22"""Support utilities for Measuring sources"""
25__all__ = [
"DipoleTestImage",
"evaluateMeanPsfFwhm",
"getPsfFwhm"]
41from lsst.utils.logging
import getLogger
42from .dipoleFitTask
import DipoleFitAlgorithm
43from .
import diffimLib
45afwDisplay.setDefaultMaskTransparency(75)
48_LOG = getLogger(__name__)
51def showSourceSet(sSet, xy0=(0, 0), frame=0, ctype=afwDisplay.GREEN, symb=
"+", size=2):
52 """Draw the (XAstrom, YAstrom) positions of a set of Sources.
54 Image has the given XY0.
56 disp = afwDisplay.afwDisplay(frame=frame)
57 with disp.Buffering():
59 xc, yc = s.getXAstrom() - xy0[0], s.getYAstrom() - xy0[1]
62 disp.dot(str(s.getId()), xc, yc, ctype=ctype, size=size)
64 disp.dot(symb, xc, yc, ctype=ctype, size=size)
72 ctype=None, ctypeUnused=None, ctypeBad=None, size=3,
73 frame=None, title="Spatial Cells"):
74 """Show the SpatialCells.
76 If symb is something that display.dot understands (e.g. "o"), the top
77 nMaxPerCell candidates will be indicated with that symbol, using ctype
80 disp = afwDisplay.Display(frame=frame)
81 disp.mtv(maskedIm, title=title)
82 with disp.Buffering():
83 origin = [-maskedIm.getX0(), -maskedIm.getY0()]
84 for cell
in kernelCellSet.getCellList():
85 afwDisplay.utils.drawBBox(cell.getBBox(), origin=origin, display=disp)
87 goodies = ctypeBad
is None
88 for cand
in cell.begin(goodies):
89 xc, yc = cand.getXCenter() + origin[0], cand.getYCenter() + origin[1]
90 if cand.getStatus() == afwMath.SpatialCellCandidate.BAD:
92 elif cand.getStatus() == afwMath.SpatialCellCandidate.GOOD:
94 elif cand.getStatus() == afwMath.SpatialCellCandidate.UNKNOWN:
100 disp.dot(symb, xc, yc, ctype=color, size=size)
103 rchi2 = cand.getChi2()
106 disp.dot(
"%d %.1f" % (cand.getId(), rchi2),
107 xc - size, yc - size - 4, ctype=color, size=size)
111 """Display Dia Sources.
117 disp = afwDisplay.Display(frame=frame)
118 for plane
in (
"BAD",
"CR",
"EDGE",
"INTERPOlATED",
"INTRP",
"SAT",
"SATURATED"):
119 disp.setMaskPlaneColor(plane, color=
"ignore")
121 mos = afwDisplay.utils.Mosaic()
122 for i
in range(len(sources)):
124 badFlag = isFlagged[i]
125 dipoleFlag = isDipole[i]
126 bbox = source.getFootprint().getBBox()
127 stamp = exposure.Factory(exposure, bbox,
True)
128 im = afwDisplay.utils.Mosaic(gutter=1, background=0, mode=
"x")
129 im.append(stamp.getMaskedImage())
130 lab =
"%.1f,%.1f:" % (source.getX(), source.getY())
132 ctype = afwDisplay.RED
135 ctype = afwDisplay.YELLOW
137 if not badFlag
and not dipoleFlag:
138 ctype = afwDisplay.GREEN
140 mos.append(im.makeMosaic(), lab, ctype)
141 title =
"Dia Sources"
142 mosaicImage = mos.makeMosaic(display=disp, title=title)
147 resids=False, kernels=False):
148 """Display the Kernel candidates.
150 If kernel is provided include spatial model and residuals;
151 If chi is True, generate a plot of residuals/sqrt(variance), i.e. chi.
157 mos = afwDisplay.utils.Mosaic(gutter=5, background=0)
159 mos = afwDisplay.utils.Mosaic(gutter=5, background=-1)
161 candidateCenters = []
162 candidateCentersBad = []
164 for cell
in kernelCellSet.getCellList():
165 for cand
in cell.begin(
False):
168 resid = cand.getDifferenceImage(diffimLib.KernelCandidateF.ORIG)
172 rchi2 = cand.getChi2()
176 if not showBadCandidates
and cand.isBad():
179 im_resid = afwDisplay.utils.Mosaic(gutter=1, background=-0.5, mode=
"x")
182 im = cand.getScienceMaskedImage()
183 im = im.Factory(im,
True)
184 im.setXY0(cand.getScienceMaskedImage().getXY0())
187 if (
not resids
and not kernels):
188 im_resid.append(im.Factory(im,
True))
190 im = cand.getTemplateMaskedImage()
191 im = im.Factory(im,
True)
192 im.setXY0(cand.getTemplateMaskedImage().getXY0())
195 if (
not resids
and not kernels):
196 im_resid.append(im.Factory(im,
True))
201 var = var.Factory(var,
True)
202 np.sqrt(var.array, var.array)
205 bbox = kernel.shrinkBBox(resid.getBBox())
206 resid = resid.Factory(resid, bbox, deep=
True)
208 kim = cand.getKernelImage(diffimLib.KernelCandidateF.ORIG).convertF()
209 resid = kim.Factory(kim,
True)
210 im_resid.append(resid)
213 ski = afwImage.ImageD(kernel.getDimensions())
214 kernel.computeImage(ski,
False, int(cand.getXCenter()), int(cand.getYCenter()))
218 sbg = background(int(cand.getXCenter()), int(cand.getYCenter()))
219 sresid = cand.getDifferenceImage(sk, sbg)
224 bbox = kernel.shrinkBBox(resid.getBBox())
225 resid = resid.Factory(resid, bbox, deep=
True)
228 resid = kim.Factory(kim,
True)
229 im_resid.append(resid)
231 im = im_resid.makeMosaic()
233 lab =
"%d chi^2 %.1f" % (cand.getId(), rchi2)
234 ctype = afwDisplay.RED
if cand.isBad()
else afwDisplay.GREEN
236 mos.append(im, lab, ctype)
238 if False and np.isnan(rchi2):
239 disp = afwDisplay.Display(frame=1)
240 disp.mtv(cand.getScienceMaskedImage.image, title=
"candidate")
241 print(
"rating", cand.getCandidateRating())
243 im = cand.getScienceMaskedImage()
244 center = (candidateIndex, cand.getXCenter() - im.getX0(), cand.getYCenter() - im.getY0())
247 candidateCentersBad.append(center)
249 candidateCenters.append(center)
256 title =
"Candidates & residuals"
258 disp = afwDisplay.Display(frame=frame)
259 mosaicImage = mos.makeMosaic(display=disp, title=title)
265 """Display a Kernel's basis images.
