bool ALSBL8XASFileLoader::loadFromFile(const QString& filepath, bool setMetaData, bool setRawDataSources, bool createDefaultAnalysisBlocks) {
// not initialized to have a scan target, or scan target is not an AMXASScan...
AMXASScan* scan = qobject_cast<AMXASScan*>(scan_);
if(!scan)
return false;
// Clear the old scan axes to ensure we don't have any extras.
scan->clearRawDataCompletely();
scan->rawData()->addScanAxis( AMAxisInfo("eV", 0, "Incident Energy", "eV") );
// information about the scan we hope to locate:
QString comments;
double integrationTime;
// used in parsing the data file
QString line;
QStringList lp;
// names of the columns, taken from headers in the data file.
QStringList colNames1;
// open the file:
QFile f(filepath);
if(!f.open(QIODevice::ReadOnly)) {
AMErrorMon::report(AMErrorReport(0, AMErrorReport::Serious, -1, "ALSBL8XASFileLoader parse error while loading scan data from file. Missing file."));
return false;
}
QTextStream fs(&f);
if(setMetaData) {
// Start reading the file. look for the count-time line.
while( !fs.atEnd() && !(line = fs.readLine()).startsWith("Count Time (s):") )
;
if(fs.atEnd()) {
AMErrorMon::report(AMErrorReport(0, AMErrorReport::Debug, -2, "ALSBL8XASFileLoader parse error while loading scan data from file. Could not find the count time (integration time)."));
fs.seek(0);
// return false; // bad format; missing the count time string
}
else {
// read it
integrationTime = line.split(':').at(1).trimmed().toDouble();
}
// Keep reading the file. look for the comment line.
while( !fs.atEnd() && !(line = fs.readLine()).startsWith("Description Length:") )
;
if(fs.atEnd()) {
AMErrorMon::report(AMErrorReport(0, AMErrorReport::Debug, -2, "ALSBL8XASFileLoader parse error while loading scan data from file. Could not find the description."));
fs.seek(0);
// return false; // bad format; missing the comment string
}
else {
// read the comment
bool descriptionLengthOk;
int descriptionLength = line.split(':').at(1).trimmed().toInt(&descriptionLengthOk);
// read this many characters now...
if(descriptionLengthOk)
comments = fs.read(descriptionLength);
}
}
// find out what columns exist. Looking for line starting with 'Time (s)'
line.clear();
while(!fs.atEnd() && !line.startsWith("Time (s)"))
line = fs.readLine();
if(fs.atEnd()) {
AMErrorMon::report(AMErrorReport(0, AMErrorReport::Serious, -2, "ALSBL8XASFileLoader parse error while loading scan data from file. Missing the Column Header line."));
return false; // bad format; missing the column header
}
colNames1 = line.split(QChar('\t'));
// translate header names into meaningful column names (ex: "Counter 0" ---> "I0".... "Counter1"--->"tey")
for(int i=0; i<colNames1.count(); i++)
header2columnName(colNames1[i]);
// ensure that we have the basic "eV" column
int eVIndex = colNames1.indexOf("eV");
if(eVIndex < 0) {
AMErrorMon::report(AMErrorReport(0, AMErrorReport::Serious, -3, "ALSBL8XASFileLoader parse error while loading scan data from file. I couldn't find the energy (eV) column."));
return false; // bad format; no primary column
}
// clear the existing raw data (and raw data sources, if we're supposed to)
if(setRawDataSources)
scan->clearRawDataPointsAndMeasurementsAndDataSources();
else
scan->clearRawDataPointsAndMeasurements();
// There is a rawData scan axis called "eV" created in the constructor. AMAxisInfo("eV", 0, "Incident Energy", "eV")
/// \todo What if there isn't? Should we check, and create the axis if none exist? What if there's more than one scan axis? Can't remove from AMDataStore... [The rest of this code assumes a single scan axis]
// add scalar (0D) measurements to the raw data store, for each data column. Also add raw data sources to the scan, which expose this data.
foreach(QString colName, colNames1) {
if(colName != "eV" && colName != "Event-ID") {
scan->rawData()->addMeasurement(AMMeasurementInfo(colName, colName)); /// \todo nice descriptions for the common column names; not just 'tey' or 'tfy'.
}
}
int eVAxisIndex = 0; // counter for each datapoint along the scan axis.
// read all the data. Add to data columns or scan properties depending on the event-ID.
while(!fs.atEnd()) {
line = fs.readLine();
// Data line. If there are the correct number of columns:
if( (lp = line.split('\t', QString::SkipEmptyParts)).count() == colNames1.count() ) {
// append a new datapoint to the data tree (supply primary eV value here)
scan->rawData()->beginInsertRows(1, -1);
scan->rawData()->setAxisValue(0, eVAxisIndex, lp.at(eVIndex).toDouble()); // insert eV
// add all columns (but ignore the eV column)
int measurementId = 0;
for(int i=1; i<colNames1.count(); i++) {
if(i!=eVIndex)
scan->rawData()->setValue(eVAxisIndex, measurementId++, AMnDIndex(), lp.at(i).toDouble());
}
eVAxisIndex++;
scan->rawData()->endInsertRows();
}
}
if(setMetaData) {
scan->setNotes(comments);
// for a date-time, there is no information saved inside the file format, so the best we can do is look at the file's creation date-time...
