lsst.meas.base  13.0-26-g0f127ff+5
forcedMeasurement.py
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1 #!/usr/bin/env python
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23 """Base classes for forced measurement plugins and the driver task for these.
24 
25 In forced measurement, a reference catalog is used to define restricted measurements (usually just fluxes)
26 on an image. As the reference catalog may be deeper than the detection limit of the measurement image, we
27 do not assume that we can use detection and deblend information from the measurement image. Instead, we
28 assume this information is present in the reference catalog and can be "transformed" in some sense to
29 the measurement frame. At the very least, this means that Footprints from the reference catalog should
30 be transformed and installed as Footprints in the output measurement catalog. If we have a procedure that
31 can transform HeavyFootprints, we can then proceed with measurement as usual, but using the reference
32 catalog's id and parent fields to define deblend families. If this transformation does not preserve
33 HeavyFootprints (this is currently the case, at least for CCD forced photometry), then we will only
34 be able to replace objects with noise one deblend family at a time, and hence measurements run in
35 single-object mode may be contaminated by neighbors when run on objects with parent != 0.
36 
37 Measurements are generally recorded in the coordinate system of the image being measured (and all
38 slot-eligible fields must be), but non-slot fields may be recorded in other coordinate systems if necessary
39 to avoid information loss (this should, of course, be indicated in the field documentation). Note that
40 the reference catalog may be in a different coordinate system; it is the responsibility of plugins
41 to transform the data they need themselves, using the reference WCS provided. However, for plugins
42 that only require a position or shape, they may simply use output SourceCatalog's centroid or shape slots,
43 which will generally be set to the transformed position of the reference object before any other plugins are
44 run, and hence avoid using the reference catalog at all.
45 
46 Command-line driver tasks for forced measurement can be found in forcedPhotImage.py, including
47 ForcedPhotImageTask, ForcedPhotCcdTask, and ForcedPhotCoaddTask.
48 """
49 from builtins import zip
50 
51 import lsst.pex.config
52 import lsst.pipe.base
53 
54 from .pluginRegistry import PluginRegistry
55 from .baseMeasurement import (BaseMeasurementPluginConfig, BaseMeasurementPlugin,
56  BaseMeasurementConfig, BaseMeasurementTask)
57 from .noiseReplacer import NoiseReplacer, DummyNoiseReplacer
58 
59 __all__ = ("ForcedPluginConfig", "ForcedPlugin",
60  "ForcedMeasurementConfig", "ForcedMeasurementTask")
61 
62 
64  """Base class for configs of forced measurement plugins."""
65  pass
66 
67 
69 
70  # All subclasses of ForcedPlugin should be registered here
71  registry = PluginRegistry(ForcedPluginConfig)
72 
73  ConfigClass = ForcedPluginConfig
74 
75  def __init__(self, config, name, schemaMapper, metadata, logName=None):
76  """Initialize the measurement object.
77 
78  @param[in] config An instance of this class's ConfigClass.
79  @param[in] name The string the plugin was registered with.
80  @param[in,out] schemaMapper A SchemaMapper that maps reference catalog fields to output
81  catalog fields. Output fields should be added to the
82  output schema. While most plugins will not need to map
83  fields from the reference schema, if they do so, those fields
84  will be transferred before any plugins are run.
85  @param[in] metadata Plugin metadata that will be attached to the output catalog
86  """
87  BaseMeasurementPlugin.__init__(self, config, name, logName=logName)
88 
89  def measure(self, measRecord, exposure, refRecord, refWcs):
90  """Measure the properties of a source on a single image, given data from a
91  reference record.
92 
93  @param[in] exposure lsst.afw.image.ExposureF, containing the pixel data to
94  be measured and the associated Psf, Wcs, etc. All
95  other sources in the image will have been replaced by
96  noise according to deblender outputs.
97  @param[in,out] measRecord lsst.afw.table.SourceRecord to be filled with outputs,
98  and from which previously-measured quantities can be
99  retreived.
