double MahalanobisDistance::operator()(const Peak& A, const Peak& B, double drt, double dmz, double dz=0., double dint=0.)
{
if(drt <= 0 || dmz <= 0){
MSPP_LOG(logERROR) << "MahalanobisDistance::operator(): drt and dmz have to be positive." << std::endl;
}
mspp_precondition(drt > 0. && dmz > 0. , "MahalanobisDistance::operator(): drt and dmz have to be positive.");
if(A.getAbundance() < dint || B.getAbundance() < dint){
// low abundance peak --> high distance
return DBL_MAX;
}
if(dz == 0.){
// only calculate distance if peaks have same charge
if(A.getCharge() != B.getCharge()){
// charge differs and dz == 0: max. distance
return DBL_MAX;
}else{
// charge equal: normal distance
double rt = (A.getRt()-B.getRt());
double mz = (A.getMz()-B.getMz());
return sqrt(rt*rt/(drt*drt) + mz*mz/(dmz*dmz));
}
}else{
// return normal distance
double rt = (A.getRt()-B.getRt());
double mz = (A.getMz()-B.getMz());
double z = A.getCharge() - B.getCharge();
return sqrt(rt*rt/(drt*drt) + mz*mz/(dmz*dmz) + z*z/(dz*dz));
}
}
/**
* Returns selected information for a "peak" at QLabFrame.
*
* @param qFrame An arbitrary position in Q-space. This does not have to
*be the
* position of a peak.
* @param labCoords Set true if the position is in the lab coordinate system,
*false if
* it is in the sample coordinate system.
* @return a vector whose elements contain different information about the
*"peak" at that position.
* each element is a pair of description of information and the string
*form for the corresponding
* value.
*/
int PeaksWorkspace::peakInfoNumber(Kernel::V3D qFrame, bool labCoords) const {
std::vector<std::pair<std::string, std::string>> Result;
std::ostringstream oss;
oss << std::setw(12) << std::fixed << std::setprecision(3) << (qFrame.norm());
std::pair<std::string, std::string> QMag("|Q|", oss.str());
Result.push_back(QMag);
oss.str("");
oss.clear();
oss << std::setw(12) << std::fixed << std::setprecision(3)
<< (2.0 * M_PI / qFrame.norm());
std::pair<std::string, std::string> dspc("d-spacing", oss.str());
oss.str("");
oss.clear();
Result.push_back(dspc);
int seqNum = -1;
double minDist = 10000000;
for (int i = 0; i < getNumberPeaks(); i++) {
Peak pk = getPeak(i);
V3D Q = pk.getQLabFrame();
if (!labCoords)
Q = pk.getQSampleFrame();
double D = qFrame.distance(Q);
if (D < minDist) {
minDist = D;
seqNum = i + 1;
}
}
return seqNum;
}
TEST(Peak, Peak2D) {
vector<vector<int> > A = {
{10, 8, 10, 10},
{14, 13, 12, 11},
{15, 9, 11, 21},
{16, 17, 19, 20}
};
Peak peak;
pair<int, int> p = peak.find2d(A);
int dr[] = {-1, 0, 1, 0};
int dc[] = {0, 1, 0, -1};
int n = A.size();
int m = A[0].size();
bool test = true;
for (int i = 0; i < 4; i++) {
int r = p.first + dr[i];
int c = p.second + dc[i];
if (r >= 0 && r < n && c >= 0 && c < m) {
test &= A[p.first][p.second] >= A[r][c];
}
}
EXPECT_TRUE(test);
}
TEST(Peak, Peak1D) {
vector<int> A = {1, 2, 3, 5, 0, 3, 1, 3, 8, 9};
Peak peak;
int n = A.size();
int i = peak.find1d(A);
EXPECT_TRUE((i == 0 && A[i] >= A[1]) ||
(i == n - 1 && A[i-1] <= A[i]) ||
(A[i-1] <= A[i] && A[i] >= A[i+1]));
}
int LuaPeak::setLabel(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const char* str = "";
if( lua_gettop(L) > 1 )
str = luaL_checkstring( L, 2 );
obj->getOwner()->setTag( obj, str );
return 0;
}
int LuaPeak::getAssig(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const Peak::Assig& a = obj->getAssig();
{
for( int i = 0; i < obj->getDimCount(); i++ )
lua_pushnumber( L, a[ i ] );
}
return obj->getDimCount();
}
int LuaPeak::getAmp(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
Spectrum* spec = 0;
if( lua_gettop( L ) > 1 )
{
spec = RefBinding<Spectrum>::cast( L, 2 );
}
lua_pushnumber(L, obj->getAmp( spec ) );
return 1;
}
int LuaPeak::setAssig(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const int n = lua_gettop(L); /* number of arguments */
if( n != ( obj->getDimCount() + 1 ) )
luaL_error( L, "Expecting %d arguments", int( obj->getDimCount() + 1 ) );
Peak::Assig a;
for( int i = 2; i <= n; i++ )
a[ i-1 ] = luaL_checknumber( L, i ); // TEST
obj->getOwner()->setAssig( obj, a );
return 0;
}
int LuaPeak::getPos(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
Spectrum* spec = 0;
if( lua_gettop( L ) > 1 )
{
spec = RefBinding<Spectrum>::cast( L, 2 );
}
const PeakPos& a = obj->getPos( spec );
for( int i = 0; i < obj->getDimCount(); i++ )
lua_pushnumber( L, a[ i ] );
return obj->getDimCount();
}
int LuaPeak::getModel(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
int n = lua_gettop(L); /* number of arguments */
Spectrum* spec = 0;
if( n > 1 )
{
spec = RefBinding<Spectrum>::cast( L, 2 );
}
PeakModel* m = obj->getModel( spec );
RefBinding<PeakModel>::create( L, m );
return 1;
}
int LuaPeak::setModel(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const int n = lua_gettop(L); /* number of arguments */
int id = 0;
if( n > 1 )
id = luaL_checknumber( L, 2 );
Spectrum* spec = 0;
if( n > 2 )
{
spec = RefBinding<Spectrum>::cast( L, 3 );
}
obj->getOwner()->setModel( obj, id, spec );
return 0;
}
int LuaPeak::setAmp(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
int n = lua_gettop(L); /* number of arguments */
Amplitude a = 0;
if( n > 1 )
a = luaL_checknumber( L, 2 );
Spectrum* spec = 0;
if( n > 2 )
{
spec = RefBinding<Spectrum>::cast( L, 3 );
}
obj->getOwner()->setAmp( obj, a, spec );
return 0;
}
