def readRawAmps(fileName, detector):
"""Given a file name read the amps and attach the detector.
Parameters
----------
fileName : `str`
The full path to a file containing data from a single CCD.
detector : `lsst.afw.cameraGeom.Detector`
Detector to associate with the amps.
Returns
-------
ampExps : `list` of `lsst.afw.image.Exposure`
All the individual amps read from the file.
"""
amps = []
for hdu in range(1, len(detector)+1):
reader = afwImage.ImageFitsReader(fileName, hdu=hdu)
exp = afwImage.makeExposure(afwImage.makeMaskedImage(reader.read(dtype=np.dtype(np.int32),
allowUnsafe=True)))
exp.setDetector(detector)
exp.setMetadata(reader.readMetadata())
amps.append(exp)
return amps
def readFitsWithOptions(filename, stamp_factory, options):
"""Read stamps from FITS file, allowing for only a
subregion of the stamps to be read.
Parameters
----------
filename : `str`
A string indicating the file to read
stamp_factory : classmethod
A factory function defined on a dataclass for constructing
stamp objects a la `lsst.meas.alrogithm.Stamp`
options : `PropertyList` or `dict`
A collection of parameters. If it contains a bounding box
(``bbox`` key), or if certain other keys (``llcX``, ``llcY``,
``width``, ``height``) are available for one to be constructed,
the bounding box is passed to the ``FitsReader`` in order to
return a sub-image.
Returns
-------
stamps : `list` of dataclass objects like `Stamp`, PropertyList
A tuple of a list of `Stamp`-like objects
metadata : `PropertyList`
The metadata
"""
# extract necessary info from metadata
metadata = afwFits.readMetadata(filename, hdu=0)
nStamps = metadata["N_STAMPS"]
has_archive = metadata["HAS_ARCHIVE"]
if has_archive:
archive_ids = metadata.getArray("ARCHIVE_IDS")
with afwFits.Fits(filename, 'r') as f:
nExtensions = f.countHdus()
# check if a bbox was provided
kwargs = {}
if options:
# gen3 API
if "bbox" in options.keys():
kwargs["bbox"] = options["bbox"]
# gen2 API
elif "llcX" in options.keys():
llcX = options["llcX"]
llcY = options["llcY"]
width = options["width"]
height = options["height"]
bbox = Box2I(Point2I(llcX, llcY), Extent2I(width, height))
kwargs["bbox"] = bbox
stamp_parts = {}
# We need to be careful because nExtensions includes the primary
# header data unit
for idx in range(nExtensions - 1):
md = afwFits.readMetadata(filename, hdu=idx + 1)
if md['EXTNAME'] in ('IMAGE', 'VARIANCE'):
reader = afwImage.ImageFitsReader(filename, hdu=idx + 1)
elif md['EXTNAME'] == 'MASK':
reader = afwImage.MaskFitsReader(filename, hdu=idx + 1)
elif md['EXTNAME'] == 'ARCHIVE_INDEX':
f.setHdu(idx + 1)
archive = afwTable.io.InputArchive.readFits(f)
continue
elif md['EXTTYPE'] == 'ARCHIVE_DATA':
continue
else:
raise ValueError(f"Unknown extension type: {md['EXTNAME']}")
stamp_parts.setdefault(
md['EXTVER'],
{})[md['EXTNAME'].lower()] = reader.read(**kwargs)
if len(stamp_parts) != nStamps:
raise ValueError(
f'Number of stamps read ({len(stamp_parts)}) does not agree with the '
f'number of stamps recorded in the metadata ({nStamps}).')
# construct stamps themselves
stamps = []
for k in range(nStamps):
# Need to increment by one since EXTVER starts at 1
maskedImage = afwImage.MaskedImageF(**stamp_parts[k + 1])
archive_element = archive.get(archive_ids[k]) if has_archive else None
stamps.append(stamp_factory(maskedImage, metadata, k, archive_element))
return stamps, metadata
def readFitsWithOptions(filename, stamp_factory, options):
"""Read stamps from FITS file, allowing for only a
subregion of the stamps to be read.
Parameters
----------
filename : `str`
A string indicating the file to read
stamp_factory : classmethod
A factory function defined on a dataclass for constructing
stamp objects a la `lsst.meas.alrogithm.Stamp`
options : `PropertyList`
A collection of parameters. If certain keys are available
(``llcX``, ``llcY``, ``width``, ``height``), a bounding box
is constructed and passed to the ``FitsReader`` in order
to return a sub-image.