QFileInfo fi(filepath);
scan->setDateTime(fi.lastModified());
/// \todo integration time... do what with?
}
// If we need to create the raw data sources...
if(setRawDataSources) {
// expose the raw data that might be useful to the users
foreach(QString visibleColumn, defaultUserVisibleColumns_) {
int measurementId = scan->rawData()->idOfMeasurement(visibleColumn);
if(measurementId >= 0)
scan->addRawDataSource(new AMRawDataSource(scan->rawData(), measurementId));
}
}
bool VESPERSXASDataLoader::loadFromFile(const QString &filepath, bool setMetaData, bool setRawDataSources, bool createDefaultAnalysisBlocks)
{
// Currently don't have meta data.
Q_UNUSED(setMetaData)
Q_UNUSED(setRawDataSources)
Q_UNUSED(createDefaultAnalysisBlocks)
AMXASScan *scan = qobject_cast<AMXASScan *>(scan_);
if (!scan) {
AMErrorMon::alert(0, 0, "VESPERS XAS File Loader: Could not load XAS data into a non-XAS scan.");
return false;
}
// Clear the old scan axes to ensure we don't have any extras.
scan->clearRawDataCompletely();
scan->rawData()->addScanAxis( AMAxisInfo("eV", 0, "Incident Energy", "eV") );
QFile file(filepath);
if(!file.open(QIODevice::ReadOnly)) {
AMErrorMon::error(0, -1, "XASFileLoader parse error while loading scan data from file.");
return false;
}
QFile spectra;
QVector<int> data;
QTextStream in(&file);
QString line;
QStringList lineTokenized;
// Need to determine if the single element or four element vortex detector was used. Also need to determine which ion chambers were used for I0 and It.
// First two lines are useless.
line = in.readLine();
line = in.readLine();
line = in.readLine();
if (line.contains("#(2)"))
line = in.readLine();
bool usingVortex = line.contains("IOC1607-004") || line.contains("dxp1607-B21-04");
if (usingVortex) {
data.resize(2048);
QString temp(filepath);
temp.chop(4);
spectra.setFileName(temp+"_spectra.dat");
if(!spectra.open(QIODevice::ReadOnly)) {
AMErrorMon::error(0, -1, QString("XASFileLoader parse error while loading scan spectra data from %1.").arg(spectra.fileName()));
return false;
}
}
else
spectra.setFileName("");
QTextStream spectraStream(&spectra);
QString spectraLine;
QStringList spectraTokenized;
while ((line = in.readLine()).contains("#")) {
//Do nothing
}
// Clear any old data so we can start fresh.
scan->clearRawDataPointsAndMeasurements();
// Some setup variables.
int axisValueIndex = 0;
if (usingVortex) {
for (int i = 0; i < scan_->rawDataSourceCount()-1; i++)
scan_->rawData()->addMeasurement(AMMeasurementInfo(scan_->rawDataSources()->at(i)->name(), scan_->rawDataSources()->at(i)->description()));
QList<AMAxisInfo> axisInfo;
AMAxisInfo ai("Energy", 2048, "Energy", "eV");
ai.increment = 10;
ai.start = AMNumber(0);
ai.isUniform = true;
axisInfo << ai;
scan_->rawData()->addMeasurement(AMMeasurementInfo(scan_->rawDataSources()->at(scan_->rawDataSourceCount()-1)->name(), scan_->rawDataSources()->at(scan_->rawDataSourceCount()-1)->description(), "eV", axisInfo));
}
else {
for (int i = 0; i < scan_->rawDataSourceCount(); i++)
scan_->rawData()->addMeasurement(AMMeasurementInfo(scan_->rawDataSources()->at(i)->name(), scan_->rawDataSources()->at(i)->description()));
}
while (!in.atEnd()) {
lineTokenized << line.split(", ");
scan->rawData()->beginInsertRows(1, -1);
scan_->rawData()->setAxisValue(0, axisValueIndex, lineTokenized.at(1).toDouble());
// This isn't the most efficient way of putting the spectra data in, but it will do for the time being.
if (usingVortex) {
// Only going to rawDataSourceCount-1 because the last raw data source is the 2D spectra scan and requires its own method of entering the data.
for (int i = 0; i < scan_->rawDataSourceCount()-1; i++)
scan_->rawData()->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
spectraTokenized.clear();
spectraLine = spectraStream.readLine();
spectraTokenized << spectraLine.split(",");
for (int j = 0; j < 2048; j++)
data[j] = spectraTokenized.at(j).toInt();
scan_->rawData()->setValue(axisValueIndex, scan_->rawDataSourceCount()-1, data.constData());
}
else {
// In transmission, there is no 2D spectra. Go through all the data sources.
for (int i = 0; i < scan_->rawDataSourceCount(); i++)
scan_->rawData()->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
scan->rawData()->endInsertRows();
axisValueIndex++;
line = in.readLine();
lineTokenized.clear();
}
file.close();
if (usingVortex)
spectra.close();
return true;
}
