Coverage for python / lsst / meas / extensions / shapeHSM / _hsm_shape.py: 40%
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1# This file is part of meas_extensions_shapeHSM.
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.
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22import logging
24import galsim
25import lsst.afw.image as afwImage
26import lsst.afw.math as afwMath
27import lsst.meas.base as measBase
28import lsst.pex.config as pexConfig
29from lsst.geom import Point2I
31__all__ = [
32 "HsmShapeBjConfig",
33 "HsmShapeBjPlugin",
34 "HsmShapeLinearConfig",
35 "HsmShapeLinearPlugin",
36 "HsmShapeKsbConfig",
37 "HsmShapeKsbPlugin",
38 "HsmShapeRegaussConfig",
39 "HsmShapeRegaussPlugin",
40]
43def inherit_doc(ref_class):
44 def decorator(func):
45 func.__doc__ = getattr(ref_class, func.__name__).__doc__
46 return func
48 return decorator
51class HsmShapeConfig(measBase.SingleFramePluginConfig):
52 """Base configuration for HSM shape measurement."""
54 deblendNChild = pexConfig.Field[str](
55 doc="Field name for number of deblend children.",
56 default="",
57 )
59 badMaskPlanes = pexConfig.ListField[str](
60 doc="Mask planes that indicate pixels that should be excluded from the fit.",
61 default=["BAD", "SAT"],
62 )
64 @property
65 def shearType(self):
66 """Base class property for the desired method of PSF correction.
68 The following options are available through GalSim. The first three
69 options return an e-type distortion, whereas the last option returns a
70 g-type shear:
72 - "REGAUSS": Regaussianization method from Hirata & Seljak (2003).
73 - "LINEAR": A modification by Hirata & Seljak (2003) of methods in
74 Bernstein & Jarvis (2002).
75 - "BJ": The method developed by Bernstein & Jarvis (2002).
76 - "KSB": The method from Kaiser, Squires, & Broadhurst (1995).
78 Subclasses can override this property, but it cannot be set externally,
79 making it effectively read-only.
80 """
81 raise NotImplementedError("The shearType property must be implemented in subclasses.")
84class HsmShapePlugin(measBase.SingleFramePlugin):
85 """Base plugin for HSM shape measurement."""
87 ConfigClass = HsmShapeConfig
88 doc = ""
90 def __init__(self, config, name, schema, metadata, logName=None):
91 if logName is None:
92 logName = __name__
93 super().__init__(config, name, schema, metadata, logName=logName)
95 # Define flags for possible issues that might arise during measurement.
96 flagDefs = measBase.FlagDefinitionList()
97 self.FAILURE = flagDefs.addFailureFlag("General failure flag, set if anything went wrong")
98 self.NO_PIXELS = flagDefs.add("flag_no_pixels", "No pixels to measure")
99 self.NOT_CONTAINED = flagDefs.add(
100 "flag_not_contained", "Center not contained in footprint bounding box"
101 )
102 self.PARENT_SOURCE = flagDefs.add("flag_parent_source", "Parent source, ignored")
103 self.GALSIM = flagDefs.add("flag_galsim", "GalSim failure")
105 # Embed the flag definitions in the schema using a flag handler.
106 self.flagHandler = measBase.FlagHandler.addFields(schema, name, flagDefs)
108 # Utilize a safe centroid extractor that uses the detection footprint
109 # as a fallback if necessary.
110 self.centroidExtractor = measBase.SafeCentroidExtractor(schema, name)
112 self.e1Key = self._addEllipticityField(name, 1, schema, self.doc)
113 self.e2Key = self._addEllipticityField(name, 2, schema, self.doc)
114 self.sigmaKey = schema.addField(
115 schema.join(name, "sigma"),
116 type=float,
117 doc=f"{self.doc} (shape measurement uncertainty per component)",
118 )
119 self.resolutionKey = schema.addField(
120 schema.join(name, "resolution"), type=float, doc="Resolution factor (0=unresolved, 1=resolved)"
121 )
122 self.hasDeblendKey = len(config.deblendNChild) > 0
124 if self.hasDeblendKey:
125 self.deblendKey = schema[config.deblendNChild].asKey()
127 self.log = logging.getLogger(self.logName)
129 @classmethod
130 def getExecutionOrder(cls):
131 return cls.SHAPE_ORDER
133 @staticmethod
134 def bboxToGalSimBounds(bbox):
135 xmin, xmax = bbox.getMinX(), bbox.getMaxX()
136 ymin, ymax = bbox.getMinY(), bbox.getMaxY()
137 return galsim._BoundsI(xmin, xmax, ymin, ymax)
139 def _addEllipticityField(self, name, n, schema, doc):
140 """
141 Helper function to add an ellipticity field to a measurement schema.
143 Parameters
144 ----------
145 name : `str`
146 Base name of the field.
147 n : `int`
148 Specifies whether the field is for the first (1) or second (2)
149 component.
