Cube¶

Cube is a class to interact with a fully reduced DRP data cube for a galaxy.

Getting Started¶

To initialize a Cube, you can specify either a mangaid, plateifu, or filename as input. Marvin will attempt to open the file locally from a file, a database, or remotely over the API.

from marvin.tools.cube import Cube
cube = Cube(mangaid='1-209232')

print(cube)
<Marvin Cube (plateifu='8485-1901', mode='local', data_origin='db')>

You can quickly grab a spaxel by slicing the Cube like an array.

# grab the central spaxel
spax_cen = cube[17, 17]
print(spax_cen)
<Marvin Spaxel (plateifu=8485-1901, x=17, y=17; x_cen=0, y_cen=0)>

The flux is available as an attribute. It is represented as a Marvin Spectrum, which is a Quantity. To quickly plot the flux, use the plot method on the flux.

# look at the flux
spax_cen.flux
<Spectrum [ 0.54676276, 0.46566465, 0.4622981 ,...,  0.        ,
            0.        , 0.        ] 1e-17 erg / (Angstrom cm2 s spaxel)>

# plot the flux
spax_cen.flux.plot()

The Cube data quality and targeting flags are available as the quality_flag and target_flags attributes, respectively. These are represented as a Maskbit objects. A good quality Cube has an empty (0) bit list.

# check the quality and bits
cube.quality_flag
<Maskbit 'MANGA_DRP3QUAL' []>

cube.quality_flag.bits
[]

# check the targeting flags
cube.target_flags
[<Maskbit 'MANGA_TARGET1' ['SECONDARY_v1_1_0', 'SECONDARY_COM2', 'SECONDARY_v1_2_0']>,
 <Maskbit 'MANGA_TARGET2' []>,
 <Maskbit 'MANGA_TARGET3' []>]

The NSA catalog information is accessible via the nsa attribute. It is a dictionary of the all the NSA parameters available for this target. Use nsa.keys() to see all of the available parameters.

# grab the NSA redshift
cube.nsa['z']
0.0407447

# and the stellar mass in log units
cube.nsa['sersic_logmass']
9.629350465781462

You can quickly navigate to the DAP MAPS using the getMaps method. See the Maps reference on how to use a Marvin Maps object.

# grab the unbinned maps object
maps = cube.getMaps()
print(maps)
<Marvin Maps (plateifu='8485-1901', mode='local', data_origin='db', bintype='SPX', template='GAU-MILESHC')>

Using Cube¶

Initializing a Cube¶

A Cube can be initialized in several ways, by filename, in which case it will always be in local mode.

cube = Cube(filename='/Users/Brian/Work/Manga/redux/v2_3_1/8485/stack/manga-8485-1901-LOGCUBE.fits.gz')
<Marvin Cube (plateifu='8485-1901', mode='local', data_origin='file')>

by plateifu or mangaid, in which case it attempts to find a local database, otherwise will open it in remote mode.

cube = Cube(plateifu='8485-1901')
<Marvin Cube (plateifu='8485-1901', mode='local', data_origin='db')>

cube = Cube(mangaid='1-209232')
<Marvin Cube (plateifu='8485-1901', mode='local', data_origin='db')>

However you can also initialize a Cube without the keyword argument and Marvin will attempt to figure out what input you mean.

cube = Cube('8485-1901')
<Marvin Cube (plateifu='8485-1901', mode='local', data_origin='db')>

Basic Attributes¶

Cubes come with some basic attributes attached, like the full header (as an Astropy Header object), cube RA and Dec, the WCS info (as an Astropy WCS object), and the NSA catalog information (as a dictionary).

# access the header
cube.header

CHECKSUM= 'HLO1KLM1HLM1HLM1'   / HDU checksum updated 2017-10-17T06:02:42
DATASUM = '3722061489'         / data unit checksum updated 2017-10-17T06:02:42
EXTNAME = 'FLUX    '
QUALDATA= 'MASK    '           / Mask extension name
ERRDATA = 'IVAR    '           / Error extension name
HDUCLAS2= 'DATA    '
HDUCLAS1= 'CUBE    '
HDUCLASS= 'SDSS    '           / SDSS format class
CUNIT2  = 'deg     '
CUNIT1  = 'deg     '
CTYPE2  = 'DEC--TAN'
CTYPE1  = 'RA---TAN'
...

# the cube RA and Dec (the OBJRA and OBJDEC)
cube.ra, cube.dec
(232.544703894, 48.6902009334)

# the NSA catalog information
cube.nsa['z']
0.0407447

c.nsa['elpetro_ba']
0.87454

# check the quality and bits
cube.quality_flag
<Maskbit 'MANGA_DRP3QUAL' []>

cube.quality_flag.bits
[]

# check the targeting flags
cube.target_flags
[<Maskbit 'MANGA_TARGET1' ['SECONDARY_v1_1_0', 'SECONDARY_COM2', 'SECONDARY_v1_2_0']>,
 <Maskbit 'MANGA_TARGET2' []>,
 <Maskbit 'MANGA_TARGET3' []>]

You can manipulate the Cube pixel mask using the pixmask attribute.

cube.pixmask
<Maskbit 'MANGA_DRP3PIXMASK' shape=(4563, 34, 34)>

The DataModel¶

The DRP datamodel is attached to Cube as the datamodel attribute. The datamodel describes the contents of the MaNGA DRP Cube, for a given release.

cube.datamodel
<DRPDataModel release='MPL-6', n_datacubes=3, n_spectra=2>>

The DRP datamodel contains both 1-d (Spectra) and 3-d (DataCubes) representations of the data within a DRP Cube.

