def check_gmos_image(filepath, calibrations=False):
from astrodata import AstroData
reason = "GMOS image"
try:
ad = AstroData(filepath)
except:
reason = "can't load file"
return False, reason
try:
fp_mask = ad.focal_plane_mask().as_pytype()
except:
fp_mask = None
if "GMOS" not in ad.types:
reason = "not GMOS"
return False, reason
elif "GMOS_DARK" in ad.types:
reason = "GMOS dark"
return False, reason
elif "GMOS_BIAS" in ad.types and not calibrations:
reason = "GMOS bias"
return False, reason
elif "GMOS_IMAGE_FLAT" in ad.types and not calibrations:
reason = "GMOS flat"
return False, reason
elif ("GMOS_IMAGE" in ad.types and
fp_mask!="Imaging"):
reason = "GMOS slit image"
return False, reason
elif (("GMOS_IMAGE" in ad.types and
fp_mask == "Imaging" and
"GMOS_DARK" not in ad.types) or
"GMOS_BIAS" in ad.types or
"GMOS_IMAGE_FLAT" in ad.types):
# Test for 3-amp mode with e2vDD CCDs
# This mode has not been commissioned.
dettype = ad.phu_get_key_value("DETTYPE")
if dettype == "SDSU II e2v DD CCD42-90":
namps = ad.phu_get_key_value("NAMPS")
if namps is not None and int(namps)==1:
reason = "uncommissioned 3-amp mode"
return False, reason
else:
return True, reason
else:
return True, reason
else:
reason = "not GMOS image"
return False, reason
def check_gmos_longslit(filepath):
from astrodata import AstroData
reason = "GMOS longslit"
try:
ad = AstroData(filepath)
except:
reason = "can't load file"
return False, reason
try:
fp_mask = ad.focal_plane_mask().as_pytype()
except:
fp_mask = None
if "GMOS" not in ad.types:
reason = "not GMOS"
return False, reason
elif "GMOS_DARK" in ad.types:
reason = "GMOS dark"
return False, reason
elif "GMOS_BIAS" in ad.types:
reason = "GMOS bias"
return False, reason
elif "GMOS_NODANDSHUFFLE" in ad.types:
reason = "GMOS nod and shuffle"
return False, reason
elif "GMOS_LS" in ad.types:
# Test for 3-amp mode with e2vDD CCDs
# This mode has not been commissioned.
dettype = ad.phu_get_key_value("DETTYPE")
if dettype == "SDSU II e2v DD CCD42-90":
namps = ad.phu_get_key_value("NAMPS")
if namps is not None and int(namps)==1:
reason = "uncommissioned 3-amp mode"
return False, reason
else:
return True, reason
else:
return True, reason
else:
reason = "not GMOS longslit"
return False, reason
def recover(self):
log.debug("OutAtList recover()")
adlist = []
for i, tmpname in enumerate(self.diskoutlist):
ad = AstroData(tmpname, mode="update")
ad.filename = self.ad_name[i]
ad = gemini_tools.obsmode_del(ad)
# Read the database back in, if it exists
try:
ad = gemini_tools.read_database(
ad, database_name=self.database_name,
input_name=self.tmpin_name[i],
output_name=ad.phu_get_key_value("ORIGNAME"))
except:
pass
adlist.append(ad)
log.fullinfo(tmpname + " was loaded into memory")
return adlist
class AcquisitionImage(object):
def __init__(self, filename, mosmask=None, mdfdir=None):
self.ad = AstroData(filename)
self.mosmask = mosmask
self.mdfdir = mdfdir
# Determine extension
nsci = len(self.ad)
debug("...nsci = ", nsci)
if nsci > 1:
l_sci_ext = 1
else:
l_sci_ext = 0
debug("...using extension [" + str(l_sci_ext) + "]")
overscan_dv = self.ad[l_sci_ext].overscan_section()
if self.is_mos_mode():
self.box_coords = parse_box_coords(self, self.get_mdf_filename())
self.box_mosaic = BoxMosaic(self, self.box_coords)
self.scidata = self.box_mosaic.get_science_data()
elif self.is_new_gmosn_ccd():
# tile the 2 center parts of the new GMOS image
self.scidata = gmultiamp(self.ad)
elif not overscan_dv.is_none():
# remove the overscan so we don't have to take it into account when guessing the slit location
self.scidata = subtract_overscan(self.ad[l_sci_ext])
# it still affects the center of rotation however
ox1, ox2, oy1, oy2 = overscan_dv.as_list()
correction = np.array([ox2 - ox1, 0])
center = self.get_binned_data_center() - correction
self.fieldcenter = center * self.detector_y_bin()
else:
self.scidata = self.ad[l_sci_ext].data
@cache
def instrument(self):
return str(self.ad.instrument())
def is_new_gmosn_ccd(self):
header = self.ad.phu.header
if "DETECTOR" not in header:
return False
if header["DETECTOR"] == "GMOS + e2v DD CCD42-90":
return True
return False
def get_science_data(self):
assert self.scidata is not None
return self.scidata
@cache
def unbinned_pixel_scale(self):
return float(self.ad.pixel_scale()) / self.detector_y_bin()
@cache
def binned_pixel_scale(self):
return float(self.ad.pixel_scale())
def _check_binning(self):
if int(self.ad.detector_x_bin()) != int(self.ad.detector_y_bin()):
error("ERROR: incorrect binning!")
