Coverage for python/lsst/meas/base/baseMeasurement.py : 22%

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1# This file is part of meas_base.
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"""Base measurement task, which subclassed by the single frame and forced
23measurement tasks.
24"""
26import lsst.pipe.base
27import lsst.pex.config
29from .pluginRegistry import PluginMap
30from .exceptions import FatalAlgorithmError, MeasurementError
31from .pluginsBase import BasePluginConfig, BasePlugin
32from .noiseReplacer import NoiseReplacerConfig
34__all__ = ("BaseMeasurementPluginConfig", "BaseMeasurementPlugin",
35 "BaseMeasurementConfig", "BaseMeasurementTask")
37# Exceptions that the measurement tasks should always propagate up to their callers
38FATAL_EXCEPTIONS = (MemoryError, FatalAlgorithmError)
41class BaseMeasurementPluginConfig(BasePluginConfig):
42 """Base config class for all measurement plugins.
44 Notes
45 -----
46 Most derived classes will want to override `setDefaults` in order to
47 customize the default `executionOrder`.
49 A derived class whose corresponding Plugin class implements a do `measureN`
50 method should additionally add a bool `doMeasureN` field to replace the
51 bool class attribute defined here.
52 """
54 doMeasure = lsst.pex.config.Field(dtype=bool, default=True,
55 doc="whether to run this plugin in single-object mode")
57 doMeasureN = False # replace this class attribute with a Field if measureN-capable
60class BaseMeasurementPlugin(BasePlugin):
61 """Base class for all measurement plugins.
63 Notes
64 -----
65 This is class is a placeholder for future behavior which will be shared
66 only between measurement plugins and is implemented for symmetry with the
67 measurement base plugin configuration class
68 """
70 pass
73class SourceSlotConfig(lsst.pex.config.Config):
74 """Assign named plugins to measurement slots.
76 Slot configuration which assigns a particular named plugin to each of a set
77 of slots. Each slot allows a type of measurement to be fetched from the
78 `lsst.afw.table.SourceTable` without knowing which algorithm was used to
79 produced the data.
81 Notes
82 -----
83 The default algorithm for each slot must be registered, even if the default
84 is not used.
85 """
87 Field = lsst.pex.config.Field
88 centroid = Field(dtype=str, default="base_SdssCentroid", optional=True,
89 doc="the name of the centroiding algorithm used to set source x,y")
90 shape = Field(dtype=str, default="base_SdssShape", optional=True,
91 doc="the name of the algorithm used to set source moments parameters")
92 psfShape = Field(dtype=str, default="base_SdssShape_psf", optional=True,
93 doc="the name of the algorithm used to set PSF moments parameters")
94 apFlux = Field(dtype=str, default="base_CircularApertureFlux_12_0", optional=True,
95 doc="the name of the algorithm used to set the source aperture instFlux slot")
96 modelFlux = Field(dtype=str, default="base_GaussianFlux", optional=True,
97 doc="the name of the algorithm used to set the source model instFlux slot")
98 psfFlux = Field(dtype=str, default="base_PsfFlux", optional=True,
99 doc="the name of the algorithm used to set the source psf instFlux slot")
100 gaussianFlux = Field(dtype=str, default="base_GaussianFlux", optional=True,
101 doc="the name of the algorithm used to set the source Gaussian instFlux slot")
102 calibFlux = Field(dtype=str, default="base_CircularApertureFlux_12_0", optional=True,
103 doc="the name of the instFlux measurement algorithm used for calibration")
105 def setupSchema(self, schema):
106 """Set up a slots in a schema following configuration directives.
108 Parameters
109 ----------
110 schema : `lsst.afw.table.Schema`
111 The schema in which slots will be set up.
113 Notes
114 -----
115 This is defined in this configuration class to support use in unit
116 tests without needing to construct an `lsst.pipe.base.Task` object.
117 """
118 aliases = schema.getAliasMap()
119 if self.centroid is not None:
120 aliases.set("slot_Centroid", self.centroid)
121 if self.shape is not None:
122 aliases.set("slot_Shape", self.shape)
123 if self.psfShape is not None:
124 aliases.set("slot_PsfShape", self.psfShape)
125 if self.apFlux is not None:
126 aliases.set("slot_ApFlux", self.apFlux)
127 if self.modelFlux is not None:
128 aliases.set("slot_ModelFlux", self.modelFlux)
129 if self.psfFlux is not None:
130 aliases.set("slot_PsfFlux", self.psfFlux)
131 if self.gaussianFlux is not None:
132 aliases.set("slot_GaussianFlux", self.gaussianFlux)
133 if self.calibFlux is not None:
134 aliases.set("slot_CalibFlux", self.calibFlux)
137class BaseMeasurementConfig(lsst.pex.config.Config):
138 """Base configuration for all measurement driver tasks.
140 Examples
141 --------
142 Subclasses should define the 'plugins' and 'undeblended' registries, e.g.
144 .. code-block:: py
146 plugins = PluginBaseClass.registry.makeField(
147 multi=True,
148 default=[],
149 doc="Plugins to be run and their configuration"
150 )
151 undeblended = PluginBaseClass.registry.makeField(
152 multi=True,
153 default=[],
154 doc="Plugins to run on undeblended image"
155 )
157 where ``PluginBaseClass`` is the appropriate base class of the plugin
158 (e.g., `SingleFramePlugin` or `ForcedPlugin`).
159 """
161 slots = lsst.pex.config.ConfigField(
162 dtype=SourceSlotConfig,
163 doc="Mapping from algorithms to special aliases in Source."
164 )
166 doReplaceWithNoise = lsst.pex.config.Field(
167 dtype=bool, default=True, optional=False,
168 doc='When measuring, replace other detected footprints with noise?')
170 noiseReplacer = lsst.pex.config.ConfigField(
171 dtype=NoiseReplacerConfig,
172 doc="configuration that sets how to replace neighboring sources with noise"
173 )
174 undeblendedPrefix = lsst.pex.config.Field(
175 dtype=str, default="undeblended_",
176 doc="Prefix to give undeblended plugins"
177 )
179 def validate(self):
180 lsst.pex.config.Config.validate(self)
181 if self.slots.centroid is not None and self.slots.centroid not in self.plugins.names:
182 raise ValueError("source centroid slot algorithm is not being run.")
183 if self.slots.shape is not None and self.slots.shape not in self.plugins.names:
184 raise ValueError("source shape slot algorithm '%s' is not being run." % self.slots.shape)
185 for slot in (self.slots.psfFlux, self.slots.apFlux, self.slots.modelFlux,
186 self.slots.gaussianFlux, self.slots.calibFlux):
187 if slot is not None:
188 for name in self.plugins.names:
189 if len(name) <= len(slot) and name == slot[:len(name)]:
190 break
191 else:
192 raise ValueError("source instFlux slot algorithm '%s' is not being run." % slot)
195class BaseMeasurementTask(lsst.pipe.base.Task):
196 """Ultimate base class for all measurement tasks.
198 Parameters
199 ----------
200 algMetadata : `lsst.daf.base.PropertyList` or `None`
201 Will be modified in-place to contain metadata about the plugins being
202 run. If `None`, an empty `~lsst.daf.base.PropertyList` will be
203 created.
204 **kwds
205 Additional arguments passed to `lsst.pipe.base.Task.__init__`.
207 Notes
208 -----
209 This base class for `SingleFrameMeasurementTask` and
210 `ForcedMeasurementTask` mostly exists to share code between the two, and
211 generally should not be used directly.
212 """
214 ConfigClass = BaseMeasurementConfig
215 _DefaultName = "measurement"
217 plugins = None
218 """Plugins to be invoked (`PluginMap`).
220 Initially empty, this will be populated as plugins are initialized. It
221 should be considered read-only.
222 """
224 algMetadata = None
225 """Metadata about active plugins (`lsst.daf.base.PropertyList`).
227 Contains additional information about active plugins to be saved with
228 the output catalog. Will be filled by subclasses.
229 """
231 def __init__(self, algMetadata=None, **kwds):
232 super(BaseMeasurementTask, self).__init__(**kwds)
233 self.plugins = PluginMap()
234 self.undeblendedPlugins = PluginMap()
235 if algMetadata is None:
236 algMetadata = lsst.daf.base.PropertyList()
237 self.algMetadata = algMetadata
239 def initializePlugins(self, **kwds):
240 """Initialize plugins (and slots) according to configuration.
242 Parameters
243 ----------
244 **kwds
245 Keyword arguments forwarded directly to plugin constructors.
247 Notes
248 -----
249 Derived class constructors should call this method to fill the
250 `plugins` attribute and add corresponding output fields and slot
251 aliases to the output schema.
253 In addition to the attributes added by `BaseMeasurementTask.__init__`,
254 a ``schema``` attribute holding the output schema must be present
255 before this method is called.
257 Keyword arguments are forwarded directly to plugin constructors,
258 allowing derived classes to use plugins with different signatures.
259 """
260 # Make a place at the beginning for the centroid plugin to run first (because it's an OrderedDict,
261 # adding an empty element in advance means it will get run first when it's reassigned to the
262 # actual Plugin).
263 if self.config.slots.centroid is not None:
264 self.plugins[self.config.slots.centroid] = None
265 # Init the plugins, sorted by execution order. At the same time add to the schema
266 for executionOrder, name, config, PluginClass in sorted(self.config.plugins.apply()):
267 # Pass logName to the plugin if the plugin is marked as using it
268 # The task will use this name to log plugin errors, regardless.
269 if hasattr(PluginClass, "hasLogName") and PluginClass.hasLogName:
270 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata,
271 logName=self.log.getChild(name).name, **kwds)
272 else:
273 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata, **kwds)
275 # In rare circumstances (usually tests), the centroid slot not be coming from an algorithm,
276 # which means we'll have added something we don't want to the plugins map, and we should
277 # remove it.
278 if self.config.slots.centroid is not None and self.plugins[self.config.slots.centroid] is None:
279 del self.plugins[self.config.slots.centroid]
280 # Initialize the plugins to run on the undeblended image
281 for executionOrder, name, config, PluginClass in sorted(self.config.undeblended.apply()):
282 undeblendedName = self.config.undeblendedPrefix + name
283 self.undeblendedPlugins[name] = PluginClass(config, undeblendedName, metadata=self.algMetadata,
284 **kwds)
286 def callMeasure(self, measRecord, *args, **kwds):
287 """Call ``measure`` on all plugins and consistently handle exceptions.
289 Parameters
290 ----------
291 measRecord : `lsst.afw.table.SourceRecord`
292 The record corresponding to the object being measured. Will be
293 updated in-place with the results of measurement.
294 *args
295 Positional arguments forwarded to ``plugin.measure``
296 **kwds
297 Keyword arguments. Two are handled locally:
299 beginOrder : `int`
300 Beginning execution order (inclusive). Measurements with
301 ``executionOrder`` < ``beginOrder`` are not executed. `None`
302 for no limit.
304 endOrder : `int`
305 Ending execution order (exclusive). Measurements with
306 ``executionOrder`` >= ``endOrder`` are not executed. `None`
307 for no limit.
309 Others are forwarded to ``plugin.measure()``.
311 Notes
312 -----
313 This method can be used with plugins that have different signatures;
314 the only requirement is that ``measRecord`` be the first argument.
315 Subsequent positional arguments and keyword arguments are forwarded
316 directly to the plugin.
318 This method should be considered "protected": it is intended for use by
319 derived classes, not users.
320 """
321 beginOrder = kwds.pop("beginOrder", None)
322 endOrder = kwds.pop("endOrder", None)
323 for plugin in self.plugins.iter():
324 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder:
325 continue
326 if endOrder is not None and plugin.getExecutionOrder() >= endOrder:
327 break
328 self.doMeasurement(plugin, measRecord, *args, **kwds)
330 def doMeasurement(self, plugin, measRecord, *args, **kwds):
331 """Call ``measure`` on the specified plugin.
333 Exceptions are handled in a consistent way.
335 Parameters
336 ----------
337 plugin : subclass of `BasePlugin`
338 Plugin that will be executed.
339 measRecord : `lsst.afw.table.SourceRecord`
340 The record corresponding to the object being measured. Will be
341 updated in-place with the results of measurement.
342 *args
343 Positional arguments forwarded to ``plugin.measure()``.
344 **kwds
345 Keyword arguments forwarded to ``plugin.measure()``.
347 Notes
348 -----
349 This method can be used with plugins that have different signatures;
350 the only requirement is that ``plugin`` and ``measRecord`` be the first
351 two arguments. Subsequent positional arguments and keyword arguments
352 are forwarded directly to the plugin.
354 This method should be considered "protected": it is intended for use by
355 derived classes, not users.
356 """
357 try:
358 plugin.measure(measRecord, *args, **kwds)
359 except FATAL_EXCEPTIONS:
360 raise
361 except MeasurementError as error:
362 self.log.getChild(plugin.name).debug(
363 "MeasurementError in %s.measure on record %s: %s",
364 plugin.name, measRecord.getId(), error)
365 plugin.fail(measRecord, error)
366 except Exception as error:
367 self.log.getChild(plugin.name).debug(
368 "Exception in %s.measure on record %s: %s",
369 plugin.name, measRecord.getId(), error)
370 plugin.fail(measRecord)
372 def callMeasureN(self, measCat, *args, **kwds):
373 """Call ``measureN`` on all plugins and consistently handle exceptions.
375 Parameters
376 ----------
377 measCat : `lsst.afw.table.SourceCatalog`
378 Catalog containing only the records for the source family to be
379 measured, and where outputs should be written.
380 *args
381 Positional arguments forwarded to ``plugin.measure()``
382 **kwds
383 Keyword arguments. Two are handled locally:
385 beginOrder:
386 Beginning execution order (inclusive): Measurements with
387 ``executionOrder`` < ``beginOrder`` are not executed. `None`
388 for no limit.
389 endOrder:
390 Ending execution order (exclusive): measurements with
391 ``executionOrder`` >= ``endOrder`` are not executed. `None` for
392 no ``limit``.
394 Others are are forwarded to ``plugin.measure()``.
396 Notes
397 -----
398 This method can be used with plugins that have different signatures;
399 the only requirement is that ``measRecord`` be the first argument.
400 Subsequent positional arguments and keyword arguments are forwarded
401 directly to the plugin.
403 This method should be considered "protected": it is intended for use by
404 derived classes, not users.
405 """
406 beginOrder = kwds.pop("beginOrder", None)
407 endOrder = kwds.pop("endOrder", None)
408 for plugin in self.plugins.iterN():
409 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder:
410 continue
411 if endOrder is not None and plugin.getExecutionOrder() >= endOrder:
412 break
413 self.doMeasurementN(plugin, measCat, *args, **kwds)
415 def doMeasurementN(self, plugin, measCat, *args, **kwds):
416 """Call ``measureN`` on the specified plugin.
418 Exceptions are handled in a consistent way.
420 Parameters
421 ----------
422 plugin : subclass of `BasePlugin`
423 Plugin that will be executed.
424 measCat : `lsst.afw.table.SourceCatalog`
425 Catalog containing only the records for the source family to be
426 measured, and where outputs should be written.
427 *args
428 Positional arguments forwarded to ``plugin.measureN()``.
429 **kwds
430 Keyword arguments forwarded to ``plugin.measureN()``.
432 Notes
433 -----
434 This method can be used with plugins that have different signatures;
435 the only requirement is that the ``plugin`` and ``measCat`` be the
436 first two arguments. Subsequent positional arguments and keyword
437 arguments are forwarded directly to the plugin.
439 This method should be considered "protected": it is intended for use by
440 derived classes, not users.
441 """
442 try:
443 plugin.measureN(measCat, *args, **kwds)
444 except FATAL_EXCEPTIONS:
445 raise
447 except MeasurementError as error:
448 for measRecord in measCat:
449 self.log.getChild(plugin.name).debug(
450 "MeasurementError in %s.measureN on records %s-%s: %s",
451 plugin.name, measCat[0].getId(), measCat[-1].getId(), error)
452 plugin.fail(measRecord, error)
453 except Exception as error:
454 for measRecord in measCat:
455 plugin.fail(measRecord)
456 self.log.getChild(plugin.name).debug(
457 "Exception in %s.measureN on records %s-%s: %s",
458 plugin.name, measCat[0].getId(), measCat[-1].getId(), error)