Merge pull request #249 from lsst/tickets/DM-39934

DM-39934: Deprecate afw MaskedImage.getArrays()

python/lsst/meas/base/tests.py

@@ -114,9 +114,9 @@ def __exit__(self, type_, value, tb):
         self.owner._installFootprint(self.parentRecord, self.parentImage)
         # Create perfect HeavyFootprints for all children; these will need to
         # be modified later to account for the noise we'll add to the image.
-        deblend = lsst.afw.image.MaskedImageF(self.owner.exposure.getMaskedImage(), True)
+        deblend = lsst.afw.image.MaskedImageF(self.owner.exposure.maskedImage, True)
         for record, image in self.children:
-            deblend.getImage().getArray()[:, :] = image.getArray()
+            deblend.image.array[:, :] = image.array
             heavyFootprint = lsst.afw.detection.HeavyFootprintF(self.parentRecord.getFootprint(), deblend)
             record.setFootprint(heavyFootprint)
 
@@ -377,7 +377,7 @@ def drawGaussian(bbox, instFlux, ellipse):
         xt = t[t.XX] * x + t[t.XY] * y + t[t.X]
         yt = t[t.YX] * x + t[t.YY] * y + t[t.Y]
         image = lsst.afw.image.ImageF(bbox)
-        image.getArray()[:, :] = np.exp(-0.5*(xt**2 + yt**2))*instFlux/(2.0*ellipse.getCore().getArea())
+        image.array[:, :] = np.exp(-0.5*(xt**2 + yt**2))*instFlux/(2.0*ellipse.getCore().getArea())
         return image
 
     def __init__(self, bbox, threshold=10.0, exposure=None, **kwds):
@@ -406,7 +406,7 @@ def _installFootprint(self, record, image, setPeakSignificance=True):
             for footprint in fpSet.getFootprints():
                 footprint.updatePeakSignificance(self.threshold.getValue())
         # Update the full exposure's mask plane to indicate the detection
-        fpSet.setMask(self.exposure.getMaskedImage().getMask(), "DETECTED")
+        fpSet.setMask(self.exposure.mask, "DETECTED")
         # Attach the new footprint to the exposure
         if len(fpSet.getFootprints()) > 1:
             raise RuntimeError("Threshold value results in multiple Footprints for a single object")
@@ -459,7 +459,7 @@ def addSource(self, instFlux, centroid, shape=None, setPeakSignificance=True):
         # Generate a footprint for this source
         self._installFootprint(record, image, setPeakSignificance)
         # Actually add the source to the full exposure
-        self.exposure.getMaskedImage().getImage().getArray()[:, :] += image.getArray()
+        self.exposure.image.array[:, :] += image.array
         return record, image
 
     def addBlend(self):
@@ -563,9 +563,8 @@ def realize(self, noise, schema, randomSeed=1):
         mapper = lsst.afw.table.SchemaMapper(self.schema)
         mapper.addMinimalSchema(self.schema, True)
         exposure = self.exposure.clone()
-        exposure.getMaskedImage().getVariance().getArray()[:, :] = noise**2
-        exposure.getMaskedImage().getImage().getArray()[:, :] \
-            += random_state.randn(exposure.getHeight(), exposure.getWidth())*noise
+        exposure.variance.array[:, :] = noise**2
+        exposure.image.array[:, :] += random_state.randn(exposure.getHeight(), exposure.getWidth())*noise
         catalog = lsst.afw.table.SourceCatalog(schema)
         catalog.extend(self.catalog, mapper=mapper)
         # Loop over sources and generate new HeavyFootprints that divide up
@@ -581,11 +580,11 @@ def realize(self, noise, schema, randomSeed=1):
             footprint = parent.getFootprint()
             parentFluxArrayNoNoise = np.zeros(footprint.getArea(), dtype=np.float32)
             footprint.spans.flatten(parentFluxArrayNoNoise,
-                                    self.exposure.getMaskedImage().getImage().getArray(),
+                                    self.exposure.image.array,
                                     self.exposure.getXY0())
             parentFluxArrayNoisy = np.zeros(footprint.getArea(), dtype=np.float32)
             footprint.spans.flatten(parentFluxArrayNoisy,
-                                    exposure.getMaskedImage().getImage().getArray(),
+                                    exposure.image.array,
                                     exposure.getXY0())
             oldHeavy = record.getFootprint()
             fraction = (oldHeavy.getImageArray() / parentFluxArrayNoNoise)

