def ncmkflats(inputs, idir='',odir='',sigma=6, clobber=False,\
suffix='default', logfile='', verbose=False):
"""
inputs = "" NICI flats and darks file list
(idir = "") Path for input directory
(odir = "") Path for output directory
(sigma=6) Set to Nan all pixel above this value from the median
(clobber = False) Clobber output file?
(suffix='default') If 'default' it will take the rootname of
the first element in the input list.
(logfile = "") Logfile
(verbose = False) Display progress on monitor
PARAMETERS:
Sigma=6 -- All pixels in the flat off (dark)
that are way above the median value
are set to NaN *** The selection is
done in the following way :
subtract a low-pass to the flat_off
to keep only single 'hot' pixels,
and select all pixels more than 6
sigma (estimated through
robust_sigma) of the median-filtered image.
DESCRIPTION:
Produces calibration given a list of fits files with flats,
darks and sky exposures
OUTPUT FILES:
flat_red_<suffix>.fits
flat_blue_<suffix>.fits
sky_red_<suffix>.fits
sky_blue_<suffix>.fits
Note: This code has skycube<color,suffix>.fits writeto commented.
EXAMPLES:
See examples in browser:
file:///<nici_dir>/doc/build/html/ReductionExamples.html
"""
global command
log.basicConfig(filename='ncmkflats.log',level=log.DEBUG)
if odir=='': odir='./'
if idir=='': idir='./'
log.info('\n\n START NICI makeFlats +++++++++++++++++++++++++')
log.info(command)
log.info( 'inputs_list_len: '+str(len(inputs)))
log.info('idir: '+idir)
log.info('odir: '+odir+'\n')
try:
odir = check_dir(odir,os.W_OK)
idir = check_dir(idir,os.R_OK)
except IOError, strerror:
log.warning('(%s)' % strerror)
return
def __init__(self, inputs, idir='', odir='', central=False, suffix='default',
bsize=5, mdfw=11, clobber=False, logfile='', verbose=True):
"""
Check input parameters
@param inputs: Input list file of the form '@in.lis', unix wilcard
or a comma separated filenames. Can be .fits or .fits.gz
file format.
@type inputs: string
@param inputdir: Input directory name to prepend to each member of the input list.
@type inputdir: string
@param outputdir: Directory name where the output files will be written.
@type outputdir: string
@param central=False:
@type central=False:
@param suffix='Object':
@type suffix='Object':
@param clobber=True:
@type clobber=True:
@param logfile='':
@type logfile='':
@param verbose=True):
"""
# Converting the verbose=True to =6 which is how it works in new log
if verbose:
verboseNew = 6
else:
verboseNew = 0
log.basicConfig(filename='ncscience.log',level=log.DEBUG)
self.log = log
print 'ncc000',inputs
# We want to write at least the strings below in the logfile,
log.info("\n START NICI SCIENCE REDUCTION +++++++++++++++++++++++++")
log.info(command)
log.info( 'inputs_list_len: '+str(len(inputs)))
log.info( 'inputdir: '+idir)
log.info( 'outdir: '+odir)
if suffix[0] != '_':
suffix = '_'+suffix
self.suffix = suffix
try:
odir = nt.check_dir(odir,os.W_OK)
idir = nt.check_dir(idir,os.R_OK)
except IOError, strerror:
log.warning('(%s)' % strerror)
sys.exit(0)
def ncmark(inputs, idir='', odir='./', oprefix='m', port=5137, logfile='', clobber=False, verbose=False):
"""
Mark by hand the mask center and update the input header
with (xcen,ycen) on the output file.
The SAOIMAGE/ds9 display must be up. If the default port is busy, then it will
use port 5199, so make sure you start "ds9 -port 5199".
"""
log = glog.getLogger(name='ncmark',verbose=verbose,logfile=logfile,
debug=True)
log.info("\n START NICI Ncprepare +++++++++++++++++++++++++")
#log.info(command)
log.info( 'inputs_list_len: '+str(len(inputs)))
log.info( 'inputdir: '+idir)
log.info( 'outdir: '+odir)
try:
odir = check_dir(odir,os.W_OK)
idir = check_dir(idir,os.R_OK)
except IOError, strerror:
log.warning('(%s)' % strerror)
#sys.exit(0)
return
def ncprepare (inputs, oprefix='n', idir='', odir='', fdir='', fsuffix='',
dobadpix=True, clobber=False, logfile='', verbose=False):
"""
inputs = Input Fits files on a list
(oprefix = 'n') Prefix for output image(s)
(idir = '') Path for input raw files
(odir = '') Output directory name
(fdir = '') Path for calibration files
(fsuffix = '') Suffix used in calibration files
(dobadpix = True) Correct bad pixels the best we can
(clobber = False) Replace output file if exits
(logfile = '') Logfile name
(verbose = False) Display details on terminal?
DESCRIPTION:
Prepare science files in 'inputs' list for further analysis
with the ncscience script.
- Shift the mask to frame center
- Map blue frame coordinates to the red frame's.
EXAMPLES:
PYRAF:
ncprepare *.fits odir=/tmp
Python_shell:
nicip.ncprepare(flis,idir='/data1/data/tmp',odir='/tmp')
Unix_shell:
ncprepare.py /data1/data/tmp/*.fits --odir='/tmp'
"""
global command
def xy_tran(out):
"""
Function to transform blue coordinates to red frame coordinates
"""
xref = out[1] - 990.5897
yref = out[0] - 37.82109
x = -0.9985259*xref - 0.0178984*yref
y = -0.0181331*xref + 0.9991414*yref
# if we want to recenter as well. Need to think about this.
#x = x + (512 -409.81)
#y = y - (512 -650.23)
return y,x
log = glog.getLogger(name='ncprepare',verbose=verbose,logfile=logfile,
debug=True)
log.info("\n START NICI Ncprepare +++++++++++++++++++++++++")
log.info(command)
log.info( 'inputs_list_len: '+str(len(inputs)))
log.info( 'inputdir: '+idir)
log.info( 'outdir: '+odir)
log.info( 'flatsdir: '+fdir)
try:
odir = nt.check_dir(odir,os.W_OK)
idir = nt.check_dir(idir,os.R_OK)
fdir = nt.check_dir(fdir,os.R_OK)
except IOError, strerror:
log.warning('(%s)' % strerror)
#sys.exit(0)
return