100  @param[in] refRecord lsst.afw.table.SimpleRecord that contains additional
101  parameters to define the fit, as measured elsewhere.
102  @param[in] refWcs The coordinate system for the reference catalog values.
103  An afw.geom.Angle may be passed, indicating that a
104  local tangent Wcs should be created for each object
105  using afw.image.makeLocalWcs and the given angle as
106  a pixel scale.
107 
108  In the normal mode of operation, the source centroid will be set to the
109  WCS-transformed position of the reference object, so plugins that only
110  require a reference position should not have to access the reference object
111  at all.
112  """
113  raise NotImplementedError()
114 
115  def measureN(self, measCat, exposure, refCat, refWcs):
116  """Measure the properties of a group of blended sources on a single image,
117  given data from a reference record.
118 
119  @param[in] exposure lsst.afw.image.ExposureF, containing the pixel data to
120  be measured and the associated Psf, Wcs, etc. Sources
121  not in the blended hierarchy to be measured will have
122  been replaced with noise using deblender outputs.
123  @param[in,out] measCat lsst.afw.table.SourceCatalog to be filled with outputs,
124  and from which previously-measured quantities can be
125  retrieved, containing only the sources that should be
126  measured together in this call.
127  @param[in] refCat lsst.afw.table.SimpleCatalog that contains additional
128  parameters to define the fit, as measured elsewhere.
129  Ordered such that zip(sources, references) may be used.
130  @param[in] refWcs The coordinate system for the reference catalog values.
131  An afw.geom.Angle may be passed, indicating that a
132  local tangent Wcs should be created for each object
133  using afw.image.makeLocalWcs and the given Angle as
134  a pixel scale.
135 
136  In the normal mode of operation, the source centroids will be set to the
137  WCS-transformed position of the reference object, so plugins that only
138  require a reference position should not have to access the reference object
139  at all.
140  """
141  raise NotImplementedError()
142 
143 
145  """Config class for forced measurement driver task."""
146 
147  plugins = ForcedPlugin.registry.makeField(
148  multi=True,
149  default=["base_PixelFlags",
150  "base_TransformedCentroid",
151  "base_TransformedShape",
152  "base_GaussianFlux",
153  "base_CircularApertureFlux",
154  "base_PsfFlux",
155  ],
156  doc="Plugins to be run and their configuration"
157  )
158  algorithms = property(lambda self: self.plugins, doc="backwards-compatibility alias for plugins")
159  undeblended = ForcedPlugin.registry.makeField(
160  multi=True,
161  default=[],
162  doc="Plugins to run on undeblended image"
163  )
164 
165  copyColumns = lsst.pex.config.DictField(
166  keytype=str, itemtype=str, doc="Mapping of reference columns to source columns",
167  default={"id": "objectId", "parent": "parentObjectId", "deblend_nChild": "deblend_nChild",
168  "coord_ra": "coord_ra", "coord_dec": "coord_dec"}
169  )
170 
171  checkUnitsParseStrict = lsst.pex.config.Field(
172  doc="Strictness of Astropy unit compatibility check, can be 'raise', 'warn' or 'silent'",
173  dtype=str,
174  default="raise",
175  )
176 
177  def setDefaults(self):
178  self.slots.centroid = "base_TransformedCentroid"
179  self.slots.shape = "base_TransformedShape"
180  self.slots.apFlux = None
181  self.slots.modelFlux = None
182  self.slots.psfFlux = None
183  self.slots.instFlux = None
184  self.slots.calibFlux = None
185 
186 
192 
193 
195  """!
196  \anchor ForcedMeasurementTask_
197 
198  \brief A subtask for measuring the properties of sources on a single
199  exposure, using an existing "reference" catalog to constrain some aspects
200  of the measurement.
201 
202  The task is configured with a list of "plugins": each plugin defines the values it
203  measures (i.e. the columns in a table it will fill) and conducts that measurement
204  on each detected source (see ForcedPlugin). The job of the
205  measurement task is to initialize the set of plugins (which includes setting up the
206  catalog schema) from their configuration, and then invoke each plugin on each
207  source.
