def test_amp_ids(self):
"""Test auto-detection of amp names"""
hdr = dict(
CCDSECA=self.header['CCDSECA'],
CCDSECB=self.header['CCDSECB'],
CCDSECC=self.header['CCDSECC'],
CCDSECD=self.header['CCDSECD'],
)
self.assertEqual(get_amp_ids(hdr), ['A', 'B', 'C', 'D'])
hdr = dict(
CCDSEC1=self.header['CCDSECA'],
CCDSEC2=self.header['CCDSECB'],
CCDSEC3=self.header['CCDSECC'],
CCDSEC4=self.header['CCDSECD'],
)
self.assertEqual(get_amp_ids(hdr), ['1', '2', '3', '4'])
hdr = dict()
with self.assertRaises(KeyError):
get_amp_ids(hdr)
def ampregion(image):
"""
Get the pixel boundary regions for amps
Args:
image: desispec.image.Image object
"""
pixboundary = []
for kk in get_amp_ids(image.meta): # A-D or 1-4
#- get the amp region in pix
ampboundary = parse_sec_keyword(image.meta["CCDSEC" + kk])
pixboundary.append(ampboundary)
return pixboundary
def cal_rdnoise(hdul, camera, ccd_calibration_filename, use_overscan_row,
overscan_per_row, use_active):
if True:
hdul_this = hdul[camera]
header = hdul_this.header
rawimage = hdul_this.data
# works! preproc.preproc(hdul['B0'].data,hdul['B0'].header,h1)
amp_ids = preproc.get_amp_ids(header)
#- Output arrays
ny = 0
nx = 0
for amp in amp_ids:
yy, xx = parse_sec_keyword(header['CCDSEC%s' % amp])
ny = max(ny, yy.stop)
nx = max(nx, xx.stop)
image = np.zeros((ny, nx))
readnoise = np.zeros_like(image)
nogain = False
cfinder = None
if ccd_calibration_filename is not False:
cfinder = CalibFinder([header, primary_header],
yaml_file=ccd_calibration_filename)
for amp in amp_ids:
# Grab the sections
ov_col = parse_sec_keyword(header['BIASSEC' + amp])
ov_row = parse_sec_keyword(header['ORSEC' + amp])
if use_active:
if amp == 'A' or amp == 'D':
ov_col2 = np.s_[ov_col[1].start:ov_col[1].stop, 0:100]
else:
ov_col2 = np.s_[ov_col[1].start:ov_col[1].stop, 0:100]
import pdb
pdb.set_trace()
if 'ORSEC' + amp in header.keys():
ov_row = parse_sec_keyword(header['ORSEC' + amp])
elif use_overscan_row:
log.error(
'No ORSEC{} keyword; not using overscan_row'.format(amp))
use_overscan_row = False
if nogain:
gain = 1.
else:
#- Initial teststand data may be missing GAIN* keywords; don't crash
if 'GAIN' + amp in header:
gain = header['GAIN' + amp] #- gain = electrons / ADU
else:
if cfinder and cfinder.haskey('GAIN' + amp):
gain = float(cfinder.value('GAIN' + amp))
log.info(
'Using GAIN{}={} from calibration data'.format(
amp, gain))
else:
gain = 1.0
log.warning(
'Missing keyword GAIN{} in header and nothing in calib data; using {}'
.format(amp, gain))
#- Add saturation level
if 'SATURLEV' + amp in header:
saturlev = header['SATURLEV' + amp] # in electrons
else:
if cfinder and cfinder.haskey('SATURLEV' + amp):
saturlev = float(cfinder.value('SATURLEV' + amp))
log.info(
'Using SATURLEV{}={} from calibration data'.format(
amp, saturlev))
else:
saturlev = 200000
log.warning(
'Missing keyword SATURLEV{} in header and nothing in calib data; using 200000'
.format(amp, saturlev))
# Generate the overscan images
raw_overscan_col = rawimage[ov_col].copy() # 2064*64
if use_overscan_row:
raw_overscan_row = rawimage[ov_row].copy() # 32*2057
overscan_row = np.zeros_like(raw_overscan_row)
# Remove overscan_col from overscan_row
raw_overscan_squared = rawimage[ov_row[0],
ov_col[1]].copy() # 32*64
for row in range(raw_overscan_row.shape[0]):
o, r = _overscan(raw_overscan_squared[row])
overscan_row[row] = raw_overscan_row[row] - o
# Now remove the overscan_col
nrows = raw_overscan_col.shape[0]
log.info("nrows in overscan=%d" % nrows)
overscan_col = np.zeros(nrows)
rdnoise = np.zeros(nrows)
if (cfinder and cfinder.haskey('OVERSCAN' + amp)
and cfinder.value("OVERSCAN" + amp).upper()
== "PER_ROW") or overscan_per_row:
log.info(
"Subtracting overscan per row for amplifier %s of camera %s"
% (amp, camera))
for j in range(nrows):
if np.isnan(np.sum(overscan_col[j])):
log.warning(
"NaN values in row %d of overscan of amplifier %s of camera %s"
% (j, amp, camera))
continue
o, r = _overscan(raw_overscan_col[j])
#log.info("%d %f %f"%(j,o,r))
overscan_col[j] = o
rdnoise[j] = r
else:
log.info(
"Subtracting average overscan for amplifier %s of camera %s"
% (amp, camera))
o, r = _overscan(raw_overscan_col)
overscan_col += o
rdnoise += r
rdnoise *= gain
median_rdnoise = np.median(rdnoise)
median_overscan = np.median(overscan_col)
return rdnoise, median_rdnoise
def bias_stats(camera='z3', use_overscan_row=True):
"""
Measure stats on bias-subtracted frames
Args:
camera:
Returns:
"""