Returns
-------
stamps : `list` of dataclass objects like `Stamp`, PropertyList
A tuple of a list of `Stamp`-like objects
metadata : `PropertyList`
The metadata
"""
# extract necessary info from metadata
metadata = afwFits.readMetadata(filename, hdu=0)
f = afwFits.Fits(filename, 'r')
nExtensions = f.countHdus()
nStamps = metadata["N_STAMPS"]
# check if a bbox was provided
kwargs = {}
if options and options.exists("llcX"):
llcX = options["llcX"]
llcY = options["llcY"]
width = options["width"]
height = options["height"]
bbox = Box2I(Point2I(llcX, llcY), Extent2I(width, height))
kwargs["bbox"] = bbox
stamp_parts = {}
# We need to be careful because nExtensions includes the primary
# header data unit
for idx in range(nExtensions - 1):
md = afwFits.readMetadata(filename, hdu=idx + 1)
if md['EXTNAME'] in ('IMAGE', 'VARIANCE'):
reader = afwImage.ImageFitsReader(filename, hdu=idx + 1)
elif md['EXTNAME'] == 'MASK':
reader = afwImage.MaskFitsReader(filename, hdu=idx + 1)
else:
raise ValueError(f"Unknown extension type: {md['EXTNAME']}")
stamp_parts.setdefault(
md['EXTVER'], {})[md['EXTNAME'].lower()] = reader.read(**kwargs)
if len(stamp_parts) != nStamps:
raise ValueError(
f'Number of stamps read ({len(stamp_parts)}) does not agree with the '
f'number of stamps recorded in the metadata ({nStamps}).')
# construct stamps themselves
stamps = []
for k in range(nStamps):
# Need to increment by one since EXTVER starts at 1
maskedImage = afwImage.MaskedImageF(**stamp_parts[k + 1])
stamps.append(stamp_factory(maskedImage, metadata, k))
return stamps, metadata
def readFits(fileName, hdu=0, flags=0):
"""Read our list of Backgrounds from a file.
Parameters
----------
fileName : `str`
FITS file to read
hdu : `int`
First Header/Data Unit to attempt to read from
flags : `int`
Flags to control details of reading; currently unused, but present
for consistency with `lsst.afw.table.BaseCatalog.readFits`.
See Also
--------
getImage()
"""
if not isinstance(fileName, MemFileManager) and not os.path.exists(fileName):
raise RuntimeError(f"File not found: {fileName}")
self = BackgroundList()
f = Fits(fileName, 'r')
nHdus = f.countHdus()
f.closeFile()
if nHdus % 3 != 0:
raise RuntimeError(f"BackgroundList FITS file {fileName} has {nHdus} HDUs;"
f"expected a multiple of 3 (compression is not supported).")
for hdu in range(0, nHdus, 3):
# It seems like we ought to be able to just use
# MaskedImageFitsReader here, but it warns about EXTTYPE and still
# doesn't work quite naturally when starting from a nonzero HDU.
imageReader = afwImage.ImageFitsReader(fileName, hdu=hdu)
maskReader = afwImage.MaskFitsReader(fileName, hdu=hdu + 1)
varianceReader = afwImage.ImageFitsReader(fileName, hdu=hdu + 2)
statsImage = afwImage.MaskedImageF(imageReader.read(), maskReader.read(), varianceReader.read())
md = imageReader.readMetadata()
x0 = md["BKGD_X0"]
y0 = md["BKGD_Y0"]
width = md["BKGD_WIDTH"]
height = md["BKGD_HEIGHT"]
imageBBox = lsst.geom.BoxI(lsst.geom.PointI(x0, y0), lsst.geom.ExtentI(width, height))
interpStyle = afwMath.Interpolate.Style(md["INTERPSTYLE"])
undersampleStyle = afwMath.UndersampleStyle(md["UNDERSAMPLESTYLE"])
# Older outputs won't have APPROX* settings. Provide alternative defaults.
# Note: Currently X- and Y-orders must be equal due to a limitation in
# math::Chebyshev1Function2. Setting approxOrderY = -1 is equivalent
# to saying approxOrderY = approxOrderX.
approxStyle = md.get("APPROXSTYLE", afwMath.ApproximateControl.UNKNOWN)
approxStyle = afwMath.ApproximateControl.Style(approxStyle)
approxOrderX = md.get("APPROXORDERX", 1)
approxOrderY = md.get("APPROXORDERY", -1)
approxWeighting = md.get("APPROXWEIGHTING", True)
bkgd = afwMath.BackgroundMI(imageBBox, statsImage)
bctrl = bkgd.getBackgroundControl()
# TODO: DM-22814: remove this after v20.
# Still needed until then because other code might call the old-style getImageF.
with suppress_deprecations():
bctrl.setInterpStyle(interpStyle)
bctrl.setUndersampleStyle(undersampleStyle)
actrl = afwMath.ApproximateControl(approxStyle, approxOrderX, approxOrderY, approxWeighting)
bctrl.setApproximateControl(actrl)
bgInfo = (bkgd, interpStyle, undersampleStyle, approxStyle,
approxOrderX, approxOrderY, approxWeighting)
self.append(bgInfo)
return self