267 mos = afwDisplay.utils.Mosaic()
269 for k
in kernel.getKernelList():
270 im = afwImage.ImageD(k.getDimensions())
271 k.computeImage(im,
False)
274 disp = afwDisplay.Display(frame=frame)
275 mos.makeMosaic(display=disp, title=
"Kernel Basis Images")
283 numSample=128, keepPlots=True, maxCoeff=10):
284 """Plot the Kernel spatial model.
287 import matplotlib.pyplot
as plt
288 import matplotlib.colors
289 except ImportError
as e:
290 print(
"Unable to import numpy and matplotlib: %s" % e)
293 x0 = kernelCellSet.getBBox().getBeginX()
294 y0 = kernelCellSet.getBBox().getBeginY()
302 for cell
in kernelCellSet.getCellList():
303 for cand
in cell.begin(
False):
304 if not showBadCandidates
and cand.isBad():
306 candCenter =
geom.PointD(cand.getXCenter(), cand.getYCenter())
308 im = cand.getTemplateMaskedImage()
312 targetFits = badFits
if cand.isBad()
else candFits
313 targetPos = badPos
if cand.isBad()
else candPos
314 targetAmps = badAmps
if cand.isBad()
else candAmps
317 kp0 = np.array(cand.getKernel(diffimLib.KernelCandidateF.ORIG).getKernelParameters())
318 amp = cand.getCandidateRating()
320 targetFits = badFits
if cand.isBad()
else candFits
321 targetPos = badPos
if cand.isBad()
else candPos
322 targetAmps = badAmps
if cand.isBad()
else candAmps
324 targetFits.append(kp0)
325 targetPos.append(candCenter)
326 targetAmps.append(amp)
328 xGood = np.array([pos.getX()
for pos
in candPos]) - x0
329 yGood = np.array([pos.getY()
for pos
in candPos]) - y0
330 zGood = np.array(candFits)
332 xBad = np.array([pos.getX()
for pos
in badPos]) - x0
333 yBad = np.array([pos.getY()
for pos
in badPos]) - y0
334 zBad = np.array(badFits)
337 xRange = np.linspace(0, kernelCellSet.getBBox().getWidth(), num=numSample)
338 yRange = np.linspace(0, kernelCellSet.getBBox().getHeight(), num=numSample)
341 maxCoeff =
min(maxCoeff, kernel.getNKernelParameters())
343 maxCoeff = kernel.getNKernelParameters()
345 for k
in range(maxCoeff):
346 func = kernel.getSpatialFunction(k)
347 dfGood = zGood[:, k] - np.array([func(pos.getX(), pos.getY())
for pos
in candPos])
351 dfBad = zBad[:, k] - np.array([func(pos.getX(), pos.getY())
for pos
in badPos])
353 yMin =
min([yMin, dfBad.min()])
354 yMax =
max([yMax, dfBad.max()])
355 yMin -= 0.05*(yMax - yMin)
356 yMax += 0.05*(yMax - yMin)
358 fRange = np.ndarray((len(xRange), len(yRange)))
359 for j, yVal
in enumerate(yRange):
360 for i, xVal
in enumerate(xRange):
361 fRange[j][i] = func(xVal, yVal)
367 fig.canvas._tkcanvas._root().lift()
371 fig.suptitle(
'Kernel component %d' % k)
374 ax = fig.add_axes((0.1, 0.05, 0.35, 0.35))
377 norm = matplotlib.colors.Normalize(vmin=vmin, vmax=vmax)
378 im = ax.imshow(fRange, aspect=
'auto', norm=norm,
379 extent=[0, kernelCellSet.getBBox().getWidth() - 1,
380 0, kernelCellSet.getBBox().getHeight() - 1])
381 ax.set_title(
'Spatial polynomial')
382 plt.colorbar(im, orientation=
'horizontal', ticks=[vmin, vmax])
385 ax = fig.add_axes((0.1, 0.55, 0.35, 0.35))
386 ax.plot(-2.5*np.log10(candAmps), zGood[:, k],
'b+')
388 ax.plot(-2.5*np.log10(badAmps), zBad[:, k],
'r+')
389 ax.set_title(
"Basis Coefficients")
390 ax.set_xlabel(
"Instr mag")
391 ax.set_ylabel(
"Coeff")
394 ax = fig.add_axes((0.55, 0.05, 0.35, 0.35))
395 ax.set_autoscale_on(
False)
396 ax.set_xbound(lower=0, upper=kernelCellSet.getBBox().getHeight())
397 ax.set_ybound(lower=yMin, upper=yMax)
398 ax.plot(yGood, dfGood,
'b+')
400 ax.plot(yBad, dfBad,
'r+')
402 ax.set_title(
'dCoeff (indiv-spatial) vs. y')
405 ax = fig.add_axes((0.55, 0.55, 0.35, 0.35))
406 ax.set_autoscale_on(
False)
407 ax.set_xbound(lower=0, upper=kernelCellSet.getBBox().getWidth())
408 ax.set_ybound(lower=yMin, upper=yMax)
409 ax.plot(xGood, dfGood,
'b+')
411 ax.plot(xBad, dfBad,
'r+')
413 ax.set_title(
'dCoeff (indiv-spatial) vs. x')
418 if keepPlots
and not keptPlots:
421 print(
"%s: Please close plots when done." % __name__)
426 print(
"Plots closed, exiting...")
