DM-31801: Prepend lsst to logger names and switch to python logging

bin.src/convert_refcat_to_nJy.py

@@ -40,6 +40,7 @@
 """
 import os.path
 import glob
+import logging
 
 import concurrent.futures
 import itertools
@@ -48,7 +49,11 @@
 from lsst.meas.algorithms import DatasetConfig
 from lsst.meas.algorithms.loadReferenceObjects import convertToNanojansky, hasNanojanskyFluxUnits
 from lsst.meas.algorithms.ingestIndexReferenceTask import addRefCatMetadata
-import lsst.log
+
+
+# Set up logging
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger("lsst.convert_refcat_to_nJy")
 
 
 def is_old_schema(config, filename):
@@ -69,9 +74,8 @@ def process_one(filename, write=False, quiet=False):
     quiet : `bool`, optional
         Do not print messages about files read/written or fields found?
     """
-    log = lsst.log.Log()
     if quiet:
-        log.setLevel(lsst.log.WARN)
+        logging.getLogger().setLevel(logging.WARNING)
 
     log.info("Reading: %s", filename)
     catalog = lsst.afw.table.SimpleCatalog.readFits(filename)

python/lsst/meas/algorithms/convertRefcatManager.py

@@ -73,7 +73,7 @@ class ConvertRefcatManager:
         The start and end HTM pixel ids.
     addRefCatMetadata : callable
         A function called to add extra metadata to each output Catalog.
-    log : `lsst.log.Log`
+    log : `lsst.log.Log` or `logging.Logger`
         The log to send messages to.
     """
     _flags = ['photometric', 'resolved', 'variable']

python/lsst/meas/algorithms/loadReferenceObjects.py

@@ -26,6 +26,7 @@
 
 import abc
 import itertools
+import logging
 
 import astropy.time
 import astropy.units
@@ -35,7 +36,6 @@
 import lsst.afw.table as afwTable
 import lsst.pex.config as pexConfig
 import lsst.pipe.base as pipeBase
-import lsst.log
 from lsst import sphgeom
 from lsst.daf.base import PropertyList
 from lsst.utils.timer import timeMethod
@@ -91,7 +91,7 @@ def convertToNanojansky(catalog, log, doConvert=True):
     ----------
     catalog : `lsst.afw.table.SimpleCatalog`
         The catalog to convert.
-    log : `lsst.log.Log`
+    log : `lsst.log.Log` or `logging.Logger`
         Log to send messages to.
     doConvert : `bool`, optional
         Return a converted catalog, or just identify the fields that need to be converted?
@@ -110,8 +110,8 @@ def convertToNanojansky(catalog, log, doConvert=True):
     """
     # Do not share the AliasMap: for refcats, that gets created when the
     # catalog is read from disk and should not be propagated.
-    mapper = lsst.afw.table.SchemaMapper(catalog.schema, shareAliasMap=False)
-    mapper.addMinimalSchema(lsst.afw.table.SimpleTable.makeMinimalSchema())
+    mapper = afwTable.SchemaMapper(catalog.schema, shareAliasMap=False)
+    mapper.addMinimalSchema(afwTable.SimpleTable.makeMinimalSchema())
     input_fields = []
     output_fields = []
     for field in catalog.schema:
@@ -124,7 +124,7 @@ def convertToNanojansky(catalog, log, doConvert=True):
                 name = oldName.replace('_fluxSigma', '_fluxErr')
             else:
                 name = oldName
-            newField = lsst.afw.table.Field[field.dtype](name, field.field.getDoc(), units)
+            newField = afwTable.Field[field.dtype](name, field.field.getDoc(), units)
             mapper.addMapping(field.getKey(), newField)
             input_fields.append(field.field)
             output_fields.append(newField)
@@ -135,7 +135,7 @@ def convertToNanojansky(catalog, log, doConvert=True):
 
     if doConvert:
         newSchema = mapper.getOutputSchema()
-        output = lsst.afw.table.SimpleCatalog(newSchema)
+        output = afwTable.SimpleCatalog(newSchema)
         output.extend(catalog, mapper=mapper)
         for field in output_fields:
             output[field.getName()] *= 1e9
@@ -236,7 +236,7 @@ def applyProperMotions(self, catalog, epoch):
 
