#include <run_metrics.h>

Public Types
typedef make_type_list< corrected_intensity_metric, dynamic_phasing_metric, error_metric, extended_tile_metric, extraction_metric, image_metric, index_metric, phasing_metric, q_metric, q_by_lane_metric, q_collapsed_metric, tile_metric, summary_run_metric >::result_t	metric_type_list_t

typedef metric_base::base_metric::id_t	id_t

typedef std::map< id_t, metric_base::base_metric >	tile_metric_map_t

typedef std::map< id_t, metric_base::base_cycle_metric >	cycle_metric_map_t

typedef metric_base::metric_set< error_metric >::id_set_t	id_set_t

Public Member Functions
	run_metrics ()

	run_metrics (const run::info &run_info, const run::parameters &run_param=run::parameters())

void	legacy_channel_update (const constants::instrument_type type)

void	set_naming_method (const constants::tile_naming_method naming_method)

size_t	count_legacy_bins (const size_t legacy_bin_count=std::numeric_limits< size_t >::max()) const

bool	is_run_parameters_required (const size_t legacy_bin_count=std::numeric_limits< size_t >::max()) const

const run::info &	run_info () const

void	run_info (const run::info &info)

const run::parameters &	run_parameters () const

void	run_parameters (const run::parameters &param)

void	list_filenames (const constants::metric_group group, std::vector< std::string > &files, const std::string &run_folder, const bool use_out=true) INTEROP_THROW_SPEC((invalid_run_info_exception))

void	list_filenames (std::vector< std::string > &files, const std::string &run_folder, const bool bycycle=false, const bool use_out=true) INTEROP_THROW_SPEC((invalid_run_info_exception))

template<class T >
void	set (const T &metrics)

template<class T >
metric_base::metric_set_helper< T >::metric_set_t &	get ()

template<class T >
const metric_base::metric_set_helper< T >::metric_set_t &	get () const

template<class T >
metric_base::metric_set< T > &	get_metric_set ()

void	copy_tile (const run_metrics &metrics, const metric_base::base_metric &tile_id)

void	append_tiles (const run_metrics &metrics, const metric_base::base_metric &tile_id)

void	check_for_data_sources (const std::string &run_folder, const size_t last_cycle)

template<class ReadFunc >
void	read_callback (ReadFunc &func)

template<class Func >
void	metrics_callback (Func &func)

template<class Func >
void	metrics_callback (Func &func) const

bool	is_group_empty (const std::string &group_name) const

bool	is_group_empty (const constants::metric_group group_id) const

void	populate_id_map (tile_metric_map_t &map) const

void	populate_id_map (cycle_metric_map_t &map) const

void	sort ()

void	clear ()

Public Attributes
void read(const std::string &run_folder, const size_t thread_count=1) INTEROP_THROW_SPEC((xml void read(const std::string &run_folder, const std::vector< unsigned char > &valid_to_load, const size_t thread_count=1, const bool skip_loaded=false) INTEROP_THROW_SPEC((xml size_t read_xml(const std::string &run_folder) INTEROP_THROW_SPEC((io void read_run_info(const std::string &run_folder) INTEROP_THROW_SPEC((xml size_t read_run_parameters(const std::string &run_folder, const bool force_load=false) INTEROP_THROW_SPEC((io void finalize_after_load(size_t count=std::numeric_limits< size_t >::max()) INTEROP_THROW_SPEC((model bool	empty () const

void read_metrics(const std::string &run_folder, const size_t last_cycle, const size_t thread_count) INTEROP_THROW_SPEC((io void read_metrics(const std::string &run_folder, const size_t last_cycle, const std::vector< unsigned char > &valid_to_load, const size_t thread_count, const bool skip_loaded=false) INTEROP_THROW_SPEC((io void write_metrics(const std::string &run_folder, const bool use_out=true) const INTEROP_THROW_SPEC((io void read_metrics_from_buffer(const constants::metric_group group,::uint8_t buffer, const size_t buffer_size) INTEROP_THROW_SPEC((io void write_metrics_to_buffer(const constants::metric_group group,::uint8_t buffer, const size_t buffer_size) const INTEROP_THROW_SPEC((io size_t calculate_buffer_size(const constants::metric_group group) const INTEROP_THROW_SPEC((io voi	validate )() INTEROP_THROW_SPEC((invalid_run_info_exception