428 atexit.register(show)
433 """Plot the individual kernel candidate and the spatial kernel solution coefficients.
438 spatialKernel : `lsst.afw.math.LinearCombinationKernel`
439 The spatial spatialKernel solution model which is a spatially varying linear combination
440 of the spatialKernel basis functions.
441 Typically returned by `lsst.ip.diffim.SpatialKernelSolution.getSolutionPair()`.
443 kernelCellSet : `lsst.afw.math.SpatialCellSet`
444 The spatial cells that was used for solution for the spatialKernel. They contain the
445 local solutions of the AL kernel for the selected sources.
447 showBadCandidates : `bool`, optional
448 If True, plot the coefficient values for kernel candidates where the solution was marked
449 bad by the numerical algorithm. Defaults to False.
451 keepPlots: `bool`, optional
452 If True, sets ``plt.show()`` to be called before the task terminates, so that the plots
453 can be explored interactively. Defaults to True.
457 This function produces 3 figures per image subtraction operation.
458 * A grid plot of the local solutions. Each grid cell corresponds to a proportional area in
459 the image. In each cell, local kernel solution coefficients are plotted of kernel candidates (color)
460 that fall into this area as a function of the kernel basis function number.
461 * A grid plot of the spatial solution. Each grid cell corresponds to a proportional area in
462 the image. In each cell, the spatial solution coefficients are evaluated for the center of the cell.
463 * Histogram of the local solution coefficients. Red line marks the spatial solution value at
466 This function is called if ``lsst.ip.diffim.psfMatch.plotKernelCoefficients==True`` in lsstDebug. This
467 function was implemented as part of DM-17825.
470 import matplotlib.pyplot
as plt
471 except ImportError
as e:
472 print(
"Unable to import matplotlib: %s" % e)
476 imgBBox = kernelCellSet.getBBox()
477 x0 = imgBBox.getBeginX()
478 y0 = imgBBox.getBeginY()
479 wImage = imgBBox.getWidth()
480 hImage = imgBBox.getHeight()
481 imgCenterX = imgBBox.getCenterX()
482 imgCenterY = imgBBox.getCenterY()
494 fig.suptitle(
"Kernel candidate parameters on an image grid")
495 arrAx = fig.subplots(nrows=nY, ncols=nX, sharex=
True, sharey=
True, gridspec_kw=dict(
499 arrAx = arrAx[::-1, :]
502 for cell
in kernelCellSet.getCellList():
505 iX = int((cellBBox.getCenterX() - x0)//wCell)
506 iY = int((cellBBox.getCenterY() - y0)//hCell)
508 for cand
in cell.begin(
False):
510 kernel = cand.getKernel(cand.ORIG)
514 if not showBadCandidates
and cand.isBad():
517 nKernelParams = kernel.getNKernelParameters()
518 kernelParams = np.array(kernel.getKernelParameters())
519 allParams.append(kernelParams)
525 arrAx[iY, iX].plot(np.arange(nKernelParams), kernelParams,
'.-',
526 color=color, drawstyle=
'steps-mid', linewidth=0.1)
527 for ax
in arrAx.ravel():
528 ax.grid(
True, axis=
'y')
533 spatialFuncs = spatialKernel.getSpatialFunctionList()
534 nKernelParams = spatialKernel.getNKernelParameters()
537 fig.suptitle(
"Hist. of parameters marked with spatial solution at img center")
538 arrAx = fig.subplots(nrows=int(nKernelParams//nX)+1, ncols=nX)
539 arrAx = arrAx[::-1, :]
540 allParams = np.array(allParams)
541 for k
in range(nKernelParams):
542 ax = arrAx.ravel()[k]
543 ax.hist(allParams[:, k], bins=20, edgecolor=
'black')
544 ax.set_xlabel(
'P{}'.format(k))
545 valueParam = spatialFuncs[k](imgCenterX, imgCenterY)
546 ax.axvline(x=valueParam, color=
'red')
547 ax.text(0.1, 0.9,
'{:.1f}'.format(valueParam),
548 transform=ax.transAxes, backgroundcolor=
'lightsteelblue')
561 fig.suptitle(
"Spatial solution of kernel parameters on an image grid")
562 arrAx = fig.subplots(nrows=nY, ncols=nX, sharex=
True, sharey=
True, gridspec_kw=dict(
564 arrAx = arrAx[::-1, :]
565 kernelParams = np.zeros(nKernelParams, dtype=float)
572 kernelParams = [f(x, y)
for f
in spatialFuncs]
573 arrAx[iY, iX].plot(np.arange(nKernelParams), kernelParams,
'.-', drawstyle=
'steps-mid')
574 arrAx[iY, iX].grid(
True, axis=
'y')
577 if keepPlots
and not keptPlots:
580 print(
"%s: Please close plots when done." % __name__)
585 print(
"Plots closed, exiting...")
