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; }