tests/test_FlagHandler.py

@@ -114,7 +114,7 @@ def measure(self, measRecord, exposure):
             raise MeasurementError(self.EDGE.doc, self.EDGE.number)
 
         # Sum the pixels inside the bounding box
-        instFlux = lsst.afw.image.ImageF(exposure.getMaskedImage().getImage(), bbox).getArray().sum()
+        instFlux = lsst.afw.image.ImageF(exposure.image, bbox).array.sum()
         measRecord.set(self.instFluxKey, instFlux)
 
         # If there was a NaN inside the bounding box, the instFlux will still
@@ -289,7 +289,7 @@ def testPluginContainsNan(self):
         task = lsst.meas.base.SingleFrameMeasurementTask(schema=schema, config=self.config)
         exposure, cat = self.dataset.realize(noise=100.0, schema=schema, randomSeed=2)
         source = cat[0]
-        exposure.getMaskedImage().getImage().getArray()[int(source.getY()), int(source.getX())] = np.nan
+        exposure.image.array[int(source.getY()), int(source.getX())] = np.nan
         task.run(cat, exposure)
         self.assertTrue(source.get(self.algName + "_flag"))
         self.assertTrue(source.get(self.algName + "_flag_containsNan"))

tests/test_ImportCentroidAlgorithm.py

@@ -89,7 +89,7 @@ def testMeasureCentroid(self):
 
         im = afwImage.MaskedImageF(lsst.geom.ExtentI(512, 512))
         im.set(0)
-        arr = im.getImage().getArray()
+        arr = im.image.array
         arr[y, x] = 1000
         exp = afwImage.makeExposure(im)
 

tests/test_InputCount.py

@@ -91,7 +91,7 @@ def ccdVennDiagram(exp, showImage=True, legendLocation='best'):
     # If showImage is true, plot the data contained in exp as well as the
     # boundaries
     if showImage:
-        plt.imshow(exp.getMaskedImage().getArrays()[0], cmap='Greys', origin='lower')
+        plt.imshow(exp.image.array, cmap='Greys', origin='lower')
         plt.colorbar()
     # Adjust plot parameters and plot
     plt.gca().relim()

tests/test_MeasureSources.py

@@ -112,8 +112,8 @@ def testPeakLikelihoodFlux(self):
         psf = afwDetection.GaussianPsf(kernelWidth, kernelWidth, sigma)
         psfKernel = psf.getLocalKernel(psf.getAveragePosition())
         psfImage = psf.computeKernelImage(psf.getAveragePosition())
-        sumPsfSq = np.sum(psfImage.getArray()**2)
-        psfSqArr = psfImage.getArray()**2
+        sumPsfSq = np.sum(psfImage.array**2)
+        psfSqArr = psfImage.array**2
 
         for instFlux in (1000, 10000):
             ctrInd = lsst.geom.Point2I(50, 51)
@@ -142,8 +142,8 @@ def testPeakLikelihoodFlux(self):
             # = sqrt(sum(unfiltered variance * PSF^2)) / sum(PSF^2)
             # and compare to that derived from filtered pixels;
             # again, this is a test of the algorithm
-            varView = afwImage.ImageF(unshMImage.getVariance(), kernelBBox)
-            varArr = varView.getArray()
+            varView = afwImage.ImageF(unshMImage.variance, kernelBBox)
+            varArr = varView.array
             unfiltPredFluxErr = math.sqrt(np.sum(varArr*psfSqArr)) / sumPsfSq
             self.assertLess(abs(unfiltPredFluxErr - predFluxErr), predFluxErr * 0.01)
 
