// process a single acquisition
int RtRoiDifference::process(ACE_Message_Block *mb) {
ACE_TRACE(("RtRoiDifference::process"));
RtStreamMessage *msg = (RtStreamMessage*) mb->rd_ptr();
cout << "PROCESSING " << endl;
// find the data with the right data IDs
RtActivation *posact
= (RtActivation*) msg->getData(posRoiModuleID,
posRoiDataName,
posRoiRoiID);
RtActivation *negact
= (RtActivation*) msg->getData(negRoiModuleID,
negRoiDataName,
negRoiRoiID);
double p = 0;
if(posact != NULL) {
p = posact->getPixel(0);
}
double n = 0;
if(negact != NULL) {
n = negact->getPixel(0);
}
// create a one element activation image
RtActivation *diff = new RtActivation(1);
// setup the data id
diff->getDataID().setFromInputData(*posact,*this);
diff->getDataID().setDataName(NAME_ROIDIFF);
diff->getDataID().setRoiID(posRoiRoiID + "-" + negRoiRoiID);
// compute the difference
diff->setPixel(0, p - n);
setResult(msg, diff);
return 0;
}
void PlotController::handleData(QString qid) {
RtDataID id;
id.setFromString(qid.toStdString());
if (id.getDataName() == NAME_DESIGN) {
baseline_box->topLeft->setCoords(0, 10);
baseline_box->bottomRight->setCoords(getNumDataPointsForErrEst(), -10);
RtDesignMatrix *design =
static_cast<RtDesignMatrix*>(getDataStore().getData(id));
updateTRIndicators();
plotDesign(design);
roi_plot->xAxis->setRange(0, design->getNumRows());
roi_plot->replot();
motion_plot->xAxis->setRange(0, design->getNumRows());
motion_plot->replot();
}
else if (id.getModuleID() == ID_ROICOMBINE) {
map<string, int>::const_iterator it = roi_graphs.find(id.getRoiID());
if (it == roi_graphs.end()) {
it = roi_graphs.insert(
pair<string, int>(id.getRoiID(), roi_plot->graphCount())).first;
roi_plot->addGraph();
roi_plot->graph(it->second)->setPen(QPen(roi_colormap.getColorForName(
id.getRoiID())));
roi_plot->graph(it->second)->setName(QString(id.getRoiID().c_str()));
roi_plot->legend->setVisible(true);
}
RtActivation *val = static_cast<RtActivation*>(getDataStore().getData(id));
roi_plot->graph(roi_graphs[id.getRoiID()])->addData(id.getTimePoint(),
val->getPixel(0));
roi_plot->replot();
}
else if (id.getModuleID() == ID_MOTION) {
plotMotion(static_cast<RtMotion*>(getDataStore().getData(id)));
}
if (id.getTimePoint() != DATAID_NUM_UNSET_VALUE &&
id.getTimePoint() > current_tr) {
current_tr = id.getTimePoint();
updateTRIndicators();
}
}
// process a single acquisition
int RtCurrentActivation::process(ACE_Message_Block *mb) {
ACE_TRACE(("RtCurrentActivation::process"));
timer tim;
if(printTiming) {
tim.start();
}
// get pointer to message
RtStreamMessage *msg = (RtStreamMessage*) mb->rd_ptr();
// get the current image to operate on
RtMRIImage *dat = (RtMRIImage*) msg->getCurrentData();
// check for validity of data
if (dat == NULL) {
cerr << "RtCurrentActivation::process: data passed is NULL" << endl;
if(logOutput) {
stringstream logs("");
logs << "RtCurrentActivation::process: data passed is NULL" << endl;
log(logs);
}
return 0;
}
// get mask from msg
RtMaskImage *mask = getMaskFromMessage(*msg);
// check validity of mask
if (mask == NULL) {
cerr << "RtCurrentActivation::process: mask is NULL" << endl;
if(logOutput) {
stringstream logs("");
logs << "RtCurrentActivation::process: mask is NULL at tr "
<< dat->getDataID().getTimePoint() << endl;
log(logs);
}
return 0;
}
// initialize the computation if necessary
if (needsInit) {
initEstimation(*dat, mask);
}
// get design
// TODO this may not work if there are more than one design matrix
RtDataID tempDataID;
tempDataID.setDataName(NAME_DESIGN);
// debug
// getDataStore().getAvailableData();
RtDesignMatrix *design = static_cast<RtDesignMatrix*>(
getDataStore().getData(tempDataID));
if(design == NULL) {
cerr << "error: could not find design matrix in datastore!" << endl;
cerr << "searched for design matrix id: " << tempDataID << endl;
return 0;
}
// allocate a new data image for the stats
RtActivation *currentActivation = new RtActivation(*dat);
// setup the data id
currentActivation->getDataID().setFromInputData(*dat, *this);
currentActivation->getDataID().setDataName(NAME_ACTIVATION);
currentActivation->getDataID().setRoiID(modelFitRoiID);
currentActivation->initToNans();
// get the residual and the beta images for discounting nuissance
// signals
// find the betas
RtActivation **betas = new RtActivation*[design->getNumColumns()];
for(unsigned int j = 0; j < design->getNumColumns(); j++) {
betas[j] = (RtActivation*) msg->getData(modelFitModuleID,
string(NAME_BETA)
+ "_" +
design->getColumnName(j),
modelFitRoiID);
// check for found
if (betas[j] == NULL) {
cerr << "RtCurrentActivation:process: beta " << j << " is null" << endl;
if(logOutput) {
stringstream logs("");
logs << "RtCurrentActivation::process: beta " << j
<< " is NULL at tr "
<< dat->getDataID().getTimePoint() << endl;
log(logs);
}
return 0;
}
}
// get residual from message if timepoint is less than
// numDataPointsForErrEst otherwise use the steady state
// residual value
RtActivation *residual;
if (dat->getDataID().getTimePoint() < numDataPointsForErrEst) {
// get residual off of msg
residual = (RtActivation *) msg->getData(modelFitModuleID,
NAME_RESIDUAL_MSE,
modelFitRoiID);
// save off residual
steadyStateResidual = residual;
}
else {
// post-numDataPointsForErrEst, use saved residual
residual = steadyStateResidual;
}
// check that residual is not null
if (residual == NULL) {
cerr << "RtCurrentActivation:process: residual is null" << endl;
if(logOutput) {
stringstream logs("");
logs << "RtCurrentActivation::process: residual is NULL at tr "
<< dat->getDataID().getTimePoint() << endl;
log(logs);
}
return 0;
}
// get this design matrix row
vnl_vector<double> Xrow = design->getRow(dat->getDataID().getTimePoint()-1);
// include this timepoint for each voxel
RtElementAccess datAc(dat, mask);
RtElementAccess resAc(residual, mask);
vector<unsigned int> inds = datAc.getElementIndices();
for(vector<unsigned int>::iterator it = inds.begin();
it != inds.end(); it++) {
// get voxel intensity
double y = datAc.getDoubleElement(*it);
double *betavals = new double[Xrow.size()];
// compute error
double err = y;
for (unsigned int j = 0; j < Xrow.size(); j++) {
if (!design->isColumnOfInterest(j)) {
double beta = betas[j]->getPixel(*it);
err -= beta * Xrow[j];
betavals[j] = beta;
}
else { // for debug output
betavals[j] = betas[j]->getPixel(*it);
}
}
// compute the dev and current activation (magic happens here)
double dev = sqrt(resAc.getDoubleElement(*it)
