DataAccessor BackgroundSuppressionShell::getCurrentFrameAccessor() const
{
if(mpRaster == NULL)
{
return DataAccessor(NULL, NULL);
}
RasterDataDescriptor *pDesc = static_cast<RasterDataDescriptor*>(mpRaster->getDataDescriptor());
VERIFYRV(pDesc != NULL, DataAccessor(NULL, NULL));
FactoryResource<DataRequest> request;
VERIFYRV(request.get() != NULL, DataAccessor(NULL, NULL));
request->setInterleaveFormat(BSQ);
DimensionDescriptor band = pDesc->getBands()[mCurrentFrame];
request->setBands(band, band, 1);
return mpRaster->getDataAccessor(request.release());
}
DynamicObject* FeatureQueryOptions::toDynamicObject() const
{
DynamicObject* pDynObj = QueryOptions::toDynamicObject();
VERIFYRV(pDynObj != NULL, NULL);
pDynObj->setAttribute(FORMAT_STRING, mFormatString);
return pDynObj;
}
QWidget* RangeProfilePlotManager::createWidget()
{
DockWindow* pWindow = getDockWindow();
VERIFYRV(pWindow, NULL);
pWindow->attach(SIGNAL_NAME(Window, SessionItemDropped), Slot(this, &RangeProfilePlotManager::dropSessionItem));
pWindow->enableSessionItemDrops(this);
if (!Service<SessionManager>()->isSessionLoading())
{
mpPlot = Service<DesktopServices>()->createPlotWidget(getName(), CARTESIAN_PLOT);
}
if (mpPlot == NULL)
{
return NULL;
}
mpView = mpPlot->getPlot();
#pragma message(__FILE__ "(" STRING(__LINE__) ") : warning : If a SHALLOW_SELECTION selection mode is added " \
"to plot view (OPTICKS-528), mpView should use it (tclarke)")
mpMode = (mpView == NULL) ? NULL : mpView->getMouseMode("SelectionMode");
if (mpMode == NULL)
{
return NULL;
}
mpView->getWidget()->installEventFilter(this);
mpPlot->attach(SIGNAL_NAME(PlotWidget, AboutToShowContextMenu),
Slot(this, &RangeProfilePlotManager::updateContextMenu));
mpView->enableMouseMode(mpMode, true);
mpView->setMouseMode(mpMode);
return mpPlot->getWidget();
}
CachedPage::UnitPtr DicomRasterPager::fetchUnit(DataRequest *pOriginalRequest)
{
VERIFYRV(pOriginalRequest != NULL, CachedPage::UnitPtr());
unsigned int frame = pOriginalRequest->getStartBand().getOriginalNumber();
if(mConvertRgb)
{
frame /= 3;
}
const RasterDataDescriptor *pDesc = static_cast<const RasterDataDescriptor*>(getRasterElement()->getDataDescriptor());
unsigned int bpp = pDesc->getBytesPerElement() * 8;
size_t bufsize = mpImage->getOutputDataSize(bpp);
char *pBuffer = new char[bufsize];
if(!mpImage->getOutputData(pBuffer, bufsize, bpp, frame, 1))
{
delete pBuffer;
return CachedPage::UnitPtr();
}
if(mConvertRgb)
{
unsigned int band = pOriginalRequest->getStartBand().getOriginalNumber();
size_t bandsize = bufsize / 3;
char *pNewBuffer = new char[bandsize];
memcpy(pNewBuffer, pBuffer + (band * bandsize), bandsize);
delete pBuffer;
pBuffer = pNewBuffer;
bufsize = bandsize;
}
return CachedPage::UnitPtr(new CachedPage::CacheUnit(pBuffer, pDesc->getRows()[0], pDesc->getRowCount(), bufsize));
}
DynamicObject* DisplayQueryOptions::toDynamicObject() const
{
DynamicObject* pDynObj = QueryOptions::toDynamicObject();
VERIFYRV(pDynObj != NULL, NULL);
pDynObj->setAttribute(UNIQUE_NAME, mUniqueName);
pDynObj->setAttribute(CHECKED, mbQueryActive);
pDynObj->setAttribute(ORDER, mOrder);
return pDynObj;
}
DynamicObject *QueryOptions::toDynamicObject() const
{
FactoryResource<DynamicObject> pDynObj;
VERIFYRV(pDynObj.get() != NULL, NULL);
pDynObj->setAttribute(QUERY_NAME, mQueryName);
pDynObj->setAttribute(QUERY_STRING, mQueryString);
pDynObj->setAttribute(SYMBOL_NAME, mSymbolName);
pDynObj->setAttribute(SYMBOL_SIZE, mSymbolSize);
pDynObj->setAttribute(LINE_STATE, mLineState);
pDynObj->setAttribute(LINE_STYLE, mLineStyle);
pDynObj->setAttribute(LINE_WIDTH, mLineWidth);
pDynObj->setAttribute(LINE_COLOR, mLineColor);