@@ -213,8 +213,8 @@ def testPixelFlags(self):
         width, height = 100, 100
         mi = afwImage.MaskedImageF(width, height)
         exp = afwImage.makeExposure(mi)
-        mi.getImage().set(0)
-        mask = mi.getMask()
+        mi.image.set(0)
+        mask = mi.mask
         sat = mask.getPlaneBitMask('SAT')
         interp = mask.getPlaneBitMask('INTRP')
         edge = mask.getPlaneBitMask('EDGE')
@@ -378,10 +378,10 @@ def makeFakeImage(bbox, centerList, instFluxList, fwhm, var):
     if len(centerList) != len(instFluxList):
         raise RuntimeError("len(centerList) != len(instFluxList)")
     maskedImage = afwImage.MaskedImageF(bbox)
-    image = maskedImage.getImage()
+    image = maskedImage.image
     for center, instFlux in zip(centerList, instFluxList):
         addStar(image, center=center, instFlux=instFlux, fwhm=fwhm)
-    variance = maskedImage.getVariance()
+    variance = maskedImage.variance
     variance[:] = image
     variance += var
     return maskedImage

tests/test_NoiseReplacer.py

@@ -51,7 +51,7 @@ def __init__(self, config, name, schema, metadata):
 
     def measure(self, measRecord, exposure):
         footprint = measRecord.getFootprint()
-        fullArray = exposure.getMaskedImage().getImage().getArray()
+        fullArray = exposure.image.array
         insideArray = np.zeros(footprint.getArea(), dtype=fullArray.dtype)
         footprint.spans.flatten(insideArray, fullArray, exposure.getXY0())
         insideFlux = float(insideArray.sum())
@@ -94,7 +94,7 @@ def testNoiseReplacer(self, noiseSource, variance):
             md['BGMEAN'] = variance
             exposure.setMetadata(md)
         task.run(catalog, exposure)
-        sumVariance = exposure.getMaskedImage().getVariance().getArray().sum()
+        sumVariance = exposure.variance.array.sum()
         for record in catalog:
             self.assertFloatsAlmostEqual(record.get("test_NoiseReplacer_inside"),
                                          record.get("truth_instFlux"), rtol=1E-3)

tests/test_PluginLogs.py

@@ -83,7 +83,7 @@ def measure(self, measRecord, exposure):
         # Sum the pixels inside the bounding box
         centerPoint = lsst.geom.Point2I(int(measRecord.getX()), int(measRecord.getY()))
         bbox = lsst.geom.Box2I(centerPoint, lsst.geom.Extent2I(1, 1))
-        instFlux = lsst.afw.image.ImageF(exposure.getMaskedImage().getImage(), bbox).getArray().sum()
+        instFlux = lsst.afw.image.ImageF(exposure.image, bbox).array.sum()
         measRecord.set(self.instFluxKey, instFlux)
 
         # If there was a NaN inside the bounding box, the instFlux will still

tests/test_PsfFlux.py

@@ -95,9 +95,9 @@ def testMasking(self):
         exposure, catalog = self.dataset.realize(10.0, schema, randomSeed=0)
         record = catalog[0]
         badPoint = lsst.geom.Point2I(self.center) + lsst.geom.Extent2I(3, 4)
-        imageArray = exposure.getMaskedImage().getImage().getArray()
-        maskArray = exposure.getMaskedImage().getMask().getArray()
-        badMask = exposure.getMaskedImage().getMask().getPlaneBitMask("BAD")
+        imageArray = exposure.image.array
+        maskArray = exposure.mask.array
+        badMask = exposure.mask.getPlaneBitMask("BAD")
         imageArray[badPoint.getY() - exposure.getY0(), badPoint.getX() - exposure.getX0()] = np.inf
         maskArray[badPoint.getY() - exposure.getY0(), badPoint.getX() - exposure.getX0()] |= badMask
         # Should get an infinite value exception, because we didn't mask that