         # Warn/raise for a catalog in an incorrect format, if epoch was specified.
         if ("pm_ra" in catalog.schema
-                and not isinstance(catalog.schema["pm_ra"].asKey(), lsst.afw.table.KeyAngle)):
+                and not isinstance(catalog.schema["pm_ra"].asKey(), afwTable.KeyAngle)):
             if self.config.requireProperMotion:
                 raise RuntimeError("requireProperMotion=True but refcat pm_ra field is not an Angle.")
             else:
@@ -275,13 +275,13 @@ def __init__(self, dataIds, refCats, config, log=None):
             Handles to load refCats on demand
         config : `lsst.pex.config.configurableField`
             Configuration for the loader.
-        log : `lsst.log.Log` or `None`, optional
-            Logger object used to write out messages. If `None` the default
-            lsst logger will be used.
+        log : `lsst.log.Log`, `logging.Logger` or `None`, optional
+            Logger object used to write out messages. If `None` a default
+            logger will be used.
         """
         self.dataIds = dataIds
         self.refCats = refCats
-        self.log = log or lsst.log.Log.getDefaultLogger()
+        self.log = log or logging.getLogger(__name__).getChild("ReferenceObjectLoader")
         self.config = config
 
     @staticmethod
@@ -1461,7 +1461,7 @@ def applyProperMotionsImpl(log, catalog, epoch):
 
     Parameters
     ----------
-    log : `lsst.log.Log`
+    log : `lsst.log.Log` or `logging.getLogger`
         Log object to write to.
     catalog : `lsst.afw.table.SimpleCatalog`
         Catalog of positions, containing:

python/lsst/meas/algorithms/objectSizeStarSelector.py

@@ -27,7 +27,7 @@
 import warnings
 from functools import reduce
 
-from lsst.log import Log
+from lsst.utils.logging import getLogger
 from lsst.pipe.base import Struct
 import lsst.geom
 from lsst.afw.cameraGeom import PIXELS, TAN_PIXELS
@@ -38,6 +38,8 @@
 
 afwDisplay.setDefaultMaskTransparency(75)
 
+_LOG = getLogger(__name__)
+
 
 class ObjectSizeStarSelectorConfig(BaseSourceSelectorTask.ConfigClass):
     doFluxLimit = pexConfig.Field(
@@ -165,7 +167,7 @@ def _assignClusters(yvec, centers):
     minDist = numpy.nan*numpy.ones_like(yvec)
     clusterId = numpy.empty_like(yvec)
     clusterId.dtype = int               # zeros_like(..., dtype=int) isn't in numpy 1.5
-    dbl = Log.getLogger("objectSizeStarSelector._assignClusters")
+    dbl = _LOG.getChild("_assignClusters")
     dbl.setLevel(dbl.INFO)
 
     # Make sure we are logging aall numpy warnings...
@@ -269,7 +271,7 @@ def _improveCluster(yvec, centers, clusterId, nsigma=2.0, nIteration=10, cluster
 def plot(mag, width, centers, clusterId, marker="o", markersize=2, markeredgewidth=0, ltype='-',
          magType="model", clear=True):
 
-    log = Log.getLogger("objectSizeStarSelector.plot")
+    log = _LOG.getChild("plot")
     try:
         import matplotlib.pyplot as plt
     except ImportError as e:

python/lsst/meas/algorithms/utils.py

@@ -27,8 +27,8 @@
 
 import math
 import numpy
+import logging
 
-import lsst.log
 import lsst.pex.exceptions as pexExcept
 import lsst.daf.base as dafBase
 import lsst.geom
@@ -46,6 +46,8 @@
 
 afwDisplay.setDefaultMaskTransparency(75)
 
+_LOG = logging.getLogger(__name__)
+
 
 def splitId(oid, asDict=True):
 
@@ -382,7 +384,7 @@ def makeSubplots(fig, nx=2, ny=2, Nx=1, Ny=1, plottingArea=(0.1, 0.1, 0.85, 0.80
         Colour of border around panels
     """
 
-    log = lsst.log.Log.getLogger("utils.makeSubplots")
+    log = _LOG.getChild("makeSubplots")
     try:
         import matplotlib.pyplot as plt
     except ImportError as e:
@@ -474,7 +476,7 @@ def plotPsfSpatialModel(exposure, psf, psfCellSet, showBadCandidates=True, numSa
                         matchKernelAmplitudes=False, keepPlots=True):
     """Plot the PSF spatial model."""
 