pDynObj->setAttribute(LINE_SCALED, mLineScaled);
pDynObj->setAttribute(FILL_COLOR, mFillColor);
pDynObj->setAttribute(FILL_STYLE, mFillStyle);
pDynObj->setAttribute(HATCH_STYLE, mHatchStyle);
return pDynObj.release();
}
CachedPage::UnitPtr DiHdfRasterPager::fetchUnit(DataRequest *pOriginalRequest)
{
VERIFYRV(pOriginalRequest != NULL, CachedPage::UnitPtr());
unsigned int frame = pOriginalRequest->getStartBand().getOnDiskNumber();
if (mHdf.toFrame(frame) == FAIL)
{
return CachedPage::UnitPtr();
}
const RasterDataDescriptor *pDesc = static_cast<const RasterDataDescriptor*>(getRasterElement()->getDataDescriptor());
unsigned int bpp = pDesc->getBytesPerElement();
size_t bufsize = pOriginalRequest->getConcurrentRows() * pDesc->getColumnCount() * bpp;
char* pBuffer = new char[bufsize];
int32 pStart[] = {pDesc->getActiveColumn(0).getOnDiskNumber(), pOriginalRequest->getStartRow().getOnDiskNumber()};
int32 pCount[] = {pDesc->getColumnCount(), pOriginalRequest->getConcurrentRows()};
int32 pStride[] = {1, 1};
if (GRreadimage(mHdf.riid(), pStart, pStride, pCount, pBuffer) == FAIL)
{
delete pBuffer;
return CachedPage::UnitPtr();
}
return CachedPage::UnitPtr(new CachedPage::CacheUnit(
pBuffer, pOriginalRequest->getStartRow(), pOriginalRequest->getConcurrentRows(),
bufsize, pOriginalRequest->getStartBand()));
}
QString LabeledSection::getText() const
{
VERIFYRV(mpTextLabel != NULL, QString());
return mpTextLabel->text();
}
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());
}
std::vector<ImportDescriptor*> VideoImporter::getImportDescriptors(const std::string &filename)
{
std::vector<ImportDescriptor*> descriptors;
AVFormatResource pFormatCtx;
{ // scope
AVFormatContext* pTmp = NULL;
if (av_open_input_file(&pTmp, filename.c_str(), NULL, 0, NULL) != 0)
{
return descriptors;
}
pFormatCtx.reset(pTmp);
}
if (av_find_stream_info(pFormatCtx) < 0)
{
return descriptors;
}
for(int streamId = 0; streamId < pFormatCtx->nb_streams; streamId++)
{
if(pFormatCtx->streams[streamId]->codec->codec_type == CODEC_TYPE_VIDEO)
{
AVCodecContext* pCodecCtx = pFormatCtx->streams[streamId]->codec;
AVCodec *pCodec = avcodec_find_decoder(pCodecCtx->codec_id);
VERIFYRV(pCodec != NULL, descriptors);
if(pCodec->capabilities & CODEC_CAP_TRUNCATED)
{
pCodecCtx->flags |= CODEC_FLAG_TRUNCATED;
}
if(avcodec_open(pCodecCtx, pCodec) < 0)
{
return descriptors;
}
ImportDescriptorResource pStreamDescriptor(filename, "VideoStream");
VERIFYRV(pStreamDescriptor.get() != NULL, descriptors);
pStreamDescriptor->getDataDescriptor()->setProcessingLocation(ON_DISK_READ_ONLY);
RasterUtilities::generateAndSetFileDescriptor(pStreamDescriptor->getDataDescriptor(), filename,
StringUtilities::toDisplayString(streamId), LITTLE_ENDIAN);
std::string rasterName = filename + QString(":%1").arg(streamId).toStdString();
ImportDescriptorResource pRasterDescriptor(rasterName,
TypeConverter::toString<RasterElement>(),
std::vector<std::string>(1, filename));
VERIFYRV(pRasterDescriptor.get() != NULL, descriptors);
RasterDataDescriptor* pDesc = static_cast<RasterDataDescriptor*>(pRasterDescriptor->getDataDescriptor());
std::vector<DimensionDescriptor> rowDims = RasterUtilities::generateDimensionVector(pCodecCtx->height);
pDesc->setRows(rowDims);
std::vector<DimensionDescriptor> colDims = RasterUtilities::generateDimensionVector(pCodecCtx->width);
pDesc->setColumns(colDims);
std::vector<DimensionDescriptor> bandDims = RasterUtilities::generateDimensionVector(3);
pDesc->setBands(bandDims);
pDesc->setInterleaveFormat(BIP);
pDesc->setDataType(INT1UBYTE);
pDesc->setProcessingLocation(IN_MEMORY);
pDesc->setDisplayMode(RGB_MODE);
