/** Remove peaks from a input workspace
*/
Workspace2D_sptr
RemovePeaks::removePeaks(API::MatrixWorkspace_const_sptr dataws, int wsindex,
double numfwhm) {
// Check
if (m_vecPeakCentre.empty())
throw runtime_error("RemovePeaks has not been setup yet. ");
// Initialize vectors
const MantidVec &vecX = dataws->readX(wsindex);
const MantidVec &vecY = dataws->readY(wsindex);
const MantidVec &vecE = dataws->readE(wsindex);
size_t sizex = vecX.size();
vector<bool> vec_useX(sizex, true);
// Exclude regions
size_t numbkgdpoints =
excludePeaks(vecX, vec_useX, m_vecPeakCentre, m_vecPeakFWHM, numfwhm);
size_t numbkgdpointsy = numbkgdpoints;
size_t sizey = vecY.size();
if (sizex > sizey)
--numbkgdpointsy;
// Construct output workspace
Workspace2D_sptr outws = boost::dynamic_pointer_cast<Workspace2D>(
WorkspaceFactory::Instance().create("Workspace2D", 1, numbkgdpoints,
numbkgdpointsy));
outws->getAxis(0)->setUnit(dataws->getAxis(0)->unit()->unitID());
MantidVec &outX = outws->dataX(0);
MantidVec &outY = outws->dataY(0);
MantidVec &outE = outws->dataE(0);
size_t index = 0;
for (size_t i = 0; i < sizex; ++i) {
if (vec_useX[i]) {
if (index >= numbkgdpoints)
throw runtime_error("Programming logic error (1)");
outX[index] = vecX[i];
++index;
}
}
index = 0;
for (size_t i = 0; i < sizey; ++i) {
if (vec_useX[i]) {
if (index >= numbkgdpointsy)
throw runtime_error("Programming logic error (2)");
outY[index] = vecY[i];
outE[index] = vecE[i];
++index;
}
}
return outws;
}
/** Construct output
*/
Workspace2D_sptr RefinePowderInstrumentParameters2::genOutputWorkspace(FunctionDomain1DVector domain,
FunctionValues rawvalues)
{
// 1. Create and set up output workspace
size_t lenx = m_dataWS->readX(m_wsIndex).size();
size_t leny = m_dataWS->readY(m_wsIndex).size();
Workspace2D_sptr outws = boost::dynamic_pointer_cast<Workspace2D>
(WorkspaceFactory::Instance().create("Workspace2D", 6, lenx, leny));
outws->getAxis(0)->setUnit("dSpacing");
TextAxis* taxis = new TextAxis(outws->getNumberHistograms());
taxis->setLabel(0, "Data");
taxis->setLabel(1, "Model");
taxis->setLabel(2, "DiffDM");
taxis->setLabel(3, "Start");
taxis->setLabel(4, "DiffDS");
taxis->setLabel(5, "Zdiff");
outws->replaceAxis(1, taxis);
// 3. Re-calculate values
FunctionValues funcvalues(domain);
m_positionFunc->function(domain, funcvalues);
// 4. Add values
// a) X axis
for (size_t iws = 0; iws < outws->getNumberHistograms(); ++iws)
{
MantidVec& vecX = outws->dataX(iws);
for (size_t n = 0; n < lenx; ++n)
vecX[n] = domain[n];
}
// b) Y axis
const MantidVec& dataY = m_dataWS->readY(m_wsIndex);
for (size_t i = 0; i < domain.size(); ++i)
{
outws->dataY(0)[i] = dataY[i];
outws->dataY(1)[i] = funcvalues[i];
outws->dataY(2)[i] = dataY[i] - funcvalues[i];
outws->dataY(3)[i] = rawvalues[i];
outws->dataY(4)[i] = dataY[i] - rawvalues[i];
}
// 5. Zscore
vector<double> zscore = Kernel::getZscore(outws->readY(2));
for (size_t i = 0; i < domain.size(); ++i)
outws->dataY(5)[i] = zscore[i];
return outws;
}
/**
* Reads the data (FITS matrix) from a single FITS file into a
* workspace (directly into the spectra, using one spectrum per image
* row).
