/**
* Generate the vtkDataSet from the objects input IMDEventWorkspace
* @param progressUpdating : Reporting object to pass progress information up the stack.
* @return fully constructed vtkDataSet.
*/
vtkDataSet* vtkSplatterPlotFactory::create(ProgressAction& progressUpdating) const
{
UNUSED_ARG(progressUpdating);
// If initialize() wasn't run, we don't have a workspace.
if(!m_workspace)
{
throw std::runtime_error("Invalid vtkSplatterPlotFactory. Workspace is null");
}
size_t nd = m_workspace->getNumDims();
Mantid::Kernel::ReadLock lock(*m_workspace);
if (nd > 3)
{
// Slice from >3D down to 3D
this->slice = true;
this->sliceMask = new bool[nd];
this->sliceImplicitFunction = new MDImplicitFunction();
// Make the mask of dimensions
// TODO: Smarter mapping
for (size_t d = 0; d < nd; d++)
this->sliceMask[d] = (d < 3);
// Define where the slice is in 4D
// TODO: Where to slice? Right now is just 0
std::vector<coord_t> point(nd, 0);
point[3] = coord_t(m_time); //Specifically for 4th/time dimension.
// Define two opposing planes that point in all higher dimensions
std::vector<coord_t> normal1(nd, 0);
std::vector<coord_t> normal2(nd, 0);
for (size_t d = 3; d < nd; d++)
{
normal1[d] = +1.0;
normal2[d] = -1.0;
}
// This creates a 0-thickness region to slice in.
sliceImplicitFunction->addPlane(MDPlane(normal1, point));
sliceImplicitFunction->addPlane(MDPlane(normal2, point));
}
else
{
// Direct 3D, so no slicing
this->slice = false;
}
// Macro to call the right instance of the
CALL_MDEVENT_FUNCTION(this->doCreate, m_workspace);
// Clean up
if (this->slice)
{
delete[] this->sliceMask;
delete this->sliceImplicitFunction;
}
// The macro does not allow return calls, so we used a member variable.
return this->dataSet;
}
/** Execute the algorithm.
*/
void FakeMDEventData::exec() {
IMDEventWorkspace_sptr in_ws = getProperty("InputWorkspace");
if (getPropertyValue("UniformParams") == "" &&
getPropertyValue("PeakParams") == "")
throw std::invalid_argument(
"You must specify at least one of PeakParams or UniformParams.");
setupDetectorCache(*in_ws);
CALL_MDEVENT_FUNCTION(this->addFakePeak, in_ws)
CALL_MDEVENT_FUNCTION(this->addFakeUniformData, in_ws)
// Mark that events were added, so the file back end (if any) needs updating
in_ws->setFileNeedsUpdating(true);
}
/** Execute the algorithm.
*/
void CreateMDWorkspace::exec()
{
// Get the properties and validate them
std::string eventType = getPropertyValue("EventType");
int ndims_prop = getProperty("Dimensions");
if (ndims_prop <= 0)
throw std::invalid_argument("You must specify a number of dimensions >= 1.");
int mind = this->getProperty("MinRecursionDepth");
int maxd = this->getProperty("MaxRecursionDepth");
if (mind > maxd)
throw std::invalid_argument("MinRecursionDepth must be <= MaxRecursionDepth.");
if (mind < 0 || maxd < 0)
throw std::invalid_argument("MinRecursionDepth and MaxRecursionDepth must be positive.");
size_t ndims = static_cast<size_t>(ndims_prop);
std::vector<double> extents = getProperty("Extents");
std::vector<std::string> names = getProperty("Names");
std::vector<std::string> units = getProperty("Units");
if (extents.size() != ndims*2)
throw std::invalid_argument("You must specify twice as many extents (min,max) as there are dimensions.");
if (names.size() != ndims)
throw std::invalid_argument("You must specify as many names as there are dimensions.");
if (units.size() != ndims)
throw std::invalid_argument("You must specify as many units as there are dimensions.");
// Have the factory create it
IMDEventWorkspace_sptr out = MDEventFactory::CreateMDWorkspace(ndims, eventType);
// Give all the dimensions
for (size_t d=0; d<ndims; d++)
{
MDHistoDimension * dim = new MDHistoDimension(names[d], names[d], units[d], static_cast<coord_t>(extents[d*2]), static_cast<coord_t>(extents[d*2+1]), 1);
out->addDimension(MDHistoDimension_sptr(dim));
}
// Initialize it using the dimension
out->initialize();
// Call the templated function to finish ints
CALL_MDEVENT_FUNCTION(this->finish, out);
// --- File back end ? ----------------
std::string filename = getProperty("Filename");
if (!filename.empty())
{
// First save to the NXS file
g_log.notice() << "Running SaveMD" << std::endl;
IAlgorithm_sptr alg = createChildAlgorithm("SaveMD");
alg->setPropertyValue("Filename", filename);
alg->setProperty("InputWorkspace", boost::dynamic_pointer_cast<IMDWorkspace>(out));
alg->executeAsChildAlg();
// And now re-load it with this file as the backing.