150 schema : `~lsst.afw.table.Schema`
151 The schema to which the field is added.
152 doc : `str`
153 The documentation string that needs to be updated to reflect the
154 type and component of the measurement.
156 Returns
157 -------
158 `~lsst.afw.table.KeyD`
159 The key associated with the added field in the schema.
160 """
161 componentLookup = {1: "+ component", 2: "x component"}
162 typeLookup = {"e": " of ellipticity", "g": " of estimated shear"}
163 name = f"{name}_{self.measTypeSymbol}{n}"
164 updatedDoc = f"{doc} ({componentLookup[n]}{typeLookup[self.measTypeSymbol]})"
165 return schema.addField(name, type=float, doc=updatedDoc)
167 def measure(self, record, exposure):
168 """
169 Measure the shape of sources given an exposure and set the results in
170 the record in place.
172 Parameters
173 ----------
174 record : `~lsst.afw.table.SourceRecord`
175 The record where measurement outputs will be stored.
176 exposure : `~lsst.afw.image.Exposure`
177 The exposure containing the source which needs measurement.
179 Raises
180 ------
181 MeasurementError
182 Raised for errors in measurement.
183 """
184 # Extract the centroid from the record.
185 center = self.centroidExtractor(record, self.flagHandler)
187 if self.hasDeblendKey and record.get(self.deblendKey) > 0:
188 raise measBase.MeasurementError(self.PARENT_SOURCE.doc, self.PARENT_SOURCE.number)
190 # Get the bounding box of the source's footprint.
191 bbox = record.getFootprint().getBBox()
193 # Check that the bounding box has non-zero area.
194 if bbox.getArea() == 0:
195 raise measBase.MeasurementError(self.NO_PIXELS.doc, self.NO_PIXELS.number)
197 # Ensure that the centroid is within the bounding box.
198 if not bbox.contains(Point2I(center)):
199 raise measBase.MeasurementError(self.NOT_CONTAINED.doc, self.NOT_CONTAINED.number)
201 # Get the PSF image evaluated at the source centroid.
202 psfImage = exposure.getPsf().computeImage(center)
203 psfImage.setXY0(0, 0)
205 # Get the trace radius of the PSF.
206 psfSigma = exposure.getPsf().computeShape(center).getTraceRadius()
208 # Turn bounding box corners into GalSim bounds.
209 bounds = self.bboxToGalSimBounds(bbox)
211 # Get the bounding box of the PSF in the parent coordinate system.
212 psfBBox = psfImage.getBBox(afwImage.PARENT)
214 # Turn the PSF bounding box corners into GalSim bounds.
215 psfBounds = self.bboxToGalSimBounds(psfBBox)
217 # Each GalSim image below will match whatever dtype the input array is.
218 # NOTE: PSF is already restricted to a small image, so no bbox for the
219 # PSF is expected.
220 image = galsim._Image(exposure.image[bbox].array, bounds, wcs=None)
221 psf = galsim._Image(psfImage.array, psfBounds, wcs=None)
223 # Get the `lsst.meas.base` mask for bad pixels.
224 subMask = exposure.mask[bbox]
225 badpix = subMask.array.copy() # Copy it since badpix gets modified.
226 bitValue = exposure.mask.getPlaneBitMask(self.config.badMaskPlanes)
227 badpix &= bitValue
229 # Turn badpix to weight where elements set to 1 indicate 'use pixel'
230 # and those set to 0 mean 'do not use pixel'. Now, weight will assume
231 # the role of badpix, and we will no longer use badpix in our call to
232 # EstimateShear().
233 gd = badpix == 0
234 badpix[gd] = 1
235 badpix[~gd] = 0
236 weight = galsim._Image(badpix, bounds, wcs=None)
238 # Get the statistics control object for sky variance estimation.
239 sctrl = afwMath.StatisticsControl()
240 sctrl.setAndMask(bitValue)
242 # Create a variance image from the exposure.
243 # NOTE: Origin defaults to PARENT in all cases accessible from Python.
244 variance = afwImage.Image(
245 exposure.variance[bbox],
246 dtype=exposure.variance.dtype,
247 deep=False,
248 )
250 # Calculate median sky variance for use in shear estimation.
251 stat = afwMath.makeStatistics(variance, subMask, afwMath.MEDIAN, sctrl)
252 skyvar = stat.getValue(afwMath.MEDIAN)
254 # Prepare various values for the GalSim's EstimateShear call.
255 recomputeFlux = "FIT"
256 precision = 1.0e-6
257 guessCentroid = galsim._PositionD(center.getX(), center.getY())
259 try:
260 # Estimate shear using GalSim.
