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;
}
std::vector<ImportDescriptor*> FitsImporter::getImportDescriptors(const std::string& fname)
{
std::string filename = fname;
std::vector<std::vector<std::string> >& errors = mErrors[fname];
std::vector<std::vector<std::string> >& warnings = mWarnings[fname];
errors.clear();
warnings.clear();
int status=0;
std::vector<ImportDescriptor*> descriptors;
FitsFileResource pFile(filename);
if (!pFile.isValid())
{
errors.resize(1);
errors[0].push_back(pFile.getStatus());
RETURN_DESCRIPTORS;
}
int hduCnt = 0;
int specificHdu = 0;
int hdu = 1;
if (!splitFilename(filename, hduCnt, specificHdu, hdu, pFile, errors, warnings))
{
RETURN_DESCRIPTORS;
}
errors.resize(hduCnt+1);
warnings.resize(hduCnt+1);
for(; hdu <= hduCnt; ++hdu)
{
std::string datasetName = filename + "[" + StringUtilities::toDisplayString(hdu) + "]";
int hduType;
CHECK_FITS(fits_movabs_hdu(pFile, hdu, &hduType, &status), hdu, false, continue);
ImportDescriptorResource pImportDescriptor(static_cast<ImportDescriptor*>(NULL));
FactoryResource<DynamicObject> pMetadata;
VERIFYRV(pMetadata.get() != NULL, descriptors);
{ // scope
std::vector<std::string> comments;
char pCard[81];
char pValue[81];
char pComment[81];
int nkeys = 0;
CHECK_FITS(fits_get_hdrspace(pFile, &nkeys, NULL, &status), hdu, true, ;);
for(int keyidx = 1; keyidx <= nkeys; ++keyidx)
{
CHECK_FITS(fits_read_keyn(pFile, keyidx, pCard, pValue, pComment, &status), hdu, true, continue);
std::string name = StringUtilities::stripWhitespace(std::string(pCard));
std::string val = StringUtilities::stripWhitespace(std::string(pValue));
std::string comment = StringUtilities::stripWhitespace(std::string(pComment));
if (!val.empty())
{
pMetadata->setAttributeByPath("FITS/" + name, val);
}
else if (!comment.empty())
{
comments.push_back(comment);
}
}
if (!comments.empty())
{
// ideally, this would add a multi-line string but Opticks doesn't display this properly
// pMetadata->setAttributeByPath("FITS/COMMENT", StringUtilities::join(comments, "\n"));
for(unsigned int idx = 0; idx < comments.size(); ++idx)
{
pMetadata->setAttributeByPath("FITS/COMMENT/" + StringUtilities::toDisplayString(idx), comments[idx]);
}
}
}
switch(hduType)
{
case IMAGE_HDU:
{
pImportDescriptor = ImportDescriptorResource(datasetName, TypeConverter::toString<RasterElement>());
VERIFYRV(pImportDescriptor.get() != NULL, descriptors);
EncodingType fileEncoding;
InterleaveFormatType interleave(BSQ);
unsigned int rows=0;
unsigned int cols=0;
unsigned int bands=1;
int bitpix;
int naxis;
long axes[3];
CHECK_FITS(fits_get_img_param(pFile, 3, &bitpix, &naxis, axes, &status), hdu, false, continue);
switch(bitpix)
{
case BYTE_IMG:
fileEncoding = INT1UBYTE;
break;
case SHORT_IMG:
fileEncoding = INT2SBYTES;
break;
case LONG_IMG:
fileEncoding = INT4SBYTES;
break;
case FLOAT_IMG:
fileEncoding = FLT4BYTES;
break;
case DOUBLE_IMG:
fileEncoding = FLT8BYTES;
break;
default:
warnings[hdu].push_back("Unsupported BITPIX value " + StringUtilities::toDisplayString(bitpix) + ".");
continue;
}
EncodingType dataEncoding = checkForOverflow(fileEncoding, pMetadata.get(), hdu, errors, warnings);
if (naxis == 1)
{
// 1-D data is a signature
pImportDescriptor = ImportDescriptorResource(datasetName, TypeConverter::toString<Signature>());
pMetadata->setAttributeByPath(METADATA_SIG_ENCODING, dataEncoding);
pMetadata->setAttributeByPath(METADATA_SIG_LENGTH, axes[0]);
RasterUtilities::generateAndSetFileDescriptor(pImportDescriptor->getDataDescriptor(), filename,
StringUtilities::toDisplayString(hdu), BIG_ENDIAN_ORDER);
// add units
SignatureDataDescriptor* pSigDd =
dynamic_cast<SignatureDataDescriptor*>(pImportDescriptor->getDataDescriptor());
if (pSigDd != NULL)
{
FactoryResource<Units> pUnits;
pUnits->setUnitName("Custom");
pUnits->setUnitType(CUSTOM_UNIT);
pSigDd->setUnits("Reflectance", pUnits.get());
}
break; // leave switch()
}
else if (naxis == 2)
{
cols = axes[0];
rows = axes[1];
}
else if (naxis == 3)
{
cols = axes[0];
rows = axes[1];
bands = axes[2];
}
else
{
errors[hdu].push_back(StringUtilities::toDisplayString(naxis) + " axis data not supported.");
}
RasterDataDescriptor* pDataDesc = RasterUtilities::generateRasterDataDescriptor(
datasetName, NULL, rows, cols, bands, interleave, dataEncoding, IN_MEMORY);
pImportDescriptor->setDataDescriptor(pDataDesc);
if (specificHdu == 0 && hdu == 1 && naxis == 2 && (axes[0] <= 5 || axes[1] <= 5))
{
// use 5 as this is a good top end for the number of astronomical band pass filters
// in general usage. this is not in a spec anywhere and is derived from various sample
// FITS files for different astronomical instruments.
