VirusHealth Class Reference

Virus Health check routines.

Public Member Functions

VirusHealth (const string &filename, unsigned int recipe, const CommonCheckOptions &)
Initiate the VirusHealth checks for a fits file and a specific recipe.
~VirusHealth ()
void write_file ()
Write the file with the header check keywords.
void check_header ()
Run all selected header checks.
void validate_size ()
Validate the image size.
void validate_keywords ()
Validate that the header contains all needed keywords.
void validate_overscan (const float mean, const float stddev, const float maxdev_mean, const float maxdev_rms)
Validate the rms of the overscan.
void validate_exptime ()
Validate the exposure time depending on the recipe.
void validate_flatbias (const float maxdiff)
Validate the overall flatness of the bias frame.
void validate_refbias (const float mean, const float stddev, const float maxdev_mean, const float maxdev_rms)
Validate that the bias and does not deviate from expected values.
void validate_saturation (const float saturation)
Validate that the image fluxes are below saturation limit.
void validate_min_flux (const float minflux, const int nfibers, const int maxbad)
Validate the flux in all fibers is above the required minimum flux.
void validate_n_fibers (const int nfibers, const int maxbad)
Validate that all expected fibers are lit.
void validate_throughput ()
Validate the throughput.
void validate_distortion (const string &distname)
Validate the position of the fibers on the chip against a reference distortion.
void validate_peaks (const string &linelist, const string &distname, int peak_tolerance, int max_missing)
Validate the arc peaks are at the expected positions and actual peaks.
void validate_sky (float skylevel)
Validate the sky level is above the minimum sky level.
int get_n_checks ()
Get the number of checks run.
int get_n_passed ()
Get the number of checks passed.
string & get_response ()
Get the string with all the error messages.

Private Member Functions

MArray< float, 2 > read_overscan_ (void)
Helper function to read the overscan region.
MArray< float, 2 > read_image_ (void)
Helper function to read the image region.
MArray< float, 2 > read_region_ (FitsIn &in, const util::Region &reg)
Read a region from the fits file.
util::Region header_to_region_ (const string &str) throw (ltl::IOException)
Convert a header region to a ltl Region.
float get_float_key_ (const string key) throw (ltl::IOException)
Get a float header keyword.
int get_int_key_ (const string key) throw (ltl::IOException)
Get an integer header keyword.
string get_string_key_ (const string key) throw (ltl::IOException)
Get a string header keyword.
bool get_bool_key_ (const string key) throw (ltl::IOException)
Get a boolean header keyword.
void set_keyword (const string &key, bool passed)
Write the header keyword for the check.
void add_error_ (const string &str)
Add an error message to the response string, prepending the current filename.
void log_test_ (const string &str)
void log_warning_ (const string &str)
void finish_check_ (const string &hkey, const string &error, const string &warn="")

Private Attributes

FitsIn fitsfile_
The open fitsfile.
string filename_
The image filename.
unsigned int recipe_
The file type recipe.
string response_
The error response string.
int n_checks_
Number of checks run.
int n_passed_
Number of checks passed.
bool verbose_
Send verbose output to stdout.
CommonCheckOptions opts_
Common check options structure.

Constructor & Destructor Documentation

VirusHealth::VirusHealth	(	const string &	filename,
		unsigned int	recipe,
		const CommonCheckOptions &	copts
	)

Initialize the VirusHealth class with the opened fits image, the recipe type (one of the vh() enum), and the optional verbose flag.

Parameters:

	fitsfile	ltl::FitsIn() of the opened fits image.
	recipe	integer specifying the recipe.
	verbose	boolean, if true write extened output to stdout.

References fitsfile_, get_string_key_(), n_checks_, n_passed_, opts_, recipe_, response_, unknown, CommonCheckOptions::verbose, and verbose_.

VirusHealth::~VirusHealth ( )

References filename_, fitsfile_, opts_, and CommonCheckOptions::write_file.

Member Function Documentation

void VirusHealth::write_file ( )

void VirusHealth::check_header ( )

Run the common header checks.

References CommonCheckOptions::chk_exptime, CommonCheckOptions::chk_keywords, CommonCheckOptions::chk_npixels, CommonCheckOptions::chk_overscan, CommonCheckOptions::maxdev_ovc_mean, CommonCheckOptions::maxdev_ovc_rms, opts_, CommonCheckOptions::overscan_mean, CommonCheckOptions::overscan_stddev, validate_exptime(), validate_keywords(), validate_overscan(), and validate_size().

Referenced by main().

void VirusHealth::validate_size ( )

Validate the image size. Check that the number of pixels along NAXIS1 is 1064 pixels (2064 / 2 + 32 pixels overscan) and along NAXIS2 is 1032 pixels (2064 binned 2 for 1).

References finish_check_(), fitsfile_, and log_test_().

