22 """Module defining connection classes for PipelineTask.
25 __all__ = [
"PipelineTaskConnections",
"InputQuantizedConnection",
"OutputQuantizedConnection",
26 "DeferredDatasetRef",
"iterConnections"]
28 from collections
import UserDict, namedtuple
29 from types
import SimpleNamespace
35 from .
import config
as configMod
36 from .connectionTypes
import (InitInput, InitOutput, Input, PrerequisiteInput,
37 Output, BaseConnection)
38 from lsst.daf.butler
import DatasetRef, Quantum
40 if typing.TYPE_CHECKING:
41 from .config
import PipelineTaskConfig
45 """Exception raised when dataset type is configured as scalar
46 but there are multiple DataIds in a Quantum for that dataset.
51 Name of the configuration field for dataset type.
52 If ``numDataIds`` is not specified, it is assumed that this parameter
53 is the full message to be reported and not the key.
54 numDataIds : `int`, optional
55 Actual number of DataIds in a Quantum for this dataset type.
58 if numDataIds
is None:
62 err_msg = f
"Expected scalar for output dataset field {key}, " \
63 f
"received {numDataIds} DataIds"
68 """This is a special dict class used by PipelineTaskConnectionMetaclass
70 This dict is used in PipelineTaskConnection class creation, as the
71 dictionary that is initially used as __dict__. It exists to
72 intercept connection fields declared in a PipelineTaskConnection, and
73 what name is used to identify them. The names are then added to class
74 level list according to the connection type of the class attribute. The
75 names are also used as keys in a class level dictionary associated with
76 the corresponding class attribute. This information is a duplicate of
77 what exists in __dict__, but provides a simple place to lookup and
78 iterate on only these variables.
85 self.data[
'inputs'] = []
86 self.data[
'prerequisiteInputs'] = []
87 self.data[
'outputs'] = []
88 self.data[
'initInputs'] = []
89 self.data[
'initOutputs'] = []
90 self.data[
'allConnections'] = {}
93 if isinstance(value, Input):
94 self.data[
'inputs'].append(name)
95 elif isinstance(value, PrerequisiteInput):
96 self.data[
'prerequisiteInputs'].append(name)
97 elif isinstance(value, Output):
98 self.data[
'outputs'].append(name)
99 elif isinstance(value, InitInput):
100 self.data[
'initInputs'].append(name)
101 elif isinstance(value, InitOutput):
102 self.data[
'initOutputs'].append(name)
105 if isinstance(value, BaseConnection):
106 object.__setattr__(value,
'varName', name)
107 self.data[
'allConnections'][name] = value
113 """Metaclass used in the declaration of PipelineTaskConnections classes
121 if isinstance(base, PipelineTaskConnectionsMetaclass):
122 for name, value
in base.allConnections.items():
127 dimensionsValueError = TypeError(
"PipelineTaskConnections class must be created with a dimensions "
128 "attribute which is an iterable of dimension names")
130 if name !=
'PipelineTaskConnections':
133 if 'dimensions' not in kwargs:
135 if hasattr(base,
'dimensions'):
136 kwargs[
'dimensions'] = base.dimensions
138 if 'dimensions' not in kwargs:
139 raise dimensionsValueError
141 dct[
'dimensions'] = set(kwargs[
'dimensions'])
142 except TypeError
as exc:
143 raise dimensionsValueError
from exc
147 stringFormatter = string.Formatter()
149 for obj
in dct[
'allConnections'].values():
152 for param
in stringFormatter.parse(nameValue):
153 if param[1]
is not None:
154 allTemplates.add(param[1])
159 for base
in bases[::-1]:
160 if hasattr(base,
'defaultTemplates'):
161 mergeDict.update(base.defaultTemplates)
162 if 'defaultTemplates' in kwargs:
163 mergeDict.update(kwargs[
'defaultTemplates'])
165 if len(mergeDict) > 0:
166 kwargs[
'defaultTemplates'] = mergeDict
171 if len(allTemplates) > 0
and 'defaultTemplates' not in kwargs:
172 raise TypeError(
"PipelineTaskConnection class contains templated attribute names, but no "
173 "defaut templates were provided, add a dictionary attribute named "
174 "defaultTemplates which contains the mapping between template key and value")
175 if len(allTemplates) > 0:
177 defaultTemplateKeys = set(kwargs[
'defaultTemplates'].keys())
178 templateDifference = allTemplates.difference(defaultTemplateKeys)
179 if templateDifference:
180 raise TypeError(f
"Default template keys were not provided for {templateDifference}")
184 nameTemplateIntersection = allTemplates.intersection(set(dct[
'allConnections'].keys()))
185 if len(nameTemplateIntersection) > 0:
186 raise TypeError(f
"Template parameters cannot share names with Class attributes")
187 dct[
'defaultTemplates'] = kwargs.get(
'defaultTemplates', {})
191 for connectionName
in (
"inputs",
"prerequisiteInputs",
"outputs",
"initInputs",
"initOutputs"):
192 dct[connectionName] = frozenset(dct[connectionName])
195 return super().