//
// There's a good chance this is really a spectrum. (0th HDU)
// We'll create an import descriptor for the spectrum version of this
// And disable the raster descriptor by default
pImportDescriptor->setImported(false);
ImportDescriptorResource pSigDesc(datasetName, TypeConverter::toString<SignatureLibrary>());
DynamicObject* pSigMetadata = pSigDesc->getDataDescriptor()->getMetadata();
pSigMetadata->merge(pMetadata.get());
std::vector<double> centerWavelengths;
unsigned int cnt = (axes[0] <= 5) ? axes[1] : axes[0];
double startVal = StringUtilities::fromDisplayString<double>(
dv_cast<std::string>(pMetadata->getAttributeByPath("FITS/MINWAVE"), "0.0"));
double endVal = StringUtilities::fromDisplayString<double>(
dv_cast<std::string>(pMetadata->getAttributeByPath("FITS/MAXWAVE"), "0.0"));
double incr = (endVal == 0.0) ? 1.0 : ((endVal - startVal) / static_cast<double>(cnt));
centerWavelengths.reserve(cnt);
for (unsigned int idx = 0; idx < cnt; idx++)
{
centerWavelengths.push_back(startVal + (idx * incr));
}
pSigMetadata->setAttributeByPath(CENTER_WAVELENGTHS_METADATA_PATH, centerWavelengths);
// Units
std::string unitsName = dv_cast<std::string>(pMetadata->getAttributeByPath("FITS/BUNIT"), std::string());
if (!unitsName.empty())
{
FactoryResource<Units> units;
units->setUnitName(unitsName);
units->setUnitType(RADIANCE);
SignatureDataDescriptor* pSigDd =
dynamic_cast<SignatureDataDescriptor*>(pSigDesc->getDataDescriptor());
if (pSigDd != NULL)
{
pSigDd->setUnits("Reflectance", units.get());
}
}
RasterUtilities::generateAndSetFileDescriptor(pSigDesc->getDataDescriptor(),
filename, StringUtilities::toDisplayString(hdu), BIG_ENDIAN_ORDER);
// If units are not available, set custom units into the data descriptor so that the user can
// modify them - this must occur after the call to RasterUtilities::generateAndSetFileDescriptor()
// so that the file descriptor will still display no defined units
if (unitsName.empty())
{
FactoryResource<Units> units;
units->setUnitName("Custom");
units->setUnitType(CUSTOM_UNIT);
SignatureDataDescriptor* pSigDd = dynamic_cast<SignatureDataDescriptor*>(pSigDesc->getDataDescriptor());
if (pSigDd != NULL)
{
pSigDd->setUnits("Reflectance", units.get());
}
}
descriptors.push_back(pSigDesc.release());
}
RasterFileDescriptor* pFileDescriptor = dynamic_cast<RasterFileDescriptor*>(
RasterUtilities::generateAndSetFileDescriptor(pDataDesc, filename,
StringUtilities::toDisplayString(hdu), BIG_ENDIAN_ORDER));
if (pFileDescriptor != NULL)
{
unsigned int bitsPerElement = RasterUtilities::bytesInEncoding(fileEncoding) * 8;
pFileDescriptor->setBitsPerElement(bitsPerElement);
}
break; // leave switch()
}
case ASCII_TBL:
case BINARY_TBL:
warnings[hdu].push_back("Tables not supported. [HDU " + StringUtilities::toDisplayString(hdu) + "]");
continue;
default:
warnings[hdu].push_back("HDU " + StringUtilities::toDisplayString(hdu) + " is an unknown type.");
continue;
}
pImportDescriptor->getDataDescriptor()->setMetadata(pMetadata.release());
pImportDescriptor->setImported(errors[hdu].empty());
descriptors.push_back(pImportDescriptor.release());
}
void SpectralLibraryMatchResults::createAverageSignature()
{
Service<DesktopServices> pDesktop;
const RasterElement* pRaster = getRasterElementForCurrentPage();
if (pRaster == NULL)
{
pDesktop->showMessageBox("Spectral Library Match",
"Unable to determine the RasterElement for the current page.");
return;
}
std::vector<Signature*> signatures = getSelectedSignatures();
if (signatures.empty())
{
pDesktop->showMessageBox("Spectral Library Match",
"No signatures are selected for use in generating an average signature.");