void read_metrics(const std::string &run_folder, const size_t last_cycle, const size_t thread_count) INTEROP_THROW_SPEC((io void read_metrics(const std::string &run_folder, const size_t last_cycle, const std::vector< unsigned char > &valid_to_load, const size_t thread_count, const bool skip_loaded=false) INTEROP_THROW_SPEC((io void write_metrics(const std::string &run_folder, const bool use_out=true) const INTEROP_THROW_SPEC((io void read_metrics_from_buffer(const constants::metric_group group,::uint8_t buffer, const size_t buffer_size) INTEROP_THROW_SPEC((io void write_metrics_to_buffer(const constants::metric_group group,::uint8_t buffer, const size_t buffer_size) const INTEROP_THROW_SPEC((io size_t calculate_buffer_size(const constants::metric_group group) const INTEROP_THROW_SPEC((io voi	invalid_run_info_cycle_exception )

Detailed Description

Collection of all metric sets for a run

See also: corrected_intensity_metrics; dynamic_phasing_metric; error_metrics; extended_tile_metric; extraction_metrics; image_metrics; index_metrics; phasing_metric; q_metrics; tile_metrics; q_by_lane_metric; q_collapsed_metric; summary_run_metric

Member Typedef Documentation

typedef std::map<id_t, metric_base::base_cycle_metric> cycle_metric_map_t

Define a map of ids to a base cycle metric

typedef metric_base::metric_set<error_metric>::id_set_t id_set_t

Define set of ids

typedef metric_base::base_metric::id_t id_t

Define an id type

typedef make_type_list< corrected_intensity_metric, dynamic_phasing_metric, error_metric, extended_tile_metric, extraction_metric, image_metric, index_metric, phasing_metric, q_metric, q_by_lane_metric, q_collapsed_metric, tile_metric, summary_run_metric >::result_t metric_type_list_t

List of metrics

typedef std::map<id_t, metric_base::base_metric> tile_metric_map_t

Define a map of ids to a base metric

Constructor & Destructor Documentation

run_metrics ( )

inline

Constructor

run_metrics	(	const run::info &	run_info,
		const run::parameters &	run_param = `run::parameters()`
	)

inline

Constructor

Parameters

run_info	run information
run_param	run parameters

Member Function Documentation

void append_tiles	(	const run_metrics &	metrics,
		const metric_base::base_metric &	tile_id
	)

Adds records only for a specific tile

Parameters

metrics	full metric set
tile_id	selected tile

Adds records only for a specific tile

Parameters

origin	full metric set
tile_id	selected tile

void check_for_data_sources	(	const std::string &	run_folder,
		const size_t	last_cycle
	)

Check if the InterOp file for each metric set exists

This will set the metric_set::data_source_exists flag.

Parameters

run_folder	run folder path
last_cycle	last cycle to search for by cycle interops

void clear ( )

Clear all the metrics

void copy_tile	(	const run_metrics &	metrics,
		const metric_base::base_metric &	tile_id
	)

Copy records only for a specific tile

Parameters

metrics	full metric set
tile_id	selected tile

Copy records only for a specific tile

Parameters

origin	full metric set
tile_id	selected tile

metric_base::metric_set_helper<T>::metric_set_t& get ( )

inline

Get a metric set

Returns: metric set

const metric_base::metric_set_helper<T>::metric_set_t& get ( ) const

inline

Get a metric set

Returns: metric set

metric_base::metric_set<T>& get_metric_set ( )

inline

Get a metric set given a metric type

bool is_group_empty ( const std::string & group_name ) const

Check if the metric group is empty

Parameters

group_name prefix of interop group metric

Returns: true if metric is empty

bool is_group_empty ( const constants::metric_group group_id ) const

Check if the metric group is empty

Parameters

group_id prefix of interop group metric id

Returns: true if metric is empty

Check if the metric group is empty

Parameters

group_id id of interop group metric

Returns: true if metric is empty

void list_filenames	(	const constants::metric_group	group,
		std::vector< std::string > &	files,
		const std::string &	run_folder,
		const bool	use_out = `true`
	)

