mangadap.proc.templatelibrary module

Class that reads and prepares template libraries for use in fitting the stellar-continuum of a spectrum. See available_template_libraries() for the list of default template libraries.

The “raw” template libraries are expected to consist of 1D fits files. The wavelength sampling can be either linear or logarithmic in wavelength. The reference frame of the template wavelengths must be defined as either vacuum or air. It is expected that the object spectra to be fit are calibrated to vacuum wavelengths. When preparing the template spectra for analysis, this class will use pydl.goddard.astro.airtovac to convert the template wavelengths to vacuum. Finally, one can specify that the template library is only valid within a certain wavelength range and above a certian flux limit; see TemplateLibraryDef.

Preparation of the template library for use in stellar-continuum fitting consists of a number of steps as described in the documentation of TemplateLibrary.process_template_library().

A template library that has been prepared for analysis is automatically written to disk for later recovery.

Two support classes are also provided. One is a derived mangadap.par.parset.KeywordParSet instance that provides the defining parameters of a DAP template library. The second is a derived mangadap.util.bitmask.BitMask instance that defines the bitmasks for the template library spectra.

Class usage examples

TODO: Update this for new datacube usage

Assuming you have the default directory structure setup, you can do:

# Imports
from mangadap.drpfits import DRPFits
from mangadap.proc.templatelibrary import TemplateLibrary
from matplotlib import pyplot

# Define the DRP file
drpf = DRPFits(7495, 12703, 'CUBE')

# Build the template library
tpl_lib = TemplateLibrary('M11MILES', drpf=drpf, directory_path='.')
# Writes: ./manga-7495-12703-LOGCUBE_M11-MILES.fits

# Plot one of the spectra
pyplot.plot(tpl_lib.hdu['WAVE'].data, tpl_lib.hdu['FLUX'].data[0,:])
pyplot.show()

As part of the instantiation of the TemplateLibrary object in the above call, the template library is prepared for use in fitting the specified DRP file. If the required processing has already been done, the instantiation of the TemplateLibrary object simply reads the existing file. If you do not have the default directory structure setup, you’ll need to define the paths to, e.g., the DRP file; see mangadap.util.drpfits.DRPFits.

If you do not want to process the template (match the spectral resolution and sampling to that of the DRP data), you can force the TemplateLibrary object to only provide the “raw” spectra:

# Imports
from mangadap.proc.templatelibrary import TemplateLibrary
from matplotlib import pyplot

# Read the raw template library
tpl_lib = TemplateLibrary('M11MILES', process=False)
# Nothing should be written to disk

# Plot one of the spectra
pyplot.plot(tpl_lib.hdu['WAVE'].data[0,:], tpl_lib.hdu['FLUX'].data[0,:])
pyplot.show()

Note that in the previous example, the wavelength data was already one-dimensional, whereas for the raw library, the wavelength vector can be spectrum-dependent.

In the above examples, the user has not provided a list of template libraries, meaning that the default set available to the DAP is used. The default set is defined in available_template_libraries(). If you want to use your own template library, you have to define its parameters using TemplateLibraryDef. Currently, the template library spectra are expected to be 1D fits files with WCS header keywords defining the wavelength solution; see above. Using an existing DAP library as an example:

# Imports
import os
from mangadap.proc.templatelibrary import TemplateLibraryDef
from mangadap.proc.templatelibrary import TemplateLibrary
from mangadap.config.defaults import dap_data_root
from matplotlib import pyplot

# Define the search string for the library
search_str = os.path.join(dap_data_root(), 'stellar_templates/miles/*.fits')

# Define the template library parameters
tpl_par = TemplateLibraryDef(key='MILES',    # Unique keyword for the library
                        file_search=search_str, # Search string
                        fwhm=2.50,              # FWHM of resolution element (assumed const)
                        in_vacuum=False,        # Wavelength in vacuum?
                        wave_limit=numpy.array([ 3575., 7400. ]),   # Range of valid lambda
                        lower_flux_limit=0.0)   # Lower limit for valid flux

# Read the raw template library
tpl_lib = TemplateLibrary('MILES', tpllib_list=tpl_par, process=False)
# Nothing should be written to disk

# Plot one of the spectra
pyplot.plot(tpl_lib.hdu['WAVE'].data[0,:], tpl_lib.hdu['FLUX'].data[0,:])
pyplot.show()

Note that the keyword you use must be provided both to the parameter set and when instantiating the TemplateLibrary object. In the example above, I have not processed the library, but you can by following a similar approach to the first example.

