#
# LSST Data Management System
# Copyright 2017 LSST Corporation.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# 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
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 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 <http://www.lsstcorp.org/LegalNotices/>.
#
import unittest
import itertools
import numpy as np
import lsst.utils.tests
import lsst.afw.image
import lsst.afw.table
import lsst.afw.cameraGeom
from lsst.afw.table import LL, LR, UL, UR
from lsst.pipe.base import Struct
from lsst.ip.isr import (IsrTask, subtractCrosstalk, extractCrosstalkRatios, measureCrosstalkCoefficients,
MeasureCrosstalkTask)
try:
debug
except NameError:
debug = False
else:
import lsst.afw.display
display = lsst.afw.display.Display(backend="ds9", frame=1)
class CrosstalkTestCase(lsst.utils.tests.TestCase):
def setUp(self):
width, height = 250, 500
self.numAmps = 4
numPixelsPerAmp = 1000
# crosstalk[i][j] is the fraction of the j-th amp present on the i-th amp.
self.crosstalk = [[0.0, 1e-4, 2e-4, 3e-4],
[3e-4, 0.0, 2e-4, 1e-4],
[4e-4, 5e-4, 0.0, 6e-4],
[7e-4, 8e-4, 9e-4, 0.0]]
self.value = 12345
self.crosstalkStr = "XTLK"
# A bit of noise is important, because otherwise the pixel distributions are razor-thin
# and then rejection doesn't work
rng = np.random.RandomState(12345)
self.noise = rng.normal(0.0, 0.1, (2*height, 2*width))
# Create amp images
withoutCrosstalk = [lsst.afw.image.ImageF(width, height) for _ in range(self.numAmps)]
for image in withoutCrosstalk:
image.set(0)
xx = rng.randint(0, width, numPixelsPerAmp)
yy = rng.randint(0, height, numPixelsPerAmp)
image.getArray()[yy, xx] = self.value
# Add in crosstalk
withCrosstalk = [image.Factory(image, True) for image in withoutCrosstalk]
for ii, iImage in enumerate(withCrosstalk):
for jj, jImage in enumerate(withoutCrosstalk):
value = self.crosstalk[ii][jj]
iImage.scaledPlus(value, jImage)
# Put amp images together
def construct(imageList):
image = lsst.afw.image.ImageF(2*width, 2*height)
image.getArray()[:height, :width] = imageList[0].getArray()
image.getArray()[:height, width:] = imageList[1].getArray()[:, ::-1] # flip in x
image.getArray()[height:, :width] = imageList[2].getArray()[::-1, :] # flip in y
image.getArray()[height:, width:] = imageList[3].getArray()[::-1, ::-1] # flip in x and y
image.getArray()[:] += self.noise
return image
# Create amp info
schema = lsst.afw.table.AmpInfoTable.makeMinimalSchema()
amplifiers = lsst.afw.table.AmpInfoCatalog(schema)
for ii, (xx, yy, corner) in enumerate([(0, 0, LL),
(width, 0, LR),
(0, height, UL),
(width, height, UR)]):
amp = amplifiers.addNew()
amp.setName("amp %d" % ii)
amp.setBBox(lsst.afw.geom.Box2I(lsst.afw.geom.Point2I(xx, yy),
lsst.afw.geom.Extent2I(width, height)))
amp.setRawDataBBox(lsst.afw.geom.Box2I(lsst.afw.geom.Point2I(xx, yy),
lsst.afw.geom.Extent2I(width, height)))
amp.setReadoutCorner(corner)
# Put everything together
ccd = lsst.afw.cameraGeom.Detector("detector", 123, lsst.afw.cameraGeom.SCIENCE, "serial",
lsst.afw.geom.Box2I(lsst.afw.geom.Point2I(0, 0),
lsst.afw.geom.Extent2I(2*width, 2*height)),
amplifiers, lsst.afw.cameraGeom.Orientation(),
lsst.afw.geom.Extent2D(1, 1), {},
np.array(self.crosstalk, dtype=np.float32))
self.exposure = lsst.afw.image.makeExposure(lsst.afw.image.makeMaskedImage(construct(withCrosstalk)))
self.exposure.setDetector(ccd)
self.corrected = construct(withoutCrosstalk)
118 ↛ 119line 118 didn't jump to line 119, because the condition on line 118 was never true if debug:
display.mtv(self.exposure)
display.incrDefaultFrame()
display.mtv(self.corrected)
display.incrDefaultFrame()
def tearDown(self):
del self.exposure
del self.corrected
def checkCoefficients(self, coeff, coeffErr, coeffNum):
"""Check that coefficients are as expected
Parameters
----------
coeff : `numpy.ndarray`
Crosstalk coefficients.
