NDData

Overview

NDData is based on numpy.ndarray-like data with additional meta attributes:

• meta, for general metadata
• unit, representing the physical unit of the data
• uncertainty for the uncertainty of the data
• mask, indicating invalid points in the data
• wcs, representing the relationship between the data grid and world coordinates

Each of these attributes can be set during initialization or directly on the instance. Only the data cannot be directly set after creating the instance.

Data

The data is the base of NDData and required to be numpy.ndarray-like. It’s the only property that is required to create an instance and it cannot be directly set on the instance.

For example:

>>> import numpy as np
>>> from astropy.nddata import NDData
>>> array = np.array([[0, 1, 0], [1, 0, 1], [0, 1, 0]])
>>> ndd = NDData(array)
>>> ndd
NDData([[0, 1, 0],
        [1, 0, 1],
        [0, 1, 0]])

and can be accessed by the data attribute:

>>> ndd.data
array([[0, 1, 0],
       [1, 0, 1],
       [0, 1, 0]])

as already mentioned it is not possible to set the data directly. So ndd.data = np.arange(9) will raise an Exception. But the data can be modified in place:

>>> ndd.data[1,1] = 100
>>> ndd.data
array([[  0,   1,   0],
       [  1, 100,   1],
       [  0,   1,   0]])

Data during initialization

During initialization it is possible to provide data that it’s not a numpy.ndarray but convertible to one. For example passing a list containing numerical values:

>>> alist = [1, 2, 3, 4]
>>> ndd = NDData(alist)
>>> ndd.data  # data will be a numpy-array:
array([1, 2, 3, 4])

Nested list or tuple are possible, but if these contain non-numerical values the conversion might fail.

Besides input that is convertible to such an array you can use the data parameter to pass implicit additional information. For example if the data is another NDData-object it implicitly uses it’s properties:

>>> ndd = NDData(ndd, unit = 'm')
>>> ndd2 = NDData(ndd)
>>> ndd2.data  # It has the same data as ndd
array([1, 2, 3, 4])
>>> ndd2.unit  # but it also has the same unit as ndd
Unit("m")

another possibility is to use a Quantity as data parameter:

>>> import astropy.units as u
>>> quantity = np.ones(3) * u.cm  # this will create a Quantity
>>> ndd3 = NDData(quantity)
>>> ndd3.data  
array([1., 1., 1.])
>>> ndd3.unit
Unit("cm")

or a numpy.ma.MaskedArray:

>>> masked_array = np.ma.array([5,10,15], mask=[False, True, False])
>>> ndd4 = NDData(masked_array)
>>> ndd4.data
array([ 5, 10, 15])
>>> ndd4.mask
array([False,  True, False]...)

If such an implicitly passed property conflicts with an explicit parameter, the explicit parameter will be used and an info-message will be issued:

>>> quantity = np.ones(3) * u.cm
>>> ndd6 = NDData(quantity, unit='m')
INFO: overwriting Quantity's current unit with specified unit. [astropy.nddata.nddata]
>>> ndd6.data  
array([1., 1., 1.])
>>> ndd6.unit
Unit("m")

The unit of the Quantity is being ignored and the unit is set to the explicitly passed one.

It might be possible to pass other classes as data parameter as long as they have the properties shape, dtype, __getitem__ and __array__.

The purpose of this mechanism is to allow considerable flexibility in the objects used to store the data while providing a useful default (numpy array).

Mask

The mask is being used to indicate if data points are valid or invalid. NDData doesn’t restrict this mask in any way but it is expected to follow the numpy.ma.MaskedArray convention that the mask:

• returns True for data points that are considered invalid.
• returns False for those points that are valid.

One possibility is to create a mask by using numpy’s comparison operators:

>>> array = np.array([0, 1, 4, 0, 2])

>>> mask = array == 0  # Mask points containing 0
>>> mask
array([ True, False, False,  True, False]...)

>>> other_mask = array > 1  # Mask points with a value greater than 1
>>> other_mask
array([False, False,  True, False,  True]...)

and initialize the NDData instance using the mask parameter:

>>> ndd = NDData(array, mask=mask)
>>> ndd.mask
array([ True, False, False,  True, False]...)

or by replacing the mask:

>>> ndd.mask = other_mask
>>> ndd.mask
array([False, False,  True, False,  True]...)

There is no requirement that the mask actually be a numpy array; for example, a function which evaluates a mask value as needed is acceptable as long as it follows the convention that True indicates a value that should be ignored.

Unit

The unit represents the unit of the data values. It is required to be Unit-like or a string that can be converted to such a Unit:

>>> import astropy.units as u
>>> ndd = NDData([1, 2, 3, 4], unit="meter")  # using a string
>>> ndd.unit
Unit("m")

..note::

Setting the unit on an instance is not possible.

