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DataClass

DataClass#

class DataClass#

Bases: BASE

The user-facing object that handles the loading and data access to the spectral data, independently of the instrument. Furthermore, this must be launched as a proxyObject (insert docs here) in order to avoid problems with data syncronization and optimize the speed of the code.

To use this class in SBART RV extraction routines, we place it in shared memory, allowing all processes to easily access

it. This is done with a proxyObject.

SBART already provides a DataClass object that is wrapped by a proxyObject:

from SBART.data_objects import DataClassManager
manager = DataClassManager()
manager.start()
data_object = manager.DataClass(*args, **kwargs)

This data_object has all the functions that the DataClass object implements!

__init__(input_files, storage_path, instrument, instrument_options, reject_subInstruments=None, target_name=None, sigma_clip_RVs=None)#
Parameters:

  • input_files (Iterable[Union[str, Path]]) – Either a path to a txt file, or a list of S2d files

  • storage_path (Union[str, Path]) – Root path of the SBART outputs

  • instrument (Type[Frame]) – Instrument that we will be loading data from. Must be an object of type SBART.Instruments

  • instrument_options (dict) –

  • reject_subInstruments (Optional[Iterable[str]]) – Iterable with names of subInstruments to automatically reject

  • target_name (Optional[str]) – Original name of the target. To be deprecated

  • sigma_clip_RVs (Optional[float]) – If it is a positive integer, reject frames with a sigma clip on the DRS RVs

load_previous_SBART_results(LoadingPath_previousRun, use_merged_cube=False)#

Load the results from a previous application of SBART, storing the RV and uncertainty inside the corresponding Frame object

Parameters:

  • LoadingPath_previousRun (Union[str, Path]) –

  • use_merged_cube (bool) –

Raises:

SBART.utils.custom_exceptions.InvalidConfiguration – If the loaded data uses a different frameID scheme than the one currently in use or if we couldn’t find the RV outputs on disk

reject_order_region_from_frame(frameID, order, region)#
remove_activity_lines(lines)#

Find the wavelength windows in which activity-related lines are expected to appear, for all valid observations

Parameters:

  • lines (Indicators) – Object with the wavelength blocks “original” positions.

  • TODO (#) –

Return type:

None

remove_telluric_features(Telluric_Template)#
Return type:

None

replace_frames_with_S2D_version(new_shape=None)#

In-place substitution of all frames with their S2D-compatible shapes!

ingest_StellarModel(Stellar_Model)#
Return type:

None

select_common_wavelengths(wave_analysis_path, subInst)#
reject_observations(conditions)#

Apply the conditions to evaluate if the VALID frame meets the specified conditions or not!

Parameters:

conditions (ConditionModel) – Conditions set by the user

Return type:

None

get_Target()#
Return type:

Target

load_frame_by_ID(frameID)#
Return type:

int

set_all_as_Zscore_frames()#
Return type:

NoReturn

normalize_all()#

Launch the normalization for all (valid) frames

Return type:

NoReturn

update_uncertainties_of_frame(frameID, new_uncerts)#

Update the flux uncertainties of a given frame

Warning

This will change your measured data, be careful with this!!!

Return type:

NoReturn

normalize_all_from_subInst(subInst)#

Normalizing all (valid) frames from a given subInstrument :type subInst: str :param subInst:

Return type:

NoReturn

scale_up_all_observations(factor)#

Multiply the flux and uncertainties by a given flux level (avoid possible SNR issues) :type factor: float :param factor:

Return type:

NoReturn

load_all_from_subInst(subInst)#

Load all valid frames from a given subInstrument

Parameters:

subInst (str) – subInstrument name

Returns:

[description]

Return type:

int

close_frame_by_ID(frameID)#
Return type:

int

min_pixel_in_order()#
Return type:

int

get_subInst_from_frameID(frameID)#
Return type:

str

get_frame_OBS_order(frameID, order, include_invalid=False)#

Request the data from one spectral order.