int LuaPeak::getGuesses(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const Peak::GuessMap& sm = obj->getGuesses();
Peak::GuessMap::const_iterator i;
lua_newtable( L );
int t = lua_gettop( L );
for( i = sm.begin(); i != sm.end(); ++i )
{
lua_pushnumber( L, (*i).first );
RefBinding<Peak::Guess>::create( L, (*i).second.deref() );
lua_rawset( L, t );
}
return 1;
}
int LuaPeak::setPos(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
const int n = lua_gettop(L); /* number of arguments */
const int dim = obj->getDimCount();
if( n < dim + 1 )
luaL_error( L, "Expecting at least %d arguments", dim );
PpmPoint a;
for( int i = 1; i <= dim; i++ )
a.push_back( luaL_checknumber( L, i + 1 ) );
Spectrum* spec = 0;
if( n > ( dim + 1 ) )
{
spec = RefBinding<Spectrum>::cast( L, n );
}
obj->getOwner()->setPos( obj, a, spec );
return 0;
}
void loop_start(float * newSpec) {
memcpy(this_spectrum, newSpec, sizeof(float) * FREQUENCY_LENGTH);
current = NO_PEAK;
for (int i = 0; i < FREQUENCY_LENGTH; ++i) {
current.update(i, this_spectrum[i]);
}
this_attr.sum = sum_over(Range::around(current));
this_attr.sdev = sdev_over();
this_attr.sdratio = sdev_except( FULL_RANGE, Range::around(current)) / this_attr.sdev;
}
int LuaPeak::setGuess(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
int n = lua_gettop(L); /* number of arguments */
Peak::Guess* g = RefBinding<Peak::Guess>::check( L, 2 );
float f = 0.0;
Peak::Assig a;
if( n > 2 )
{
f = luaL_checknumber( L, 3 );
if( f < 0.0 || f > 1.0 )
luaL_error( L, "Invalid probability value" );
const int off = 4;
for( int i = off; i <= n; i++ )
{
if( i - off >= Peak::Assig::MAX_DIM )
luaL_error( L, "Invalid number of dimensions" );
a[ i - off ] = luaL_checknumber( L, i );
}
}
obj->getOwner()->setGuess( obj, g->getId(), a, f );
return 0;
}
/** Compare two peaks using the stored criteria */
inline bool operator()(const Peak& a, const Peak& b)
{
for (size_t i = 0; i < criteria.size(); i++)
{
std::string & col = criteria[i].first;
bool ascending = criteria[i].second;
bool lessThan = false;
if (col == "BankName")
{
// If this criterion is equal, move on to the next one
std::string valA = a.getBankName();
std::string valB = b.getBankName();
// Move on to lesser criterion if equal
if (valA == valB)
continue;
lessThan = (valA < valB);
}
else
{
// General double comparison
double valA = a.getValueByColName(col);
double valB = b.getValueByColName(col);
// Move on to lesser criterion if equal
if (valA == valB)
continue;
lessThan = (valA < valB);
}
// Flip the sign of comparison if descending.
if (ascending)
return lessThan;
else
return !lessThan;
}
// If you reach here, all criteria were ==; so not <, so return false
return false;
}
bool FindUBUsingIndexedPeaks::isPeakIndexed(Peak &peak) {
V3D hkl(peak.getIntHKL()); // ##### KEEP
V3D mnp(peak.getIntMNP());
return (IndexingUtils::ValidIndex(hkl, 1.0) ||
IndexingUtils::ValidIndex(mnp, 1.0));
}
void FindPeaksMD::findPeaks(typename MDEventWorkspace<MDE, nd>::sptr ws)
{
if (nd < 3)
throw std::invalid_argument("Workspace must have at least 3 dimensions.");
progress(0.01, "Refreshing Centroids");
// TODO: This might be slow, progress report?
// Make sure all centroids are fresh
ws->getBox()->refreshCentroid();
typedef IMDBox<MDE,nd>* boxPtr;
if (ws->getNumExperimentInfo() == 0)
throw std::runtime_error("No instrument was found in the MDEventWorkspace. Cannot find peaks.");
// TODO: Do we need to pick a different instrument info?
ExperimentInfo_sptr ei = ws->getExperimentInfo(0);
// Instrument associated with workspace
Geometry::Instrument_const_sptr inst = ei->getInstrument();
// Find the run number
int runNumber = ei->getRunNumber();
// Check that the workspace dimensions are in Q-sample-frame or Q-lab-frame.
eDimensionType dimType;
std::string dim0 = ws->getDimension(0)->getName();
if (dim0 == "H")
{
dimType = HKL;
throw std::runtime_error("Cannot find peaks in a workspace that is already in HKL space.");
}
else if (dim0 == "Q_lab_x")
{
dimType = QLAB;
}
else if (dim0 == "Q_sample_x")
dimType = QSAMPLE;
else
throw std::runtime_error("Unexpected dimensions: need either Q_lab_x or Q_sample_x.");
// Find the goniometer rotation matrix
Mantid::Kernel::Matrix<double> goniometer(3,3, true); // Default IDENTITY matrix
try
{
goniometer = ei->mutableRun().getGoniometerMatrix();
}
catch (std::exception & e)
{
g_log.warning() << "Error finding goniometer matrix. It will not be set in the peaks found." << std::endl;
g_log.warning() << e.what() << std::endl;
}
/// Arbitrary scaling factor for density to make more manageable numbers, especially for older file formats.
signal_t densityScalingFactor = 1e-6;
// Calculate a threshold below which a box is too diffuse to be considered a peak.
signal_t thresholdDensity = 0.0;
thresholdDensity = ws->getBox()->getSignalNormalized() * DensityThresholdFactor * densityScalingFactor;
g_log.notice() << "Threshold signal density: " << thresholdDensity << std::endl;
// We will fill this vector with pointers to all the boxes (up to a given depth)
typename std::vector<boxPtr> boxes;
// Get all the MDboxes
progress(0.10, "Getting Boxes");
ws->getBox()->getBoxes(boxes, 1000, true);
// TODO: Here keep only the boxes > e.g. 3 * mean.
typedef std::pair<double, boxPtr> dens_box;
// Map that will sort the boxes by increasing density. The key = density; value = box *.