error("Sorry about that, better luck next time.")
sys.exit(1)
@cache
def detector_x_bin(self):
self._check_binning()
return int(self.ad.detector_x_bin())
@cache
def detector_y_bin(self):
self._check_binning()
return int(self.ad.detector_y_bin())
@cache
def program_id(self):
return str(self.ad.program_id())
@cache
def observation_id(self):
return str(self.ad.observation_id())
@cache
def saturation_level(self):
dv = self.ad.saturation_level()
return min(dv.as_list())
@cache
def focal_plane_mask(self):
return str(self.ad.focal_plane_mask())
@cache
def grating(self):
return str(self.ad.grating())
def get_detector_size(self):
# mos mode acquisitions don't necessarily have the entire
# field of view in their data sections, so we have to rely on
# other tricks to figure out the center of rotation.
detsize = self.ad.phu_get_key_value("DETSIZE")
xmin, xdim, ymin, ydim = extract_dimensions(detsize)
# adjust for chip gaps
nccds = int(self.ad.phu_get_key_value("NCCDS"))
xdim += ((nccds - 1) * _obtain_unbinned_arraygap(self.ad))
# adjust for un-illuminated pixels
if self.is_gmos():
ydim -= 36 # magic number that should be replaced with a lookup table later
return xdim, ydim
def get_field_center(self):
""" The center of rotation in pixels. """
if hasattr(self, "fieldcenter"):
return self.fieldcenter
if self.is_mos_mode():
xdim, ydim = self.get_detector_size()
return np.array([float(xdim) / 2.0, float(ydim) / 2.0])
return self.get_data_center()
def get_data_center(self):
ydim, xdim = self.get_science_data().shape
return np.array([float(xdim) / 2.0, float(ydim) / 2.0]) * self.detector_y_bin()
def get_binned_data_center(self):
return self.get_data_center() / self.detector_y_bin()
def set_goal_center(self, center):
self.goal_center = np.array(center)
def get_goal_center(self):
default = self.get_data_center()
return getattr(self, "goal_center", default)
def set_binned_custom_center(self, center):
self.set_binned_goal_center(center)
self.custom_center = True
def has_custom_center(self):
return getattr(self, "custom_center", False)
def get_binned_goal_center(self):
return self.get_goal_center() / self.detector_y_bin()
def set_binned_goal_center(self, center):
center = np.array(center) * self.detector_y_bin()
self.set_goal_center(center)
def get_mask_width(self):
debug("...finding slit dimensions...")