List all filenames for a specific metric

Parameters

group	metric group type
files	destination interop file names (first one is legacy, all subsequent are by cycle)
run_folder	run folder location
use_out	use the copied version

void list_filenames	(	std::vector< std::string > &	files,
		const std::string &	run_folder,
		const bool	bycycle = `false`,
		const bool	use_out = `true`
	)

List all filenames for all metrics

Parameters

files	destination interop file names (first one is legacy, all subsequent are by cycle)
run_folder	run folder location
bycycle	if true, list all by cycle file name
use_out	use the copied version

void metrics_callback ( Func & func )

inline

Read binary metrics from the run folder

Parameters

func	call back for metric reading

void metrics_callback ( Func & func ) const

inline

Read binary metrics from the run folder

Parameters

func	call back for metric reading

void populate_id_map ( tile_metric_map_t & map ) const

Populate a map of valid tiles

Parameters

map	mapping between tile has and base_metric

void populate_id_map ( cycle_metric_map_t & map ) const

Populate a map of valid tiles and cycles

Parameters

map	mapping between tile has and base_cycle_metric

Populate a map of valid tiles and cycles

Parameters

map	mapping between tile has and base_metric

void read_callback ( ReadFunc & func )

inline

Read binary metrics and XML files from the run folder

Parameters

func	call back for metric and XML reading

const run::parameters& run_parameters ( ) const

inline

Get parameters describing the run

Returns: run parameters

void run_parameters ( const run::parameters & param )

inline

Set parameters describing the run

Parameters

param run parameters

void set ( const T & metrics )

inline

Set a given metric set

Parameters

metrics metric set

void sort ( )

Sort the metrics by id

Sort the metrics by lane, then tile, then cycle

Member Data Documentation

void read_metrics (const std::string &run_folder, const size_t last_cycle, const size_t thread_count) INTEROP_THROW_SPEC(( io void read_metrics (const std::string &run_folder, const size_t last_cycle, const std::vector<unsigned char>& valid_to_load, const size_t thread_count, const bool skip_loaded=false) INTEROP_THROW_SPEC(( io void write_metrics (const std::string &run_folder, const bool use_out=true) const INTEROP_THROW_SPEC(( io void read_metrics_from_buffer (const constants::metric_group group, ::uint8_t* buffer, const size_t buffer_size) INTEROP_THROW_SPEC(( io void write_metrics_to_buffer (const constants::metric_group group, ::uint8_t* buffer, const size_t buffer_size) const INTEROP_THROW_SPEC(( io size_t calculate_buffer_size (const constants::metric_group group) const INTEROP_THROW_SPEC(( io voi invalid_run_info_cycle_exception)

void validate

Read binary metrics from the run folder

This function ignores:

Missing InterOp files
Incomplete InterOp files
Missing RunParameters.xml for non-legacy run folders

Parameters

run_folder	run folder path
last_cycle	last cycle of run
thread_count	number of threads to use for network loading Read binary metrics from the run folder

This function ignores:

Missing InterOp files
Incomplete InterOp files
Missing RunParameters.xml for non-legacy run folders

Parameters

run_folder	run folder path
last_cycle	last cycle of run
valid_to_load	boolean vector indicating which files to load
thread_count	number of threads to use for network loading
skip_loaded	skip metrics that are already loaded Write binary metrics to the run folder
run_folder	run folder path
use_out	use the copied version Read a single metric set from a binary buffer
group	metric set to write
buffer	binary buffer
buffer_size	size of binary buffer Write a single metric set to a binary buffer
group	metric set to write
buffer	binary buffer
buffer_size	size of binary buffer Calculate the required size of the buffer for writing
group	metric set to write

Returns: required size of the binary buffer Validate whether the RunInfo.xml matches the InterOp files

Exceptions

invalid_run_info_exception
invalid_run_info_cycle_exception	Validate whether the RunInfo.xml matches the InterOp files
invalid_run_info_exception

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

/io/interop/model/run_metrics.h
/io/src/interop/model/run_metrics.cpp
/io/src/interop/model/run_metrics_helper.cpp

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation