pyreduce.instruments package

Submodules

pyreduce.instruments.common module

Abstract parent module for all other instruments Contains some general functionality, which may be overridden by the children of course

class pyreduce.instruments.common.COMMON

Bases: pyreduce.instruments.common.Instrument

class pyreduce.instruments.common.Instrument

Bases: object

Abstract parent class for all instruments Handles the handling of instrument specific information

add_header_info(header, mode, **kwargs)

read data from header and add it as REDUCE keyword back to the header

Parameters:

• header (fits.header, dict) – header to read/write info from/to
• mode (str) – instrument mode

Returns:

header – header with added information

Return type:

fits.header, dict

apply_filters(files, expected, allow_calibration_only=False)

Determine the relevant files for a given set of expected values.

Parameters:

• files (list(files)) – list if fits files
• expected (dict) – dictionary with expected header values for each reduction step

Returns:

files – list of files. The first element of each tuple is the used setting, and the second are the files for each step.

Return type:

list((dict, dict))

find_files(input_dir)

Find fits files in the given folder

Parameters:input_dir (string) – directory to look for fits and fits.gz files in, may include bash style wildcards Returns:files – absolute path filenames Return type:array(string)

get(key, header, mode, alt=None)

get_expected_values(target, night, *args, **kwargs)

get_extension(header, mode)

get_mask_filename(mode, **kwargs)

get_supported_modes()

get_wavecal_filename(header, mode, **kwargs)

Get the filename of the pre-existing wavelength solution for the current setting

Parameters:

• header (fits.header, dict) – header of the wavelength calibration file
• mode (str) – instrument mode

Returns:

filename – name of the wavelength solution file

Return type:

str

get_wavelength_range(header, mode, **kwargs)

info = None

Information about the instrument

Type:dict

load_fits(fname, mode, extension=None, mask=None, header_only=False, dtype=None)

load fits file, REDUCE style

primary and extension header are combined modeinfo is applied to header data is clipnflipped mask is applied

Parameters:

• fname (str) – filename
• instrument (str) – name of the instrument
• mode (str) – instrument mode
• extension (int) – data extension of the FITS file to load
• mask (array, optional) – mask to add to the data
• header_only (bool, optional) – only load the header, not the data
• dtype (str, optional) – numpy datatype to convert the read data to

Returns:

• data (masked_array) – FITS data, clipped and flipped, and with mask
• header (fits.header) – FITS header (Primary and Extension + Modeinfo)
• ONLY the header is returned if header_only is True

load_info()

Load static instrument information Either as fits header keywords or static values

Returns:info – dictionary of REDUCE names for properties to Header keywords/static values Return type:dict(str:object)

name = None

Name of the instrument (lowercase)

Type:str

populate_filters(files)

Extract values from the fits headers and store them in self.filters

Parameters:files (list(str)) – list of fits files Returns:filters – list of populated filters (identical to self.filters) Return type:list(Filter)

sort_files(input_dir, target, night, *args, allow_calibration_only=False, **kwargs)

Sort a set of fits files into different categories types are: bias, flat, wavecal, orderdef, spec

Parameters:

• input_dir (str) – input directory containing the files to sort
• target (str) – name of the target as in the fits headers
• night (str) – observation night, possibly with wildcards
• mode (str) – instrument mode

Returns:

• files_per_night (list[dict{str:dict{str:list[str]}}]) – a list of file sets, one entry per night, where each night consists of a dictionary with one entry per setting, each fileset has five lists of filenames: “bias”, “flat”, “order”, “wave”, “spec”, organised in another dict
• nights_out (list[datetime]) – a list of observation times, same order as files_per_night

class pyreduce.instruments.common.InstrumentWithModes

Bases: pyreduce.instruments.common.Instrument

get_expected_values(target, night, mode)

pyreduce.instruments.common.create_custom_instrument(name, extension=0, info=None, mask_file=None, wavecal_file=None, hasModes=False)

pyreduce.instruments.common.find_first_index(arr, value)

find the first element equal to value in the array arr

class pyreduce.instruments.common.getter(header, info, mode)

Bases: object

Get data from a header/dict, based on the given mode, and applies replacements

get(key, alt=None)

Get data

Parameters:

• key (str) – key of the data in the header
• alt (obj, optional) – alternative value, if key does not exist (default: None)

Returns:

value – value found in header (or alternatively alt)

Return type:

obj

pyreduce.instruments.common.observation_date_to_night(observation_date)

Convert an observation timestamp into the date of the observation night Nights start at 12am and end at 12 am the next day

Parameters:observation_date (datetime) – timestamp of the observation Returns:night – night of the observation Return type:datetime.date

pyreduce.instruments.harps module

Handles instrument specific info for the HARPS spectrograph

Mostly reading data from the header

class pyreduce.instruments.harps.FiberFilter(keyword='ESO DPR TYPE')

Bases: pyreduce.instruments.filters.Filter

collect(header)

class pyreduce.instruments.harps.HARPS

Bases: pyreduce.instruments.common.Instrument

add_header_info(header, mode, **kwargs)

read data from header and add it as REDUCE keyword back to the header

get_expected_values(target, night, mode, fiber, polarimetry)

Determine the default expected values in the headers for a given observation configuration

Any parameter may be None, to indicate that all values are allowed

Parameters:

• target (str) – Name of the star / observation target
• night (str) – Observation night/nights
• fiber ("A", "B", "AB") – Which of the fibers should carry observation signal
• polarimetry ("none", "linear", "circular", bool) – Whether the instrument is used in HARPS or HARPSpol mode and which polarization is observed. Set to true for both kinds of polarisation.

Returns:

expectations – Dictionary of expected header values, with one entry per step. The entries for each step refer to the filters defined in self.filters

Return type:

dict

Raises:

ValueError – Invalid combination of parameters

get_extension(header, mode)

get_wavecal_filename(header, mode, polarimetry, **kwargs)

Get the filename of the wavelength calibration config file

get_wavelength_range(header, mode, **kwargs)

class pyreduce.instruments.harps.PolarizationFilter(keyword='ESO INS RET?? POS')

Bases: pyreduce.instruments.filters.Filter

collect(header)

class pyreduce.instruments.harps.TypeFilter(keyword='ESO DPR TYPE')

Bases: pyreduce.instruments.filters.Filter

classify(value)

pyreduce.instruments.instrument_info module

Interface for all instrument specific information The actual info is contained in the instruments/{name}.py modules/classes, which are all subclasses of “common”

pyreduce.instruments.instrument_info.get_instrument_info(instrument)

Load instrument specific information

Parameters:instrument (str) – Name of the instrument Returns:dict{str – Dictionary with information Return type:obj}

pyreduce.instruments.instrument_info.get_supported_modes(instrument)

pyreduce.instruments.instrument_info.get_wavecal_filename(header, instrument, mode, **kwargs)

Get the filename of the pre-existing wavelength solution for the current settings

Parameters:

• header (fits.header, dict) – header of the wavelength calibration file
• instrument (str) – instrument name
• mode (str) – instrument mode (e.g. red/blue for HARPS)

Returns:

filename – wavelength solution file

Return type:

str

pyreduce.instruments.instrument_info.load_instrument(instrument) → pyreduce.instruments.common.Instrument

Load an python instrument module

Parameters:instrument (str) – name of the instrument Returns:instrument – Instance of the {instrument} class Return type:Instrument

pyreduce.instruments.instrument_info.modeinfo(header, instrument, mode, **kwargs)

Add instrument specific information to a header/dict

Parameters:

• header (fits.header, dict) – header to add information to
• instrument (str) – instrument name
• mode (str) – instrument mode (e.g. red/blue for HARPS)

Returns:

header with added information

Return type:

header

pyreduce.instruments.instrument_info.sort_files(input_dir, target, night, instrument, mode, **kwargs)

Sort a list of files into different categories and discard files that are not used

Parameters:

• input_dir (str) – directory containing all files (with tags for target, night, and instrument)
• target (str) – observation target name, as found in the files
• night (str) – observation night of interest, as found in the files
• instrument (str) – instrument name
• mode (str) – instrument mode, if applicable (e.g. red/blue for HARPS)

Returns:

• biaslist (list(str)) – list of bias files
• flatlist (list(str)) – list of flat field files
• wavelist (list(str)) – list of wavelength calibration files
• orderlist (list(str)) – list of order definition files (for order tracing)
• speclist (list(str)) – list of science files, i.e. observations

pyreduce.instruments.uves module

Handles instrument specific info for the UVES spectrograph

Mostly reading data from the header

class pyreduce.instruments.uves.UVES

Bases: pyreduce.instruments.common.Instrument

add_header_info(header, mode, **kwargs)

read data from header and add it as REDUCE keyword back to the header

get_mask_filename(mode, **kwargs)

get_wavecal_filename(header, mode, **kwargs)

Get the filename of the wavelength calibration config file

Module contents