slitxbin = self.detector_x_bin()
slitybin = self.detector_y_bin()
debug("...slit image binning = ", slitxbin, " x ", slitybin)
if slitxbin > 1 or slitybin > 1:
warning("! WARNING: Slit image is binned " + slitxbin + " x " + slitybin)
slitmask = self.focal_plane_mask()
return float(slitmask.replace("arcsec", ""))
def get_mask_width_in_pixels(self):
return self.get_mask_width() / self.unbinned_pixel_scale()
def get_slit_size_in_pixels(self):
xsize = self.get_mask_width_in_pixels()
ysize = self.get_science_data().shape[0]
return xsize, ysize
def get_expected_slit_tilt(self):
if self.is_gmos():
return 0.0
error("Instrument is not supported, need to know an expected slit tilt")
sys.exit(1)
@property
def phu(self):
return self.ad.phu
@property
def filename(self):
return self.ad.filename
def get_program_id_parts(self):
gemprgid = str(self.ad.program_id())
parts = gemprgid.split("-")
if len(parts) != 4:
msg = "Cannot parse program id '%s'" % gemprgid
error(msg)
raise ValueError(msg)
observatory, semester, prgtype, queuenum = parts
return observatory, semester, prgtype, int(queuenum)
def get_semester(self):
""" Return something in the form of '2006B' """
observatory, semester, prgtype, queuenum = self.get_program_id_parts()
return semester
def get_observatory_prefix(self):
""" Return something in the form of 'GN' """
observatory, semester, prgtype, queuenum = self.get_program_id_parts()
return observatory
def is_mos_mode(self):
return self.mosmask is not None or self.has_mos_mask()
@cache
def has_mos_mask(self):
if not self.is_gmos() and not self.is_f2():
return False
maskname = self.focal_plane_mask()
if ("Q" in maskname or # Queue program
"C" in maskname or # Classical program
"D" in maskname or # DD program
"V" in maskname): # SV program
xbin = self.detector_x_bin()
ybin = self.detector_y_bin()
if xbin != 1 or ybin != 1:
error ("MOS acquisition image binning must be 1x1, found %ix%i binning." % (xbin, ybin))
clean()
return True
return False
def has_mask_in_beam(self):
maskname = self.focal_plane_mask().lower()
if "imag" in maskname:
return False
slitmask = self.focal_plane_mask()
if self.is_gmos() and "arcsec" in slitmask:
return True
if self.is_gnirs() and "arcsec" in slitmask:
acqmir = slitimage_ad.phu.header["ACQMIR"]
debug("...acqmir = ", acqmir)
if acqmir == "In":
return True
if self.is_niri() and "cam" not in slitmask:
return True
if self.is_f2() and "slit" in slitmask:
return True
if self.is_f2() and "mos" in slitmask:
return True
return self.has_mos_mask()
def get_mdf_filename(self):
if hasattr(self, "mdffile"):
return self.mdffile
self.mdffile = self._get_mdf_filename()
return self.mdffile
def _get_mdf_filename(self):
if self.mosmask is not None:
mdffile = self.mosmask
# Expand the MOS mask number
if is_number(self.mosmask):
observatory, semester, prgtype, queuenum = self.get_program_id_parts()
mdffile = "%s%s%s%03i-%02i" % (observatory, semester, prgtype, queuenum, int(self.mosmask))
debug("...mosmask =", mdffile)
else:
mdffile = self.focal_plane_mask()
mdffile = fits_filename(mdffile)
#-----------------------------------------------------------------------
# Start searching around willy nilly for the MDF file
if os.path.exists(mdffile):
return mdffile
# note, the order in which directories are added to this list gives priority
dirs = []
if self.mdfdir is not None:
dirs.append(self.mdfdir)
dname = os.path.dirname(self.filename)
if dname and dname != ".":
dirs.append(dname)
dirs.append(os.getcwd())
# search through semester directories as well
semester_dir = self.get_observatory_prefix() + self.get_semester()
directories_to_search = []
for dname in dirs:
directories_to_search.append(dname)
dname = os.path.join(dname, semester_dir)
directories_to_search.append(dname)
# now search through the directories
for dname in directories_to_search:
fname = os.path.join(dname, mdffile)
debug("...trying", fname)
if os.path.exists(fname):
return fname
raise ValueError("Unable to find MDF file named '%s'" % mdffile)
def get_num_mos_boxes(self):
return self.box_mosaic.get_num_mos_boxes()