-    log = lsst.log.Log.getLogger("utils.plotPsfSpatialModel")
+    log = _LOG.getChild("plotPsfSpatialModel")
     try:
         import matplotlib.pyplot as plt
         import matplotlib as mpl

src/CR.cc

@@ -574,10 +574,10 @@ std::vector<std::shared_ptr<afw::detection::Footprint>> findCosmicRays(
         // find the sum of pixel values within the CR
         (*cr)->getSpans()->applyFunctor(CountDN, *mimage.getImage());
 
-        LOGL_DEBUG("TRACE4.algorithms.CR", "CR at (%d, %d) has %g DN", (*cr)->getBBox().getMinX(),
+        LOGL_DEBUG("TRACE4.lsst.algorithms.CR", "CR at (%d, %d) has %g DN", (*cr)->getBBox().getMinX(),
                    (*cr)->getBBox().getMinY(), CountDN.getCounts());
         if (CountDN.getCounts() < minDn) { /* not bright enough */
-            LOGL_DEBUG("TRACE5.algorithms.CR", "Erasing CR");
+            LOGL_DEBUG("TRACE5.lsst.algorithms.CR", "Erasing CR");
 
             cr = CRs.erase(cr);
             --cr;  // back up to previous CR (we're going to increment it)
@@ -591,7 +591,7 @@ std::vector<std::shared_ptr<afw::detection::Footprint>> findCosmicRays(
                        */
     bool const debias_values = true;
     bool grow = false;
-    LOGL_DEBUG("TRACE2.algorithms.CR", "Removing initial list of CRs");
+    LOGL_DEBUG("TRACE2.lsst.algorithms.CR", "Removing initial list of CRs");
     removeCR(mimage, CRs, bkgd, crBit, saturBit, badMask, debias_values, grow);
 #if 0  // Useful to see phase 2 in display; debugging only
     (void)setMaskFromFootprintList(mimage.getMask().get(), CRs,
@@ -607,7 +607,7 @@ std::vector<std::shared_ptr<afw::detection::Footprint>> findCosmicRays(
     bool too_many_crs = false;  // we've seen too many CR pixels
     int nextra = 0;             // number of pixels added to list of CRs
     for (int i = 0; i != niteration && !too_many_crs; ++i) {
-        LOGL_DEBUG("TRACE1.algorithms.CR", "Starting iteration %d", i);
+        LOGL_DEBUG("TRACE1.lsst.algorithms.CR", "Starting iteration %d", i);
         for (std::vector<std::shared_ptr<afw::detection::Footprint>>::iterator fiter = CRs.begin();
              fiter != CRs.end(); fiter++) {
             std::shared_ptr<afw::detection::Footprint> cr = *fiter;
@@ -709,7 +709,7 @@ std::vector<std::shared_ptr<afw::detection::Footprint>> findCosmicRays(
     } else {
         if (true || nextra > 0) {
             grow = true;
-            LOGL_DEBUG("TRACE2.algorithms.CR", "Removing final list of CRs, grow = %d", grow);
+            LOGL_DEBUG("TRACE2.lsst.algorithms.CR", "Removing final list of CRs, grow = %d", grow);
             removeCR(mimage, CRs, bkgd, crBit, saturBit, badMask, debias_values, grow);
         }
         /*
@@ -919,7 +919,7 @@ class RemoveCR {
          * estimate
          */
         if (ngood > 0) {
-            LOGL_DEBUG("TRACE3.algorithms.CR", "Adopted min==%g at (%d, %d) (ngood=%d)",
+            LOGL_DEBUG("TRACE3.lsst.algorithms.CR", "Adopted min==%g at (%d, %d) (ngood=%d)",
                        static_cast<double>(min), x, y, ngood);
         }
 