587 atexit.register(show)
592 showCenter=True, showEllipticity=True):
593 """Show a mosaic of Kernel images.
595 mos = afwDisplay.utils.Mosaic()
597 x0 = bbox.getBeginX()
598 y0 = bbox.getBeginY()
599 width = bbox.getWidth()
600 height = bbox.getHeight()
603 ny = int(nx*float(height)/width + 0.5)
607 schema = afwTable.SourceTable.makeMinimalSchema()
608 centroidName =
"base_SdssCentroid"
609 shapeName =
"base_SdssShape"
610 control = measBase.SdssCentroidControl()
611 schema.getAliasMap().
set(
"slot_Centroid", centroidName)
612 schema.getAliasMap().
set(
"slot_Centroid_flag", centroidName +
"_flag")
613 centroider = measBase.SdssCentroidAlgorithm(control, centroidName, schema)
614 sdssShape = measBase.SdssShapeControl()
615 shaper = measBase.SdssShapeAlgorithm(sdssShape, shapeName, schema)
616 table = afwTable.SourceTable.make(schema)
617 table.defineCentroid(centroidName)
618 table.defineShape(shapeName)
624 x = int(ix*(width - 1)/(nx - 1)) + x0
625 y = int(iy*(height - 1)/(ny - 1)) + y0
627 im = afwImage.ImageD(kernel.getDimensions())
628 ksum = kernel.computeImage(im,
False, x, y)
629 lab =
"Kernel(%d,%d)=%.2f" % (x, y, ksum)
if False else ""
635 w, h = im.getWidth(), im.getHeight()
636 centerX = im.getX0() + w//2
637 centerY = im.getY0() + h//2
638 src = table.makeRecord()
641 foot.addPeak(centerX, centerY, 1)
642 src.setFootprint(foot)
645 centroider.measure(src, exp)
646 centers.append((src.getX(), src.getY()))
648 shaper.measure(src, exp)
649 shapes.append((src.getIxx(), src.getIxy(), src.getIyy()))
653 disp = afwDisplay.Display(frame=frame)
654 mos.makeMosaic(display=disp, title=title
if title
else "Model Kernel", mode=nx)
656 if centers
and frame
is not None:
657 disp = afwDisplay.Display(frame=frame)
659 with disp.Buffering():
660 for cen, shape
in zip(centers, shapes):
661 bbox = mos.getBBox(i)
663 xc, yc = cen[0] + bbox.getMinX(), cen[1] + bbox.getMinY()
665 disp.dot(
"+", xc, yc, ctype=afwDisplay.BLUE)
668 ixx, ixy, iyy = shape
669 disp.dot(
"@:%g,%g,%g" % (ixx, ixy, iyy), xc, yc, ctype=afwDisplay.RED)
675 """Plot whisker diagram of astromeric offsets between results.matches.
677 refCoordKey = results.matches[0].first.getTable().getCoordKey()
678 inCentroidKey = results.matches[0].second.getTable().getCentroidSlot().getMeasKey()
679 positions = [m.first.get(refCoordKey)
for m
in results.matches]
680 residuals = [m.first.get(refCoordKey).getOffsetFrom(
681 newWcs.pixelToSky(m.second.get(inCentroidKey)))
for
682 m
in results.matches]
683 import matplotlib.pyplot
as plt
685 sp = fig.add_subplot(1, 1, 0)
686 xpos = [x[0].asDegrees()
for x
in positions]
687 ypos = [x[1].asDegrees()
for x
in positions]
688 xpos.append(0.02*(
max(xpos) -
min(xpos)) +
min(xpos))
689 ypos.append(0.98*(
max(ypos) -
min(ypos)) +
min(ypos))
690 xidxs = np.isfinite(xpos)
691 yidxs = np.isfinite(ypos)
692 X = np.asarray(xpos)[xidxs]
693 Y = np.asarray(ypos)[yidxs]
694 distance = [x[1].asArcseconds()
for x
in residuals]
696 distance = np.asarray(distance)[xidxs]
699 bearing = [x[0].asRadians()
for x
in residuals]
701 bearing = np.asarray(bearing)[xidxs]
702 U = (distance*np.cos(bearing))
703 V = (distance*np.sin(bearing))
704 sp.quiver(X, Y, U, V)
705 sp.set_title(
"WCS Residual")
710 """Utility class for dipole measurement testing.
712 Generate an image with simulated dipoles and noise; store the original
713 "pre-subtraction" images and catalogs as well.
714 Used to generate test data for DMTN-007 (http://dmtn-007.lsst.io).
717 def __init__(self, w=101, h=101, xcenPos=[27.], ycenPos=[25.], xcenNeg=[23.], ycenNeg=[25.],
718 psfSigma=2., flux=[30000.], fluxNeg=None, noise=10., gradientParams=None):
735 """Generate an exposure and catalog with the given dipole source(s).
