def lris_read_amp(inp, ext):
"""
Read one amplifier of an LRIS multi-extension FITS image
Parameters
----------
inp: tuple
(str,int) filename, extension
(hdu,int) FITS hdu, extension
Returns
-------
data
predata
postdata
x1
y1
;------------------------------------------------------------------------
function lris_read_amp, filename, ext, $
linebias=linebias, nobias=nobias, $
predata=predata, postdata=postdata, header=header, $
x1=x1, x2=x2, y1=y1, y2=y2, GAINDATA=gaindata
;------------------------------------------------------------------------
; Read one amp from LRIS mHDU image
;------------------------------------------------------------------------
"""
from pypit import arload
# Parse input
if isinstance(inp, basestring):
hdu = pyfits.open(inp)
else:
hdu = inp
#; Get the pre and post pix values
#; for LRIS red POSTLINE = 20, POSTPIX = 80, PRELINE = 0, PRECOL = 12
head0 = hdu[0].header
precol = head0['precol']
postpix = head0['postpix']
#; Deal with binning
binning = head0['BINNING']
xbin, ybin = [int(ibin) for ibin in binning.split(',')]
precol = precol//xbin
postpix = postpix//xbin
#; get entire extension...
temp = hdu[ext].data.transpose() # Silly Python nrow,ncol formatting
tsize = temp.shape
nxt = tsize[0]
#; parse the DETSEC keyword to determine the size of the array.
header = hdu[ext].header
detsec = header['DETSEC']
x1, x2, y1, y2 = np.array(arload.load_sections(detsec, msgs)).flatten()
#; parse the DATASEC keyword to determine the size of the science region (unbinned)
datasec = header['DATASEC']
xdata1, xdata2, ydata1, ydata2 = np.array(arload.load_sections(datasec, msgs)).flatten()
#; grab the components...
predata = temp[0:precol, :]
# datasec appears to have the x value for the keywords that are zero
# based. This is only true in the image header extensions
# not true in the main header. They also appear inconsistent between
# LRISr and LRISb!
#data = temp[xdata1-1:xdata2-1,*]
#data = temp[xdata1:xdata2+1, :]
if (xdata1-1) != precol:
msgs.error("Something wrong in LRIS datasec or precol")
xshape = 1024 // xbin
if (xshape+precol+postpix) != temp.shape[0]:
msgs.error("Wrong size for in LRIS detector somewhere. Funny binning?")
data = temp[precol:precol+xshape,:]
postdata = temp[nxt-postpix:nxt, :]
#; flip in X as needed...
if x1 > x2:
xt = x2
x2 = x1
x1 = xt
data = np.flipud(data) #reverse(temporary(data),1)
#; flip in Y as needed...
if y1 > y2:
yt = y2
y2 = y1
y1 = yt
data = np.fliplr(data)
predata = np.fliplr(predata)
postdata = np.fliplr(postdata)
'''
#; correct gain if requested...
if keyword_set(GAINDATA) then begin
gain = gainvalue( gaindata, header)
data = FLOAT(temporary(data)) * gain
predata = FLOAT(temporary(predata)) * gain
postdata = FLOAT(temporary(postdata)) * gain
endif
'''
'''
;; optional bias subtraction...
if ~ keyword_set(NOBIAS) then begin
if keyword_set( LINEBIAS) then begin
;; compute a bias for each line...
bias = median( postdata, dim=1)
;; subtract for data...
buf = size(data)
nx = buf[1]
ny = buf[2]
data2 = fltarr(nx,ny)
for i=0,nx-1 do begin
data2[i,*] = float(data[i,*]) - bias
endfor
data = data2
endif else begin
;; compute a scalar bias....
bias = median( postdata)
data -= bias
endelse
endif
'''
return data, predata, postdata, x1, y1
def read_lris(raw_file, det=None, TRIM=False):
"""
Read a raw LRIS data frame (one or more detectors)
Packed in a multi-extension HDU
Based on readmhdufits.pro
Parameters
----------
raw_file : str
Filename
det : int, optional
Detector number; Default = both
TRIM : bool, optional
Trim the image?