typename std::multimap<double, boxPtr> sortedBoxes;
progress(0.20, "Sorting Boxes by Density");
typename std::vector<boxPtr>::iterator it1;
typename std::vector<boxPtr>::iterator it1_end = boxes.end();
for (it1 = boxes.begin(); it1 != it1_end; it1++)
{
boxPtr box = *it1;
double density = box->getSignalNormalized() * densityScalingFactor;
// Skip any boxes with too small a signal density.
if (density > thresholdDensity)
sortedBoxes.insert(dens_box(density,box));
}
// List of chosen possible peak boxes.
std::vector<boxPtr> peakBoxes;
prog = new Progress(this, 0.30, 0.95, MaxPeaks);
int64_t numBoxesFound = 0;
// Now we go (backwards) through the map
// e.g. from highest density down to lowest density.
typename std::multimap<double, boxPtr>::reverse_iterator it2;
typename std::multimap<double, boxPtr>::reverse_iterator it2_end = sortedBoxes.rend();
for (it2 = sortedBoxes.rbegin(); it2 != it2_end; it2++)
{
signal_t density = it2->first;
boxPtr box = it2->second;
#ifndef MDBOX_TRACK_CENTROID
coord_t boxCenter[nd];
box->calculateCentroid(boxCenter);
#else
const coord_t * boxCenter = box->getCentroid();
#endif
// Compare to all boxes already picked.
bool badBox = false;
for (typename std::vector<boxPtr>::iterator it3=peakBoxes.begin(); it3 != peakBoxes.end(); it3++)
{
#ifndef MDBOX_TRACK_CENTROID
coord_t otherCenter[nd];
(*it3)->calculateCentroid(otherCenter);
#else
const coord_t * otherCenter = (*it3)->getCentroid();
#endif
// Distance between this box and a box we already put in.
coord_t distSquared = 0.0;
for (size_t d=0; d<nd; d++)
{
coord_t dist = otherCenter[d] - boxCenter[d];
distSquared += (dist * dist);
}
// Reject this box if it is too close to another previously found box.
if (distSquared < peakRadiusSquared)
{
badBox = true;
break;
}
}
// The box was not rejected for another reason.
if (!badBox)
{
if (numBoxesFound++ >= MaxPeaks)
{
g_log.notice() << "Number of peaks found exceeded the limit of " << MaxPeaks << ". Stopping peak finding." << std::endl;
break;
}
peakBoxes.push_back(box);
g_log.information() << "Found box at ";
for (size_t d=0; d<nd; d++)
g_log.information() << (d>0?",":"") << boxCenter[d];
g_log.information() << "; Density = " << density << std::endl;
// Report progres for each box found.
prog->report("Finding Peaks");
}
}
prog->resetNumSteps(numBoxesFound, 0.95, 1.0);
// Copy the instrument, sample, run to the peaks workspace.
peakWS->copyExperimentInfoFrom(ei.get());
// --- Convert the "boxes" to peaks ----
for (typename std::vector<boxPtr>::iterator it3=peakBoxes.begin(); it3 != peakBoxes.end(); it3++)
{
// The center of the box = Q in the lab frame
boxPtr box = *it3;
#ifndef MDBOX_TRACK_CENTROID
coord_t boxCenter[nd];
box->calculateCentroid(boxCenter);
#else
const coord_t * boxCenter = box->getCentroid();
#endif
V3D Q(boxCenter[0], boxCenter[1], boxCenter[2]);
// Create a peak and add it
// Empty starting peak.
Peak p;
try
{
if (dimType == QLAB)
{
// Build using the Q-lab-frame constructor
p = Peak(inst, Q);
// Save gonio matrix for later
p.setGoniometerMatrix(goniometer);
}
else if (dimType == QSAMPLE)
{
// Build using the Q-sample-frame constructor
p = Peak(inst, Q, goniometer);
}
}
catch (std::exception &e)
{
g_log.notice() << "Error creating peak at " << Q << " because of '" << e.what() << "'. Peak will be skipped." << std::endl;
continue;
}
try
{ // Look for a detector
p.findDetector();
}
catch (...)
{ /* Ignore errors in ray-tracer TODO: Handle for WISH data later */ }
// The "bin count" used will be the box density.
p.setBinCount( box->getSignalNormalized() * densityScalingFactor);
// Save the run number found before.
p.setRunNumber(runNumber);
peakWS->addPeak(p);
// Report progres for each box found.
prog->report("Adding Peaks");
} // for each box found
}
int LuaPeak::setColor(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
obj->getOwner()->setColor( obj, luaL_checknumber( L, 2 ) );
return 0;
}
/**
* Calculates the h,k, and l offsets from an integer for (some of )the peaks,
*given the parameter values.
*
* @param out For each peak there are 3 consecutive elements in this array. The
*first is for the h offset from an
* integer, the second is the k offset and the 3rd is the l offset
* @param xValues xValues give the index in the PeaksWorkspace for the peak.
