Merge pull request #213 from lsst/tickets/DM-10302

DM-10302 Change flux->instFlux

examples/photoCalTask.py

@@ -61,7 +61,7 @@ def loadData():
     # Read sources
     #
     srcCat = afwTable.SourceCatalog.readFits(os.path.join(mypath, "tests", "v695833-e0-c000.xy.fits"))
-    srcCat.getPsfFluxErr()[:] = np.sqrt(srcCat.getPsfFlux())
+    srcCat.getPsfInstFluxErr()[:] = np.sqrt(srcCat.getPsfInstFlux())
 
     return exposure, srcCat
 
@@ -88,7 +88,7 @@ def run():
     config = PhotoCalTask.ConfigClass()
     config.applyColorTerms = False      # we don't have any available, so this suppresses a warning
     # The associated data has been prepared on the basis that we use PsfFlux to perform photometry.
-    config.fluxField = "base_PsfFlux_flux"
+    config.fluxField = "base_PsfFlux_instFlux"
     pTask = PhotoCalTask(config=config, schema=schema)
     #
     # The tasks may have added extra elements to the schema (e.g. AstrometryTask's centroidKey to
@@ -102,7 +102,7 @@ def run():
         print("Adding columns to the source catalogue")
         cat = afwTable.SourceCatalog(schema)
         cat.table.defineCentroid(srcCat.table.getCentroidDefinition())
-        cat.table.definePsfFlux(srcCat.table.getPsfFluxDefinition())
+        cat.table.definePsfFlux(srcCat.table.schema.get("slot_psfFlux"))
 
         scm = afwTable.SchemaMapper(srcCat.getSchema(), schema)
         for schEl in srcCat.getSchema():

python/lsst/pipe/tasks/imageDifference.py

@@ -629,8 +629,9 @@ def runDataRef(self, sensorRef, templateIdList=None):
                     exposure, diaSources, subtractedExposure.getWcs())
                 self.forcedMeasurement.run(forcedSources, exposure, diaSources, subtractedExposure.getWcs())
                 mapper = afwTable.SchemaMapper(forcedSources.schema, diaSources.schema)
-                mapper.addMapping(forcedSources.schema.find("base_PsfFlux_flux")[0], "totFlux", True)
-                mapper.addMapping(forcedSources.schema.find("base_PsfFlux_fluxErr")[0], "totFluxErr", True)
+                mapper.addMapping(forcedSources.schema.find("base_PsfFlux_instFlux")[0], "totFlux", True)
+                mapper.addMapping(forcedSources.schema.find("base_PsfFlux_instFluxErr")[0],
+                                  "totFluxErr", True)
                 for diaSource, forcedSource in zip(diaSources, forcedSources):
                     diaSource.assign(forcedSource, mapper)
 

python/lsst/pipe/tasks/mocks/mockObservation.py

@@ -241,8 +241,8 @@ def makeRandomBoundedField():
         bbox = detector.getBBox()
         apCorrMap = lsst.afw.image.ApCorrMap()
         for name in getApCorrNameSet():
-            apCorrMap.set(name + "_flux", makeRandomBoundedField())
-            apCorrMap.set(name + "_fluxErr", makeRandomBoundedField())
+            apCorrMap.set(name + "_instFlux", makeRandomBoundedField())
+            apCorrMap.set(name + "_instFluxErr", makeRandomBoundedField())
         return apCorrMap
 
     def buildTransmissionCurve(self, detector):

python/lsst/pipe/tasks/multiBand.py

@@ -1542,8 +1542,8 @@ def __init__(self, butler=None, schema=None, **kwargs):
         inputSchema = self.getInputSchema(butler=butler, schema=schema)
         self.schemaMapper = afwTable.SchemaMapper(inputSchema, True)
         self.schemaMapper.addMinimalSchema(inputSchema, True)
-        self.fluxKey = inputSchema.find(self.config.snName + "_flux").getKey()
-        self.fluxErrKey = inputSchema.find(self.config.snName + "_fluxErr").getKey()
+        self.instFluxKey = inputSchema.find(self.config.snName + "_instFlux").getKey()
+        self.instFluxErrKey = inputSchema.find(self.config.snName + "_instFluxErr").getKey()
         self.fluxFlagKey = inputSchema.find(self.config.snName + "_flag").getKey()
 
         self.flagKeys = {}
@@ -1626,10 +1626,10 @@ def run(self, catalogs, patchRef):
                         break
 
