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#!/usr/bin/env python
# LSST Data Management System
# Copyright 2008, 2009, 2010 LSST Corporation.
# This product includes software developed by the
# LSST Project (
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# GNU General Public License for more details.
# You should have received a copy of the LSST License Statement and
# the GNU General Public License along with this program. If not,
# see <>.
import os
import sys
import numpy as np
import lsst.utils
import lsst.daf.base as dafBase
import lsst.afw.table as afwTable
import lsst.afw.image as afwImage
import lsst.afw.display as afwDisplay
import lsst.meas.algorithms as measAlg
from lsst.meas.algorithms.detection import SourceDetectionTask
from lsst.meas.base import SingleFrameMeasurementTask
def loadData():
"""Prepare the data we need to run the example"""
# Load sample input from disk
afwdataDir = lsst.utils.getPackageDir('afwdata')
imFile = os.path.join(afwdataDir, "CFHT", "D4", "cal-53535-i-797722_small_1.fits")
exposure = afwImage.ExposureF(imFile)
psf = measAlg.SingleGaussianPsf(21, 21, 2)
im = exposure.getMaskedImage().getImage()
im -= float(np.median(im.getArray()))
return exposure
def run(display=False):
exposure = loadData()
schema = afwTable.SourceTable.makeMinimalSchema()
# Create the detection task
config = SourceDetectionTask.ConfigClass()
config.thresholdPolarity = "both"
config.background.isNanSafe = True
config.thresholdValue = 3
detectionTask = SourceDetectionTask(config=config, schema=schema)
# And the measurement Task
config = SingleFrameMeasurementTask.ConfigClass()
config.algorithms.names = ["base_SdssCentroid", "base_SdssShape", "base_CircularApertureFlux"]
config.algorithms["base_CircularApertureFlux"].radii = [1, 2, 4, 8, 12, 16] # pixels
config.slots.gaussianFlux = None
config.slots.modelFlux = None
config.slots.psfFlux = None
algMetadata = dafBase.PropertyList()
measureTask = SingleFrameMeasurementTask(schema, algMetadata=algMetadata, config=config)
radii = algMetadata.getArray("base_CircularApertureFlux_radii")
# Create the output table
tab = afwTable.SourceTable.make(schema)
# Process the data
result =, exposure)
sources = result.sources
print("Found %d sources (%d +ve, %d -ve)" % (len(sources), result.fpSets.numPos, result.fpSets.numNeg)), exposure)
if display: # display image (see also --debug argparse option)
frame = 1
disp = afwDisplay.Display(frame=frame)
with disp.Buffering():
for s in sources:
xy = s.getCentroid()'+', *xy, ctype=afwDisplay.CYAN if s.get("flags_negative") else afwDisplay.GREEN), *xy, ctype=afwDisplay.RED)
for radius in radii:'o', *xy, size=radius, ctype=afwDisplay.YELLOW)
if __name__ == "__main__":
import argparse
parser = argparse.ArgumentParser(description="Demonstrate the use of Source{Detection,Measurement}Task")
parser.add_argument('--debug', '-d', action="store_true", help="Load", default=False)
parser.add_argument('--doDisplay', action="store_true", help="Display sources", default=False)
args = parser.parse_args()
if args.debug:
import debug # noqa F401
except ImportError as e:
print(e, file=sys.stderr)
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