https://github.com/RadioAstronomySoftwareGroup/pyuvdata
Tip revision: 090b4b9efedd04671d2ea3967cc85d898f3c3d49 authored by Bryna Hazelton on 30 November 2022, 23:32:39 UTC
Fix the incorrect version in the changelog, add a missed item earlier
Fix the incorrect version in the changelog, add a missed item earlier
Tip revision: 090b4b9
uvbase.py
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""
Base class for objects with UVParameter attributes.
Subclassed by UVData and Telescope.
"""
import copy
import warnings
import numpy as np
from astropy.coordinates import SkyCoord
from astropy.units import Quantity
from . import __version__
from . import parameter as uvp
from .utils import _get_iterable
__all__ = ["UVBase"]
def _warning(msg, *a, **kwargs):
"""
Improve the printing of user warnings.
Parameters
----------
msg : str
Input warning message.
a
postional parameters not used by this formatting method.
kwargs
named parameters not used by this formatting method.
Returns
-------
str
Input warning message with new line character appended to improve warning
formatting.
"""
return str(msg) + "\n"
class UVBase(object):
"""
Base class for objects with UVParameter attributes.
This class is intended to be subclassed and its init method should be
called in the subclass init after all associated UVParameter attributes are
defined. The init method of this base class creates properties
(named using UVParameter.name) from all the UVParameter attributes on the subclass.
AngleParameter and LocationParameter attributes also have extra convenience
properties defined:
AngleParameter:
UVParameter.name+'_degrees'
LocationParameter:
UVParameter.name+'_lat_lon_alt'
UVParameter.name+'_lat_lon_alt_degrees'
"""
def _setup_parameters(self):
"""Set up parameter objects to be able to be referenced by their names."""
# set any UVParameter attributes to be properties
for p in self:
this_param = getattr(self, p)
attr_name = this_param.name
setattr(
self.__class__,
attr_name,
property(self.prop_fget(p), self.prop_fset(p)),
)
if isinstance(this_param, uvp.AngleParameter):
setattr(
self.__class__,
attr_name + "_degrees",
property(self.degree_prop_fget(p), self.degree_prop_fset(p)),
)
elif isinstance(this_param, uvp.LocationParameter):
setattr(
self.__class__,
attr_name + "_lat_lon_alt",
property(
self.lat_lon_alt_prop_fget(p), self.lat_lon_alt_prop_fset(p)
),
)
setattr(
self.__class__,
attr_name + "_lat_lon_alt_degrees",
property(
self.lat_lon_alt_degrees_prop_fget(p),
self.lat_lon_alt_degrees_prop_fset(p),
),
)
return
def __init__(self):
"""Create properties from UVParameter attributes."""
warnings.formatwarning = _warning
self._setup_parameters()
# String to add to history of any files written with this version of pyuvdata
self.pyuvdata_version_str = (
f" Read/written with pyuvdata version: {__version__ }."
)
def __setstate__(self, state):
"""
Set the state of the object from given input state.
This is useful for pickling.
Parameters
----------
state
input state to assign to the __dict__.
"""
self.__dict__ = state
self._setup_parameters()
def prop_fget(self, param_name):
"""
Getter method for UVParameter properties.
Parameters
----------
param_name : str
Property name to get, corresponds the the UVParameter.name.
Returns
-------
fget
getter method to use for the property definition.
"""
# Create method to return
def fget(self):
this_param = getattr(self, param_name)
return this_param.value
return fget
def prop_fset(self, param_name):
"""
Setter method for UVParameter properties.
Parameters
----------
param_name : str
Property name to set, corresponds the the UVParameter.name.
Returns
-------
fset
setter method to use for the property definition.
"""
# Create method to return
def fset(self, value):
this_param = getattr(self, param_name)
this_param.value = value
setattr(self, param_name, this_param)
return fset
def degree_prop_fget(self, param_name):
"""
Degree getter method for AngleParameter properties.
Parameters
----------
param_name : str
Property name to get, corresponds the the UVParameter.name with "_degrees"
appended.
Returns
-------
fget
getter method to use for the property definition.
"""
# Create method to return
def fget(self):
this_param = getattr(self, param_name)
return this_param.degrees()
return fget
def degree_prop_fset(self, param_name):
"""
Degree setter method for AngleParameter properties.
Parameters
----------
param_name : str
Property name to set, corresponds the the UVParameter.name with "_degrees"
appended.
Returns
-------
fset
setter method to use for the property definition.
"""
# Create method to return
def fset(self, value):
this_param = getattr(self, param_name)
this_param.set_degrees(value)
setattr(self, param_name, this_param)
return fset
def lat_lon_alt_prop_fget(self, param_name):
"""
Lat/lon/alt getter method for LocationParameter properties.
Parameters
----------
param_name : str
Property name to get, corresponds the the UVParameter.name with
"_lat_lon_alt" appended.
Returns
-------
fget
getter method to use for the property definition.
"""
# Create method to return
def fget(self):
this_param = getattr(self, param_name)
return this_param.lat_lon_alt()
return fget
def lat_lon_alt_prop_fset(self, param_name):
"""
Lat/lon/alt setter method for LocationParameter properties.
Parameters
----------
param_name : str
Property name to set, corresponds the the UVParameter.name with
"_lat_lon_alt" appended.
Returns
-------
fset
setter method to use for the property definition.
"""
# Create method to return
def fset(self, value):
this_param = getattr(self, param_name)
this_param.set_lat_lon_alt(value)
setattr(self, param_name, this_param)
return fset
def lat_lon_alt_degrees_prop_fget(self, param_name):
"""
Lat/lon/alt degree getter method for LocationParameter properties.
Parameters
----------
param_name : str
Property name to get, corresponds the the UVParameter.name with
"_lat_lon_alt_degrees" appended.
Returns
-------
fget
getter method to use for the property definition.
"""
# Create method to return
def fget(self):
this_param = getattr(self, param_name)
return this_param.lat_lon_alt_degrees()
return fget
def lat_lon_alt_degrees_prop_fset(self, param_name):
"""
Lat/lon/alt degree setter method for LocationParameter properties.
Parameters
----------
param_name : str
Property name to set, corresponds the the UVParameter.name with
"_lat_lon_alt_degrees" appended.
Returns
-------
fset
setter method to use for the property definition.
"""
# Create method to return
def fset(self, value):
this_param = getattr(self, param_name)
this_param.set_lat_lon_alt_degrees(value)
setattr(self, param_name, this_param)
return fset
def __iter__(self, uvparams_only=True):
"""
Iterate over all (UVParameter) attributes.
Parameters
----------
uvparams_only : bool
Option to only iterate over UVParameter attributes.
Yields
------
attribute : UVParameter or any type
Object attributes, exclusively UVParameter objects if uvparams_only is True.
"""
attribute_list = [
a
for a in dir(self)
if not a.startswith("__") and not callable(getattr(self, a))
]
param_list = []
for a in attribute_list:
if uvparams_only:
attr = getattr(self, a)
if isinstance(attr, uvp.UVParameter):
param_list.append(a)
else:
param_list.append(a)
for a in param_list:
yield a
def required(self):
"""
Iterate over all required UVParameter attributes.
Yields
------
UVParameter
required UVParameters on this object.
"""
attribute_list = [
a
for a in dir(self)
if not a.startswith("__") and not callable(getattr(self, a))
]
required_list = []
for a in attribute_list:
attr = getattr(self, a)
if isinstance(attr, uvp.UVParameter):
if attr.required:
required_list.append(a)
for a in required_list:
yield a
def extra(self):
"""
Iterate over all non-required UVParameter attributes.
Yields
------
UVParameter
optional (non-required) UVParameters on this object.
"""
attribute_list = [
a
for a in dir(self)
if not a.startswith("__") and not callable(getattr(self, a))
]
extra_list = []
for a in attribute_list:
attr = getattr(self, a)
if isinstance(attr, uvp.UVParameter):
if not attr.required:
extra_list.append(a)
for a in extra_list:
yield a
def __eq__(self, other, check_extra=True, allowed_failures=("filename",)):
"""
Test if classes match and parameters are equal.
Parameters
----------
other : class
Other class instance to check
check_extra : bool
Option to specify whether to include all parameters, or just the
required ones. Default is True.
allowed_failures : iterable of str, optional
List or tuple of parameter names that are allowed to fail while
still passing an overall equality check. These should only include
optional parameters. By default, the `filename` parameter will be
ignored.
Returns
-------
bool
True if the two instances are equivalent.
"""
if isinstance(other, self.__class__):
# only check that required parameters are identical
self_required = []
other_required = []
for param in self.required():
self_required.append(param)
for param in other.required():
other_required.append(param)
if set(self_required) != set(other_required):
print(
"Sets of required parameters do not match. "
f"Left is {self_required},"
f" right is {other_required}."
)
return False
if check_extra:
self_extra = []
other_extra = []
for param in self.extra():
self_extra.append(param)
for param in other.extra():
other_extra.append(param)
if set(self_extra) != set(other_extra):
print(
"Sets of extra parameters do not match. "
f"Left is {self_extra},"
f" right is {other_extra}."
)
return False
p_check = self_required + self_extra
else:
p_check = self_required
if allowed_failures is not None:
if isinstance(allowed_failures, str):
# convert a single string into a length-1 list
allowed_failures = [allowed_failures]
if isinstance(allowed_failures, tuple):
# convert a tuple into a list
allowed_failures = list(allowed_failures)
for i, param in enumerate(allowed_failures):
if not param.startswith("_"):
param = "_" + param
allowed_failures[i] = param
if param not in self_required:
if param in p_check:
p_check.remove(param)
p_equal = True
for param in p_check:
self_param = getattr(self, param)
other_param = getattr(other, param)
if self_param != other_param:
print(
f"parameter {param} does not match. Left is "
f"{self_param.value}, right is {other_param.value}."