pDesc->setDisplayBand(RED, pDesc->getActiveBand(0));
pDesc->setDisplayBand(GREEN, pDesc->getActiveBand(1));
pDesc->setDisplayBand(BLUE, pDesc->getActiveBand(2));
RasterUtilities::generateAndSetFileDescriptor(pDesc, filename, StringUtilities::toDisplayString(streamId), LITTLE_ENDIAN);
descriptors.push_back(pStreamDescriptor.release());
descriptors.push_back(pRasterDescriptor.release());
}
}
return descriptors;
}
CachedPage::UnitPtr Jpeg2000Pager::populateImageData(const DimensionDescriptor& startRow,
const DimensionDescriptor& startColumn,
unsigned int concurrentRows, unsigned int concurrentColumns) const
{
VERIFYRV(startRow.isOnDiskNumberValid() == true, CachedPage::UnitPtr());
VERIFYRV(startColumn.isOnDiskNumberValid() == true, CachedPage::UnitPtr());
VERIFYRV(concurrentRows > 0, CachedPage::UnitPtr());
VERIFYRV(concurrentColumns > 0, CachedPage::UnitPtr());
// Get the rows, colums, and bands to load
unsigned int onDiskStartRow = startRow.getOnDiskNumber();
unsigned int onDiskStopRow = onDiskStartRow + concurrentRows;
unsigned int onDiskStartColumn = startColumn.getOnDiskNumber();
unsigned int onDiskStopColumn = onDiskStartColumn + concurrentColumns;
const RasterElement* pRaster = getRasterElement();
VERIFYRV(pRaster != NULL, CachedPage::UnitPtr());
const RasterDataDescriptor* pDescriptor = dynamic_cast<const RasterDataDescriptor*>(pRaster->getDataDescriptor());
VERIFYRV(pDescriptor != NULL, CachedPage::UnitPtr());
const RasterFileDescriptor* pFileDescriptor =
dynamic_cast<const RasterFileDescriptor*>(pDescriptor->getFileDescriptor());
VERIFYRV(pFileDescriptor != NULL, CachedPage::UnitPtr());
const std::vector<DimensionDescriptor>& allBands = pFileDescriptor->getBands();
if (allBands.empty() == true)
{
return CachedPage::UnitPtr();
}
// Create the output data
unsigned int numPixels = concurrentRows * concurrentColumns * allBands.size();
unsigned int numBytes = numPixels * getBytesPerBand();
if (numPixels > static_cast<unsigned int>(std::numeric_limits<int>::max())) // ArrayResource only allocates up
// to INT_MAX number of values
{
return CachedPage::UnitPtr();
}
ArrayResource<Out> pDestination(numPixels, true);
char* pDest = reinterpret_cast<char*>(pDestination.get());
if (pDest == NULL)
{
return CachedPage::UnitPtr();
}
memset(pDest, 0, numPixels);
// Decode the image from the file, first trying the codestream format then the file format
opj_image_t* pImage = decodeImage(onDiskStartRow, onDiskStartColumn, onDiskStopRow, onDiskStopColumn,
Jpeg2000Utilities::J2K_CFMT);
if (pImage == NULL)
{
pImage = decodeImage(onDiskStartRow, onDiskStartColumn, onDiskStopRow, onDiskStopColumn,
Jpeg2000Utilities::JP2_CFMT);
}
if (pImage == NULL)
{
return CachedPage::UnitPtr();
}
// Populate the output image data
int bandFactor = 1;
std::string filename = pRaster->getFilename();
if (filename.empty() == false)
{
QStringList parts = QString::fromStdString(filename).split('.');
foreach (QString part, parts)
{
bool error;
EncodingType dataType = StringUtilities::fromXmlString<EncodingType>(part.toStdString(), &error);
if (dataType.isValid() == true && error == false)
{
int currentBandFactor = Jpeg2000Utilities::get_num_bands(dataType);
if (currentBandFactor > 0)
{
bandFactor = currentBandFactor;
break;
}
}
}
CachedPage::UnitPtr Jpeg2000Pager::fetchUnit(DataRequest* pOriginalRequest)
{
if (pOriginalRequest == NULL)
{
return CachedPage::UnitPtr();
}
// Check for interleave conversions, which are not supported by this pager
const RasterElement* pRaster = getRasterElement();
VERIFYRV(pRaster != NULL, CachedPage::UnitPtr());
const RasterDataDescriptor* pDescriptor = dynamic_cast<const RasterDataDescriptor*>(pRaster->getDataDescriptor());
