LSST Applications  21.0.0+04719a4bac,21.0.0-1-ga51b5d4+f5e6047307,21.0.0-11-g2b59f77+a9c1acf22d,21.0.0-11-ga42c5b2+86977b0b17,21.0.0-12-gf4ce030+76814010d2,21.0.0-13-g1721dae+760e7a6536,21.0.0-13-g3a573fe+768d78a30a,21.0.0-15-g5a7caf0+f21cbc5713,21.0.0-16-g0fb55c1+b60e2d390c,21.0.0-19-g4cded4ca+71a93a33c0,21.0.0-2-g103fe59+bb20972958,21.0.0-2-g45278ab+04719a4bac,21.0.0-2-g5242d73+3ad5d60fb1,21.0.0-2-g7f82c8f+8babb168e8,21.0.0-2-g8f08a60+06509c8b61,21.0.0-2-g8faa9b5+616205b9df,21.0.0-2-ga326454+8babb168e8,21.0.0-2-gde069b7+5e4aea9c2f,21.0.0-2-gecfae73+1d3a86e577,21.0.0-2-gfc62afb+3ad5d60fb1,21.0.0-25-g1d57be3cd+e73869a214,21.0.0-3-g357aad2+ed88757d29,21.0.0-3-g4a4ce7f+3ad5d60fb1,21.0.0-3-g4be5c26+3ad5d60fb1,21.0.0-3-g65f322c+e0b24896a3,21.0.0-3-g7d9da8d+616205b9df,21.0.0-3-ge02ed75+a9c1acf22d,21.0.0-4-g591bb35+a9c1acf22d,21.0.0-4-g65b4814+b60e2d390c,21.0.0-4-gccdca77+0de219a2bc,21.0.0-4-ge8a399c+6c55c39e83,21.0.0-5-gd00fb1e+05fce91b99,21.0.0-6-gc675373+3ad5d60fb1,21.0.0-64-g1122c245+4fb2b8f86e,21.0.0-7-g04766d7+cd19d05db2,21.0.0-7-gdf92d54+04719a4bac,21.0.0-8-g5674e7b+d1bd76f71f,master-gac4afde19b+a9c1acf22d,w.2021.13
LSST Data Management Base Package
baseMeasurement.py
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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 #
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20 # along with this program. If not, see <https://www.gnu.org/licenses/>.
21 
22 """Base measurement task, which subclassed by the single frame and forced
23 measurement tasks.
24 """
25 
26 import lsst.pipe.base
27 import lsst.pex.config
28 
29 from .pluginRegistry import PluginMap
30 from .exceptions import FatalAlgorithmError, MeasurementError
31 from .pluginsBase import BasePluginConfig, BasePlugin
32 from .noiseReplacer import NoiseReplacerConfig
33 
34 __all__ = ("BaseMeasurementPluginConfig", "BaseMeasurementPlugin",
35  "BaseMeasurementConfig", "BaseMeasurementTask")
36 
37 # Exceptions that the measurement tasks should always propagate up to their callers
38 FATAL_EXCEPTIONS = (MemoryError, FatalAlgorithmError)
39 
40 
42  """Base config class for all measurement plugins.
43 
44  Notes
45  -----
46  Most derived classes will want to override `setDefaults` in order to
47  customize the default `executionOrder`.
48 
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  """
53 
54  doMeasure = lsst.pex.config.Field(dtype=bool, default=True,
55  doc="whether to run this plugin in single-object mode")
56 
57  doMeasureN = False # replace this class attribute with a Field if measureN-capable
58 
59 
61  """Base class for all measurement plugins.
62 
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  """
69 
70  pass
71 
72 
74  """Assign named plugins to measurement slots.
75 
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.
80 
81  Notes
82  -----
83  The default algorithm for each slot must be registered, even if the default
84  is not used.
85  """
86 
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")
104 
105  def setupSchema(self, schema):
106  """Set up a slots in a schema following configuration directives.
107 
108  Parameters
109  ----------
110  schema : `lsst.afw.table.Schema`
111  The schema in which slots will be set up.
112 
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.centroidcentroid is not None:
120  aliases.set("slot_Centroid", self.centroidcentroid)
121  if self.shapeshape is not None:
122  aliases.set("slot_Shape", self.shapeshape)
123  if self.psfShapepsfShape is not None:
124  aliases.set("slot_PsfShape", self.psfShapepsfShape)
125  if self.apFluxapFlux is not None:
126  aliases.set("slot_ApFlux", self.apFluxapFlux)
127  if self.modelFluxmodelFlux is not None:
128  aliases.set("slot_ModelFlux", self.modelFluxmodelFlux)
129  if self.psfFluxpsfFlux is not None:
130  aliases.set("slot_PsfFlux", self.psfFluxpsfFlux)
131  if self.gaussianFluxgaussianFlux is not None:
132  aliases.set("slot_GaussianFlux", self.gaussianFluxgaussianFlux)
133  if self.calibFluxcalibFlux is not None:
134  aliases.set("slot_CalibFlux", self.calibFluxcalibFlux)
135 
136 
138  """Base configuration for all measurement driver tasks.
139 
140  Examples
141  --------
142  Subclasses should define the 'plugins' and 'undeblended' registries, e.g.
143 
144  .. code-block:: py
145 
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  )
156 
157  where ``PluginBaseClass`` is the appropriate base class of the plugin
158  (e.g., `SingleFramePlugin` or `ForcedPlugin`).
159  """
160 
162  dtype=SourceSlotConfig,
163  doc="Mapping from algorithms to special aliases in Source."
164  )
165 
166  doReplaceWithNoise = lsst.pex.config.Field(
167  dtype=bool, default=True, optional=False,
168  doc='When measuring, replace other detected footprints with noise?')