208 
209  Most of the time, ForcedMeasurementTask will be used via one of the subclasses of
210  ForcedPhotImageTask, ForcedPhotCcdTask and ForcedPhotCoaddTask. These combine
211  this measurement subtask with a "references" subtask (see BaseReferencesTask and
212  CoaddSrcReferencesTask) to perform forced measurement using measurements performed on
213  another image as the references. There is generally little reason to use
214  ForcedMeasurementTask outside of one of these drivers, unless it is necessary to avoid
215  using the Butler for I/O.
216 
217  ForcedMeasurementTask has only three methods: __init__(), run(), and generateMeasCat().
218  For configuration options, see SingleFrameMeasurementConfig.
219  """
220 
221  ConfigClass = ForcedMeasurementConfig
222 
223  def __init__(self, refSchema, algMetadata=None, **kwds):
224  """!
225  Initialize the task. Set up the execution order of the plugins and initialize
226  the plugins, giving each plugin an opportunity to add its measurement fields to
227  the output schema and to record information in the task metadata.
228 
229  Note that while SingleFrameMeasurementTask is passed an initial Schema that is
230  appended to in order to create the output Schema, ForcedMeasurementTask is
231  initialized with the Schema of the reference catalog, from which a new Schema
232  for the output catalog is created. Fields to be copied directly from the
233  reference Schema are added before Plugin fields are added.
234 
235  @param[in] refSchema Schema of the reference catalog. Must match the catalog
236  later passed to generateMeasCat() and/or run().
237  @param[in,out] algMetadata lsst.daf.base.PropertyList used to record information about
238  each algorithm. An empty PropertyList will be created if None.
239  @param[in] **kwds Keyword arguments passed from lsst.pipe.base.Task.__init__
240  """
241  super(ForcedMeasurementTask, self).__init__(algMetadata=algMetadata, **kwds)
242  self.mapper = lsst.afw.table.SchemaMapper(refSchema)
243  self.mapper.addMinimalSchema(lsst.afw.table.SourceTable.makeMinimalSchema(), False)
244  self.config.slots.setupSchema(self.mapper.editOutputSchema())
245  for refName, targetName in self.config.copyColumns.items():
246  refItem = refSchema.find(refName)
247  self.mapper.addMapping(refItem.key, targetName)
248  self.config.slots.setupSchema(self.mapper.editOutputSchema())
249  self.initializePlugins(schemaMapper=self.mapper)
250  self.schema = self.mapper.getOutputSchema()
251  self.schema.checkUnits(parse_strict=self.config.checkUnitsParseStrict)
252 
253  def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None):
254  """!
255  Perform forced measurement.
256 
257  @param[in] exposure lsst.afw.image.ExposureF to be measured; must have at least a Wcs attached.
258  @param[in] measCat Source catalog for measurement results; must be initialized with empty
259  records already corresponding to those in refCat (via e.g. generateMeasCat).
260  @param[in] refCat A sequence of SourceRecord objects that provide reference information
261  for the measurement. These will be passed to each Plugin in addition
262  to the output SourceRecord.
263  @param[in] refWcs Wcs that defines the X,Y coordinate system of refCat
264  @param[in] exposureId optional unique exposureId used to calculate random number
265  generator seed in the NoiseReplacer.
266  @param[in] beginOrder beginning execution order (inclusive): measurements with
267  executionOrder < beginOrder are not executed. None for no limit.
268  @param[in] endOrder ending execution order (exclusive): measurements with
269  executionOrder >= endOrder are not executed. None for no limit.
270 
271  Fills the initial empty SourceCatalog with forced measurement results. Two steps must occur
272  before run() can be called:
273  - generateMeasCat() must be called to create the output measCat argument.
274  - Footprints appropriate for the forced sources must be attached to the measCat records. The
275  attachTransformedFootprints() method can be used to do this, but this degrades HeavyFootprints
276  to regular Footprints, leading to non-deblended measurement, so most callers should provide
277  Footprints some other way. Typically, calling code will have access to information that will
278  allow them to provide HeavyFootprints - for instance, ForcedPhotCoaddTask uses the HeavyFootprints
279  from deblending run in the same band just before non-forced is run measurement in that band.