VERIFYRV(pDescriptor != NULL, CachedPage::UnitPtr());
const RasterFileDescriptor* pFileDescriptor =
dynamic_cast<const RasterFileDescriptor*>(pDescriptor->getFileDescriptor());
VERIFYRV(pFileDescriptor != NULL, CachedPage::UnitPtr());
if (pFileDescriptor->getBandCount() > 1)
{
InterleaveFormatType requestedInterleave = pOriginalRequest->getInterleaveFormat();
InterleaveFormatType fileInterleave = pFileDescriptor->getInterleaveFormat();
if (requestedInterleave != fileInterleave)
{
return CachedPage::UnitPtr();
}
VERIFYRV(requestedInterleave == BIP, CachedPage::UnitPtr()); // The JPEG2000 data is stored BIP
}
// Get and validate the extents of the data to be loaded
DimensionDescriptor startRow = pOriginalRequest->getStartRow();
DimensionDescriptor stopRow = pOriginalRequest->getStopRow();
unsigned int concurrentRows = pOriginalRequest->getConcurrentRows();
DimensionDescriptor startColumn = pOriginalRequest->getStartColumn();
DimensionDescriptor stopColumn = pOriginalRequest->getStopColumn();
unsigned int concurrentColumns = pOriginalRequest->getConcurrentColumns();
DimensionDescriptor startBand = pOriginalRequest->getStartBand();
DimensionDescriptor stopBand = pOriginalRequest->getStopBand();
if ((startRow.isOnDiskNumberValid() == false) || (stopRow.isOnDiskNumberValid() == false) ||
(startColumn.isOnDiskNumberValid() == false) || (stopColumn.isOnDiskNumberValid() == false) ||
(startBand.isOnDiskNumberValid() == false) || (stopBand.isOnDiskNumberValid() == false))
{
return CachedPage::UnitPtr();
}
if ((startRow.getOnDiskNumber() > stopRow.getOnDiskNumber()) ||
(startColumn.getOnDiskNumber() > stopColumn.getOnDiskNumber()) ||
(startBand.getOnDiskNumber() > stopBand.getOnDiskNumber()))
{
return CachedPage::UnitPtr();
}
if ((startRow.getActiveNumber() + concurrentRows - 1) > stopRow.getActiveNumber())
{
concurrentRows = stopRow.getActiveNumber() - startRow.getActiveNumber() + 1;
}
if ((startColumn.getActiveNumber() + concurrentColumns - 1) > stopColumn.getActiveNumber())
{
concurrentColumns = stopColumn.getActiveNumber() - startColumn.getActiveNumber() + 1;
}
// Populate the image data based on the output data type
EncodingType outputDataType = pDescriptor->getDataType();
switch (outputDataType)
{
case INT1UBYTE:
return populateImageData<unsigned char>(startRow, startColumn, concurrentRows, concurrentColumns);
case INT1SBYTE:
return populateImageData<signed char>(startRow, startColumn, concurrentRows, concurrentColumns);
case INT2UBYTES:
return populateImageData<unsigned short>(startRow, startColumn, concurrentRows, concurrentColumns);
case INT2SBYTES:
return populateImageData<signed short>(startRow, startColumn, concurrentRows, concurrentColumns);
case INT4UBYTES:
return populateImageData<unsigned int>(startRow, startColumn, concurrentRows, concurrentColumns);
case INT4SBYTES:
return populateImageData<signed int>(startRow, startColumn, concurrentRows, concurrentColumns);
case FLT4BYTES:
return populateImageData<float>(startRow, startColumn, concurrentRows, concurrentColumns);
case FLT8BYTES:
return populateImageData<double>(startRow, startColumn, concurrentRows, concurrentColumns);
default:
break;
}
return CachedPage::UnitPtr();
}
RasterPage* ConvertToBsqPager::getPage(DataRequest* pOriginalRequest, DimensionDescriptor startRow,
DimensionDescriptor startColumn, DimensionDescriptor startBand)
{
VERIFYRV(pOriginalRequest != NULL, NULL);
if (pOriginalRequest->getWritable())
{
return NULL;
}
InterleaveFormatType requestedType = pOriginalRequest->getInterleaveFormat();
DimensionDescriptor stopRow = pOriginalRequest->getStopRow();