coeffErr : `numpy.ndarray`
Crosstalk coefficient errors.
coeffNum : `numpy.ndarray`
Number of pixels to produce each coefficient.
"""
for matrix in (coeff, coeffErr, coeffNum):
self.assertEqual(matrix.shape, (self.numAmps, self.numAmps))
for ii in range(self.numAmps):
self.assertEqual(matrix[ii, ii], 0)
self.assertFloatsAlmostEqual(coeff, np.array(self.crosstalk), atol=1.0e-6)
145 ↛ exitline 145 didn't run the generator expression on line 145 self.assertTrue(np.all(coeffErr[ii, jj] > 0 for ii, jj in
itertools.product(range(self.numAmps), range(self.numAmps)) if ii != jj))
147 ↛ exitline 147 didn't run the generator expression on line 147 self.assertTrue(np.all(coeffNum[ii, jj] > 0 for ii, jj in
itertools.product(range(self.numAmps), range(self.numAmps)) if ii != jj))
def checkSubtracted(self, exposure):
"""Check that the subtracted image is as expected
Parameters
----------
exposure : `lsst.afw.image.Exposure`
Crosstalk-subtracted exposure.
"""
image = exposure.getMaskedImage().getImage()
mask = exposure.getMaskedImage().getMask()
self.assertFloatsAlmostEqual(image.getArray(), self.corrected.getArray(), atol=2.0e-2)
self.assertIn(self.crosstalkStr, mask.getMaskPlaneDict())
self.assertGreater((mask.getArray() & mask.getPlaneBitMask(self.crosstalkStr) > 0).sum(), 0)
def testDirectAPI(self):
"""Test that individual function calls work"""
ratios = extractCrosstalkRatios(self.exposure, threshold=self.value - 1)
coeff, coeffErr, coeffNum = measureCrosstalkCoefficients(ratios)
self.checkCoefficients(coeff, coeffErr, coeffNum)
subtractCrosstalk(self.exposure, minPixelToMask=self.value - 1,
crosstalkStr=self.crosstalkStr)
self.checkSubtracted(self.exposure)
def testTaskAPI(self):
"""Test that the Tasks work
Checks both MeasureCrosstalkTask and the CrosstalkTask.
"""
# make exposure available to NullIsrTask
# without NullIsrTask's `self` hiding this test class's `self`
exposure = self.exposure
class NullIsrTask(IsrTask):
def runDataRef(self, dataRef):
return Struct(exposure=exposure)
config = MeasureCrosstalkTask.ConfigClass()
config.isr.retarget(NullIsrTask)
config.threshold = self.value - 1
measure = MeasureCrosstalkTask(config=config)
fakeDataRef = Struct(dataId={'fake': 1})
coeff, coeffErr, coeffNum = measure.reduce([measure.run(fakeDataRef)])
self.checkCoefficients(coeff, coeffErr, coeffNum)
config = IsrTask.ConfigClass()
config.crosstalk.minPixelToMask = self.value - 1
config.crosstalk.crosstalkMaskPlane = self.crosstalkStr
isr = IsrTask(config=config)
isr.crosstalk.run(self.exposure)
self.checkSubtracted(self.exposure)
class MemoryTester(lsst.utils.tests.MemoryTestCase):
pass
def setup_module(module):
lsst.utils.tests.init()
210 ↛ 211line 210 didn't jump to line 211, because the condition on line 210 was never trueif __name__ == "__main__":
import sys
setup_module(sys.modules[__name__])
unittest.main()
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