#include <image_metric.h>

Inheritance diagram for image_metric:

Public Types
enum	{ MAX_CHANNELS = image_metric_header::MAX_CHANNELS, TYPE = constants::Image, LATEST_VERSION = 3 }

typedef image_metric_header	header_type

typedef std::vector< ushort_t >	ushort_array_t

typedef ::uint16_t *	ushort_pointer_t

Public Types inherited from base_cycle_metric
typedef base_cycle_metric_header	header_type

typedef constants::base_cycle_t	base_t

typedef uint16_t	cycle_t

Public Types inherited from base_metric
enum	{ LANE_BIT_COUNT = 6, TILE_BIT_COUNT = 26, CYCLE_BIT_COUNT = 16, READ_BIT_COUNT = 16, RESERVED_BIT_COUNT = 16, READ_BIT_SHIFT = RESERVED_BIT_COUNT, CYCLE_BIT_SHIFT = RESERVED_BIT_COUNT, TILE_BIT_SHIFT = CYCLE_BIT_SHIFT+CYCLE_BIT_COUNT, LANE_BIT_SHIFT = TILE_BIT_SHIFT+TILE_BIT_COUNT }

typedef ::uint64_t	ulong_t

typedef ulong_t	id_t

typedef ::uint16_t	ushort_t

typedef ::uint32_t	uint_t

typedef base_metric_header	header_type

typedef ::uint8_t	lane_t

typedef ::uint32_t	tile_t

typedef constants::base_tile_t	base_t

Public Types inherited from empty_metric
typedef ::uint32_t	id_t

typedef ::uint32_t	uint_t

typedef constants::base_run_t	base_t

Public Member Functions
	image_metric ()

	image_metric (const header_type &header)

	image_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_t channel_count, const ushort_array_t &min_contrast, const ushort_array_t &max_contrast)

	image_metric (const uint_t lane, const uint_t tile, const uint_t cycle, const ushort_t channel_count, const ushort_pointer_t min_contrast, const ushort_pointer_t max_contrast)

ushort_t	min_contrast (const size_t channel) const INTEROP_THROW_SPEC((model

ushort_t	max_contrast (const size_t channel) const INTEROP_THROW_SPEC((model

const ushort_array_t &	min_contrast_array () const

const ushort_array_t &	max_contrast_array () const

ushort_t	channel_count () const

bool	is_any_channel_blank () const

void	trim (const size_t channel_count)

ushort_t	minContrast (size_t channel) const

ushort_t	maxContrast (size_t channel) const

const ushort_array_t &	minContrast () const

const ushort_array_t &	maxContrast () const

ushort_t	channelCount () const

Public Member Functions inherited from base_cycle_metric
	base_cycle_metric (const uint_t lane=0, const uint_t tile=0, const uint_t cycle=0)

void	set_base (const uint_t lane, const uint_t tile)

void	set_base (const uint_t lane, const uint_t tile, const uint_t cycle)

template<class BaseCycleMetric >
void	set_base (const BaseCycleMetric &base)

uint_t	cycle () const

id_t	id () const

id_t	cycle_hash () const

bool	operator< (const base_cycle_metric &metric2) const

Public Member Functions inherited from base_metric
	base_metric (const uint_t lane=0, const uint_t tile=0)

void	set_base (const uint_t lane, const uint_t tile)

template<class BaseMetric >
void	set_base (const BaseMetric &base)

id_t	id () const

id_t	tile_hash () const

uint_t	lane () const

uint_t	tile () const

uint_t	number (const illumina::interop::constants::tile_naming_method) const

uint_t	section (const illumina::interop::constants::tile_naming_method method) const

uint_t	surface (const illumina::interop::constants::tile_naming_method method) const

uint_t	swath (const illumina::interop::constants::tile_naming_method method) const

uint_t	phyiscalLocationIndex (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationColumn (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	phyiscalLocationRow (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

size_t	physical_location_index (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_column (const illumina::interop::constants::tile_naming_method method, const uint_t swath_count, const bool all_surfaces) const

uint_t	physical_location_row (const illumina::interop::constants::tile_naming_method method, const uint_t section_per_lane, const uint_t tile_count) const

bool	operator< (const base_metric &metric2) const

Public Member Functions inherited from empty_metric
template<class BaseMetric >
void	set_base (const BaseMetric &)

void	set_base (const uint_t, const uint_t)

bool	operator< (const empty_metric &) const

Static Public Member Functions
static const char *	prefix ()

