/**
* Populate this object with the data from the file
*/
void FileBackedExperimentInfo::populateFromFile() const {
try {
::NeXus::File nxFile(m_filename);
nxFile.openPath(m_nxpath);
// The loadExperimentInfo calls things such as mutableSample()
// and if m_loaded is not true then this function is
// will be called recursively.
m_loaded = true;
std::string parameterStr;
const_cast<FileBackedExperimentInfo *>(this)
->loadExperimentInfoNexus(m_filename, &nxFile, parameterStr);
const_cast<FileBackedExperimentInfo *>(this)
->readParameterMap(parameterStr);
} catch (::NeXus::Exception &exc) {
std::ostringstream os;
os << "Unable to load experiment information from NeXus file: "
<< exc.what() << "\n";
throw std::runtime_error(os.str());
}
}
/**
* Creates the format for the output file if it doesn't exist
* @returns the structured nexus file to write the data to
*
* @throw runtime_error Thrown if nexus file cannot be opened or created
*/
::NeXus::File SaveNXTomo::setupFile() {
// Try and open the file, if it doesn't exist, create it.
NXhandle fileHandle;
NXstatus status = NXopen(this->m_filename.c_str(), NXACC_RDWR, &fileHandle);
if (status != NX_ERROR && !m_overwriteFile) {
// Appending to an existing file, return reference to the file
::NeXus::File nxFile(fileHandle);
return nxFile;
}
// Either overwriting the file or creating a new one now
if (status != NX_ERROR) {
::NeXus::File f(fileHandle);
f.close();
}
// If not overwriting, ensure it has a .nxs extension
if ((!m_overwriteFile || status == NX_ERROR) &&
!boost::ends_with(this->m_filename, ".nxs"))
m_filename = m_filename + ".nxs";
status = NXopen(this->m_filename.c_str(), NXACC_CREATE5, &fileHandle);
if (status == NX_ERROR)
throw std::runtime_error("Unable to open or create nexus file.");
// *********************************
// Now genererate file and structure
::NeXus::File nxFile(fileHandle);
// Make the top level entry (and open it)
nxFile.makeGroup("entry1", "NXentry", true);
// Make an entry to store log values from the original files.
nxFile.makeGroup("log_info", "NXsubentry", false);
// Make a sub-group for the entry to work with DAWN software (and open it)
nxFile.makeGroup("tomo_entry", "NXsubentry", true);
// Title
nxFile.writeData("title", this->m_filename);
// Definition name and version
nxFile.writeData("definition", "NXtomo");
nxFile.openData("definition");
nxFile.putAttr("version", NXTOMO_VER);
nxFile.closeData();
// Originating program name and version
nxFile.writeData("program_name", "mantid");
nxFile.openData("program_name");
nxFile.putAttr("version", Mantid::Kernel::MantidVersion::version());
nxFile.closeData();
// ******************************************
// NXinstrument
nxFile.makeGroup("instrument", "NXinstrument", true);
// Write the instrument name | could add short_name attribute to name
nxFile.writeData("name", m_workspaces[0]->getInstrument()->getName());
// detector group - diamond example file contains
// {data,distance,image_key,x_pixel_size,y_pixel_size}
nxFile.makeGroup("detector", "NXdetector", true);
std::vector<int64_t> infDim;
infDim.push_back(NX_UNLIMITED);
nxFile.makeData("image_key", ::NeXus::FLOAT64, infDim, false);
nxFile.closeGroup(); // detector
// source group // from diamond file contains {current,energy,name,probe,type}
// - probe = [neutron | x-ray | electron]
nxFile.closeGroup(); // NXinstrument
// ******************************************
// NXsample
nxFile.makeGroup("sample", "NXsample", true);
nxFile.makeData("rotation_angle", ::NeXus::FLOAT64, infDim, true);
// Create a link object for rotation_angle to use later
NXlink rotationLink = nxFile.getDataID();
nxFile.closeData();
nxFile.closeGroup(); // NXsample
// ******************************************
// Make the NXmonitor group - Holds base beam intensity for each image
nxFile.makeGroup("control", "NXmonitor", true);
nxFile.makeData("data", ::NeXus::FLOAT64, infDim, false);
nxFile.closeGroup(); // NXmonitor
nxFile.makeGroup("data", "NXdata", true);
nxFile.putAttr<int>("NumFiles", 0);
nxFile.makeLink(rotationLink);
nxFile.makeData("data", ::NeXus::FLOAT64, m_infDimensions, true);
// Create a link object for the data
NXlink dataLink = nxFile.getDataID();
nxFile.closeData();
if (m_includeError)
nxFile.makeData("error", ::NeXus::FLOAT64, m_infDimensions, false);
nxFile.closeGroup(); // Close Data group
// Put a link to the data in instrument/detector
nxFile.openGroup("instrument", "NXinstrument");
nxFile.openGroup("detector", "NXdetector");
nxFile.makeLink(dataLink);
nxFile.closeGroup();
nxFile.closeGroup();
nxFile.closeGroup(); // tomo_entry sub-group
nxFile.closeGroup(); // Top level NXentry
return nxFile;
}