return;
}
// now need to get the resampled sigs from the library
SpectralLibraryManager* pLibMgr(NULL);
std::vector<PlugIn*> plugIns =
Service<PlugInManagerServices>()->getPlugInInstances(SpectralLibraryMatch::getNameLibraryManagerPlugIn());
if (!plugIns.empty())
{
pLibMgr = dynamic_cast<SpectralLibraryManager*>(plugIns.front());
}
if (pLibMgr == NULL)
{
pDesktop->showMessageBox("Spectral Library Match",
"Unable to access the Spectral Library Manager.");
return;
}
const RasterDataDescriptor* pDesc = dynamic_cast<const RasterDataDescriptor*>(pRaster->getDataDescriptor());
if (pDesc == NULL)
{
pDesktop->showMessageBox("Spectral Library Match",
"Unable to access the RasterDataDescriptor for the RasterElement of the current page.");
return;
}
unsigned int numBands = pDesc->getBandCount();
std::vector<double> averageValues(numBands, 0);
std::vector<double> values;
for (std::vector<Signature*>::iterator it = signatures.begin(); it != signatures.end(); ++it)
{
if (pLibMgr->getResampledSignatureValues(pRaster, *it, values) == false)
{
pDesktop->showMessageBox("Spectral Library Match",
"Unable to access the resampled signature values for " + (*it)->getDisplayName(true));
return;
}
for (unsigned int band = 0; band < numBands; ++band)
{
averageValues[band] += values[band];
}
}
unsigned int numSigs = signatures.size();
for (unsigned int band = 0; band < numBands; ++band)
{
averageValues[band] /= static_cast<double>(numSigs);
}
QString avgName = QInputDialog::getText(pDesktop->getMainWidget(), "Spectral Library Match",
"Enter the name to use for the average signature:");
if (avgName.isEmpty())
{
return;
}
ModelResource<Signature> pAvgSig(avgName.toStdString(), const_cast<RasterElement*>(pRaster));
pAvgSig->setData("Reflectance", averageValues);
const DynamicObject* pMetaData = pRaster->getMetadata();
FactoryResource<Wavelengths> pWavelengths;
pWavelengths->initializeFromDynamicObject(pMetaData, false);
const std::vector<double>& centerValues = pWavelengths->getCenterValues();
pAvgSig->setData("Wavelength", centerValues);
SignatureDataDescriptor* pSigDesc = dynamic_cast<SignatureDataDescriptor*>(pAvgSig->getDataDescriptor());
VERIFYNRV(pSigDesc != NULL);
FactoryResource<Units> pUnits;
const Units* pRasterUnits = pDesc->getUnits();
pUnits->setUnitName(pRasterUnits->getUnitName());
pUnits->setUnitType(pRasterUnits->getUnitType());
pUnits->setScaleFromStandard(1.0); // the rescaled values are already corrected for the original scaling factor
pUnits->setRangeMin(pRasterUnits->getRangeMin());
pUnits->setRangeMax(pRasterUnits->getRangeMax());
pSigDesc->setUnits("Reflectance", pUnits.get());
pAvgSig.release();
}
vector<ImportDescriptor*> EnviLibraryImporter::getImportDescriptors(const string& filename)
{
vector<ImportDescriptor*> descriptors;
string headerFile = filename;
string dataFile;
// assume filename is a header file and try to parse
bool bSuccess = mFields.populateFromHeader(filename);
if (bSuccess == false)
{
dataFile = filename; // was passed data file name instead of header file name
headerFile = findHeaderFile(dataFile);
if (headerFile.empty() == false)
{
bSuccess = mFields.populateFromHeader(headerFile);
}
}
if (bSuccess == true)
{
if (dataFile.empty()) // was passed header file name and now need to find the data file name
{
dataFile = findDataFile(headerFile);
}
if (dataFile.empty()) // no data file found for the header
{
return descriptors;
}
EnviField* pField = mFields.find("file type");
if (pField != NULL)
{
if (pField->mValue == "ENVI Spectral Library" ||
pField->mValue == "Spectral Library")
{