DimensionDescriptor stopColumn = pOriginalRequest->getStopColumn();
DimensionDescriptor stopBand = pOriginalRequest->getStopBand();
unsigned int concurrentRows = std::min(pOriginalRequest->getConcurrentRows(),
stopRow.getActiveNumber() - startRow.getActiveNumber() + 1);
unsigned int concurrentBands = pOriginalRequest->getConcurrentBands();
VERIFY(requestedType == BSQ);
VERIFY(startBand == stopBand && concurrentBands == 1);
VERIFY(mpRaster != NULL);
const RasterDataDescriptor* pDd = dynamic_cast<const RasterDataDescriptor*>(mpRaster->getDataDescriptor());
VERIFY(pDd != NULL);
InterleaveFormatType interleave = pDd->getInterleaveFormat();
VERIFY(interleave == BIL || interleave == BIP);
unsigned int numRows = pDd->getRowCount();
unsigned int numCols = pDd->getColumnCount();
unsigned int numBands = pDd->getBandCount();
if (startRow.getActiveNumber() >= numRows || stopRow.getActiveNumber() >= numRows ||
startColumn.getActiveNumber() >= numCols || stopColumn.getActiveNumber() >= numCols ||
startBand.getActiveNumber() >= numBands || stopBand.getActiveNumber() >= numBands)
{
return NULL;
}
unsigned int cols = stopColumn.getActiveNumber() - startColumn.getActiveNumber() + 1;
std::auto_ptr<ConvertToBsqPage> pPage(new ConvertToBsqPage(concurrentRows, cols, mBytesPerElement));
unsigned char* pDst = reinterpret_cast<unsigned char*>(pPage->getRawData());
if (pDst == NULL)
{
return NULL;
}
FactoryResource<DataRequest> pRequest;
pRequest->setRows(startRow, stopRow);
pRequest->setColumns(startColumn, stopColumn, cols);
pRequest->setBands(startBand, startBand, 1);
DataAccessor da = mpRaster->getDataAccessor(pRequest.release());
if (interleave == BIP)
{
for (unsigned int row = 0; row < concurrentRows; ++row)
{
for (unsigned int col = 0; col < cols; ++col)
{
if (da.isValid() == false)
{
return NULL;
}
memcpy(pDst, da->getColumn(), mBytesPerElement);
pDst += mBytesPerElement;
da->nextColumn();
}
da->nextRow();
}
}
else if (interleave == BIL)
{
for (unsigned int row = 0; row < concurrentRows; ++row)
{
if (da.isValid() == false)
{
return NULL;
}
memcpy(pDst, da->getRow(), mBytesPerElement * cols);
pDst += mBytesPerElement * cols;
da->nextRow();
}
}
return pPage.release();
}
bool RangeProfilePlotManager::plotProfile(Signature* pSignature)
{
VERIFY(mpView && pSignature);
std::string plotName = pSignature->getDisplayName();
if (plotName.empty())
{
plotName = pSignature->getName();
}
if (plotName == "Difference")
{
QMessageBox::warning(Service<DesktopServices>()->getMainWidget(),
"Invalid signature", "Signatures can not be named 'Difference' as this is a reserved "
"name for this plot. Please rename your signature and try again.");
return false;
}
const Units* pXUnits = NULL;
const Units* pYUnits = NULL;
std::vector<double> xData;
std::vector<double> yData;
std::set<std::string> dataNames = pSignature->getDataNames();
for (std::set<std::string>::const_iterator dataName = dataNames.begin();
dataName != dataNames.end() && (pXUnits == NULL || pYUnits == NULL);
++dataName)
{
const Units* pUnits = pSignature->getUnits(*dataName);
if (pUnits == NULL)
{
continue;
}
if (pUnits->getUnitType() == DISTANCE)
{
if (pXUnits == NULL)
{
pXUnits = pUnits;
xData = dv_cast<std::vector<double> >(pSignature->getData(*dataName), std::vector<double>());
}
}
else if (pYUnits == NULL)
{
pYUnits = pUnits;
yData = dv_cast<std::vector<double> >(pSignature->getData(*dataName), std::vector<double>());
}
}
if (xData.empty() || xData.size() != yData.size())
{
QMessageBox::warning(Service<DesktopServices>()->getMainWidget(),
"Invalid signature", QString("Signatures must have a distance axis. '%1' does not and will not be plotted.")