*For each peak considered there are
* three consecutive entries all with the same index
* @param nData The size of the xValues and out arrays
*/
void PeakHKLErrors::function1D(double *out, const double *xValues,
const size_t nData) const {
PeaksWorkspace_sptr Peaks =
AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(
PeakWorkspaceName);
boost::shared_ptr<Geometry::Instrument> instNew = getNewInstrument(Peaks);
if (!Peaks)
throw std::invalid_argument("Peaks not stored under the name " +
PeakWorkspaceName);
std::map<int, Mantid::Kernel::Matrix<double>> RunNum2GonMatrixMap;
getRun2MatMap(Peaks, OptRuns, RunNum2GonMatrixMap);
const DblMatrix &UBx = Peaks->sample().getOrientedLattice().getUB();
DblMatrix UBinv(UBx);
UBinv.Invert();
UBinv /= (2 * M_PI);
double GonRotx = getParameter("GonRotx");
double GonRoty = getParameter("GonRoty");
double GonRotz = getParameter("GonRotz");
Matrix<double> GonRot = RotationMatrixAboutRegAxis(GonRotx, 'x') *
RotationMatrixAboutRegAxis(GonRoty, 'y') *
RotationMatrixAboutRegAxis(GonRotz, 'z');
double ChiSqTot = 0.0;
for (size_t i = 0; i < nData; i += 3) {
int peakNum = boost::math::iround(xValues[i]);
IPeak &peak_old = Peaks->getPeak(peakNum);
int runNum = peak_old.getRunNumber();
std::string runNumStr = std::to_string(runNum);
Peak peak = createNewPeak(peak_old, instNew, 0, peak_old.getL1());
size_t N = OptRuns.find("/" + runNumStr + "/");
if (N < OptRuns.size()) {
peak.setGoniometerMatrix(GonRot * RunNum2GonMatrixMap[runNum]);
} else {
peak.setGoniometerMatrix(GonRot * peak.getGoniometerMatrix());
}
V3D sampOffsets(getParameter("SampleXOffset"),
getParameter("SampleYOffset"),
getParameter("SampleZOffset"));
peak.setSamplePos(peak.getSamplePos() + sampOffsets);
V3D hkl = UBinv * peak.getQSampleFrame();
for (int k = 0; k < 3; k++) {
double d1 = hkl[k] - floor(hkl[k]);
if (d1 > .5)
d1 = d1 - 1;
if (d1 < -.5)
d1 = d1 + 1;
out[i + k] = d1;
ChiSqTot += d1 * d1;
}
}
g_log.debug() << "------------------------Function---------------------------"
"--------------------\n";
for (size_t p = 0; p < nParams(); p++) {
g_log.debug() << parameterName(p) << "(" << getParameter(p) << "),";
if ((p + 1) % 6 == 0)
g_log.debug() << '\n';
}
g_log.debug() << '\n';
g_log.debug() << "Off constraints=";
for (size_t p = 0; p < nParams(); p++) {
IConstraint *constr = getConstraint(p);
if (constr)
if ((constr->check() > 0))
g_log.debug() << "(" << parameterName(p) << "=" << constr->check()
<< ");";
}
g_log.debug() << '\n';
g_log.debug() << " Chi**2 = " << ChiSqTot << " nData = " << nData
<< '\n';
}
int LuaPeak::getLabel(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
lua_pushstring(L, obj->getTag().data() );
return 1;
}
void PeakHKLErrors::functionDeriv1D(Jacobian *out, const double *xValues,
const size_t nData) {
PeaksWorkspace_sptr Peaks =
AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(
PeakWorkspaceName);
boost::shared_ptr<Geometry::Instrument> instNew = getNewInstrument(Peaks);
const DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
DblMatrix UBinv(UB);
UBinv.Invert();
UBinv /= 2 * M_PI;
double GonRotx = getParameter("GonRotx");
double GonRoty = getParameter("GonRoty");
double GonRotz = getParameter("GonRotz");
Matrix<double> InvGonRotxMat = RotationMatrixAboutRegAxis(GonRotx, 'x');
Matrix<double> InvGonRotyMat = RotationMatrixAboutRegAxis(GonRoty, 'y');
Matrix<double> InvGonRotzMat = RotationMatrixAboutRegAxis(GonRotz, 'z');
Matrix<double> GonRot = InvGonRotxMat * InvGonRotyMat * InvGonRotzMat;
InvGonRotxMat.Invert();
InvGonRotyMat.Invert();
InvGonRotzMat.Invert();
std::map<int, Kernel::Matrix<double>> RunNums2GonMatrix;
getRun2MatMap(Peaks, OptRuns, RunNums2GonMatrix);
g_log.debug()
<< "----------------------------Derivative------------------------\n";
V3D samplePosition = instNew->getSample()->getPos();
IPeak &ppeak = Peaks->getPeak(0);
double L0 = ppeak.getL1();
double velocity = (L0 + ppeak.getL2()) / ppeak.getTOF();
double K =
2 * M_PI / ppeak.getWavelength() / velocity; // 2pi/lambda = K* velocity
V3D beamDir = instNew->getBeamDirection();
size_t paramNums[] = {parameterIndex(std::string("SampleXOffset")),
parameterIndex(std::string("SampleYOffset")),
parameterIndex(std::string("SampleZOffset"))};
for (size_t i = 0; i < nData; i += 3) {
int peakNum = boost::math::iround(xValues[i]);
IPeak &peak_old = Peaks->getPeak(peakNum);
Peak peak = createNewPeak(peak_old, instNew, 0, peak_old.getL1());
int runNum = peak_old.getRunNumber();
std::string runNumStr = std::to_string(runNum);
for (int kk = 0; kk < static_cast<int>(nParams()); kk++) {
out->set(i, kk, 0.0);
out->set(i + 1, kk, 0.0);
out->set(i + 2, kk, 0.0);
}
double chi, phi, omega;
size_t chiParamNum, phiParamNum, omegaParamNum;
size_t N = OptRuns.find("/" + runNumStr);
if (N < OptRuns.size()) {
chi = getParameter("chi" + (runNumStr));
phi = getParameter("phi" + (runNumStr));
omega = getParameter("omega" + (runNumStr));
peak.setGoniometerMatrix(GonRot * RunNums2GonMatrix[runNum]);
chiParamNum = parameterIndex("chi" + (runNumStr));
phiParamNum = parameterIndex("phi" + (runNumStr));
omegaParamNum = parameterIndex("omega" + (runNumStr));
} else {
Geometry::Goniometer Gon(peak.getGoniometerMatrix());
std::vector<double> phichiOmega = Gon.getEulerAngles("YZY");
chi = phichiOmega[1];
phi = phichiOmega[2];
omega = phichiOmega[0];
// peak.setGoniometerMatrix( GonRot*Gon.getR());
chiParamNum = phiParamNum = omegaParamNum = nParams() + 10;
peak.setGoniometerMatrix(GonRot * peak.getGoniometerMatrix());
}
V3D sampOffsets(getParameter("SampleXOffset"),
getParameter("SampleYOffset"),
getParameter("SampleZOffset"));
peak.setSamplePos(peak.getSamplePos() + sampOffsets);
// NOTE:Use getQLabFrame except for below.
// For parameters the getGoniometerMatrix should remove GonRot, for derivs
// wrt GonRot*, wrt chi*,phi*,etc.
// Deriv wrt chi phi and omega
if (phiParamNum < nParams()) {
Matrix<double> chiMatrix = RotationMatrixAboutRegAxis(chi, 'z');
Matrix<double> phiMatrix = RotationMatrixAboutRegAxis(phi, 'y');
Matrix<double> omegaMatrix = RotationMatrixAboutRegAxis(omega, 'y');
Matrix<double> dchiMatrix = DerivRotationMatrixAboutRegAxis(chi, 'z');
Matrix<double> dphiMatrix = DerivRotationMatrixAboutRegAxis(phi, 'y');
Matrix<double> domegaMatrix = DerivRotationMatrixAboutRegAxis(omega, 'y');
Matrix<double> InvG = omegaMatrix * chiMatrix * phiMatrix;
InvG.Invert();
// Calculate Derivatives wrt chi(phi,omega) in degrees
Matrix<double> R = omegaMatrix * chiMatrix * dphiMatrix;
Matrix<double> InvR = InvG * R * InvG * -1;
V3D lab = peak.getQLabFrame();
V3D Dhkl0 = UBinv * InvR * lab;
R = omegaMatrix * dchiMatrix * phiMatrix;
InvR = InvG * R * InvG * -1;
V3D Dhkl1 = UBinv * InvR * peak.getQLabFrame();
R = domegaMatrix * chiMatrix * phiMatrix;
InvR = InvG * R * InvG * -1;
V3D Dhkl2 =
UBinv * InvR * peak.getQLabFrame(); // R.transpose should be R inverse
out->set(i, chiParamNum, Dhkl1[0]);
out->set(i + 1, chiParamNum, Dhkl1[1]);
out->set(i + 2, chiParamNum, Dhkl1[2]);
out->set(i, phiParamNum, Dhkl0[0]);
out->set(i + 1, phiParamNum, Dhkl0[1]);
out->set(i + 2, phiParamNum, Dhkl0[2]);
out->set(i, omegaParamNum, Dhkl2[0]);
out->set(i + 1, omegaParamNum, Dhkl2[1]);
out->set(i + 2, omegaParamNum, Dhkl2[2]);
} // if optimize for chi phi and omega on this peak
//------------------------Goniometer Rotation Derivatives
//-----------------------
Matrix<double> InvGonRot(GonRot);
InvGonRot.Invert();
Matrix<double> InvGon = InvGonRot * peak.getGoniometerMatrix();
InvGon.Invert();
V3D DGonx = (UBinv * InvGon * InvGonRotzMat * InvGonRotyMat *
DerivRotationMatrixAboutRegAxis(
-GonRotx, 'x') * // - gives inverse of GonRot
peak.getQLabFrame()) *
-1;
V3D DGony = (UBinv * InvGon * InvGonRotzMat *
DerivRotationMatrixAboutRegAxis(-GonRoty, 'y') *
InvGonRotxMat * peak.getQLabFrame()) *
-1;
V3D DGonz =
(UBinv * InvGon * DerivRotationMatrixAboutRegAxis(-GonRotz, 'z') *
InvGonRotyMat * InvGonRotxMat * peak.getQLabFrame()) *
-1;
size_t paramnum = parameterIndex("GonRotx");
out->set(i, paramnum, DGonx[0]);
out->set(i + 1, paramnum, DGonx[1]);
out->set(i + 2, paramnum, DGonx[2]);
out->set(i, parameterIndex("GonRoty"), DGony[0]);
out->set(i + 1, parameterIndex("GonRoty"), DGony[1]);
out->set(i + 2, parameterIndex("GonRoty"), DGony[2]);
out->set(i, parameterIndex("GonRotz"), DGonz[0]);
out->set(i + 1, parameterIndex("GonRotz"), DGonz[1]);
out->set(i + 2, parameterIndex("GonRotz"), DGonz[2]);
//-------------------- Sample Orientation derivatives
//----------------------------------
// Qlab = -KV + k|V|*beamdir
// D = pos-sampPos
//|V|= vmag=(L0 + D )/tof
// t1= tof - L0/|V| {time from sample to pixel}
// V = D/t1
V3D D = peak.getDetPos() - samplePosition;
double vmag = (L0 + D.norm()) / peak.getTOF();
double t1 = peak.getTOF() - L0 / vmag;
// Derivs wrt sample x, y, z
// Ddsx =( - 1, 0, 0), d|D|^2/dsx -> 2|D|d|D|/dsx =d(tranp(D)* D)/dsx =2
// Ddsx* tranp(D)
//|D| also called Dmag
V3D Dmagdsxsysz(D);
Dmagdsxsysz *= (-1 / D.norm());
V3D vmagdsxsysz = Dmagdsxsysz / peak.getTOF();
V3D t1dsxsysz = vmagdsxsysz * (L0 / vmag / vmag);
Matrix<double> Gon = peak.getGoniometerMatrix();
Gon.Invert();
// x=0 is deriv wrt SampleXoffset, x=1 is deriv wrt SampleYoffset, etc.
for (int x = 0; x < 3; x++) {
V3D pp;
pp[x] = 1;
V3D dQlab1 = pp / -t1 - D * (t1dsxsysz[x] / t1 / t1);
V3D dQlab2 = beamDir * vmagdsxsysz[x];
V3D dQlab = dQlab2 - dQlab1;
dQlab *= K;
V3D dQSamp = Gon * dQlab;
V3D dhkl = UBinv * dQSamp;
out->set(i, paramNums[x], dhkl[0]);
out->set(i + 1, paramNums[x], dhkl[1]);
out->set(i + 2, paramNums[x], dhkl[2]);
}
}
}
void PeaksWorkspace::saveNexus(::NeXus::File * file) const
{
//Number of Peaks
const size_t np(peaks.size());
// Column vectors for peaks table
std::vector<int> detectorID(np);
std::vector<double> H(np);
std::vector<double> K(np);
std::vector<double> L(np);
std::vector<double> intensity(np);
std::vector<double> sigmaIntensity(np);
std::vector<double> binCount(np);
std::vector<double> initialEnergy(np);
std::vector<double> finalEnergy(np);
std::vector<double> waveLength(np);
std::vector<double> scattering(np);
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<double> goniometerMatrix(9 * np);
// Populate column vectors from Peak Workspace
for (size_t i = 0; i < np; i++)
{
Peak p = peaks[i];
detectorID[i] = p.getDetectorID();
H[i] = p.getH();
K[i] = p.getK();
L[i] = p.getL();
intensity[i] = p.getIntensity();
sigmaIntensity[i] = p.getSigmaIntensity();
binCount[i] = p.getBinCount();
initialEnergy[i] = p.getInitialEnergy();
finalEnergy[i] = p.getFinalEnergy();
waveLength[i] = p.getWavelength();
scattering[i] = p.getScattering();
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
goniometerMatrix[9 * i + 1] = gm[1][0];
goniometerMatrix[9 * i + 2] = gm[2][0];
goniometerMatrix[9 * i + 3] = gm[0][1];
goniometerMatrix[9 * i + 4] = gm[1][1];
goniometerMatrix[9 * i + 5] = gm[2][1];
goniometerMatrix[9 * i + 6] = gm[0][2];
goniometerMatrix[9 * i + 7] = gm[1][2];
goniometerMatrix[9 * i + 8] = gm[1][2];
}
// etc.
