def bypass_defects(self, datasetType, pythonType, butlerLocation, dataId):
"""Return a defect based on the butler location returned by map_defects
Parameters
----------
butlerLocation : `lsst.daf.persistence.ButlerLocation`
locationList = path to defects FITS file
dataId : `dict`
Butler data ID; "ccd" must be set.
Note: the name "bypass_XXX" means the butler makes no attempt to
convert the ButlerLocation into an object, which is what we want for
now, since that conversion is a bit tricky.
"""
detectorName = self._extractDetectorName(dataId)
defectsFitsPath = butlerLocation.locationList[0]
with fits.open(defectsFitsPath) as hduList:
for hdu in hduList[1:]:
if hdu.header["name"] != detectorName:
continue
defectList = Defects()
for data in hdu.data:
bbox = geom.Box2I(
geom.Point2I(int(data['x0']), int(data['y0'])),
geom.Extent2I(int(data['width']), int(data['height'])),
)
defectList.append(bbox)
return defectList
raise RuntimeError("No defects for ccd %s in %s" % (detectorName, defectsFitsPath))
def read_defects_one_chip(root, chip_name, chip_id):
"""Read defects for a particular sensor from the standard format at a particular root.
Parameters
----------
root : str
Path to the top level of the defects tree. This is expected to hold directories
named after the sensor names. They are expected to be lower case.
chip_name : str
The name of the sensor for which to read defects.
chip_id : int
The identifier for the sensor in question.
Returns
-------
dict
A dictionary of `lsst.meas.algorithms.Defects`.
The key is the validity start time as a `datetime` object.
"""
files = glob.glob(os.path.join(root, chip_name, '*.ecsv'))
parts = os.path.split(root)
instrument = os.path.split(
parts[0])[1] # convention is that these reside at <instrument>/defects
defect_dict = {}
for f in files:
date_str = os.path.splitext(os.path.basename(f))[0]
valid_start = dateutil.parser.parse(date_str)
defect_dict[valid_start] = Defects.readText(f)
check_metadata(defect_dict[valid_start], valid_start, instrument,
chip_id, f)
return defect_dict
def makeDefectList(self):
"""Generate a simple single-entry defect list.
Returns
-------
defectList : `lsst.meas.algorithms.Defects`
Simulated defect list
"""
return Defects([lsst.geom.Box2I(lsst.geom.Point2I(0, 0),
lsst.geom.Extent2I(40, 50))])
detectorName = "0"
"""Detector name."""
detectorSerial = "0000011"
"""Detector serial code"""
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=f"""Construct a defects file from the mask plane of a test camera bias frame.
To use this command you must setup ip_isr and astropy.
Output is written to the current directory as file {DefectsPath}, which must not already exist.
"""
)
parser.add_argument("bias", help="path to bias image for the test camera")
args = parser.parse_args()
biasMI = afwImage.MaskedImageF(args.bias)
defectList = Defects.fromMask(biasMI, "BAD")
valid_start = dateutil.parser.parse('19700101T000000')
md = defectList.getMetadata()
md['INSTRUME'] = 'test'
md['DETECTOR'] = detectorName
md['CALIBDATE'] = valid_start.isoformat()
md['FILTER'] = None
defect_file = defectList.writeText(DefectsPath)
print("wrote defects file %r" % (DefectsPath,))
test2defectList = Defects.readText(defect_file)
assert defectList == test2defectList
print("verified that defects file %r round trips correctly" % (DefectsPath,))