*
* @param fileInfo information on the FITS file to load, including its path
* @param cmpp centimeters per pixel, to scale/normalize values
* @param ws workspace with the required dimensions
* @param buffer pre-allocated buffer to read from file
*
* @throws std::runtime_error if there are file input issues
*/
void LoadFITS::readDataToWorkspace(const FITSInfo &fileInfo, double cmpp,
Workspace2D_sptr ws,
std::vector<char> &buffer) {
const size_t bytespp = (fileInfo.bitsPerPixel / 8);
const size_t len = m_pixelCount * bytespp;
readInBuffer(fileInfo, buffer, len);
const size_t nrows(fileInfo.axisPixelLengths[1]),
ncols(fileInfo.axisPixelLengths[0]);
// Treat buffer as a series of bytes
uint8_t *buffer8 = reinterpret_cast<uint8_t *>(buffer.data());
PARALLEL_FOR_NO_WSP_CHECK()
for (int i = 0; i < static_cast<int>(nrows); ++i) {
auto &dataX = ws->dataX(i);
auto &dataY = ws->dataY(i);
auto &dataE = ws->dataE(i);
std::fill(dataX.begin(), dataX.end(), static_cast<double>(i) * cmpp);
for (size_t j = 0; j < ncols; ++j) {
// Map from 2D->1D index
const size_t start = ((i * (bytespp)) * nrows) + (j * (bytespp));
uint8_t const *const buffer8Start = buffer8 + start;
// Reverse byte order of current value. Make sure we allocate enough
// enough space to hold the size
uint8_t byteValue[g_maxBytesPP];
std::reverse_copy(buffer8Start, buffer8Start + bytespp, byteValue);
double val = 0;
if (fileInfo.bitsPerPixel == 8) {
val = toDouble<uint8_t>(byteValue);
} else if (fileInfo.bitsPerPixel == 16) {
val = toDouble<uint16_t>(byteValue);
} else if (fileInfo.bitsPerPixel == 32 && !fileInfo.isFloat) {
val = toDouble<uint32_t>(byteValue);
} else if (fileInfo.bitsPerPixel == 64 && !fileInfo.isFloat) {
val = toDouble<uint32_t>(byteValue);
} else if (fileInfo.bitsPerPixel == 32 && fileInfo.isFloat) {
val = toDouble<float>(byteValue);
} else if (fileInfo.bitsPerPixel == 64 && fileInfo.isFloat) {
val = toDouble<double>(byteValue);
}
val = fileInfo.scale * val - fileInfo.offset;
dataY[j] = val;
dataE[j] = sqrt(val);
}
}
}
/** Filter non-background data points out and create a background workspace
*/
Workspace2D_sptr
ProcessBackground::filterForBackground(BackgroundFunction_sptr bkgdfunction) {
double posnoisetolerance = getProperty("NoiseTolerance");
double negnoisetolerance = getProperty("NegativeNoiseTolerance");
if (isEmpty(negnoisetolerance))
negnoisetolerance = posnoisetolerance;
// Calcualte theoretical values
const std::vector<double> x = m_dataWS->readX(m_wsIndex);
API::FunctionDomain1DVector domain(x);
API::FunctionValues values(domain);
bkgdfunction->function(domain, values);
g_log.information() << "Function used to select background points : "
<< bkgdfunction->asString() << "\n";
// Optional output
string userbkgdwsname = getPropertyValue("UserBackgroundWorkspace");
if (userbkgdwsname.size() == 0)
throw runtime_error("In mode SelectBackgroundPoints, "
"UserBackgroundWorkspace must be given!");
size_t sizex = domain.size();
size_t sizey = values.size();
MatrixWorkspace_sptr visualws = boost::dynamic_pointer_cast<MatrixWorkspace>(
