Coverage for python/lsst/meas/base/sfm.py: 29%
91 statements
« prev ^ index » next coverage.py v7.11.0, created at 2025-11-06 01:42 -0800
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/>.
22r"""Base classes for single-frame measurement plugins and the associated task.
24In single-frame measurement, we assume that detection and probably deblending
25have already been run on the same frame, so a `~lsst.afw.table.SourceCatalog`
26has already been created with `lsst.afw.detection.Footprint`\ s (which may be
27"heavy" — that is, include pixel data). Measurements are generally recorded in
28the coordinate system of the image being measured (and all slot-eligible
29fields must be), but non-slot fields may be recorded in other coordinate
30systems if necessary to avoid information loss (this should, of course, be
31indicated in the field documentation).
32"""
34from lsst.utils.logging import PeriodicLogger
35from lsst.utils.timer import timeMethod
37from .pluginRegistry import PluginRegistry
38from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
39 BaseMeasurementConfig, BaseMeasurementTask)
40from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer
42__all__ = ("SingleFramePluginConfig", "SingleFramePlugin",
43 "SingleFrameMeasurementConfig", "SingleFrameMeasurementTask")
46class SingleFramePluginConfig(BaseMeasurementPluginConfig):
47 """Base class for single-frame plugin configuration classes.
48 """
49 pass
52class SingleFramePlugin(BaseMeasurementPlugin):
53 """Base class for single-frame measurement plugin.
55 Parameters
56 ----------
57 config : `SingleFramePlugin.ConfigClass`
58 Configuration for this plugin.
59 name : `str`
60 The string with which the plugin was registered.
61 schema : `lsst.afw.table.Schema`
62 The schema for the source table . New fields are added here to
63 hold measurements produced by this plugin.
64 metadata : `lsst.daf.base.PropertySet`
65 Plugin metadata that will be attached to the output catalog
66 logName : `str`, optional
67 Name to use when logging errors.
69 Notes
70 -----
71 New plugins can be created in Python by inheriting directly from this
72 class and implementing the `measure`, `fail` (from `BasePlugin`), and
73 optionally `__init__` and `measureN` methods. Plugins can also be defined
74 in C++ via the `WrappedSingleFramePlugin` class.
75 """
77 registry = PluginRegistry(SingleFramePluginConfig)
78 """Registry of subclasses of `SingleFramePlugin` (`PluginRegistry`).
79 """
81 ConfigClass = SingleFramePluginConfig
83 def __init__(self, config, name, schema, metadata, logName=None, **kwds):
84 BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
86 def measure(self, measRecord, exposure):
87 """Measure the properties of a source on a single image.
89 The image may be from a single epoch, or it may be a coadd.
91 Parameters
92 ----------
93 measRecord : `lsst.afw.table.SourceRecord`
94 Record describing the object being measured. Previously-measured
95 quantities may be retrieved from here, and it will be updated
96 in-place tih the outputs of this plugin.
97 exposure : `lsst.afw.image.ExposureF`
98 The pixel data to be measured, together with the associated PSF,
99 WCS, etc. All other sources in the image should have been replaced
100 by noise according to deblender outputs.
101 """
102 raise NotImplementedError()
104 def measureN(self, measCat, exposure):
105 """Measure the properties of blended sources on a single image.
107 This operates on all members of a blend family at once. The image may
108 be from a single epoch, or it may be a coadd.
110 Parameters
111 ----------
112 measCat : `lsst.afw.table.SourceCatalog`
113 Catalog describing the objects (and only those objects) being
114 measured. Previously-measured quantities will be retrieved from
115 here, and it will be updated in-place with the outputs of this
116 plugin.
117 exposure : `lsst.afw.image.ExposureF`
118 The pixel data to be measured, together with the associated PSF,
119 WCS, etc. All other sources in the image should have been replaced
120 by noise according to deblender outputs.
122 Notes
123 -----
124 Derived classes that do not implement ``measureN`` should just inherit
125 this disabled version. Derived classes that do implement ``measureN``
126 should additionally add a bool doMeasureN config field to their config
127 class to signal that measureN-mode is available.
128 """
129 raise NotImplementedError()
132class SingleFrameMeasurementConfig(BaseMeasurementConfig):
133 """Config class for single frame measurement driver task.
134 """
136 plugins = SingleFramePlugin.registry.makeField(
137 multi=True,
138 default=["base_PixelFlags",
139 "base_SdssCentroid",
140 "base_SdssShape",
141 "base_GaussianFlux",
142 "base_PsfFlux",
143 "base_CircularApertureFlux",
144 "base_SkyCoord",
145 "base_Variance",
146 "base_Blendedness",
147 "base_LocalBackground",
148 "base_CompensatedTophatFlux",
149 "base_ClassificationSizeExtendedness",
150 ],
151 doc="Plugins to be run and their configuration"
152 )
153 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins")
154 undeblended = SingleFramePlugin.registry.makeField(
155 multi=True,
156 default=[],
157 doc="Plugins to run on undeblended image"
158 )
161class SingleFrameMeasurementTask(BaseMeasurementTask):
162 """A subtask for measuring the properties of sources on a single exposure.
164 Parameters
165 ----------
166 schema : `lsst.afw.table.Schema`
167 Schema of the output resultant catalog. Will be updated to provide
168 fields to accept the outputs of plugins which will be executed by this
169 task.
170 algMetadata : `lsst.daf.base.PropertyList`, optional
171 Used to record metadaa about algorithm execution. An empty
172 `lsst.daf.base.PropertyList` will be created if `None`.
173 **kwds
174 Keyword arguments forwarded to `BaseMeasurementTask`.
175 """
177 ConfigClass = SingleFrameMeasurementConfig
179 NOISE_SEED_MULTIPLIER = "NOISE_SEED_MULTIPLIER"
180 """Name by which the noise seed multiplier is recorded in metadata ('str').
181 """
183 NOISE_SOURCE = "NOISE_SOURCE"
184 """Name by which the noise source is recorded in metadata ('str').
185 """
187 NOISE_OFFSET = "NOISE_OFFSET"
188 """Name by which the noise offset is recorded in metadata ('str').
189 """
191 NOISE_EXPOSURE_ID = "NOISE_EXPOSURE_ID"
192 """Name by which the noise exposire ID is recorded in metadata ('str').
193 """
195 def __init__(self, schema, algMetadata=None, **kwds):
196 super(SingleFrameMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
197 self.schema = schema
198 self.config.slots.setupSchema(self.schema)
199 self.initializePlugins(schema=self.schema)
200 self.addInvalidPsfFlag(self.schema)
202 # Check to see if blendedness is one of the plugins
203 if 'base_Blendedness' in self.plugins:
204 self.doBlendedness = True
205 self.blendPlugin = self.plugins['base_Blendedness']
206 else:
207 self.doBlendedness = False
209 @timeMethod
210 def run(
211 self,
212 measCat,
213 exposure,
214 noiseImage=None,
215 exposureId=None,
216 beginOrder=None,
217 endOrder=None,
218 footprints=None,
219 ):
220 r"""Run single frame measurement over an exposure and source catalog.
222 Parameters
223 ----------
224 measCat : `lsst.afw.table.SourceCatalog`
225 Catalog to be filled with the results of measurement. Must contain
226 all the `lsst.afw.table.SourceRecord`\ s to be measured (with
227 `lsst.afw.detection.Footprint`\ s attached), and have a schema
228 that is a superset of ``self.schema``.
229 exposure : `lsst.afw.image.ExposureF`
230 Image containing the pixel data to be measured together with
231 associated PSF, WCS, etc.
232 noiseImage : `lsst.afw.image.ImageF`, optional
233 Can be used to specify the a predictable noise replacement field
234 for testing purposes.
235 exposureId : `int`, optional
236 Unique exposure identifier used to calculate the random number
237 generator seed during noise replacement.
238 beginOrder : `float`, optional
239 Start execution order (inclusive): measurements with
240 ``executionOrder < beginOrder`` are not executed. `None` for no
241 limit.
242 endOrder : `float`, optional
243 Final execution order (exclusive): measurements with
244 ``executionOrder >= endOrder`` are not executed. `None` for no
245 limit.
246 footprints : `dict` {`int`: `lsst.afw.detection.Footprint`}, optional
247 List of footprints to use for noise replacement. If this is not
248 supplied then the footprints from the measCat are used.
249 """
250 assert measCat.getSchema().contains(self.schema)
251 if footprints is None:
252 footprints = self.getFootprintsFromCatalog(measCat)
254 # noiseReplacer is used to fill the footprints with noise and save
255 # heavy footprints of the source pixels so that they can be restored
256 # one at a time for measurement. After the NoiseReplacer is
257 # constructed, all pixels in the exposure.getMaskedImage() which
258 # belong to objects in measCat will be replaced with noise
260 if self.config.doReplaceWithNoise:
261 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure, footprints,
262 noiseImage=noiseImage, log=self.log, exposureId=exposureId)
263 algMetadata = measCat.getMetadata()
264 if algMetadata is not None:
265 algMetadata.addInt(self.NOISE_SEED_MULTIPLIER, self.config.noiseReplacer.noiseSeedMultiplier)
266 algMetadata.addString(self.NOISE_SOURCE, self.config.noiseReplacer.noiseSource)
267 algMetadata.addDouble(self.NOISE_OFFSET, self.config.noiseReplacer.noiseOffset)
268 if exposureId is not None:
269 algMetadata.addLong(self.NOISE_EXPOSURE_ID, exposureId)
270 else:
271 noiseReplacer = DummyNoiseReplacer()
273 self.runPlugins(noiseReplacer, measCat, exposure, beginOrder, endOrder)
275 def runPlugins(self, noiseReplacer, measCat, exposure, beginOrder=None, endOrder=None):
276 r"""Call the configured measument plugins on an image.
