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SBART.Base_Models.Frame

SBART.Base_Models.Frame#

Classes

Frame

Base Class for the different Instruments, providing a shared interface to spectral data and header information.
class Frame#

Bases: Spectrum, Spectral_Modelling, Spectral_Normalization

Base Class for the different Instruments, providing a shared interface to spectral data and header information.

This class defines a set of Keywords, consistent for all s-BART supported Instruments, which can be accessed through the proper methods. The internal keywords are initialized to a default value, which the Frame will use if the instrument does not provide that metric/value. Furthermore, all RV-related metrics are returned as astropy.Quantity objects (or lists of such objects). For such cases, one can use convert_data() to convert data to different units and/or to floats

The supported list of keywords, and the default initialization values is:

Internal KW name

Default intialization

BERV

np.nan * kilometer_second

MAX_BERV

np.nan * kilometer_second

previous_SBART_RV

np.nan * kilometer_second

previous_SBART_RV_ERR

np.nan * kilometer_second

DRS_RV_ERR

np.nan * kilometer_second

DRS_RV_ERR

np.nan * kilometer_second

drift

np.nan * kilometer_second

drift_ERR

np.nan * kilometer_second

relative_humidity

np.nan

ambient_temperature

np.nan

airmass

np.nan

orderwise_SNRs

[]

OBJECT

None

BJD

None

MJD

None

DRS-VERSION

None

MD5-CHECK

None

ISO-DATE

None

CONTRAST

0

FWHM

0

BIS SPAN

0

RA

None

DEC

None

SPEC_TYPE

“”

User parameters:

Parameter name

Mandatory

Default Value

Valid Values

Comment

bypass_QualCheck

False

False

boolean

If True, avoid checking the pixel-wise QC checks

reject_order_percentage

False

0.25

range [0 ,1]

Smallest percentage of “valid” pixels in a “valid” order

minimum_order_SNR

False

20

int/float >= 0

If the order’s SNR is below this value, reject the order

spectra_format

False

S2D

“S2D”

Indicates where we are using S2D or S1D data. Not all instruments support S1D

use_air_wavelengths

False

False

boolean

Use air wavelengths, instead of vacuum. Only used in S1D files!

open_without_BervCorr

False

False

boolean

If True, remove any BERV correction

Note

This class also uses the User parameters defined by the Spectral_Modelling

class

Note

Also check the User parameters of the parent classes for further customization options of SBART

sub_instruments = {}#
__init__(inst_name, array_size, file_path, frameID, KW_map, available_indicators, user_configs=None, reject_subInstruments=None, need_external_data_load=False, init_log=True, quiet_user_params=True)#

The Frame object is initialized with the following set of Keywords:

Parameters:

  • inst_name (str) – Name of the instrument

  • array_size (Dict[str, tuple]) – Size of the data that will be loaded from disk. Follow the format [Number order, Number pixels]

  • file_path (Path) – Path to the file that is going to be opened

  • frameID (int) – Numerical value that represents the frame’s ID inside the DataClass

  • KW_map (Dict[str, str]) – Dictionary where the keys are names of internal Keywords and the values represent the keyword name on the header of the .fits files

  • available_indicators (tuple) – Names of available activity indicators for the instrument

  • user_configs (Optional[Dict[str, Any]]) – User configs information to be loaded in the parent class

  • reject_subInstruments (Optional[Iterable[str]]) – List of subInstruments to completely reject

  • need_external_data_load (bool) – True if the instrument must load data from a file that is not the one specified on the “file_path” argument

  • init_log (bool) – If True create a log entry with the filename

  • quiet_user_params (bool) – If True, there are no logs for the generation of the user parameters of each Frame

get_spectral_type()#

Check the filename to see if we are using an S1D or S2D file

Return type:

str

copy_into_S2D(new_S2D_size=None)#

Return a new object which contains the S1D that that has been converted into a S2D

