Coverage for python/lsst/meas/base/baseMeasurement.py : 23%

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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 getPluginLogName(self, pluginName):
240 return self.log.getName() + '.' + pluginName
242 def initializePlugins(self, **kwds):
243 """Initialize plugins (and slots) according to configuration.
245 Parameters
246 ----------
247 **kwds
248 Keyword arguments forwarded directly to plugin constructors.
250 Notes
251 -----
252 Derived class constructors should call this method to fill the
253 `plugins` attribute and add corresponding output fields and slot
254 aliases to the output schema.
256 In addition to the attributes added by `BaseMeasurementTask.__init__`,
257 a ``schema``` attribute holding the output schema must be present
258 before this method is called.
260 Keyword arguments are forwarded directly to plugin constructors,
261 allowing derived classes to use plugins with different signatures.
262 """
263 # Make a place at the beginning for the centroid plugin to run first (because it's an OrderedDict,
264 # adding an empty element in advance means it will get run first when it's reassigned to the
265 # actual Plugin).
266 if self.config.slots.centroid is not None:
267 self.plugins[self.config.slots.centroid] = None
268 # Init the plugins, sorted by execution order. At the same time add to the schema
269 for executionOrder, name, config, PluginClass in sorted(self.config.plugins.apply()):
270 # Pass logName to the plugin if the plugin is marked as using it
271 # The task will use this name to log plugin errors, regardless.
272 if hasattr(PluginClass, "hasLogName") and PluginClass.hasLogName:
273 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata,
274 logName=self.getPluginLogName(name), **kwds)
275 else:
276 self.plugins[name] = PluginClass(config, name, metadata=self.algMetadata, **kwds)
278 # In rare circumstances (usually tests), the centroid slot not be coming from an algorithm,
279 # which means we'll have added something we don't want to the plugins map, and we should
280 # remove it.
281 if self.config.slots.centroid is not None and self.plugins[self.config.slots.centroid] is None:
282 del self.plugins[self.config.slots.centroid]
283 # Initialize the plugins to run on the undeblended image
284 for executionOrder, name, config, PluginClass in sorted(self.config.undeblended.apply()):
285 undeblendedName = self.config.undeblendedPrefix + name
286 self.undeblendedPlugins[name] = PluginClass(config, undeblendedName, metadata=self.algMetadata,
287 **kwds)
289 def callMeasure(self, measRecord, *args, **kwds):
290 """Call ``measure`` on all plugins and consistently handle exceptions.
292 Parameters
293 ----------
294 measRecord : `lsst.afw.table.SourceRecord`
295 The record corresponding to the object being measured. Will be
296 updated in-place with the results of measurement.
297 *args
298 Positional arguments forwarded to ``plugin.measure``
299 **kwds
300 Keyword arguments. Two are handled locally:
302 beginOrder : `int`
303 Beginning execution order (inclusive). Measurements with
304 ``executionOrder`` < ``beginOrder`` are not executed. `None`
305 for no limit.
307 endOrder : `int`
308 Ending execution order (exclusive). Measurements with
309 ``executionOrder`` >= ``endOrder`` are not executed. `None`
310 for no limit.
312 Others are forwarded to ``plugin.measure()``.
314 Notes
315 -----
316 This method can be used with plugins that have different signatures;
317 the only requirement is that ``measRecord`` be the first argument.
318 Subsequent positional arguments and keyword arguments are forwarded
319 directly to the plugin.
321 This method should be considered "protected": it is intended for use by
322 derived classes, not users.
323 """
324 beginOrder = kwds.pop("beginOrder", None)
325 endOrder = kwds.pop("endOrder", None)
326 for plugin in self.plugins.iter():
327 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder:
328 continue
329 if endOrder is not None and plugin.getExecutionOrder() >= endOrder:
330 break
331 self.doMeasurement(plugin, measRecord, *args, **kwds)
333 def doMeasurement(self, plugin, measRecord, *args, **kwds):
334 """Call ``measure`` on the specified plugin.
336 Exceptions are handled in a consistent way.
338 Parameters
339 ----------
340 plugin : subclass of `BasePlugin`
341 Plugin that will be executed.
342 measRecord : `lsst.afw.table.SourceRecord`
343 The record corresponding to the object being measured. Will be
344 updated in-place with the results of measurement.
