/// Overwrites Algorithm exec method
void LoadSpice2D::exec()
{
std::string fileName = getPropertyValue("Filename");
const double wavelength_input = getProperty("Wavelength");
const double wavelength_spread_input = getProperty("WavelengthSpread");
// Set up the DOM parser and parse xml file
DOMParser pParser;
Document* pDoc;
try
{
pDoc = pParser.parse(fileName);
} catch (...)
{
throw Kernel::Exception::FileError("Unable to parse File:", fileName);
}
// Get pointer to root element
Element* pRootElem = pDoc->documentElement();
if (!pRootElem->hasChildNodes())
{
throw Kernel::Exception::NotFoundError("No root element in Spice XML file", fileName);
}
// Read in start time
const std::string start_time = pRootElem->getAttribute("start_time");
Element* sasEntryElem = pRootElem->getChildElement("Header");
throwException(sasEntryElem, "Header", fileName);
// Read in scan title
Element* element = sasEntryElem->getChildElement("Scan_Title");
throwException(element, "Scan_Title", fileName);
std::string wsTitle = element->innerText();
// Read in instrument name
element = sasEntryElem->getChildElement("Instrument");
throwException(element, "Instrument", fileName);
std::string instrument = element->innerText();
// Read sample thickness
double sample_thickness = 0;
from_element<double>(sample_thickness, sasEntryElem, "Sample_Thickness", fileName);
double source_apert = 0.0;
from_element<double>(source_apert, sasEntryElem, "source_aperture_size", fileName);
double sample_apert = 0.0;
from_element<double>(sample_apert, sasEntryElem, "sample_aperture_size", fileName);
double source_distance = 0.0;
from_element<double>(source_distance, sasEntryElem, "source_distance", fileName);
// Read in wavelength and wavelength spread
double wavelength = 0;
double dwavelength = 0;
if ( isEmpty(wavelength_input) ) {
from_element<double>(wavelength, sasEntryElem, "wavelength", fileName);
from_element<double>(dwavelength, sasEntryElem, "wavelength_spread", fileName);
}
else
{
wavelength = wavelength_input;
dwavelength = wavelength_spread_input;
}
// Read in positions
sasEntryElem = pRootElem->getChildElement("Motor_Positions");
throwException(sasEntryElem, "Motor_Positions", fileName);
// Read in the number of guides
int nguides = 0;
from_element<int>(nguides, sasEntryElem, "nguides", fileName);
// Read in sample-detector distance in mm
double distance = 0;
from_element<double>(distance, sasEntryElem, "sample_det_dist", fileName);
distance *= 1000.0;
// Read in beam trap positions
double highest_trap = 0;
double trap_pos = 0;
from_element<double>(trap_pos, sasEntryElem, "trap_y_25mm", fileName);
double beam_trap_diam = 25.4;
from_element<double>(highest_trap, sasEntryElem, "trap_y_101mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 101.6;
}
from_element<double>(trap_pos, sasEntryElem, "trap_y_50mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 50.8;
}
from_element<double>(trap_pos, sasEntryElem, "trap_y_76mm", fileName);
if (trap_pos>highest_trap)
{
highest_trap = trap_pos;
beam_trap_diam = 76.2;
}
// Read in counters
sasEntryElem = pRootElem->getChildElement("Counters");
throwException(sasEntryElem, "Counters", fileName);
double countingTime = 0;
from_element<double>(countingTime, sasEntryElem, "time", fileName);
double monitorCounts = 0;
from_element<double>(monitorCounts, sasEntryElem, "monitor", fileName);
// Read in the data image
Element* sasDataElem = pRootElem->getChildElement("Data");
throwException(sasDataElem, "Data", fileName);
// Read in the data buffer
element = sasDataElem->getChildElement("Detector");
throwException(element, "Detector", fileName);
std::string data_str = element->innerText();
// Read in the detector dimensions from the Detector tag
int numberXPixels = 0;
int numberYPixels = 0;
std::string data_type = element->getAttribute("type");
boost::regex b_re_sig("INT\\d+\\[(\\d+),(\\d+)\\]");
if (boost::regex_match(data_type, b_re_sig))
{
boost::match_results<std::string::const_iterator> match;
boost::regex_search(data_type, match, b_re_sig);
// match[0] is the full string
Kernel::Strings::convert(match[1], numberXPixels);
Kernel::Strings::convert(match[2], numberYPixels);
}
if (numberXPixels==0 || numberYPixels==0)
g_log.notice() << "Could not read in the number of pixels!" << std::endl;
// We no longer read from the meta data because that data is wrong
//from_element<int>(numberXPixels, sasEntryElem, "Number_of_X_Pixels", fileName);
//from_element<int>(numberYPixels, sasEntryElem, "Number_of_Y_Pixels", fileName);
// Store sample-detector distance
declareProperty("SampleDetectorDistance", distance, Kernel::Direction::Output);
// Create the output workspace
// Number of bins: we use a single dummy TOF bin
int nBins = 1;
// Number of detectors: should be pulled from the geometry description. Use detector pixels for now.
