Coverage for python / lsst / meas / base / forcedMeasurement.py: 25%
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22r"""Base classes for forced measurement plugins and the driver task for these.
24In forced measurement, a reference catalog is used to define restricted
25measurements (usually just fluxes) on an image. As the reference catalog may
26be deeper than the detection limit of the measurement image, we do not assume
27that we can use detection and deblend information from the measurement image.
28Instead, we assume this information is present in the reference catalog and
29can be "transformed" in some sense to the measurement frame. At the very
30least, this means that `~lsst.afw.detection.Footprint`\ s from the reference
31catalog should be transformed and installed as Footprints in the output
32measurement catalog. If we have a procedure that can transform "heavy"
33Footprints (ie, including pixel data), we can then proceed with measurement as
34usual, but using the reference catalog's ``id`` and ``parent`` fields to
35define deblend families. If this transformation does not preserve
36heavy Footprints (this is currently the case, at least for CCD forced
37photometry), then we will only be able to replace objects with noise one
38deblend family at a time, and hence measurements run in single-object mode may
39be contaminated by neighbors when run on objects with ``parent != 0``.
41Measurements are generally recorded in the coordinate system of the image
42being measured (and all slot-eligible fields must be), but non-slot fields may
43be recorded in other coordinate systems if necessary to avoid information loss
44(this should, of course, be indicated in the field documentation). Note that
45the reference catalog may be in a different coordinate system; it is the
46responsibility of plugins to transform the data they need themselves, using
47the reference WCS provided. However, for plugins that only require a position
48or shape, they may simply use output `~lsst.afw.table.SourceCatalog`\'s
49centroid or shape slots, which will generally be set to the transformed
50position of the reference object before any other plugins are run, and hence
51avoid using the reference catalog at all.
53Command-line driver tasks for forced measurement include
54`ForcedPhotCcdTask`, and `ForcedPhotCoaddTask`.
55"""
57import lsst.pex.config
58import lsst.pipe.base
59from lsst.utils.logging import PeriodicLogger
61from .pluginRegistry import PluginRegistry
62from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
63 BaseMeasurementConfig, BaseMeasurementTask)
65__all__ = ("ForcedPluginConfig", "ForcedPlugin",
66 "ForcedMeasurementConfig", "ForcedMeasurementTask")
69class ForcedPluginConfig(BaseMeasurementPluginConfig):
70 """Base class for configs of forced measurement plugins."""
72 pass
75class ForcedPlugin(BaseMeasurementPlugin):
76 """Base class for forced measurement plugins.
78 Parameters
79 ----------
80 config : `ForcedPlugin.ConfigClass`
81 Configuration for this plugin.
82 name : `str`
83 The string with which the plugin was registered.
84 schemaMapper : `lsst.afw.table.SchemaMapper`
85 A mapping from reference catalog fields to output catalog fields.
86 Output fields should be added to the output schema. While most plugins
87 will not need to map fields from the reference schema, if they do so,
88 those fields will be transferred before any plugins are run.
89 metadata : `lsst.daf.base.PropertySet`
90 Plugin metadata that will be attached to the output catalog.
91 logName : `str`, optional
92 Name to use when logging errors.
93 """
95 registry = PluginRegistry(ForcedPluginConfig)
96 """Subclasses of `ForcedPlugin` must be registered here (`PluginRegistry`).
97 """
99 ConfigClass = ForcedPluginConfig
101 def __init__(self, config, name, schemaMapper, metadata, logName=None):
102 BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
104 def measure(self, measRecord, exposure, refRecord, refWcs):
105 """Measure the properties of a source given an image and a reference.
107 Parameters
108 ----------
109 exposure : `lsst.afw.image.ExposureF`
110 The pixel data to be measured, together with the associated PSF,
111 WCS, etc. All other sources in the image should have been replaced
112 by noise according to deblender outputs.
113 measRecord : `lsst.afw.table.SourceRecord`
114 Record describing the object being measured. Previously-measured
115 quantities will be retrieved from here, and it will be updated
116 in-place with the outputs of this plugin.
117 refRecord : `lsst.afw.table.SimpleRecord`
118 Additional parameters to define the fit, as measured elsewhere.
119 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
120 The coordinate system for the reference catalog values. An
121 `~lsst.geom.Angle` may be passed, indicating that a local tangent
122 WCS should be created for each object using the given angle as a
123 pixel scale.
125 Notes
126 -----
127 In the normal mode of operation, the source centroid will be set to
128 the WCS-transformed position of the reference object, so plugins that
129 only require a reference position should not have to access the
130 reference object at all.
