void RtDataStore::setAvailableData(RtDataID dataID) {
// remove timepoint if one is set
if(dataID.getTimePoint() != DATAID_NUM_UNSET_VALUE) {
dataID.setTimePoint(DATAID_NUM_WILDCARD_VALUE);
}
// put data id into available data (insert will only add a unique value)
// TODO will a position iterator add any efficiency here?
availableData.insert(dataID);
}
// process a single acquisition
int RtDataViewer::process(ACE_Message_Block *mb) {
ACE_TRACE(("RtDataViewer::process"));
RtStreamMessage *msg = (RtStreamMessage*) mb->rd_ptr();
// get the current time
unsigned int time = msg->getCurrentData()->getDataID().getTimePoint();
// debug
getDataStore().getAvailableData();
RtDataID id;
// find all data requested
for(vector<string>::iterator i = dataIds.begin(); i != dataIds.end(); i++) {
id.setFromString(*i);
if(id.getTimePoint() != DATAID_NUM_UNSET_VALUE
&& id.getTimePoint() != DATAID_NUM_WILDCARD_VALUE) {
id.setTimePoint(time);
}
cout << "RtDataViewer::process: searching for " << id
<< " from " << *i << endl;
// find the data with the right ID
RtData *dat = getDataStore().getData(id);
if(dat == NULL) {
cout << "RtDataViewer::process: could not find " << id << endl;
if(logOutput) {
stringstream logs("");
logs << "RtDataViewer::process: could not find " << id << endl;
log(logs);
}
}
else {
cout << "RtDataViewer::process: found " << dat->getDataID() << endl;
if(logOutput) {
stringstream logs("");
logs << "RtDataViewer::process: found "
<< dat->getDataID() << endl;
log(logs);
}
}
}
return 0;
}
// hand off some data to be output
void RtDataStore::setData(RtData *data) {
mut.acquire();
// special check for processing done
if(data->getDataID().getModuleID() == "end-task") {
// update value of latestTR
if (data->getDataID().getTimePoint() != DATAID_NUM_UNSET_VALUE &&
data->getDataID().getTimePoint() != DATAID_NUM_WILDCARD_VALUE) {
latestTR = data->getDataID().getTimePoint();
}
mut.release();
return;
}
// don't allow wildcards on insertion
RtDataID insert = data->getDataID();
if(insert.hasWildcards()) {
insert.eliminateWildcards();
}
// put data into datastore with its dataID as the key
store[data->getDataID()] = data;
// add to availableData (needs a hard copy of the dataID)
setAvailableData(data->getDataID());
mut.release();
//debug
// set<RtDataID>::const_iterator it = getAvailableData();
//endebug
// notify listeners
for(vector<RtDataListener*>::iterator i = notifyList.begin();
i != notifyList.end(); i++) {
(*i)->notify(data->getDataID());
}
}
// 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;
}
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();
}
}
// get data by id
//
// NOTE: this function is much more efficient if the requested data is
// specified fully, i.e. there are no wildcards in the dataID (see RtDataID.h)
// avoid using wildcards if possible
RtData *RtDataStore::getData(RtDataID dataID) {
// fill in wildcards (search through available data makes this inefficient)
if(dataID.hasWildcards()) {
// find corresponding full id by an exhaustive search through available
// data
for(set<RtDataID>::const_iterator id = availableData.begin();
id != availableData.end(); id++) {
RtDataID avail = (*id);
// handle potential timepoint-less data
unsigned int tp = avail.getTimePoint();
if(dataID.getTimePoint() != DATAID_NUM_UNSET_VALUE) {
avail.setTimePoint(DATAID_NUM_WILDCARD_VALUE);
}
else {
avail.setTimePoint(DATAID_NUM_UNSET_VALUE);
}
if (avail == dataID) { // == respects wildcards
// copy, preserving timepoint if not a timepointless datum
unsigned int origTp = dataID.getTimePoint();
dataID = avail;
if(tp != DATAID_NUM_UNSET_VALUE) {
dataID.setTimePoint(origTp);
}
else {
dataID.setTimePoint(tp);
}
break;
}
}
// finally, handle wildcard in timepoint field by using the latest timepoint
if (dataID.getTimePoint() == DATAID_NUM_WILDCARD_VALUE) {
dataID.setTimePoint(latestTR);
}
if(dataID.hasWildcards()) {
cerr << "filling in wildcards failed. no match found." << endl;
return NULL;
}
}
// iterator for map
map<RtDataID,RtData*,RtDataIDCompare>::const_iterator it;
mut.acquire();
it = store.find(dataID);
// if not found
if(it == store.end()) {
mut.release();
return NULL;
}
mut.release();
return (*it).second;
}
void MainWindow::notify(const RtDataID &id) {
ui->imageWidget->handleData(id);
emit dataReady(QString(id.toString().c_str()));
}