WorkspaceFactory::Instance().create("Workspace2D", 4, sizex, sizey));
for (size_t i = 0; i < sizex; ++i) {
for (size_t j = 0; j < 4; ++j) {
visualws->dataX(j)[i] = domain[i];
}
}
for (size_t i = 0; i < sizey; ++i) {
visualws->dataY(0)[i] = values[i];
visualws->dataY(1)[i] = m_dataWS->readY(m_wsIndex)[i] - values[i];
visualws->dataY(2)[i] = posnoisetolerance;
visualws->dataY(3)[i] = -negnoisetolerance;
}
setProperty("UserBackgroundWorkspace", visualws);
// Filter for background
std::vector<double> vecx, vecy, vece;
for (size_t i = 0; i < domain.size(); ++i) {
// double y = m_dataWS->readY(m_wsIndex)[i];
// double theoryy = values[i]; y-theoryy
double purey = visualws->readY(1)[i];
if (purey < posnoisetolerance && purey > -negnoisetolerance) {
// Selected
double x = domain[i];
double y = m_dataWS->readY(m_wsIndex)[i];
double e = m_dataWS->readE(m_wsIndex)[i];
vecx.push_back(x);
vecy.push_back(y);
vece.push_back(e);
}
}
g_log.information() << "Found " << vecx.size() << " background points out of "
<< m_dataWS->readX(m_wsIndex).size()
<< " total data points. "
<< "\n";
// Build new workspace for OutputWorkspace
size_t nspec = 3;
Workspace2D_sptr outws =
boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", nspec,
vecx.size(), vecy.size()));
for (size_t i = 0; i < vecx.size(); ++i) {
for (size_t j = 0; j < nspec; ++j)
outws->dataX(j)[i] = vecx[i];
outws->dataY(0)[i] = vecy[i];
outws->dataE(0)[i] = vece[i];
}
return outws;
}
/**
* Executes the algorithm.
* Saves the workspace specified by the user to the VTK XML format
*/
void SaveVTK::exec()
{
std::string filename = getProperty("Filename");
g_log.debug() << "Parameters: Filename='" << filename << "'" << std::endl;
//add extension
filename += ".vtu";
MatrixWorkspace_sptr inputWorkspace = getProperty("InputWorkspace");
if( !inputWorkspace )
{
g_log.error("Failed to retrieve inputWorkspace.");
throw Exception::NullPointerException("SaveVTK::exec()", "inputWorkspace");
}
checkOptionalProperties();
//Open file for writing
std::ofstream outVTP(filename.c_str());
if( !outVTP )
{
g_log.error("Failed to open file: " + filename);
throw Exception::FileError("Failed to open file ", filename);
}
// First write document level XML header
outVTP << "<?xml version=\"1.0\"?>\n"
"<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n"
"<UnstructuredGrid>\n";
const std::string workspaceID = inputWorkspace->id();
if( workspaceID.find("Workspace2D") != std::string::npos )
{
const Workspace2D_sptr localWorkspace =
boost::dynamic_pointer_cast<Workspace2D>(inputWorkspace);
// const size_t numberOfHist = localWorkspace->getNumberHistograms();
//Write out whole range
bool xMin(m_Xmin > 0.0), xMax(m_Xmax > 0.0);
Progress prog(this,0.0,1.0,97);
if( !xMin && !xMax )
{
for( int hNum = 2; hNum < 100; ++hNum )
{
writeVTKPiece(outVTP, localWorkspace->dataX(hNum), localWorkspace->dataY(hNum),
localWorkspace->dataE(hNum), hNum);
prog.report();
}
}
else
{
for( int hNum = 2; hNum < 100; ++hNum )
{
std::vector<double> xValue, yValue, errors;