280  """
281  # First check that the reference catalog does not contain any children for which
282  # any member of their parent chain is not within the list. This can occur at
283  # boundaries when the parent is outside and one of the children is within.
284  # Currently, the parent chain is always only one deep, but just in case, this
285  # code checks for any case where when the parent chain to a child's topmost
286  # parent is broken and raises an exception if it occurs.
287  #
288  # I.e. this code checks that this precondition is satisfied by whatever reference
289  # catalog provider is being paired with it.
290  refCatIdDict = {ref.getId(): ref.getParent() for ref in refCat}
291  for ref in refCat:
292  refId = ref.getId()
293  topId = refId
294  while(topId > 0):
295  if topId not in refCatIdDict:
296  raise RuntimeError("Reference catalog contains a child for which at least "
297  "one parent in its parent chain is not in the catalog.")
298  topId = refCatIdDict[topId]
299 
300  # Construct a footprints dict which looks like
301  # {ref.getId(): (ref.getParent(), source.getFootprint())}
302  # (i.e. getting the footprint from the transformed source footprint)
303  footprints = {ref.getId(): (ref.getParent(), measRecord.getFootprint())
304  for (ref, measRecord) in zip(refCat, measCat)}
305 
306  self.log.info("Performing forced measurement on %d sources" % (len(refCat),))
307 
308  if self.config.doReplaceWithNoise:
309  noiseReplacer = NoiseReplacer(self.config.noiseReplacer, exposure,
310  footprints, log=self.log, exposureId=exposureId)
311  algMetadata = measCat.getTable().getMetadata()
312  if algMetadata is not None:
313  algMetadata.addInt("NOISE_SEED_MULTIPLIER", self.config.noiseReplacer.noiseSeedMultiplier)
314  algMetadata.addString("NOISE_SOURCE", self.config.noiseReplacer.noiseSource)
315  algMetadata.addDouble("NOISE_OFFSET", self.config.noiseReplacer.noiseOffset)
316  if exposureId is not None:
317  algMetadata.addLong("NOISE_EXPOSURE_ID", exposureId)
318  else:
319  noiseReplacer = DummyNoiseReplacer()
320 
321  # Create parent cat which slices both the refCat and measCat (sources)
322  # first, get the reference and source records which have no parent
323  refParentCat, measParentCat = refCat.getChildren(0, measCat)
324  for parentIdx, (refParentRecord, measParentRecord) in enumerate(zip(refParentCat, measParentCat)):
325 
326  # first process the records which have the current parent as children
327  refChildCat, measChildCat = refCat.getChildren(refParentRecord.getId(), measCat)
328  # TODO: skip this loop if there are no plugins configured for single-object mode
329  for refChildRecord, measChildRecord in zip(refChildCat, measChildCat):
330  noiseReplacer.insertSource(refChildRecord.getId())
331  self.callMeasure(measChildRecord, exposure, refChildRecord, refWcs,
332  beginOrder=beginOrder, endOrder=endOrder)
333  noiseReplacer.removeSource(refChildRecord.getId())
334 
335  # then process the parent record
336  noiseReplacer.insertSource(refParentRecord.getId())
337  self.callMeasure(measParentRecord, exposure, refParentRecord, refWcs,
338  beginOrder=beginOrder, endOrder=endOrder)
339  self.callMeasureN(measParentCat[parentIdx:parentIdx+1], exposure,
340  refParentCat[parentIdx:parentIdx+1],
341  beginOrder=beginOrder, endOrder=endOrder)
342  # measure all the children simultaneously
343  self.callMeasureN(measChildCat, exposure, refChildCat,
344  beginOrder=beginOrder, endOrder=endOrder)
345  noiseReplacer.removeSource(refParentRecord.getId())
346  noiseReplacer.end()
347 
348  # Undeblended plugins only fire if we're running everything
349  if endOrder is None:
350  for measRecord, refRecord in zip(measCat, refCat):
351  for plugin in self.undeblendedPlugins.iter():
352  self.doMeasurement(plugin, measRecord, exposure, refRecord, refWcs)
353 
354  def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None):
355  """!Initialize an output SourceCatalog using information from the reference catalog.
