AM1DRunningAverageFilterAB::AM1DRunningAverageFilterAB(int filterSize, const QString &outputName, QObject *parent) :
AMStandardAnalysisBlock(outputName, parent)
{
inputSource_ = 0;
filterSize_ = filterSize;
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
// Returns a bunch of information about a particular axis.
AMAxisInfo AM1DExpressionAB::axisInfoAt(int axisNumber) const {
if(axisNumber != 0)
return AMAxisInfo("invalid", 0);
axisInfo_.size = size_;
/// \todo: optimization: the axis is uniform if its a direct output of the axisValue() of a source with a uniform axis.
axisInfo_.isUniform = false;
return axisInfo_;
}
AM1DInterpolationAB::AM1DInterpolationAB(int interpolationPoints, const QString &outputName, QObject *parent) :
AMStandardAnalysisBlock(outputName, parent)
{
inputSource_ = 0;
interpolationPoints_ = interpolationPoints;
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
AMDeadTimeAB::AMDeadTimeAB(const QString &outputName, QObject *parent)
: AMStandardAnalysisBlock(outputName, parent)
{
spectra_ = 0;
icr_ = 0;
ocr_ = 0;
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
AM1DDerivativeAB::AM1DDerivativeAB(const QString &outputName, QObject *parent) :
AMStandardAnalysisBlock(outputName, parent)
{
inputSource_ = 0;
analyzedName_ = "";
canAnalyze_ = false;
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
AM4DBinningAB::AM4DBinningAB(AMDatabase *db, int id)
: AMStandardAnalysisBlock("tempName")
{
sumAxis_ = 3;
sumRangeMin_ = 0;
sumRangeMax_ = 0;
inputSource_ = 0;
cacheCompletelyInvalid_ = true;
// leave sources_ empty for now.
axes_ << AMAxisInfo("invalid", 0, "No input data") << AMAxisInfo("invalid", 0, "No input data") << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
loadFromDb(db, id);
// will restore sumAxis, sumRangeMin, and sumRangeMax. We'll remain invalid until we get connected.
AMDataSource::name_ = AMDbObject::name(); // normally it's not okay to change a dataSource's name. Here we get away with it because we're within the constructor, and nothing's watching us yet.
}
void REIXSXESImageInterpolationAB::setInputDataSourcesImplementation(const QList<AMDataSource *> &dataSources)
{
// disconnect connections from old source, if it exists.
if(inputSource_) {
disconnect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
inputSource_ = 0;
}
if(dataSources.isEmpty()) {
inputSource_ = 0;
sources_.clear();
axes_[0] = AMAxisInfo("invalid", 0, "No input data");
}
// we know that this will only be called with one valid input source
else {
inputSource_ = dataSources.at(0);
sources_ = dataSources;
axes_[0] = inputSource_->axisInfoAt(0); // take the X axis info from the data source.
axes_[0].description = "Emission Energy";
axes_[0].units = "eV";
axes_[0].size /= binningLevel_;
cacheUpdateRequired_ = true;
axisValueCacheInvalid_ = true;
cachedData_ = QVector<double>(axes_.at(0).size);
cachedAxisValues_ = QVector<double>(axes_.at(0).size);
if(shiftValues1_.isEmpty()) {
for(int i=0,cc=inputSource_->size(1); i<cc; i++)
shiftValues1_ << 0; // make a null shift list, matching the size of the input data. Don't do this if we already have a shift list.
}
if(shiftValues2_.isEmpty()) {
for(int i=0,cc=inputSource_->size(1); i<cc; i++)
shiftValues2_ << 0; // make a null shift list, matching the size of the input data. Don't do this if we already have a shift list.