278 Parameters
279 ----------
280 noiseReplacer : `NoiseReplacer`
281 Used to fill sources not being measured with noise.
282 measCat : `lsst.afw.table.SourceCatalog`
283 Catalog to be filled with the results of measurement. Must contain
284 all the `lsst.afw.table.SourceRecord`\ s to be measured (with
285 `lsst.afw.detection.Footprint`\ s attached), and have a schema
286 that is a superset of ``self.schema``.
287 exposure : `lsst.afw.image.ExposureF`
288 Image containing the pixel data to be measured together with
289 associated PSF, WCS, etc.
290 beginOrder : `float`, optional
291 Start execution order (inclusive): measurements with
292 ``executionOrder < beginOrder`` are not executed. `None` for no
293 limit.
294 endOrder : `float`, optional
295 Final execution order (exclusive): measurements with
296 ``executionOrder >= endOrder`` are not executed. `None` for no
297 limit.
298 """
299 # First, create a catalog of all parentless sources. Loop through all
300 # the parent sources, first processing the children, then the parent.
301 measParentCat = measCat.getChildren(0)
303 nMeasCat = len(measCat)
304 nMeasParentCat = len(measParentCat)
305 self.log.info("Measuring %d source%s (%d parent%s, %d child%s) ",
306 nMeasCat, ("" if nMeasCat == 1 else "s"),
307 nMeasParentCat, ("" if nMeasParentCat == 1 else "s"),
308 nMeasCat - nMeasParentCat, ("" if nMeasCat - nMeasParentCat == 1 else "ren"))
310 # Wrap the task logger into a period logger
311 periodicLog = PeriodicLogger(self.log)
313 childrenIter = measCat.getChildren([measParentRecord.getId() for measParentRecord in measParentCat])
314 for parentIdx, (measParentRecord, measChildCat) in enumerate(zip(measParentCat, childrenIter)):
315 # first get all the children of this parent, insert footprint in
316 # turn, and measure
317 # TODO: skip this loop if there are no plugins configured for
318 # single-object mode
319 for measChildRecord in measChildCat:
320 noiseReplacer.insertSource(measChildRecord.getId())
321 self.callMeasure(measChildRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
323 if self.doBlendedness:
324 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measChildRecord)
326 noiseReplacer.removeSource(measChildRecord.getId())
328 # Then insert the parent footprint, and measure that
329 noiseReplacer.insertSource(measParentRecord.getId())
330 self.callMeasure(measParentRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
332 if self.doBlendedness:
333 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measParentRecord)
335 # Finally, process both parent and child set through measureN
336 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
337 beginOrder=beginOrder, endOrder=endOrder)
338 self.callMeasureN(measChildCat, exposure, beginOrder=beginOrder, endOrder=endOrder)
339 noiseReplacer.removeSource(measParentRecord.getId())
340 # Log a message if it has been a while since the last log.
341 periodicLog.log("Measurement complete for %d parents (and their children) out of %d",
342 parentIdx + 1, nMeasParentCat)
344 # When done, restore the exposure to its original state
345 noiseReplacer.end()
347 # Undeblended plugins only fire if we're running everything
348 if endOrder is None:
349 for sourceIndex, source in enumerate(measCat):
350 for plugin in self.undeblendedPlugins.iter():
351 self.doMeasurement(plugin, source, exposure)
352 # Log a message if it has been a while since the last log.
353 periodicLog.log("Undeblended measurement complete for %d sources out of %d",
354 sourceIndex + 1, nMeasCat)
356 # Now we loop over all of the sources one more time to compute the
357 # blendedness metrics
358 if self.doBlendedness:
359 for source in measCat:
360 self.blendPlugin.cpp.measureParentPixels(exposure.getMaskedImage(), source)
362 def measure(self, measCat, exposure):
363 """Backwards-compatibility alias for `run`.
364 """
365 self.run(measCat, exposure)