// Get the name and dataset from the header values
string name;
string dataset;
EnviField* pBandNamesField = mFields.find("band names");
if (pBandNamesField != NULL)
{
if (pBandNamesField->mChildren.empty() == false)
{
EnviField* pNameField = pBandNamesField->mChildren.front();
if (pNameField != NULL)
{
name = pNameField->mValue;
}
}
}
EnviField* pDescriptionField = mFields.find("description");
if (pDescriptionField != NULL)
{
// Library name
if (name.empty() == true)
{
EnviField* pNameField = pDescriptionField->find("library name");
if (pNameField != NULL)
{
name = pNameField->mValue;
}
}
// Dataset
EnviField* pDatasetField = pDescriptionField->find("dataset");
if (pDatasetField != NULL)
{
dataset = pDatasetField->mValue;
}
}
// Create the data descriptor
Service<ModelServices> pModel;
RasterElement* pRasterElement = NULL;
if (dataset.empty() == false)
{
pRasterElement = dynamic_cast<RasterElement*>(pModel->getElement(dataset, "RasterElement", NULL));
}
if (name.empty() == true)
{
// Create a unique default name
unsigned int libraryNumber = pModel->getElements(pRasterElement, "SignatureLibrary").size();
DataElement* pSignatureLibrary = NULL;
do
{
char buffer[64];
sprintf(buffer, "%u", ++libraryNumber);
name = "Spectral Library " + string(buffer);
pSignatureLibrary = pModel->getElement(name, "SignatureLibrary", pRasterElement);
}
while (pSignatureLibrary != NULL);
}
ImportDescriptor* pImportDescriptor =
pModel->createImportDescriptor(name, "SignatureLibrary", pRasterElement);
if (pImportDescriptor != NULL)
{
SignatureDataDescriptor* pDescriptor =
dynamic_cast<SignatureDataDescriptor*>(pImportDescriptor->getDataDescriptor());
if (pDescriptor != NULL)
{
// Metadata
FactoryResource<DynamicObject> pMetadata;
if (pDescriptionField != NULL)
{
vector<EnviField*>& children = pDescriptionField->mChildren;
for (vector<EnviField*>::iterator iter = children.begin(); iter != children.end(); ++iter)
{
EnviField* pField = *iter;
if (pField != NULL)
{
if ((pField->mTag.empty() == false) && (pField->mValue.empty() == false))
{
pMetadata->setAttribute(pField->mTag, pField->mValue);
}
}
}
}
// Signature names
EnviField* pSigNamesField = mFields.find("spectra names");
if (pSigNamesField != NULL)
{
vector<string> sigNames;
for (unsigned int i = 0; i < pSigNamesField->mChildren.size(); i++)
{
EnviField* pField = pSigNamesField->mChildren[i];
if (pField != NULL)
{
vector<char> bufferVector(pField->mValue.size() + 1);
char* pBuffer = &bufferVector.front();
strcpy(pBuffer, pField->mValue.c_str());
char* pPtr = strtok(pBuffer, ",");
while (pPtr != NULL)
{
string sigName = StringUtilities::stripWhitespace(string(pPtr));
sigNames.push_back(sigName);
pPtr = strtok(NULL, ",");
}
}
}
if (sigNames.empty() == false)
{
pMetadata->setAttribute("Signature Names", sigNames);
}
}
// Signature units - Set custom units into the data descriptor so that the
// user can modify them even though units are not loaded from the file
FactoryResource<Units> pUnits;
pUnits->setUnitName("Custom");
pUnits->setUnitType(CUSTOM_UNIT);
pDescriptor->setUnits("Reflectance", pUnits.get());
// Wavelengths
EnviField* pSamplesField = mFields.find("samples");
if (pSamplesField != NULL)
{
unsigned int numWavelengths = StringUtilities::fromXmlString<unsigned int>(pSamplesField->mValue);
vector<double> wavelengths;
unsigned int uiNanometerValues = 0;
EnviField* pWavelengthField = mFields.find("wavelength");
if (pWavelengthField != NULL)
{
vector<unsigned int> goodBands;
EnviField* pBblField = mFields.find("bbl");
if (pBblField != NULL)
{
// Parse the bad bands list. This method puts the indices of good bands in ascending order.
