Coverage for python/lsst/meas/extensions/shapeHSM/_hsm_higher_moments.py: 23%
141 statements
« prev ^ index » next coverage.py v7.5.0, created at 2024-05-04 10:18 +0000
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.
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/>.
22__all__ = (
23 "HigherOrderMomentsConfig",
24 "HigherOrderMomentsPlugin",
25 "HigherOrderMomentsPSFConfig",
26 "HigherOrderMomentsPSFPlugin",
27 "HigherOrderMomentsSourceConfig",
28 "HigherOrderMomentsSourcePlugin",
29)
31import lsst.geom as geom
32import lsst.meas.base as measBase
33import numpy as np
34from lsst.pex.config import Field, FieldValidationError, ListField
37class HigherOrderMomentsConfig(measBase.SingleFramePluginConfig):
38 min_order = Field[int](
39 doc="Minimum order of the higher order moments to compute",
40 default=3,
41 )
43 max_order = Field[int](
44 doc="Maximum order of the higher order moments to compute",
45 default=4,
46 )
48 def validate(self):
49 if self.min_order > self.max_order:
50 raise FieldValidationError(
51 self.__class__.min_order, self, "min_order must be less than or equal to max_order"
52 )
53 super().validate()
56class HigherOrderMomentsPlugin(measBase.SingleFramePlugin):
57 """Base plugin for higher moments measurement"""
59 ConfigClass = HigherOrderMomentsConfig
61 def __init__(self, config, name, schema, metadata, logName=None):
62 super().__init__(config, name, schema, metadata, logName=logName)
64 # Define flags for possible issues that might arise during measurement.
65 flagDefs = measBase.FlagDefinitionList()
66 self.FAILURE = flagDefs.addFailureFlag("General failure flag, set if anything went wrong")
68 # Embed the flag definitions in the schema using a flag handler.
69 self.flagHandler = measBase.FlagHandler.addFields(schema, name, flagDefs)
71 self.pqlist = self._get_pq_full()
73 @classmethod
74 def getExecutionOrder(cls):
75 return cls.FLUX_ORDER
77 def fail(self, record, error=None):
78 # Docstring inherited.
79 self.flagHandler.handleFailure(record)
81 def _get_pq_full(self):
82 """Get a list of the orders to measure as a tuple.
84 Returns
85 -------
86 pqlist: `list` [`tuples`]
87 A list of tuples of the form (p, q) where p and q denote the order
88 in x and y direction.
89 """
90 pq_list = []
92 for n in range(self.config.min_order, self.config.max_order + 1):
93 p = 0
94 q = n
96 pq_list.append((p, q))
98 while p < n:
99 p += 1
100 q -= 1
101 pq_list.append((p, q))
103 return pq_list
105 def _generate_suffixes(self):
106 """Generator of suffixes 'pq'."""
107 for p, q in self.pqlist:
108 yield f"{p}{q}"
110 def _generate_powers_of_standard_positions(self, std_x, std_y):
111 std_x_powers, std_y_powers = {0: 1.0, 1: std_x}, {0: 1.0, 1: std_y}
113 for p in range(2, self.config.max_order + 1):
114 std_x_powers[p] = std_x_powers[p - 1] * std_x
116 for q in range(2, self.config.max_order + 1):
117 std_y_powers[q] = std_y_powers[q - 1] * std_y
119 return std_x_powers, std_y_powers
121 def _calculate_higher_order_moments(
122 self,
123 image,
124 center,
125 M,
126 badpix=None,
127 set_masked_pixels_to_zero=False,
128 use_linear_algebra=False,
129 ):
130 """
131 Calculate the higher order moments of an image.
133 Parameters
134 ----------
135 image : `~lsst.afw.image.Image`
136 Image from which the moments need to be measured (source or PSF).
137 center: `~lsst.geom.Point2D`
138 First order moments of ``image``. This is used as the peak of the
139 Gaussian weight image.
140 M : `~numpy.ndarray`
141 A 2x2 numpy array representing the second order moments of
142 ``image``. This is used to generate the Gaussian weight image.
143 badpix : `~numpy.ndarray` or None
144 A 2D array having the same shape and orientation as ``image.array``
145 that denotes which pixels are bad and should not be accounted for
146 when computing the moments.
147 set_masked_pixels_to_zero: `bool`
148 Whether to treat pixels corresponding to ``badpix`` should be set
149 to zero, or replaced by a scaled version of the weight image.
150 This is ignored if ``badpix`` is None.
151 use_linear_algebra: `bool`
152 Use linear algebra operations (eigen decomposition and inverse) to
153 calculate the moments? If False, use the specialized formulae for
154 2x2 matrix.
156 Returns
157 -------
158 results : `dict`
159 A dictionary mapping the order of the moments expressed as tuples
160 to the corresponding higher order moments.