744 dipole = posImage.clone()
745 di = dipole.getMaskedImage()
746 di -= negImage.getMaskedImage()
749 = dipole, posImage, posCatalog, negImage, negCatalog
751 def _makeStarImage(self, xc=[15.3], yc=[18.6], flux=[2500], schema=None, randomSeed=None):
752 """Generate an exposure and catalog with the given stellar source(s).
756 dataset = TestDataset(bbox, psfSigma=self.
psfSigma, threshold=1.)
758 for i
in range(len(xc)):
759 dataset.addSource(instFlux=flux[i], centroid=
geom.Point2D(xc[i], yc[i]))
762 schema = TestDataset.makeMinimalSchema()
763 exposure, catalog = dataset.realize(noise=self.
noise, schema=schema, randomSeed=randomSeed)
766 y, x = np.mgrid[:self.
w, :self.
h]
768 gradient = gp[0] + gp[1]*x + gp[2]*y
770 gradient += gp[3]*x*y + gp[4]*x*x + gp[5]*y*y
771 imgArr = exposure.image.array
774 return exposure, catalog
778 fitResult = alg.fitDipole(source, **kwds)
782 """Utility function for detecting dipoles.
784 Detect pos/neg sources in the diffim, then merge them. A
785 bigger "grow" parameter leads to a larger footprint which
786 helps with dipole measurement for faint dipoles.
791 Whether to merge the positive and negagive detections into a single
793 diffim : `lsst.afw.image.exposure.exposure.ExposureF`
794 Difference image on which to perform detection.
795 detectSigma : `float`
796 Threshold for object detection.
798 Number of pixels to grow the footprints before merging.
800 Minimum bin size for the background (re)estimation (only applies if
801 the default leads to min(nBinX, nBinY) < fit order so the default
802 config parameter needs to be decreased, but not to a value smaller
803 than ``minBinSize``, in which case the fitting algorithm will take
804 over and decrease the fit order appropriately.)
808 sources : `lsst.afw.table.SourceCatalog`
809 If doMerge=True, the merged source catalog is returned OR
810 detectTask : `lsst.meas.algorithms.SourceDetectionTask`
811 schema : `lsst.afw.table.Schema`
812 If doMerge=False, the source detection task and its schema are
819 schema = afwTable.SourceTable.makeMinimalSchema()
822 detectConfig = measAlg.SourceDetectionConfig()
823 detectConfig.returnOriginalFootprints =
False
826 detectConfig.thresholdPolarity =
"both"
827 detectConfig.thresholdValue = detectSigma
829 detectConfig.reEstimateBackground =
True
830 detectConfig.thresholdType =
"pixel_stdev"
831 detectConfig.excludeMaskPlanes = [
"EDGE"]
833 while ((
min(diffim.getWidth(), diffim.getHeight()))//detectConfig.background.binSize
834 < detectConfig.background.approxOrderX
and detectConfig.background.binSize > minBinSize):
835 detectConfig.background.binSize =
max(minBinSize, detectConfig.background.binSize//2)
838 detectTask = measAlg.SourceDetectionTask(schema, config=detectConfig)
840 table = afwTable.SourceTable.make(schema)
841 catalog = detectTask.run(table, diffim)
845 fpSet = catalog.positive
846 fpSet.merge(catalog.negative, grow, grow,
False)
848 fpSet.makeSources(sources)
853 return detectTask, schema
857 vec = image.take(peaks[1 - axis], axis=axis)
858 low = np.interp(threshold, vec[:peaks[axis] + 1], np.arange(peaks[axis] + 1))
859 high = np.interp(threshold, vec[:peaks[axis] - 1:-1], np.arange(len(vec) - 1, peaks[axis] - 1, -1))
864 """Directly calculate the horizontal and vertical widths
865 of a PSF at half its maximum value.
869 psf : `~lsst.afw.detection.Psf`
870 Point spread function (PSF) to evaluate.
871 average : `bool`, optional
872 Set to return the average width over Y and X axes.
873 position : `~lsst.geom.Point2D`, optional
874 The position at which to evaluate the PSF. If `None`, then the
875 average position is used.
879 psfSize : `float` | `tuple` [`float`]
880 The FWHM of the PSF computed at its average position.
881 Returns the widths along the Y and X axes,
882 or the average of the two if `average` is set.
889 position = psf.getAveragePosition()
890 image = psf.computeKernelImage(position).array
891 peak = psf.computePeak(position)
892 peakLocs = np.unravel_index(np.argmax(image), image.shape)
894 return np.nanmean(width)
if average
else width
898 fwhmExposureBuffer: float, fwhmExposureGrid: int) -> float:
899 """Get the mean PSF FWHM by evaluating it on a grid within an exposure.
903 exposure : `~lsst.afw.image.Exposure`
904 The exposure for which the mean FWHM of the PSF is to be computed.
905 The exposure must contain a `psf` attribute.
906 fwhmExposureBuffer : `float`
907 Fractional buffer margin to be left out of all sides of the image
908 during the construction of the grid to compute mean PSF FWHM in an
910 fwhmExposureGrid : `int`
911 Grid size to compute the mean FWHM in an exposure.
916 The mean PSF FWHM on the exposure.
921 Raised if the PSF cannot be computed at any of the grid points.
931 bbox = exposure.getBBox()
932 xmax, ymax = bbox.getMax()
933 xmin, ymin = bbox.getMin()
935 xbuffer = fwhmExposureBuffer*(xmax-xmin)
936 ybuffer = fwhmExposureBuffer*(ymax-ymin)
939 for (x, y)
in itertools.product(np.linspace(xmin+xbuffer, xmax-xbuffer, fwhmExposureGrid),
940 np.linspace(ymin+ybuffer, ymax-ybuffer, fwhmExposureGrid)
944 fwhm = getPsfFwhm(psf, average=
True, position=pos)
945 except InvalidParameterError:
946 _LOG.debug(
"Unable to compute PSF FWHM at position (%f, %f).", x, y)
952 raise ValueError(
"Unable to compute PSF FWHM at any position on the exposure.")
954 return np.nanmean(width)
958 psfExposureBuffer: float, psfExposureGrid: int) -> afwImage.ImageD:
959 """Get the average PSF by evaluating it on a grid within an exposure.
963 exposure : `~lsst.afw.image.Exposure`
964 The exposure for which the average PSF is to be computed.
965 The exposure must contain a `psf` attribute.
966 psfExposureBuffer : `float`
967 Fractional buffer margin to be left out of all sides of the image
968 during the construction of the grid to compute average PSF in an
970 psfExposureGrid : `int`
971 Grid size to compute the average PSF in an exposure.
975 psfImage : `~lsst.afw.image.Image`
976 The average PSF across the exposure.
981 Raised if the PSF cannot be computed at any of the grid points.
985 `evaluateMeanPsfFwhm`
990 bbox = exposure.getBBox()
991 xmax, ymax = bbox.getMax()
992 xmin, ymin = bbox.getMin()
994 xbuffer = psfExposureBuffer*(xmax-xmin)
995 ybuffer = psfExposureBuffer*(ymax-ymin)
999 for (x, y)
in itertools.product(np.linspace(xmin+xbuffer, xmax-xbuffer, psfExposureGrid),
1000 np.linspace(ymin+ybuffer, ymax-ybuffer, psfExposureGrid)
1004 singleImage = psf.computeKernelImage(pos)
1005 except InvalidParameterError:
1006 _LOG.debug(
"Unable to compute PSF image at position (%f, %f).", x, y)
1009 if psfArray
is None:
1010 psfArray = singleImage.array
1012 psfArray += singleImage.array
1015 if psfArray
is None:
1016 raise ValueError(
"Unable to compute PSF image at any position on the exposure.")
1018 psfImage = afwImage.ImageD(psfArray/nImg)
1023 """Minimal source detection wrapper suitable for unit tests.
1027 exposure : `lsst.afw.image.Exposure`
1028 Exposure on which to run detection/measurement
1029 The exposure is modified in place to set the 'DETECTED' mask plane.
1030 addMaskPlanes : `list` of `str`, optional
1031 Additional mask planes to add to the maskedImage of the exposure.
1036 Source catalog containing candidates
1038 if addMaskPlanes
is None:
1041 addMaskPlanes = [
"STREAK",
"INJECTED",
"INJECTED_TEMPLATE"]
1043 schema = afwTable.SourceTable.makeMinimalSchema()
1044 selectDetection = measAlg.SourceDetectionTask(schema=schema)
1045 selectMeasurement = measBase.SingleFrameMeasurementTask(schema=schema)
1046 table = afwTable.SourceTable.make(schema)
1048 detRet = selectDetection.run(
1054 for mp
in addMaskPlanes:
1055 exposure.mask.addMaskPlane(mp)
1057 selectSources = detRet.sources
1058 selectMeasurement.run(measCat=selectSources, exposure=exposure)
1060 return selectSources
1064 """Make a fake, affine Wcs.
1068 cdMatrix = np.array([[5.19513851e-05, -2.81124812e-07],
1069 [-3.25186974e-07, -5.19112119e-05]])
1074 noiseSeed=6, fluxLevel=500., fluxRange=2.,
1075 kernelSize=32, templateBorderSize=0,
1082 doApplyCalibration=False,
1086 clearEdgeMask=False,
1089 """Make a reproduceable PSF-convolved exposure for testing.
1093 seed : `int`, optional
1094 Seed value to initialize the random number generator for sources.
1095 nSrc : `int`, optional
1096 Number of sources to simulate.
1097 psfSize : `float`, optional
1098 Width of the PSF of the simulated sources, in pixels.
1099 noiseLevel : `float`, optional
1100 Standard deviation of the noise to add to each pixel.
1101 noiseSeed : `int`, optional
1102 Seed value to initialize the random number generator for noise.
1103 fluxLevel : `float`, optional
1104 Reference flux of the simulated sources.
1105 fluxRange : `float`, optional
1106 Range in flux amplitude of the simulated sources.
1107 kernelSize : `int`, optional
1108 Size in pixels of the kernel for simulating sources.
1109 templateBorderSize : `int`, optional
1110 Size in pixels of the image border used to pad the image.
1111 background : `lsst.afw.math.Chebyshev1Function2D`, optional
1112 Optional background to add to the output image.
1113 xSize, ySize : `int`, optional
1114 Size in pixels of the simulated image.
1115 x0, y0 : `int`, optional
1116 Origin of the image.
1117 calibration : `float`, optional
1118 Conversion factor between instFlux and nJy.
1119 doApplyCalibration : `bool`, optional
1120 Apply the photometric calibration and return the image in nJy?
1121 xLoc, yLoc : `list` of `float`, optional
1122 User-specified coordinates of the simulated sources.
1123 If specified, must have length equal to ``nSrc``
1124 flux : `list` of `float`, optional
1125 User-specified fluxes of the simulated sources.
1126 If specified, must have length equal to ``nSrc``
1127 clearEdgeMask : `bool`, optional
1128 Clear the "EDGE" mask plane after source detection.
1129 addMaskPlanes : `list` of `str`, optional
1130 Mask plane names to add to the image.
1134 modelExposure : `lsst.afw.image.Exposure`
1135 The model image, with the mask and variance planes. The DETECTED
1136 plane is filled in for the injected source footprints.