)
p_equal = False
if allowed_failures is not None:
for param in allowed_failures:
if hasattr(self, param):
self_param = getattr(self, param)
other_param = getattr(other, param)
if self_param != other_param:
print(
f"parameter {param} does not match, but is not "
"required to for equality. Left is "
f"{self_param.value}, right is {other_param.value}."
)
return p_equal
else:
print("Classes do not match")
return False
def __ne__(self, other, check_extra=True, allowed_failures=("filename",)):
"""
Test if classes match and parameters are not equal.
Parameters
----------
other : class
Other class instance to check
check_extra : bool
Option to specify whether to include all parameters, or just the
required ones. Default is True.
allowed_failures : iterable of str, optional
List or tuple of parameter names that are allowed to fail while
still passing an overall equality check. These should only include
optional parameters. By default, the `filename` parameter will be
ignored.
Returns
-------
bool
True if the two instances are equivalent.
"""
return not self.__eq__(
other, check_extra=check_extra, allowed_failures=allowed_failures
)
def check(
self, check_extra=True, run_check_acceptability=True, ignore_requirements=False
):
"""
Check that required parameters exist and have the correct shapes.
Optionally, check that the values are acceptable.
Parameters
----------
check_extra : bool
If true, check shapes and values on all parameters,
otherwise only check required parameters.
run_check_acceptability : bool
Option to check if values in parameters are acceptable.
ignore_requirements : bool
Do not error if a required parameter isn't set.
This allows the user to run the shape/acceptability checks
on parameters in a partially-defined UVData object.
Returns
-------
bool
True if the checks pass.
Raises
------
ValueError
If required UVParameter values have not been set or if set UVParameters
values do not have the expected names, shapes, types or values.
"""
if check_extra:
p_check = list(self.required()) + list(self.extra())
else:
p_check = list(self.required())
for p in p_check:
param = getattr(self, p)
if p != ("_" + param.name):
raise ValueError(
f"UVParameter {p} does not follow the required naming convention"
f"(expected be {'_' + param.name})."
)
# Check required parameter exists
if param.value is None:
if ignore_requirements:
continue
if param.required is True:
raise ValueError(f"Required UVParameter {p} has not been set.")
else:
# Check parameter shape
eshape = param.expected_shape(self)
# default value of eshape is ()
if eshape == "str" or (eshape == () and param.expected_type == "str"):
# Check that it's a string
if not isinstance(param.value, str):
raise ValueError(
f"UVParameter {p} expected to be string, but is not."
)
else:
# Check the shape of the parameter value. Note that np.shape
# returns an empty tuple for single numbers.
# eshape should do the same.
if not np.shape(param.value) == eshape:
raise ValueError(
"UVParameter {param} is not expected shape. "
"Parameter shape is {pshape}, expected shape is "
"{eshape}.".format(
param=p, pshape=np.shape(param.value), eshape=eshape
)
)
# Handle SkyCoord objects separately
if isinstance(param, uvp.SkyCoordParameter):
if not issubclass(param.value.__class__, SkyCoord):
raise ValueError(
f"UVParameter {p} should be a subclass of a "
f"SkyCoord object but it is {type(param.value)}."
)
else:
# matches expected type. Don't need to iterate through it.
continue # pragma: no cover
# Quantity objects complicate things slightly
# Do a separate check with warnings until a quantity based
# parameter value is created
if isinstance(param.value, Quantity):
# check if user put expected type as a type of quantity
# not a more generic type of number.
if any(
issubclass(param_type, Quantity)
for param_type in _get_iterable(param.expected_type)
):
# Verify the param is an instance
# of the specific Quantity type
if not isinstance(param.value, param.expected_type):
raise ValueError(
f"UVParameter {p} is a Quantity object "
"but not the appropriate type. "
f"Is {type(param.value)} but "
f"expected {param.expected_type}."
)
else:
# matches expected type
continue # pragma: no cover
else:
# Expected type is not a Quantity subclass
# Assuming it is a data type like float, int, etc
# continuing with check below
warnings.warn(
f"Parameter {p} is a Quantity object, "
"but the expected type is a precision identifier: "
f"{param.expected_type}. "
"Testing the precision of the value, but this "
"check will fail in a future version."
)
check_vals = [param.value.item(0).value]
elif eshape == ():
# Single element
check_vals = [param.value]
else:
if isinstance(param.value, (list, tuple)):
# List & tuples needs to be handled differently than array
# list values may be different types, so they all
# need to be checked
check_vals = list(param.value)
else:
# numpy array
check_vals = [param.value.item(0)]
for val in check_vals:
if not isinstance(val, param.expected_type):
raise ValueError(
f"UVParameter {p} is not the appropriate"
f" type. Is: {type(val)}. "
f"Should be: {param.expected_type}."
)
if run_check_acceptability:
accept, message = param.check_acceptability()
if not accept:
raise ValueError(
f"UVParameter {p} has unacceptable values. {message}"
)
return True
def copy(self):
"""
Make and return a copy of the object.
Returns
-------
UVBase
A deep copy of this object.
"""
return copy.deepcopy(self)