261 shape = galsim.hsm.EstimateShear(
262 image,
263 psf,
264 weight=weight,
265 badpix=None, # Already incorporated into `weight_image`.
266 sky_var=skyvar,
267 shear_est=self.config.shearType.upper(),
268 recompute_flux=recomputeFlux.upper(),
269 guess_sig_gal=2.5 * psfSigma,
270 guess_sig_PSF=psfSigma,
271 precision=precision,
272 guess_centroid=guessCentroid,
273 strict=True, # Raises GalSimHSMError if estimation fails.
274 check=False, # This speeds up the code!
275 hsmparams=None,
276 )
277 except galsim.hsm.GalSimHSMError as error:
278 raise measBase.MeasurementError(str(error), self.GALSIM.number)
280 # Set ellipticity and error values based on measurement type.
281 if shape.meas_type == "e":
282 record.set(self.e1Key, shape.corrected_e1)
283 record.set(self.e2Key, shape.corrected_e2)
284 record.set(self.sigmaKey, 2.0 * shape.corrected_shape_err)
285 else:
286 record.set(self.e1Key, shape.corrected_g1)
287 record.set(self.e2Key, shape.corrected_g2)
288 record.set(self.sigmaKey, shape.corrected_shape_err)
290 record.set(self.resolutionKey, shape.resolution_factor)
291 self.flagHandler.setValue(record, self.FAILURE.number, shape.correction_status != 0)
293 def fail(self, record, error=None):
294 # Docstring inherited.
295 self.flagHandler.handleFailure(record)
296 if error:
297 centroid = self.centroidExtractor(record, self.flagHandler)
298 self.log.debug(
299 "Failed to measure shape for %d at (%f, %f): %s",
300 record.getId(),
301 centroid.getX(),
302 centroid.getY(),
303 error,
304 )
307class HsmShapeBjConfig(HsmShapeConfig):
308 """Configuration for HSM shape measurement for the BJ estimator."""
310 @HsmShapeConfig.shearType.getter
311 @inherit_doc(HsmShapeConfig)
312 def shearType(self):
313 # Docstring inherited.
314 return "BJ"
317@measBase.register("ext_shapeHSM_HsmShapeBj")
318class HsmShapeBjPlugin(HsmShapePlugin):
319 """Plugin for HSM shape measurement for the BJ estimator."""
321 ConfigClass = HsmShapeBjConfig
322 measTypeSymbol = "e"
323 doc = "PSF-corrected shear using Bernstein & Jarvis (2002) method"
326class HsmShapeLinearConfig(HsmShapeConfig):
327 """Configuration for HSM shape measurement for the LINEAR estimator."""
329 @HsmShapeConfig.shearType.getter
330 @inherit_doc(HsmShapeConfig)
331 def shearType(self):
332 # Docstring inherited.
333 return "LINEAR"
336@measBase.register("ext_shapeHSM_HsmShapeLinear")
337class HsmShapeLinearPlugin(HsmShapePlugin):
338 """Plugin for HSM shape measurement for the LINEAR estimator."""
340 ConfigClass = HsmShapeLinearConfig
341 measTypeSymbol = "e"
342 doc = "PSF-corrected shear using Hirata & Seljak (2003) 'linear' method"
345class HsmShapeKsbConfig(HsmShapeConfig):
346 """Configuration for HSM shape measurement for the KSB estimator."""
348 @HsmShapeConfig.shearType.getter
349 @inherit_doc(HsmShapeConfig)
350 def shearType(self):
351 # Docstring inherited.
352 return "KSB"
355@measBase.register("ext_shapeHSM_HsmShapeKsb")
356class HsmShapeKsbPlugin(HsmShapePlugin):
357 """Plugin for HSM shape measurement for the KSB estimator."""
359 ConfigClass = HsmShapeKsbConfig
360 measTypeSymbol = "g"
361 doc = "PSF-corrected shear using Kaiser, Squires, & Broadhurst (1995) method"
364class HsmShapeRegaussConfig(HsmShapeConfig):
365 """Configuration for HSM shape measurement for the REGAUSS estimator."""
367 @HsmShapeConfig.shearType.getter
368 @inherit_doc(HsmShapeConfig)
369 def shearType(self):
370 # Docstring inherited.
371 return "REGAUSS"
374@measBase.register("ext_shapeHSM_HsmShapeRegauss")
375class HsmShapeRegaussPlugin(HsmShapePlugin):
376 """Plugin for HSM shape measurement for the REGAUSS estimator."""
378 ConfigClass = HsmShapeRegaussConfig
379 measTypeSymbol = "e"
380 doc = "PSF-corrected shear using Hirata & Seljak (2003) 'regaussianization' method"