Uncertainties

The uncertainty represents an arbitrary representation of the error of the data values. To indicate which kind of uncertainty representation is used the uncertainty should have an uncertainty_type property. If no such property is found it will be wrapped inside a UnknownUncertainty.

The uncertainty_type should follow the StdDevUncertainty convention that it returns a short string like "std" for an uncertainty given in standard deviation. Other examples are VarianceUncertainty and InverseVariance.

Like the other properties the uncertainty can be set during initialization:

>>> from astropy.nddata import StdDevUncertainty
>>> array = np.array([10, 7, 12, 22])
>>> uncert = StdDevUncertainty(np.sqrt(array))
>>> ndd = NDData(array, uncertainty=uncert)
>>> ndd.uncertainty  
StdDevUncertainty([3.16227766, 2.64575131, 3.46410162, 4.69041576])

or on the instance directly:

>>> other_uncert = StdDevUncertainty([2,2,2,2])
>>> ndd.uncertainty = other_uncert
>>> ndd.uncertainty
StdDevUncertainty([2, 2, 2, 2])

but it will print an info message if there is no uncertainty_type:

>>> ndd.uncertainty = np.array([5, 1, 2, 10])
INFO: uncertainty should have attribute uncertainty_type. [astropy.nddata.nddata]
>>> ndd.uncertainty
UnknownUncertainty([ 5,  1,  2, 10])

WCS

The wcs should contain a mapping from the gridded data to world coordinates. There are no restrictions placed on the property currently but it may be restricted to an WCS object or a more generalized WCS object in the future.

Note

Like the unit the wcs cannot be set on an instance.

Meta-data

The meta property contains all further meta information that don’t fit any other property.

If given it must be dict-like:

>>> ndd = NDData([1,2,3], meta={'observer': 'myself'})
>>> ndd.meta
{'observer': 'myself'}

dict-like means it must be a mapping from some keys to some values. This also includes Header objects:

>>> from astropy.io import fits
>>> header = fits.Header()
>>> header['observer'] = 'Edwin Hubble'
>>> ndd = NDData(np.zeros([10, 10]), meta=header)
>>> ndd.meta['observer']
'Edwin Hubble'

If the meta isn’t provided or explicitly set to None it will default to an empty collections.OrderedDict:

>>> ndd.meta = None
>>> ndd.meta
OrderedDict()

>>> ndd = NDData([1,2,3])
>>> ndd.meta
OrderedDict()

The meta object therefore supports adding or updating these values:

>>> ndd.meta['exposure_time'] = 340.
>>> ndd.meta['filter'] = 'J'

Elements of the meta-data dictionary can be set to any valid Python object:

>>> ndd.meta['history'] = ['calibrated', 'aligned', 'flat-fielded']

Initialization with copy

The default way to create an NDData instance is to try saving the parameters as references to the original rather than as copy. Sometimes this is not possible because the internal mechanics don’t allow for this. For example if the data is a list then during initialization this is copied while converting to a ndarray. But it is also possible to enforce copies during initialization by setting the copy parameter to True:

>>> array = np.array([1, 2, 3, 4])
>>> ndd = NDData(array)
>>> ndd.data[2] = 10
>>> array[2]  # Original array has changed
10

>>> ndd2 = NDData(array, copy=True)
>>> ndd2.data[2] = 3
>>> array[2]  # Original array hasn't changed.
10

Note

In some cases setting copy=True will copy the data twice. Known cases are if the data is a list or tuple.

Converting NDData to other classes

There is limited to support to convert a NDData instance to other classes. In the process some properties might be lost.

>>> data = np.array([1, 2, 3, 4])
>>> mask = np.array([True, False, False, True])
>>> unit = 'm'
>>> ndd = NDData(data, mask=mask, unit=unit)

numpy.ndarray

Converting the data to an array:

>>> array = np.asarray(ndd.data)
>>> array
array([1, 2, 3, 4])

Though using np.asarray is not required in most cases it will ensure that the result is always a numpy.ndarray

numpy.ma.MaskedArray

Converting the data and mask to a MaskedArray:

>>> masked_array = np.ma.array(ndd.data, mask=ndd.mask)
>>> masked_array  
masked_array(data=[--, 2, 3, --],
             mask=[ True, False, False,  True],
       fill_value=999999)

Quantity

Converting the data and unit to a Quantity:

>>> quantity = u.Quantity(ndd.data, unit=ndd.unit)
>>> quantity  
<Quantity [1., 2., 3., 4.] m>

Note

Ideally, one would construct masked quantities, but these are not properly supported: many operations on them fail.