LSSTApplications  17.0+11,17.0+34,17.0+56,17.0+57,17.0+59,17.0+7,17.0-1-g377950a+33,17.0.1-1-g114240f+2,17.0.1-1-g4d4fbc4+28,17.0.1-1-g55520dc+49,17.0.1-1-g5f4ed7e+52,17.0.1-1-g6dd7d69+17,17.0.1-1-g8de6c91+11,17.0.1-1-gb9095d2+7,17.0.1-1-ge9fec5e+5,17.0.1-1-gf4e0155+55,17.0.1-1-gfc65f5f+50,17.0.1-1-gfc6fb1f+20,17.0.1-10-g87f9f3f+1,17.0.1-11-ge9de802+16,17.0.1-16-ga14f7d5c+4,17.0.1-17-gc79d625+1,17.0.1-17-gdae4c4a+8,17.0.1-2-g26618f5+29,17.0.1-2-g54f2ebc+9,17.0.1-2-gf403422+1,17.0.1-20-g2ca2f74+6,17.0.1-23-gf3eadeb7+1,17.0.1-3-g7e86b59+39,17.0.1-3-gb5ca14a,17.0.1-3-gd08d533+40,17.0.1-30-g596af8797,17.0.1-4-g59d126d+4,17.0.1-4-gc69c472+5,17.0.1-6-g5afd9b9+4,17.0.1-7-g35889ee+1,17.0.1-7-gc7c8782+18,17.0.1-9-gc4bbfb2+3,w.2019.22
LSSTDataManagementBasePackage
references.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 #
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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
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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 """
23 Subtasks for creating the reference catalogs used in forced measurement.
24 """
25 
26 import lsst.geom
27 import lsst.pex.config
28 import lsst.pipe.base
29 
30 __all__ = ("BaseReferencesTask", "CoaddSrcReferencesTask")
31 
32 
34  """Default configuration for reference source selection.
35  """
36 
37  removePatchOverlaps = lsst.pex.config.Field(
38  doc="Only include reference sources for each patch that lie within the patch's inner bbox",
39  dtype=bool,
40  default=True
41  )
43  doc="Bandpass for reference sources; None indicates chi-squared detections.",
44  dtype=str,
45  optional=True
46  )
47 
48 
50  """Base class for forced photometry subtask that fetches reference sources.
51 
52  Parameters
53  ----------
54  schema : `lsst.afw.table.Schema`, optional
55  The schema of the reference catalog.
56  butler : `lsst.daf.persistence.butler.Butler`, optional
57  A butler that will allow the task to load its schema from disk.
58 
59  Notes
60  -----
61  At least one of the ``schema`` and ``butler`` arguments must be present;
62  if both are, ``schema`` takes precedence.
63 
64  ``BaseReferencesTask`` defines the required API for the references task,
65  which consists of:
66 
67  - ``getSchema(butler)``
68  - ``fetchInPatches(butler, tract, filter, patchList)``
69  - ``fetchInBox(self, butler, tract, filter, bbox, wcs)``
70  - the ``removePatchOverlaps`` config option
71 
72  It also provides the ``subset`` method, which may be of use to derived
73  classes when reimplementing ``fetchInBox``.
74  """
75 
76  ConfigClass = BaseReferencesConfig
77  """Configuration class associated with this task (`lsst.pex.config.Config`).
78  """
79 
80  def __init__(self, butler=None, schema=None, **kwargs):
81  lsst.pipe.base.Task.__init__(self, **kwargs)
82 
83  def getSchema(self, butler):
84  """Return the schema for the reference sources.
85 
86  Parameters
87  ----------
88  butler : `lsst.daf.persistence.butler.Butler`
89  Data butler from which the schema will be fetched.
90 
91  Notes
92  -----
93  Must be available even before any data has been processed.
94  """
95  raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")
96 
97  def getWcs(self, dataRef):
98  """Return the WCS for reference sources.
99 
100  Parameters
101  ----------
102  dataRef : `lsst.daf.persistence.ButlerDataRef`
103  The data reference from which the WCS will be fetched. This must
104  include the tract in its dataId.
105  """
106  raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")
107 
108  def fetchInBox(self, dataRef, bbox, wcs):
109  """Return reference sources within a given bounding box.
110 
111  Reference sources are selected if they overlap a region defined by a
112  pixel-coordinate bounding box and corresponding WCS.
113 
114  Parameters
115  ----------
116  dataRef : `lsst.daf.persistence.ButlerDataRef`
117  Butler data reference. The implied data ID must contain the
118  ``tract`` key.
119  bbox : `lsst.afw.geom.Box2I` or `lsst.afw.geom.Box2D`
120  Defines the selection region in pixel coordinates.
121  wcs : `lsst.afw.image.SkyWcs`
122  Maps ``bbox`` to sky coordinates.
123 
124  Returns
125  -------
126  sources : iterable of `~lsst.afw.table.SourceRecord`
127  Reference sources. May be any Python iterable, including a lazy
128  iterator.
129 
130  Notes
131  -----
132  The returned set of sources should be complete and close to minimal.
133  """
134  raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")
135 
136  def fetchInPatches(self, dataRef, patchList):
137  """Return reference sources within one or more patches.
138 
139  Parameters
140  ----------
141  dataRef : `lsst.daf.persistence.ButlerDataRef`
142  Butler data reference. The implied data ID must contain the
143  ``tract`` key.
144  patchList : `list` of `lsst.skymap.PatchInfo`
145  Patches for which to fetch reference sources.
146 
147  Returns
148  -------
149  sources : iterable of `~lsst.afw.table.SourceRecord`
150  Reference sources. May be any Python iterable, including a lazy
151  iterator.
152 
153  Notes
154  -----
155  The returned set of sources should be complete and close to minimal.
156 
157  If ``config.removePatchOverlaps`` is `True`, only sources within each
158  patch's "inner" bounding box should be returned.
159  """
160  raise NotImplementedError("BaseReferencesTask is pure abstract, and cannot be used directly.")
161 
162  def subset(self, sources, bbox, wcs):
163  """Filter a list of sources to only those within the bounding box.
164 
165  Parameters
166  ----------
167  sources : iterable of `~lsst.afw.table.SourceRecord`
168  Reference sources. May be any Python iterable, including a lazy
169  iterator.
170  bbox : `lsst.afw.geom.Box2I` or `lsst.afw.geom.Box2D`
171  Defines the selection region.
172  wcs : `lsst.afw.image.SkyWcs`
173  Maps ``bbox`` to sky coordinates.
174 
175  Returns
176  -------
177  sources : iterable of `~lsst.afw.table.SourceRecord`
178  Filtered sources. May be any Python iterable, including a lazy
179  iterator.
180 
181  Notes
182  -----
183  Instead of filtering sources directly via their positions, we filter
184  based on the positions of parent objects, then include or discard all
185  children based on their parent's status. This is necessary to support
186  replacement with noise in measurement, which requires all child
187  sources have their parent present.
188 
189  This is not a part of the required `BaseReferencesTask` interface;
190  it's a convenience function used in implementing `fetchInBox` that may
191  be of use to subclasses.
192  """
193  boxD = lsst.geom.Box2D(bbox)
194  # We're passed an arbitrary iterable, but we need a catalog so we can
195  # iterate over parents and then children.
196  catalog = lsst.afw.table.SourceCatalog(self.schema)
197  catalog.extend(sources)
198  # catalog must be sorted by parent ID for lsst.afw.table.getChildren
199  # to work
201  # Iterate over objects that have no parent.
