mangadap.util.pixelmask module

A class hierarchy for pixel masks.

License

Copyright © 2019, SDSS-IV/MaNGA Pipeline Group

class mangadap.util.pixelmask.PixelMask[source]

Bases: object

Base class for a general 1D or 2D pixel mask.

shape

Shape of the array for the mask.

Type

tuple

_empty_mask(x, ny=None)[source]

Return an empty mask with the correct shape.

Parameters

  • x (numpy.ndarray) – Coordinate vector

  • ny (int) – (Optional) Size of the second dimension. Default is that there is only one dimension.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray

_mask_coordinate_ranges(x, rng, ny=None)[source]

Flag any x coordinates between a set of range limits as True. The mask is repeated in the second dimension, if requested.

Parameters

  • x (numpy.ndarray) – Coordinate vector

  • rng (list, numpy.ndarray) – (List of) Coordinate ranges that should be masked.

  • ny (int) – (Optional) Size of the second dimension. Default is that there is only one dimension.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray

_set_shape(x, ny=None)[source]

Set shape of the object

Parameters

  • x (numpy.ndarray) – Vector with the x-coordinates

  • ny (int) – (Optional) Size of the second dimension. Default is that there is no second dimension.

class mangadap.util.pixelmask.SpectralPixelMask(artdb=None, emldb=None, waverange=None, nsig=None)[source]

Bases: PixelMask

Container that produces a mask for the stellar continuum based on a set of emission lines and artifacts.

Parameters

  • artdb (mangadap.proc.artifactdb.ArtifactDB) – (Optional) Database with the list of artifacts to mask.

  • emldb (mangadap.proc.emissionlinedb.EmissionLineDB) – (Optional) Database with the list of emission lines to mask.

  • waverange (numpy.ndarray) – (Optional) Any pixels outside this wavelength range are masked.

artdb

Database with the list of artifacts to mask.

Type

mangadap.proc.artifactdb.ArtifactDB

emldb

Database with the list of emission lines to mask.

Type

mangadap.proc.emissionlinedb.EmissionLineDB

waverange

Any pixels outside this wavelength range are masked.

Type

numpy.ndarray

_artifact_mask(wave, nspec=None)[source]

Mask the pixels in the wavelength range(s) defined by the artifact database.

Parameters

  • wave (numpy.ndarray) – Wavelength coordinate vector

  • nspec (int) – (Optional) Number of spectra to mask. Default is just one.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray

_check_eml_kin_argument(kin)[source]

Check and return the correct kinematics vectors. If a single number is provided, the function returns the number repeated for each emission line.

Parameters

kin (float, list, numpy.ndarray) – An input set of kinematics to used by the mask.

Returns

A 1D float array of the correct shape with the kinematics

Return type

numpy.ndarray

Raises

ValueError – Raised if the length of the kin array is not the same as the number of emission lines in emldb.

_emission_line_mask(wave, nspec=None, velocity_offsets=0.0, sigma=250.0)[source]

Mask the pixels in the wavelength range(s) defined by the emission-line database that has been adjusted by a set of velocities and dispersions.

Currently, the velocity offsets are applied to all lines for each spectrum, whereas sigma and nsigma are applied to all spectra for each line.

Parameters

  • wave (numpy.ndarray) – Wavelength coordinate vector

  • nspec (int) – (Optional) Number of spectra to mask. Default is just one.

  • velocity_offsets (float, numpy.ndarray) – (Optional) One or more velocity offsets to apply to the emission-line bands on a spectrum-by-spectrum basis. Default is to apply no velocity offset.

  • sigma (float, numpy.ndarray) – (Optional) One or more velocity dispersions to use for setting the width of the emission-line band on a line-by-line basis. Default is a width based on a dispersion of 250 km/s.

  • nsigma (float, numpy.ndarray) – (Optional) One or more numbers that sets the width of the band in units of the provided velocity dipsersions band on a line-by-line basis.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray

_get_emission_line_bands(velocity_offsets=0.0, sigma=250.0)[source]

Set the emission-line masks, using the emission-line parameters defined by emldb (see mangadap.par.emissionlinedb.EmissionLineDB.

All emission lines in the database, except for those marked with action==i are masked.

The center of the masked region is constructed using emldb[‘restwave’] and the provided velocity (velocity_offset). The velocity of any lines marked as sky (action==s) is always set to 0.