EnviImporter::parseBbl(pBblField, goodBands);
// Sort in descending order so that the last one can be popped later
// A pop_back is much faster than an erase on the first element
reverse(goodBands.begin(), goodBands.end());
}
unsigned int numWavelengthsRead = 0;
for (std::vector<EnviField*>::const_iterator iter = pWavelengthField->mChildren.begin();
iter != pWavelengthField->mChildren.end();
++iter)
{
EnviField* pField = *iter;
if (pField != NULL)
{
vector<char> bufferVector(pField->mValue.size() + 1);
char* pBuffer = &(bufferVector.front());
strcpy(pBuffer, pField->mValue.c_str());
char* pPtr = strtok(pBuffer, ",");
while (pPtr != NULL)
{
double dWavelength = 0.0;
if (sscanf(pPtr, "%lf", &dWavelength) == 1)
{
if (dWavelength > 50.0) // Assumed to be in nanometers
{
uiNanometerValues++;
}
// Restrict the number of wavelengths to the number of samples in the header file
if (numWavelengthsRead < numWavelengths)
{
// Only write the wavelength if the value is valid
// Since the bands are in descending order,
// goodBands.back() always holds the next good band.
if (pBblField == NULL ||
(goodBands.empty() == false && goodBands.back() == numWavelengthsRead))
{
if (goodBands.empty() == false)
{
goodBands.pop_back();
}
wavelengths.push_back(dWavelength);
}
}
++numWavelengthsRead;
}
pPtr = strtok(NULL, ",");
}
}
}
VERIFYNR(goodBands.empty() == true);
}
// Wavelength units
bool bConvertWavelengths = false;
bool bDetermineUnits = true;
EnviField* pUnitsField = mFields.find("wavelength units");
if (pUnitsField != NULL)
{
if (pUnitsField->mValue == "Micrometers")
{
bDetermineUnits = false;
}
else if (pUnitsField->mValue == "Nanometers")
{
bDetermineUnits = false;
bConvertWavelengths = true;
}
}
if (bDetermineUnits)
{
if ((uiNanometerValues * 100) / wavelengths.size() > 50)
{
bConvertWavelengths = true;
}
}
if (bConvertWavelengths == true)
{
for (vector<double>::size_type i = 0; i < wavelengths.size(); i++)
{
wavelengths[i] *= 0.001;
}
}
string pCenterPath[] = { SPECIAL_METADATA_NAME, BAND_METADATA_NAME,
CENTER_WAVELENGTHS_METADATA_NAME, END_METADATA_NAME };
pMetadata->setAttributeByPath(pCenterPath, wavelengths);
}
if (pMetadata->getNumAttributes() > 0)
{
pDescriptor->setMetadata(pMetadata.get());
}
// Create the file descriptor
FactoryResource<SignatureFileDescriptor> pFileDescriptor;
if (pFileDescriptor.get() != NULL)
{
pFileDescriptor->setFilename(dataFile);
pDescriptor->setFileDescriptor(pFileDescriptor.get());
}
}
descriptors.push_back(pImportDescriptor);
}
}
}
}
return descriptors;
}
vector<ImportDescriptor*> SignatureImporter::getImportDescriptors(const string& filename)
{
vector<ImportDescriptor*> descriptors;
if (filename.empty())
{
return descriptors;
}
LargeFileResource pSigFile;
if (!pSigFile.open(filename, O_RDONLY | O_BINARY, S_IREAD))
{
return descriptors;
}
// load the data
FactoryResource<DynamicObject> pMetadata;
VERIFYRV(pMetadata.get() != NULL, descriptors);
bool readError = false;
string line;
string unitName("Reflectance");
UnitType unitType(REFLECTANCE);
double unitScale(1.0);
// parse the metadata
for (line = pSigFile.readLine(&readError);
(readError == false) && (line.find('=') != string::npos);
line = pSigFile.readLine(&readError))
{
vector<string> metadataEntry;
trim(line);
split(metadataEntry, line, is_any_of("="));
if (metadataEntry.size() == 2)
{
string key = metadataEntry[0];
string value = metadataEntry[1];
trim(key);
trim(value);
if (ends_with(key, "Bands") || key == "Pixels")
{
pMetadata->setAttribute(key, StringUtilities::fromXmlString<unsigned long>(value));
}
else if (key == "UnitName")
{
unitName = value;
}
else if (key == "UnitType")
{
unitType = StringUtilities::fromXmlString<UnitType>(value);
}
else if (key == "UnitScale")
{
unitScale = StringUtilities::fromXmlString<double>(value);
}
else
{
pMetadata->setAttribute(key, value);
}
}
}
if ((readError == true) && (pSigFile.eof() != 1))
{
return descriptors;
}
// Verify that the next line contains float float pairs
