void SaveISISNexus::user() {
NXmakegroup(handle, "user_1", "NXuser");
NXopengroup(handle, "user_1", "NXuser");
saveChar("name", m_isisRaw->user.r_user, 20);
saveChar("affiliation", m_isisRaw->user.r_instit, 20);
NXclosegroup(handle); // user_1
}
void SaveISISNexus::sample() {
NXmakegroup(handle, "sample", "NXsample");
NXopengroup(handle, "sample", "NXsample");
saveChar("name", m_isisRaw->spb.e_name, 40);
saveFloat("height", &m_isisRaw->spb.e_height, 1);
saveFloat("width", &m_isisRaw->spb.e_width, 1);
saveFloat("thickness", &m_isisRaw->spb.e_thick, 1);
saveString("id", " ");
float tmp(0.0);
saveFloat("distance", &tmp, 1);
std::string shape[] = {"cylinder", "flat plate", "HRPD slab", "unknown"};
int i = m_isisRaw->spb.e_geom - 1;
if (i < 0 || i > 3)
i = 3;
saveString("shape", shape[i]);
std::string type[] = {"sample+can", "empty can", "vanadium", "absorber",
"nothing", "sample, no can", "unknown"};
i = m_isisRaw->spb.e_type - 1;
if (i < 0 || i > 6)
i = 6;
saveString("type", type[i]);
NXclosegroup(handle); // sample
}
QHash<QString, QString> UrlEncode::getConfiguration()
{
QHash<QString, QString> properties = TransformAbstract::getConfiguration();
properties.insert(XMLPERCENTCHAR,saveChar(percentSign));
properties.insert(XMLINCLUDE,QString(include.toBase64()));
properties.insert(XMLEXCLUDE,QString(exclude.toBase64()));
return properties;
}
/** Execute the algorithm. Currently just calls SaveISISNexusProcessed but could
* call write other formats if support added
*
* @throw runtime_error Thrown if algorithm cannot execute
*/
void SaveISISNexus::exec() {
// Retrieve the filename from the properties
inputFilename = getPropertyValue("InputFileName");
m_isisRaw = new ISISRAW2;
rawFile = fopen(inputFilename.c_str(), "rb");
if (rawFile == nullptr) {
throw Exception::FileError("Cannot open file ", inputFilename);
}
m_isisRaw->ioRAW(rawFile, true);
nper = m_isisRaw->t_nper; // number of periods
nsp = m_isisRaw->t_nsp1; // number of spectra
ntc = m_isisRaw->t_ntc1; // number of time channels
nmon = m_isisRaw->i_mon; // number of monitors
ndet = m_isisRaw->i_det; // number of detectors
std::string outputFilename = getPropertyValue("OutputFileName");
NXstatus status;
float flt;
status = NXopen(outputFilename.c_str(), NXACC_CREATE5, &handle);
if (status != NX_OK) {
throw std::runtime_error("Cannot open file " + outputFilename +
" for writing.");
}
NXmakegroup(handle, "raw_data_1", "NXentry");
NXopengroup(handle, "raw_data_1", "NXentry");
write_isis_vms_compat();
saveString("beamline", " ");
flt = static_cast<float>(m_isisRaw->rpb.r_dur); // could be wrong
saveFloatOpen("collection_time", &flt, 1);
putAttr("units", "second");
close();
saveStringOpen("definition", "TOFRAW");
putAttr("version", "1.0");
putAttr("url",
"http://definition.nexusformat.org/instruments/TOFRAW/?version=1.0");
close();
saveStringOpen("definition_local", "ISISTOFRAW");
putAttr("version", "1.0");
putAttr("url",
"http://svn.isis.rl.ac.uk/instruments/ISISTOFRAW/?version=1.0");
close();
flt = static_cast<float>(m_isisRaw->rpb.r_dur);
saveFloatOpen("duration", &flt, 1);
putAttr("units", "second");
close();
start_time_str.assign(m_isisRaw->hdr.hd_date, m_isisRaw->hdr.hd_date + 12);
toISO8601(start_time_str);
start_time_str += 'T';
start_time_str +=
std::string(m_isisRaw->hdr.hd_time, m_isisRaw->hdr.hd_time + 8);
saveCharOpen("start_time", &start_time_str[0], 19);
putAttr("units", "ISO8601");
close();
std::string str;
str.assign(m_isisRaw->rpb.r_enddate, m_isisRaw->rpb.r_enddate + 12);
toISO8601(str);
str += 'T';
str += std::string(m_isisRaw->rpb.r_endtime, m_isisRaw->rpb.r_endtime + 8);
saveCharOpen("end_time", &str[0], 19);
putAttr("units", "ISO8601");
close();
saveChar("title", m_isisRaw->r_title, 80);
saveInt("good_frames", &m_isisRaw->rpb.r_goodfrm);
std::string experiment_identifier = std::to_string(m_isisRaw->rpb.r_prop);