You can also process the spectra to a user-provided resolution and pixel sampling, toggle on/off the renormalization of the library to a mean flux of unity and define various paths if you’re not working within the nominal DAP directory structure. See the optional instantiation arguments for TemplateLibrary.

Revision history

23 Apr 2015: Implementation begun by K. Westfall (KBW)
26 May 2015: (KBW) Added some Sphinx documentation.
17 Jun 2015: (KBW) Added flexibility in definition of template libraries from which to choose using the new TemplateLibraryDef class.
23 Jun 2015: (KBW) Allow user to provided non-DRP input spectra, meaning they need to provide the velocity scale and the wavelength and spectral resolution vectors. They must also directly set the name of the output processed file.
01 Feb 2016: (KBW) Propagated changes to TemplateLibraryDef and changed procedure for reading raw template library.
04 Feb 2016: (KBW) Converted from mangadap.util.instrument.log_rebin() to mangadap.util.instrument.resample_vector(). Allows input library to be logarithmically sampled and provides a different approach to subsampling spectra. Implemented other convenience operations, such as selecting a certain wavelength range for the processed library.
19 May 2016: (KBW) Added loggers and quiet keyword arguments to TemplateLibrary
22 Jun 2016: (KBW) Included MILESHC library in documentation. Allow to specify how the resolution and sampling are matched to the DRP data. The TemplateLibrary class should be generalized to make this more transparent (and unnecessary).
03 Apr 2017: (KBW) Include arguments for mangadap.util.instrument.match_spectral_resolution() that specify the minimum sigma in pixels for the convolution kernel and any offset in the resolution required in the call for the template library. Check that the resampling of the spectrum does not reach the two-pixel resolution limit; flag the spectrum in those regions that do and change the resolution to the two pixel limit.
30 Aug 2017: (KBW) Switch from using mangadap.util.instrument.resample_vector() to mangadap.util.instrument.resample1d()
30 Aug 2018: (KBW) Switch from using resample1d to mangadap.util.sampling.Resample.
License

Copyright © 2019, SDSS-IV/MaNGA Pipeline Group

class mangadap.proc.templatelibrary.TemplateLibrary(library_key, tpllib_list=None, cube=None, match_resolution=True, velscale_ratio=None, sres=None, velocity_offset=0.0, min_sig_pix=0.0, no_offset=True, spectral_step=None, log=True, wavelength_range=None, renormalize=True, dapver=None, analysis_path=None, directory_path=None, processed_file=None, read=True, process=True, hardcopy=True, symlink_dir=None, clobber=False, checksum=False, loggers=None, quiet=False)[source]

Bases: object

TODO: Revisit these docs.

Object used to read, store, and prepare template libraries for use in analyzing object spectra.

The default list of available libraries provided by the MaNGA DAP defined in available_template_libraries(). The user can provide their own library for use with this class provided they are contained in 1D fits spectra, sampled linearly in wavelength with the wavelength coordinates available via the WCS keywords (CRPIX1, CRVAL1, CDELT1), and they have an appropriately defined spectral resolution. See TemplateLibraryDef and _build_raw_hdu().

The class is optimized for use in analyzing MaNGA DRP files; however, one can provide the necessary information so that the class can be used with a non-DRP spectrum. In the latter case, the user must supply the velocity scale of the pixel for the logarithmically resampled template library, and a mangadap.util.resolution.SpectralResolution object the defines the instrumental resolution of the spectrum/spectra to be analyzed.

Todo

  • Docs are out of date.

  • Update the list of attributes.

  • Allow for velocity scale input instead of spectral_step?

  • Only works with DRP files that have log-linear wavelength binning!

  • Allow to process, where process is just to change the sampling or the resolution (not necessarily both).

  • Need to make this more general, removing all dependence on DRPFits object. This would simplify the functionality to change how the resolution and sampling matching is specified.

On initialization, if the datacube object is not provided (is None), the default behavior is to read the raw template library if read=True. If the datacube is provided, the routine will check for the resolution matched fits file; if it doesn’t exist and read is True, it will prepare the template library for use in analyzing the datacube and write the prepared library file (if hardcopy is True). If clobber=True, the preparation and writing of the template library will be done even if the library already exists.

Todo

Change sres to be a standard input object?

Parameters

  • library_key (str) – Keyword selecting the library to use.

  • tpllib_list (list, optional) – List of TemplateLibraryDef objects that define the parameters required to read and interpret a template library. The library_key must select one of the objects in this list.

  • cube (mangadap.datacube.datacube.DataCube, optional) – The datacube to be analyzed using the template library.

  • match_resolution (bool, optional) – Match the spectral resolution of the template library to the resolution provided by the cube; the latter must be provided for this argument to have any use.

  • velscale_ratio (int, optional) – Resample the template spectra such that the ratio of the pixel scale in the provided cube is this many times larger than the pixels in the resampled template spectrum.

  • sres (mangadap.util.resolution.SpectralResolution, optional) – The object is used simply to access the spectral resolution and associated wavelength coordinate vector needed when matching the spectral resolution of the template library; this is used in lieu of a datacube.

  • velocity_offset (float, optional) – Velocity offset to use when matching the spectral resolution between the template library and the galaxy spectra.

  • min_sig_pix (float, optional) – Minimum value of the LSF standard deviation in pixels allowed before assuming the kernel is a Delta function. See mangadap.util.resolution.match_spectral_resolution().

  • no_offset (bool, optional) – Prohibit the spectral resolution matching to introduce an offset in spectral resolution required to match the relative shape of the resolution vectors. See mangadap.util.resolution.match_spectral_resolution() and mangadap.util.resolution.SpectralResolution.GaussianKernelDifference().

  • spectral_step (float, optional) – Logarithmic (log=True) or linear (log=False) step in wavelength for the template library.

  • log (bool, optional) – Flag to force the library to be logarithmically sampled in wavelength.

  • wavelength_range (array-like, optional) – Force the template library to cover this spectral range. Unobserved spectral regions will be masked.

  • renormalize (bool, optional) – After processing, renormalize the flux of the full library to unity. The relative fluxes of the templates are maintained.

  • dapver (str, optional) – DAP version, which is used to define the default DAP analysis path. Default is defined by mangadap.config.defaults.dap_version()

  • analysis_path (str, optional) – The path to the top-level directory for the DAP output files. Default is defined by mangadap.config.defaults.dap_analysis_path().

  • directory_path (str, optional) – The exact path to the processed template library file. Default is defined by mangadap.config.defaults.dap_common_path().

  • processed_file (str, optional) – The name of the file containing the prepared template library output file. The file should be found at directory_path/processed_file. Default is defined by mangadap.config.defaults.dap_file_name().

  • read (bool, optional) – Flag to read the template library data.

  • process (bool, optional) – Process (spectral resolution and sampling operations) the template library in preparation for use in fitting the provided datacube.

  • hardcopy (bool, optional) – Flag to keep a hardcopy of the processed template library.

  • symlink_dir (str, optional) – Create a symlink to the file in this directory. If None, no symbolic link is created.

  • clobber (bool, optional) – Overwrite any saved, processed template library file.

  • checksum (bool, optional) – Use the checksum in the fits header to confirm that the data has not been corrupted. The checksum is always written to the fits header when the file is created.

  • loggers (list, optional) – List of logging.Logger objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output(). If None, no logging is performed and output is just written to stdout.

  • quiet (bool, optional) – Suppress all terminal and logging output.

bitmask (class

mangadap.util.bitmask.BitMask): Object used to toggle mask values; see TemplateLibraryBitMask().

library

Parameter set required to read and prepare the library.

Type

TemplateLibraryDef

file_list

The list of files found using glob.glob and file_search.

Type

list

ntpl

Number of template spectra in the library

Type

int

cube

The datacube to be analyzed using the template library.

Type

mangadap.datacube.datacube.DataCube

sres

The object is used simply to access the spectral resolution and associated wavelength coordinate vector needed when matching the spectral resolution of the template library; this is used in place of the attributes in any provided DRP file object.

Type

mangadap.util.resolution.SpectralResolution

velocity_offset

Velocity offset to use when matching the spectral resolution between the template library and the galaxy spectra.

Type

float

spectral_step

Target logarithmic (log10_sampling=True) or linear (log10_sampling=False) step in wavelength for the template library.

Type

float

log10_sampling

Flag that the processed template library is logarithmically sampled in wavelength.

Type

bool

directory_path

The exact path to the processed template library file.

Type

str

processed_file

The name of the file containing (to contain) the prepared template library output file. The file should be found at directory_path/processed_file.

Type

str

processed

Flag that the template library has been prepared for use in the DAP.

Type

bool

hardcopy

Flag to keep a hardcopy of the processed template library.

Type

bool

Symlink created to the file in this directory

Type

str

hdu

HDUList read from the DAP file

Type

astropy.io.fits.HDUList

_build_raw_hdu(npix)[source]

Build the “raw” template library arrays.

This simply reads the provided list of fits files and puts them into arrays of size \(N_{\rm tpl} \times N_{\rm pix}\).

This will force reading of the data, even if the hdu is already initialized.

The hdu will contain the appropriate extensions, but it is important to note that the wavelength vectors will not necessarily be the same. That is, reading of the raw template spectra can accommodate spectra that have different wavelength coordinates. Any pixels that have no data are masked using the ‘NO_DATA’ bitmask flag; see TemplateLibraryBitMask().

The spectral resolution is set using the fwhm or sres_ext values in the library parameters.

Warning

Currently no errors are saved because none are expected for the template libraries.

Parameters

npix (int) – Number of spectral channels for the output arrays

_can_set_paths(directory_path, cube, processed_file, quiet=False)[source]

Determine if the paths are fully defined.

Parameters

  • directory_path (str) – The exact path to the processed template library file.

  • cube (mangadap.datacube.datacube.DataCube) – The datacube to be analyzed using the template library.

  • processed_file (str) – The name of the file containing (to contain) the prepared template library output file. The file should be found at directory_path/processed_file.

  • quiet (bool, optional) – Suppress terminal output.

Returns

True if the paths can be set.

Return type

bool

_get_file_list()[source]

Use the search string to find the template library fits files.

The file list read by the search key is sorted for consistency.

Returns

The sorted list of files found with glob.glob.

Return type

list

Raises

ValueError – Raised if no files are found.

_get_nchannels()[source]

Get the maximum number of wavelength channels needed to store all the template spectra in a single array.

Todo

  • What happens if the spectrum has an empty primary extension?

Returns

Maximum number of pixels used by the listed spectra.

Return type

int

Raises

ValueError – Raised if the input template spectra are not one-dimensional.

_minimum_sampling()[source]

Return the minimum sampling of the available wavelength vectors.

Returns

Minimum sampling of all (will just be one if the library has been processed) wavelength vectors.

Return type

float

_modify_spectral_resolution()[source]

Modify the spectral resolution to match the provided sres.

Returns

Redshift used when matching the spectral resolution.

Return type

float

_process_library(wavelength_range=None, renormalize=True)[source]

Process the template library for use in analyzing object spectra. See process_template_library().

Todo

  • Add wavelength coordinate WCS information to the appropriate extension headers.

  • Include ‘step’ as an argument

  • Include limit on covering fraction used to mask data as an argument

Parameters

  • wavelength_range (array-like, optional) – A two-element object with the lower and upper limits for the wavelength range of the library.

  • renormalize (bool, optional) – Renormalize the flux of the full library to unity. Relative fluxes of spectra in the library are maintained.

_read_raw()[source]

Read the ‘raw’ versions of the template library.

The “raw” library is the data before its sampling or resolution have been altered.

This is a simple wrapper for _get_file_list(), _get_channels() and _build_raw_hdu().

_rebin_masked(i, flag, fullRange, rmsk_lim=0.5)[source]

Determine the mask value to adopt for a rebinned spectrum by rebinning the mask pixels, setting a masked pixel to unity, and an unmasked pixel to zero. After rebinning, any pixel with a value of larger than rmsk_lim is masked; otherwise it is left unmasked.

Although the function can be used with multiple flags, its intended use is to determine which pixels should be masked with a specific flag.

Parameters

  • i (int) – Index of the spectrum to be rebinned.

  • flag (str, list) – Flags to consider when determining which pixels to mask; see mangadap.util.bitmasks.BitMask.flagged().

  • fullRange (numpy.ndarray) – Two-element array with the wavelength range for the rebinned spectrum.

  • rmsk_lim (float) – Limit of the rebinned mask value that is allowed before considering the pixel as masked.

Returns

Boolean array indicating which pixels in the rebinned spectrum should be masked.

Return type

numpy.ndarray

_reset_hdu(wave, flux, mask, sres, soff)[source]

(Re)Set hdu to a new HDUList object using the input arrays. Also sets the header items indicating the version of the template reader and the keyword for the library.

Warning

No checking is done concerning the size of each array!

Parameters

  • wave (numpy.ndarray) – Array with the wavelengths of each pixel.

  • flux (numpy.ndarray) – Array with the flux in each pixel.

  • mask (numpy.ndarray) – Bitmask values for each pixel.

  • sres (numpy.ndarray) – Spectral resolution, \(R=\lambda/\delta\lambda\), at each pixel.

  • soff (numpy.ndarray) – The spectral resolution offset for each spectrum (see mangadap.util.resolution.GaussianKernelDifference()).

_set_paths(directory_path, dapver, analysis_path, cube, processed_file)[source]

Set the I/O path to the processed template library.

Used to set directory_path and processed_file. If not provided, the defaults are set using, respectively, mangadap.config.defaults.dap_common_path() and mangadap.config.defaults.dap_file_name().

Parameters

  • directory_path (str) – The exact path to the DAP template library file. See directory_path.

  • dapver (str) – DAP version.

  • analysis_path (str) – The path to the top-level directory containing the DAP output files for a given DRP and DAP version.

  • cube (mangadap.datacube.datacube.DataCube) – The datacube to be analyzed using the template library.

  • processed_file (str) – The name of the file containing (to contain) the prepared template library output file. The file should be found at directory_path/processed_file.

_wavelength_range(flag=None)[source]

Return the valid wavelength range for each spectrum based on the first and last unmasked pixel; interspersed masked regions are not considered.

Parameters

flag (str, list, optional) – Flags to consider when determining the wavelength range; see mangadap.util.bitmasks.BitMask.flagged().

Returns

Two-element vector with wavelengths of the first and last valid pixels.

Return type

numpy.ndarray

static define_library(library_key, tpllib_list=None)[source]

Select the library from the provided list. Used to set library; see mangadap.proc.util.select_proc_method().

Parameters

  • library_key (str) – Keyword of the selected library. Available libraries are proved by available__template_libraries()

  • tpllib_list (list, optional) – List of TemplateLibraryDef objects that define the parameters required to read and interpret a template library.

file_name()[source]

Return the name of the processed file.

file_path()[source]

Return the full path to the processed file.

process_template_library(library_key=None, tpllib_list=None, cube=None, match_resolution=True, velscale_ratio=None, sres=None, velocity_offset=0.0, min_sig_pix=0.0, no_offset=True, spectral_step=None, log=True, wavelength_range=None, renormalize=True, dapver=None, analysis_path=None, directory_path=None, processed_file=None, hardcopy=True, symlink_dir=None, clobber=False, loggers=None, quiet=False)[source]

Process the template library for use in analyzing spectra.

Todo

  • Docs need to be updated

  • type checking

  • If a DRP file is provided, the processing to a logarithmic binning is done by default (log=True). But linearly sampled DRP data are available, so need to have mangadap.util.drpfits.DRPFits return the spectral sampling type.

  • Documentation needs updating!

Primary steps are to:

  • Read the raw 1D fits files; see _read_raw().

  • Convert the wavelengths to vacuum, if necessary; see pydl.goddard.astro.airtovac.

  • Mask wavelengths outside the rest wavelength range of the datacube spectra, due to need to extrapolate these values; see mangadap.util.bitmasks.HDUList_mask_wavelengths().

  • Match the spectral resolution of the template to that of the datacube (if match_resolution is True); see mangadap.util.resolution.match_spectral_resolution().

  • Mask the template pixels where the spectral resolution was too low to match to datacube; see mangadap.util.bitmasks.BitMask.turn_on().

  • Force a common wavelength range and sampling for all templates, where the sampling is forced to match the sampling of the DRP spectra; see mangadap.util.sampling.resample_vector_pix(). The masks are appropriately resampled as well; see _rebin_masked().

Warning

The routine does not check that that an existing processed file or the existing object has been processed using the same datacube, velocity_offset, velscale, or sres input. If unsure, use clobber=True.

Parameters

  • library_key (str) – Keyword selecting the library to use.

  • tpllib_list (list, optional) – List of TemplateLibraryDef objects that define the parameters required to read and interpret a template library. The library_key must select one of the objects in this list.

  • cube (mangadap.datacube.datacube.DataCube, optional) – The datacube to be analyzed using the template library.

  • match_resolution (bool, optional) – Match the spectral resolution of the template library to the resolution provided by the cube; the latter must be provided for this argument to have any use.

  • velscale_ratio (int, optional) – Resample the template spectra such that the ratio of the pixel scale in the provided cube is this many times larger than the pixels in the resampled template spectrum.

  • sres (mangadap.util.resolution.SpectralResolution, optional) – The object is used simply to access the spectral resolution and associated wavelength coordinate vector needed when matching the spectral resolution of the template library; this is used in lieu of a datacube.

  • velocity_offset (float, optional) – Velocity offset to use when matching the spectral resolution between the template library and the galaxy spectra.

  • min_sig_pix (float, optional) – Minimum value of the LSF standard deviation in pixels allowed before assuming the kernel is a Delta function. See mangadap.util.resolution.match_spectral_resolution().

  • no_offset (bool, optional) – Prohibit the spectral resolution matching to introduce an offset in spectral resolution required to match the relative shape of the resolution vectors. See mangadap.util.resolution.match_spectral_resolution() and mangadap.util.resolution.SpectralResolution.GaussianKernelDifference().

  • spectral_step (float, optional) – Logarithmic (log=True) or linear (log=False) step in wavelength for the template library.

  • log (bool, optional) – Flag to force the library to be logarithmically sampled in wavelength.

  • wavelength_range (array-like, optional) – Force the template library to cover this spectral range. Unobserved spectral regions will be masked.

  • renormalize (bool, optional) – After processing, renormalize the flux of the full library to unity. The relative fluxes of the templates are maintained.

  • dapver (str, optional) – DAP version, which is used to define the default DAP analysis path. Default is defined by mangadap.config.defaults.dap_version()

  • analysis_path (str, optional) – The path to the top-level directory for the DAP output files. Default is defined by mangadap.config.defaults.dap_analysis_path().

  • directory_path (str, optional) – The exact path to the processed template library file. Default is defined by mangadap.config.defaults.dap_common_path().

  • processed_file (str, optional) – The name of the file containing the prepared template library output file. The file should be found at directory_path/processed_file. Default is defined by mangadap.config.defaults.dap_file_name().

  • hardcopy (bool, optional) – Flag to keep a hardcopy of the processed template library.

  • symlink_dir (str, optional) – Create a symlink to the file in this directory. If None, no symbolic link is created.

  • clobber (bool, optional) – Overwrite any saved, processed template library file.

  • loggers (list, optional) – List of logging.Logger objects to log progress; ignored if quiet=True. Logging is done using mangadap.util.log.log_output(). If None, no logging is performed and output is just written to stdout.

  • quiet (bool, optional) – Suppress all terminal and logging output.

Raises

ValueError – If the sampling is undefined, or if a hardcopy is requested but the output file could not be defined.

read_raw_template_library(library_key=None, tpllib_list=None)[source]

Read the identified template library. If all the arguments are the default, the preset attributes from the initialization of the object are used.

Parameters

  • library_key (str, optional) – Keyword selecting the library to use.

  • tpllib_list (list, optional) – List of TemplateLibraryDef objects that define the parameters required to read and interpret a template library.

single_spec_to_fits(i, ofile, clobber=True)[source]

Write one of the template spectra to a 1D fits file.

Output is a one-dimensional fits file with a single extension containing the flux measurements and header keywords needed to determine the wavelength of each pixel.

Parameters

  • i (int) – Index of the spectrum in the avaiable list to output.

  • ofile (str) – Name of the file to write

  • clobber (bool, optional) – Overwrite any existing file.

Raises

ValueError – Raised if the selected index is not available.

supported_libraries = ['BC03', 'BPASS', 'M11ELODIE', 'M11MARCS', 'M11MILES', 'M11STELIB', 'M11STELIBZSOL', 'MASTARHC', 'MASTARHC2', 'MILES', 'MILESAVG', 'MILESHC', 'MILESTHIN', 'MIUSCAT', 'MIUSCATTHIN', 'STELIB']

Provides the keywords of the supported libraries.

class mangadap.proc.templatelibrary.TemplateLibraryBitMask[source]

Bases: mangadap.util.dapbitmask.DAPBitMask

Derived class that specifies the mask bits for the template library data. The maskbits defined are:

Key

Bit

Description

NO_DATA

0

Pixel has no data

WAVE_INVALID

1

Used to designate pixels in the 1D spectra that are outside the valid wavelength range defined by default_template_libraries().

FLUX_INVALID

2

Used to designate pixels in the 1D spectra that are below the valid flux limit defined by default_template_libraries().

SPECRES_EXTRAP

3

The spectral resolution has been matched to a value that was an extrapolation of the target spectral resolution samples.

SPECRES_LOW

4

The spectral resolution was not matched to the target value because the target value was higher than the existing spectral resolution.

SPECRES_2PIXEL

5

Resampling has lead to the resolution being below the two pixel limit. The spectral resolution has been changed to be exactly the two pixel limit for these pixels.

SPECRES_NOFLUX

6

Resolution matching has lead a template flux <= 0.
cfg_root = 'spectral_template_bits'
class mangadap.proc.templatelibrary.TemplateLibraryDef(key=None, file_search=None, fwhm=None, sres_ext=None, in_vacuum=False, wave_limit=None, lower_flux_limit=None, log10=False)[source]

Bases: mangadap.par.parset.KeywordParSet

Class with parameters used to define the template library. See mangadap.par.parset.ParSet for attributes.

The defined parameters are:

Key

Type

Options

Default

Description

key

str

Keyword to distinguish the template library.

file_search

str

Search string used by glob to find the 1D fits spectra to include in the template library.

fwhm

int, float

FWHM of the resolution element in angstroms.

sres_ext

str

Extension in the fits files with measurements of the spectral resolution as a function of wavelength.

in_vacuum

bool

Flag that the wavelengths of the spectra are in vacuum, not air.

wave_limit

ndarray

Two-element array with the starting and ending wavelengths for the valid spectral range of the templates.

lower_flux_limit

int, float

Minimum valid flux in the template spectra.

log10

bool

Flag that the template spectra have been binned logarithmically in wavelength.
mangadap.proc.templatelibrary.available_template_libraries()[source]

Return the list of available template libraries.

The available libraries are construced by looking for configuration files in the relevant DAP configuration directory.

Todo

  • Point to where the library format is described.

  • Somehow add a python call that reads the databases and constructs the table for presentation in sphinx so that the text above doesn’t have to be edited with changes in the available databases.

Returns

A list of mangadap.proc.templatelibrary.TemplateLibraryDef() objects, each defining a separate template library.

Return type

list

Raises

  • IOError – Raised if no template configuration files could be found.

  • KeyError – Raised if the template-library keywords are not all unique.

  • ValueError – Raised if the configuration file provides an invalid set of wavelength limits.

mangadap.proc.templatelibrary.validate_spectral_template_config(cnfg)[source]

Validate the mangadap.util.parser.DefaultConfig object with the template library parameters.

Parameters

cnfg (mangadap.util.parser.DefaultConfig) – Object with the template library parameters to validate.

Raises

  • KeyError – Raised if required keyword does not exist.

  • ValueError – Raised if key has unacceptable value.