131 """
132 raise NotImplementedError()
134 def measureN(self, measCat, exposure, refCat, refWcs):
135 """Measure the properties of blended sources from image & reference.
137 This operates on all members of a blend family at once.
139 Parameters
140 ----------
141 exposure : `lsst.afw.image.ExposureF`
142 The pixel data to be measured, together with the associated PSF,
143 WCS, etc. Sources not in the blended hierarchy to be measured
144 should have been replaced with noise using deblender outputs.
145 measCat : `lsst.afw.table.SourceCatalog`
146 Catalog describing the objects (and only those objects) being
147 measured. Previously-measured quantities will be retrieved from
148 here, and it will be updated in-place with the outputs of this
149 plugin.
150 refCat : `lsst.afw.table.SimpleCatalog`
151 Additional parameters to define the fit, as measured elsewhere.
152 Ordered such that ``zip(measCat, refcat)`` may be used.
153 refWcs : `lsst.afw.geom.SkyWcs` or `lsst.afw.geom.Angle`
154 The coordinate system for the reference catalog values. An
155 `~lsst.geom.Angle` may be passed, indicating that a local tangent
156 WCS should be created for each object using the given angle as a
157 pixel scale.
159 Notes
160 -----
161 In the normal mode of operation, the source centroids will be set to
162 the WCS-transformed position of the reference object, so plugins that
163 only require a reference position should not have to access the
164 reference object at all.
165 """
166 raise NotImplementedError()
169class ForcedMeasurementConfig(BaseMeasurementConfig):
170 """Config class for forced measurement driver task.
171 """
173 plugins = ForcedPlugin.registry.makeField(
174 multi=True,
175 default=["base_PixelFlags",
176 "base_TransformedCentroid",
177 "base_SdssCentroid",
178 "base_TransformedShape",
179 "base_SdssShape",
180 "base_GaussianFlux",
181 "base_CircularApertureFlux",
182 "base_PsfFlux",
183 "base_LocalBackground",
184 ],
185 doc="Plugins to be run and their configuration"
186 )
187 algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins")
188 undeblended = ForcedPlugin.registry.makeField(
189 multi=True,
190 default=[],
191 doc="Plugins to run on undeblended image"
192 )
193 copyColumns = lsst.pex.config.DictField(
194 keytype=str, itemtype=str, doc="Mapping of reference columns to source columns",
195 default={"id": "objectId", "parent": "parentObjectId", "deblend_nChild": "deblend_nChild",
196 "coord_ra": "coord_ra", "coord_dec": "coord_dec"}
197 )
198 checkUnitsParseStrict = lsst.pex.config.Field(
199 doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
200 dtype=str,
201 default="raise",
202 )
204 def setDefaults(self):
205 self.slots.centroid = "base_TransformedCentroid"
206 self.slots.shape = "base_TransformedShape"
207 self.slots.apFlux = None
208 self.slots.modelFlux = None
209 self.slots.psfFlux = None
210 self.slots.gaussianFlux = None
211 self.slots.calibFlux = None
214class ForcedMeasurementTask(BaseMeasurementTask):
215 """Measure sources on an image, constrained by a reference catalog.
217 A subtask for measuring the properties of sources on a single image,
218 using an existing "reference" catalog to constrain some aspects of the
219 measurement.
221 Parameters
222 ----------
223 refSchema : `lsst.afw.table.Schema`
224 Schema of the reference catalog. Must match the catalog later passed
225 to 'ForcedMeasurementTask.generateMeasCat` and/or
226 `ForcedMeasurementTask.run`.
227 algMetadata : `lsst.daf.base.PropertyList` or `None`
228 Will be updated in place to to record information about each
229 algorithm. An empty `~lsst.daf.base.PropertyList` will be created if
230 `None`.
231 **kwds
232 Keyword arguments are passed to the supertask constructor.
234 Notes
235 -----
236 Note that while `SingleFrameMeasurementTask` is passed an initial
237 `~lsst.afw.table.Schema` that is appended to in order to create the output
238 `~lsst.afw.table.Schema`, `ForcedMeasurementTask` is initialized with the
239 `~lsst.afw.table.Schema` of the reference catalog, from which a new
240 `~lsst.afw.table.Schema` for the output catalog is created. Fields to be
241 copied directly from the reference `~lsst.afw.table.Schema` are added
242 before ``Plugin`` fields are added.