161 """
163 bbox = image.getBBox()
164 image_array = image.array
166 y, x = np.mgrid[: image_array.shape[0], : image_array.shape[1]]
168 if use_linear_algebra:
169 inv_M = np.linalg.inv(M)
171 evalues, evectors = np.linalg.eig(inv_M)
173 sqrt_inv_M = evectors * np.sqrt(evalues) @ np.linalg.inv(evectors)
174 else:
175 # This is the implementation of Eq. 6 in Hirata & Seljak (2003):
176 # https://arxiv.org/pdf/astro-ph/0301054.pdf
177 D = M[0, 0] * M[1, 1] - M[0, 1] * M[1, 0]
178 sqrt_D = D**0.5
179 sqrt_eta = (D * (M[0, 0] + M[1, 1] + 2 * sqrt_D)) ** 0.5
180 sqrt_inv_M = (1 / sqrt_eta) * np.array(
181 [[M[1, 1] + sqrt_D, -M[0, 1]], [-M[1, 0], M[0, 0] + sqrt_D]]
182 )
184 pos = np.array([x - (center.getX() - bbox.getMinX()), y - (center.getY() - bbox.getMinY())])
186 std_pos = np.einsum("ij,jqp->iqp", sqrt_inv_M, pos)
187 weight = np.exp(-0.5 * np.einsum("ijk,ijk->jk", std_pos, std_pos))
189 image_weight = weight * image_array
191 # Modify only the weight, not the image_array, since it will change the
192 # pixel values forever!!!
193 if badpix is not None and badpix.any():
194 if set_masked_pixels_to_zero:
195 # This is how HSM treats bad pixels to compute the quadrupole
196 # moments.
197 image_weight[badpix] = 0.0
198 else:
199 # This is how Piff treats bad pixels to compute the
200 # higher-order moments.
201 scale = image_array[~badpix].sum() / weight[~badpix].sum()
202 image_weight[badpix] = (weight[badpix] ** 2) * scale
204 normalization = np.sum(image_weight)
206 std_x, std_y = std_pos
207 std_x_powers, std_y_powers = self._generate_powers_of_standard_positions(std_x, std_y)
209 results = {}
210 for p, q in self.pqlist:
211 results[(p, q)] = np.sum(std_x_powers[p] * std_y_powers[q] * image_weight) / normalization
213 return results
216class HigherOrderMomentsSourceConfig(HigherOrderMomentsConfig):
217 """Configuration for the measurement of higher order moments of objects."""
219 badMaskPlanes = ListField[str](
220 doc="Mask planes used to reject bad pixels.",
221 default=["BAD", "SAT"],
222 )
224 setMaskedPixelsToZero = Field[bool](
225 doc="Set masked pixels to zero? If False, they are replaced by the "
226 "scaled version of the adaptive weights.",
227 default=False,
228 )
231@measBase.register("ext_shapeHSM_HigherOrderMomentsSource")
232class HigherOrderMomentsSourcePlugin(HigherOrderMomentsPlugin):
233 """Plugin for Higher Order Moments measurement of objects.
235 The moments are measured in normalized coordinates, where the normalized x
236 axis is along the major axis and the normalized y axis along the minor.
237 The moments are dependent only on the light profile, and does not scale
238 with the size or orientation of the object.
240 For any well-sampled image, the zeroth order moment is 1,
241 the first order moments are 0, and the second order moments are 0.5 for xx
242 and yy and 0 for xy. For a symmetric profile, the moments are zeros if
243 either of the indices is odd.
245 Notes
246 -----
247 This plugin requires the `ext_shapeHSM_HsmSourceMoments` plugin to be
248 enabled in order to measure the higher order moments, and raises a
249 FatalAlgorithmError otherwise. For accurate results, the weight function
250 used must match those used for first and second order moments. Hence, this
251 plugin does not use slots for centroids and shapes, but instead uses those
252 measured by the `ext_shapeHSM_HsmSourceMoments` explicitly.
254 The only known failure mode of this plugin is if
255 `ext_shapeHSM_HsmSourceMoments` measurement failed. The flags of that
256 plugin are informative here as well and should be used to filter out
257 unreliable measurements.
258 """
260 ConfigClass = HigherOrderMomentsSourceConfig
262 def __init__(self, config, name, schema, metadata, logName=None):
263 super().__init__(config, name, schema, metadata, logName=logName)
265 for suffix in self._generate_suffixes():
266 schema.addField(
267 schema.join(name, suffix),
268 type=float,
269 doc=f"Higher order moments M_{suffix} for source",
270 )
272 def measure(self, record, exposure):
273 # Docstring inherited.
274 M = np.zeros((2, 2))
275 try:
276 center = geom.Point2D(
277 record["ext_shapeHSM_HsmSourceMoments_x"],
278 record["ext_shapeHSM_HsmSourceMoments_y"],
279 )
280 M[0, 0] = record["ext_shapeHSM_HsmSourceMoments_xx"]
281 M[1, 1] = record["ext_shapeHSM_HsmSourceMoments_yy"]
282 M[0, 1] = M[1, 0] = record["ext_shapeHSM_HsmSourceMoments_xy"]
283 except KeyError:
284 raise measBase.FatalAlgorithmError("'ext_shapeHSM_HsmSourceMoments' plugin must be enabled.")