}
connect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
reviewState();
emitSizeChanged();
emitValuesChanged();
emitAxisInfoChanged();
emitInfoChanged();
}
VESPERSEnergyScanActionController::VESPERSEnergyScanActionController(VESPERSEnergyScanConfiguration *configuration, QObject *parent)
: AMStepScanActionController(configuration, parent), VESPERSScanController(configuration)
{
configuration_ = configuration;
scan_ = new AMXASScan();
scan_->setName(configuration_->name());
scan_->setScanConfiguration(configuration_);
scan_->setFileFormat("amCDFv1");
scan_->setIndexType("fileSystem");
scan_->setNotes(buildNotes());
scan_->rawData()->addScanAxis(AMAxisInfo("eV", 0, "Incident Energy", "eV"));
useFeedback_ = true;
originalEnergy_ = VESPERSBeamline::vespers()->mono()->energy();
AMControlInfoList list;
list.append(VESPERSBeamline::vespers()->energy()->toInfo());
configuration_->setAxisControlInfos(list);
AMDetectorInfoSet detectors;
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("SplitIonChamber")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("PreKBIonChamber")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("MiniIonChamber")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("PostIonChamber")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("EnergySetpoint")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("MasterDwellTime")->toInfo());
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("RingCurrent")->toInfo());
VESPERS::CCDDetectors ccdDetector = configuration_->ccdDetector();
if (ccdDetector.testFlag(VESPERS::Roper))
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("RoperFileNumber")->toInfo());
if (ccdDetector.testFlag(VESPERS::Mar))
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("MarFileNumber")->toInfo());
if (ccdDetector.testFlag(VESPERS::Pilatus))
detectors.addDetectorInfo(VESPERSBeamline::vespers()->exposedDetectorByName("PilatusFileNumber")->toInfo());
configuration_->setDetectorConfigurations(detectors);
secondsElapsed_ = 0;
secondsTotal_ = configuration_->totalTime();
elapsedTime_.setInterval(1000);
connect(this, SIGNAL(started()), &elapsedTime_, SLOT(start()));
connect(this, SIGNAL(cancelled()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(paused()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(resumed()), &elapsedTime_, SLOT(start()));
connect(this, SIGNAL(failed()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(finished()), &elapsedTime_, SLOT(stop()));
connect(&elapsedTime_, SIGNAL(timeout()), this, SLOT(onScanTimerUpdate()));
}
AM1DDarkCurrentCorrectionAB::AM1DDarkCurrentCorrectionAB(const QString &outputName, QObject *parent)
: AMStandardAnalysisBlock(outputName, parent)
{
data_ = 0;
dwellTime_ = 0;
darkCurrent_ = 0;
canAnalyze_ = false;
dataName_ = "";
dwellTimeName_ = "";
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
void AMAdditionAB::setInputDataSourcesImplementation(const QList<AMDataSource*>& dataSources)
{
// disconnect connections from old sources, if they exist.
if(!sources_.isEmpty()) {
for (int i = 0; i < sources_.size(); i++) {
disconnect(sources_.at(i)->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(sources_.at(i)->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(sources_.at(i)->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
}
if(dataSources.isEmpty()) {
sources_.clear();
for (int i = 0, size = rank(); i < size; i++)
axes_[i] = AMAxisInfo("invalid", 0, "No input data");
setDescription("-- No input data --");
}
// we know that this will only be called with valid input source
else {
sources_ = dataSources;
for (int i = 0, size = rank(); i < size; i++)
axes_[i] = sources_.at(0)->axisInfoAt(i);
cacheUpdateRequired_ = true;
cachedData_ = QVector<double>(size().product());
setDescription(QString("Sum of spectra from %1 maps").arg(sources_.size()));
for (int i = 0; i < sources_.size(); i++) {
connect(sources_.at(i)->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(sources_.at(i)->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(sources_.at(i)->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
}
reviewState();
emitSizeChanged();
emitValuesChanged();
emitAxisInfoChanged();
emitInfoChanged();
}
AM1DNormalizationAB::AM1DNormalizationAB(const QString &outputName, QObject *parent)
: AMStandardAnalysisBlock(outputName, parent)
{
data_ = 0;
normalizer_ = 0;
canAnalyze_ = false;
dataName_ = "";
normalizationName_ = "";
cacheUpdateRequired_ = false;
cachedDataRange_ = AMRange();
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
REIXSXESImageInterpolationAB::REIXSXESImageInterpolationAB(const QString &outputName, QObject *parent) :
AMStandardAnalysisBlock(outputName, parent)
{
// Live correlation turned off by default. Prevents correlation while loading from db and no shift is really better than a random shift, initially.
liveCorrelation_ = false;
curve1Smoother_ = 0;
curve2Smoother_ = 0;
sumRangeMinY_ = 10;
sumRangeMaxY_ = 53;
sumRangeMinX_ = 75;
sumRangeMaxX_ = 925;
rangeRound_ = 0.6;
curve2Disabled_ = false;
correlation1CenterPx_ = 250;
correlation2CenterPx_ = 700;
correlation1HalfWidth_ = 40;
correlation2HalfWidth_ = 40;
setCorrelation1Smoothing(QPair<int,int>(3,5)); //poly,quadratic
setCorrelation2Smoothing(QPair<int,int>(3,5)); //poly,quadratic
energyCalibrationOffset_ = 0;
tiltCalibrationOffset_ = 0;
interpolationLevel_ = 10;
binningLevel_ = 2;
inputSource_ = 0;
cacheUpdateRequired_ = false;
cachedDataRange_ = AMRange();
axisValueCacheInvalid_ = true;
axisValuesInvalid_ = false;
// leave sources_ empty for now.
axes_ << AMAxisInfo("invalid", 0, "No input data");
connect(&callCorrelation_, SIGNAL(executed()), this, SLOT(correlateNow()));
setDescription("XES Interpolated Spectrum");
// shift values can start out empty.