202  parentSources = catalog.getChildren(0)
203  skyCoordList = [source.getCoord() for source in parentSources]
204  pixelPosList = wcs.skyToPixel(skyCoordList)
205  for parent, pixel in zip(parentSources, pixelPosList):
206  if boxD.contains(pixel):
207  yield parent
208  for child in catalog.getChildren(parent.getId()):
209  yield child
210 
211 
212 class CoaddSrcReferencesConfig(BaseReferencesTask.ConfigClass):
213  """Default configuration for coadd reference source selection.
214  """
215 
217  doc="Coadd name: typically one of deep or goodSeeing.",
218  dtype=str,
219  default="deep",
220  )
221  skipMissing = lsst.pex.config.Field(
222  doc="Silently skip patches where the reference catalog does not exist.",
223  dtype=bool,
224  default=False
225  )
226 
227  def validate(self):
228  if (self.coaddName == "chiSquared") != (self.filter is None):
230  field=CoaddSrcReferencesConfig.coaddName,
231  config=self,
232  msg="filter may be None if and only if coaddName is chiSquared"
233  )
234 
235 
237  """Select reference sources by loading the “coadd source” dataset directly.
238 
239  The name of the dataset to read is generated by appending the
240  `datasetSuffix` attribute to the string ``Coadd_``. The dataset is then
241  read directly from disk using the Butler.
242 
243  Parameters
244  ----------
245  schema : `lsst.afw.table.Schema`, optional
246  The schema of the detection catalogs used as input to this one.
247  butler : `lsst.daf.persistence.butler.Butler`, optional
248  A Butler used to read the input schema from disk. Required if
249  ``schema`` is `None`.
250 
251  Notes
252  -----
253  The task will set its own ``self.schema`` attribute to the schema of the
254  output merged catalog.
255  """
256 
257  ConfigClass = CoaddSrcReferencesConfig
258  """Configuration class associated with this task (`lsst.pex.config.Config`).
259  """
260 
261  datasetSuffix = "src"
262  """Suffix to append to ``Coadd_`` to generate the dataset name (`str`).
263  """
264 
265  def __init__(self, butler=None, schema=None, **kwargs):
266  BaseReferencesTask.__init__(self, butler=butler, schema=schema, **kwargs)
267  if schema is None:
268  assert butler is not None, "No butler nor schema provided"
269  schema = butler.get("{}Coadd_{}_schema".format(self.config.coaddName, self.datasetSuffix),
270  immediate=True).getSchema()
271  self.schema = schema
272 
273  def getWcs(self, dataRef):
274  """Return the WCS for reference sources.
275 
276  Parameters
277  ----------
278  dataRef : `lsst.daf.persistence.ButlerDataRef`
279  Butler data reference. Must includ the trac in its dataId.
280  """
281  skyMap = dataRef.get(self.config.coaddName + "Coadd_skyMap", immediate=True)
282  return skyMap[dataRef.dataId["tract"]].getWcs()
283 
284  def fetchInPatches(self, dataRef, patchList):
285  """Fetch the source catalog using the Butler.
286 
287  Parameters
288  ----------
289  dataRef : `lsst.daf.persistence.ButlerDataRef`
290  Butler data reference. The implied data ID must contain the
291  ``tract`` key.
292  patchList : `list` of `lsst.skymap.PatchInfo`
293  Patches for which to fetch reference sources.
294 
295  Returns
296  -------
297  sources : iterable of `~lsst.afw.table.SourceRecord`
298  Reference sources. May be any Python iterable, including a lazy
299  iterator.
300 
301  Notes
302  -----
303  An implementation of `BaseReferencesTask.fetchInPatches` that loads
304  ``Coadd_`` + `datasetSuffix` catalogs using the butler.
