Mixins¶

class marvin.tools.mixins.mma.MMAMixIn(input=None, filename=None, mangaid=None, plateifu=None, mode=None, data=None, release=None, drpall=None, download=None, ignore_db=False)[source]¶

A mixin that provides multi-modal data access.

Add this mixin to any new class object to provide that class with the Multi-Modal Data Access System for using local files, database, or remote connection when initializing new objects. See decision tree

Parameters:

Parameters:	input (str) – A string that can be a filename, plate-ifu, or mangaid. It will be automatically identified based on its unique format. This argument is always the first one, so it can be defined without the keyword for convenience. filename (str) – The path of the file containing the file to load. If set, `input` is ignored. mangaid (str) – The mangaid of the file to load. If set, `input` is ignored. plateifu (str) – The plate-ifu of the data cube to load. If set, `input` is ignored. mode ({'local', 'remote', 'auto'}) – The load mode to use. See Mode Decision Tree. data (`HDUList`, SQLAlchemy object, or None) – An astropy `HDUList` or a SQLAlchemy object, to be used for initialisation. If `None`, the normal <marvin-dma>` mode will be used. release (str) – The MPL/DR version of the data to use. drpall (str) – The path to the drpall file to use. If not set it will use the default path for the file based on the `release` download (bool) – If `True`, the data will be downloaded on instantiation. See Downloading Objects. ignore_db (bool) – If `True`, the local data-origin `db` will be ignored.
Variables:	data (`HDUList`, SQLAlchemy object, or dict) – Depending on the access mode, `data` is populated with the `HDUList` from the FITS file, a SQLAlchemy object, or a dictionary of values returned by an API call. data_origin ({'file', 'db', 'api'}) – Indicates the origin of the data, either from a file, the DB, or an API call. filename (str) – The path of the file used, if any. mangaid (str) – The mangaid of the target. plateifu – The plateifu of the target release – The data release

input (str) – A string that can be a filename, plate-ifu, or mangaid. It will be automatically identified based on its unique format. This argument is always the first one, so it can be defined without the keyword for convenience.
filename (str) – The path of the file containing the file to load. If set, input is ignored.
mangaid (str) – The mangaid of the file to load. If set, input is ignored.
plateifu (str) – The plate-ifu of the data cube to load. If set, input is ignored.
mode ({'local', 'remote', 'auto'}) – The load mode to use. See Mode Decision Tree.
data (HDUList, SQLAlchemy object, or None) – An astropy HDUList or a SQLAlchemy object, to be used for initialisation. If None, the normal <marvin-dma>` mode will be used.
release (str) – The MPL/DR version of the data to use.
drpall (str) – The path to the drpall file to use. If not set it will use the default path for the file based on the release
download (bool) – If True, the data will be downloaded on instantiation. See Downloading Objects.
ignore_db (bool) – If True, the local data-origin db will be ignored.

Variables:

data (HDUList, SQLAlchemy object, or dict) – Depending on the access mode, data is populated with the HDUList from the FITS file, a SQLAlchemy object, or a dictionary of values returned by an API call.
data_origin ({'file', 'db', 'api'}) – Indicates the origin of the data, either from a file, the DB, or an API call.
filename (str) – The path of the file used, if any.
mangaid (str) – The mangaid of the target.
plateifu – The plateifu of the target
release – The data release

download(pathType=None, **pathParams)[source]¶: Download using sdss_access Rsync

ifu¶: Returns the IFU.

plate¶: Returns the plate id.

release¶: Returns the release.

class marvin.tools.mixins.nsa.NSAMixIn(nsa_source='auto')[source]¶

A mixin that provides access to NSA paremeters.

Must be used in combination with MarvinToolsClass and initialised before nsa can be called.

Parameters: nsa_source ({'auto', 'drpall', 'nsa'}) – Defines how the NSA data for this object should loaded when .nsa is first called. If drpall, the drpall file will be used (note that this will only contain a subset of all the NSA information); if nsa, the full set of data from the DB will be retrieved. If the drpall file or a database are not available, a remote API call will be attempted. If nsa_source='auto', the source will depend on how the parent object has been instantiated. If the parent has data_origin='file', the drpall file will be used (as it is more likely that the user has that file in their system). Otherwise, nsa_source='nsa' will be assumed. This behaviour can be modified during runtime by modifying the nsa_mode attribute with one of the valid values.