shiftValues1_ << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0;
shiftValues2_ << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0 << 0;
}
// Set the data source inputs.
void AM1DSummingAB::setInputDataSourcesImplementation(const QList<AMDataSource*>& dataSources)
{
// disconnect connections from old sources, if they exist.
if(!sources_.isEmpty()) {
for (int i = 0; i < sources_.size(); i++){
disconnect(sources_.at(i)->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(sources_.at(i)->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(sources_.at(i)->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
}
if(dataSources.isEmpty()) {
sources_.clear();
axes_[0] = AMAxisInfo("invalid", 0, "No input data");
setDescription("-- No input data --");
}
// we know that this will only be called with valid input source
else {
sources_ = dataSources;
axes_[0] = sources_.at(0)->axisInfoAt(0);
setDescription(QString("Sum of %1 spectra").arg(sources_.size()));
for (int i = 0; i < sources_.size(); i++){
connect(sources_.at(i)->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(sources_.at(i)->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(sources_.at(i)->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
}
reviewState();
emitSizeChanged(0);
emitValuesChanged();
emitAxisInfoChanged(0);
emitInfoChanged();
}
VESPERSEnergyDacqScanController::VESPERSEnergyDacqScanController(VESPERSEnergyScanConfiguration *cfg, QObject *parent)
: AMDacqScanController(cfg, parent), VESPERSScanController(cfg)
{
config_ = cfg;
secondsElapsed_ = 0;
secondsTotal_ = config_->totalTime();
elapsedTime_.setInterval(1000);
connect(this, SIGNAL(started()), &elapsedTime_, SLOT(start()));
connect(this, SIGNAL(cancelled()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(paused()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(resumed()), &elapsedTime_, SLOT(start()));
connect(this, SIGNAL(failed()), &elapsedTime_, SLOT(stop()));
connect(this, SIGNAL(finished()), &elapsedTime_, SLOT(stop()));
connect(&elapsedTime_, SIGNAL(timeout()), this, SLOT(onScanTimerUpdate()));
scan_ = new AMXASScan(); // MB: Moved from line 363 in startImplementation.
scan_->setName(config_->name());
scan_->setScanConfiguration(config_);
scan_->setRunId(AMUser::user()->currentRunId());
scan_->setIndexType("fileSystem");
scan_->setFilePath(AMUserSettings::defaultRelativePathForScan(QDateTime::currentDateTime())+".cdf");
scan_->setFileFormat("amCDFv1");
scan_->replaceRawDataStore(new AMCDFDataStore(AMUserSettings::userDataFolder % scan_->filePath(), false));
scan_->rawData()->addScanAxis(AMAxisInfo("eV", 0, "Incident Energy", "eV"));
scan_->setNotes(buildNotes());
AMOldDetectorSet *ionChambers = VESPERSBeamline::vespers()->ionChambers();
AMMeasurementInfo temp = AMMeasurementInfo("", "");
for (int i = 0; i < ionChambers->count(); i++) {
temp = AMMeasurementInfo(*(ionChambers->detectorAt(i)->toInfo()));
temp.name = ionChambers->detectorAt(i)->detectorName();
scan_->rawData()->addMeasurement(temp);
scan_->addRawDataSource(new AMRawDataSource(scan_->rawData(), scan_->rawData()->measurementCount() - 1), true, false);
}
addExtraDatasources();
useDwellTimes(VESPERSBeamline::vespers()->dwellTimeTrigger(), VESPERSBeamline::vespers()->dwellTimeConfirmed());
}
// Set the data source inputs.
void AM1DRunningAverageFilterAB::setInputDataSourcesImplementation(const QList<AMDataSource*>& dataSources) {
// disconnect connections from old source, if it exists.
if(inputSource_) {
disconnect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
if(dataSources.isEmpty()) {
inputSource_ = 0;
sources_.clear();
axes_[0] = AMAxisInfo("invalid", 0, "No input data");
setDescription("-- No input data --");
}
// we know that this will only be called with valid input source
else {
inputSource_ = dataSources.at(0);
sources_ = dataSources;
axes_[0] = inputSource_->axisInfoAt(0);
setDescription(QString("Running Average of %1")
.arg(inputSource_->name()));
connect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
reviewState();
emitSizeChanged(0);
emitValuesChanged();
emitAxisInfoChanged(0);
emitInfoChanged();
}
void AM1DDerivativeAB::setInputDataSourcesImplementation(const QList<AMDataSource*>& dataSources)
{
// disconnect connections from old source, if it exists.