dpath = '/home/xavier/DESI/DESI_SCRATCH/minisv2/data/20200304/'
bias_files = glob.glob(dpath + '000*/desi-*.fz')
bias_files.sort()
# Load bias images
hdul = fits.open(bias_files[0])
hdu = hdul[camera.upper()]
smnum = hdu.header['SPECID']
new_bias_file = os.path.join(dpath, 'bias_{}.fits'.format(camera))
new_bias = fits.open(new_bias_file)[0].data
old_bias_file = os.path.join(
os.getenv('DESI_SPECTRO_CALIB'), 'ccd',
'bias-sm{}-{}-20191021.fits'.format(smnum, camera[0]))
old_bias = fits.open(old_bias_file)[0].data
calib_file = os.path.join(os.getenv('DESI_SPECTRO_CALIB'), 'spec',
'sm{}'.format(smnum),
'sm{}-{}.yaml'.format(smnum, camera[0]))
# Loop and process
stat_tbl = None
for ss, bias_file in enumerate(bias_files):
hdul = fits.open(bias_file)
# Process
tdict = dict(file=[os.path.basename(bias_file)])
lbias = 'new'
for lbias, bimg in zip(['new', 'old'], [new_bias, old_bias]):
img = preproc.preproc(hdu.data,
hdu.header,
hdul[0].header,
pixflat=False,
mask=False,
nocrosstalk=True,
ccd_calibration_filename=calib_file,
use_overscan_row=use_overscan_row,
dark=False,
flag_savgol=False,
bias_img=bimg)
# Stats
amp_ids = preproc.get_amp_ids(hdu.header)
for amp in amp_ids:
kk = preproc.parse_sec_keyword(hdu.header['CCDSEC' + amp])
zero, rms = preproc._overscan(img.pix[kk])
tdict[lbias + amp + '_zero'] = [zero]
tdict[lbias + amp + '_rms'] = [rms]
# Add to Table
if stat_tbl is None:
stat_tbl = Table(tdict)
else:
stat_tbl.add_row(tdict)
# Write
if use_overscan_row:
root = '_'
else:
root = '_norow_'
outbase = 'bias_stats{}{}.fits'.format(root, camera)
outfile = os.path.join(dpath, 'Stats', outbase)
stat_tbl.write(outfile, overwrite=True)
print("Wrote: {}".format(outfile))
def fiducialregion(frame, psf):
"""
Get the fiducial amplifier regions on the CCD pixel to fiber by wavelength space
Args:
frame: desispec.frame.Frame object
psf: desispec.psf.PSF like object
"""
startspec = 0 #- will be None if don't have fibers on the right of the CCD.
endspec = 499 #- will be None if don't have fibers on the right of the CCD
startwave0 = 0 #- lower index for the starting fiber
startwave1 = 0 #- lower index for the last fiber for the amp region
endwave0 = frame.wave.shape[0] #- upper index for the starting fiber
endwave1 = frame.wave.shape[
0] #- upper index for the last fiber for that amp
pixboundary = []
fidboundary = []
#- Adding the min, max boundary individually for the benefit of dumping to yaml.
leftmax = 499 #- for amp 1 and 3
rightmin = 0 #- for amp 2 and 4
bottommax = frame.wave.shape[0] #- for amp 1 and 2
topmin = 0 #- for amp 3 and 4
#- Loop over each amp
for kk in get_amp_ids(frame.meta): # A-D or 1-4
#- get the amp region in pix
ampboundary = parse_sec_keyword(frame.meta["CCDSEC" + kk])
pixboundary.append(ampboundary)
for ispec in range(frame.flux.shape[0]):
if np.all(psf.x(ispec) > ampboundary[1].start):
startspec = ispec
#-cutting off wavelenth boundaries from startspec
yy = psf.y(ispec, frame.wave)
k = np.where(yy > ampboundary[0].start)[0]
startwave0 = k[0]
yy = psf.y(ispec, frame.wave)
k = np.where(yy < ampboundary[0].stop)[0]
endwave0 = k[-1]
break
else:
startspec = None
startwave0 = None
endwave0 = None
if startspec is not None:
for ispec in range(frame.flux.shape[0])[::-1]:
if np.all(psf.x(ispec) < ampboundary[1].stop):
endspec = ispec
#-cutting off wavelenth boundaries from startspec
yy = psf.y(ispec, frame.wave)
k = np.where(yy > ampboundary[0].start)[0]
startwave1 = k[0]
yy = psf.y(ispec, frame.wave)
k = np.where(yy < ampboundary[0].stop)[0]
endwave1 = k[-1]
break
else:
endspec = None
startwave1 = None
endwave1 = None
if startwave0 is not None and startwave1 is not None:
startwave = max(startwave0, startwave1)
else:
startwave = None
if endwave0 is not None and endwave1 is not None:
endwave = min(endwave0, endwave1)
else:
endwave = None
if endspec is not None:
#endspec+=1 #- last entry exclusive in slice, so add 1
#endwave+=1
if endspec < leftmax:
leftmax = endspec
if startspec > rightmin:
rightmin = startspec
if endwave < bottommax:
bottommax = endwave
if startwave > topmin:
topmin = startwave
else:
rightmin = 0 #- Only if no spec in right side of CCD. passing 0 to encertain valid data type. Nontype throws a type error in yaml.dump.
#fiducialb=(slice(startspec,endspec,None),slice(startwave,endwave,None)) #- Note: y,x --> spec, wavelength
#fidboundary.append(fiducialb)
#- return pixboundary,fidboundary
return leftmax, rightmin, bottommax, topmin