286 # Obtain the bounding box of the source footprint
287 bbox = record.getFootprint().getBBox()
289 bitValue = exposure.mask.getPlaneBitMask(self.config.badMaskPlanes)
290 badpix = (exposure.mask[bbox].array & bitValue) != 0
292 # Measure all the moments together to save time
293 try:
294 hm_measurement = self._calculate_higher_order_moments(
295 exposure.image[bbox],
296 center,
297 M,
298 badpix,
299 set_masked_pixels_to_zero=self.config.setMaskedPixelsToZero,
300 )
301 except Exception as e:
302 raise measBase.MeasurementError(e)
304 # Record the moments
305 for (p, q), M_pq in hm_measurement.items():
306 column_key = self.name + f"_{p}{q}"
307 record.set(column_key, M_pq)
310class HigherOrderMomentsPSFConfig(HigherOrderMomentsConfig):
311 """Configuration for the higher order moments of the PSF."""
313 useSourceCentroidOffset = Field[bool](
314 doc="Use source centroid offset?",
315 default=False,
316 )
319@measBase.register("ext_shapeHSM_HigherOrderMomentsPSF")
320class HigherOrderMomentsPSFPlugin(HigherOrderMomentsPlugin):
321 """Plugin for Higher Order Moments measurement of PSF models.
323 The moments are measured in normalized coordinates, where the normalized x
324 axis is along the major axis and the normalized y axis along the minor.
325 The moments are dependent only on the light profile, and does not scale
326 with the size or orientation of the object.
328 For any well-sampled image, the zeroth order moment is 1,
329 the first order moments are 0, and the second order moments are 0.5 for xx
330 and yy and 0 for xy. For a symmetric profile, the moments are zeros if
331 either of the indices is odd.
333 Notes
334 -----
335 This plugin requires the `ext_shapeHSM_HsmPsfMoments` plugin to be
336 enabled in order to measure the higher order moments, and raises a
337 FatalAlgorithmError otherwise. The weight function is parametrized by the
338 shape measured from `ext_shapeHSM_HsmPsfMoments` but for efficiency
339 reasons, uses the slot centroid to evaluate the PSF model.
341 The only known failure mode of this plugin is if
342 `ext_shapeHSM_HsmPsfMoments` measurement failed. The flags of that
343 plugin are informative here as well and should be used to filter out
344 unreliable measurements.
345 """
347 ConfigClass = HigherOrderMomentsPSFConfig
349 def __init__(self, config, name, schema, metadata, logName=None):
350 super().__init__(config, name, schema, metadata, logName=logName)
351 # Use the standard slot centroid to use the shared PSF model with
352 # other plugins.
353 self.centroidExtractor = measBase.SafeCentroidExtractor(schema, name)
355 for suffix in self._generate_suffixes():
356 schema.addField(
357 schema.join(name, suffix),
358 type=float,
359 doc=f"Higher order moments M_{suffix} for PSF",
360 )
362 def measure(self, record, exposure):
363 # Docstring inherited.
364 M = np.zeros((2, 2))
365 try:
366 M[0, 0] = record["ext_shapeHSM_HsmPsfMoments_xx"]
367 M[1, 1] = record["ext_shapeHSM_HsmPsfMoments_yy"]
368 M[0, 1] = M[1, 0] = record["ext_shapeHSM_HsmPsfMoments_xy"]
369 except KeyError:
370 raise measBase.FatalAlgorithmError("'ext_shapeHSM_HsmPsfMoments' plugin must be enabled.")
372 psf = exposure.getPsf()
374 centroid = self.centroidExtractor(record, self.flagHandler)
375 if self.config.useSourceCentroidOffset:
376 psfImage = psf.computeImage(centroid)
377 psfCenter = centroid
378 # Undo what subtractCenter config did.
379 # This operation assumes subtractCenter was set to True (default)
380 # in the ext_shapeHSM_HsmPsfMomentsConfig and does not have
381 # access to it.
382 psfCenter.x += record["ext_shapeHSM_HsmPsfMoments_x"]
383 psfCenter.y += record["ext_shapeHSM_HsmPsfMoments_y"]
384 else:
385 psfImage = psf.computeKernelImage(centroid)
386 center0 = geom.Point2I(centroid)
387 xy0 = geom.Point2I(center0.x + psfImage.getX0(), center0.y + psfImage.getY0())
388 psfImage.setXY0(xy0)
389 psfBBox = psfImage.getBBox()
390 psfCenter = geom.Point2D(psfBBox.getMin() + psfBBox.getDimensions() // 2)
392 # Measure all the moments together to save time
393 try:
394 hm_measurement = self._calculate_higher_order_moments(psfImage, psfCenter, M)
395 except Exception as e:
396 raise measBase.MeasurementError(e)
398 # Record the moments
399 for (p, q), M_pq in hm_measurement.items():
400 column_key = self.name + f"_{p}{q}"
401 record.set(column_key, M_pq)