if(inputSource_) {
disconnect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
inputSource_ = 0;
}
if(dataSources.isEmpty()) {
inputSource_ = 0;
sources_.clear();
canAnalyze_ = false;
axes_[0] = AMAxisInfo("invalid", 0, "No input data");
setDescription("Derivative");
}
// we know that this will only be called with valid input source
else if (dataSources.count() == 1){
inputSource_ = dataSources.at(0);
sources_ = dataSources;
canAnalyze_ = true;
axes_[0] = inputSource_->axisInfoAt(0);
cacheUpdateRequired_ = true;
cachedData_ = QVector<double>(size(0));
setDescription(QString("Derivative of %1").arg(inputSource_->name()));
connect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
bool ALSBL8XASFileLoaderPlugin::load(AMScan *scan, const QString &userDataFolder, AMErrorMon *errorMonitor){
if(columns2fileFormatHeaders_.count() == 0) {
columns2fileFormatHeaders_.set("eV", "Mono Energy");
columns2fileFormatHeaders_.set("ringCurrent", "Beam Current");
columns2fileFormatHeaders_.set("I0", "Counter 0");
columns2fileFormatHeaders_.set("TEY", "Counter 1");
columns2fileFormatHeaders_.set("TFY", "Counter 2");
}
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") );
QFileInfo sourceFileInfo(scan->filePath());
if(sourceFileInfo.isRelative()){
sourceFileInfo.setFile(userDataFolder + "/" + scan->filePath());
}
// 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(sourceFileInfo.filePath());
if(!f.open(QIODevice::ReadOnly)) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, ALSBL8XASFileLoaderPLUGIN_CANNOT_OPEN_FILE, "ALSBL8XASFileLoader parse error while loading scan data from file. Missing file."));
return false;
}
QTextStream fs(&f);
// find out what columns exist. Looking for line starting with 'Time (s)'
while(!fs.atEnd() && !line.startsWith("Time (s)"))
line = fs.readLine();
if(fs.atEnd()) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, ALSBL8XASFileLoaderPLUGIN_BAD_FORMAT_NO_EVENT1_HEADER, "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) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, ALSBL8XASFileLoaderPLUGIN_BAD_FORMAT_NO_ENERGY_COLUMN, "ALSBL8XASFileLoader parse error while loading scan data from file. I couldn't find the energy (eV) column."));
return false; // bad format. No primary column
}
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();
}
}
/// Not supposed to create the raw data sources. Do an integrity check on the pre-existing data sources instead... If there's a raw data source, but it's pointing to a non-existent measurement in the data store, that's a problem. Remove it. \todo Is there any way to incorporate this at a higher level, so that import-writers don't need to bother?
for(int i=0; i<scan->rawDataSources()->count(); i++) {
if(scan->rawDataSources()->at(i)->measurementId() >= scan->rawData()->measurementCount()) {
errorMonitor->exteriorReport(AMErrorReport(scan, AMErrorReport::Debug, ALSBL8XASFileLoaderPLUGIN_DATA_COLUMN_MISMATCH, QString("The data in the file didn't match the raw data columns we were expecting. Removing the raw data column '%1')").arg(scan->rawDataSources()->at(i)->name())));
scan->deleteRawDataSource(i);
}
}
return true;
}
bool VESPERS2012SpatialLineScanFileLoaderPlugin::load(AMScan *scan, const QString &userDataFolder, AMErrorMon *errorMonitor)
{
// Check for null scan reference.
if (!scan)
return false;
QFileInfo sourceFileInfo(scan->filePath());
if(sourceFileInfo.isRelative())
sourceFileInfo.setFile(userDataFolder + "/" + scan->filePath());
QFile file(sourceFileInfo.filePath());
if(!file.open(QIODevice::ReadOnly)) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, VESPERS201SPATIALLINESCANFILELOADERPLUGIN_CANNOT_OPEN_FILE, "Line Scan File Loader parse error while loading scan data from file."));
return false;
}
QTextStream in(&file);
QString line;
QStringList lineTokenized;
bool usingSingleElement = false;
bool usingFourElement = false;
if (scan->fileFormat() == "vespers2012LineScanXRF1El" || scan->fileFormat() == "vespers2012LineScanXRF1ElXRD")
usingSingleElement = true;
else if (scan->fileFormat() == "vespers2012LineScanXRF4El" || scan->fileFormat() == "vespers2012LineScanXRF4ElXRD")
usingFourElement = true;
else if (scan->fileFormat() == "vespers2012LineScan1Eln4El" || scan->fileFormat() == "vespers2012LineScan1Eln4ElXRD"){
usingSingleElement = true;
usingFourElement = true;
}
in.readLine();
in.readLine();
in.readLine();
// Grab the first PV, it tells us what the axis was.