169 
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  )
178 
179  def validate(self):
180  lsst.pex.config.Config.validate(self)
181  if self.slotsslots.centroid is not None and self.slotsslots.centroid not in self.plugins.names:
182  raise ValueError("source centroid slot algorithm is not being run.")
183  if self.slotsslots.shape is not None and self.slotsslots.shape not in self.plugins.names:
184  raise ValueError("source shape slot algorithm '%s' is not being run." % self.slotsslots.shape)
185  for slot in (self.slotsslots.psfFlux, self.slotsslots.apFlux, self.slotsslots.modelFlux,
186  self.slotsslots.gaussianFlux, self.slotsslots.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)
193 
194 
196  """Ultimate base class for all measurement tasks.
197 
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__`.
206 
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  """
213 
214  ConfigClass = BaseMeasurementConfig
215  _DefaultName = "measurement"
216 
217  plugins = None
218  """Plugins to be invoked (`PluginMap`).
219 
220  Initially empty, this will be populated as plugins are initialized. It
221  should be considered read-only.
222  """
223 
224  algMetadata = None
225  """Metadata about active plugins (`lsst.daf.base.PropertyList`).
226 
227  Contains additional information about active plugins to be saved with
228  the output catalog. Will be filled by subclasses.
229  """
230 
231  def __init__(self, algMetadata=None, **kwds):
232  super(BaseMeasurementTask, self).__init__(**kwds)
233  self.pluginsplugins = PluginMap()
234  self.undeblendedPluginsundeblendedPlugins = PluginMap()
235  if algMetadata is None:
236  algMetadata = lsst.daf.base.PropertyList()
237  self.algMetadataalgMetadata = algMetadata
238 
239  def getPluginLogName(self, pluginName):
240  return self.loglog.getName() + '.' + pluginName
241 
242  def initializePlugins(self, **kwds):
243  """Initialize plugins (and slots) according to configuration.
244 
245  Parameters
246  ----------
247  **kwds
248  Keyword arguments forwarded directly to plugin constructors.
249 
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.
255 
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.
259 
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.configconfig.slots.centroid is not None:
267  self.pluginsplugins[self.configconfig.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.configconfig.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.pluginsplugins[name] = PluginClass(config, name, metadata=self.algMetadataalgMetadata,
274  logName=self.getPluginLogNamegetPluginLogName(name), **kwds)
275  else:
276  self.pluginsplugins[name] = PluginClass(config, name, metadata=self.algMetadataalgMetadata, **kwds)
277 
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.configconfig.slots.centroid is not None and self.pluginsplugins[self.configconfig.slots.centroid] is None:
282  del self.pluginsplugins[self.configconfig.slots.centroid]
283  # Initialize the plugins to run on the undeblended image
284  for executionOrder, name, config, PluginClass in sorted(self.configconfig.undeblended.apply()):
285  undeblendedName = self.configconfig.undeblendedPrefix + name
286  self.undeblendedPluginsundeblendedPlugins[name] = PluginClass(config, undeblendedName, metadata=self.algMetadataalgMetadata,
287  **kwds)
288 
289  def callMeasure(self, measRecord, *args, **kwds):
290  """Call ``measure`` on all plugins and consistently handle exceptions.
291 
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:
301 
302  beginOrder : `int`
303  Beginning execution order (inclusive). Measurements with
304  ``executionOrder`` < ``beginOrder`` are not executed. `None`
305  for no limit.
306 
307  endOrder : `int`
308  Ending execution order (exclusive). Measurements with
309  ``executionOrder`` >= ``endOrder`` are not executed. `None`
310  for no limit.
311 
312  Others are forwarded to ``plugin.measure()``.
313 
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.
320 
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.pluginsplugins.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.doMeasurementdoMeasurement(plugin, measRecord, *args, **kwds)
332 
333  def doMeasurement(self, plugin, measRecord, *args, **kwds):
334  """Call ``measure`` on the specified plugin.
335 
336  Exceptions are handled in a consistent way.
337 
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()``.
349 
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.
356 
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.getPluginLogNamegetPluginLogName(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.getPluginLogNamegetPluginLogName(plugin.name)).debug(
371  "Exception in %s.measure on record %s: %s"
372  % (plugin.name, measRecord.getId(), error))
373  plugin.fail(measRecord)
374 
375  def callMeasureN(self, measCat, *args, **kwds):
376  """Call ``measureN`` on all plugins and consistently handle exceptions.
377 
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:
387 
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``.
396 
397  Others are are forwarded to ``plugin.measure()``.
398 
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.
405 
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.pluginsplugins.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.doMeasurementNdoMeasurementN(plugin, measCat, *args, **kwds)
417 
418  def doMeasurementN(self, plugin, measCat, *args, **kwds):
419  """Call ``measureN`` on the specified plugin.
420 
421  Exceptions are handled in a consistent way.
422 
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()``.
434 
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.
441 
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
449 
450  except MeasurementError as error:
451  for measRecord in measCat:
452  lsst.log.Log.getLogger(self.getPluginLogNamegetPluginLogName(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.getPluginLogNamegetPluginLogName(plugin.name)).debug(
460  "Exception in %s.measureN on records %s-%s: %s"
461  % (plugin.name, measCat[0].getId(), measCat[-1].getId(), error))
Class for storing ordered metadata with comments.
Definition: PropertyList.h:68
static Log getLogger(Log const &logger)
Definition: Log.h:760
def doMeasurement(self, plugin, measRecord, *args, **kwds)
def doMeasurementN(self, plugin, measCat, *args, **kwds)
def callMeasure(self, measRecord, *args, **kwds)
def __init__(self, algMetadata=None, **kwds)
def callMeasureN(self, measCat, *args, **kwds)
def getName(self)
Definition: task.py:274