class CVScene represents a base class for opencv based representations of raster images contained in a medical slide. More...

#include <cvscene.hpp>

Inherits slideio::RefCounter.

Inherited by slideio::CVSmallScene, slideio::CZIScene, slideio::DCMScene, slideio::GDALScene, slideio::NDPIScene, slideio::PKEScene, slideio::SCNScene, slideio::SVSScene, slideio::TransformerScene, slideio::WSIScene, slideio::ZVIScene, slideio::ometiff::OTScene, and slideio::vsi::VSIScene.

Public Member Functions
virtual	~CVScene ()=default
	default constructor

virtual std::string	getFilePath () const =0
	returns path of the slide

virtual std::string	getName () const =0
	returns scene name

virtual cv::Rect	getRect () const =0
	returns image rectangle. More...

virtual int	getNumChannels () const =0
	returns number of image channels.

virtual int	getNumZSlices () const
	returns number of z-slices in the images. More...

virtual int	getNumTFrames () const
	returns number of time frames in the image. More...

virtual slideio::DataType	getChannelDataType (int channel) const =0
	returns channel data type. More...

virtual std::string	getChannelName (int channel) const

virtual Resolution	getResolution () const =0
	returns image resolution in x and y direction. More...

virtual double	getZSliceResolution () const
	returns thickness of a Z slice in meters for 3D images.

virtual double	getTFrameResolution () const
	returns time between 2 time frames in seconds for images with time frames.

virtual double	getMagnification () const =0
	returns slide magnification extracted from the slide metadata.

virtual Compression	getCompression () const =0
	returns compression of the raster data

virtual void	readBlock (const cv::Rect &blockRect, cv::OutputArray output)
	reads raster rectangle of a plane image. More...

virtual void	readBlockChannels (const cv::Rect &blockRect, const std::vector< int > &channelIndices, cv::OutputArray output)
	reads selected channels of raster rectangle of a plane image. More...

virtual void	readResampledBlock (const cv::Rect &blockRect, const cv::Size &blockSize, cv::OutputArray output)
	reads raster rectangle of a plane image with resizing. More...

virtual void	readResampledBlockChannels (const cv::Rect &blockRect, const cv::Size &blockSize, const std::vector< int > &channelIndices, cv::OutputArray output)
	reads selected channels raster rectangle of a plane image with resizing. More...

virtual void	read4DBlock (const cv::Rect &blockRect, const cv::Range &zSliceRange, const cv::Range &timeFrameRange, cv::OutputArray output)
	reads multi-dimensional raster block. More...

virtual void	read4DBlockChannels (const cv::Rect &blockRect, const std::vector< int > &channelIndices, const cv::Range &zSliceRange, const cv::Range &timeFrameRange, cv::OutputArray output)
	multi-dimensional raster block with resizing. More...

virtual void	readResampled4DBlock (const cv::Rect &blockRect, const cv::Size &blockSize, const cv::Range &zSliceRange, const cv::Range &timeFrameRange, cv::OutputArray output)
	reads multi-dimensional raster block with resizing. More...

virtual void	readResampled4DBlockChannels (const cv::Rect &blockRect, const cv::Size &blockSize, const std::vector< int > &channelIndices, const cv::Range &zSliceRange, const cv::Range &timeFrameRange, cv::OutputArray output)
	reads selected channels of multi-dimensional raster block. More...

virtual const std::list< std::string > &	getAuxImageNames () const
	returns list of auxiliary image names.

virtual int	getNumAuxImages () const
	returns number of auxiliary images in the scene object.

virtual std::shared_ptr< CVScene >	getAuxImage (const std::string &imageName) const
	returns a slideio::CVScene object that represents an auxiliary image. More...

virtual std::string	getRawMetadata () const
	returns string of serialized metadata. Content of the string depends on image format.

const Metadata &	getMetadata () const
	returns metadata as a navigable tree. Built lazily on first call.

virtual void	readResampledLevelBlockChannelsEx (int level, const cv::Rect &levelRect, const cv::Size &blockSize, const std::vector< int > &channelIndices, int zSliceIndex, int tFrameIndex, cv::OutputArray output)
	reads a raster rectangle from an explicitly selected zoom level. More...

