bool ResamplerPlugIn::execute(PlugInArgList* pInArgList, PlugInArgList* pOutArgList)
{
VERIFY(pInArgList != NULL && pOutArgList != NULL);
ProgressTracker progress(pInArgList->getPlugInArgValue<Progress>(Executable::ProgressArg()),
"Executing Spectral Resampler.", "spectral", "{88CD3E49-A522-431A-AE2A-96A6B2EB4012}");
Service<DesktopServices> pDesktop;
const DataElement* pElement(NULL);
std::string waveFilename;
// get default resampling options from user config
std::string resampleMethod = ResamplerOptions::getSettingResamplerMethod();
double dropOutWindow = ResamplerOptions::getSettingDropOutWindow();
double fwhm = ResamplerOptions::getSettingFullWidthHalfMax();
bool useFillValue = ResamplerOptions::getSettingUseFillValue();
double fillValue = ResamplerOptions::getSettingSignatureFillValue();
std::vector<Signature*> originalSignatures;
std::auto_ptr<std::vector<Signature*> > pResampledSignatures(new std::vector<Signature*>);
std::string errorMsg;
if (isBatch())
{
VERIFY(pInArgList->getPlugInArgValue("Signatures to resample", originalSignatures));
if (originalSignatures.empty())
{
Signature* pSignature = pInArgList->getPlugInArgValue<Signature>("Signature to resample");
if (pSignature != NULL)
{
originalSignatures.push_back(pSignature);
}
}
if (originalSignatures.empty())
{
progress.report("No signatures are available to be resampled.", 0, ERRORS, true);
return false;
}
pElement = pInArgList->getPlugInArgValue<DataElement>("Data element wavelength source");
Filename* pWaveFilename = pInArgList->getPlugInArgValue<Filename>("Wavelengths Filename");
if (pWaveFilename != NULL)
{
waveFilename = pWaveFilename->getFullPathAndName();
}
VERIFY(pInArgList->getPlugInArgValue("Resampling Method", resampleMethod));
VERIFY(pInArgList->getPlugInArgValue("Drop out window", dropOutWindow));
VERIFY(pInArgList->getPlugInArgValue("FWHM", fwhm));
VERIFY(pInArgList->getPlugInArgValue("Use fill value", useFillValue));
VERIFY(pInArgList->getPlugInArgValue("Fill value", fillValue));
}
else
{
ResamplerPlugInDlg dlg(pDesktop->getMainWidget());
if (dlg.exec() == QDialog::Rejected)
{
progress.report("User canceled resampling.", 0, ABORT, true);
progress.upALevel();
return false;
}
originalSignatures = dlg.getSignaturesToResample();
resampleMethod = dlg.getResamplingMethod();
dropOutWindow = dlg.getDropOutWindow();
fwhm = dlg.getFWHM();
useFillValue = dlg.getUseFillValue();
fillValue = dlg.getFillValue();
pElement = dlg.getWavelengthsElement();
waveFilename = dlg.getWavelengthsFilename();
}
std::string resampledTo;
FactoryResource<Wavelengths> pWavelengths;
if (pElement != NULL) // try loading wavelengths from user specified data element
{
if (getWavelengthsFromElement(pElement, pWavelengths.get(), errorMsg) == false)
{
progress.report(errorMsg, 0, ERRORS, true);
return false;
}
resampledTo = pElement->getName();
}
else if (waveFilename.empty() == false) // if no user provided raster, look for a wavelengths file
{
if (QFile::exists(QString::fromStdString(waveFilename)))
{
if (getWavelengthsFromFile(waveFilename, pWavelengths.get(), errorMsg) == false)
{
progress.report(errorMsg, 0, ERRORS, true);
return false;
}
}
else
{
errorMsg = "The wavelengths file \"" + waveFilename + "\" could not be found.";
progress.report(errorMsg, 0, ERRORS, true);
return false;
}
resampledTo = waveFilename;
}
else // if no wavelength source provided, look for raster in current active spatial data view
{
SpatialDataView* pView = dynamic_cast<SpatialDataView*>(pDesktop->getCurrentWorkspaceWindowView());
if (pView != NULL)
{
LayerList* pLayerList = pView->getLayerList();
if (pLayerList != NULL)
{
pElement = pLayerList->getPrimaryRasterElement();