line = in.readLine();
lineTokenized = line.split(" ");
line = lineTokenized.at(2);
QString temp = sourceFileInfo.filePath();
temp.replace(".dat", ".cdf");
AMCDFDataStore *cdfData = new AMCDFDataStore(temp, false);
if (line == "TS1607-2-B21-01:H:user:mm")
cdfData->addScanAxis(AMAxisInfo("H", 0, "Horizontal Position", "mm"));
else if (line == "TS1607-2-B21-01:V:user:mm")
cdfData->addScanAxis(AMAxisInfo("V", 0, "Vertical Position", "mm"));
else if (line == "SVM1607-2-B21-02:mm")
cdfData->addScanAxis(AMAxisInfo("X", 0, "Horizontal Position", "mm"));
else if (line == "SVM1607-2-B21-01:mm")
cdfData->addScanAxis(AMAxisInfo("Z", 0, "Vertical Position", "mm"));
else if (line == "07B2_Mono_SineB_Egec:eV")
cdfData->addScanAxis(AMAxisInfo("eV", 0, "Incident Energy", "eV"));
in.readLine();
in.readLine();
in.readLine();
// Clear any old data so we can start fresh.
scan->clearRawDataPointsAndMeasurements();
int axisValueIndex = 0;
int count = scan->rawDataSourceCount();
// Note! Not general!
QList<AMAxisInfo> axisInfo;
AMAxisInfo ai("Energy", 2048, "Energy", "eV");
ai.increment = 10;
ai.start = AMNumber(0);
ai.isUniform = true;
axisInfo << ai;
if (usingSingleElement && usingFourElement){
// The last 6 raw data sources are spectra.
for (int i = 0; i < count-6; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
for (int i = count-6; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description(), "eV", axisInfo));
}
else if (usingSingleElement){
// The last raw data source is a spectrum.
for (int i = 0; i < count-1; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(scan->rawDataSourceCount()-1)->name(), scan->rawDataSources()->at(scan->rawDataSourceCount()-1)->description(), "eV", axisInfo));
}
else if (usingFourElement){
// The last 5 raw data sources are spectra.
for (int i = 0; i < count-5; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
for (int i = count-5; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description(), "eV", axisInfo));
}
else{
for (int i = 0; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
}
lineTokenized.clear();
QStringList fileLines;
while(!in.atEnd())
fileLines << in.readLine();
file.close();
// Add in the data at the right spot.
cdfData->beginInsertRows(fileLines.size(), -1);
foreach(QString currentLine, fileLines){
lineTokenized = currentLine.split(", ");
cdfData->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 (usingSingleElement && usingFourElement){
// Only going to rawDataSourceCount-6 because the last 6 raw data sources are the 2D spectra scan and requires its own method of entering the data.
for (int i = 0; i < count-6; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else if (usingSingleElement){
// 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 < count-1; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else if (usingFourElement){
// Only going to rawDataSourceCount-5 because the last 5 raw data sources are the 2D spectra scan and requires its own method of entering the data.
for (int i = 0; i < count-5; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else{
for (int i = 0; i < count; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
// Advance to the next spot.
axisValueIndex++;
}
bool SGM2013FastFileLoaderPlugin::load(AMScan *scan, const QString &userDataFolder, AMErrorMon *errorMonitor){
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") );
QFileInfo sourceFileInfo(scan->filePath());
if(sourceFileInfo.isRelative())
sourceFileInfo.setFile(userDataFolder + "/" + scan->filePath());
// open the file:
QFile f(sourceFileInfo.filePath());
if(!f.open(QIODevice::ReadOnly)) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, SGM2013FASTFILELOADERPLUGIN_CANNOT_OPEN_FILE, "SGM2013FastFileLoader parse error while loading scan data from file. Missing file."));
return false;
}
QTextStream fs(&f);
QMap<int, QList<int> > measurementOrderByRank;
// used in parsing the data file
QString line;
QStringList lp;
QString versionString;
int index;
double dataValue;
int insertionIndex = 0;
bool informationSection = false;
bool finishedHeader = false;
while(!fs.atEnd()){
if(!finishedHeader)
line = fs.readLine();
if(line == "Start Info")
informationSection = true;
else if(line.contains("Version: "))
versionString = line.remove("Version: ");
else if(line == "End Info"){
informationSection = false;
finishedHeader = true;
line = "";
}
else if(informationSection){
if(versionString == "SGM Generic Fast 0.1"){
if(!line.contains("Encoder Start Value:") && !line.contains("SpacingParam:") && !line.contains("C1Param:") && !line.contains("C2Param:") && !line.contains("SParam:") && !line.contains("ThetaParam:")){
lp = line.split("|!|!|");
index = lp.at(0).toInt();
if(index >= 0){
QString oneString = lp.at(1);
AMTextStream measurementInfoStreamOut(&oneString);
AMMeasurementInfo oneMeasurementInfo = AMMeasurementInfo(QString(), QString());
measurementInfoStreamOut.read(oneMeasurementInfo);
if(measurementOrderByRank.contains(oneMeasurementInfo.rank())){
QList<int> thisRankList = measurementOrderByRank.value(oneMeasurementInfo.rank());
thisRankList.append(index);
measurementOrderByRank.insert(oneMeasurementInfo.rank(), thisRankList);
}
else{
QList<int> newRankList;
newRankList.append(index);
measurementOrderByRank.insert(oneMeasurementInfo.rank(), newRankList);
}
scan->rawData()->addMeasurement(oneMeasurementInfo);
}
}
}
}
else{
if(!fs.atEnd()){
fs >> dataValue;
if(!fs.atEnd()){
scan->rawData()->beginInsertRows(1, -1);
scan->rawData()->setAxisValue(0, insertionIndex, dataValue); // insert eV
QList<int> rank0Measurements = measurementOrderByRank.value(0);
for(int x = 0; x < rank0Measurements.count(); x++){
fs >> dataValue;
scan->rawData()->setValue(AMnDIndex(insertionIndex), rank0Measurements.at(x), AMnDIndex(), dataValue);
}
scan->rawData()->endInsertRows();
insertionIndex++;
}
}
}
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;
}
// Set the data source inputs.