void	readResampledLevelBlockChannels (int level, const cv::Rect &levelRect, const cv::Size &blockSize, const std::vector< int > &channelIndices, cv::OutputArray output)
	reads a plane raster rectangle from an explicitly selected zoom level. More...

void	readResampledLevel4DBlockChannels (int level, const cv::Rect &levelRect, const cv::Size &blockSize, const std::vector< int > &channelIndices, const cv::Range &zSliceRange, const cv::Range &timeFrameRange, cv::OutputArray output)
	reads a multi-dimensional raster block from an explicitly selected zoom level. More...

virtual MetadataFormat	getMetadataFormat () const
	returns metadata format of the image

const Metadata &	getChannelAttributes () const
	returns channel attributes as a Metadata tree. More...

Protected Member Functions
virtual void	setChannelAttribute (int channelIndex, const std::string &attributeName, const std::string &attributeValue)
	adds a new attribute to channels

virtual void	setChannelAttribute (int channelIndex, const std::string &attributeName, const char *attributeValue)
	adds a string-literal attribute to a channel

virtual void	setChannelAttribute (int channelIndex, const std::string &attributeName, bool attributeValue)
	adds a boolean attribute to a channel

virtual void	setChannelAttribute (int channelIndex, const std::string &attributeName, int64_t attributeValue)
	adds an integer attribute to a channel

virtual void	setChannelAttribute (int channelIndex, const std::string &attributeName, double attributeValue)
	adds a floating-point attribute to a channel

void	validateLevel (int level) const
	throws unless level names a zoom level of this scene.

virtual MetadataBuilder	buildMetadataTree () const
	Driver hook: convert m_rawMetadata into a Metadata tree. More...

Detailed Description

class CVScene represents a base class for opencv based representations of raster images contained in a medical slide.

Most of the class methods are pure virtual and must be overriten by child classes that implement specific image format. The class exposes methods for extraction raster data as well as metadata for the image. The class supports 2D, 3D and 4D multi-channel images and provides methods for extraction of arbitrary image regions, optionally with resizing. Methods for working with raster data deliver image blocks as opencv Mat objects.

Member Function Documentation

◆ buildMetadataTree()

MetadataBuilder CVScene::buildMetadataTree ( ) const

protectedvirtual

Driver hook: convert m_rawMetadata into a Metadata tree.

The default implementation handles MetadataFormat::{None,Text,JSON,XML}. Drivers that need semantic structure override and return a MetadataBuilder. To wrap an existing JSON tree, use slideio::detail::builderFromJson from "slideio/core/metadata_internal.hpp".

◆ getAuxImage()

std::shared_ptr< CVScene > CVScene::getAuxImage ( const std::string & imageName ) const

virtual

returns a slideio::CVScene object that represents an auxiliary image.

Parameters

imageName : name of the auxiliary image.

◆ getChannelAttributes()

const Metadata & CVScene::getChannelAttributes ( ) const

returns channel attributes as a Metadata tree.

Always an Array of length getNumChannels(). Each element is an Object keyed by attribute name; channels with no attributes get an empty Object. Built lazily on first call; neither the channel count nor the attribute values must change after the first read.

◆ getChannelDataType()

virtual slideio::DataType slideio::CVScene::getChannelDataType ( int channel ) const

pure virtual

returns channel data type.

Some image format may have channels with different data types.

◆ getChannelName()

std::string CVScene::getChannelName ( int channel ) const

virtual

@ returns channel name by channel index.

Some formats provide human readable names for image channels. The method returns such names extracted from image metadata.

◆ getNumTFrames()

virtual int slideio::CVScene::getNumTFrames ( ) const

inlinevirtual

returns number of time frames in the image.

The method returns 1 for single frame images (images without time sequences).

◆ getNumZSlices()

virtual int slideio::CVScene::getNumZSlices ( ) const

inlinevirtual

returns number of z-slices in the images.

The method returns 1 for plain images.