243 """
245 ConfigClass = ForcedMeasurementConfig
247 def __init__(self, refSchema, algMetadata=None, **kwds):
248 super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
249 self.mapper = lsst.afw.table.SchemaMapper(refSchema)
250 self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False)
251 self.config.slots.setupSchema(self.mapper.editOutputSchema())
252 for refName, targetName in self.config.copyColumns.items():
253 refItem = refSchema.find(refName)
254 self.mapper.addMapping(refItem.key, targetName)
255 self.config.slots.setupSchema(self.mapper.editOutputSchema())
256 self.initializePlugins(schemaMapper=self.mapper)
257 self.addInvalidPsfFlag(self.mapper.editOutputSchema())
258 self.schema = self.mapper.getOutputSchema()
259 self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
261 def run(
262 self,
263 measCat,
264 exposure,
265 refCat,
266 refWcs,
267 exposureId=None,
268 beginOrder=None,
269 endOrder=None,
270 ):
271 r"""Perform forced measurement.
273 Parameters
274 ----------
275 exposure : `lsst.afw.image.exposureF`
276 Image to be measured. Must have at least a `lsst.afw.geom.SkyWcs`
277 attached.
278 measCat : `lsst.afw.table.SourceCatalog`
279 Source catalog for measurement results; must be initialized with
280 empty records already corresponding to those in ``refCat`` (via
281 e.g. `generateMeasCat`).
282 refCat : `lsst.afw.table.SourceCatalog`
283 A sequence of `lsst.afw.table.SourceRecord` objects that provide
284 reference information for the measurement. These will be passed
285 to each plugin in addition to the output
286 `~lsst.afw.table.SourceRecord`.
287 refWcs : `lsst.afw.geom.SkyWcs`
288 Defines the X,Y coordinate system of ``refCat``.
289 exposureId : `int`, optional
290 Optional unique exposureId used to calculate random number
291 generator seed in the NoiseReplacer.
292 beginOrder : `int`, optional
293 Beginning execution order (inclusive). Algorithms with
294 ``executionOrder`` < ``beginOrder`` are not executed. `None` for no limit.
295 endOrder : `int`, optional
296 Ending execution order (exclusive). Algorithms with
297 ``executionOrder`` >= ``endOrder`` are not executed. `None` for no limit.
299 Notes
300 -----
301 Fills the initial empty `~lsst.afw.table.SourceCatalog` with forced
302 measurement results. Two steps must occur before `run` can be called:
304 - `generateMeasCat` must be called to create the output ``measCat``
305 argument.
306 - `~lsst.afw.detection.Footprint`\ s appropriate for the forced sources
307 must be attached to the ``measCat`` records. The
308 `attachTransformedFootprints` method can be used to do this, but
309 this degrades "heavy" (i.e., including pixel values)
310 `~lsst.afw.detection.Footprint`\s to regular
311 `~lsst.afw.detection.Footprint`\s, leading to non-deblended
312 measurement, so most callers should provide
313 `~lsst.afw.detection.Footprint`\s some other way. Typically, calling
314 code will have access to information that will allow them to provide
315 heavy footprints - for instance, `ForcedPhotCoaddTask` uses the
316 heavy footprints from deblending run in the same band just before
317 non-forced is run measurement in that band.
318 """
319 # Construct a footprints dict which looks like
320 # {ref.getId(): (ref.getParent(), source.getFootprint())}
321 # (i.e. getting the footprint from the transformed source footprint)
322 footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint())
323 for (ref, measRecord) in zip(refCat, measCat)}
325 self.log.info("Performing forced measurement on %d source%s", len(refCat),
326 "" if len(refCat) == 1 else "s")
328 # Wrap the task logger into a periodic logger.
329 periodicLog = PeriodicLogger(self.log)
331 # Initialize the noise replacer
332 noiseReplacer = self.initNoiseReplacer(exposure, measCat, footprints, exposureId)
334 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)):
335 # Insert source into noise replacer
336 noiseReplacer.insertSource(refRecord.getId())
337 self.callMeasure(measRecord, exposure, refRecord, refWcs,
338 beginOrder=beginOrder, endOrder=endOrder)
339 noiseReplacer.removeSource(refRecord.getId())
340 periodicLog.log("Forced measurement complete for %d sources out of %d",
341 recordIndex + 1, len(refCat))
343 # When done, restore the exposure to its original state
344 noiseReplacer.end()
346 # Undeblended plugins only fire if we're running everything
347 if endOrder is None:
348 for recordIndex, (measRecord, refRecord) in enumerate(zip(measCat, refCat)):
349 for plugin in self.undeblendedPlugins.iter():
350 self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
351 periodicLog.log("Undeblended forced measurement complete for %d sources out of %d",
352 recordIndex + 1, len(refCat))
354 def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
355 r"""Initialize an output catalog from the reference catalog.