}
// Start Peaks Workspace in Nexus File
std::string specifyInteger = "An integer";
std::string specifyDouble = "A double";
file->makeGroup("peaks_workspace", "NXentry", true); // For when peaksWorkspace can be loaded
// Detectors column
file->writeData("column_1", detectorID);
file->openData("column_1");
file->putAttr("name", "Dectector ID");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known");
file->closeData();
// H column
file->writeData("column_2", H);
file->openData("column_2");
file->putAttr("name", "H");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// K column
file->writeData("column_3", K);
file->openData("column_3");
file->putAttr("name", "K");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// L column
file->writeData("column_4", L);
file->openData("column_4");
file->putAttr("name", "L");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Intensity column
file->writeData("column_5", intensity);
file->openData("column_5");
file->putAttr("name", "Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Sigma Intensity column
file->writeData("column_6", sigmaIntensity);
file->openData("column_6");
file->putAttr("name", "Sigma Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Bin Count column
file->writeData("column_7", binCount);
file->openData("column_7");
file->putAttr("name", "Bin Count");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Initial Energy column
file->writeData("column_8", initialEnergy);
file->openData("column_8");
file->putAttr("name", "Initial Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Final Energy column
file->writeData("column_9", finalEnergy);
file->openData("column_9");
file->putAttr("name", "Final Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Wave Length Column
file->writeData("column_10", waveLength);
file->openData("column_10");
file->putAttr("name", "Wave Length");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Scattering Column
file->writeData("column_11", scattering);
file->openData("column_11");
file->putAttr("name", "Scattering");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// D Spacing Column
file->writeData("column_12", dSpacing);
file->openData("column_12");
file->putAttr("name", "D Spacing");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// TOF Column
file->writeData("column_13", TOF);
file->openData("column_13");
file->putAttr("name", "TOF");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
//Run Number column
file->writeData("column_14", runNumber);
file->openData("column_14");
file->putAttr("name", "Run Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
array_dims.push_back(9);
file->writeData("column_15", goniometerMatrix, array_dims);
file->openData("column_15");
file->putAttr("name", "Goniometer Matrix");
file->putAttr("interpret_as", "A matrix of 3x3 doubles");
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// QLab & QSample are calculated and do not need to be saved
file->closeGroup(); // end of peaks workpace
}
void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
// Number of Peaks
const size_t np(peaks.size());
// Column vectors for peaks table
std::vector<int> detectorID(np);
std::vector<double> H(np);
std::vector<double> K(np);
std::vector<double> L(np);
std::vector<double> intensity(np);
std::vector<double> sigmaIntensity(np);
std::vector<double> binCount(np);
std::vector<double> initialEnergy(np);
std::vector<double> finalEnergy(np);
std::vector<double> waveLength(np);
std::vector<double> scattering(np);
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<double> goniometerMatrix(9 * np);
std::vector<std::string> shapes(np);
// Populate column vectors from Peak Workspace
size_t maxShapeJSONLength = 0;
for (size_t i = 0; i < np; i++) {
Peak p = peaks[i];
detectorID[i] = p.getDetectorID();
H[i] = p.getH();
K[i] = p.getK();
L[i] = p.getL();
intensity[i] = p.getIntensity();
sigmaIntensity[i] = p.getSigmaIntensity();
binCount[i] = p.getBinCount();
initialEnergy[i] = p.getInitialEnergy();
finalEnergy[i] = p.getFinalEnergy();
waveLength[i] = p.getWavelength();
scattering[i] = p.getScattering();
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
goniometerMatrix[9 * i + 1] = gm[1][0];
goniometerMatrix[9 * i + 2] = gm[2][0];
goniometerMatrix[9 * i + 3] = gm[0][1];
goniometerMatrix[9 * i + 4] = gm[1][1];
goniometerMatrix[9 * i + 5] = gm[2][1];
goniometerMatrix[9 * i + 6] = gm[0][2];
goniometerMatrix[9 * i + 7] = gm[1][2];
goniometerMatrix[9 * i + 8] = gm[2][2];
}
const std::string shapeJSON = p.getPeakShape().toJSON();
shapes[i] = shapeJSON;
if (shapeJSON.size() > maxShapeJSONLength) {
maxShapeJSONLength = shapeJSON.size();
}
}
// Start Peaks Workspace in Nexus File
const std::string specifyInteger = "An integer";
const std::string specifyDouble = "A double";
const std::string specifyString = "A string";
file->makeGroup("peaks_workspace", "NXentry",
true); // For when peaksWorkspace can be loaded
// Coordinate system
file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
// Write out the Qconvention
// ki-kf for Inelastic convention; kf-ki for Crystallography convention
std::string m_QConvention = this->getConvention();
file->putAttr("QConvention", m_QConvention);
// Detectors column
file->writeData("column_1", detectorID);
file->openData("column_1");
file->putAttr("name", "Detector ID");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known");
file->closeData();
// H column
file->writeData("column_2", H);
file->openData("column_2");
file->putAttr("name", "H");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// K column
file->writeData("column_3", K);
file->openData("column_3");
file->putAttr("name", "K");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// L column
file->writeData("column_4", L);
file->openData("column_4");
file->putAttr("name", "L");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Intensity column
file->writeData("column_5", intensity);
file->openData("column_5");