◆ getRect()

virtual cv::Rect slideio::CVScene::getRect ( ) const

pure virtual

returns image rectangle.

Origins of the rectangle define shift of top left image corner from top left slide corner.

◆ getResolution()

virtual Resolution slideio::CVScene::getResolution ( ) const

pure virtual

returns image resolution in x and y direction.

Resolution is returned as class Resolution with pixel sizes in meters for x and y directions.

◆ read4DBlock()

void CVScene::read4DBlock	(	const cv::Rect &	blockRect,
		const cv::Range &	zSliceRange,
		const cv::Range &	timeFrameRange,
		cv::OutputArray	output
	)

virtual

reads multi-dimensional raster block.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
zSliceRange	: range of z-slices to be read. Defined as a std::tuple<indexOfFirstSliceToRead,numberOfSlicesToRead>
timeFrameRange	: range of time frames to be read. Defined as a std::tuple<indexOfFirstTimeFrameToRead,numberOfTimeFramesToRead>;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ read4DBlockChannels()

void CVScene::read4DBlockChannels	(	const cv::Rect &	blockRect,
		const std::vector< int > &	channelIndices,
		const cv::Range &	zSliceRange,
		const cv::Range &	timeFrameRange,
		cv::OutputArray	output
	)

virtual

multi-dimensional raster block with resizing.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
channelIndices	: vector of indices of channels to be extracted;
zSliceRange	: range of z-slices to be read. Defined as a std::tuple<indexOfFirstSliceToRead,numberOfSlicesToRead>
timeFrameRange	: range of time frames to be read. Defined as a std::tuple<indexOfFirstTimeFrameToRead,numberOfTimeFramesToRead>;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readBlock()

void CVScene::readBlock	(	const cv::Rect &	blockRect,
		cv::OutputArray	output
	)

virtual

reads raster rectangle of a plane image.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readBlockChannels()

void CVScene::readBlockChannels	(	const cv::Rect &	blockRect,
		const std::vector< int > &	channelIndices,
		cv::OutputArray	output
	)

virtual

reads selected channels of raster rectangle of a plane image.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure.
channelIndices	: vector of indices of channels to be extracted;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readResampled4DBlock()

void CVScene::readResampled4DBlock	(	const cv::Rect &	blockRect,
		const cv::Size &	blockSize,
		const cv::Range &	zSliceRange,
		const cv::Range &	timeFrameRange,
		cv::OutputArray	output
	)

virtual

reads multi-dimensional raster block with resizing.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
blockSize	: size of the block after resizing.
zSliceRange	: range of z-slices to be read. Defined as a std::tuple<indexOfFirstSliceToRead,numberOfSlicesToRead>
timeFrameRange	: range of time frames to be read. Defined as a std::tuple<indexOfFirstTimeFrameToRead,numberOfTimeFramesToRead>;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readResampled4DBlockChannels()

void CVScene::readResampled4DBlockChannels	(	const cv::Rect &	blockRect,
		const cv::Size &	blockSize,
		const std::vector< int > &	channelIndices,
		const cv::Range &	zSliceRange,
		const cv::Range &	timeFrameRange,
		cv::OutputArray	output
	)

virtual

reads selected channels of multi-dimensional raster block.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
blockSize	: size of the block after resizing.
channelIndices	: vector of indices of channels to be extracted;
zSliceRange	: range of z-slices to be read. Defined as a std::tuple<indexOfFirstSliceToRead,numberOfSlicesToRead>
timeFrameRange	: range of time frames to be read. Defined as a std::tuple<indexOfFirstTimeFrameToRead,numberOfTimeFramesToRead>;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readResampledBlock()

void CVScene::readResampledBlock	(	const cv::Rect &	blockRect,
		const cv::Size &	blockSize,
		cv::OutputArray	output
	)

virtual

reads raster rectangle of a plane image with resizing.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
blockSize	: size of the block after resizing.
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readResampledBlockChannels()

void CVScene::readResampledBlockChannels	(	const cv::Rect &	blockRect,
		const cv::Size &	blockSize,
		const std::vector< int > &	channelIndices,
		cv::OutputArray	output
	)

virtual

reads selected channels raster rectangle of a plane image with resizing.