Parameters:

new_S2D_size (Optional[Tuple[int, int]]) – Size of the new S2D size, should be a tuple with two elements: (number orders, pixel in order). If it is None, then uses the standard size of S2D files of this instrument. Default: None

import_KW_from_outside(KW, value, optional)#

Allow to manually override frame parameters from the outside

reject_wavelength_region_from_order(order, region)#

Flag a wavelength region from an order to be marked as invalid during the creation of the stellar mask

mark_wavelength_region(reason, wavelength_blocks)#

Add wavelength regions to be removed whenever the S2D file is opened

Parameters:

  • reason (Flag) – Flag for the removal type

  • wavelength_blocks (List[list]) – List with lists of wavelength limits. [[lambda_0, lambda_1], [lambda_2, lambda_3]]

Return type:

None

select_wavelength_region(order, wavelength_blocks)#
finalize_data_load(bad_flag=None)#

Called for all Instruments, even those that do not need an external data load. Checks if the non-fatal Flag “LOADING_EXTERNAL_DATA” exists in the Status. If so, add the fatal Flag “MISSING_EXTERNAL_DATA”. Otherwise, does nothing

Return type:

NoReturn

finalized_external_data_load()#

Tuns an invalid CARMENES::KOBE frame into a valid one (assuming that the only problem is missing the SHAQ loads)

If the status of the frame is different than MISSING_SHAQ_DATA (meaning that something went bad with the data load) :rtype: NoReturn

add_to_status(new_flag)#
Return type:

NoReturn

property status: Status#

Return the Status of the entire Frame

Return type:

Status

build_mask(bypass_QualCheck=False, assess_bad_orders=True)#

Build a spectral mask based on the S2D data

Parameters:

bypass_QualCheck (bool, optional) – Do not check the QUAL_DATA array for non-zero values, by default False

Return type:

None

assess_bad_orders()#

Evaluate the masked points to find those that can always be discarded!

Return type:

None

check_header_QC(header)#

Check if the header keywords are in accordance with their default value. Each instrument should do this check on its own

This function will check for two things: 1. Fatal keywords - will mark the Frame as invalid 2. Warning Keywords - the frame is still valid, but it has a warning issued in the logs

If any of those conditions is met, make sure that the flags meet the following naming conditions (so that we can filter by them later on):

For fatal flags ` msg = f"QC flag {flag} has taken the bad value of {bad_value}" self.add_to_status(FATAL_KW(msg)) `

For warnings: ` msg = f"QC flag {flag} meets the bad value" self._status.store_warning(KW_WARNING(msg)) `

find_instrument_type()#
get_S1D_name()#

Build the S1D name that should be associated with this Frame. If it is already a S1D, returns the actual name. If it is not, remove “blaze” from the filename and replaces “S2D” with “S1D”

Return type:

str

load_data()#
Return type:

None

load_S1D_data()#

To be overriden by the children classes

load_S2D_data()#

To be overriden by the children classes

load_instrument_specific_KWs(header)#

Load the KW values that can not be loaded in a general fashion (e.g. needs UT number or units) To be overriden by the different instruments :param header: [description] :type header: [type]

store_previous_SBART_result(RV, RV_err)#

Store, from the outside, RV and uncertainty from a previous SBART application

Parameters:

  • RV (Quantity) –

  • RV_err (Quantity) –

Return type:

NoReturn

load_header_info()#

Open the header of the fits file and load the necessary keywords. To be overriden by the children classes

Return type:

None

get_KW_value(KW)#
property is_S1D#
property is_S2D#
property has_warnings#
is_Instrument(Instrument)#
Return type:

bool

is_SubInstrument(sub_instrument)#

Check if the current instrument is from the given time_block (e.g ESPRESSO18/ESPRESSO19)

Parameters:

sub_instrument (str) – Name of the time block that is going to be checked

Returns:

Results from the comparison

Return type:

[type]

property previous_RV_measurements#
property bare_fname: str#

Returns the file name without the _S2D (and similar) parts

The children classes must overload this property. Otherwise, returns the full filename

Return type:

str

property fname#
property min_pixel_in_order: int#
Return type:

int

property spectrum_information#