Coverage for python/lsst/afw/table/_schema.py : 35%

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1# This file is part of afw.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# This program is free software: you can redistribute it and/or modify
10# it under the terms of the GNU General Public License as published by
11# the Free Software Foundation, either version 3 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17# GNU General Public License for more details.
18#
19# You should have received a copy of the GNU General Public License
20# along with this program. If not, see <https://www.gnu.org/licenses/>.
22__all__ = ["Key", "Field", "SchemaItem"]
24import numpy as np
25import fnmatch
26import re
27import collections
28import astropy.units
30import lsst.geom
31from lsst.utils import continueClass, TemplateMeta
33from ._table import _Key, _Field, _SchemaItem, Schema
35# Objects we prefer to use over the C++ string name for
36# Key/Field/SchemaItem types.
37_dtypes = {
38 "String": str,
39 "B": np.uint8,
40 "U": np.uint16,
41 "I": np.int32,
42 "L": np.int64,
43 "F": np.float32,
44 "D": np.float64,
45 "Angle": lsst.geom.Angle,
46}
49class Key(metaclass=TemplateMeta):
50 pass
53class Field(metaclass=TemplateMeta):
54 pass
57class SchemaItem(metaclass=TemplateMeta):
58 pass
61def _registerInstantiations(abc, types):
62 """Iterate over a private dict (filled by template instantiations in C++)
63 to register template instantiations a TemplateMeta ABCs.
65 If an entry for the type string exists in _dtypes, we use that instead of
66 the string as the key, and use the string as an alias.
67 """
68 for k, v in types.items():
69 dtype = _dtypes.get(k, None)
70 if dtype is not None:
71 abc.register(dtype, v)
72 abc.alias(k, v)
73 else:
74 abc.register(k, v)
77# _Key, _Field, and _SchemaItem are {str: class} dicts populated by the C++
78# wrappers. The keys are a superset of those in _dtypes.
79_registerInstantiations(Key, _Key)
80_registerInstantiations(Field, _Field)
81_registerInstantiations(SchemaItem, _SchemaItem)
83# Also register `float->D` as an alias; can't include
84# in _dtypes because we have (and prefer) np.float64 there.
85Key.alias(float, _Key["D"])
86Field.alias(float, _Field["D"])
87SchemaItem.alias(float, _SchemaItem["D"])
90@continueClass # noqa: F811
91class Schema:
93 def getOrderedNames(self):
94 """Return a list of field names in the order the fields were added to the Schema.
96 Returns
97 -------
98 names : `List`
99 Field names in order they were added to the Schema.
100 """
101 names = []
103 def func(item):
104 names.append(item.field.getName())
105 self.forEach(func)
106 return names
108 def __iter__(self):
109 """Iterate over the items in the Schema.
110 """
111 items = []
112 self.forEach(items.append)
113 return iter(items)
115 def checkUnits(self, parse_strict='raise'):
116 """Check that all units in the Schema are valid Astropy unit strings.
118 Parameters
119 ----------
120 parse_strict : `str`, optional
121 One of 'raise' (default), 'warn', or 'strict', indicating how to
122 handle unrecognized unit strings. See also astropy.units.Unit.
123 """
124 def func(item):
125 astropy.units.Unit(item.field.getUnits(),
126 parse_strict=parse_strict)
127 self.forEach(func)
129 def addField(self, field, type=None, doc="", units="", size=None,
130 doReplace=False, parse_strict="raise"):
131 """Add a field to the Schema.
133 Parameters
134 ----------
135 field : `str` or `Field`
136 The string name of the Field, or a fully-constructed Field object.
137 If the latter, all other arguments besides doReplace are ignored.
138 type : `str`, optional
139 The type of field to create. Valid types are the keys of the
140 afw.table.Field dictionary.
141 doc : `str`
142 Documentation for the field.
143 unit : `str`
144 Units for the field, or an empty string if unitless.
145 size : `int`
146 Size of the field; valid for string and array fields only.
147 doReplace : `bool`
148 If a field with this name already exists, replace it instead of
149 raising pex.exceptions.InvalidParameterError.
150 parse_strict : `str`
151 One of 'raise' (default), 'warn', or 'strict', indicating how to
152 handle unrecognized unit strings. See also astropy.units.Unit.
154 Returns
155 -------
156 result :
157 Result of the `Field` addition.
158 """
159 if isinstance(field, str):
160 field = Field[type](field, doc=doc, units=units,
161 size=size, parse_strict=parse_strict)
162 return field._addTo(self, doReplace)
164 def extract(self, *patterns, **kwargs):
165 """Extract a dictionary of {<name>: <schema-item>} in which the field names
166 match the given shell-style glob pattern(s).
168 Any number of glob patterns may be passed; the result will be the union of all
169 the result of each glob considered separately.
171 Parameters
172 ----------
173 patterns : Array of `str`
174 List of glob patterns to use to select field names.
175 kwargs : `dict`
176 Dictionary of additional keyword arguments. May contain:
177 - ``regex`` : `str` or `re` pattern
178 A regular expression to be used in addition to any
179 glob patterns passed as positional arguments. Note
180 that this will be compared with re.match, not
181 re.search.
182 - ``sub`` : `str`
183 A replacement string (see re.MatchObject.expand) used
184 to set the dictionary keys of any fields matched by
185 regex.
186 - ``ordered`` : `bool`, optional
187 If True, a collections.OrderedDict will be returned
188 instead of a standard dict, with the order
189 corresponding to the definition order of the
190 Schema. Default is False.
192 Returns
193 -------
194 d : `dict`
195 Dictionary of extracted name-schema item sets.
197 Raises
198 ------
199 ValueError
200 Raised if the `sub` keyword argument is invalid without
201 the `regex` argument.
203 Also raised if an unknown keyword argument is supplied.
204 """
205 if kwargs.pop("ordered", False):
206 d = collections.OrderedDict()
207 else:
208 d = dict()
209 regex = kwargs.pop("regex", None)
210 sub = kwargs.pop("sub", None)
211 if sub is not None and regex is None:
212 raise ValueError(
213 "'sub' keyword argument to extract is invalid without 'regex' argument")
214 if kwargs:
215 kwargsStr = ", ".join(kwargs.keys())
216 raise ValueError(f"Unrecognized keyword arguments for extract: {kwargsStr}")
217 for item in self:
218 trueName = item.field.getName()
219 names = [trueName]
220 for alias, target in self.getAliasMap().items():
221 if trueName.startswith(target):
222 names.append(trueName.replace(target, alias, 1))
223 for name in names:
224 if regex is not None:
225 m = re.match(regex, name)
226 if m is not None:
227 if sub is not None:
228 name = m.expand(sub)
229 d[name] = item
230 continue # continue middle loop so we don't match the same name twice
231 for pattern in patterns:
232 if fnmatch.fnmatchcase(name, pattern):
233 d[name] = item
234 break # break inner loop so we don't match the same name twice
235 return d
237 def __reduce__(self):
238 """For pickle support."""
239 fields = []
240 for item in self:
241 fields.append(item.field)
242 return (makeSchemaFromFields, (fields,))
245def makeSchemaFromFields(fields):
246 """Create a Schema from a sequence of Fields. For pickle support.
248 Parameters
249 ----------
250 fields : `tuple` ['lsst.afw.table.Field']
251 The fields to construct the new Schema from.
253 Returns
254 -------
255 schema : `lsst.afw.table.Schema`
256 The constructed Schema.
257 """
258 schema = Schema()
259 for field in fields:
260 schema.addField(field)
261 return schema