def get_mos_boxes(self):
return self.box_mosaic.get_boxes()
def get_mos_box_borders(self):
for border in self.box_mosaic.get_box_borders():
yield border
@cache
def get_min_slitsize(self):
mdffile_ad = AstroData(self.get_mdf_filename())
xsize = Ellipsis
ysize = Ellipsis
for row in mdffile_ad["MDF"].data:
# select the alignment boxes, designated by priority 0
if row["priority"] not in ["1", "2", "3"]:
continue
xsize = min(xsize, row["slitsize_x"])
ysize = min(ysize, row["slitsize_y"])
return xsize, ysize
def get_extensions(self):
for ext in self.ad:
yield ext
def _get_lazy_detector_section_finder(self):
if not hasattr(self, "detsec_finder"):
self.detsec_finder = DetectorSectionFinder(self)
return self.detsec_finder
def get_box_size(self):
return self._get_lazy_detector_section_finder().get_box_size()
def find_detector_section(self, point):
return self._get_lazy_detector_section_finder().find_detector_section(point)
def get_full_field_of_view(self):
return self._get_lazy_detector_section_finder().get_full_field_of_view()
def is_altair(self):
aofold = self.ad.phu.header["AOFOLD"]
if aofold == "IN":
return True
return False
def is_south_port(self):
inportnum = int(self.ad.phu.header["INPORT"])
if inportnum == 1:
return True
return False
def is_type(self, typename):
return self.ad.is_type(typename)
def is_gmos(self):
return self.is_type("GMOS")
def is_gmosn(self):
return self.is_type("GMOS_N")
def is_gmoss(self):
return self.is_type("GMOS_S")
def is_gnirs(self):
return self.is_type("GNIRS")
def is_f2(self):
return self.is_type("F2")
def is_nifs(self):
return self.is_type("NIFS")
def is_niri(self):
return self.is_type("NIRI")
def test_method_phu_get_key_val_6():
ad = AstroData(TESTFILE2)
with pytest.raises(TypeError):
assert ad.phu_get_key_value()
def test_method_phu_get_key_val_5():
ad = AstroData(TESTFILE2)
assert ad.phu_get_key_value('FOO') is None
def test_method_phu_get_key_val_3():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('RA'), float)
def test_method_phu_get_key_val_2():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('BITPIX'), int)
def test_method_phu_get_key_val_1():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('SIMPLE'), bool)
def test_method_phu_get_key_val_3():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('RA'), float)
def test_method_phu_get_key_val_2():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('BITPIX'), int)
def test_method_phu_get_key_val_1():
ad = AstroData(TESTFILE2)
assert isinstance(ad.phu_get_key_value('SIMPLE'), bool)
def test_method_phu_get_key_val_6():
ad = AstroData(TESTFILE2)
with pytest.raises(TypeError):
assert ad.phu_get_key_value()
def test_method_phu_get_key_val_5():
ad = AstroData(TESTFILE2)
assert ad.phu_get_key_value('FOO') is None
def main():
options, args, parser = handleClArgs()
# If clean, call superclean to clear out cache and kill old reduce
# and adcc processes.
if options.clean:
print "\nRestoring redux to default state:" + \
"\nall stack and calibration associations will be lost;" + \
"\nall temporary files will be removed.\n"
subprocess.call(["superclean", "--safe"])
print
sys.exit()
# Get local site
if time.timezone / 3600 == 10: # HST = UTC + 10
localsite = GEMINI_NORTH
elif time.timezone / 3600 == 4: # CST = UTC + 4
localsite = GEMINI_SOUTH
else:
print "ERROR - timezone is not HST or CST. Local site cannot " + \
"be determined"
sys.exit()
# Check arguments
if len(args) < 1:
print "ERROR - No input file specified"
parser.print_help()
sys.exit()
elif len(args) > 2:
print "ERROR - Too many arguments"
parser.print_help()
sys.exit()
elif len(args) == 2:
date = gemini_date(args[0])
if date != "":
prefix = OBSPREF[localsite] + date + "S"
else:
print "ERROR - Date %s not recognized." % args[0]
parser.print_help()
sys.exit()
filenm = prefix + "%04i" % int(args[1])
else:
filenm = args[0]
# Get file prefix from user; otherwise, use auto
prefix = "auto"
if options.prefix:
prefix = options.prefix
# Get data directory from user or from site defaults
directory = "."