.arg(QString::fromStdString(pSignature->getName())));
return false;
}
std::map<Signature*, std::string>::iterator oldPointSet = mSigPointSets.find(pSignature);
PointSet* pSet = getPointSet(pSignature);
if (pSet != NULL)
{
pSet->clear(true);
}
std::list<PlotObject*> curObjects;
mpView->getObjects(POINT_SET, curObjects);
if (pSet == NULL)
{
std::vector<ColorType> excluded;
excluded.push_back(ColorType(255, 255, 255)); // background
excluded.push_back(ColorType(200, 0, 0)); // color for the difference plot
for (std::list<PlotObject*>::const_iterator cur = curObjects.begin(); cur != curObjects.end(); ++cur)
{
excluded.push_back(static_cast<PointSet*>(*cur)->getLineColor());
}
pSet = static_cast<PointSet*>(mpView->addObject(POINT_SET, true));
mSigPointSets[pSignature] = plotName;
pSignature->attach(SIGNAL_NAME(Subject, Deleted), Slot(this, &RangeProfilePlotManager::signatureDeleted));
pSignature->getDataDescriptor()->attach(SIGNAL_NAME(DataDescriptor, Renamed),
Slot(this, &RangeProfilePlotManager::signatureRenamed));
std::vector<ColorType> colors;
ColorType::getUniqueColors(1, colors, excluded);
if (!colors.empty())
{
pSet->setLineColor(colors.front());
}
}
pSet->setObjectName(plotName);
for (size_t idx = 0; idx < xData.size(); ++idx)
{
pSet->addPoint(xData[idx], yData[idx]);
}
VERIFY(mpPlot);
Axis* pBottom = mpPlot->getAxis(AXIS_BOTTOM);
Axis* pLeft = mpPlot->getAxis(AXIS_LEFT);
VERIFYRV(pBottom && pLeft, NULL);
if (pBottom->getTitle().empty())
{
pBottom->setTitle(pXUnits->getUnitName());
}
if (pLeft->getTitle().empty())
{
pLeft->setTitle(pYUnits->getUnitName());
}
else if (pLeft->getTitle() != pYUnits->getUnitName())
{
Axis* pRight = mpPlot->getAxis(AXIS_RIGHT);
VERIFYRV(pRight, NULL);
if (pRight->getTitle().empty())
{
pRight->setTitle(pYUnits->getUnitName());
}
}
std::string classificationText = dv_cast<std::string>(pSignature->getMetadata()->getAttribute("Raw Classification"),
mpPlot->getClassificationText());
if (classificationText.empty() == false)
{
FactoryResource<Classification> pClassification;
if (pClassification->setClassification(classificationText) == true)
{
mpPlot->setClassification(pClassification.get());
}
else
{
QMessageBox::warning(Service<DesktopServices>()->getMainWidget(), QString::fromStdString(getName()),
"The plot could not be updated with the signature classification. Please ensure that the plot "
"has the proper classification.");
}
}
getDockWindow()->show();
mpView->zoomExtents();
mpView->refresh();
return true;
}
std::vector<ImportDescriptor*> DicomImporter::getImportDescriptors(const std::string &filename)
{
mErrors.clear();
mWarnings.clear();
std::vector<ImportDescriptor*> descriptors;
DcmFileFormat fileformat;
OFCondition status;
if((status = fileformat.loadFile(filename.c_str())).bad())
{
return descriptors;
}
ImportDescriptorResource pImportDescriptor(filename, TypeConverter::toString<RasterElement>());
VERIFYRV(pImportDescriptor.get() != NULL, descriptors);
descriptors.push_back(pImportDescriptor.release());
DicomImage img(fileformat.getDataset(), fileformat.getDataset()->getOriginalXfer());
if(img.getStatus() != EIS_Normal)
{
mErrors.push_back(std::string("Unable to decode image: ") + DicomImage::getString(img.getStatus()));
pImportDescriptor->setDataDescriptor(RasterUtilities::generateRasterDataDescriptor(filename, NULL, 0, 0, INT1UBYTE, IN_MEMORY));
return descriptors;
}
InterleaveFormatType interleave(BSQ);
EncodingType encoding(INT4UBYTES);
bool rgb = false;
unsigned long rows = img.getHeight(), columns = img.getWidth(), frames = img.getFrameCount();
int imgDepth = img.getDepth();
switch(img.getPhotometricInterpretation())
{
case EPI_Monochrome1:
case EPI_Monochrome2:
// do nothing special....this is single or multi-frame grayscale, 1 or 2 byte
break;
case EPI_RGB:
case EPI_PaletteColor:
// supported if there's only 1 frame
if(frames == 1)
{
frames = 3;
rgb = true;
}
else
{
mWarnings.push_back("RGB and palette color not supported when multiple frames are present. Converting to grayscale.");
}
break;
default:
mWarnings.push_back(std::string(DicomImage::getString(img.getPhotometricInterpretation())) +
" not supported. Attempting to convert to grayscale.");
}
if(imgDepth <= 8)
{
encoding = INT1UBYTE;
}
else if(imgDepth <= 16)
{
encoding = INT2UBYTES;
}
else if(imgDepth <= 32)
{
encoding = INT4UBYTES;
}
else
{
mWarnings.push_back("Bit depth " + StringUtilities::toDisplayString(imgDepth) + " not supported. Downgrading to 32 bits.");
encoding = INT4UBYTES;
}
RasterDataDescriptor *pDescriptor = RasterUtilities::generateRasterDataDescriptor(
filename, NULL, rows, columns, frames, interleave, encoding, IN_MEMORY);
if(pDescriptor != NULL)
{
if(rgb)
{
pDescriptor->setDisplayBand(RED, pDescriptor->getBands()[0]);
pDescriptor->setDisplayBand(GREEN, pDescriptor->getBands()[1]);
pDescriptor->setDisplayBand(BLUE, pDescriptor->getBands()[2]);
pDescriptor->setDisplayMode(RGB_MODE);
}
pImportDescriptor->setDataDescriptor(pDescriptor);
FactoryResource<DynamicObject> pMeta;
int idx = 0;
DcmElement *pElmnt;
while((pElmnt = fileformat.getDataset()->getElement(idx++)) != NULL)
{
if(pElmnt->error().bad())
{
continue;
}
const DcmTag &tag = pElmnt->getTag();
std::string name = const_cast<DcmTag&>(tag).getTagName();
if(name.empty())
{
name = QString("(%1,%2)").arg(pElmnt->getGTag(), 4, 16, QChar('0')).arg(pElmnt->getETag(), 4, 16, QChar('0')).toStdString();
}
pMeta->setAttributeByPath(std::string("DICOM/") + name, dcmElementToDataVariant(*pElmnt));
}
pImportDescriptor->getDataDescriptor()->setMetadata(pMeta.release());
}
RasterUtilities::generateAndSetFileDescriptor(pImportDescriptor->getDataDescriptor(), filename, std::string(), LITTLE_ENDIAN_ORDER);
return descriptors;
}
std::vector<ImportDescriptor*> DiHdfImporter::getImportDescriptors(const std::string &filename)
{
mErrors.clear();
mWarnings.clear();
std::vector<ImportDescriptor*> descriptors;
ImportDescriptorResource pImportDescriptor(filename, TypeConverter::toString<RasterElement>());
VERIFYRV(pImportDescriptor.get(), descriptors);
descriptors.push_back(pImportDescriptor.release());
HdfContext hdf(filename);
if (hdf.grid() == FAIL)
{
mErrors.push_back("Invalid DI HDF file.");
return descriptors;
}
int32 frames = 0;
int32 attrs = 0;
GRfileinfo(hdf.grid(), &frames, &attrs);
if (frames <= 0)
{
mErrors.push_back("Dataset does not contain and frames.");
return descriptors;
}
if (hdf.toFrame(0) == FAIL)
{
mErrors.push_back("Unable to access image data.");
return descriptors;
}
char pName[256];
int32 comps = 0;
int32 data_type = 0;
int32 interlace_mode = 0;
int32 pDims[2] = {0,0};
EncodingType encoding;
GRgetiminfo(hdf.riid(), pName, &comps, &data_type, &interlace_mode, pDims, &attrs);
switch(data_type)
{
case DFNT_FLOAT32:
encoding = FLT4BYTES;
break;
case DFNT_FLOAT64:
encoding = FLT8BYTES;
break;
case DFNT_CHAR8:
case DFNT_INT8:
encoding = INT1SBYTE;
break;
case DFNT_UCHAR8:
case DFNT_UINT8:
encoding = INT1UBYTE;
break;
case DFNT_INT16:
encoding = INT2SBYTES;
break;
case DFNT_UINT16:
encoding = INT2UBYTES;
break;
case DFNT_INT32:
encoding = INT4SBYTES;
break;
case DFNT_UINT32:
encoding = INT4UBYTES;
break;
case DFNT_INT64:
case DFNT_UINT64:
default:
mErrors.push_back("Unknown data encoding.");
break;
}
pImportDescriptor->setDataDescriptor(RasterUtilities::generateRasterDataDescriptor(
filename, NULL, pDims[1], pDims[0], frames, BSQ, encoding, IN_MEMORY));