Referenced by check_header().

void VirusHealth::validate_keywords ( )

Validate the presence of various header keywords, keywords checked are:

`AIRMASS`
`DITHER`
`IMAGETYP`

References finish_check_(), get_float_key_(), get_int_key_(), get_string_key_(), and log_test_().

Referenced by check_header().

void VirusHealth::validate_overscan	(	const float	mean,
		const float	stddev,
		const float	maxdev_mean,
		const float	maxdev_rms
	)

Validate the rms of the overscan by checking that the standard deviation of the overscan region is below the given maximum. The overscan region is read from the `BIASSEC` header keyword.

Parameters:

	mean	float expected mean.
	stddev	float expected standard deviation.
	maxdev_mean	float maximum allowed fractional difference of the mean.
	maxdev_mean	float maximum allowed fractional difference of the standard deviation.

References finish_check_(), log_test_(), and read_overscan_().

Referenced by check_header().

void VirusHealth::validate_exptime ( )

Validate the exposure time depending on the image type recipe. For bias frames, the exposure time must be zero seconds, for other images it must be not zero. For HETDEX observations the exposure time must be at least 3600 seconds.

References bias, finish_check_(), get_float_key_(), log_test_(), and recipe_.

Referenced by check_header().

void VirusHealth::validate_flatbias ( const float maxdiff )

Validate the overall flatness of the bias frame, by comparing the standard deviation and average of different sub images at 250:500,500:1000, 250:500,1500:2000, 750:1000,500:1000, 750:1000,1500:2000, and the overcan. If any of the differences exceeds the difference allowed by the relative difference given by maxdiff.

Parameters:

maxdiff

float giving the maximum difference relative to the average / rms.

References finish_check_(), log_test_(), read_image_(), and read_overscan_().

Referenced by main().

void VirusHealth::validate_refbias	(	const float	mean,
		const float	stddev,
		const float	maxdev_mean,
		const float	maxdev_rms
	)

Validate that the bias and the reference bias frame are not too deviant. Check that the average image flux of the bias frame and the reference bias frame or the standard deviation of bias frame and the reference bias frame do not differ more than the maximum given by maxdiff.

Parameters:

	mean	float expected mean.
	stddev	float expected standard deviation.
	maxdev_mean	float maximum allowed fractional difference of the mean.
	maxdev_mean	float maximum allowed fractional difference of the standard deviation.

References finish_check_(), log_test_(), and read_image_().

Referenced by main().

void VirusHealth::validate_saturation ( const float saturation )

Validate that the image fluxes are below saturation limit.

Parameters:

saturation

The saturation limit of the chip.

References finish_check_(), log_test_(), and read_image_().

Referenced by main().

void VirusHealth::validate_min_flux	(	const float	minflux,
		const int	nfibers,
		const int	maxbad
	)

Validate the flux in all fibers is above the required minimum flux.

Parameters:

minflux

The expected minimum flux

References finish_check_(), log_test_(), read_image_(), read_overscan_(), and Measure::search().

Referenced by main().

void VirusHealth::validate_n_fibers	(	const int	nfibers,
		const int	maxbad
	)

Validate that all expected fibers are lit.

Parameters:

	nfibers	Expected number of active fibers.
	maxbad	Maximum number of fibers allowed to go dark with only a warning raised. If more fibers fail an error is logged.

References finish_check_(), log_test_(), read_image_(), read_overscan_(), and Measure::search().

Referenced by main().

void VirusHealth::validate_throughput ( )

Validate the throughput.

Not yet implemented, the check always succeeds.

References finish_check_(), and log_test_().

Referenced by main().

void VirusHealth::validate_distortion ( const string & distname )

Validate the position of the fibers on the chip against a reference distortion.

Parameters:

distname

The name of the reference distortion

Not yet implemented, the check always succeeds.

References finish_check_(), and log_test_().

Referenced by main().

void VirusHealth::validate_peaks	(	const string &	linelist,
		const string &	distname,
		int	peak_tolerance,
		int	max_missing
	)

Validate the arc peaks are at the expected positions and actual peaks.

Parameters:

	linelist	string The name of the arc line lists.
	distname	string The name of the reference distortion
	peak_tolerance	int maximum pixel offset from the expected position and half size of the patch used to perform the arc peak fit
	max_missing	int maximum number of missing fibers before giving up

References finish_check_(), gauss2Dfit(), Distortion::get_numfibers(), Distortion::get_reference_f(), get_string_key_(), ArcLineList::getActiveWLs(), ArcLineList::getNumActiveLines(), header_to_region_(), log_test_(), log_warning_(), Distortion::map_wf_x(), Distortion::map_wf_y(), read_image_(), read_overscan_(), and verbose_.

Referenced by main().

void VirusHealth::validate_sky ( float skylevel )

Validate the sky level is above the minimum sky level.