345 *args
346 Positional arguments forwarded to ``plugin.measure()``.
347 **kwds
348 Keyword arguments forwarded to ``plugin.measure()``.
350 Notes
351 -----
352 This method can be used with plugins that have different signatures;
353 the only requirement is that ``plugin`` and ``measRecord`` be the first
354 two arguments. Subsequent positional arguments and keyword arguments
355 are forwarded directly to the plugin.
357 This method should be considered "protected": it is intended for use by
358 derived classes, not users.
359 """
360 try:
361 plugin.measure(measRecord, *args, **kwds)
362 except FATAL_EXCEPTIONS:
363 raise
364 except MeasurementError as error:
365 lsst.log.Log.getLogger(self.getPluginLogName(plugin.name)).debug(
366 "MeasurementError in %s.measure on record %s: %s"
367 % (plugin.name, measRecord.getId(), error))
368 plugin.fail(measRecord, error)
369 except Exception as error:
370 lsst.log.Log.getLogger(self.getPluginLogName(plugin.name)).debug(
371 "Exception in %s.measure on record %s: %s"
372 % (plugin.name, measRecord.getId(), error))
373 plugin.fail(measRecord)
375 def callMeasureN(self, measCat, *args, **kwds):
376 """Call ``measureN`` on all plugins and consistently handle exceptions.
378 Parameters
379 ----------
380 measCat : `lsst.afw.table.SourceCatalog`
381 Catalog containing only the records for the source family to be
382 measured, and where outputs should be written.
383 *args
384 Positional arguments forwarded to ``plugin.measure()``
385 **kwds
386 Keyword arguments. Two are handled locally:
388 beginOrder:
389 Beginning execution order (inclusive): Measurements with
390 ``executionOrder`` < ``beginOrder`` are not executed. `None`
391 for no limit.
392 endOrder:
393 Ending execution order (exclusive): measurements with
394 ``executionOrder`` >= ``endOrder`` are not executed. `None` for
395 no ``limit``.
397 Others are are forwarded to ``plugin.measure()``.
399 Notes
400 -----
401 This method can be used with plugins that have different signatures;
402 the only requirement is that ``measRecord`` be the first argument.
403 Subsequent positional arguments and keyword arguments are forwarded
404 directly to the plugin.
406 This method should be considered "protected": it is intended for use by
407 derived classes, not users.
408 """
409 beginOrder = kwds.pop("beginOrder", None)
410 endOrder = kwds.pop("endOrder", None)
411 for plugin in self.plugins.iterN():
412 if beginOrder is not None and plugin.getExecutionOrder() < beginOrder:
413 continue
414 if endOrder is not None and plugin.getExecutionOrder() >= endOrder:
415 break
416 self.doMeasurementN(plugin, measCat, *args, **kwds)
418 def doMeasurementN(self, plugin, measCat, *args, **kwds):
419 """Call ``measureN`` on the specified plugin.
421 Exceptions are handled in a consistent way.
423 Parameters
424 ----------
425 plugin : subclass of `BasePlugin`
426 Plugin that will be executed.
427 measCat : `lsst.afw.table.SourceCatalog`
428 Catalog containing only the records for the source family to be
429 measured, and where outputs should be written.
430 *args
431 Positional arguments forwarded to ``plugin.measureN()``.
432 **kwds
433 Keyword arguments forwarded to ``plugin.measureN()``.
435 Notes
436 -----
437 This method can be used with plugins that have different signatures;
438 the only requirement is that the ``plugin`` and ``measCat`` be the
439 first two arguments. Subsequent positional arguments and keyword
440 arguments are forwarded directly to the plugin.
442 This method should be considered "protected": it is intended for use by
443 derived classes, not users.
444 """
445 try:
446 plugin.measureN(measCat, *args, **kwds)
447 except FATAL_EXCEPTIONS:
448 raise
450 except MeasurementError as error:
451 for measRecord in measCat:
452 lsst.log.Log.getLogger(self.getPluginLogName(plugin.name)).debug(
453 "MeasurementError in %s.measureN on records %s-%s: %s"
454 % (plugin.name, measCat[0].getId(), measCat[-1].getId(), error))
455 plugin.fail(measRecord, error)
456 except Exception as error:
457 for measRecord in measCat:
458 plugin.fail(measRecord)
459 lsst.log.Log.getLogger(self.getPluginLogName(plugin.name)).debug(
460 "Exception in %s.measureN on records %s-%s: %s"
461 % (plugin.name, measCat[0].getId(), measCat[-1].getId(), error))