# see the available Datacubes
cube.datamodel.datacubes
[<DataCube 'flux', release='MPL-6', unit=u'1e-17 erg / (Angstrom cm2 s spaxel)'>,
 <DataCube 'dispersion', release='MPL-6', unit=u'Angstrom'>,
 <DataCube 'dispersion_prepixel', release='MPL-6', unit=u'Angstrom'>]

 # see the available Spectra
[<Spectrum 'spectral_resolution', release='MPL-6', unit=u'Angstrom'>,
 <Spectrum 'spectral_resolution_prepixel', release='MPL-6', unit=u'Angstrom'>]

DataCubes and Spectra¶

The datamodel provides DataCubes and Spectra objects for each target for a given release. These objects are Quantities. For example, in MPL-6, there are three available DataCubes, the flux, dispersion, and dispersion_prepixel, and two Spectra, the spectral_resolution and spectral_resolution_prepixel.

# access the cube flux
cube.flux
<DataCube [[[ 0., 0., 0.,...,  0., 0., 0.],
            [ 0., 0., 0.,...,  0., 0., 0.],
            [ 0., 0., 0.,...,  0., 0., 0.],
            ...,
            [ 0., 0., 0.,...,  0., 0., 0.],
            [ 0., 0., 0.,...,  0., 0., 0.],
            [ 0., 0., 0.,...,  0., 0., 0.]]] 1e-17 erg / (Angstrom cm2 s spaxel)>

type(cube.flux)
marvin.tools.quantities.datacube.DataCube

You can always get back the numpy array values using the value attribute.

# retrieve the underlying data
cube.flux.value
array([[[ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        ...,
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.]],

       [[ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        ...

DataCubes and Spectra behave as quantities, so may have available wavelength, ivar and mask attached.

# get the wavelength
cube.flux.wavelength
<Quantity [  3621.6 ,  3622.43,  3623.26,...,  10349.  , 10351.4 , 10353.8 ] Angstrom>

# get the flux ivar and mask
cube.flux.ivar
array([[[ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        ...,
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.]],

       [[ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        [ 0.,  0.,  0., ...,  0.,  0.,  0.],
        ...

cube.flux.mask
array([[[1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        ...,
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027]],

       [[1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        [1027, 1027, 1027, ..., 1027, 1027, 1027],
        ...

Extracting a Spaxel¶

From a Cube you can access Marvin objects related to this particular target. To access a Spaxel, you can slice like an array

# slice a cube by i, j
spaxel = cube[17, 17]
<Marvin Spaxel (plateifu=8485-1901, x=17, y=17; x_cen=0, y_cen=0)>

When slicing a Cube, the xy origin is always the lower left corner of the array, xyorig="lower". Remember Numpy arrays are in row-major. You can also use the getSpaxel method, which provides addionional keyword options. The cube[i, j] is a shorthand for cube.getSpaxel(x=j, y=i, xyorig='lower').

# get the central spaxel
spaxel = cube.getSpaxel(x=17, y=17, xyorig='lower')
<Marvin Spaxel (plateifu=8485-1901, x=17, y=17; x_cen=0, y_cen=0)>

By default, the xy origin in getSpaxel is the center of the Cube, xyorig="center".

spaxel = cube.getSpaxel(x=1, y=1)
<Marvin Spaxel (plateifu=8485-1901, x=18, y=18; x_cen=1, y_cen=1)>

Accessing Maps¶

Maps are also available from the Cube object, using the getMaps method. By default, this grabs the unbinned SPX maps.

# grab the Marvin Maps object
cube.getMaps()
<Marvin Maps (plateifu='8485-1901', mode='local', data_origin='db', bintype='SPX', template='GAU-MILESHC')>

Saving and Restoring¶

You can save a Cube locally as a Python pickle object, using the save method.

cube.save('mycube.mpf')

as well as restore a Cube pickle object using the restore class method

from marvin.tools.cube import Cube

cube = Cube.restore('mycube.mpf')

Reference/API¶

Class Inheritance Diagram

Inheritance diagram of marvin.tools.cube.Cube

Class

marvin.tools.cube.Cube([input, filename, …]) A class to interface with MaNGA DRP data cubes.

Methods

`marvin.tools.cube.Cube.getMaps`(**kwargs)	Retrieves the DAP `Maps` for this cube.
`marvin.tools.cube.Cube.getSpaxel`([x, y, ra, …])	Returns the `Spaxel` matching certain coordinates.
`marvin.tools.cube.Cube.download`()	Downloads the cube using sdss_access - Rsync,
`marvin.tools.cube.Cube.save`([path, overwrite])	Pickles the object.
`marvin.tools.cube.Cube.restore`(path[, delete])	Restores a MarvinToolsClass object from a pickled file.