RasterUtilities::generateAndSetFileDescriptor(pImportDescriptor->getDataDescriptor(), filename,
std::string(), LITTLE_ENDIAN_ORDER);
return descriptors;
}
std::vector<ImportDescriptor*> NefImporter::getImportDescriptors(const std::string &filename)
{
std::vector<ImportDescriptor*> descriptors;
try
{
ImportDescriptorResource pImportDescriptor(filename, TypeConverter::toString<RasterElement>());
VERIFYRV(pImportDescriptor.get() != NULL, descriptors);
descriptors.push_back(pImportDescriptor.release());
InterleaveFormatType interleave(BSQ);
EncodingType encoding(INT4UBYTES);
//bool rgb = false;
LibRaw iProcessor;
const char *fn=filename.c_str();
iProcessor.open_file(fn);
unsigned long rows = iProcessor.imgdata.sizes.iheight, columns = iProcessor.imgdata.sizes.iwidth,frames=3;
RasterDataDescriptor *pDescriptor = RasterUtilities::generateRasterDataDescriptor(
filename, NULL, rows, columns, frames, interleave, encoding, IN_MEMORY);
if(pDescriptor != NULL)
{
pDescriptor->setDisplayBand(RED, pDescriptor->getBands()[0]);
pDescriptor->setDisplayBand(GREEN, pDescriptor->getBands()[1]);
pDescriptor->setDisplayBand(BLUE, pDescriptor->getBands()[2]);
pDescriptor->setDisplayMode(RGB_MODE);
}
pImportDescriptor->setDataDescriptor(pDescriptor);
RasterUtilities::generateAndSetFileDescriptor(pImportDescriptor->getDataDescriptor(), filename, std::string(), LITTLE_ENDIAN_ORDER);
descriptors.push_back(pImportDescriptor.release());
//return descriptors;
/*
Endian e;
DynamicObject* pMeta = NULL;
{ // scope the geotiff importer
ImporterResource geotiff("GeoTIFF Importer", filename);
if (geotiff.get() == NULL)
{
return descriptors;
}
std::vector<ImportDescriptor*> tiffDescriptors = geotiff->getImportDescriptors();
if (tiffDescriptors.size() != 1)
{
return descriptors;
}
e = Endian(tiffDescriptors.front()->getDataDescriptor()->getFileDescriptor()->getEndian());
pMeta = tiffDescriptors.front()->getDataDescriptor()->getMetadata();
}
if (dv_cast<std::string>(pMeta->getAttributeByPath("TIFF/Make")) != "NIKON CORPORATION")
{
return descriptors;
}
// Reload the file and parse the RAW IFD
FileResource pNef(filename.c_str(), "rb");
if (pNef.get() == NULL)
{
return descriptors;
}
// JpegImageOffset, RawOffset
std::vector<unsigned int> ifds = dv_cast<std::vector<unsigned int> >(pMeta->getAttributeByPath("TIFF/SubIFD"));
if (ifds.size() != 2)
{
return descriptors;
}
fseek(pNef, ifds[1], SEEK_SET);
unsigned int rows = 0;
unsigned int cols = 0;
unsigned int bpp = 0;
// parse the entries
size_t entryCount = getVal<uint16_t>(pNef, e);
while (--entryCount >= 0)
{
uint16_t tag = getVal<uint16_t>(pNef, e);
uint16_t type = getVal<uint16_t>(pNef, e);
uint16_t count = getVal<uint32_t>(pNef, e);
bool compressed = false;
switch(tag)
{
case 254: // SubfileType == 0 (full resolution)
if (type != 4 && count != 1 && getVal<uint32_t>(pNef, e) != 0)
{
return descriptors;
}
break;
case 256: // ImageWidth
if (type != 4 && count != 1)
{
return descriptors;
}
cols = getVal<uint32_t>(pNef, e);
break;
case 257: // ImageHight
if (type != 4 && count != 1)
{
return descriptors;
}
rows = getVal<uint32_t>(pNef, e);
break;
case 258: // BitsPerSample
if (type != 1 && count != 1)
{
return descriptors;
}
bpp = getVal<unsigned char>(pNef, e);
fseek(pNef, 3, SEEK_CUR);
break;
case 259: // Compression
if (type != 3 && count != 1)
{
return descriptors;
}
{
uint16_t comp = getVal<uint16_t>(pNef, e);
fseek(pNef, 2, SEEK_CUR);
if (comp == 1)
{
compressed = false;
}
else if (comp == 34713)
{
compressed = true;
}
else
{
return descriptors;
}
}
break;
default:
fseek(pNef, 4, SEEK_CUR);
break;
}
}
*/
}
catch (const std::bad_cast&)
{
// metadata not present, wrong kind of file
}
return descriptors;
}