g_log.notice() << "Running LoadMD" << std::endl;
alg = createChildAlgorithm("LoadMD");
alg->setPropertyValue("Filename", filename);
alg->setProperty("FileBackEnd", true);
alg->setPropertyValue("Memory", getPropertyValue("Memory"));
alg->executeAsChildAlg();
// Replace the workspace with the loaded, file-backed one
IMDWorkspace_sptr temp;
temp = alg->getProperty("OutputWorkspace");
out = boost::dynamic_pointer_cast<IMDEventWorkspace>(temp);
}
// Save it on the output.
setProperty("OutputWorkspace", boost::dynamic_pointer_cast<Workspace>(out));
}
/** Execute the algorithm.
*/
void ImportMDEventWorkspace::exec() {
std::string filename = getProperty("Filename");
std::ifstream file;
try {
file.open(filename.c_str(), std::ios::in);
} catch (std::ifstream::failure &e) {
g_log.error() << "Cannot open file: " << filename;
throw(e);
}
// Extract data from the file, excluding comment lines.
std::string line;
std::string lastLine;
size_t nActualColumns = 0;
while (std::getline(file, line)) {
boost::algorithm::trim(line);
if (std::string::npos == line.find_first_of(CommentLineStartFlag())) {
std::stringstream buffer(line);
std::copy(std::istream_iterator<std::string>(buffer),
std::istream_iterator<std::string>(),
std::back_inserter(m_file_data));
if (lastLine == MDEventBlockFlag()) {
std::vector<std::string> strVec;
boost::algorithm::split(strVec, line, boost::is_any_of("\t "),
boost::token_compress_on);
nActualColumns = strVec.size();
}
}
lastLine = line;
}
file.close();
// Check the file format.
quickFileCheck();
// Extract some well used posisions
m_posDimStart =
std::find(m_file_data.begin(), m_file_data.end(), DimensionBlockFlag());
m_posMDEventStart =
std::find(m_file_data.begin(), m_file_data.end(), MDEventBlockFlag());
// Calculate the dimensionality
int posDiffDims =
static_cast<int>(std::distance(m_posDimStart, m_posMDEventStart));
m_nDimensions = (posDiffDims - 1) / 4;
// Calculate the actual number of columns in the MDEvent data.
int posDiffMDEvent =
static_cast<int>(std::distance(m_posMDEventStart, m_file_data.end()));
const size_t columnsForFullEvents =
m_nDimensions + 4; // signal, error, run_no, detector_no
m_IsFullDataObjects = (nActualColumns == columnsForFullEvents);
if (0 == nActualColumns) {
m_nDataObjects = 0;
g_log.warning() << "The number of actual columns found in the file "
"(exlcuding comments) is zero" << std::endl;
} else {
m_nDataObjects = posDiffMDEvent / nActualColumns;
}
// Get the min and max extents in each dimension.
std::vector<double> extentMins(m_nDimensions);
std::vector<double> extentMaxs(m_nDimensions);
DataCollectionType::iterator mdEventEntriesIterator = m_posMDEventStart;
for (size_t i = 0; i < m_nDataObjects; ++i) {
mdEventEntriesIterator += 2;
if (m_IsFullDataObjects) {
mdEventEntriesIterator += 2;
}
for (size_t j = 0; j < m_nDimensions; ++j) {
double coord = convert<double>(*(++mdEventEntriesIterator));
extentMins[j] = coord < extentMins[j] ? coord : extentMins[j];
extentMaxs[j] = coord > extentMaxs[j] ? coord : extentMaxs[j];
}
}
// Create a target output workspace.
IMDEventWorkspace_sptr outWs = MDEventFactory::CreateMDWorkspace(
m_nDimensions, m_IsFullDataObjects ? "MDEvent" : "MDLeanEvent");
// Extract Dimensions and add to the output workspace.
DataCollectionType::iterator dimEntriesIterator = m_posDimStart;
auto unitFactory = makeMDUnitFactoryChain();
for (size_t i = 0; i < m_nDimensions; ++i) {
std::string id = convert<std::string>(*(++dimEntriesIterator));
std::string name = convert<std::string>(*(++dimEntriesIterator));
std::string units = convert<std::string>(*(++dimEntriesIterator));
int nbins = convert<int>(*(++dimEntriesIterator));
auto mdUnit = unitFactory->create(units);
Mantid::Geometry::GeneralFrame frame(
Mantid::Geometry::GeneralFrame::GeneralFrameName, std::move(mdUnit));
outWs->addDimension(MDHistoDimension_sptr(new MDHistoDimension(
id, name, frame, static_cast<coord_t>(extentMins[i]),
static_cast<coord_t>(extentMaxs[i]), nbins)));
}
CALL_MDEVENT_FUNCTION(this->addEventsData, outWs)
// set output
this->setProperty("OutputWorkspace", outWs);
}