void AM4DBinningAB::setInputDataSourcesImplementation(const QList<AMDataSource*>& dataSources) {
// disconnect connections from old source, if it exists.
if(inputSource_) {
disconnect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
disconnect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
disconnect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
inputSource_ = 0;
}
if(dataSources.isEmpty()) {
inputSource_ = 0;
sources_.clear();
canAnalyze_ = false;
axes_[0] = AMAxisInfo("invalid", 0, "No input data");
axes_[1] = AMAxisInfo("invalid", 0, "No input data");
axes_[2] = AMAxisInfo("invalid", 0, "No input data");
setDescription("-- No input data --");
}
// we know that this will only be called with valid input source
else if (dataSources.count() == 1) {
inputSource_ = dataSources.at(0);
sources_ = dataSources;
canAnalyze_ = true;
switch (sumAxis_) {
case 0:
axes_[0] = inputSource_->axisInfoAt(1);
axes_[1] = inputSource_->axisInfoAt(2);
axes_[2] = inputSource_->axisInfoAt(3);
break;
case 1:
axes_[0] = inputSource_->axisInfoAt(0);
axes_[1] = inputSource_->axisInfoAt(2);
axes_[2] = inputSource_->axisInfoAt(3);
break;
case 2:
axes_[0] = inputSource_->axisInfoAt(0);
axes_[1] = inputSource_->axisInfoAt(1);
axes_[2] = inputSource_->axisInfoAt(3);
break;
case 3:
axes_[0] = inputSource_->axisInfoAt(0);
axes_[1] = inputSource_->axisInfoAt(1);
axes_[2] = inputSource_->axisInfoAt(2);
}
cacheUpdateRequired_ = true;
cachedData_ = QVector<double>(size().product());
setDescription(QString("%1 Summed (over %2)")
.arg(inputSource_->name())
.arg(inputSource_->axisInfoAt(sumAxis_).name));
connect(inputSource_->signalSource(), SIGNAL(valuesChanged(AMnDIndex,AMnDIndex)), this, SLOT(onInputSourceValuesChanged(AMnDIndex,AMnDIndex)));
connect(inputSource_->signalSource(), SIGNAL(sizeChanged(int)), this, SLOT(onInputSourceSizeChanged()));
connect(inputSource_->signalSource(), SIGNAL(stateChanged(int)), this, SLOT(onInputSourceStateChanged()));
}
AM1DSummingAB::AM1DSummingAB(const QString &outputName, QObject *parent)
: AMStandardAnalysisBlock(outputName, parent)
{
axes_ << AMAxisInfo("invalid", 0, "No input data");
setState(AMDataSource::InvalidFlag);
}
bool VESPERS2011XASFileLoaderPlugin::load(AMScan *scan, const QString &userDataFolder, AMErrorMon *errorMonitor)
{
// Check for null scan reference.
if (!scan)
return false;
QFileInfo sourceFileInfo(scan->filePath());
if(sourceFileInfo.isRelative())
sourceFileInfo.setFile(userDataFolder + "/" + scan->filePath());
QFile file(sourceFileInfo.filePath());
if(!file.open(QIODevice::ReadOnly)) {
errorMonitor->exteriorReport(AMErrorReport(0, AMErrorReport::Serious, VESPERS2011XASFILELOADERPLUGIN_CANNOT_OPEN_FILE, "XASFileLoader parse error while loading scan data from file."));
return false;
}
QString temp = sourceFileInfo.filePath();
temp.replace(".dat", ".cdf");
AMCDFDataStore *cdfData = new AMCDFDataStore(temp, false);
cdfData->addScanAxis( AMAxisInfo("eV", 0, "Incident Energy", "eV") );
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 usingSingleElement = line.contains("IOC1607-004");
bool usingFourElement = line.contains("dxp1607-B21-04");
while ((line = in.readLine()).contains("#")){
//Do nothing
}
// Clear any old data so we can start fresh.
scan->clearRawDataPointsAndMeasurements();
// Some setup variables.
int axisValueIndex = 0;
int count = scan->rawDataSourceCount();
// Note! Not general!
