Coverage for python/lsst/meas/base/sfm.py: 30%
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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/>.
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_NaiveCentroid",
141 "base_SdssShape",
142 "base_GaussianFlux",
143 "base_PsfFlux",
144 "base_CircularApertureFlux",
145 "base_SkyCoord",
146 "base_Variance",
147 "base_Blendedness",
148 "base_LocalBackground",
149 "base_CompensatedGaussianFlux"
150 ],
151 doc="Plugins to be run and their configuration"
152 )
153 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins") 153 ↛ exitline 153 didn't run the lambda on line 153
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)
201 # Check to see if blendedness is one of the plugins
202 if 'base_Blendedness' in self.plugins:
203 self.doBlendedness = True
204 self.blendPlugin = self.plugins['base_Blendedness']
205 else:
206 self.doBlendedness = False
208 @timeMethod
209 def run(self, measCat, exposure, noiseImage=None, exposureId=None, beginOrder=None, endOrder=None):
210 r"""Run single frame measurement over an exposure and source catalog.
212 Parameters
213 ----------
214 measCat : `lsst.afw.table.SourceCatalog`
215 Catalog to be filled with the results of measurement. Must contain
216 all the `lsst.afw.table.SourceRecord`\ s to be measured (with
217 `lsst.afw.detection.Footprint`\ s attached), and have a schema
218 that is a superset of ``self.schema``.
219 exposure : `lsst.afw.image.ExposureF`
220 Image containing the pixel data to be measured together with
221 associated PSF, WCS, etc.
222 noiseImage : `lsst.afw.image.ImageF`, optional
223 Can be used to specify the a predictable noise replacement field
224 for testing purposes.
225 exposureId : `int`, optional
226 Unique exposure identifier used to calculate the random number
227 generator seed during noise replacement.
228 beginOrder : `float`, optional
229 Start execution order (inclusive): measurements with
230 ``executionOrder < beginOrder`` are not executed. `None` for no
231 limit.
232 endOrder : `float`, optional
233 Final execution order (exclusive): measurements with
234 ``executionOrder >= endOrder`` are not executed. `None` for no
235 limit.
236 """
237 assert measCat.getSchema().contains(self.schema)
238 footprints = {measRecord.getId(): (measRecord.getParent(), measRecord.getFootprint())
239 for measRecord in measCat}
241 # noiseReplacer is used to fill the footprints with noise and save
242 # heavy footprints of the source pixels so that they can be restored
243 # one at a time for measurement. After the NoiseReplacer is
244 # constructed, all pixels in the exposure.getMaskedImage() which
245 # belong to objects in measCat will be replaced with noise
247 if self.config.doReplaceWithNoise:
248 noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure, footprints,
249 noiseImage=noiseImage, log=self.log, exposureId=exposureId)
250 algMetadata = measCat.getMetadata()
251 if algMetadata is not None:
252 algMetadata.addInt(self.NOISE_SEED_MULTIPLIER, self.config.noiseReplacer.noiseSeedMultiplier)
253 algMetadata.addString(self.NOISE_SOURCE, self.config.noiseReplacer.noiseSource)
254 algMetadata.addDouble(self.NOISE_OFFSET, self.config.noiseReplacer.noiseOffset)
255 if exposureId is not None:
256 algMetadata.addLong(self.NOISE_EXPOSURE_ID, exposureId)
257 else:
258 noiseReplacer = DummyNoiseReplacer()
260 self.runPlugins(noiseReplacer, measCat, exposure, beginOrder, endOrder)
262 def runPlugins(self, noiseReplacer, measCat, exposure, beginOrder=None, endOrder=None):
263 r"""Call the configured measument plugins on an image.
265 Parameters
266 ----------
267 noiseReplacer : `NoiseReplacer`
268 Used to fill sources not being measured with noise.
269 measCat : `lsst.afw.table.SourceCatalog`
270 Catalog to be filled with the results of measurement. Must contain
271 all the `lsst.afw.table.SourceRecord`\ s to be measured (with
272 `lsst.afw.detection.Footprint`\ s attached), and have a schema
273 that is a superset of ``self.schema``.
274 exposure : `lsst.afw.image.ExposureF`
275 Image containing the pixel data to be measured together with
276 associated PSF, WCS, etc.
277 beginOrder : `float`, optional
278 Start execution order (inclusive): measurements with
279 ``executionOrder < beginOrder`` are not executed. `None` for no
280 limit.
281 endOrder : `float`, optional
282 Final execution order (exclusive): measurements with
283 ``executionOrder >= endOrder`` are not executed. `None` for no
284 limit.
285 """
286 # First, create a catalog of all parentless sources. Loop through all
287 # the parent sources, first processing the children, then the parent.
288 measParentCat = measCat.getChildren(0)
290 nMeasCat = len(measCat)
291 nMeasParentCat = len(measParentCat)
292 self.log.info("Measuring %d source%s (%d parent%s, %d child%s) ",
293 nMeasCat, ("" if nMeasCat == 1 else "s"),
294 nMeasParentCat, ("" if nMeasParentCat == 1 else "s"),
295 nMeasCat - nMeasParentCat, ("" if nMeasCat - nMeasParentCat == 1 else "ren"))
297 # Wrap the task logger into a period logger
298 periodicLog = PeriodicLogger(self.log)
300 childrenIter = measCat.getChildren([measParentRecord.getId() for measParentRecord in measParentCat])
301 for parentIdx, (measParentRecord, measChildCat) in enumerate(zip(measParentCat, childrenIter)):
302 # first get all the children of this parent, insert footprint in
303 # turn, and measure
304 # TODO: skip this loop if there are no plugins configured for
305 # single-object mode
306 for measChildRecord in measChildCat:
307 noiseReplacer.insertSource(measChildRecord.getId())
308 self.callMeasure(measChildRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
310 if self.doBlendedness:
311 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measChildRecord)
313 noiseReplacer.removeSource(measChildRecord.getId())
315 # Then insert the parent footprint, and measure that
316 noiseReplacer.insertSource(measParentRecord.getId())
317 self.callMeasure(measParentRecord, exposure, beginOrder=beginOrder, endOrder=endOrder)
319 if self.doBlendedness:
320 self.blendPlugin.cpp.measureChildPixels(exposure.getMaskedImage(), measParentRecord)
322 # Finally, process both parent and child set through measureN
323 self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
324 beginOrder=beginOrder, endOrder=endOrder)
325 self.callMeasureN(measChildCat, exposure, beginOrder=beginOrder, endOrder=endOrder)
326 noiseReplacer.removeSource(measParentRecord.getId())
327 # Log a message if it has been a while since the last log.
328 periodicLog.log("Measurement complete for %d parents (and their children) out of %d",
329 parentIdx + 1, nMeasParentCat)
331 # When done, restore the exposure to its original state
332 noiseReplacer.end()
334 # Undeblended plugins only fire if we're running everything
335 if endOrder is None:
336 for sourceIndex, source in enumerate(measCat):
337 for plugin in self.undeblendedPlugins.iter():
338 self.doMeasurement(plugin, source, exposure)
339 # Log a message if it has been a while since the last log.
340 periodicLog.log("Undeblended measurement complete for %d sources out of %d",
341 sourceIndex + 1, nMeasCat)
343 # Now we loop over all of the sources one more time to compute the
344 # blendedness metrics
345 if self.doBlendedness:
346 for source in measCat:
347 self.blendPlugin.cpp.measureParentPixels(exposure.getMaskedImage(), source)
349 def measure(self, measCat, exposure):
350 """Backwards-compatibility alias for `run`.
351 """
352 self.run(measCat, exposure)