def testReadFits(self):
"""Test reading FITS files"""
dataDir = eups.productDir("afwdata")
if dataDir:
dataDir = os.path.join(dataDir, "data")
else:
print >> sys.stderr, "Warning: afwdata is not set up; not running the FITS I/O tests"
return
hdus = {}
fileName = os.path.join(dataDir, "small_MI.fits")
hdus["img"] = 2 # an S16 fits HDU
hdus["msk"] = 3 # an U8 fits HDU
hdus["var"] = 4 # an F32 fits HDU
imgU = afwImage.DecoratedImageU(fileName, hdus["img"]) # read as unsigned short
imgF = afwImage.DecoratedImageF(fileName, hdus["img"]) # read as float
self.assertEqual(imgU.getHeight(), 256)
self.assertEqual(imgF.getImage().getWidth(), 256)
self.assertEqual(imgU.getImage().get(0, 0), imgF.getImage().get(0, 0))
#
# Check the metadata
#
meta = self.trueMetadata
for k in meta.keys():
self.assertEqual(imgU.getMetadata().getAsDouble(k), meta[k])
self.assertEqual(imgF.getMetadata().getAsDouble(k), meta[k])
#
# Read an F32 image
#
varU = afwImage.DecoratedImageF(fileName, hdus["var"]) # read as unsigned short
varF = afwImage.DecoratedImageF(fileName, hdus["var"]) # read as float
self.assertEqual(varU.getHeight(), 256)
self.assertEqual(varF.getImage().getWidth(), 256)
self.assertEqual(varU.getImage().get(0, 0), varF.getImage().get(0, 0))
#
# Read a char image
#
maskImg = afwImage.DecoratedImageU(fileName, hdus["msk"]).getImage() # read a char file
self.assertEqual(maskImg.getHeight(), 256)
self.assertEqual(maskImg.getWidth(), 256)
self.assertEqual(maskImg.get(0, 0), 1)
#
# Read a U16 image
#
tmpFile = "foo.fits"
imgU.writeFits(tmpFile)
try:
imgU16 = afwImage.DecoratedImageF(tmpFile) # read as unsigned short
except:
os.remove(tmpFile)
raise
os.remove(tmpFile)
def testReadFits(self):
"""Test reading FITS files"""
try:
dataDir = lsst.utils.getPackageDir("afwdata")
except Exception:
print >> sys.stderr, "Warning: afwdata is not set up; not running the FITS I/O tests"
return
dataDir = os.path.join(dataDir, "data")
hdus = {}
fileName = os.path.join(dataDir, "small_MI.fits")
hdus["img"] = 2 # an S16 fits HDU
hdus["msk"] = 3 # an U8 fits HDU
hdus["var"] = 4 # an F32 fits HDU
imgU = afwImage.DecoratedImageU(fileName, hdus["img"]) # read as unsigned short
imgF = afwImage.DecoratedImageF(fileName, hdus["img"]) # read as float
self.assertEqual(imgU.getHeight(), 256)
self.assertEqual(imgF.getImage().getWidth(), 256)
self.assertEqual(imgU.getImage().get(0, 0), imgF.getImage().get(0, 0))
#
# Check the metadata
#
meta = self.trueMetadata
for k in meta.keys():
self.assertEqual(imgU.getMetadata().getAsDouble(k), meta[k])
self.assertEqual(imgF.getMetadata().getAsDouble(k), meta[k])
#
# Read an F32 image
#
varU = afwImage.DecoratedImageF(fileName, hdus["var"]) # read as unsigned short
varF = afwImage.DecoratedImageF(fileName, hdus["var"]) # read as float
self.assertEqual(varU.getHeight(), 256)
self.assertEqual(varF.getImage().getWidth(), 256)
self.assertEqual(varU.getImage().get(0, 0), varF.getImage().get(0, 0))
#
# Read a char image
#
maskImg = afwImage.DecoratedImageU(fileName, hdus["msk"]).getImage() # read a char file
self.assertEqual(maskImg.getHeight(), 256)
self.assertEqual(maskImg.getWidth(), 256)
self.assertEqual(maskImg.get(0, 0), 1)
#
# Read a U16 image
#
with utilsTests.getTempFilePath(".fits") as tmpFile:
imgU.writeFits(tmpFile)
afwImage.DecoratedImageF(tmpFile) # read as unsigned short
def testReadFits(self):
"""Test reading FITS files"""
hdus = {}
hdus["img"] = 1 # an S16 fits HDU
hdus["msk"] = 2 # an U8 fits HDU
hdus["var"] = 3 # an F32 fits HDU
# read as unsigned short
imgU = afwImage.DecoratedImageU(self.fileForMetadata,
hdus["img"],
allowUnsafe=True)
# read as float
imgF = afwImage.DecoratedImageF(self.fileForMetadata, hdus["img"])
self.assertEqual(imgU.getHeight(), 256)
self.assertEqual(imgF.image.getWidth(), 256)
self.assertEqual(imgU.image[0, 0, afwImage.LOCAL],
imgF.image[0, 0, afwImage.LOCAL])
#
# Check the metadata
#
meta = self.trueMetadata
for k in meta.keys():
self.assertEqual(imgU.getMetadata().getAsDouble(k), meta[k])
self.assertEqual(imgF.getMetadata().getAsDouble(k), meta[k])
#
# Read an F32 image
#
# read as unsigned short
varU = afwImage.DecoratedImageF(self.fileForMetadata, hdus["var"])
# read as float
varF = afwImage.DecoratedImageF(self.fileForMetadata, hdus["var"])
self.assertEqual(varU.getHeight(), 256)
self.assertEqual(varF.image.getWidth(), 256)
self.assertEqual(varU.image[0, 0, afwImage.LOCAL],
varF.image[0, 0, afwImage.LOCAL])
#
# Read a char image
#
maskImg = afwImage.DecoratedImageU(
self.fileForMetadata, hdus["msk"]).image # read a char file
self.assertEqual(maskImg.getHeight(), 256)
self.assertEqual(maskImg.getWidth(), 256)
self.assertEqual(maskImg[0, 0, afwImage.LOCAL], 1)
#
# Read a U16 image
#
with lsst.utils.tests.getTempFilePath(".fits") as tmpFile:
imgU.writeFits(tmpFile)
afwImage.DecoratedImageF(tmpFile) # read as unsigned short
def bypass_raw(self, datasetType, pythonType, location, dataId):
"""Read raw image with hacked metadata"""
filename = location.getLocations()[0]
md = self.bypass_raw_md(datasetType, pythonType, location, dataId)
image = afwImage.DecoratedImageU(filename)
image.setMetadata(md)
return self.std_raw(image, dataId)
def makeRampDecoratedImage(bbox, start, **metadataDict):
"""Make a DecoratedImageU that is a ramp."""