Static Public Member Functions inherited from base_cycle_metric
static id_t	cycle_from_id (const id_t id)

static id_t	reserved_from_id (const id_t id)

static id_t	create_id (const id_t lane, const id_t tile, const id_t cycle)

Static Public Member Functions inherited from base_metric
static id_t	create_id (const id_t lane, const id_t tile, const id_t=0)

static id_t	lane_from_id (const id_t id)

static id_t	tile_hash_from_id (const id_t id)

static id_t	tile_from_id (const id_t id)

static const char *	suffix ()

Static Public Member Functions inherited from empty_metric
static const char *	suffix ()

static id_t	create_id (const id_t, const id_t, const id_t=0)

Friends
template<class MetricType , int Version>
struct	io::generic_layout

Detailed Description

Image metric

Per tile per cycle per channel percentiles of pixel values used to autocontrast thumbnail images

Note: Supported versions: 1, 2 and 3

Test:

Confirm version 1 of the metric can be written to and read from a stream

Confirm version 1 of the metric matches known binary file

Confirm version 2 of the metric can be written to and read from a stream

Confirm version 2 of the metric matches known binary file

Member Typedef Documentation

typedef image_metric_header header_type

Image metric header

typedef std::vector<ushort_t> ushort_array_t

Define a uint16_t array using an underlying vector

typedef ::uint16_t* ushort_pointer_t

Define a uint16_t pointer to a uint16_t array

Member Enumeration Documentation

anonymous enum

Enumerator
MAX_CHANNELS	Maximum number of channels supported
TYPE	Unique type code for metric
LATEST_VERSION	Latest version of the InterOp format

Constructor & Destructor Documentation

image_metric ( )

inline

Constructor

image_metric ( const header_type & header )

inline

Constructor

Parameters

header metric set header

image_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const ushort_t	channel_count,
		const ushort_array_t &	min_contrast,
		const ushort_array_t &	max_contrast
	)

inline

Constructor

Note: Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
channel_count	number of channels
min_contrast	minimum contrast for each channel
max_contrast	maximum contrast for each channel

image_metric	(	const uint_t	lane,
		const uint_t	tile,
		const uint_t	cycle,
		const ushort_t	channel_count,
		const ushort_pointer_t	min_contrast,
		const ushort_pointer_t	max_contrast
	)

inline

Constructor

Note: Version 2

Parameters

lane	lane number
tile	tile number
cycle	cycle number
channel_count	number of channels
min_contrast	minimum contrast for each channel
max_contrast	maximum contrast for each channel

Member Function Documentation

ushort_t channelCount ( ) const

inline

Number of channels

Deprecated:

Will be removed in 1.1.x (use channel_count instead)

Returns: number of channels

ushort_t maxContrast ( size_t channel ) const

inline

Maximum contrast intensity

Deprecated:

Will be removed in 1.1.x (use max_contrast instead)

Returns: maximum contrast intensity

const ushort_array_t& maxContrast ( ) const

inline

Maximum contrast intensity

Deprecated:

Will be removed in 1.1.x (use max_contrast_array instead)

Returns: maximum contrast intensity

ushort_t minContrast ( size_t channel ) const

inline

Minimum contrast intensity

Deprecated:

Will be removed in 1.1.x (use min_contrast instead)

Returns: minimum contrast intensity

const ushort_array_t& minContrast ( ) const

inline

Minimum contrast intensity

Deprecated:

Will be removed in 1.1.x (use min_contrast_array instead)

Returns: minimum contrast intensity

static const char* prefix ( )

inlinestatic

Get the prefix of the InterOp filename

Returns: prefix

void trim ( const size_t channel_count )

inline

Trim unused channel values

Parameters

channel_count actual number of channels

Friends And Related Function Documentation

friend struct io::generic_layout

friend

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

/io/interop/model/metrics/image_metric.h

Public Types

Public Member Functions

Static Public Member Functions

Friends

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation