Most unit tests pass. Ccd assembly still needs work.

Also, there are no unit tests for IsrTask methods.

python/lsst/ip/isr/__init__.py

@@ -22,7 +22,6 @@
 
 from .version import *
 from .isrLib import *
-from .assembleCcdTask import *
 from .isr import *
+from .assembleCcdTask import *
 from .isrTask import *
-

python/lsst/ip/isr/assembleCcdTask.py

@@ -28,14 +28,26 @@
 __all__ = ["AssembleCcdTask"]
 
 class AssembleCcdConfig(pexConfig.Config):
-    setGain = pexConfig.ConfigField(dtype = bool, default = True,
-        doc = "set gain?")
-    doRenorm = pexConfig.ConfigField(dtype = bool, default = True,
-        doc = "renormalize to a gain of 1? (ignored if setGain false)")
-    doTrim = pexConfig.ConfigField(dtype = bool, default = True,
-        doc = "trim out non-data regions?")
-    keysToRemove = pexConfig.ListField(dtype = str, default = (),
-        doc = "FITS headers to remove (in addition to DATASEC, BIASSEC, TRIMSEC and perhaps GAIN)")
+    setGain = pexConfig.Field(
+        doc = "set gain?",
+        dtype = bool,
+        default = True,
+    )
+    doRenorm = pexConfig.Field(
+        doc = "renormalize to a gain of 1? (ignored if setGain false)",
+        dtype = bool,
+        default = True,
+    )
+    doTrim = pexConfig.Field(
+        doc = "trim out non-data regions?",
+        dtype = bool,
+        default = True,
+    )
+    keysToRemove = pexConfig.ListField(
+        doc = "FITS headers to remove (in addition to DATASEC, BIASSEC, TRIMSEC and perhaps GAIN)",
+        dtype = str,
+        default = (),
+    )
 
 
 class AssembleCcdTask(pipeBase.Task):
@@ -47,13 +59,7 @@ class AssembleCcdTask(pipeBase.Task):
     def __init__(self, **kwargs):
         pipeBase.Task.__init__(self, **kwargs)
 
-        if self.config.setGain and self.config.doRenorm:
-            #Don't want to remove GAIN keyword as it is set by the renormalization.
-            self.allKeysToRemove = ['DATASEC', 'BIASSEC', 'TRIMSEC']
-        else:
-            self.allKeysToRemove = ['DATASEC', 'BIASSEC', 'TRIMSEC', 'GAIN']
-        for key in self.config.keysToRemove:
-            self.allKeysToRemove.append(key)
+        self.allKeysToRemove = ('DATASEC', 'BIASSEC', 'TRIMSEC', 'GAIN') + tuple(self.config.keysToRemove)
 
     def run(self, inExposure):
         """Assemble a CCD by trimming non-data areas

python/lsst/ip/isr/isr.py

@@ -89,10 +89,10 @@ def calculateSdqaCcdRatings(maskedImage, metadata):
     badmaskim = afwImage.ImageU(badmask.getBBox(afwImage.PARENT))
     badmaskim <<= badmask
     thresh = afwDetection.Threshold(0.5)
-    fs = afwDetection.makeFootprintSet(satmaskim, thresh)
+    fs = afwDetection.FootprintSet(satmaskim, thresh)
     for f in fs.getFootprints():
         metrics['nSaturatePix'] += f.getNpix()
-    fs = afwDetection.makeFootprintSet(badmaskim, thresh)
+    fs = afwDetection.FootprintSet(badmaskim, thresh)
     for f in fs.getFootprints():
         metrics['nBadCalibPix'] += f.getNpix()
     stats = afwMath.makeStatistics(maskedImage, afwMath.MEANCLIP | \
@@ -125,7 +125,7 @@ def calculateSdqaAmpRatings(maskedImage, metadata, biasBBox, dataBBox):
     satmaskim = afwImage.ImageU(satmask.getBBox(afwImage.PARENT))
     satmaskim <<= satmask
     thresh = afwDetection.Threshold(0.5)
-    fs = afwDetection.makeFootprintSet(satmaskim, thresh)
+    fs = afwDetection.FootprintSet(satmaskim, thresh)
     for f in fs.getFootprints():
         metrics['nSaturatePix'] += f.getNpix()
     stats = afwMath.makeStatistics(biasmi, afwMath.MEAN | \
@@ -232,7 +232,7 @@ def getDefectListFromMask(maskedImage, maskName, growFootprints=1):
     thresh = afwDetection.Threshold(0.5)
     maskimg = afwImage.ImageU(workmask.getBBox(afwImage.PARENT))
     maskimg <<= workmask
-    ds = afwDetection.makeFootprintSet(maskimg, thresh)
+    ds = afwDetection.FootprintSet(maskimg, thresh)
     fpList = ds.getFootprints()
     return defectListFromFootprintList(fpList, growFootprints)
 
@@ -246,7 +246,7 @@ def makeThresholdMask(maskedImage, threshold, growFootprints=1, maskName = 'SAT'
     """
     # find saturated regions
     thresh = afwDetection.Threshold(threshold)
-    ds = afwDetection.makeFootprintSet(maskedImage, thresh)
+    ds = afwDetection.FootprintSet(maskedImage, thresh)
     fpList = ds.getFootprints()
     # set mask
     mask = maskedImage.getMask()

python/lsst/ip/isr/isrTask.py

@@ -354,10 +354,10 @@ def maskAndInterpNan(self, exposure):
         unc.apply(exposure.getMaskedImage())
         nnans = unc.getNpix()
         self.metadata.set("NUMNANS", nnans)
-        if not nnans == 0:
-		raise RuntimeError("There were %i unmasked NaNs"%(nnans))
+
         #get footprints of bad pixels not in the camera class
         if nnans > 0:
+            self.log.log(self.log.WARN, "There were %i unmasked NaNs" % (nnans,))
             undefects = isr.getDefectListFromMask(exposure.getMaskedImage(), maskName='UNMASKEDNAN', growFootprints=grow)
             #interpolate all bad pixels
             if self.transposeForInterpolation:

tests/testBiasAndDarkCorrection.py

@@ -21,88 +21,66 @@
 # the GNU General Public License along with this program.  If not, 
 # see <http://www.lsstcorp.org/LegalNotices/>.
 #
-
 import os
-
 import unittest
-import lsst.utils.tests as tests
 
-import eups
-import lsst.afw.detection as afwDetection
+import lsst.utils.tests as tests
 import lsst.afw.image as afwImage
 import lsst.afw.geom as afwGeom
-import lsst.pex.policy as pexPolicy
-from lsst.ip.isr import Isr
-import lsst.pex.logging as logging
-
-import lsst.afw.display.ds9 as ds9
-
-Verbosity = 4
-logging.Trace_setVerbosity('lsst.ip.isr', Verbosity)
-
-isrDir     = eups.productDir('ip_isr')
-
-
-# Policy file
-InputIsrPolicy = os.path.join(isrDir, 'pipeline', 'isrPolicy.paf')
+import lsst.ip.isr as ipIsr
 
 class IsrTestCases(unittest.TestCase):
-
     def setUp(self):
-        self.policy = pexPolicy.Policy.createPolicy(InputIsrPolicy)
         self.pmin = afwGeom.Point2I(1,1)
         self.pmax = afwGeom.Point2I(10,10)
-        self.isr = Isr()
+        self.meanCountsKeyword = "IMMODE"
+        self.filenameKeyword = "filename"
 
     def tearDown(self):
-        del self.policy
         del self.pmin
         del self.pmax
-        del self.isr
+        del self.meanCountsKeyword
+        del self.filenameKeyword
 
     def testBias(self):
-        meanCountsKeyword = self.policy.getString('biasPolicy.meanCountsKeyword')
-        filenameKeyword   = self.policy.getString('filenameKeyword')
-        mi = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
-        mi.getImage().set(10)
-        exposure = afwImage.ExposureF(mi, afwImage.Wcs())
+        maskedImage = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
+        maskedImage.getImage().set(10)
+        exposure = afwImage.ExposureF(maskedImage, afwImage.Wcs())
 
         bias = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
         bias.getImage().set(1)
         biasexposure = afwImage.ExposureF(bias, afwImage.Wcs())
         bmetadata = biasexposure.getMetadata()
-        bmetadata.setDouble(meanCountsKeyword, 1.)
-        bmetadata.setString(filenameKeyword, 'Unittest Bias')
+        bmetadata.setDouble(self.meanCountsKeyword, 1.)
+        bmetadata.setString(self.filenameKeyword, 'Unittest Bias')
 
-        self.isr.biasCorrection(exposure.getMaskedImage(), biasexposure.getMaskedImage())
+        ipIsr.biasCorrection(maskedImage, biasexposure.getMaskedImage())
 
-        height        = mi.getHeight()
-        width         = mi.getWidth()
+        height = maskedImage.getHeight()
+        width  = maskedImage.getWidth()
         for j in range(height):
             for i in range(width):
-                self.assertEqual(mi.getImage().get(i,j), 9)
+                self.assertEqual(maskedImage.getImage().get(i,j), 9)
 
     def doDark(self, scaling):
-        filenameKeyword  = self.policy.getString('filenameKeyword')
-
-        mi = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
-        mi.getImage().set(10)
-        exposure = afwImage.ExposureF(mi, afwImage.Wcs())
+        maskedImage = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
+        maskedImage.getImage().set(10)
+        exposure = afwImage.ExposureF(maskedImage, afwImage.Wcs())
         metadata = exposure.getMetadata()
 
         dark = afwImage.MaskedImageF(afwGeom.Box2I(self.pmin, self.pmax))
         dark.getImage().set(1)
         darkexposure = afwImage.ExposureF(dark, afwImage.Wcs())
         dmetadata = darkexposure.getMetadata()
-        dmetadata.setString(filenameKeyword, 'Unittest Dark')
+        dmetadata.setString(self.filenameKeyword, 'Unittest Dark')
 
-        self.isr.darkCorrection(exposure.getMaskedImage(), darkexposure.getMaskedImage(), 1., scaling)
+        ipIsr.darkCorrection(maskedImage, darkexposure.getMaskedImage(), 1., scaling)
 
-        height        = mi.getHeight()
-        width         = mi.getWidth()
+        height        = maskedImage.getHeight()
+        width         = maskedImage.getWidth()
         for j in range(height):
             for i in range(width):
-                self.assertAlmostEqual(mi.getImage().get(i,j), 10 - 1./scaling, 5)
+                self.assertAlmostEqual(maskedImage.getImage().get(i,j), 10 - 1./scaling, 5)
 
     def testDark1(self):
         self.doDark(scaling=10)
@@ -112,9 +90,8 @@ def testDark2(self):
 
     def testDark3(self):
         self.doDark(scaling=3.7)
-
-#####
-
+
+
 def suite():
     """Returns a suite containing all the test cases in this module."""
     tests.init()

tests/testCcdAssemble.py

@@ -21,7 +21,6 @@
 # the GNU General Public License along with this program.  If not, 
 # see <http://www.lsstcorp.org/LegalNotices/>.
 #
-
 import os
 
 import unittest
@@ -46,12 +45,11 @@
 afwDir = eups.productDir('afw')
 
 # Policy file
-cameraPolicy = os.path.join(afwDir, 'tests', 'TestCameraGeom.paf')
+CameraPolicyPath = os.path.join(afwDir, 'tests', 'TestCameraGeom.paf')
 
 class IsrTestCases(unittest.TestCase):
-
     def setUp(self):
-        self.cameraPolicy = cameraGeomUtils.getGeomPolicy(cameraPolicy)
+        self.cameraPolicy = cameraGeomUtils.getGeomPolicy(CameraPolicyPath)
         afwImage.Filter.reset()
         afwImage.FilterProperty.reset()
 
@@ -75,8 +73,12 @@ def testCcdAssemble(self):
             exp.setFilter(afwImage.Filter("g"))
             exp.getCalib().setExptime(15)
             exposureList.append(exp)
-        assembler = ipIsr.CcdAssembler(exposureList, reNorm = False, isTrimmed=True)
-        aexp = assembler.assembleCcd()
+
+        assemblerConfig = ipIsr.AssembleCcdTask.ConfigClass()
+        assemblerConfig.reNorm = False
+        assembler = ipIsr.AssembleCcdTask(config=assemblerConfig)
+
+        aexp = assembler.run(exposureList).exposure
         xpos = [50,150]
         ypos = [25,76,137,188]
         ind = 0
@@ -87,7 +89,6 @@ def testCcdAssemble(self):
         if display:
             ds9.mtv(aexp)
 
-#####
 
 def suite():
     """Returns a suite containing all the test cases in this module."""