tests/nopytest_ingestIndexReferenceCatalog.py

@@ -107,7 +107,7 @@ def runTest(withRaDecErr):
             # (otherwise it logs to `root`); only show WARN logs because each
             # loadRegion (called once per source) in the check below will log
             # twice to INFO.
-            log = lsst.log.Log.getLogger('ReferenceObjectLoader')
+            log = lsst.log.Log.getLogger('lsst.ReferenceObjectLoader')
             log.setLevel(lsst.log.WARN)
             loader = ReferenceObjectLoader([dataRef.dataId for dataRef in datasetRefs],
                                            handlers,
@@ -130,7 +130,7 @@ def setUp(self):
         np.random.seed(10)
 
         tempPath = tempfile.mkdtemp()
-        self.log = lsst.log.Log.getLogger("TestIngestIndexManager")
+        self.log = lsst.log.Log.getLogger("lsst.TestIngestIndexManager")
         self.config = ingestIndexTestBase.makeConvertConfig(withRaDecErr=True)
         self.config.id_name = 'id'
         self.depth = 2  # very small depth, for as few pixels as possible.

tests/test_cr.py

@@ -35,7 +35,7 @@
 import lsst.utils.tests
 
 # Increase the number for more verbose messages
-logUtils.traceSetAt("algorithms.CR", 3)
+logUtils.traceSetAt("lsst.algorithms.CR", 3)
 
 try:
     display

tests/test_htmIndex.py

@@ -363,10 +363,10 @@ def testRequireProperMotion(self):
         config.anyFilterMapsToThis = "g"  # to use a catalog not made for obs_test
         loader = LoadIndexedReferenceObjectsTask(butler=self.testButler, config=config)
         with unittest.mock.patch.object(self.testButler, 'get', return_value=refcatData):
-            with lsst.log.UsePythonLogging(), self.assertLogs(level="WARNING") as cm:
+            with self.assertLogs("lsst.LoadIndexedReferenceObjectsTask", level="WARNING") as cm:
                 loader.loadSkyCircle(center, self.searchRadius, epoch=epoch)
             warnLog1 = "Reference catalog pm_ra field is not an Angle; cannot apply proper motion."
-            self.assertEqual(cm.output, [f"WARNING:LoadIndexedReferenceObjectsTask:{warnLog1}"])
+            self.assertEqual(cm.records[0].message, warnLog1)
 
     def testLoadVersion0(self):
         """Test reading a pre-written format_version=0 (Jy flux) catalog.

tests/test_measure.py

@@ -36,7 +36,7 @@
 import lsst.utils.tests
 
 # Change the level to Log.DEBUG or Log.TRACE to see debug messages
-Log.getLogger("measurement").setLevel(Log.INFO)
+Log.getLogger("lsst.measurement").setLevel(Log.INFO)
 
 try:
     type(display)

tests/test_psfDetermination.py

@@ -47,8 +47,8 @@
     afwDisplay.setDefaultMaskTransparency(75)
 
 # Change the level to Log.DEBUG or Log.TRACE to see debug messages
-Log.getLogger("measurement").setLevel(Log.INFO)
-Log.getLogger("psfDeterminer").setLevel(Log.TRACE)
+Log.getLogger("lsst.measurement").setLevel(Log.INFO)
+Log.getLogger("lsst.psfDeterminer").setLevel(Log.TRACE)
 
 
 def psfVal(ix, iy, x, y, sigma1, sigma2, b):

tests/test_psfIO.py

@@ -45,7 +45,7 @@
     afwDisplay.setDefaultMaskTransparency(75)
 
 # Change the level to Log.DEBUG or Log.TRACE to see debug messages
-Log.getLogger("measurement").setLevel(Log.INFO)
+Log.getLogger("lsst.measurement").setLevel(Log.INFO)
 
 
 def roundTripPsf(key, psf):