// The number of spectram also includes the monitor and the timer.
int numSpectra = numberXPixels*numberYPixels + LoadSpice2D::nMonitors;
DataObjects::Workspace2D_sptr ws = boost::dynamic_pointer_cast<DataObjects::Workspace2D>(
API::WorkspaceFactory::Instance().create("Workspace2D", numSpectra, nBins+1, nBins));
ws->setTitle(wsTitle);
ws->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create("Wavelength");
ws->setYUnit("");
API::Workspace_sptr workspace = boost::static_pointer_cast<API::Workspace>(ws);
setProperty("OutputWorkspace", workspace);
// Parse out each pixel. Pixels can be separated by white space, a tab, or an end-of-line character
Poco::StringTokenizer pixels(data_str, " \n\t", Poco::StringTokenizer::TOK_TRIM | Poco::StringTokenizer::TOK_IGNORE_EMPTY);
Poco::StringTokenizer::Iterator pixel = pixels.begin();
// Check that we don't keep within the size of the workspace
size_t pixelcount = pixels.count();
if( pixelcount != static_cast<size_t>(numberXPixels*numberYPixels) )
{
throw Kernel::Exception::FileError("Inconsistent data set: "
"There were more data pixels found than declared in the Spice XML meta-data.", fileName);
}
if( numSpectra == 0 )
{
throw Kernel::Exception::FileError("Empty data set: the data file has no pixel data.", fileName);
}
// Go through all detectors/channels
int ipixel = 0;
// Store monitor count
store_value(ws, ipixel++, monitorCounts, monitorCounts>0 ? sqrt(monitorCounts) : 0.0,
wavelength, dwavelength);
// Store counting time
store_value(ws, ipixel++, countingTime, 0.0, wavelength, dwavelength);
// Store detector pixels
while (pixel != pixels.end())
{
//int ix = ipixel%npixelsx;
//int iy = (int)ipixel/npixelsx;
// Get the count value and assign it to the right bin
double count = 0.0;
from_string<double>(count, *pixel, std::dec);
// Data uncertainties, computed according to the HFIR/IGOR reduction code
// The following is what I would suggest instead...
// error = count > 0 ? sqrt((double)count) : 0.0;
double error = sqrt( 0.5 + fabs( count - 0.5 ));
store_value(ws, ipixel, count, error, wavelength, dwavelength);
// Set the spectrum number
ws->getAxis(1)->setValue(ipixel, ipixel);
++pixel;
ipixel++;
}
// run load instrument
runLoadInstrument(instrument, ws);
runLoadMappingTable(ws, numberXPixels, numberYPixels);
// Set the run properties
ws->mutableRun().addProperty("sample-detector-distance", distance, "mm", true);
ws->mutableRun().addProperty("beam-trap-diameter", beam_trap_diam, "mm", true);
ws->mutableRun().addProperty("number-of-guides", nguides, true);
ws->mutableRun().addProperty("source-sample-distance", source_distance, "mm", true);
ws->mutableRun().addProperty("source-aperture-diameter", source_apert, "mm", true);
ws->mutableRun().addProperty("sample-aperture-diameter", sample_apert, "mm", true);
ws->mutableRun().addProperty("sample-thickness", sample_thickness, "cm", true);
ws->mutableRun().addProperty("wavelength", wavelength, "Angstrom", true);
ws->mutableRun().addProperty("wavelength-spread", dwavelength, "Angstrom", true);
ws->mutableRun().addProperty("timer", countingTime, "sec", true);
ws->mutableRun().addProperty("monitor", monitorCounts, "", true);
ws->mutableRun().addProperty("start_time", start_time, "", true);
ws->mutableRun().addProperty("run_start", start_time, "", true);
// Move the detector to the right position
API::IAlgorithm_sptr mover = createChildAlgorithm("MoveInstrumentComponent");
// Finding the name of the detector object.
std::string detID = ws->getInstrument()->getStringParameter("detector-name")[0];
g_log.information("Moving "+detID);
try
{
mover->setProperty<API::MatrixWorkspace_sptr> ("Workspace", ws);
mover->setProperty("ComponentName", detID);
mover->setProperty("Z", distance/1000.0);
mover->execute();
} catch (std::invalid_argument& e)
{
g_log.error("Invalid argument to MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
} catch (std::runtime_error& e)
{
g_log.error("Unable to successfully run MoveInstrumentComponent Child Algorithm");
g_log.error(e.what());
}
// Release the XML document memory
pDoc->release();
}