QList<AMAxisInfo> axisInfo;
AMAxisInfo ai("Energy", 2048, "Energy", "eV");
ai.increment = 10;
ai.start = AMNumber(0);
ai.isUniform = true;
axisInfo << ai;
if (usingSingleElement && usingFourElement){
// The last 6 raw data sources are spectra.
for (int i = 0; i < count-6; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
for (int i = count-6; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description(), "eV", axisInfo));
}
else if (usingSingleElement){
// The last raw data source is a spectrum.
for (int i = 0; i < count-1; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(scan->rawDataSourceCount()-1)->name(), scan->rawDataSources()->at(scan->rawDataSourceCount()-1)->description(), "eV", axisInfo));
}
else if (usingFourElement){
// The last 5 raw data sources are spectra.
for (int i = 0; i < count-5; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
for (int i = count-5; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description(), "eV", axisInfo));
}
else{
for (int i = 0; i < count; i++)
cdfData->addMeasurement(AMMeasurementInfo(scan->rawDataSources()->at(i)->name(), scan->rawDataSources()->at(i)->description()));
}
QStringList fileLines;
fileLines << line;
while(!in.atEnd())
fileLines << in.readLine();
file.close();
// Add in the data at the right spot.
cdfData->beginInsertRows(fileLines.size(), -1);
foreach(QString currentLine, fileLines){
lineTokenized = currentLine.split(", ");
cdfData->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 (usingSingleElement && usingFourElement){
// Only going to rawDataSourceCount-6 because the last 6 raw data sources are the 2D spectra scan and requires its own method of entering the data.
for (int i = 0; i < count-6; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else if (usingSingleElement){
// 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 < count-1; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else if (usingFourElement){
// Only going to rawDataSourceCount-5 because the last 5 raw data sources are the 2D spectra scan and requires its own method of entering the data.
for (int i = 0; i < count-5; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
else{
// In transmission, there is no 2D spectra. Go through all the data sources.
for (int i = 0; i < count; i++)
cdfData->setValue(axisValueIndex, i, AMnDIndex(), lineTokenized.at(i+2).toDouble());
}
axisValueIndex++;
}
SGMXASScanController::SGMXASScanController(SGMXASScanConfiguration *cfg){
config_ = cfg;
initializationActions_ = 0; //NULL
cleanUpActions_ = 0; //NULL
beamlineInitialized_ = false;
specificScan_ = new AMXASScan();
specificScan_->setFileFormat("sgm2011XAS");
specificScan_->setRunId(AMUser::user()->currentRunId());
specificScan_->setScanConfiguration(config_);
specificScan_->setSampleId(SGMBeamline::sgm()->currentSampleId());
specificScan_->setIndexType("fileSystem");
specificScan_->rawData()->addScanAxis(AMAxisInfo("eV", 0, "Incident Energy", "eV"));
QString scanName;
QString sampleName;
if(specificScan_->sampleId() == -1)
sampleName = "Unknown Sample";
else
sampleName = AMSamplePre2013(specificScan_->sampleId(), AMUser::user()->database()).name();
if(config_->userScanName() == ""){
scanName = config_->autoScanName();
specificScan_->setName(QString("%1 - %2").arg(sampleName).arg(scanName));
}
else{
scanName = config_->userScanName();
specificScan_->setName(QString("%1 - %2").arg(scanName).arg(sampleName));
}
// Create space in raw data store, and create raw data channels, for each detector.