Parameters

blockRect	: rectangle of the block to be read. The rectangle is represented by cv::Rect structure where x and y properties define shift of the top left corner of the block from the top left corner of the image.
blockSize	: size of the block after resizing.
channelIndices	: vector of indices of channels to be extracted;
output	: reference to cv::OutputArray object. The method creates cv::Mat object for the parameters and allocate memory for the object if it is not yet allocated or allocated not enough memory. All channels have to be of the same type. The method will throw an error by attempt to put read several channels of different types in one block.

◆ readResampledLevel4DBlockChannels()

void CVScene::readResampledLevel4DBlockChannels	(	int	level,
		const cv::Rect &	levelRect,
		const cv::Size &	blockSize,
		const std::vector< int > &	channelIndices,
		const cv::Range &	zSliceRange,
		const cv::Range &	timeFrameRange,
		cv::OutputArray	output
	)

reads a multi-dimensional raster block from an explicitly selected zoom level.

Parameters

zSliceRange	: range of z-slices to be read.
timeFrameRange	: range of time frames to be read. Other parameters are those of readResampledLevelBlockChannelsEx.

◆ readResampledLevelBlockChannels()

void CVScene::readResampledLevelBlockChannels	(	int	level,
		const cv::Rect &	levelRect,
		const cv::Size &	blockSize,
		const std::vector< int > &	channelIndices,
		cv::OutputArray	output
	)

reads a plane raster rectangle from an explicitly selected zoom level.

Parameters are those of readResampledLevelBlockChannelsEx, with the z slice and the time frame fixed at 0.

◆ readResampledLevelBlockChannelsEx()

void CVScene::readResampledLevelBlockChannelsEx	(	int	level,
		const cv::Rect &	levelRect,
		const cv::Size &	blockSize,
		const std::vector< int > &	channelIndices,
		int	zSliceIndex,
		int	tFrameIndex,
		cv::OutputArray	output
	)

virtual

reads a raster rectangle from an explicitly selected zoom level.

Unlike the readBlock family, this method does not choose a zoom level: it reads from the level named by level and from no other. It exists for callers that already know the level they want – tiled viewers above all – and that would otherwise have to convert their rectangle to scene coordinates and let the library convert it back, rounding twice on the way.

Parameters

level	: zoom level index, in the range [0, getNumZoomLevels()).
levelRect	: rectangle in the pixel coordinate system of `level`. It is not scene coordinates and receives no scaling. The part of it lying outside the level is filled with the background value.
blockSize	: size of the returned block. Resampling is performed from `level` only; a blockSize that would suit a different level does not cause one to be selected. blockSize equal to levelRect.size() means no resampling at all.
channelIndices	: vector of indices of channels to be extracted. Empty means every channel.
zSliceIndex	: index of the z slice to read.
tFrameIndex	: index of the time frame to read.
output	: reference to a cv::OutputArray object.

The default implementation clamps levelRect to the level, maps it to scene coordinates through LevelInfo::getScale() and delegates to readResampledBlockChannelsEx. For a single level scene that mapping is the identity. Drivers with a real pyramid override it to read the named level directly.

The documentation for this class was generated from the following files:

src/slideio/core/cvscene.hpp
src/slideio/core/cvscene.cpp

Public Member Functions

Protected Member Functions

Detailed Description

Member Function Documentation

◆ buildMetadataTree()

◆ getAuxImage()

◆ getChannelAttributes()

◆ getChannelDataType()

◆ getChannelName()

◆ getNumTFrames()

◆ getNumZSlices()

◆ getRect()

◆ getResolution()

◆ read4DBlock()

◆ read4DBlockChannels()

◆ readBlock()

◆ readBlockChannels()

◆ readResampled4DBlock()

◆ readResampled4DBlockChannels()

◆ readResampledBlock()

◆ readResampledBlockChannels()

◆ readResampledLevel4DBlockChannels()

◆ readResampledLevelBlockChannels()

◆ readResampledLevelBlockChannelsEx()