vector<string> dataEntry;
trim(line);
split(dataEntry, line, is_space());
if (dataEntry.size() != 2)
{
return descriptors;
}
bool error = false;
StringUtilities::fromXmlString<float>(dataEntry[0], &error);
!error && StringUtilities::fromXmlString<float>(dataEntry[1], &error);
if (error)
{
return descriptors;
}
string datasetName = dv_cast<string>(pMetadata->getAttribute("Name"), filename);
ImportDescriptorResource pImportDescriptor(datasetName, "Signature");
VERIFYRV(pImportDescriptor.get() != NULL, descriptors);
SignatureDataDescriptor* pDataDescriptor =
dynamic_cast<SignatureDataDescriptor*>(pImportDescriptor->getDataDescriptor());
VERIFYRV(pDataDescriptor != NULL, descriptors);
FactoryResource<SignatureFileDescriptor> pFileDescriptor;
VERIFYRV(pFileDescriptor.get() != NULL, descriptors);
pFileDescriptor->setFilename(filename);
FactoryResource<Units> pReflectanceUnits;
VERIFYRV(pReflectanceUnits.get() != NULL, descriptors);
pReflectanceUnits->setUnitName(unitName);
pReflectanceUnits->setUnitType(unitType);
if (unitScale != 0.0)
{
pReflectanceUnits->setScaleFromStandard(1.0 / unitScale);
}
pDataDescriptor->setUnits("Reflectance", pReflectanceUnits.get());
pFileDescriptor->setUnits("Reflectance", pReflectanceUnits.get());
pDataDescriptor->setFileDescriptor(pFileDescriptor.get());
pDataDescriptor->setMetadata(pMetadata.get());
descriptors.push_back(pImportDescriptor.release());
return descriptors;
}
bool EditDataDescriptor::execute(PlugInArgList* pInArgList, PlugInArgList* pOutArgList)
{
StepResource pStep("Execute Wizard Item", "app", "055486F4-A9DB-4FDA-9AA7-75D1917E2C87");
pStep->addProperty("Item", getName());
mpStep = pStep.get();
if (extractInputArgs(pInArgList) == false)
{
return false;
}
// Set the values in the data descriptor
VERIFY(mpDescriptor != NULL);
// File descriptor
if (mpFileDescriptor != NULL)
{
mpDescriptor->setFileDescriptor(mpFileDescriptor);
}
// Processing location
if (mpProcessingLocation != NULL)
{
mpDescriptor->setProcessingLocation(*mpProcessingLocation);
}
RasterDataDescriptor* pRasterDescriptor = dynamic_cast<RasterDataDescriptor*>(mpDescriptor);
RasterFileDescriptor* pRasterFileDescriptor = dynamic_cast<RasterFileDescriptor*>(mpFileDescriptor);
SignatureDataDescriptor* pSignatureDescriptor = dynamic_cast<SignatureDataDescriptor*>(mpDescriptor);
SignatureFileDescriptor* pSignatureFileDescriptor = dynamic_cast<SignatureFileDescriptor*>(mpFileDescriptor);
if (pRasterDescriptor != NULL)
{
if (pRasterFileDescriptor != NULL)
{
// Set the rows and columns to match the rows and columns in the file descriptor before creating the subset
const vector<DimensionDescriptor>& rows = pRasterFileDescriptor->getRows();
pRasterDescriptor->setRows(rows);
const vector<DimensionDescriptor>& columns = pRasterFileDescriptor->getColumns();
pRasterDescriptor->setColumns(columns);
const vector<DimensionDescriptor>& bands = pRasterFileDescriptor->getBands();
pRasterDescriptor->setBands(bands);
}
// Data type
if (mpDataType != NULL)
{
pRasterDescriptor->setDataType(*mpDataType);
}
// InterleaveFormat
if (mpInterleave != NULL)
{
pRasterDescriptor->setInterleaveFormat(*mpInterleave);
}
// Bad values
if (mpBadValues != NULL)
{
pRasterDescriptor->setBadValues(*mpBadValues);
}
// Rows
if ((mpStartRow != NULL) || (mpEndRow != NULL) || (mpRowSkipFactor != NULL))
{
// We need to obtain this origRows from the FileDescriptor if present since an importer
// may generate a subset by default in which case the DataDescriptor will not contain all
// the rows and subsetting will not work correctly. We
// can't just set mpFileDescriptor = pRasterDescriptor->getFileDescriptor() since we only
// want to replace the DataDescriptor's row list if one of the subset options is specified
const RasterFileDescriptor* pFileDesc(pRasterFileDescriptor);
if (pFileDesc == NULL)
{
pFileDesc = dynamic_cast<const RasterFileDescriptor*>(pRasterDescriptor->getFileDescriptor());
}
const vector<DimensionDescriptor>& origRows = (pFileDesc != NULL) ?