__new__(cls, name, bases, dict(dct))
207 """A Namespace to map defined variable names of connections to their
208 `lsst.daf.buter.DatasetRef`s
210 This class maps the names used to define a connection on a
211 PipelineTaskConnectionsClass to the corresponding
212 `lsst.daf.butler.DatasetRef`s provided by a `lsst.daf.butler.Quantum`
213 instance. This will be a quantum of execution based on the graph created
214 by examining all the connections defined on the
215 `PipelineTaskConnectionsClass`.
220 object.__setattr__(self,
"_attributes", set())
222 def __setattr__(self, name: str, value: typing.Union[DatasetRef, typing.List[DatasetRef]]):
224 self._attributes.add(name)
228 object.__delattr__(self, name)
229 self._attributes.remove(name)
231 def __iter__(self) -> typing.Generator[typing.Tuple[str, typing.Union[DatasetRef,
232 typing.List[DatasetRef]]], None, None]:
233 """Make an Iterator for this QuantizedConnection
235 Iterating over a QuantizedConnection will yield a tuple with the name
236 of an attribute and the value associated with that name. This is
237 similar to dict.items() but is on the namespace attributes rather than
240 yield from ((name, getattr(self, name))
for name
in self._attributes)
242 def keys(self) -> typing.Generator[str, None, None]:
243 """Returns an iterator over all the attributes added to a
244 QuantizedConnection class
246 yield from self._attributes
253 class OutputQuantizedConnection(QuantizedConnection):
258 """Class which denotes that a datasetRef should be treated as deferred when
259 interacting with the butler
263 datasetRef : `lsst.daf.butler.DatasetRef`
264 The `lsst.daf.butler.DatasetRef` that will be eventually used to
271 """PipelineTaskConnections is a class used to declare desired IO when a
272 PipelineTask is run by an activator
276 config : `PipelineTaskConfig`
277 A `PipelineTaskConfig` class instance whose class has been configured
278 to use this `PipelineTaskConnectionsClass`
282 ``PipelineTaskConnection`` classes are created by declaring class
283 attributes of types defined in `lsst.pipe.base.connectionTypes` and are
286 * ``InitInput`` - Defines connections in a quantum graph which are used as
287 inputs to the ``__init__`` function of the `PipelineTask` corresponding
289 * ``InitOuput`` - Defines connections in a quantum graph which are to be
290 persisted using a butler at the end of the ``__init__`` function of the
291 `PipelineTask` corresponding to this class. The variable name used to
292 define this connection should be the same as an attribute name on the
293 `PipelineTask` instance. E.g. if an ``InitOutput`` is declared with
294 the name ``outputSchema`` in a ``PipelineTaskConnections`` class, then
295 a `PipelineTask` instance should have an attribute
296 ``self.outputSchema`` defined. Its value is what will be saved by the
298 * ``PrerequisiteInput`` - An input connection type that defines a
299 `lsst.daf.butler.DatasetType` that must be present at execution time,
300 but that will not be used during the course of creating the quantum
301 graph to be executed. These most often are things produced outside the
302 processing pipeline, such as reference catalogs.
303 * ``Input`` - Input `lsst.daf.butler.DatasetType` objects that will be used
304 in the ``run`` method of a `PipelineTask`. The name used to declare
305 class attribute must match a function argument name in the ``run``
306 method of a `PipelineTask`. E.g. If the ``PipelineTaskConnections``
307 defines an ``Input`` with the name ``calexp``, then the corresponding
308 signature should be ``PipelineTask.run(calexp, ...)``
309 * ``Output`` - A `lsst.daf.butler.DatasetType` that will be produced by an
310 execution of a `PipelineTask`. The name used to declare the connection
311 must correspond to an attribute of a `Struct` that is returned by a
312 `PipelineTask` ``run`` method. E.g. if an output connection is
313 defined with the name ``measCat``, then the corresponding
314 ``PipelineTask.run`` method must return ``Struct(measCat=X,..)`` where
315 X matches the ``storageClass`` type defined on the output connection.
317 The process of declaring a ``PipelineTaskConnection`` class involves
318 parameters passed in the declaration statement.
320 The first parameter is ``dimensions`` which is an iterable of strings which
321 defines the unit of processing the run method of a corresponding
322 `PipelineTask` will operate on. These dimensions must match dimensions that
323 exist in the butler registry which will be used in executing the
324 corresponding `PipelineTask`.
326 The second parameter is labeled ``defaultTemplates`` and is conditionally
327 optional. The name attributes of connections can be specified as python
328 format strings, with named format arguments. If any of the name parameters
329 on connections defined in a `PipelineTaskConnections` class contain a
330 template, then a default template value must be specified in the
331 ``defaultTemplates`` argument. This is done by passing a dictionary with
332 keys corresponding to a template identifier, and values corresponding to
333 the value to use as a default when formatting the string. For example if
334 ``ConnectionClass.calexp.name = '{input}Coadd_calexp'`` then
335 ``defaultTemplates`` = {'input': 'deep'}.