                 isBad = any(inputRecord.get(flag) for flag in self.badFlags)
-                if isBad or inputRecord.get(self.fluxFlagKey) or inputRecord.get(self.fluxErrKey) == 0:
+                if isBad or inputRecord.get(self.fluxFlagKey) or inputRecord.get(self.instFluxErrKey) == 0:
                     sn = 0.
                 else:
-                    sn = inputRecord.get(self.fluxKey)/inputRecord.get(self.fluxErrKey)
+                    sn = inputRecord.get(self.instFluxKey)/inputRecord.get(self.instFluxErrKey)
                 if numpy.isnan(sn) or sn < 0.:
                     sn = 0.
                 if (parent or child) and priorityRecord is None:

python/lsst/pipe/tasks/photoCal.py

@@ -43,8 +43,8 @@ class PhotoCalConfig(pexConf.Config):
     reserve = pexConf.ConfigurableField(target=ReserveSourcesTask, doc="Reserve sources from fitting")
     fluxField = pexConf.Field(
         dtype=str,
-        default="slot_CalibFlux_flux",
-        doc=("Name of the source flux field to use.  The associated flag field\n"
+        default="slot_CalibFlux_instFlux",
+        doc=("Name of the source instFlux field to use.  The associated flag field\n"
              "('<name>_flags') will be implicitly included in badFlags."),
     )
     applyColorTerms = pexConf.Field(
@@ -259,15 +259,26 @@ def __init__(self, refObjLoader, schema=None, **kwds):
                          doc="set if source was reserved from photometric calibration")
 
     def getSourceKeys(self, schema):
-        """!Return a struct containing the source catalog keys for fields used by PhotoCalTask.
+        """Return a struct containing the source catalog keys for fields used
+        by PhotoCalTask.
 
-        Returned fields include:
-        - flux
-        - fluxErr
+
+        Parameters
+        ----------
+        schema : `lsst.afw.table.schema`
+            Schema of the catalog to get keys from.
+
+        Returns
+        -------
+        result : `lsst.pipe.base.Struct`
+            Result struct with components:
+
+            - ``instFlux``: Instrument flux key.
+            - ``instFluxErr``: Instrument flux error key.
         """
-        flux = schema.find(self.config.fluxField).key
-        fluxErr = schema.find(self.config.fluxField + "Err").key
-        return pipeBase.Struct(flux=flux, fluxErr=fluxErr)
+        instFlux = schema.find(self.config.fluxField).key
+        instFluxErr = schema.find(self.config.fluxField + "Err").key
+        return pipeBase.Struct(instFlux=instFlux, instFluxErr=instFluxErr)
 
     @pipeBase.timeMethod
     def extractMagArrays(self, matches, filterName, sourceKeys):
@@ -286,17 +297,17 @@ def extractMagArrays(self, matches, filterName, sourceKeys):
         @note These magnitude arrays are the @em inputs to the photometric calibration, some may have been
         discarded by clipping while estimating the calibration (https://jira.lsstcorp.org/browse/DM-813)
         """
-        srcFluxArr = np.array([m.second.get(sourceKeys.flux) for m in matches])
-        srcFluxErrArr = np.array([m.second.get(sourceKeys.fluxErr) for m in matches])
-        if not np.all(np.isfinite(srcFluxErrArr)):
+        srcInstFluxArr = np.array([m.second.get(sourceKeys.instFlux) for m in matches])
+        srcInstFluxErrArr = np.array([m.second.get(sourceKeys.instFluxErr) for m in matches])
+        if not np.all(np.isfinite(srcInstFluxErrArr)):
             # this is an unpleasant hack; see DM-2308 requesting a better solution
             self.log.warn("Source catalog does not have flux uncertainties; using sqrt(flux).")
-            srcFluxErrArr = np.sqrt(srcFluxArr)
+            srcInstFluxErrArr = np.sqrt(srcInstFluxArr)
 
-        # convert source flux from DN to an estimate of Jy
+        # convert source instFlux from DN to an estimate of Jy
         JanskysPerABFlux = 3631.0
-        srcFluxArr = srcFluxArr * JanskysPerABFlux
-        srcFluxErrArr = srcFluxErrArr * JanskysPerABFlux
+        srcInstFluxArr = srcInstFluxArr * JanskysPerABFlux
+        srcInstFluxErrArr = srcInstFluxErrArr * JanskysPerABFlux
 
         if not matches:
             raise RuntimeError("No reference stars are available")
@@ -364,16 +375,19 @@ def extractMagArrays(self, matches, filterName, sourceKeys):
         else:
             refMagArr = np.array([abMagFromFlux(rf) for rf in refFluxArrList[0]])
 
-        srcMagArr = np.array([abMagFromFlux(sf) for sf in srcFluxArr])
+        srcMagArr = np.array([abMagFromFlux(sf) for sf in srcInstFluxArr])
 