Parameters:	nsa_source ({'auto', 'drpall', 'nsa'}) – Defines how the NSA data for this object should loaded when `.nsa` is first called. If `drpall`, the drpall file will be used (note that this will only contain a subset of all the NSA information); if `nsa`, the full set of data from the DB will be retrieved. If the drpall file or a database are not available, a remote API call will be attempted. If `nsa_source='auto'`, the source will depend on how the parent object has been instantiated. If the parent has `data_origin='file'`, the drpall file will be used (as it is more likely that the user has that file in their system). Otherwise, `nsa_source='nsa'` will be assumed. This behaviour can be modified during runtime by modifying the `nsa_mode` attribute with one of the valid values.

nsa¶: Returns the contents of the NSA catalogue for this target.

class marvin.tools.mixins.dapall.DAPallMixIn[source]¶

A mixin that provides access to DAPall paremeters.

Must be used in combination with MarvinToolsClass and initialised before dapall can be called.

DAPallMixIn uses the MarvinToolsClass.data_origin of the object to determine how to obtain the DAPall information. However, if the object contains a dapall attribute with the path to a DAPall file, that file will be used.

dapall¶: Returns the contents of the DAPall data for this target.

class marvin.tools.mixins.aperture.MarvinAperture[source]¶

Bases: object

Extends photutils.Aperture allowing to extract spaxels in the aperture.

This class is not intended for general use and it is dynamically set as the base for a Aperture instance.

getSpaxels(threshold=0.5, lazy=True, mask=None, **kwargs)[source]¶

Returns the spaxels that fall within the aperture.

Parameters:

Parameters:	threshold (float) – The minimum fractional overlap between the spaxel and the aperture grid for the spaxel to be returned. lazy (bool) – Whether the returned spaxels must be fully loaded or lazily instantiated. mask (numpy.ndarray) – A mask that defines the fractional pixel overlap with the apertures. If `None`, the mask returned by `MarvinAperture.mask` will be used. kwargs (dict) – Additional parameters to be passed to the parent `getSpaxel` method. Can be used to define what information is loaded in the spaxels.

threshold (float) – The minimum fractional overlap between the spaxel and the aperture grid for the spaxel to be returned.
lazy (bool) – Whether the returned spaxels must be fully loaded or lazily instantiated.
mask (numpy.ndarray) – A mask that defines the fractional pixel overlap with the apertures. If None, the mask returned by MarvinAperture.mask will be used.
kwargs (dict) – Additional parameters to be passed to the parent getSpaxel method. Can be used to define what information is loaded in the spaxels.

mask¶

Returns the fractional overlap mask.

Equivalent to using photutils.PixelAperture.to_mask followed by photutils.ApertureMask.to_image using the shape of the parent object. Combines all the apertures in a single mask.

parent¶: Returns or sets the parent object.

class marvin.tools.mixins.aperture.GetApertureMixIn[source]¶

getAperture(coords, aperture_params, aperture_type='circular', coord_type='pixel')[source]¶

Defines an aperture.

This method is mostly a wrapper around the aperture classes defined in photutils. It allows to

Parameters:

Parameters:	coords (tuple or `ndarray`) – Either a 2-element tuple `(x, y)` or `(ra, dec)` to define the centre of a single aperture, or a list of N tuples or a Nx2 array to define N apertures. aperture_params (tuple) – A tuple with the parameters of the aperture. For `aperture_type='rectangular'`: If `coord_type='pixel'`, a tuple `(w, h, theta)` where `w` is the full width of the aperture (for `theta=0` the width side is along the `x` axis); `h` is the full height of the aperture (for `theta=0` the height side is along the `y` axis); and `theta` is the rotation angle in radians of the width (`w`) side from the positive `x` axis (the rotation angle increases counterclockwise). If `coord_type='sky'`, same format but `w` and `h` must be in arcsec and `theta` is the position angle (in degrees) of the width side. The position angle increases counterclockwise, from North (PA=0) towards East. For `aperture_type='circular'`: The radius `r` in units of pixels or arcsec depending on the value of `coord_type`. Can be a tuple or a float. For `aperture_type='elliptical'`: If `coord_type='pixel'`, a tuple `(a, b, theta)` where `a` and `b` are the semi-major and semi-minor axes of the ellipse, respectively, and `theta` is the rotation angle in radians of the semi-major axis from the positive x axis (the rotation angle increases counterclockwise). If `coord_type='sky'`, `a` and `b` must be in arcsec, and `theta` is the position angle (in degrees) of the semi-major axis. The position angle increases counterclockwise, from North (PA=0) towards East. aperture_type ({'rectangular', 'circular', 'elliptical'}) – The type of aperture to define. coord_type ({'pixel', 'sky'}) – Determines whether the coordinates and aperture parameters refer to to the frame of the image or to sky coordinates. The conversion between the image and sky frames is determined using the WCS headers from the image.
Returns:	marvin_aperture (MarvinAperture object) – A `MarvinAperture` instance with the definition of the aperture, which can be used to extract the associated spaxels or to return the mask.

coords (tuple or ndarray) – Either a 2-element tuple (x, y) or (ra, dec) to define the centre of a single aperture, or a list of N tuples or a Nx2 array to define N apertures.
aperture_params (tuple) –
A tuple with the parameters of the aperture.
- For aperture_type='rectangular':
  - If coord_type='pixel', a tuple (w, h, theta) where w is the full width of the aperture (for theta=0 the width side is along the x axis); h is the full height of the aperture (for theta=0 the height side is along the y axis); and theta is the rotation angle in radians of the width (w) side from the positive x axis (the rotation angle increases counterclockwise).
  - If coord_type='sky', same format but w and h must be in arcsec and theta is the position angle (in degrees) of the width side. The position angle increases counterclockwise, from North (PA=0) towards East.
- For aperture_type='circular':
  - The radius r in units of pixels or arcsec depending on the value of coord_type. Can be a tuple or a float.
- For aperture_type='elliptical':
  - If coord_type='pixel', a tuple (a, b, theta) where a and b are the semi-major and semi-minor axes of the ellipse, respectively, and theta is the rotation angle in radians of the semi-major axis from the positive x axis (the rotation angle increases counterclockwise). If coord_type='sky', a and b must be in arcsec, and theta is the position angle (in degrees) of the semi-major axis. The position angle increases counterclockwise, from North (PA=0) towards East.
aperture_type ({'rectangular', 'circular', 'elliptical'}) – The type of aperture to define.
coord_type ({'pixel', 'sky'}) – Determines whether the coordinates and aperture parameters refer to to the frame of the image or to sky coordinates. The conversion between the image and sky frames is determined using the WCS headers from the image.

Returns:

marvin_aperture (MarvinAperture object) – A MarvinAperture instance with the definition of the aperture, which can be used to extract the associated spaxels or to return the mask.

Examples

A single circular aperture with a radius of 3 pixels can created as

>>> cube = marvin.tools.Cube('8485-1901')
>>> aperture = cube.getAperture((17, 15), 3)

aperture can then be used to return all spaxels that have a fractional overlap with the aperture of more than 0.6 pixels

>>> spaxels = aperture.getSpaxels(threshold=0.6, lazy=True)
>>> spaxels[0]
<Marvin Spaxel (x=15, y=13, loaded=False)

Apertures can also be defined from sky coordinates. To define two elliptical apertures with semi-axes 3 and 1 arcsec and rotated 30 degrees we do

>>> ap_ell = cube.getAperture([(232.546173, 48.6892288), (232.544069, 48.6906177)],
                              (3, 1, 30), aperture_type='elliptical')
>>> ap_ell
<MarvinAperture([[232.546173 ,  48.6892288],
     [232.544069 ,  48.6906177]], a=3.0, b=1.0, theta=30.0)>