/ (residual->getDataID().getTimePoint()));
currentActivation->setPixel(*it, err / dev);
if (dumpAlgoVars && dat->getDataID().getTimePoint() > 2) {
dumpFile
<< dat->getDataID().getTimePoint() << " "
<< *it << " "
<< y << " "
<< err << " "
<< Xrow[0] << " "
<< residual->getPixel(*it) << " "
<< dev << " "
<< currentActivation->getPixel(*it) << " ";
for (unsigned int b = 0; b < design->getNumColumns(); b++) {
dumpFile << betavals[b] << " ";
}
dumpFile << endl;
}
delete [] betavals;
}
setResult(msg, currentActivation);
setResult(msg, residual);
delete [] betas;
if(printTiming) {
tim.stop();
cout << "RtCurrentActivation process at tr "
<< dat->getDataID().getTimePoint()
<< " elapsed time: " << tim.elapsed_time()*1000 << "ms" << endl;
}
if(print) {
cout << "RtCurrentActivation: done at tr "
<< dat->getDataID().getTimePoint() << endl;
}
if(logOutput) {
stringstream logs("");
logs << "RtCurrentActivation: done at tr "
<< dat->getDataID().getTimePoint() << endl;
log(logs);
}
if(saveResult) {
string fn = getExperimentConfig().getVolFilename(
dat->getDataID().getSeriesNum(),
dat->getDataID().getTimePoint());
string stem = getExperimentConfig().get("study:volumeFileStem").str();
currentActivation->setFilename(fn.replace(fn.rfind(stem), stem.size(),
"curact"));
currentActivation->save();
}
return 0;
}
// process a single acquisition
int RtSingleImageCor::process(ACE_Message_Block *mb) {
ACE_TRACE(("RtSingleImageCor::process"));
RtStreamMessage *msg = (RtStreamMessage*) mb->rd_ptr();
// get the current image to operate on
RtMRIImage *dat = (RtMRIImage*) msg->getCurrentData();
if (dat == NULL) {
cout << "RtSingleImageCor::process: data passed is NULL" << endl;
ACE_DEBUG((LM_INFO, "RtSingleImageCor:process: data passed is NULL\n"));
return 0;
}
RtMaskImage *mask = getMaskFromMessage(*msg);
numTimepoints++;
// initialize the computation if necessary
if (needsInit) {
initEstimation(*dat, mask);
}
// allocate a new data images for the stats
RtActivation *stat = new RtActivation(*dat);
// setup the data id
stat->getDataID().setFromInputData(*dat, *this);
stat->getDataID().setDataName(NAME_ACTIVATION);
stat->getDataID().setRoiID(mask->getDataID().getRoiID());
stat->initToZeros();
// residual sum of squares map
RtActivation *res = new RtActivation(*dat);
// setup the data id
res->getDataID().setFromInputData(*dat, *this);
res->getDataID().setDataName(NAME_RESIDUAL_MSE);
res->getDataID().setRoiID(mask->getDataID().getRoiID());
res->initToZeros();
//// element independent setup
/// build a design matrix row
vnl_vector<double> Xrow = design.getRow(dat->getDataID().getTimePoint());
bool anyOverZero = false;
for (unsigned int i = 0; i < design.getNumColumns(); i++) {
// check for on condition for any stimulus
if (design.isColumnOfInterest(i)
&& Xrow[i] > std::numeric_limits<double>::epsilon()) {
anyOverZero = true;
break;
}
}
if (DEBUG_LEVEL & MODERATE) {
cout << " xrow " << numTimepoints << ":";
for (unsigned int i = 0; i < Xrow.size(); i++) {
cout << Xrow[i] << " ";
}
cout << endl;
}
// check if we should include this timepoint in variance computation
bool includeInErr;
if ((numTimepoints > numDataPointsForErrEst)
|| (onlyEstErrInBaseline && anyOverZero)) {
includeInErr = false;
}