305  """
306  dataset = "{}Coadd_{}".format(self.config.coaddName, self.datasetSuffix)
307  tract = dataRef.dataId["tract"]
308  butler = dataRef.butlerSubset.butler
309  for patch in patchList:
310  dataId = {'tract': tract, 'patch': "%d,%d" % patch.getIndex()}
311  if self.config.filter is not None:
312  dataId['filter'] = self.config.filter
313 
314  if not butler.datasetExists(dataset, dataId):
315  if self.config.skipMissing:
316  continue
317  raise lsst.pipe.base.TaskError("Reference %s doesn't exist" % (dataId,))
318  self.log.info("Getting references in %s" % (dataId,))
319  catalog = butler.get(dataset, dataId, immediate=True)
320  if self.config.removePatchOverlaps:
321  bbox = lsst.geom.Box2D(patch.getInnerBBox())
322  for source in catalog:
323  if bbox.contains(source.getCentroid()):
324  yield source
325  else:
326  for source in catalog:
327  yield source
328 
329  def fetchInBox(self, dataRef, bbox, wcs, pad=0):
330  """Return reference sources within a given bounding box.
331 
332  Reference sources are selected if they overlap a region defined by a
333  pixel-coordinate bounding box and corresponding WCS.
334 
335  Parameters
336  ----------
337  dataRef : `lsst.daf.persistence.ButlerDataRef`
338  Butler data reference. The implied data ID must contain the
339  ``tract`` key.
340  bbox : `lsst.afw.geom.Box2I` or `lsst.afw.geom.Box2D`
341  Defines the selection region in pixel coordinates.
342  wcs : `lsst.afw.image.SkyWcs`
343  Maps ``bbox`` to sky coordinates.
344  pad : `int`
345  a buffer to grow the bounding box by after catalogs have been loaded, but
346  before filtering them to include just the given bounding box.
347 
348  Returns
349  -------
350  sources : iterable of `~lsst.afw.table.SourceRecord`
351  Reference sources. May be any Python iterable, including a lazy
352  iterator.
353  """
354  skyMap = dataRef.get(self.config.coaddName + "Coadd_skyMap", immediate=True)
355  tract = skyMap[dataRef.dataId["tract"]]
356  coordList = [wcs.pixelToSky(corner) for corner in lsst.geom.Box2D(bbox).getCorners()]
357  self.log.info("Getting references in region with corners %s [degrees]" %
358  ", ".join("(%s)" % (coord.getPosition(lsst.geom.degrees),) for coord in coordList))
359  patchList = tract.findPatchList(coordList)
360  # After figuring out which patch catalogs to read from the bbox, pad out the bbox if desired
361  # But don't add any new patches while padding
362  if pad:
363  bbox.grow(pad)
364  return self.subset(self.fetchInPatches(dataRef, patchList), bbox, wcs)
365 
366 
367 class MultiBandReferencesConfig(CoaddSrcReferencesTask.ConfigClass):
368  """Default configuration for multi-band reference source selection.
369  """
370 
371  def validate(self):
372  if self.filter is not None:
374  field=MultiBandReferencesConfig.filter,
375  config=self,
376  msg="Filter should not be set for the multiband processing scheme")
377  # Delegate to ultimate base class, because the direct one has a check we don't want.
378  BaseReferencesTask.ConfigClass.validate(self)
379 
380 
382  """Loads references from the multi-band processing scheme.
383  """
384 
385  ConfigClass = MultiBandReferencesConfig
386  datasetSuffix = "ref" # Documented in superclass
def fetchInBox(self, dataRef, bbox, wcs, pad=0)
Definition: references.py:329
A floating-point coordinate rectangle geometry.
Definition: Box.h:305
def fetchInBox(self, dataRef, bbox, wcs)
Definition: references.py:108
def format(config, name=None, writeSourceLine=True, prefix="", verbose=False)
Definition: history.py:168
def fetchInPatches(self, dataRef, patchList)
Definition: references.py:284
def __init__(self, butler=None, schema=None, kwargs)
Definition: references.py:265
def __init__(self, butler=None, schema=None, kwargs)
Definition: references.py:80
static Key< RecordId > getParentKey()
Key for the parent ID.
Definition: Source.h:277
def fetchInPatches(self, dataRef, patchList)
Definition: references.py:136
def subset(self, sources, bbox, wcs)
Definition: references.py:162