file->putAttr("name", "Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Sigma Intensity column
file->writeData("column_6", sigmaIntensity);
file->openData("column_6");
file->putAttr("name", "Sigma Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Bin Count column
file->writeData("column_7", binCount);
file->openData("column_7");
file->putAttr("name", "Bin Count");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Initial Energy column
file->writeData("column_8", initialEnergy);
file->openData("column_8");
file->putAttr("name", "Initial Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Final Energy column
file->writeData("column_9", finalEnergy);
file->openData("column_9");
file->putAttr("name", "Final Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Wave Length Column
file->writeData("column_10", waveLength);
file->openData("column_10");
file->putAttr("name", "Wave Length");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Scattering Column
file->writeData("column_11", scattering);
file->openData("column_11");
file->putAttr("name", "Scattering");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// D Spacing Column
file->writeData("column_12", dSpacing);
file->openData("column_12");
file->putAttr("name", "D Spacing");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// TOF Column
file->writeData("column_13", TOF);
file->openData("column_13");
file->putAttr("name", "TOF");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Run Number column
file->writeData("column_14", runNumber);
file->openData("column_14");
file->putAttr("name", "Run Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
array_dims.push_back(9);
file->writeData("column_15", goniometerMatrix, array_dims);
file->openData("column_15");
file->putAttr("name", "Goniometer Matrix");
file->putAttr("interpret_as", "A matrix of 3x3 doubles");
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Shape
std::vector<int64_t> dims;
dims.push_back(np);
dims.push_back(static_cast<int>(maxShapeJSONLength));
const std::string name = "column_16";
file->makeData(name, NeXus::CHAR, dims, false);
file->openData(name);
auto toNexus = new char[maxShapeJSONLength * np];
for (size_t ii = 0; ii < np; ii++) {
std::string rowStr = shapes[ii];
for (size_t ic = 0; ic < rowStr.size(); ic++)
toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
for (size_t ic = rowStr.size();
ic < static_cast<size_t>(maxShapeJSONLength); ic++)
toNexus[ii * maxShapeJSONLength + ic] = ' ';
}
file->putData((void *)(toNexus));
delete[] toNexus;
file->putAttr("units", "Not known"); // Units may need changing when known
file->putAttr("name", "Shape");
file->putAttr("interpret_as", specifyString);
file->closeData();
// QLab & QSample are calculated and do not need to be saved
file->closeGroup(); // end of peaks workpace
}
int LuaPeak::getId(lua_State *L)
{
Peak* obj = RefBinding<Peak>::check( L, 1);
lua_pushnumber(L, obj->getId() );
return 1;
}
/** Append the peaks from a .peaks file into the workspace
* @param outWS :: the workspace in which to place the information
* @param filename :: path to the .peaks file
*/
void LoadIsawPeaks::appendFile( PeaksWorkspace_sptr outWS, std::string filename )
{
// Open the file
std::ifstream in( filename.c_str() );
// Read the header, load the instrument
double T0;
std::string s = readHeader( outWS, in , T0);
// set T0 in the run parameters
API::Run & m_run = outWS->mutableRun();
m_run.addProperty<double>("T0", T0, true);
if( !in.good() || s.length() < 1 )
throw std::runtime_error( "End of Peaks file before peaks" );
if( s.compare( std::string( "0" ) ) != 0 )
throw std::logic_error( "No header for Peak segments" );
readToEndOfLine( in , true );
s = getWord( in , false );
int run, bankNum;
double chi , phi , omega , monCount;
// Build the universal goniometer that will build the rotation matrix.
Mantid::Geometry::Goniometer uniGonio;
uniGonio.makeUniversalGoniometer();
// TODO: Can we find the number of peaks to get better progress reporting?
Progress prog(this, 0.0, 1.0, 100);
while( in.good() )
{
// Read the header if necessary
s = readPeakBlockHeader( s , in , run , bankNum , chi , phi ,
omega , monCount );
// Build the Rotation matrix using phi,chi,omega
uniGonio.setRotationAngle("phi", phi);
uniGonio.setRotationAngle("chi", chi);
uniGonio.setRotationAngle("omega", omega);
//Put goniometer into peaks workspace
outWS->mutableRun().setGoniometer(uniGonio, false);
std::ostringstream oss;
std::string bankString = "bank";
if (outWS->getInstrument()->getName() == "WISH") bankString = "WISHpanel0";
oss << bankString << bankNum;
std::string bankName = oss.str();
int seqNum = -1;
try
{
// Read the peak
Peak peak = readPeak(outWS, s, in, seqNum, bankName);
// Get the calculated goniometer matrix
Matrix<double> gonMat = uniGonio.getR();
peak.setGoniometerMatrix(gonMat);
peak.setRunNumber(run);
peak.setMonitorCount( monCount );
double tof = peak.getTOF();
Kernel::Units::Wavelength wl;
wl.initialize(peak.getL1(), peak.getL2(), peak.getScattering(), 0,
peak.getInitialEnergy(), 0.0);
peak.setWavelength(wl.singleFromTOF( tof));
// Add the peak to workspace
outWS->addPeak(peak);
}
catch (std::runtime_error & e)
{
g_log.warning() << "Error reading peak SEQN " << seqNum << " : " << e.what() << std::endl;
}
prog.report();
}
}
//Merge Peaklists merge_lower and merge_upper
void PeakListCollection::mergePeakLists_(unsigned int merge_lower, unsigned int merge_upper, std::vector<PeakList>& c,
double drt, double dmz, double dz, double dint = 0.)
{
PeakList newPeakList; //Peaklists will be merged into newPeakList
std::vector<map_item> newCorrespondenceMapColumn; //correspondenceMap information will be merged in here
//get assignments via StableMarriage
StableMarriage sm(c[merge_lower], c[merge_upper], drt, dmz, dz, dint);
//set limit: do not assign Peaks with distance larger than 1. Note: normalization constants
//drt and dmz must be adjusted properly.