saveChar("experiment_identifier", &experiment_identifier[0],
static_cast<int>(experiment_identifier.size()));
int tmp_int(0);
saveInt("measurement_first_run", &tmp_int);
saveString("measurement_id", " ");
saveString("measurement_label", " ");
saveString("measurement_subid", " ");
saveString("measurement_type", " ");
saveCharOpen("name", &m_isisRaw->i_inst, 8);
putAttr("short_name", m_isisRaw->hdr.inst_abrv, 3);
close();
logNotes();
saveString("program_name", "isisicp");
saveFloatOpen("proton_charge", &m_isisRaw->rpb.r_gd_prtn_chrg, 1);
putAttr("units", "uamp.hour");
close();
saveFloatOpen("proton_charge_raw", &m_isisRaw->rpb.r_tot_prtn_chrg, 1);
putAttr("units", "uamp.hour");
close();
saveInt("raw_frames", &m_isisRaw->rpb.r_rawfrm);
run_cycle();
saveInt("run_number", &m_isisRaw->r_number);
// script_name
// seci_config
instrument();
make_detector_1_link();
write_monitors();
user();
sample();
runlog();
selog();
NXclosegroup(handle); // raw_data_1
status = NXclose(&handle);
delete m_isisRaw;
}
/// Write isis_vms_compat
void SaveISISNexus::write_isis_vms_compat() {
NXmakegroup(handle, "isis_vms_compat", "IXvms");
NXopengroup(handle, "isis_vms_compat", "IXvms");
int ndet = m_isisRaw->i_det;
int nmon = m_isisRaw->i_mon;
saveInt("ADD", &m_isisRaw->add, 9);
saveInt("CODE", m_isisRaw->code, ndet);
saveInt("CRAT", m_isisRaw->crat, ndet);
write_rpb();
write_spb();
write_vpb();
saveInt("DAEP", &m_isisRaw->daep, 64);
saveInt("DELT", m_isisRaw->delt, ndet);
saveInt("FORM", &m_isisRaw->data_format);
saveChar("HDR", &m_isisRaw->hdr, 80);
saveFloat("LEN2", m_isisRaw->len2, ndet);
saveInt("MDET", m_isisRaw->mdet, nmon);
saveInt("MODN", m_isisRaw->modn, ndet);
saveInt("MONP", m_isisRaw->monp, nmon);
saveInt("MPOS", m_isisRaw->mpos, ndet);
saveChar("NAME", m_isisRaw->i_inst, 8);
saveInt("NDET", &ndet);
saveInt("NFPP", &m_isisRaw->t_nfpp);
saveInt("NMON", &nmon);
saveInt("NPER", &m_isisRaw->t_nper);
saveInt("NSER", &m_isisRaw->e_nse);
saveInt("NSP1", &m_isisRaw->t_nsp1);
saveInt("NTC1", &m_isisRaw->t_ntc1);
saveInt("NTRG", &m_isisRaw->t_ntrg);
saveInt("NUSE", &m_isisRaw->i_use);
saveInt("PMAP", &m_isisRaw->t_pmap, 256);
saveInt("PRE1", &m_isisRaw->t_pre1);
saveInt("RUN", &m_isisRaw->r_number);
saveInt("SPEC", m_isisRaw->spec, ndet);
saveInt("TCM1", &m_isisRaw->t_tcm1);
saveFloat("TCP1", m_isisRaw->t_tcp1, 20);
saveInt("TIMR", m_isisRaw->timr, ndet);
saveChar("TITL", m_isisRaw->r_title, 80);
saveFloat("TTHE", m_isisRaw->tthe, ndet);
saveInt("UDET", m_isisRaw->udet, ndet);
saveInt("ULEN", &m_isisRaw->u_len);
std::string user_info(160, ' ');
if (m_isisRaw->u_len > 0) {
std::copy(reinterpret_cast<char *>(&m_isisRaw->user),
reinterpret_cast<char *>(&m_isisRaw->user) + m_isisRaw->u_len,
user_info.begin());
}
saveString("USER", user_info);
saveInt("VER1", &m_isisRaw->frmt_ver_no);
saveInt("VER2", &m_isisRaw->ver2);
saveInt("VER3", &m_isisRaw->ver3);
saveInt("VER4", &m_isisRaw->ver4);
saveInt("VER5", &m_isisRaw->ver5);
saveInt("VER6", &m_isisRaw->ver6);
saveInt("VER7", &m_isisRaw->ver7);
saveInt("VER8", &m_isisRaw->ver8);
int tmp_int(0);
saveInt("VER9", &tmp_int);
int n = m_isisRaw->logsect.nlines;
log_notes.resize(n);
for (int i = 0; i < n; ++i) {
log_notes[i].assign(m_isisRaw->logsect.lines[i].data,
m_isisRaw->logsect.lines[i].len);
}
int ll = saveStringVectorOpen("NOTE", log_notes);
saveInt("NTNL", &n);
saveInt("NTLL", &ll);
NXclosegroup(handle); // isis_vms_compat
}
/**
* Save a string in a dataset.
* @param name :: Name of the data set
* @param str :: The vector to save
*/
void SaveISISNexus::saveString(const char *name, const std::string &str) {
if (str.empty())
return;
std::string buff(str);
saveChar(name, &buff[0], static_cast<int>(buff.size()));
}
QHash<QString, QString> NumberToChar::getConfiguration()
{
QHash<QString, QString> properties = TransformAbstract::getConfiguration();
properties.insert(XMLSEPARATOR,saveChar(separator));
return properties;
}