Parameters:

skylevel

The minimum expected sky level.

Not yet implemented, the check always succeeds.

References finish_check_(), and log_test_().

Referenced by main().

int VirusHealth::get_n_checks ( ) [inline]

Get the number of checks run.

Returns:: Number of checks run

References n_checks_.

Referenced by main().

int VirusHealth::get_n_passed ( ) [inline]

Get the number of checks passed.

Returns:: Number of checks passed.

References n_passed_.

Referenced by main().

string& VirusHealth::get_response ( ) [inline]

Get the string with all the error messages.

Returns:: The error message string.

References response_.

Referenced by main().

MArray<float,2> VirusHealth::read_overscan_ ( void ) [inline, private]

References fitsfile_, get_string_key_(), header_to_region_(), and read_region_().

Referenced by validate_flatbias(), validate_min_flux(), validate_n_fibers(), validate_overscan(), and validate_peaks().

MArray<float,2> VirusHealth::read_image_ ( void ) [inline, private]

References fitsfile_, get_string_key_(), header_to_region_(), and read_region_().

Referenced by validate_flatbias(), validate_min_flux(), validate_n_fibers(), validate_peaks(), validate_refbias(), and validate_saturation().

MArray< float, 2 > VirusHealth::read_region_	(	FitsIn &	in,
		const util::Region &	reg
	)			`[private]`

Read a region from the fits file.

Parameters:

	in	The ltl::FitIn() object to read the region from.
	reg	The util::Region to read.

Returns:: ltl::MArray() the read image region.

Referenced by read_image_(), and read_overscan_().

util::Region VirusHealth::header_to_region_ ( const string & key ) throw (ltl::IOException) [private]

Convert a header region to a ltl Region. Read the region string from the header, and convert it to a util::Region object.

Parameters:

key

The header key from which to read the region string

Returns:: util::Region() object.

Exceptions:

ltl::IOException

Thrown if the header key cannot be found.

Referenced by read_image_(), read_overscan_(), and validate_peaks().

float VirusHealth::get_float_key_ ( const string key ) throw (ltl::IOException) [private]

Get a float header keyword.

Parameters:

key

The keyword to read from the checked image.

Returns:: float The read and converted keyword

Exceptions:

util::IOException()

Thrown if the keyword cannot be found

Referenced by validate_exptime(), and validate_keywords().

int VirusHealth::get_int_key_ ( const string key ) throw (ltl::IOException) [private]

Get a integer header keyword.

Parameters:

key

The keyword to read from the checked image.

Returns:: int The read and converted keyword

Exceptions:

util::IOException()

Thrown if the keyword cannot be found

Referenced by validate_keywords().

string VirusHealth::get_string_key_ ( const string key ) throw (ltl::IOException) [private]

Get a string header keyword.

Parameters:

key

The keyword to read from the checked image.

Returns:: string The read and converted keyword

Exceptions:

util::IOException()

Thrown if the keyword cannot be found

Referenced by read_image_(), read_overscan_(), validate_keywords(), validate_peaks(), and VirusHealth().

bool VirusHealth::get_bool_key_ ( const string key ) throw (ltl::IOException) [private]

Get a boolean header keyword.

Parameters:

key

The keyword to read from the checked image.

Returns:: bool The read and converted keyword

Exceptions:

util::IOException()

Thrown if the keyword cannot be found

void VirusHealth::set_keyword	(	const string &	key,
		bool	passed
	)			`[private]`

void VirusHealth::add_error_ ( const string & str ) [inline, private]

Add an error message to the response string, prepending the current filename.

Parameters:

str

The string to add.

References filename_, and response_.

Referenced by finish_check_().

void VirusHealth::log_test_ ( const string & str ) [inline, private]

References filename_, and fitsfile_.

Referenced by validate_distortion(), validate_exptime(), validate_flatbias(), validate_keywords(), validate_min_flux(), validate_n_fibers(), validate_overscan(), validate_peaks(), validate_refbias(), validate_saturation(), validate_size(), validate_sky(), and validate_throughput().

void VirusHealth::log_warning_ ( const string & str ) [inline, private]

References filename_.

Referenced by validate_peaks().

void VirusHealth::finish_check_	(	const string &	hkey,
		const string &	error,
		const string &	warn = `""`
	)			`[private]`

Finish a check.

Parameters:

	hkey	The keyword to be set in the header
	error	The check error message. If it is "", the check is considered passed.
	warn	Optional warning generated by the test, placed into the key comment.

References add_error_(), fitsfile_, n_checks_, and n_passed_.

Referenced by validate_distortion(), validate_exptime(), validate_flatbias(), validate_keywords(), validate_min_flux(), validate_n_fibers(), validate_overscan(), validate_peaks(), validate_refbias(), validate_saturation(), validate_size(), validate_sky(), and validate_throughput().