The width of the mask is set to be \(\pm n_\sigma \sigma\) about this center, where both \(n_\sigma\) and \(\sigma\) are parameters (nsigma, sigma). If sigma is None, emldb[‘sig’] is used for each line.

Parameters

  • velocity_offsets (float, numpy.ndarray) – (Optional) The velocity offset to apply to each emission-line mask. Must be either a single number or one number per emission line. Assumed to be 0 if set to None.

  • sigma (float, numpy.ndarray) – (Optional) Line velocity dispersions used to set the mask width. Must be either a single number or one number per emission line. If None, the dispersion provided by the emission-line database is used (emldb[‘sig’]).

  • nsigma (float, numpy.ndarray) – (Optional) The half-width of the band in units of the provided velocity dipsersions. Must be either a single number or one number per emission line. Cannot be None.

Returns

A \(N_l \times 2\) array with the wavelength limits of the emission-line bands.

Return type

numpy.ndarray

Raises

ValueError – Raised if nsigma is None, or any nsigma is not greater than 0; raised if the half-width of any mask is not greater than 0.

_waverange_mask(wave, nspec=None)[source]

Mask the pixels not within the selected wavelength range.

Parameters

  • wave (numpy.ndarray) – Wavelength coordinate vector

  • nspec (int) – (Optional) Number of spectra to mask. Default is just one.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray

bits(bitmask, wave, nspec=None, mask=None, velocity_offsets=0.0, sigma=250.0, waverange_flag='OUTSIDE_RANGE', art_flag='ARTIFACT', eml_flag='EML_REGION')[source]

Construct a bit mask that signifies pixels as outside the desired wavelength range, as being affected by an artifact, and being designated as an emission-line region. To simply flag the pixels as a binary masked or unmasked, use boolean().

Parameters

  • bitmask (mangadap.util.bitmask.BitMask) – Bitmask used to flag pixels. The flags waverange_flag, art_flag, and eml_flag must be defined in the provided instance of BitMask.

  • wave (numpy.ndarray) – Wavelength coordinate vector

  • nspec (int) – (Optional) Number of spectra to mask. Default is just one.

  • mask (numpy.array) – (Optional) Baseline mask to add pixels masks. Should have data type that matches provided bitmask. Default is to start with all pixels unmasked.

  • velocity_offsets (float, numpy.ndarray) – (Optional) One or more velocity offsets to apply to the emission-line bands on a spectrum-by-spectrum basis. Default is to apply no velocity offset.

  • sigma (float, numpy.ndarray) – (Optional) One or more velocity dispersions to use for setting the width of the emission-line band on a line-by-line basis. Default is a width based on a dispersion of 250 km/s.

  • nsigma (float, numpy.ndarray) – (Optional) One or more numbers that sets the width of the band in units of the provided velocity dipsersions band on a line-by-line basis.

  • waverange_flag (str) – (Optional) Bitmask name used to flag a pixel as outside of the desired wavelength range. Default is ‘OUTSIDE_RANGE’.

  • art_flag (str) – (Optional) Bitmask name used to flag a pixel being affected by an artifact. Default is ‘ARTIFACT’.

  • eml_flag (str) – (Optional) Bitmask name used to flag a pixel being within an emission-line region. Default is ‘EML_REGION’.

Returns

Bit mask of the correct shape.

Return type

numpy.ndarray

boolean(wave, nspec=None, velocity_offsets=0.0, sigma=250.0)[source]

Construct the full boolean mask that includes the desired wavelength range, omitting artifacts, and omitting emission lines.

Parameters

  • wave (numpy.ndarray) – Wavelength coordinate vector

  • nspec (int) – (Optional) Number of spectra to mask. Default is just one.

  • velocity_offsets (float, numpy.ndarray) – (Optional) One or more velocity offsets to apply to the emission-line bands on a spectrum-by-spectrum basis. Default is to apply no velocity offset.

  • sigma (float, numpy.ndarray) – (Optional) One or more velocity dispersions to use for setting the width of the emission-line band on a line-by-line basis. Default is a width based on a dispersion of 250 km/s.

  • nsigma (float, numpy.ndarray) – (Optional) One or more numbers that sets the width of the band in units of the provided velocity dipsersions band on a line-by-line basis.

Returns

Boolean mask of the correct shape.

Return type

numpy.ndarray