Subclassing¶
NDData
¶
This class serves as the base for subclasses that use a numpy.ndarray
(or
something that presents a numpy-like interface) as the data
attribute.
Note
Each attribute is saved as attribute with one leading underscore. For example
the data
is saved as _data
and the mask
as _mask
, and so on.
Adding another property¶
>>> from astropy.nddata import NDData
>>> class NDDataWithFlags(NDData):
... def __init__(self, *args, **kwargs):
... # Remove flags attribute if given and pass it to the setter.
... self.flags = kwargs.pop('flags') if 'flags' in kwargs else None
... super().__init__(*args, **kwargs)
...
... @property
... def flags(self):
... return self._flags
...
... @flags.setter
... def flags(self, value):
... self._flags = value
>>> ndd = NDDataWithFlags([1,2,3])
>>> ndd.flags is None
True
>>> ndd = NDDataWithFlags([1,2,3], flags=[0, 0.2, 0.3])
>>> ndd.flags
[0, 0.2, 0.3]
Note
To simplify subclassing each setter (except for data
) is called during
__init__
so putting restrictions on any attribute can be done inside
the setter and will also apply during instance creation.
Customize the setter for a property¶
>>> import numpy as np
>>> class NDDataMaskBoolNumpy(NDData):
...
... @NDData.mask.setter
... def mask(self, value):
... # Convert mask to boolean numpy array.
... self._mask = np.array(value, dtype=np.bool_)
>>> ndd = NDDataMaskBoolNumpy([1,2,3])
>>> ndd.mask = [True, False, True]
>>> ndd.mask
array([ True, False, True]...)
Extend the setter for a property¶
unit
, meta
and uncertainty
implement some additional logic in their
setter so subclasses might define a call to the superclass and let the
super property set the attribute afterwards:
>>> import numpy as np
>>> class NDDataUncertaintyShapeChecker(NDData):
...
... @NDData.uncertainty.setter
... def uncertainty(self, value):
... value = np.asarray(value)
... if value.shape != self.data.shape:
... raise ValueError('uncertainty must have the same shape as the data.')
... # Call the setter of the super class in case it might contain some
... # important logic (only True for meta, unit and uncertainty)
... super(NDDataUncertaintyShapeChecker, self.__class__).uncertainty.fset(self, value)
... # Unlike "super(cls_name, cls_name).uncertainty.fset" or
... # or "NDData.uncertainty.fset" this will respect Pythons method
... # resolution order.
>>> ndd = NDDataUncertaintyShapeChecker([1,2,3], uncertainty=[2,3,4])
INFO: uncertainty should have attribute uncertainty_type. [astropy.nddata.nddata]
>>> ndd.uncertainty
UnknownUncertainty([2, 3, 4])
Having a setter for the data¶
>>> class NDDataWithDataSetter(NDData):
...
... @NDData.data.setter
... def data(self, value):
... self._data = np.asarray(value)
>>> ndd = NDDataWithDataSetter([1,2,3])
>>> ndd.data = [3,2,1]
>>> ndd.data
array([3, 2, 1])
NDDataRef
¶
NDDataRef
itself inherits from NDData
so
any of the possibilities there also apply to NDDataRef. But NDDataRef also
inherits from the Mixins:
which allow additional operations.
Add another arithmetic operation¶
Adding another possible operations is quite easy provided the data
and
unit
allow it within the framework of Quantity
.
For example adding a power function:
>>> from astropy.nddata import NDDataRef
>>> import numpy as np
>>> from astropy.utils import sharedmethod
>>> class NDDataPower(NDDataRef):
... @sharedmethod # sharedmethod to allow it also as classmethod
... def pow(self, operand, operand2=None, **kwargs):
... # the uncertainty doesn't allow propagation so set it to None
... kwargs['propagate_uncertainties'] = None
... # Call the _prepare_then_do_arithmetic function with the
... # numpy.power ufunc.
... return self._prepare_then_do_arithmetic(np.power, operand,
... operand2, **kwargs)
This can be used like the other arithmetic methods like
add()
. So it works when calling it
on the class or the instance:
>>> ndd = NDDataPower([1,2,3])
>>> # using it on the instance with one operand
>>> ndd.pow(3)
NDDataPower([ 1, 8, 27])
>>> # using it on the instance with two operands
>>> ndd.pow([1,2,3], [3,4,5])
NDDataPower([ 1, 16, 243])
>>> # or using it as classmethod
>>> NDDataPower.pow(6, [1,2,3])
NDDataPower([ 6, 36, 216])
To allow propagation also with uncertainty
see subclassing
NDUncertainty
.
The _prepare_then_do_arithmetic
implements the relevant checks if it was
called on the class or the instance, and, if one or two operands were given,
and converts the operands, if necessary, to the appropriate classes. Overriding
_prepare_then_do_arithmetic
in subclasses should be avoided if
possible.
Arithmetic on an existing property¶
Customizing how an existing property is handled during arithmetic is possible
with some arguments to the function calls like
add()
but it’s possible to hardcode
behavior too. The actual operation on the attribute (except for unit
) is
done in a method _arithmetic_*
where *
is the name of the property.
For example to customize how the meta
will be affected during arithmetics:
>>> from astropy.nddata import NDDataRef
>>> from copy import deepcopy
>>> class NDDataWithMetaArithmetics(NDDataRef):
...
... def _arithmetic_meta(self, operation, operand, handle_mask, **kwds):
... # the function must take the arguments:
... # operation (numpy-ufunc like np.add, np.subtract, ...)
... # operand (the other NDData-like object, already wrapped as NDData)
... # handle_mask (see description for "add")
...
... # The meta is dict like but we want the keywords exposure to change
... # Anticipate that one or both might have no meta and take the first one that has
... result_meta = deepcopy(self.meta) if self.meta else deepcopy(operand.meta)
... # Do the operation on the keyword if the keyword exists
... if result_meta and 'exposure' in result_meta:
... result_meta['exposure'] = operation(result_meta['exposure'], operand.data)
... return result_meta # return it
To trigger this method the handle_meta
argument to arithmetic methods can
be anything except None
or "first_found"
:
>>> ndd = NDDataWithMetaArithmetics([1,2,3], meta={'exposure': 10})
>>> ndd2 = ndd.add(10, handle_meta='')
>>> ndd2.meta
{'exposure': 20}
>>> ndd3 = ndd.multiply(0.5, handle_meta='')
>>> ndd3.meta
{'exposure': 5.0}
Warning
To use these internal _arithmetic_*
methods there are some restrictions on
the attributes when calling the operation:
mask
:handle_mask
must not beNone
,"ff"
or"first_found"
.wcs
:compare_wcs
argument with the same restrictions as mask.meta
:handle_meta
argument with the same restrictions as mask.uncertainty
:propagate_uncertainties
must beNone
or evaluate toFalse
.arithmetic_uncertainty
must also accepts different arguments:operation, operand, result, correlation, **kwargs
Changing default argument for arithmetic operations¶
If the goal is to change the default value of an existing parameter for
arithmetic methods, maybe because explicitly specifying the parameter each
time you’re calling an arithmetic operation is too much effort, you can easily
change the default value of existing parameters by changing it in the method
signature of _arithmetic
:
>>> from astropy.nddata import NDDataRef
>>> import numpy as np
>>> class NDDDiffAritDefaults(NDDataRef):
... def _arithmetic(self, *args, **kwargs):
... # Changing the default of handle_mask to None
... if 'handle_mask' not in kwargs:
... kwargs['handle_mask'] = None
... # Call the original with the updated kwargs
... return super()._arithmetic(*args, **kwargs)
>>> ndd1 = NDDDiffAritDefaults(1, mask=False)
>>> ndd2 = NDDDiffAritDefaults(1, mask=True)
>>> ndd1.add(ndd2).mask is None # it will be None
True
>>> # But giving other values is still possible:
>>> ndd1.add(ndd2, handle_mask=np.logical_or).mask
True
>>> ndd1.add(ndd2, handle_mask="ff").mask
False
The parameter controlling how properties are handled are all keyword-only
so using the *args, **kwargs
approach allows one to only alter one default
without needing to care about the positional order of arguments.
Arithmetic with an additional property¶
This also requires overriding the _arithmetic
method. Suppose we have a
flags
attribute again:
>>> from copy import deepcopy
>>> import numpy as np
>>> class NDDataWithFlags(NDDataRef):
... def __init__(self, *args, **kwargs):
... # Remove flags attribute if given and pass it to the setter.
... self.flags = kwargs.pop('flags') if 'flags' in kwargs else None
... super().__init__(*args, **kwargs)
...
... @property
... def flags(self):
... return self._flags
...
... @flags.setter
... def flags(self, value):
... self._flags = value
...
... def _arithmetic(self, operation, operand, *args, **kwargs):
... # take all args and kwargs to allow arithmetic on the other properties
... # to work like before.
...
... # do the arithmetics on the flags (pop the relevant kwargs, if any!!!)
... if self.flags is not None and operand.flags is not None:
... result_flags = np.logical_or(self.flags, operand.flags)
... # np.logical_or is just a suggestion you can do what you want
... else:
... if self.flags is not None:
... result_flags = deepcopy(self.flags)
... else:
... result_flags = deepcopy(operand.flags)
...
... # Let the superclass do all the other attributes note that
... # this returns the result and a dictionary containing other attributes
... result, kwargs = super()._arithmetic(operation, operand, *args, **kwargs)
... # The arguments for creating a new instance are saved in kwargs
... # so we need to add another keyword "flags" and add the processed flags
... kwargs['flags'] = result_flags
... return result, kwargs # these must be returned
>>> ndd1 = NDDataWithFlags([1,2,3], flags=np.array([1,0,1], dtype=bool))
>>> ndd2 = NDDataWithFlags([1,2,3], flags=np.array([0,0,1], dtype=bool))
>>> ndd3 = ndd1.add(ndd2)
>>> ndd3.flags
array([ True, False, True]...)