pFileDesc->getRows() : pRasterDescriptor->getRows();
unsigned int startRow = 0;
if (mpStartRow != NULL)
{
startRow = *mpStartRow;
}
else if (origRows.empty() == false)
{
startRow = origRows.front().getOriginalNumber() + 1;
}
unsigned int endRow = 0;
if (mpEndRow != NULL)
{
endRow = *mpEndRow;
}
else if (origRows.empty() == false)
{
endRow = origRows.back().getOriginalNumber() + 1;
}
unsigned int rowSkip = 0;
if (mpRowSkipFactor != NULL)
{
rowSkip = *mpRowSkipFactor;
}
vector<DimensionDescriptor> rows;
for (unsigned int i = 0; i < origRows.size(); ++i)
{
DimensionDescriptor rowDim = origRows[i];
unsigned int originalNumber = rowDim.getOriginalNumber() + 1;
if ((originalNumber >= startRow) && (originalNumber <= endRow))
{
rows.push_back(rowDim);
i += rowSkip;
}
}
pRasterDescriptor->setRows(rows);
}
// Columns
if ((mpStartColumn != NULL) || (mpEndColumn != NULL) || (mpColumnSkipFactor != NULL))
{
// We need to obtain this origColumns from the FileDescriptor if present since an importer
// may generate a subset by default in which case the DataDescriptor will not contain all
// the columns and subsetting will not work correctly. We
// can't just set mpFileDescriptor = pRasterDescriptor->getFileDescriptor() since we only
// want to replace the DataDescriptor's column list if one of the subset options is specified
const RasterFileDescriptor* pFileDesc(pRasterFileDescriptor);
if (pFileDesc == NULL)
{
pFileDesc = dynamic_cast<const RasterFileDescriptor*>(pRasterDescriptor->getFileDescriptor());
}
const vector<DimensionDescriptor>& origColumns = (pFileDesc != NULL) ?
pFileDesc->getColumns() : pRasterDescriptor->getColumns();
unsigned int startColumn = 0;
if (mpStartColumn != NULL)
{
startColumn = *mpStartColumn;
}
else if (origColumns.empty() == false)
{
startColumn = origColumns.front().getOriginalNumber() + 1;
}
unsigned int endColumn = 0;
if (mpEndColumn != NULL)
{
endColumn = *mpEndColumn;
}
else if (origColumns.empty() == false)
{
endColumn = origColumns.back().getOriginalNumber() + 1;
}
unsigned int columnSkip = 0;
if (mpColumnSkipFactor != NULL)
{
columnSkip = *mpColumnSkipFactor;
}
vector<DimensionDescriptor> columns;
for (unsigned int i = 0; i < origColumns.size(); ++i)
{
DimensionDescriptor columnDim = origColumns[i];
unsigned int originalNumber = columnDim.getOriginalNumber() + 1;
if ((originalNumber >= startColumn) && (originalNumber <= endColumn))
{
columns.push_back(columnDim);
i += columnSkip;
}
}
pRasterDescriptor->setColumns(columns);
}
// Bands
if ((mpStartBand != NULL) || (mpEndBand != NULL) || (mpBandSkipFactor != NULL) || (mpBadBandsFile != NULL))
{
// We need to obtain this origBands from the FileDescriptor if present since an importer
// may generate a subset by default in which case the DataDescriptor will not contain all
// the bands and subsetting (especially by bad band file) will not work correctly. We
// can't just set mpFileDescriptor = pRasterDescriptor->getFileDescriptor() since we only
// want to replace the DataDescriptor's band list if one of the subset options is specified
const RasterFileDescriptor* pFileDesc(pRasterFileDescriptor);
if (pFileDesc == NULL)
{
pFileDesc = dynamic_cast<const RasterFileDescriptor*>(pRasterDescriptor->getFileDescriptor());
}
const vector<DimensionDescriptor>& origBands = (pFileDesc != NULL) ?