356 
357  This generates a new blank SourceRecord for each record in refCat. Note that this
358  method does not attach any Footprints. Doing so is up to the caller (who may
359  call attachedTransformedFootprints or define their own method - see run() for more
360  information).
361 
362  @param[in] exposure Exposure to be measured
363  @param[in] refCat Sequence (not necessarily a SourceCatalog) of reference SourceRecords.
364  @param[in] refWcs Wcs that defines the X,Y coordinate system of refCat
365  @param[in] idFactory factory for creating IDs for sources
366 
367  @return Source catalog ready for measurement
368  """
369  if idFactory is None:
370  idFactory = lsst.afw.table.IdFactory.makeSimple()
371  table = lsst.afw.table.SourceTable.make(self.schema, idFactory)
372  measCat = lsst.afw.table.SourceCatalog(table)
373  table = measCat.table
374  table.setMetadata(self.algMetadata)
375  table.preallocate(len(refCat))
376  for ref in refCat:
377  newSource = measCat.addNew()
378  newSource.assign(ref, self.mapper)
379  return measCat
380 
381  def attachTransformedFootprints(self, sources, refCat, exposure, refWcs):
382  """!Default implementation for attaching Footprints to blank sources prior to measurement
383 
384  Footprints for forced photometry must be in the pixel coordinate system of the image being
385  measured, while the actual detections may start out in a different coordinate system.
386  This default implementation transforms the Footprints from the reference catalog from the
387  refWcs to the exposure's Wcs, which downgrades HeavyFootprints into regular Footprints,
388  destroying deblend information.
389 
390  Note that ForcedPhotImageTask delegates to this method in its own attachFootprints method.
391  attachFootprints can then be overridden by its subclasses to define how their Footprints
392  should be generated.
393 
394  See the documentation for run() for information about the relationships between run(),
395  generateMeasCat(), and attachTransformedFootprints().
396  """
397  exposureWcs = exposure.getWcs()
398  region = exposure.getBBox(lsst.afw.image.PARENT)
399  for srcRecord, refRecord in zip(sources, refCat):
400  srcRecord.setFootprint(refRecord.getFootprint().transform(refWcs, exposureWcs, region))
Base config class for all measurement plugins.
def callMeasure(self, measRecord, args, kwds)
Call the measure() method on all plugins, handling exceptions in a consistent way.
def __init__(self, refSchema, algMetadata=None, kwds)
Initialize the task.
A subtask for measuring the properties of sources on a single exposure, using an existing "reference"...
def callMeasureN(self, measCat, args, kwds)
Call the measureN() method on all plugins, handling exceptions in a consistent way.
def run(self, measCat, exposure, refCat, refWcs, exposureId=None, beginOrder=None, endOrder=None)
Perform forced measurement.
int iter
def attachTransformedFootprints(self, sources, refCat, exposure, refWcs)
Default implementation for attaching Footprints to blank sources prior to measurement.
def __init__(self, config, name, schemaMapper, metadata, logName=None)
def generateMeasCat(self, exposure, refCat, refWcs, idFactory=None)
Initialize an output SourceCatalog using information from the reference catalog.
def measure(self, measRecord, exposure, refRecord, refWcs)
Base class for plugin registries.
A do-nothing standin for NoiseReplacer, used when we want to disable NoiseReplacer.
def measureN(self, measCat, exposure, refCat, refWcs)
Class that handles replacing sources with noise during measurement.
Ultimate base class for all measurement tasks.
Base config class for all measurement driver tasks.
def doMeasurement(self, plugin, measRecord, args, kwds)
Call the measure() method on the nominated plugin, handling exceptions in a consistent way...