Parameters:

  • frameID (int) – FrameID of the observation

  • order (int) – NUmber of order

  • include_invalid (bool) – Orders can also be flagged as “invalid”. If False, the frame will raise an error when requesting the data

update_interpol_properties_of_all_frames(new_properties)#
update_interpol_properties_of_stellar_model(new_properties)#
update_frame_interpol_properties(frameID, new_properties)#

Allow to update the interpolation settings from the outside, so that any object can configure the interpolation as it wishes

Return type:

NoReturn

interpolate_frame_order(frameID, order, new_wavelengths, shift_RV_by, RV_shift_mode, include_invalid=False)#

Interpolate a given order to a new wavelength solution

get_frame_arrays_by_ID(frameID)#

Access data from the entire spectral range (i.e. all orders come as a matrix) :type frameID: int :param frameID:

get_KW_from_frameID(KW, frameID)#
get_filename_from_frameID(frameID, full_path=False)#
Return type:

str

get_status_by_frameID(frameID)#
Return type:

Status

collect_KW_observations(KW, subInstruments, include_invalid=False, conditions=None, return_frameIDs=False)#

Parse through the loaded observations and retrieve a specific KW from all of them. There is no sort of the files. The output will follow the order of the files loaded in memory!

Parameters:

  • return_frameIDs (bool) –

  • KW (str) – KW from the Frame.observation_info dictionary

  • subInstruments (Union[tuple, list]) – List of the subInstruments for which we want to retrieve the KW. If there are multiple entries, the output will follow the order of this list

  • include_invalid (bool, optional) – If True, also retrieve the KWs of Frames deemed to not be valid. By default False

Returns:

List of the KW

Return type:

list

collect_RV_information(KW, subInst, frameIDs=None, include_invalid=False, units=None, as_value=True)#

Return the RV measurements (or BERV) from the observations of a given sub-Instrument

Parameters:

  • KW (KW to request) – previousRV, previousRV_ERR or BERV

  • subInst (str) – Name of the sub-Instrument

  • frameIDs (None | list) – If not None, retrive only for the frameIDs inside the list. If they are not from subInst, an exception will be raised

  • include_invalid (bool, optional) – Include invalid observations, by default False

  • units ([type], optional) – units to convert the measurements, by default None

  • as_value (bool, optional) – provide a value instead of “units”, by default True

Returns:

[description]

Return type:

list

Raises:

InvalidConfiguration – [description]

get_valid_frameIDS()#

Get list of all available frame IDs (across all subInstruments)

Returns:

[description]

Return type:

list

get_frameIDs_from_subInst(subInstrument, include_invalid=False)#

Get all frameIDs associated with a given instrument. By default, only returns the valid ones

Parameters:

  • subInstrument (str) – SubInstrument name

  • include_invalid (bool, optional) – If True, also return IDs associated with the invalid frames, by default False

Returns:

[description]

Return type:

list

get_frame_by_ID(frameID)#

Return the frame object that is associated with a given ID

Parameters:

frameID (int) –

Return type:

Frame

get_subInstruments_with_valid_frames()#

Find all subInstruments that have at least one valid observation

Returns:

SubInstruments that have at least one valid observation

Return type:

list

get_available_subInstruments()#
Return type:

list

get_instrument_information()#
Return type:

dict

get_stellar_template(subInst)#
get_stellar_model()#
Return type:

StellarModel

get_metaData()#
Return type:

MetaData

get_internalPaths()#
trigger_data_storage()#
Return type:

None

generate_root_path(storage_path)#

Triggers the parent routine and also generates the root path for the Frames

Parameters:

storage_path (Path) –

Return type:

NoReturn

has_instrument_data(instrument)#

Check if the first loaded frame is of a given Instrument

Warning

in the off-chance that we mix data this will give problems…

Return type:

bool

show_loadedData_table()#

Compute the number of observations available in each subInstrument. Find the number of valid ( with and without warnings) and the invalid ones!

Return type:

Table

load_instrument_extra_information()#

See if the given instrument is one of the ones that has extra information to load. If so, then

load_CARMENES_extra_information()#

CARMENES pipeline does not give RVs, we have to do an external load of the information

Parameters:

shaq_folder (str) – Path to the main folder of shaq-outputs. where all the KOBE-*** targets live

Return type:

None

add_relative_path(path_name, relative_structure)#
add_to_status(new_flag)#
Return type:

NoReturn

classmethod config_help()#

Prints a message to terminal, showing all possible configurations and their constraints

classmethod control_parameters()#
is_object_type(type_to_check)#

Check if this object is of a given type

Parameters:

type_to_check (str) –

Return type:

bool

property is_valid: bool#
Return type:

bool

json_ready()#

Concerts the current class into a json entry that can be easily saved/loaded to/from disk

Return type:

Dict[str, Any]

load_from_file(root_path, loading_path)#
Return type:

None

property name: str#
Return type:

str

property storage_name: str#
Return type:

str