tests/test_SdssCentroid.py

@@ -169,7 +169,7 @@ def testNo2ndDerivative(self):
         bbox.grow(20)
         subImage = lsst.afw.image.ExposureF(exposure, bbox)
         # A completely flat image will trigger the no 2nd derivative error
-        subImage.getMaskedImage().getImage().getArray()[:] = 0
+        subImage.image.array[:] = 0
         task.measure(catalog, subImage)
         self.assertTrue(catalog[0].get("base_SdssCentroid_flag"))
         self.assertTrue(catalog[0].get("base_SdssCentroid_flag_noSecondDerivative"))
@@ -182,7 +182,7 @@ def testNotAtMaximum(self):
         bbox.grow(20)
         subImage = lsst.afw.image.ExposureF(exposure, bbox)
         # zero out the central region, which will destroy the maximum
-        subImage.getMaskedImage().getImage().getArray()[18:22, 18:22] = 0
+        subImage.image.array[18:22, 18:22] = 0
         task.measure(catalog, subImage)
         self.assertTrue(catalog[0].get("base_SdssCentroid_flag"))
         self.assertTrue(catalog[0].get("base_SdssCentroid_flag_notAtMaximum"))

tests/test_Variance.py

@@ -55,12 +55,12 @@ def setUp(self):
 
         # Initial setup of an image
         exp = afwImage.ExposureF(size, size)
-        image = exp.getMaskedImage().getImage()
-        mask = exp.getMaskedImage().getMask()
-        var = exp.getMaskedImage().getVariance()
+        image = exp.image
+        mask = exp.mask
+        var = exp.variance
         image.set(0.0)
         mask.set(0)
-        var.getArray()[:, :] = variancePlane
+        var.array[:, :] = variancePlane
 
         # Put down a PSF
         psfSize = int(6*width + 1)  # Size of PSF image; must be odd
@@ -74,17 +74,17 @@ def setUp(self):
         # Put in some bad pixels to ensure they're ignored
         for i in range(-5, 6):
             bad = size//2 + i*width
-            var.getArray()[bad, :] = float("nan")
-            mask.getArray()[bad, :] = mask.getPlaneBitMask("BAD")
-            var.getArray()[:, bad] = float("nan")
-            mask.getArray()[:, bad] = mask.getPlaneBitMask("BAD")
+            var.array[bad, :] = float("nan")
+            mask.array[bad, :] = mask.getPlaneBitMask("BAD")
+            var.array[:, bad] = float("nan")
+            mask.array[:, bad] = mask.getPlaneBitMask("BAD")
 
         # Put in some unmasked bad pixels outside the expected aperture, to
         # ensure the aperture is working
-        var.getArray()[0, 0] = float("nan")
-        var.getArray()[0, -1] = float("nan")
-        var.getArray()[-1, 0] = float("nan")
-        var.getArray()[-1, -1] = float("nan")
+        var.array[0, 0] = float("nan")
+        var.array[0, -1] = float("nan")
+        var.array[-1, 0] = float("nan")
+        var.array[-1, -1] = float("nan")
 
         if display:
             import lsst.afw.display as afwDisplay
@@ -149,7 +149,7 @@ def testVariance(self):
 
     def testEmptyFootprint(self):
         # Set the pixel mask for all pixels to ``BAD`` and remeasure.
-        self.mask.getArray()[:, :] = self.mask.getPlaneBitMask("BAD")
+        self.mask.array[:, :] = self.mask.getPlaneBitMask("BAD")
         self.task.run(self.catalog, self.exp)
 
         # The computed variance should be NaN and flag_emptyFootprint should