else {
includeInErr = true;
numDataPointsCount++;
}
//// compute t map for each element
RtElementAccess elAc(dat, mask);
vector<unsigned int> indices = elAc.getElementIndices();
unsigned int curSolver = 0;
for (vector<unsigned int>::iterator i = indices.begin(); i != indices.end();
i++, curSolver++) {
if (!mask->getPixel(*i)) {
stat->setPixel(*i, numeric_limits<double>::quiet_NaN()); // assign nan
res->setPixel(*i, numeric_limits<double>::quiet_NaN()); // assign nan
continue;
}
// include this timepoint in the solver for this voxel
double y = dat->getElement(*i);
solvers[curSolver]->include(&y, Xrow.data_block(), 1.0);
// get stats and residual
double *beta = solvers[curSolver]->regress(0);
// note that residual is always the standard L2 version, despite which
// norm we are using for the stat scaling
res->setPixel(*i, sqrt(solvers[curSolver]->getTotalSquaredError(0)
/ (numTimepoints - 1)));
// compute stat
double err = y;
double meanCondActivity = 0;
for (unsigned int j = 0; j < Xrow.size(); j++) {
if (!design.isColumnOfInterest(j)) {
err -= beta[j] * Xrow[j];
}
else {
meanCondActivity += beta[j] * Xrow[j];
}
}
if (DEBUG_LEVEL & ADVANCED) {
static double lastErr = 0;
cerr << *i << ": err is " << err << " ?= "
<< sqrt(solvers[curSolver]->getTotalSquaredError(0)) - lastErr
<< endl;
lastErr = sqrt(solvers[curSolver]->getTotalSquaredError(0));
}
// update the error in the estimate for the voxel
// get estimation error and compute the standard deviation based on
// the error sum and current error norm and include the error in the
// estimate if desired
double dev;
switch (errorNorm) {
case L1:
if (includeInErr) {
estErrSum->setPixel(*i, estErrSum->getPixel(*i) + fabs(err));
}
dev = estErrSum->getPixel(*i) / (numDataPointsCount - 1);
break;
case L2:
default:
if (includeInErr) {
estErrSum->setPixel(*i, estErrSum->getPixel(*i) + err * err);
}
dev = sqrt(estErrSum->getPixel(*i) / (numDataPointsCount - 1));
break;
case LINF:
if (includeInErr) {
estErrSum->setPixel(*i, std::max(estErrSum->getPixel(*i), fabs(err)));
}
dev = estErrSum->getPixel(*i);
break;
}
if (DEBUG_LEVEL & ADVANCED) {
cerr << dev << " ?= "
<< sqrt(solvers[curSolver]->getTotalSquaredError(0)
/ (numTimepoints - 1))
<< endl;
}
// compute the sds away from the mean (magic kinda happens here)
if (includeConditionMean) {
stat->setPixel(*i, (meanCondActivity + err) / dev);
}
else {
stat->setPixel(*i, (meanCondActivity) + (err / dev));
}
if (DEBUG_LEVEL & ADVANCED) {
cerr
<< numTimepoints << " "
<< *i << " "
<< y << " "
<< err + meanCondActivity << " "
<< err << " "
<< dev << " "
<< stat->getPixel(*i) << " " << endl;
}
if (DEBUG_LEVEL & MODERATE) {
cerr << err << "/" << dev << "=" << stat->getPixel(*i) << endl;
}
if (numTimepoints > 2) {
dumpFile
<< numTimepoints << " "
<< *i << " "
<< y << " "
<< err + meanCondActivity << " "
<< Xrow[0] << " "
<< err << " "
<< dev << " "
<< stat->getPixel(*i) << " ";
for (unsigned int b = 0; b < design.getNumColumns(); b++) {
dumpFile << beta[b] << " ";
}
dumpFile << endl;
}
delete beta;
}
if (DEBUG_LEVEL & BASIC) {
cout << "done processing single image correlation at ";
printNow(cout);
cout << endl;
}
// set the results
setResult(msg, stat);
setResult(msg, res);
return 0;
}