mag = np.where((dqflag==0), mag, None)
# Now ditch the values out of the arrays where mag is None
# NB do mag last
magerr = magerr[np.flatnonzero(mag)]
refmag = refmag[np.flatnonzero(mag)]
refmagerr = refmagerr[np.flatnonzero(mag)]
mag = mag[np.flatnonzero(mag)]
if(len(mag) == 0):
print "No good sources to plot"
sys.exit(1)
# Now apply the exposure time and nom_at_ext corrections to mag
et = float(ad.exposure_time())
if(ad.is_type('GMOS_NODANDSHUFFLE')):
print "Imaging Nod-And-Shuffle. Photometry may be dubious"
et /= 2.0
etmag = 2.5*math.log10(et)
nom_at_ext = float(ad.nominal_atmospheric_extinction())
mag += etmag
mag += nom_at_ext
# Can now calculate the zp array
zp = refmag - mag
zperr = np.sqrt(refmagerr*refmagerr + magerr*magerr)
# Trim values out of zp where the zeropoint error is > 0.1
zp_trim = np.where((zperr<0.1), zp, None)
def __init__(self,fname,linelist=None,extv=1,nsum=10,match=6,radius=10):
self.extv = extv
self.nsum = nsum
self.match = match
self.radius = radius
ad = AstroData(fname)
self.imdata = ad['SCI',extv].data
if ad.dispersion_axis() == 2:
# Transpose to work on the X-axis.
self.imdata = self.imdata.transpose()
self.filename = ad.filename
self.ad = ad
linelist_file = linelist
scrpix = 'crpix1'
scrval = 'crval1'
scdelt = 'cd1_1'
fpath=os.path.dirname(spu.__file__)
if ad.is_type('F2_SPECT') or self.ad.is_type('GNIRS'):
reffile = 'calibrated_arc.fits'
wmin = 7035.14 # x*0.24321 + 7035.1381. wavelength at [0]
wmax = 25344.54 # wavelength at [-1]
scrpix = 'crpix2'
scrval = 'crval2'
scdelt = 'cd2_2'
sz = np.shape(self.imdata)
if len(sz) == 3:
self.imdata = self.imdata.reshape(sz[1],sz[2])
if linelist_file==None:
linelist_file = 'argon.dat'
#linelist_file = 'lowresargon.dat'
elif ad.is_type('GMOS_SPECT'):
if linelist_file==None:
linelist_file = 'cuar.dat'
reffile = 'cuar.fits'
wmin = 3053. # x*0.25 + 3053. cuar.fits wavelength at cuarf[0]
wmax = 10423. # cuar.fits wavelength at cuarf[-1]
elif ad.is_type('NIRI_SPECT'):
reffile = 'calibrated_arc.fits'
wmin = 7032.706
wmax = 25342.113
if linelist_file==None:
linelist_file = 'lowresargon.dat'
elif ad.is_type('NIFS_SPECT'):
filtername = str(self.ad.filter_name())
if 'JH' in filtername:
if linelist_file==None:
linelist_file = 'argon.dat'
wmin = 7032.706
wmax = 25342.113
reffile = 'calibrated_arc.fits'
elif 'HK' in filtername:
if linelist_file==None:
linelist_file = 'ArXe_K.dat'
wmin = 20140.259
wmax = 24491.320
reffile = 'NIFS_K_arc_1D.fits'
elif 'ZJ' in filtername:
if linelist_file==None:
linelist_file = 'argon.dat'
wmin = 7035.14
wmax = 25344.54
reffile = 'calibrated_arc.fits'
else:
raise ValueError('Input file is not supported: '+ad.filename)
self.reffile = os.path.join(fpath,reffile)
self.wmin = wmin
self.wmax = wmax
self.pixs=[]
self.users=[]
linelist_file = os.path.join(fpath,linelist_file)
linelist = np.loadtxt(linelist_file,usecols=(0,))
hdr = ad['SCI',extv].header
self.wcs={'crpix':hdr[scrpix], 'crval':hdr[scrval], 'cdelt':hdr[scdelt]}
cdelt = self.wcs['cdelt']
if cdelt < 0:
linelist = linelist[::-1] # Change to decreasing order
self.cuar = linelist # cuar is the IRAF name
self.ad = ad
sz = np.shape(self.imdata)
nsum = 6
if len(sz) == 2:
ny = max(3,nsum/2)
ym = sz[0]/2
lpix = np.mean(self.imdata[ym-ny:ym+ny],axis=0)
elif len(sz) == 1:
lpix = self.imdata
else:
raise ValueError("Image dimesions are greater than 2.")
self.lpix = lpix
# Now find the arc peaks pixel coordinates
upeaks,uflux,fw = spu.find_upeaks(self.lpix, 2, nmax=50, cradius=12)
self.xfluxs = uflux
self.xpeaks = upeaks # A synonim
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")
except:
log.warning('getBPM: CCDSUM value not supported with BPM: '+indx)
return None
# Find where are these BPM files
fp, pathname, description = imp.find_module('detectSources')
fname = os.path.join(os.path.dirname(pathname),dq)
return AstroData(fname)
if __name__ == '__main__':
import sys,glob
#ad = AstroData('/home/nzarate/zp/zzz.fits')
#ff = Fluxcal(ad) # Create object
#ff.runFC() # run the scripts
for ifile in glob.glob('[g,m]*.fits'):
if 'rgS20110125S' in ifile: continue
if 'zp_' in ifile: continue
ad = AstroData(ifile)
if ad.is_type('CAL'):
print "\nWARNING: 'CAL' type for file:",ifile," not supported."
continue
print "\n >>>>>>>>>>>>>>>>>>FluxCAL for:",ifile
ff = Fluxcal(ad,addBPM=False) # Create object
ff.runFC()