for(int i = 0; i < config_->allDetectorConfigurations().count(); i++){
AMOldDetectorInfo* detectorInfo = config_->allDetectorConfigurations().detectorInfoAt(i);
if(config_->allDetectorConfigurations().isActiveAt(i)){
if(specificScan_->rawData()->addMeasurement(AMMeasurementInfo(*detectorInfo)))
specificScan_->addRawDataSource(new AMRawDataSource(specificScan_->rawData(), specificScan_->rawData()->measurementCount()-1));
else
AMErrorMon::alert(0, SGMXASSCANCONTROLLER_CANNOT_ADD_MEASUREMENT, QString("Could not add measurement to SGMXASScanController by name %1").arg(detectorInfo->name()) );
}
}
QList<AMDataSource*> raw1DDataSources;
for(int i=0; i<specificScan_->rawDataSources()->count(); i++)
if(specificScan_->rawDataSources()->at(i)->rank() == 1)
raw1DDataSources << specificScan_->rawDataSources()->at(i);
int rawTeyIndex = specificScan_->rawDataSources()->indexOfKey(SGMBeamline::sgm()->teyDetector()->description().remove(" "));
int rawTfyIndex = specificScan_->rawDataSources()->indexOfKey(SGMBeamline::sgm()->tfyDetector()->description().remove(" "));
int rawI0Index = specificScan_->rawDataSources()->indexOfKey(SGMBeamline::sgm()->i0Detector()->description().remove(" "));
if(rawTeyIndex != -1 && rawI0Index != -1) {
AM1DExpressionAB* teyChannel = new AM1DExpressionAB(QString("%1Norm").arg(SGMBeamline::sgm()->teyDetector()->description().remove(" ")));
teyChannel->setDescription("Normalized TEY");
teyChannel->setInputDataSources(raw1DDataSources);
teyChannel->setExpression(QString("%1/%2").arg(SGMBeamline::sgm()->teyDetector()->description().remove(" ")).arg(SGMBeamline::sgm()->i0Detector()->description().remove(" ")));
specificScan_->addAnalyzedDataSource(teyChannel);
}
if(rawTfyIndex != -1 && rawI0Index != -1) {
AM1DExpressionAB* tfyChannel = new AM1DExpressionAB(QString("%1Norm").arg(SGMBeamline::sgm()->tfyDetector()->description().remove(" ")));
tfyChannel->setDescription("Normalized TFY");
tfyChannel->setInputDataSources(raw1DDataSources);
tfyChannel->setExpression(QString("%1/%2").arg(SGMBeamline::sgm()->tfyDetector()->description().remove(" ")).arg(SGMBeamline::sgm()->i0Detector()->description().remove(" ")));
specificScan_->addAnalyzedDataSource(tfyChannel);
}
/*
if(SGMBeamline::sgm()->pgtDetector()){
int rawSddIndex = specificScan_->rawDataSources()->indexOfKey(SGMBeamline::sgm()->pgtDetector()->description().remove(" "));
if(rawSddIndex != -1) {
AMRawDataSource* sddRaw = specificScan_->rawDataSources()->at(rawSddIndex);
AM2DSummingAB* pfy = new AM2DSummingAB("PFY");
QList<AMDataSource*> pfySource;
pfySource << sddRaw;
pfy->setInputDataSources(pfySource);
pfy->setSumAxis(1);
pfy->setSumRangeMax(sddRaw->size(1)-1);
specificScan_->addAnalyzedDataSource(pfy);
if(rawSddIndex != -1 && rawI0Index != -1) {
AM1DExpressionAB* ipfyChannel = new AM1DExpressionAB(QString("IPFY"));
ipfyChannel->setDescription("IPFY");
QList<AMDataSource*> ipfySources;
ipfySources.append(raw1DDataSources);
ipfySources.append(pfy);
ipfyChannel->setInputDataSources(ipfySources);
ipfyChannel->setExpression(QString("%1/%2").arg(SGMBeamline::sgm()->i0Detector()->description().remove(" ")).arg("PFY"));
specificScan_->addAnalyzedDataSource(ipfyChannel);
}
}
}
*/
if(SGMBeamline::sgm()->oos65000Detector()){
int rawOOSIndex = specificScan_->rawDataSources()->indexOfKey(SGMBeamline::sgm()->oos65000Detector()->description().remove('\n'));
if(rawOOSIndex != -1) {
AMRawDataSource* oosRaw = specificScan_->rawDataSources()->at(rawOOSIndex);
AM2DSummingAB* ply = new AM2DSummingAB("PLY");
QList<AMDataSource*> plySource;
plySource << oosRaw;
ply->setInputDataSources(plySource);
ply->setSumAxis(1);
ply->setSumRangeMax(oosRaw->size(1)-1);
specificScan_->addAnalyzedDataSource(ply);
if(rawOOSIndex != -1 && rawI0Index != -1) {
AM1DExpressionAB* plyNormChannel = new AM1DExpressionAB(QString("PLYNorm"));
plyNormChannel->setDescription("PLYNorm");
QList<AMDataSource*> plyNormSources;
plyNormSources.append(raw1DDataSources);
plyNormSources.append(ply);
plyNormChannel->setInputDataSources(plyNormSources);
plyNormChannel->setExpression(QString("%1/%2").arg("PLY").arg(SGMBeamline::sgm()->i0Detector()->description().remove(" ")));
specificScan_->addAnalyzedDataSource(plyNormChannel);
}
}
}
}