sm.setLimit(1.);
StableMarriage::Assignment assign = sm.getAssignment();
//process peaks with a partner
for(unsigned int i = 0; i < assign.ass12.size(); i++){
if(assign.ass12[i] > -1){
//write matched Peaks into newPeaklist
//calculate average Rt, Mz and Intensity values
//Peak1: PL: merge_lower ; Item: i ; plContent: correspondenceMap_[merge_lower][i].size()
//Peak2: PL: merge_upper ; Item: assign.ass12[i] ; plContent: correspondenceMap_[merge_upper][assign.ass12[i]].size()
//Number of peaks merged into single peak = size of originInformation vector
double plc_lower = correspondenceMap_[merge_lower][i].size();
double plc_upper = correspondenceMap_[merge_upper][assign.ass12[i]].size();
double avRt = (c[merge_lower][i].getRt()*plc_lower +
c[merge_upper][assign.ass12[i]].getRt()*plc_upper) /
(plc_lower + plc_upper);
double avMz = (c[merge_lower][i].getMz()*plc_lower +
c[merge_upper][assign.ass12[i]].getMz()*plc_upper) /
(plc_lower + plc_upper);
double avInt = (c[merge_lower][i].getAbundance()*plc_lower +
c[merge_upper][assign.ass12[i]].getAbundance()*plc_upper) /
(plc_lower + plc_upper);
//create temporary peak and fill with averaged values
Peak temp;
temp.setCharge(c[merge_lower][i].getCharge()); //charge is assumed to be equal
temp.setRt(avRt);
temp.setMz(avMz);
temp.setAbundance(avInt);
//add temporary peak to peaklist
newPeakList.push_back(temp);
//write origin information of matched peaks
map_item tempItem;
//copy all origin information from merge_lower
for(unsigned int j = 0; j < correspondenceMap_[merge_lower][i].size(); j++){
tempItem.push_back(correspondenceMap_[merge_lower][i][j]);
}
//copy all origin information from merge_upper
for(unsigned int j = 0; j < correspondenceMap_[merge_upper][assign.ass12[i]].size(); j++){
tempItem.push_back(correspondenceMap_[merge_upper][assign.ass12[i]][j]);
}
//add item to column
newCorrespondenceMapColumn.push_back(tempItem);
}
}
//process PeakList merge_lower
for(unsigned int i = 0; i < assign.ass12.size(); i++){
if(assign.ass12[i] == -1){
newPeakList.push_back(c[merge_lower][i]);
map_item tempItem;
//copy all origin information
for(unsigned int j = 0; j < correspondenceMap_[merge_lower][i].size(); j++){
tempItem.push_back(correspondenceMap_[merge_lower][i][j]);
}
newCorrespondenceMapColumn.push_back(tempItem);
}
}
//process PeakList merge_upper
for(unsigned int i = 0; i < assign.ass21.size(); i++){
if(assign.ass21[i] == -1){
newPeakList.push_back(c[merge_upper][i]);
map_item tempItem;
//copy all origin information
for(unsigned int j = 0; j < correspondenceMap_[merge_upper][i].size(); j++){
tempItem.push_back(correspondenceMap_[merge_upper][i][j]);
}
newCorrespondenceMapColumn.push_back(tempItem);
}
}
//refresh correspondence map
//erase merged columns
correspondenceMap_.erase(correspondenceMap_.begin()+merge_upper);
correspondenceMap_.erase(correspondenceMap_.begin()+merge_lower);
//add new column
correspondenceMap_.push_back(newCorrespondenceMapColumn);
//refresh peaklist collection c
//erase merged peaklists
c.erase(c.begin()+merge_upper);
c.erase(c.begin()+merge_lower);
//add new peaklist
c.push_back(newPeakList);
//update plContent_
plContent_.push_back(plContent_[merge_lower] + plContent_[merge_upper]);
plContent_.erase(plContent_.begin()+merge_upper);
plContent_.erase(plContent_.begin()+merge_lower);
return;
}
int PeakProcessor::DiscoverPeaks (std::vector<double> *vect_mz, std::vector<double> *vect_intensity, double start_mz, double stop_mz)
{
if(vect_intensity->size() < 1)
return 0 ;
mobj_peak_data->Clear() ;
int num_data_pts = (int) (*vect_intensity).size() ;
int ilow ;
int ihigh ;
Peak peak ;
int start_index = mobj_pk_index.GetNearestBinary(*vect_mz, start_mz, 0, num_data_pts-1) ;
int stop_index = mobj_pk_index.GetNearestBinary(*vect_mz, stop_mz, start_index, num_data_pts-1) ;
if (start_index <= 0)
start_index = 1 ;
if (stop_index >= (int)vect_mz->size() -2)
stop_index = (int)vect_mz->size() - 2 ;
for (int index = start_index ; index <= stop_index ; index++)
{
double FWHM = -1 ;
double current_intensity = (*vect_intensity)[index] ;
double last_intensity = (*vect_intensity)[index-1] ;
double next_intensity = (*vect_intensity)[index+1] ;
double current_mz = (*vect_mz)[index] ;
if (menm_profile_type == CENTROIDED)
{
if (current_intensity >= mdbl_peak_intensity_threshold)
{
double mass_ = (*vect_mz)[index] ;
double SN = current_intensity / mdbl_peak_intensity_threshold ;
double FWHM = 0.6 ;
peak.Set(mass_, current_intensity, SN, mobj_peak_data->GetNumPeaks(), index, FWHM) ;
mobj_peak_data->AddPeak(peak) ;
}
}
else if (menm_profile_type == PROFILE)
{
if(current_intensity >= last_intensity && current_intensity >= next_intensity
&& current_intensity >= this->mdbl_peak_intensity_threshold)
{
//See if the peak meets the conditions.
//The peak data will be found at _transformData->begin()+i+1.
double SN = 0 ;
if (!mbln_thresholded_data)
SN = this->mobj_peak_statistician.FindSignalToNoise(current_intensity, (*vect_intensity), index);
else
SN = current_intensity / mdbl_background_intensity ;
// Run Full-Width Half-Max algorithm to try and squeak out a higher SN
if(SN < this->mdbl_signal_2_noise_threshold)
{
double mass_ = (*vect_mz)[index] ;
FWHM = this->mobj_peak_statistician.FindFWHM((*vect_mz), (*vect_intensity), index, SN);
if(FWHM > 0 && FWHM < 0.5)
{
ilow = mobj_pk_index.GetNearestBinary((*vect_mz), current_mz - FWHM, 0, index);
ihigh = mobj_pk_index.GetNearestBinary((*vect_mz), current_mz + FWHM, index, stop_index);
double low_intensity = (*vect_intensity)[ilow] ;
double high_intensity = (*vect_intensity)[ihigh] ;
double sum_intensity = low_intensity + high_intensity ;
if(sum_intensity)
SN = (2.0 * current_intensity) / sum_intensity ;
else
SN = 10;
}
}
// Found a peak, make sure it is in the attention list, if there is one.
if(SN >= this->mdbl_signal_2_noise_threshold && ( !this->mbln_chk_attention_list || this->IsInAttentionList(current_mz)))
{
// Find a more accurate m/z location of the peak.
double fittedPeak = mobj_peak_fit.Fit(index, (*vect_mz), (*vect_intensity));
if (FWHM == -1)
{
FWHM = this->mobj_peak_statistician.FindFWHM((*vect_mz), (*vect_intensity), index, SN);
}
if (FWHM > 0)
{
peak.Set(fittedPeak, current_intensity, SN, mobj_peak_data->GetNumPeaks(), index, FWHM) ;
mobj_peak_data->AddPeak(peak) ;
}
// move beyond peaks have the same intensity.
bool incremented = false ;
while( index < num_data_pts && (*vect_intensity)[index] == current_intensity)
{
incremented = true ;
index++ ;
}
if(index > 0 && index < num_data_pts
&& incremented)
index-- ;
}
}
}
}
mobj_peak_data->mptr_vect_mzs = vect_mz ;
mobj_peak_data->mptr_vect_intensities = vect_intensity ;
return mobj_peak_data->GetNumPeaks() ;
}