Slicing an existing property¶
Suppose you have a class expecting a 2 dimensional data
but the mask is
only 1D. This would lead to problems if one were to slice in two dimensions.
>>> from astropy.nddata import NDDataRef
>>> import numpy as np
>>> class NDDataMask1D(NDDataRef):
... def _slice_mask(self, item):
... # Multidimensional slices are represented by tuples:
... if isinstance(item, tuple):
... # only use the first dimension of the slice
... return self.mask[item[0]]
... # Let the superclass deal with the other cases
... return super()._slice_mask(item)
>>> ndd = NDDataMask1D(np.ones((3,3)), mask=np.ones(3, dtype=bool))
>>> nddsliced = ndd[1:3,1:3]
>>> nddsliced.mask
array([ True, True]...)
Note
The methods doing the slicing of the attributes are prefixed by a
_slice_*
where *
can be mask
, uncertainty
or wcs
. So
simply overriding them is the easiest way to customize how the are sliced.
Note
If slicing should affect the unit
or meta
see the next example.
Slicing an additional property¶
Building on the added property flags
we want them to be sliceable:
>>> class NDDataWithFlags(NDDataRef):
... def __init__(self, *args, **kwargs):
... # Remove flags attribute if given and pass it to the setter.
... self.flags = kwargs.pop('flags') if 'flags' in kwargs else None
... super().__init__(*args, **kwargs)
...
... @property
... def flags(self):
... return self._flags
...
... @flags.setter
... def flags(self, value):
... self._flags = value
...
... def _slice(self, item):
... # slice all normal attributes
... kwargs = super()._slice(item)
... # The arguments for creating a new instance are saved in kwargs
... # so we need to add another keyword "flags" and add the sliced flags
... kwargs['flags'] = self.flags[item]
... return kwargs # these must be returned
>>> ndd = NDDataWithFlags([1,2,3], flags=[0, 0.2, 0.3])
>>> ndd2 = ndd[1:3]
>>> ndd2.flags
[0.2, 0.3]
If you wanted to keep just the original flags
instead of the sliced ones
you could use kwargs['flags'] = self.flags
and omit the [item]
.
NDDataBase
¶
The class NDDataBase
is a metaclass – when subclassing it,
all properties of NDDataBase
must be overridden in the
subclass.
Subclassing from NDDataBase
gives you complete flexibility
in how you implement data storage and the other properties. If your data is
stored in a numpy array (or something that behaves like a numpy array), it may
be more straightforward to subclass NDData
instead of
NDDataBase
.
Implementing the NDDataBase interface¶
For example to create a readonly container:
>>> from astropy.nddata import NDDataBase
>>> class NDDataReadOnlyNoRestrictions(NDDataBase):
... def __init__(self, data, unit, mask, uncertainty, meta, wcs):
... self._data = data
... self._unit = unit
... self._mask = mask
... self._uncertainty = uncertainty
... self._meta = meta
... self._wcs = wcs
...
... @property
... def data(self):
... return self._data
...
... @property
... def unit(self):
... return self._unit
...
... @property
... def mask(self):
... return self._mask
...
... @property
... def uncertainty(self):
... return self._uncertainty
...
... @property
... def meta(self):
... return self._meta
...
... @property
... def wcs(self):
... return self._wcs
>>> # A meaningless test to show that creating this class is possible:
>>> NDDataReadOnlyNoRestrictions(1,2,3,4,5,6) is not None
True
Note
Actually defining an __init__
is not necessary and the properties could
return arbitrary values but the properties must be defined.
Subclassing NDUncertainty
¶
Warning
The internal interface of NDUncertainty and subclasses is experimental and might change in future versions.
Subclasses deriving from NDUncertainty
need to implement:
property
uncertainty_type
, should return a string describing the uncertainty for example"ivar"
for inverse variance.methods for propagation:
_propagate_*
where*
is the name of the UFUNC that is used on theNDData
parent.
Creating an uncertainty without propagation¶
UnknownUncertainty
is a minimal working implementation
without error propagation. So let’s create an uncertainty just storing
systematic uncertainties:
>>> from astropy.nddata import NDUncertainty
>>> class SystematicUncertainty(NDUncertainty):
... @property
... def uncertainty_type(self):
... return 'systematic'
...
... def _data_unit_to_uncertainty_unit(self, value):
... return None
...
... def _propagate_add(self, other_uncert, *args, **kwargs):
... return None
...
... def _propagate_subtract(self, other_uncert, *args, **kwargs):
... return None
...
... def _propagate_multiply(self, other_uncert, *args, **kwargs):
... return None
...
... def _propagate_divide(self, other_uncert, *args, **kwargs):
... return None
>>> SystematicUncertainty([10])
SystematicUncertainty([10])