout << " Ny = " << m_Geometry->N_y << std::endl;
std::cout << " Nz = " << m_Geometry->N_z << std::endl;
#ifdef NHICD
std::cout << "Number of equivalet iterations taken =" << EffIterCount / MBIR::Constants::k_NumNonHomogeniousIter << std::endl;
#else
std::cout << "Number of equivalet iterations taken =" << EffIterCount / MBIR::Constants::k_NumHomogeniousIter << std::endl;
#endif //NHICD
}
notify("Reconstruction Complete", 100, Observable::UpdateProgressValueAndMessage);
setErrorCondition(0);
if (getVerbose()) {std::cout << "Total Running Time for Execute: " << (EIMTOMO_getMilliSeconds() - totalTime) / 1000 << std::endl;}
return;
}
int main(int argc, char* argv[] )
{
srand(time(NULL));
int verbose = 0;
char outputFile[256];
int doOutput = getWriteToFile( argc, argv, outputFile, 256);
if (argc == 1)
{
showUsageAndExit();
}
moleculizer* pMoleculizer = createNewMoleculizerObject();
setRateExtrapolation( pMoleculizer, 1 );
int result = loadModelFile( pMoleculizer, argc, argv);
switch(result)
{
case 0:
printf("Model loaded successfully.\n");
break;
case 1:
printf("Unknown error on load. Aborting\n");
return 1;
case 2:
printf("Document unparsable. Aborting.\n");
return 1;
case 3:
printf("Moleculizer has already loaded rules. Ignoring and continuing.\n");
return 1;
}
int numIter = getNumberOfIterations(argc, argv);
int maxSpecies = getMaxNumSpecies( argc, argv);
int maxRxns = getMaxNumReactions( argc, argv);
if (numIter > 0 && (maxSpecies > 0 || maxRxns > 0) )
{
// ANCHOR
printf("Error, if either (max species and/or max rxns) can be set or numIters. ");
showUsageAndExit();
}
verbose = getVerbose(argc, argv);
if(numIter == -1 )
{
int numRxns;
int numSpec;
species** speciesArray;
reaction** rxnArray;
int errorCode = \
getBoundedNetwork( pMoleculizer, maxSpecies, maxRxns, &speciesArray, &numSpec, &rxnArray, &numRxns );
if (errorCode)
{
printf("Unknown erorr. Check error messages for description. Exiting...\n");
exit(1);
}
else
{
numIter = 10;
printf("Network generated to %d species and %d reactions.\n", numSpec, numRxns);
}
}
else
{
int iter = 0;
for( iter = 0; iter != numIter; ++iter)
{
species** theSpecies;
int numSpecies = 0;
getAllExteriorSpecies( pMoleculizer, &theSpecies, &numSpecies);
if (numSpecies == 0)
{
printf("Entire network has been generated on the %dth iteration.\n", iter);
freeSpeciesArray( theSpecies, numSpecies);
break;
}
/* Get a random number in the range [0, numSpecies) */
int speciesNumber = rand() % numSpecies;
printf("Iteration %d: Expanding %s\n", iter + 1, theSpecies[speciesNumber]->name);
incrementSpecies( pMoleculizer, theSpecies[speciesNumber]->name);
freeSpeciesArray( theSpecies, numSpecies);
}
}
if (numIter == -1)
{
printf("Expanded entire network.\n");
}
else
{
printf("Expanded %d iterations.", numIter);
}
printf("\n##########################################\n");
printf("There are %d species and %d reactions.\n",
getNumberOfSpecies(pMoleculizer),
getNumberOfReactions(pMoleculizer) );
if ( verbose )
{
showAllSpecies( pMoleculizer );
showAllReactions( pMoleculizer);
}
if (doOutput)
{
writeDotFile(pMoleculizer, outputFile);
}
freeMoleculizerObject( pMoleculizer );
return 0;
}