std::vector<double>::size_type nVals(localWorkspace->dataY(hNum).size());
for( int i = 0; i < (int)nVals; ++i )
{
if( xMin && localWorkspace->dataX(hNum)[i] < m_Xmin ) continue;
if( xMax && localWorkspace->dataX(hNum)[i+1] > m_Xmax)
{
xValue.push_back(localWorkspace->dataX(hNum)[i]);
break;
}
xValue.push_back(localWorkspace->dataX(hNum)[i]);
if( i == (int)nVals - 1 )
{
xValue.push_back(localWorkspace->dataX(hNum)[i+1]);
}
yValue.push_back(localWorkspace->dataY(hNum)[i]);
errors.push_back(localWorkspace->dataE(hNum)[i]);
}
//sanity check
assert( (int)xValue.size() == (int)yValue.size() + 1 );
writeVTKPiece(outVTP, xValue, yValue, errors, hNum);
prog.report();
}
}
}
else
{
outVTP.close();
Poco::File(filename).remove();
throw Exception::NotImplementedError("SaveVTK only implemented for Workspace2D\n");
}
// Final XML end block tags
outVTP << "</UnstructuredGrid>\n</VTKFile>\n";
outVTP.close();
}
/** Output distributions in order for a better understanding of the log
* Result is written to a Workspace2D
*
* @param timevec :: a vector of time stamps
* @param stepsize :: resolution of the delta time count bin
*/
Workspace2D_sptr GetTimeSeriesLogInformation::calDistributions(
std::vector<Kernel::DateAndTime> timevec, double stepsize) {
// 1. Get a vector of delta T (in unit of seconds)
double dtmin = static_cast<double>(timevec.back().totalNanoseconds() -
timevec[0].totalNanoseconds()) *
1.0E-9;
double dtmax = 0.0;
vector<double> vecdt(timevec.size() - 1, 0.0);
for (size_t i = 1; i < timevec.size(); ++i) {
vecdt[i - 1] = static_cast<double>(timevec[i].totalNanoseconds() -
timevec[i - 1].totalNanoseconds()) *
1.0E-9;
if (vecdt[i - 1] < dtmin)
dtmin = vecdt[i - 1];
else if (vecdt[i - 1] > dtmax)
dtmax = vecdt[i - 1];
}
// 2. Create a vector of counts
size_t numbins;
if (m_ignoreNegativeTime && dtmin < 0) {
numbins = static_cast<size_t>(ceil((dtmax) / stepsize)) + 2;
} else {
numbins = static_cast<size_t>(ceil((dtmax - dtmin) / stepsize)) + 2;
}
g_log.notice() << "Distribution has " << numbins << " bins. Delta T = ("
<< dtmin << ", " << dtmax << ")\n";
Workspace2D_sptr distws = boost::dynamic_pointer_cast<Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", 1, numbins,
numbins));
MantidVec &vecDeltaT = distws->dataX(0);
MantidVec &vecCount = distws->dataY(0);
double countmin = dtmin;
if (m_ignoreNegativeTime && dtmin < 0)
countmin = 0;
for (size_t i = 0; i < numbins; ++i)
vecDeltaT[i] = countmin + (static_cast<double>(i) - 1) * stepsize;
for (size_t i = 0; i < numbins; ++i)
vecCount[i] = 0;
// 3. Count
for (double dt : vecdt) {
int index;
if (dt < 0 && m_ignoreNegativeTime) {
index = 0;
} else {
auto viter = lower_bound(vecDeltaT.begin(), vecDeltaT.end(), dt);
index = static_cast<int>(viter - vecDeltaT.begin());
if (index >= static_cast<int>(vecDeltaT.size())) {
// Out of upper boundary
g_log.error() << "Find index = " << index
<< " > vecX.size = " << vecDeltaT.size() << ".\n";
} else if (dt < vecDeltaT[index]) {
--index;
}
if (index < 0)
throw runtime_error("How can this happen.");
}
vecCount[index] += 1;
}
return distws;
}