pWavelengths->initializeFromDynamicObject(pElement->getMetadata(), false);
if (pWavelengths->isEmpty())
{
progress.report("No target wavelengths are available for resampling the signatures.", 0, ERRORS, true);
return false;
}
resampledTo = pElement->getName();
}
}
}
PlugInResource pPlugIn("Resampler");
Resampler* pResampler = dynamic_cast<Resampler*>(pPlugIn.get());
if (pResampler == NULL)
{
progress.report("The \"Resampler\" plug-in is not available so the signatures can not be resampled.",
0, ERRORS, true);
return false;
}
std::string dataName("Reflectance");
std::string wavelengthName("Wavelength");
// save user config settings - Resampler doesn't have interface to set them separately from user config
std::string configMethod = ResamplerOptions::getSettingResamplerMethod();
ResamplerOptions::setSettingResamplerMethod(resampleMethod);
double configDropout = ResamplerOptions::getSettingDropOutWindow();
ResamplerOptions::setSettingDropOutWindow(dropOutWindow);
double configFwhm = ResamplerOptions::getSettingFullWidthHalfMax();
ResamplerOptions::setSettingFullWidthHalfMax(fwhm);
std::vector<double> toWavelengths = pWavelengths->getCenterValues();
std::vector<double> toFwhm = pWavelengths->getFwhm();
if (toFwhm.size() != toWavelengths.size())
{
toFwhm.clear(); // Resampler will use the default config setting fwhm if this vector is empty
}
unsigned int numSigs = originalSignatures.size();
unsigned int numSigsResampled(0);
progress.report("Begin resampling signatures...", 0, NORMAL);
for (unsigned int index = 0; index < numSigs; ++index)
{
if (isAborted())
{
progress.report("Resampling aborted by user", 100 * index / numSigs, ABORT, true);
return false;
}
if (originalSignatures[index] == NULL)
{
continue;
}
// check if signature has target wavelength centers and doesn't need to be resampled
if (needToResample(originalSignatures[index], pWavelengths.get()) == false)
{
pResampledSignatures->push_back(originalSignatures[index]);
++numSigsResampled;
continue;
}
DataVariant var = originalSignatures[index]->getData(dataName);
if (var.isValid() == false)
{
continue;
}
std::vector<double> fromData;
if (!var.getValue(fromData))
{
continue;
}
var = originalSignatures[index]->getData(wavelengthName);
if (var.isValid() == false)
{
continue;
}
std::vector<double> fromWavelengths;
if (!var.getValue(fromWavelengths))
{
continue;
}
std::string resampledSigName = originalSignatures[index]->getName() + "_resampled";
int suffix(2);
ModelResource<Signature> pSignature(resampledSigName, NULL);
// probably not needed but just in case resampled name already used
while (pSignature.get() == NULL)
{
pSignature = ModelResource<Signature>(resampledSigName + StringUtilities::toDisplayString(suffix), NULL);
++suffix;
}
if (resampledTo.empty() == false)
{
DynamicObject* pMetaData = pSignature->getMetadata();
if (pMetaData != NULL)
{
pMetaData->setAttribute(CommonSignatureMetadataKeys::ResampledTo(), resampledTo);
}
}
std::vector<double> toData;
std::vector<int> toBands;
if (pResampler->execute(fromData, toData, fromWavelengths, toWavelengths, toFwhm, toBands, errorMsg))
{
if (toWavelengths.size() != toBands.size())
{
if (toBands.size() < 2) // no need to try if only one point
{
continue;
}
if (useFillValue)
{
std::vector<double> values(toWavelengths.size(), fillValue);
for (unsigned int i = 0; i < toBands.size(); ++i)
{
values[static_cast<unsigned int>(toBands[i])] = toData[i];
}
toData.swap(values);
DynamicObject* pMetaData = pSignature->getMetadata();
if (pMetaData != NULL)
{
pMetaData->setAttribute(CommonSignatureMetadataKeys::FillValue(), fillValue);
}
}
else
{
std::vector<double> wavelengths(toBands.size());
for (unsigned int i = 0; i < toBands.size(); ++i)
{