337 Once a `PipelineTaskConnections` class is created, it is used in the
338 creation of a `PipelineTaskConfig`. This is further documented in the
339 documentation of `PipelineTaskConfig`. For the purposes of this
340 documentation, the relevant information is that the config class allows
341 configuration of connection names by users when running a pipeline.
343 Instances of a `PipelineTaskConnections` class are used by the pipeline
344 task execution framework to introspect what a corresponding `PipelineTask`
345 will require, and what it will produce.
349 >>> from lsst.pipe.base import connectionTypes as cT
350 >>> from lsst.pipe.base import PipelineTaskConnections
351 >>> from lsst.pipe.base import PipelineTaskConfig
352 >>> class ExampleConnections(PipelineTaskConnections,
353 ... dimensions=("A", "B"),
354 ... defaultTemplates={"foo": "Example"}):
355 ... inputConnection = cT.Input(doc="Example input",
356 ... dimensions=("A", "B"),
357 ... storageClass=Exposure,
358 ... name="{foo}Dataset")
359 ... outputConnection = cT.Output(doc="Example output",
360 ... dimensions=("A", "B"),
361 ... storageClass=Exposure,
362 ... name="{foo}output")
363 >>> class ExampleConfig(PipelineTaskConfig,
364 ... pipelineConnections=ExampleConnections):
366 >>> config = ExampleConfig()
367 >>> config.connections.foo = Modified
368 >>> config.connections.outputConnection = "TotallyDifferent"
369 >>> connections = ExampleConnections(config=config)
370 >>> assert(connections.inputConnection.name == "ModifiedDataset")
371 >>> assert(connections.outputConnection.name == "TotallyDifferent")
374 def __init__(self, *, config:
'PipelineTaskConfig' =
None):
381 if config
is None or not isinstance(config, configMod.PipelineTaskConfig):
382 raise ValueError(
"PipelineTaskConnections must be instantiated with"
383 " a PipelineTaskConfig instance")
388 templateValues = {name: getattr(config.connections, name)
for name
in getattr(self,
389 'defaultTemplates').keys()}
393 self.
_nameOverrides = {name: getattr(config.connections, name).format(**templateValues)
394 for name
in self.allConnections.keys()}
402 OutputQuantizedConnection]:
403 """Builds QuantizedConnections corresponding to input Quantum
407 quantum : `lsst.daf.butler.Quantum`
408 Quantum object which defines the inputs and outputs for a given
413 retVal : `tuple` of (`InputQuantizedConnection`,
414 `OutputQuantizedConnection`) Namespaces mapping attribute names
415 (identifiers of connections) to butler references defined in the
416 input `lsst.daf.butler.Quantum`
422 for refs, names
in zip((inputDatasetRefs, outputDatasetRefs),
425 for attributeName
in names:
427 attribute = getattr(self, attributeName)
429 if attribute.name
in quantum.predictedInputs:
431 quantumInputRefs = quantum.predictedInputs[attribute.name]
434 if attribute.deferLoad:
438 if not attribute.multiple:
439 if len(quantumInputRefs) > 1:
440 raise ScalarError(attributeName, len(quantumInputRefs))
441 if len(quantumInputRefs) == 0:
443 quantumInputRefs = quantumInputRefs[0]
445 setattr(refs, attributeName, quantumInputRefs)
447 elif attribute.name
in quantum.outputs:
448 value = quantum.outputs[attribute.name]
451 if not attribute.multiple:
454 setattr(refs, attributeName, value)
458 raise ValueError(f
"Attribute with name {attributeName} has no counterpoint "
460 return inputDatasetRefs, outputDatasetRefs
463 """Override to make adjustments to `lsst.daf.butler.DatasetRef` objects
464 in the `lsst.daf.butler.core.Quantum` during the graph generation stage
469 datasetRefMap : `dict`
470 Mapping with keys of dataset type name to `list` of
471 `lsst.daf.butler.DatasetRef` objects
475 datasetRefMap : `dict`
476 Modified mapping of input with possible adjusted
477 `lsst.daf.butler.DatasetRef` objects
482 Overrides of this function have the option of raising an Exception
483 if a field in the input does not satisfy a need for a corresponding
484 pipelineTask, i.e. no reference catalogs are found.
489 def iterConnections(connections: PipelineTaskConnections, connectionType: str) -> typing.Generator:
490 """Creates an iterator over the selected connections type which yields
491 all the defined connections of that type.
495 connections: `PipelineTaskConnections`
496 An instance of a `PipelineTaskConnections` object that will be iterated
498 connectionType: `str`
499 The type of connections to iterate over, valid values are inputs,
500 outputs, prerequisiteInputs, initInputs, initOutputs.
504 connection: `BaseConnection`
505 A connection defined on the input connections object of the type
506 supplied. The yielded value Will be an derived type of
509 for name
in getattr(connections, connectionType):
510 yield getattr(connections, name)