Returns
-------
array : ndarray
Combined image
header : FITS header
sections : list
List of datasec, oscansec, ampsec sections
"""
from pypit import arload
# Check for file; allow for extra .gz, etc. suffix
fil = glob.glob(raw_file+'*')
if len(fil) != 1:
msgs.error("Found {:d} files matching {:s}".format(len(fil)))
# Read
msgs.info("Reading LRIS file: {:s}".format(fil[0]))
hdu = pyfits.open(fil[0])
head0 = hdu[0].header
# Get post, pre-pix values
precol = head0['PRECOL']
postpix = head0['POSTPIX']
preline = head0['PRELINE']
postline = head0['POSTLINE']
# Setup for datasec, oscansec, ampsec
dsec = []
osec = []
asec = []
# get the x and y binning factors...
binning = head0['BINNING']
xbin, ybin = [int(ibin) for ibin in binning.split(',')]
# First read over the header info to determine the size of the output array...
n_ext = len(hdu)-1 # Number of extensions (usually 4)
xcol = []
xmax = 0
ymax = 0
xmin = 10000
ymin = 10000
for i in np.arange(1, n_ext+1):
theader = hdu[i].header
detsec = theader['DETSEC']
if detsec != '0':
# parse the DETSEC keyword to determine the size of the array.
x1, x2, y1, y2 = np.array(arload.load_sections(detsec, msgs)).flatten()
# find the range of detector space occupied by the data
# [xmin:xmax,ymin:ymax]
xt = max(x2, x1)
xmax = max(xt, xmax)
yt = max(y2, y1)
ymax = max(yt, ymax)
# find the min size of the array
xt = min(x1, x2)
xmin = min(xmin, xt)
yt = min(y1, y2)
ymin = min(ymin, yt)
# Save
xcol.append(xt)
#; determine the output array size...
nx = xmax - xmin + 1
ny = ymax - ymin + 1
#; change size for binning...
nx = nx // xbin
ny = ny // ybin
#; Update PRECOL and POSTPIX
precol = precol // xbin
postpix = postpix // xbin
# Deal with detectors
if det in [1,2]:
nx = nx // 2
n_ext = n_ext // 2
det_idx = np.arange(n_ext, dtype=np.int) + (det-1)*n_ext
ndet = 1
elif det is None:
ndet = 2
det_idx = np.arange(n_ext).astype(int)
else:
raise ValueError('Bad value for det')
#; change size for pre/postscan...
if not TRIM:
nx += n_ext*(precol+postpix)
ny += preline + postline
#; allocate output array...
array = np.zeros( (nx, ny) )
order = np.argsort(np.array(xcol))
#; insert extensions into master image...
for kk, i in enumerate(order[det_idx]):
#; grab complete extension...
data, predata, postdata, x1, y1 = lris_read_amp(hdu, i+1)
#, linebias=linebias, nobias=nobias, $
#x1=x1, x2=x2, y1=y1, y2=y2, gaindata=gaindata)
#; insert components into output array...
if not TRIM:
#; insert predata...
buf = predata.shape
nxpre = buf[0]
xs = kk*precol
xe = xs + nxpre
'''
if keyword_set(VERBOSE) then begin
section = '['+stringify(xs)+':'+stringify(xe)+',*]'
message, 'inserting extension '+stringify(i)+ $
' predata in '+section, /info
endif
'''
array[xs:xe, :] = predata
#; insert data...
buf = data.shape
nxdata = buf[0]
nydata = buf[1]
xs = n_ext*precol + kk*nxdata #(x1-xmin)/xbin
xe = xs + nxdata
# Data section
section = '[{:d}:{:d},{:d}:{:d}]'.format(preline,nydata-postline, xs, xe) # Eliminate lines
dsec.append(section)
section = '[:,{:d}:{:d}]'.format(xs, xe) # Amp section
asec.append(section)
#print('data',xs,xe)
array[xs:xe, :] = data # Include postlines
#; insert postdata...
buf = postdata.shape
nxpost = buf[0]
xs = nx - n_ext*postpix + kk*postpix
xe = xs + nxpost
section = '[:,{:d}:{:d}]'.format(xs, xe)
osec.append(section)
'''
if keyword_set(VERBOSE) then begin
section = '['+stringify(xs)+':'+stringify(xe)+',*]'
message, 'inserting extension '+stringify(i)+ $
' postdata in '+section, /info
endif
'''
array[xs:xe, :] = postdata
else:
buf = data.shape
nxdata = buf[0]
nydata = buf[1]
xs = (x1-xmin)//xbin
xe = xs + nxdata
ys = (y1-ymin)//ybin
ye = ys + nydata - postline
yin1 = preline
yin2 = nydata - postline
'''
if keyword_set(VERBOSE) then begin
section = '['+stringify(xs)+':'+stringify(xe)+ $
','+stringify(ys)+':'+stringify(ye)+']'
message, 'inserting extension '+stringify(i)+ $
' data in '+section, /info
endif
'''
array[xs:xe, ys:ye] = data[:, yin1:yin2]
#; make sure BZERO is a valid integer for IRAF
obzero = head0['BZERO']
head0['O_BZERO'] = obzero
head0['BZERO'] = 32768-obzero
# Return, transposing array back to goofy Python indexing
return array.T, head0, (dsec, osec, asec)