if options.directory:
directory = options.directory
else:
if os.path.exists(OPSDATAPATH[localsite]):
directory = OPSDATAPATH[localsite]
elif os.path.exists(OPSDATAPATHBKUP[localsite]):
directory = OPSDATAPATHBKUP[localsite]
else:
print "Cannot find %s or %s. Please specify a directory." % \
(OPSDATAPATH[localsite], OPSDATAPATHBKUP[localsite])
directory = directory.rstrip("/") + "/"
# Check for stacking option
recipe = None
if options.stack:
# Check for _forStack image in local directory
if os.path.exists(filenm):
stack_filenm = os.path.basename(filenm)
else:
stack_filenm = filenm
imgpath = image_path(stack_filenm, ".",
prefix=prefix, localsite=localsite,
suffix="_forStack")
if imgpath is None:
# If not found, check for raw image in specified directory
# and use full reduction recipe
imgpath = image_path(filenm, directory,
prefix=prefix, localsite=localsite)
recipe = "qaReduceAndStack"
else:
# If found, just use stacking recipe
recipe = "qaStack"
else:
imgpath = image_path(filenm, directory,
prefix=prefix, localsite=localsite)
if imgpath is None:
print "\nFile %s was not found.\n" % filenm
sys.exit()
imgname = os.path.basename(imgpath)
print "Image path: "+imgpath
# Check that file is GMOS LONGSLIT or IMAGE; other types are not yet supported
# (but do allow biases and flats, too)
try:
ad = AstroData(imgpath)
except IOError:
print "\nProblem accessing file %s.\n" % filenm
sys.exit()
try:
fp_mask = ad.focal_plane_mask()
except:
fp_mask = None
if "RAW" not in ad.types and "PREPARED" in ad.types:
print "AstroDataType 'RAW' not found in types."
print "AstroDataType 'PREPARED' found in types."
print "\nFile %s appears to have been processed." % imgname
print "redux halting ..."
sys.exit()
if "GMOS" not in ad.types:
print "\nFile %s is not a GMOS file." % imgname
print "Only GMOS longslit and images can be reduced at this time.\n"
sys.exit()
elif "GMOS_DARK" in ad.types:
print "\nFile %s is a GMOS dark." % imgname
print "Only GMOS longslit and images can be reduced at this time.\n"
sys.exit()
elif ("GMOS_IMAGE" in ad.types and
fp_mask!="Imaging"):
print "\nFile %s is a slit image." % imgname
print "Only GMOS longslit and images can be reduced at this time.\n"
sys.exit()
elif (("GMOS_IMAGE" in ad.types and
fp_mask=="Imaging" and
"GMOS_DARK" not in ad.types) or
"GMOS_BIAS" in ad.types or
"GMOS_IMAGE_FLAT" in ad.types or
"GMOS_LS" in ad.types):
# Test for 3-amp mode with e2vDD CCDs. NOT commissioned.
dettype = ad.phu_get_key_value("DETTYPE")
if dettype=="SDSU II e2v DD CCD42-90":
namps = ad.phu_get_key_value("NAMPS")
if namps is not None and int(namps)==1:
print "\nERROR: The GMOS e2v detectors should " \
"not use 3-amp mode!"
print "Please set the GMOS CCD Readout Characteristics " \
"to use 6 amplifiers.\n"
sys.exit()
print "\nBeginning reduction for file %s, %s\n" % (imgname,
ad.data_label())
if options.upload:
context = "QA,upload"
else:
context = "QA"
# Check for an alternate recipe for science reductions
if ("GMOS_IMAGE" in ad.types and
"GMOS_BIAS" not in ad.types and
"GMOS_IMAGE_FLAT" not in ad.types and
recipe is not None):
reduce_cmd = ["reduce",
"-r", recipe,
"--context",context,
"--loglevel","stdinfo",
"--logfile","gemini.log",
"-p", "clobber=True",
imgpath]
else:
# Otherwise call reduce with auto-selected reduction recipe
reduce_cmd = ["reduce",
"--context",context,
"--loglevel","stdinfo",
"--logfile","gemini.log",
"-p", "clobber=True",
imgpath]
subprocess.call(reduce_cmd)
print ""
else:
print "\nFile %s is not a supported type." % imgname
print "Only GMOS longslit and images can be reduced at this time.\n"
sys.exit()