         # Fitting with error bars in both axes is hard
         # for now ignore reference flux error, but ticket DM-2308 is a request for a better solution
-        magErrArr = np.array([abMagErrFromFluxErr(fe, sf) for fe, sf in zip(srcFluxErrArr, srcFluxArr)])
+        magErrArr = np.array([abMagErrFromFluxErr(fe, sf)
+                             for fe, sf in zip(srcInstFluxErrArr, srcInstFluxArr)])
         if self.config.magErrFloor != 0.0:
             magErrArr = (magErrArr**2 + self.config.magErrFloor**2)**0.5
 
-        srcMagErrArr = np.array([abMagErrFromFluxErr(sfe, sf) for sfe, sf in zip(srcFluxErrArr, srcFluxArr)])
-        refMagErrArr = np.array([abMagErrFromFluxErr(rfe, rf) for rfe, rf in zip(refFluxErrArr, refFluxArr)])
+        srcMagErrArr = np.array([abMagErrFromFluxErr(sfe, sf)
+                                for sfe, sf in zip(srcInstFluxErrArr, srcInstFluxArr)])
+        refMagErrArr = np.array([abMagErrFromFluxErr(rfe, rf)
+                                for rfe, rf in zip(refFluxErrArr, refFluxArr)])
 
         good = np.isfinite(srcMagArr) & np.isfinite(refMagArr)
 

tests/test_fakeProcessing.py

@@ -170,7 +170,7 @@ def checkSourceCatalog(self, srcCat, thresh=5):
             for fakePos, fakeIntensity in FakeSourcesTestTask.fakeSources:
                 distSq = (srcX - fakePos.x)**2 + (srcY - fakePos.y)**2
                 if distSq <= thresh**2:
-                    fluxDiff = abs(source.getPsfFlux() - fakeIntensity)
+                    fluxDiff = abs(source.getPsfInstFlux() - fakeIntensity)
                     self.assertLessEqual(fluxDiff, 5*np.sqrt(fakeIntensity))
                     fakeSourceCounter += 1
         # Verify the correct number of fake sources were found

tests/test_photoCal.py

@@ -63,8 +63,8 @@ def setUp(self):
         self.srcCat = afwTable.SourceCatalog.readFits(
             os.path.join(testDir, "data", "v695833-e0-c000.xy.fits"))
 
-        self.srcCat["slot_ApFlux_fluxErr"] = 1
-        self.srcCat["slot_PsfFlux_fluxErr"] = 1
+        self.srcCat["slot_ApFlux_instFluxErr"] = 1
+        self.srcCat["slot_PsfFlux_instFluxErr"] = 1
 
         # The .xy.fits file has sources in the range ~ [0,2000],[0,4500]
         # which is bigger than the exposure
@@ -92,15 +92,15 @@ def setUp(self):
         self.config.match.matchRadius = 0.5
         self.config.match.referenceSelection.doMagLimit = True
         self.config.match.referenceSelection.magLimit.maximum = 22.0
-        self.config.match.referenceSelection.magLimit.fluxField = "i_flux"
+        self.config.match.referenceSelection.magLimit.fluxField = "i_instFlux"
         self.config.match.referenceSelection.doFlags = True
         self.config.match.referenceSelection.flags.good = ['photometric']
         self.config.match.referenceSelection.flags.bad = ['resolved']
         self.config.match.sourceSelection.doUnresolved = False  # Don't have star/galaxy in the srcCat
 
         # The test and associated data have been prepared on the basis that we
         # use the PsfFlux to perform photometry.
-        self.config.fluxField = "base_PsfFlux_flux"
+        self.config.fluxField = "base_PsfFlux_instFlux"
 
     def tearDown(self):
         del self.srcCat
@@ -123,7 +123,7 @@ def _runTask(self):
             if refFlux <= 0:
                 continue
             refMag = afwImage.abMagFromFlux(refFlux)  # reference catalog mag
-            instFlux = m[1].getPsfFlux()  # Instrumental Flux
+            instFlux = m[1].getPsfInstFlux()  # Instrumental Flux
             if instFlux <= 0:
                 continue
             instMag = pCal.calib.getMagnitude(instFlux)  # Instrumental mag

tests/test_transform.py

@@ -225,7 +225,7 @@ def testInterface(self):
         cfg.calibrate.measurement.slots.shape = None
         cfg.calibrate.measurement.slots.psfFlux = None
         cfg.calibrate.measurement.slots.apFlux = None
-        cfg.calibrate.measurement.slots.instFlux = None
+        cfg.calibrate.measurement.slots.gaussianFlux = None
         cfg.calibrate.measurement.slots.modelFlux = None
         cfg.calibrate.measurement.slots.calibFlux = None
         # no reference catalog, so...