pFileDesc->getBands() : pRasterDescriptor->getBands();
unsigned int startBand = 0;
if (mpStartBand != NULL)
{
startBand = *mpStartBand;
}
else if (origBands.empty() == false)
{
startBand = origBands.front().getOriginalNumber() + 1;
}
unsigned int endBand = 0;
if (mpEndBand != NULL)
{
endBand = *mpEndBand;
}
else if (origBands.empty() == false)
{
endBand = origBands.back().getOriginalNumber() + 1;
}
unsigned int bandSkip = 0;
if (mpBandSkipFactor != NULL)
{
bandSkip = *mpBandSkipFactor;
}
// Get the bad bands from the file
vector<unsigned int> badBands;
if (mpBadBandsFile != NULL)
{
string filename = *mpBadBandsFile;
if (filename.empty() == false)
{
FILE* pFile = fopen(filename.c_str(), "rb");
if (pFile != NULL)
{
char line[1024];
while (fgets(line, 1024, pFile) != NULL)
{
unsigned int bandNumber = 0;
int iValues = sscanf(line, "%u", &bandNumber);
if (iValues == 1)
{
badBands.push_back(bandNumber);
}
}
fclose(pFile);
}
}
}
vector<DimensionDescriptor> bands;
for (unsigned int i = 0; i < origBands.size(); ++i)
{
DimensionDescriptor bandDim = origBands[i];
unsigned int originalNumber = bandDim.getOriginalNumber() + 1;
if ((originalNumber >= startBand) && (originalNumber <= endBand))
{
bool bBad = false;
for (unsigned int j = 0; j < badBands.size(); ++j)
{
unsigned int badBandNumber = badBands[j];
if (originalNumber == badBandNumber)
{
bBad = true;
break;
}
}
if (bBad == false)
{
bands.push_back(bandDim);
i += bandSkip;
}
}
}
pRasterDescriptor->setBands(bands);
}
// X pixel size
if (mpPixelSizeX != NULL)
{
pRasterDescriptor->setXPixelSize(*mpPixelSizeX);
}
// Y pixel size
if (mpPixelSizeY != NULL)
{
pRasterDescriptor->setYPixelSize(*mpPixelSizeY);
}
// Units
if ((mpUnitsName != NULL) || (mpUnitsType != NULL) ||
(mpUnitsScale != NULL) || (mpUnitsRangeMin != NULL) || (mpUnitsRangeMax != NULL))
{
const Units* pOrigUnits = pRasterDescriptor->getUnits();
FactoryResource<Units> pUnits;
VERIFY(pUnits.get() != NULL);
// Name
if (mpUnitsName != NULL)
{
pUnits->setUnitName(*mpUnitsName);
}
else if (pOrigUnits != NULL)
{
pUnits->setUnitName(pOrigUnits->getUnitName());
}
// Type
if (mpUnitsType != NULL)
{
pUnits->setUnitType(*mpUnitsType);
}
else if (pOrigUnits != NULL)
{
pUnits->setUnitType(pOrigUnits->getUnitType());
}
// Scale
if (mpUnitsScale != NULL)
{
pUnits->setScaleFromStandard(*mpUnitsScale);
}
else if (pOrigUnits != NULL)
{
pUnits->setScaleFromStandard(pOrigUnits->getScaleFromStandard());
}
// Range minimum
if (mpUnitsRangeMin != NULL)
{
pUnits->setRangeMin(*mpUnitsRangeMin);
}
else if (pOrigUnits != NULL)
{
pUnits->setRangeMin(pOrigUnits->getRangeMin());
}
// Range maximum
if (mpUnitsRangeMax != NULL)
{
pUnits->setRangeMax(*mpUnitsRangeMax);
}
else if (pOrigUnits != NULL)
{
pUnits->setRangeMax(pOrigUnits->getRangeMax());
}
pRasterDescriptor->setUnits(pUnits.get());
}
// Display mode
if (mpDisplayMode != NULL)
{
pRasterDescriptor->setDisplayMode(*mpDisplayMode);
}
// Display bands
// Gray
if (mpGrayBand != NULL)
{
DimensionDescriptor band = pRasterDescriptor->getOriginalBand(*mpGrayBand - 1);
pRasterDescriptor->setDisplayBand(GRAY, band);
}
// Red
if (mpRedBand != NULL)
{
DimensionDescriptor band = pRasterDescriptor->getOriginalBand(*mpRedBand - 1);
pRasterDescriptor->setDisplayBand(RED, band);
}
// Green
if (mpGreenBand != NULL)
{
DimensionDescriptor band = pRasterDescriptor->getOriginalBand(*mpGreenBand - 1);
pRasterDescriptor->setDisplayBand(GREEN, band);
}
// Blue
if (mpBlueBand != NULL)
{
DimensionDescriptor band = pRasterDescriptor->getOriginalBand(*mpBlueBand - 1);
pRasterDescriptor->setDisplayBand(BLUE, band);
}
}
else if (pSignatureDescriptor != NULL)
{
if (mpComponentName != NULL)
{
const Units* pOrigUnits = pSignatureDescriptor->getUnits(*mpComponentName);
FactoryResource<Units> pUnits;
if (pOrigUnits != NULL)
{
*pUnits = *pOrigUnits;
}
if (mpUnitsName != NULL)
{
pUnits->setUnitName(*mpUnitsName);
}
if (mpUnitsType != NULL)
{
pUnits->setUnitType(*mpUnitsType);
}
if (mpUnitsScale != NULL)
{
pUnits->setScaleFromStandard(*mpUnitsScale);
}
if (mpUnitsRangeMin != NULL)
{
pUnits->setRangeMin(*mpUnitsRangeMin);
}
if (mpUnitsRangeMax != NULL)
{
pUnits->setRangeMax(*mpUnitsRangeMax);
}
pSignatureDescriptor->setUnits(*mpComponentName, pUnits.get());
}
}
reportComplete();
return true;
}