wavelengths[i] = toWavelengths[static_cast<unsigned int>(toBands[i])];
}
toWavelengths.swap(wavelengths);
}
}
pSignature->setData(dataName, toData);
pSignature->setData(wavelengthName, toWavelengths);
SignatureDataDescriptor* pDesc = dynamic_cast<SignatureDataDescriptor*>(pSignature->getDataDescriptor());
if (pDesc == NULL)
{
continue;
}
pDesc->setUnits(dataName, originalSignatures[index]->getUnits(dataName));
pResampledSignatures->push_back(pSignature.release());
++numSigsResampled;
}
std::string progressStr =
QString("Resampled signature %1 of %2 signatures").arg(index + 1).arg(numSigs).toStdString();
progress.report(progressStr, (index + 1) * 100 / numSigs, NORMAL);
}
// reset config options
ResamplerOptions::setSettingResamplerMethod(configMethod);
ResamplerOptions::setSettingDropOutWindow(configDropout);
ResamplerOptions::setSettingFullWidthHalfMax(configFwhm);
if (numSigsResampled == numSigs)
{
progress.report("Complete", 100, NORMAL);
progress.upALevel();
}
else
{
errorMsg = QString("Only %1 of the %2 signatures were successfully resampled.").arg(
numSigsResampled).arg(numSigs).toStdString();
progress.report(errorMsg, 100, WARNING, true);
}
VERIFY(pOutArgList->setPlugInArgValue("Resampled signatures", pResampledSignatures.release()));
return true;
}
bool SpectralLibraryManager::generateResampledLibrary(const RasterElement* pRaster)
{
VERIFY(pRaster != NULL);
// check that lib sigs are in same units as the raster element
const RasterDataDescriptor* pDesc = dynamic_cast<const RasterDataDescriptor*>(pRaster->getDataDescriptor());
VERIFY(pDesc != NULL);
const Units* pUnits = pDesc->getUnits();
if (pDesc->getUnits()->getUnitType() != mLibraryUnitType)
{
if (Service<DesktopServices>()->showMessageBox("Mismatched Units", "The data are not in the "
"same units as the spectral library.\n Do you want to continue anyway?", "Yes", "No") == 1)
{
return false;
}
}
FactoryResource<Wavelengths> pWavelengths;
pWavelengths->initializeFromDynamicObject(pRaster->getMetadata(), false);
// populate the library with the resampled signatures
PlugInResource pPlugIn("Resampler");
Resampler* pResampler = dynamic_cast<Resampler*>(pPlugIn.get());
VERIFY(pResampler != NULL);
if (pWavelengths->getNumWavelengths() != pDesc->getBandCount())
{
mpProgress->updateProgress("Wavelength information in metadata does not match the number of bands "
"in the raster element", 0, ERRORS);
return false;
}
// get resample suitable signatures - leave out signatures that don't cover the spectral range of the data
std::vector<std::vector<double> > resampledData;
resampledData.reserve(mSignatures.size());
std::vector<Signature*> resampledSignatures;
resampledSignatures.reserve(mSignatures.size());
std::vector<std::string> unsuitableSignatures;
std::vector<double> sigValues;
std::vector<double> sigWaves;
std::vector<double> rasterWaves = pWavelengths->getCenterValues();
std::vector<double> rasterFwhm = pWavelengths->getFwhm();
std::vector<double> resampledValues;
std::vector<int> bandIndex;
DataVariant data;
for (std::vector<Signature*>::const_iterator it = mSignatures.begin(); it != mSignatures.end(); ++it)
{
data = (*it)->getData(SpectralLibraryMatch::getNameSignatureWavelengthData());
VERIFY(data.isValid());
VERIFY(data.getValue(sigWaves));
resampledValues.clear();
data = (*it)->getData(SpectralLibraryMatch::getNameSignatureAmplitudeData());
VERIFY(data.isValid());
VERIFY(data.getValue(sigValues));
double scaleFactor = (*it)->getUnits(
SpectralLibraryMatch::getNameSignatureAmplitudeData())->getScaleFromStandard();
for (std::vector<double>::iterator sit = sigValues.begin(); sit != sigValues.end(); ++sit)
{
*sit *= scaleFactor;
}
std::string msg;