357 Parameters
358 ----------
359 exposure : `lsst.afw.image.exposureF`
360 Image to be measured.
361 refCat : iterable of `lsst.afw.table.SourceRecord`
362 Catalog of reference sources.
363 refWcs : `lsst.afw.geom.SkyWcs`
364 Defines the X,Y coordinate system of ``refCat``.
365 This parameter is not currently used.
366 idFactory : `lsst.afw.table.IdFactory`, optional
367 Factory for creating IDs for sources.
369 Returns
370 -------
371 meascat : `lsst.afw.table.SourceCatalog`
372 Source catalog ready for measurement.
374 Notes
375 -----
376 This generates a new blank `~lsst.afw.table.SourceRecord` for each
377 record in ``refCat``. Note that this method does not attach any
378 `~lsst.afw.detection.Footprint`\ s. Doing so is up to the caller (who
379 may call `attachedTransformedFootprints` or define their own method -
380 see `run` for more information).
381 """
382 if idFactory is None:
383 idFactory = lsst.afw.table.IdFactory.makeSimple()
384 table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
385 measCat = lsst.afw.table.SourceCatalog(table)
386 table = measCat.table
387 table.setMetadata(self.algMetadata)
388 table.preallocate(len(refCat))
389 for ref in refCat:
390 newSource = measCat.addNew()
391 newSource.assign(ref, self.mapper)
392 return measCat
394 def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
395 r"""Attach Footprints to blank sources prior to measurement, by
396 transforming Footprints attached to the reference catalog.
398 Notes
399 -----
400 `~lsst.afw.detection.Footprint`\s for forced photometry must be in the
401 pixel coordinate system of the image being measured, while the actual
402 detections may start out in a different coordinate system. This
403 default implementation transforms the Footprints from the reference
404 catalog from the WCS to the exposure's WCS, which downgrades
405 ``HeavyFootprint``\s into regular `~lsst.afw.detection.Footprint`\s,
406 destroying deblend information.
408 See the documentation for `run` for information about the
409 relationships between `run`, `generateMeasCat`, and
410 `attachTransformedFootprints`.
411 """
412 exposureWcs = exposure.getWcs()
413 region = exposure.getBBox(lsst.afw.image.PARENT)
414 for srcRecord, refRecord in zip(sources, refCat):
415 srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))
417 def attachPsfShapeFootprints(self, sources, exposure, scaling=3):
418 """Attach Footprints to blank sources prior to measurement, by
419 creating elliptical Footprints from the PSF moments.
421 Parameters
422 ----------
423 sources : `lsst.afw.table.SourceCatalog`
424 Blank catalog (with all rows and columns, but values other than
425 ``coord_ra``, ``coord_dec`` unpopulated).
426 to which footprints should be attached.
427 exposure : `lsst.afw.image.Exposure`
428 Image object from which peak values and the PSF are obtained.
429 scaling : `int`, optional
430 Scaling factor to apply to the PSF second-moments ellipse in order
431 to determine the footprint boundary.
433 Notes
434 -----
435 This is a utility function for use by parent tasks; see
436 `attachTransformedFootprints` for more information.
437 """
438 psf = exposure.getPsf()
439 if psf is None:
440 raise RuntimeError("Cannot construct Footprints from PSF shape without a PSF.")
441 bbox = exposure.getBBox()
442 wcs = exposure.getWcs()
443 for record in sources:
444 localPoint = wcs.skyToPixel(record.getCoord())
445 localIntPoint = lsst.geom.Point2I(localPoint)
446 assert bbox.contains(localIntPoint), (
447 f"Center for record {record.getId()} is not in exposure; this should be guaranteed by "
448 "generateMeasCat."
449 )
450 ellipse = lsst.afw.geom.ellipses.Ellipse(psf.computeShape(localPoint), localPoint)
451 ellipse.getCore().scale(scaling)
452 spans = lsst.afw.geom.SpanSet.fromShape(ellipse)
453 footprint = lsst.afw.detection.Footprint(spans.clippedTo(bbox), bbox)
454 footprint.addPeak(localIntPoint.getX(), localIntPoint.getY(),
455 exposure.image._get(localIntPoint, lsst.afw.image.PARENT))
456 record.setFootprint(footprint)