1137 sourceCat : `lsst.afw.table.SourceCatalog`
1138 Catalog of sources inserted in the model image.
1143 If `xloc`, `yloc`, or `flux` are supplied with inconsistant lengths.
1147 bufferSize = kernelSize/2 + templateBorderSize + 1
1150 if templateBorderSize > 0:
1151 bbox.grow(templateBorderSize)
1153 rng = np.random.RandomState(seed)
1154 rngNoise = np.random.RandomState(noiseSeed)
1155 x0, y0 = bbox.getBegin()
1156 xSize, ySize = bbox.getDimensions()
1158 xLoc = rng.rand(nSrc)*(xSize - 2*bufferSize) + bufferSize + x0
1160 if len(xLoc) != nSrc:
1161 raise ValueError(
"xLoc must have length equal to nSrc. %f supplied vs %f", len(xLoc), nSrc)
1163 yLoc = rng.rand(nSrc)*(ySize - 2*bufferSize) + bufferSize + y0
1165 if len(yLoc) != nSrc:
1166 raise ValueError(
"yLoc must have length equal to nSrc. %f supplied vs %f", len(yLoc), nSrc)
1169 flux = (rng.rand(nSrc)*(fluxRange - 1.) + 1.)*fluxLevel
1171 if len(flux) != nSrc:
1172 raise ValueError(
"flux must have length equal to nSrc. %f supplied vs %f", len(flux), nSrc)
1173 sigmas = [psfSize
for src
in range(nSrc)]
1174 injectList = list(zip(xLoc, yLoc, flux, sigmas))
1177 modelExposure = plantSources(bbox, kernelSize, skyLevel, injectList, addPoissonNoise=
False)
1179 noise = rngNoise.randn(ySize, xSize)*noiseLevel
1180 noise -= np.mean(noise)
1181 modelExposure.variance.array = np.sqrt(np.abs(modelExposure.image.array)) + noiseLevel**2
1182 modelExposure.image.array += noise
1187 modelExposure.mask &= ~modelExposure.mask.getPlaneBitMask(
"EDGE")
1189 if background
is not None:
1190 modelExposure.image += background
1191 modelExposure.maskedImage /= calibration
1192 modelExposure.info.setId(seed)
1193 if doApplyCalibration:
1194 modelExposure.maskedImage = modelExposure.photoCalib.calibrateImage(modelExposure.maskedImage)
1198 return modelExposure, truth
1202 """Make a schema for the truth catalog produced by `makeTestImage`.
1206 keys : `dict` [`str`]
1207 Fields added to the catalog, to make it easier to set them.
1208 schema : `lsst.afw.table.Schema`
1209 Schema to use to make a "truth" SourceCatalog.
1210 Calib, Ap, and Psf flux slots all are set to ``truth_instFlux``.
1212 schema = afwTable.SourceTable.makeMinimalSchema()
1215 keys[
"instFlux"] = schema.addField(
"truth_instFlux", type=np.float64,
1216 doc=
"true instFlux", units=
"count")
1217 keys[
"instFluxErr"] = schema.addField(
"truth_instFluxErr", type=np.float64,
1218 doc=
"true instFluxErr", units=
"count")
1219 keys[
"centroid"] = afwTable.Point2DKey.addFields(schema,
"truth",
"true simulated centroid",
"pixel")
1220 schema.addField(
"truth_flag",
"Flag",
"truth flux failure flag.")
1222 schema.addField(
"sky_source",
"Flag",
"testing flag.")
1223 schema.addField(
"base_PixelFlags_flag_interpolated",
"Flag",
"testing flag.")
1224 schema.addField(
"base_PixelFlags_flag_saturated",
"Flag",
"testing flag.")
1225 schema.addField(
"base_PixelFlags_flag_bad",
"Flag",
"testing flag.")
1226 schema.getAliasMap().
set(
"slot_Centroid",
"truth")
1227 schema.getAliasMap().
set(
"slot_CalibFlux",
"truth")
1228 schema.getAliasMap().
set(
"slot_ApFlux",
"truth")
1229 schema.getAliasMap().
set(
"slot_PsfFlux",
"truth")
1234 """Add injected sources to the truth catalog.
1238 injectList : `list` [`float`]
1239 Sources that were injected; tuples of (x, y, flux, size).
1243 catalog : `lsst.afw.table.SourceCatalog`
1244 Catalog with centroids and instFlux/instFluxErr values filled in and
1245 appropriate slots set.
1249 catalog.reserve(len(injectList))
1250 for x, y, flux, size
in injectList:
1251 record = catalog.addNew()
1253 keys[
"instFlux"].
set(record, flux)
1255 keys[
"instFluxErr"].
set(record, 20)
1258 footprint = afwDetection.Footprint(afwGeom.SpanSet.fromShape(circle))
1259 footprint.addPeak(x, y, flux)
1260 record.setFootprint(footprint)
1266 """Create a statistics control for configuring calculations on images.
1270 badMaskPlanes : `list` of `str`, optional
1271 List of mask planes to exclude from calculations.
1275 statsControl : ` lsst.afw.math.StatisticsControl`
1276 Statistics control object for configuring calculations on images.
1278 if badMaskPlanes
is None:
1279 badMaskPlanes = (
"INTRP",
"EDGE",
"DETECTED",
"SAT",
"CR",
1280 "BAD",
"NO_DATA",
"DETECTED_NEGATIVE")
1282 statsControl.setNumSigmaClip(3.)