if (pResampler->execute(sigValues, resampledValues, sigWaves, rasterWaves, rasterFwhm, bandIndex, msg) == false
|| resampledValues.size() != rasterWaves.size())
{
unsuitableSignatures.push_back((*it)->getName());
continue;
}
resampledData.push_back(resampledValues);
resampledSignatures.push_back(*it);
}
if (resampledSignatures.empty())
{
std::string errMsg = "None of the signatures in the library cover the spectral range of the data.";
if (mpProgress != NULL)
{
mpProgress->updateProgress(errMsg, 0, ERRORS);
return false;
}
}
if (unsuitableSignatures.empty() == false)
{
std::string warningMsg = "The following library signatures do not cover the spectral range of the data:\n";
for (std::vector<std::string>::iterator it = unsuitableSignatures.begin();
it != unsuitableSignatures.end(); ++it)
{
warningMsg += *it + "\n";
}
warningMsg += "These signatures will not be searched for in the data.";
Service<DesktopServices>()->showMessageBox("SpectralLibraryManager", warningMsg);
StepResource pStep("Spectral LibraryManager", "spectral", "64B6C87A-A6C3-4378-9B6E-221D89D8707B");
pStep->finalize(Message::Unresolved, warningMsg);
}
std::string libName = "Resampled Spectral Library";
// Try to get the resampled lib element in case session was restored. If NULL, create a new raster element with
// num rows = num valid signatures, num cols = 1, num bands = pRaster num bands
RasterElement* pLib = dynamic_cast<RasterElement*>(Service<ModelServices>()->getElement(libName,
TypeConverter::toString<RasterElement>(), pRaster));
if (pLib != NULL)
{
// check that pLib has same number of sigs as SpectralLibraryManager
RasterDataDescriptor* pLibDesc = dynamic_cast<RasterDataDescriptor*>(pLib->getDataDescriptor());
VERIFY(pLibDesc != NULL);
if (pLibDesc->getRowCount() != mSignatures.size())
{
mpProgress->updateProgress("An error occurred during session restore and some signatures were not restored."
" Check the spectral library before using.", 0, ERRORS);
Service<ModelServices>()->destroyElement(pLib);
pLib = NULL;
}
}
bool isNewElement(false);
if (pLib == NULL)
{
pLib = RasterUtilities::createRasterElement(libName,
static_cast<unsigned int>(resampledData.size()), 1, pDesc->getBandCount(), FLT8BYTES, BIP,
true, const_cast<RasterElement*>(pRaster));
isNewElement = true;
}
if (pLib == NULL)
{
mpProgress->updateProgress("Error occurred while trying to create the resampled spectral library", 0, ERRORS);
return false;
}
RasterDataDescriptor* pLibDesc = dynamic_cast<RasterDataDescriptor*>(pLib->getDataDescriptor());
VERIFY(pLibDesc != NULL);
// copy resampled data into new element
if (isNewElement)
{
FactoryResource<DataRequest> pRequest;
pRequest->setWritable(true);
pRequest->setRows(pLibDesc->getActiveRow(0), pLibDesc->getActiveRow(pLibDesc->getRowCount()-1), 1);
DataAccessor acc = pLib->getDataAccessor(pRequest.release());
for (std::vector<std::vector<double> >::iterator sit = resampledData.begin(); sit != resampledData.end(); ++sit)
{
VERIFY(acc->isValid());
void* pData = acc->getColumn();
memcpy(acc->getColumn(), &(sit->begin()[0]), pLibDesc->getBandCount() * sizeof(double));
acc->nextRow();
}
// set wavelength info in resampled library
pWavelengths->applyToDynamicObject(pLib->getMetadata());
FactoryResource<Units> libUnits;
libUnits->setUnitType(mLibraryUnitType);
libUnits->setUnitName(StringUtilities::toDisplayString<UnitType>(mLibraryUnitType));
pLibDesc->setUnits(libUnits.get());
}
pLib->attach(SIGNAL_NAME(Subject, Deleted), Slot(this, &SpectralLibraryManager::resampledElementDeleted));
mLibraries[pRaster] = pLib;
mResampledSignatures[pLib] = resampledSignatures;
const_cast<RasterElement*>(pRaster)->attach(SIGNAL_NAME(Subject, Deleted),
Slot(this, &SpectralLibraryManager::elementDeleted));
return true;
}