rampArr = makeRampImage(bbox=bbox, start=start,
imageClass=afwImage.ImageU).getArray()
decoratedImage = afwImage.DecoratedImageU(bbox)
imarr = decoratedImage.getImage().getArray()
imarr[:] = rampArr
md = decoratedImage.getMetadata()
for (key, val) in metadataDict.items():
md.set(key, val)
return decoratedImage
def openChannelImage(dirPath, x, y):
"""Open an LSSTSim channel raw image
"""
globStr = os.path.join(dirPath, "imsim_*_R22_S00_C%d%d*" % (y, x))
inDecoImagePathList = glob.glob(globStr)
if len(inDecoImagePathList) != 1:
raise RuntimeError("Found %s instead of 1 file" %
(inDecoImagePathList, ))
inDecoImagePath = inDecoImagePathList[0]
inDecoImageFileName = os.path.basename(inDecoImagePath)
# calib images (which are float) have names such as imsim_2_R22_S00_C00.fits
# raw images (which are unsigned int) have names such as imsim_890104911_R22_S00_C00_E000....
if not re.match(r"imsim_\d\d\d\d\d", inDecoImageFileName):
raise RuntimeError("Not raw data")
print("loading %s as raw unsigned integer data" % (inDecoImageFileName, ))
return afwImage.DecoratedImageU(inDecoImagePath)
def assembleImage(dirPath):
"""Make one image by combining half of amplifiers C00, C01, C10, C11 of lsstSim data
"""
# views and assembly operations require a masked image, not a DecoratedImage
inDecoImage = openChannelImage(dirPath, 0, 0)
fullInDim = inDecoImage.getDimensions()
yStart = fullInDim[1] - SizeY
if yStart < 0:
raise RuntimeError("channel image unexpectedly small")
subDim = afwGeom.Extent2I(
fullInDim[0],
SizeY) # dimensions of the portion of a channel that we use
inSubBBox = afwGeom.Box2I(afwGeom.Point2I(0, yStart), subDim)
outBBox = afwGeom.Box2I(afwGeom.Point2I(0, 0), subDim * 2)
outDecoImage = afwImage.DecoratedImageU(outBBox)
# copy metadata
outDecoImage.setMetadata(inDecoImage.getMetadata())
for x in (0, 1):
for y in (0, 1):
inDecoImage = openChannelImage(dirPath, x, y)
inImage = inDecoImage.getImage()
inView = inImage.Factory(inImage, inSubBBox)
# flip image about x axis for the y = 1 channels
if y == 1:
arr = inView.getArray()
if numpy.any(arr != 0):
arr[:, :] = numpy.flipud(arr)
xStart = x * subDim[0]
yStart = y * subDim[1]
outSubBBox = afwGeom.Box2I(afwGeom.Point2I(xStart, yStart), subDim)
outImage = outDecoImage.getImage()
outView = outImage.Factory(outImage, outSubBBox)
outView[:] = inView
outDecoImage.writeFits(OutFileName)
print("wrote assembled data as %r" % (OutFileName, ))
from lsst.pex.harness import Dataset
lm = dafBase.PropertySet()
lm.add("input", "tests")
lm.add("output", ".")
dafPersist.LogicalLocation.setLocationMap(lm)
ps = dafBase.PropertySet()
ps.add("field", "D4")
clip0 = {
'inputDatasets': [
Dataset('postIsr', visit=707911, snap=0, ccd=13, amp=0),
Dataset('postIsr', visit=707911, snap=0, ccd=13, amp=1)
],
'root':
"raw",
'ps':
ps
}
policy = pexPolicy.Policy.createPolicy("tests/policy/TestIO_2.policy")
t1 = SST.SimpleStageTester(IOStage.InputStage(policy))
clip1 = t1.run(clip0, 0)
el = clip1.get("exposureSet")
assert len(el) == 2
e = afwImage.DecoratedImageU()
assert type(el[0]) == type(e)
assert type(el[1]) == type(e)
assert el[0].getWidth() == 1056
assert el[1].getHeight() == 1153
assert el[0].getMetadata().get("LSSTAMP") == 0
assert el[1].getMetadata().get("LSSTAMP") == 1