1283 statsControl.setNumIter(3)
1284 statsControl.setAndMask(afwImage.Mask.getPlaneBitMask(badMaskPlanes))
1289 """Calculate a robust mean of the variance plane of an exposure.
1293 image : `lsst.afw.image.Image`
1294 Image or variance plane of an exposure to evaluate.
1295 mask : `lsst.afw.image.Mask`
1296 Mask plane to use for excluding pixels.
1297 statsCtrl : `lsst.afw.math.StatisticsControl`
1298 Statistics control object for configuring the calculation.
1299 statistic : `lsst.afw.math.Property`, optional
1300 The type of statistic to compute. Typical values are
1301 ``afwMath.MEANCLIP`` or ``afwMath.STDEVCLIP``.
1306 The result of the statistic calculated from the unflagged pixels.
1309 return statObj.getValue(statistic)
1313 """Compute the noise equivalent area for an image psf
1317 psf : `lsst.afw.detection.Psf`
1323 psfImg = psf.computeImage(psf.getAveragePosition())
1324 nea = 1./np.sum(psfImg.array**2)
A compact representation of a collection of pixels.
An ellipse defined by an arbitrary BaseCore and a center point.
The photometric calibration of an exposure.
A kernel created from an Image.
Pass parameters to a Statistics object.
A floating-point coordinate rectangle geometry.
An integer coordinate rectangle.
Point in an unspecified spherical coordinate system.
detectDipoleSources(self, doMerge=True, diffim=None, detectSigma=5.5, grow=3, minBinSize=32)
_makeStarImage(self, xc=[15.3], yc=[18.6], flux=[2500], schema=None, randomSeed=None)
__init__(self, w=101, h=101, xcenPos=[27.], ycenPos=[25.], xcenNeg=[23.], ycenNeg=[25.], psfSigma=2., flux=[30000.], fluxNeg=None, noise=10., gradientParams=None)
fitDipoleSource(self, source, **kwds)
daf::base::PropertySet * set
std::shared_ptr< SkyWcs > makeSkyWcs(daf::base::PropertySet &metadata, bool strip=false)
Construct a SkyWcs from FITS keywords.
MaskedImage< ImagePixelT, MaskPixelT, VariancePixelT > * makeMaskedImage(typename std::shared_ptr< Image< ImagePixelT > > image, typename std::shared_ptr< Mask< MaskPixelT > > mask=Mask< MaskPixelT >(), typename std::shared_ptr< Image< VariancePixelT > > variance=Image< VariancePixelT >())
A function to return a MaskedImage of the correct type (cf.
std::shared_ptr< Exposure< ImagePixelT, MaskPixelT, VariancePixelT > > makeExposure(MaskedImage< ImagePixelT, MaskPixelT, VariancePixelT > &mimage, std::shared_ptr< geom::SkyWcs const > wcs=std::shared_ptr< geom::SkyWcs const >())
A function to return an Exposure of the correct type (cf.
Statistics makeStatistics(lsst::afw::image::Image< Pixel > const &img, lsst::afw::image::Mask< image::MaskPixel > const &msk, int const flags, StatisticsControl const &sctrl=StatisticsControl())
Handle a watered-down front-end to the constructor (no variance)
afwImage.ImageD computeAveragePsf(afwImage.Exposure exposure, float psfExposureBuffer, int psfExposureGrid)
makeTestImage(seed=5, nSrc=20, psfSize=2., noiseLevel=5., noiseSeed=6, fluxLevel=500., fluxRange=2., kernelSize=32, templateBorderSize=0, background=None, xSize=256, ySize=256, x0=12345, y0=67890, calibration=1., doApplyCalibration=False, xLoc=None, yLoc=None, flux=None, clearEdgeMask=False, addMaskPlanes=None)
plotKernelSpatialModel(kernel, kernelCellSet, showBadCandidates=True, numSample=128, keepPlots=True, maxCoeff=10)
_sliceWidth(image, threshold, peaks, axis)
detectTestSources(exposure, addMaskPlanes=None)
makeStats(badMaskPlanes=None)
showKernelMosaic(bbox, kernel, nx=7, ny=None, frame=None, title=None, showCenter=True, showEllipticity=True)
showSourceSet(sSet, xy0=(0, 0), frame=0, ctype=afwDisplay.GREEN, symb="+", size=2)
showKernelSpatialCells(maskedIm, kernelCellSet, showChi2=False, symb="o", ctype=None, ctypeUnused=None, ctypeBad=None, size=3, frame=None, title="Spatial Cells")
plotWhisker(results, newWcs)
showKernelBasis(kernel, frame=None)
_fillTruthCatalog(injectList)
showDiaSources(sources, exposure, isFlagged, isDipole, frame=None)
computePSFNoiseEquivalentArea(psf)
showKernelCandidates(kernelCellSet, kernel, background, frame=None, showBadCandidates=True, resids=False, kernels=False)
plotKernelCoefficients(spatialKernel, kernelCellSet, showBadCandidates=False, keepPlots=True)
getPsfFwhm(psf, average=True, position=None)
float evaluateMeanPsfFwhm(afwImage.Exposure exposure, float fwhmExposureBuffer, int fwhmExposureGrid)
computeRobustStatistics(image, mask, statsCtrl, statistic=afwMath.MEANCLIP)