def _medfilter(self,im,r,rad):
"""
Median filtering of each slice in the cube
"""
log = self.log
pa = self.pa
bsize = self.boxcar_size # Boxcar smoothing size (def:5)
mdfw = self.medfilt_width # Medfiltering width (def:11)
# to accelerate the code, we bin the image and the 'r'
# image down to 256x256 and do the radial profile on the binned versions
sz = np.shape(im)
bsy = sz[0]/4
bsx = sz[1]/4
rbin = nt.rebin(r,bsy,bsx)
tmp = np.zeros(self.imsize,dtype=np.float32)
# COPY: We are not modifying input image
tmp[:,:] = im
#NOTE: We are not using reset_num so far
imbin = nt.rebin(tmp, bsy,bsx) # bin down to 256x256
for rr in range(8,np.size(rad)):
# determine the median profile beyond r=8
# (irrelevant inside this because of focal plane mask)
if rr < 50:
ss = tmp[abs(r-rr) < .5]
rad[rr] = np.median(ss[np.where(np.isfinite(ss))])
else:
ss = imbin[abs(rbin-rr) < 3]
rad[rr] = np.median(ss[np.where(np.isfinite(ss))])
# smooth the radial profile beyond r=22
rad[22:] = boxcar(rad,(bsize,))[22:]
rad[40:] = boxcar(rad,(bsize,))[40:] # smooth even more
tmp[:,:] -= gi.ginterpolate(rad,r)
tmp[:,:] -= scipy.signal.medfilt2d(np.nan_to_num(tmp),mdfw)
#t = time.time()
#line = '%.2f' % (t-ti)
#log.info('medfilter['+chan+']: ['+str(i+1)+'/'+str(sz[0])+']' +line)
return tmp
def ncqlook(inputs, idir='', odir='./', log=True,lists=True, saturate=5000, nodisplay=False, full=False, port=5137):
"""
nqlook
Get NICI data from SBF: /net/petrohue/dataflow repository
for last night date. Produces a quick display of each
frame plus log file and lists that can be used with
niciprepare, nicimkflats and niciscience scripts.
The output lists are written in the working directory.
nqlook inputs='20081116' saturate=2000 display=False
Get data from 20081116 with a saturation limit at 2000
and does not display (for speed)'
nqlook @inlis idir='/data/myfiles' saturate=2000 display=False
Get data from 'inlis' which is a list of input FITS files
pathnames -one per line. The actual files are in the directory
'idir'
Use a saturation limit at 2000 and does not display (for speed)'
Even though you have 'inputs' parameter in here, it is not
taken into account since all the FITS files from the input
directory will be read.
NOTE: The files bad_r.fits ans bad_b.fits are read from
the nici directory wherever is it installed.
"""
if (inputs == None):
today = datetime.date.today()
dd = today.timetuple()
inputs = str(dd[0]) + '%.2d'%dd[1] + '%.2d'%dd[2]
if nodisplay == False:
# NOTE: pyds9 should be installed in ritchie.
# Needs to be part of the general installation and
# an explanatory should be given in the installation Guide
#ds9 = sao.ds9()
try:
pp = 'inet:%d' % port
ndis.open(imtdev=pp)
except:
print "\n ****************** WARNING: Please start ds9."
return
#else:
# ndis.close()
# We need to know were we are. 'nici' is the package name
fp, pathname, description = imp.find_module('nici')
pathname += '/'
#loads the badpixels list for the blue and red channel
bad_b = pf.getdata(pathname+'bad_b.fits')
bad_r = pf.getdata(pathname+'bad_r.fits')
# Chech that we can write in the current directory
# the output FITS file is written here.
odir = os.path.join(odir,'') # Make sure odir has '/'
if not os.access(odir,os.W_OK):
print "\nERROR: You do not have write access to \
this directory (output FITS file)\n"
return
if idir != '':
idir = os.path.join(idir,'') # Make sure odir has '/'
if not os.access(idir,os.R_OK):
print "\nERROR: No access to input directory:",idir
return
pathS = '/net/petrohue/dataflow/S'
froot = 'ncqlook'
if 'list' not in str(type(inputs)):
date = str(inputs)
fits_files = getFileList(date)
# see if it date format 20yymmdd. Will not work for 20?.fits
if len(fits_files) == 1:
dd = fits_files[0]
if len(dd) == 8 and dd[:2] == '20':
print 'Looking for files: ' +pathS+date+'S*.fits'
fits_files = glob.glob(pathS+date+'S*.fits')
froot = date
else:
# it is already a list:
fits_files = inputs
command = 'ncqlook ('+str(inputs)+',idir='+idir+',odir='+odir+',log=' \
+str(log)+',lists='+str(lists)+',saturate='+str(saturate)\
+',nodisplay='+str(nodisplay)+',full='+str(full)+')'
fits_files = np.sort(fits_files)
if len(fits_files)==0:
print 'couldn''t find files for :'+pathS +inputs+'S*.fits'
return
print '\nfound '+str(len(fits_files))+ ' files.'
previous_angle = -999 #define a few dummy variables
previous_time = -999
previous_ra = -99
previous_dec = -999
previous_mode = 'NONE'
nfiles = 0
nff = len(fits_files)
cube = np.zeros((nff,256,512),dtype=np.float32)
hh = 'NAME DATALAB EXPTIME CEN_WAVE FILTER_R FILTER_B (MIN-MAX rms)'+\
' [ext1,ext2 median] OBJECT CLASS MODE NCOADD CORE2HALO'
print command
print hh
lg = 0
if nff > 0 and (log or lists): # Open outputfiles
if log:
lg = open(odir+froot+'.log','w+')
lg.write('COMMAND: '+command+'\n')
lg.write(hh+'\n')
if lists:
flis_1 = open(odir+froot+'.1_flats','w+')
flis_2 = open(odir+froot+'.2_flats','w+')
slis_adi = open(odir+froot+'.adi','w+')
slis_sdi = open(odir+froot+'.sdi','w+')
slis_asdi = open(odir+froot+'.asdi','w+')
slis_other = open(odir+froot+'.other','w+')
parser = mathtext.MathTextParser("Bitmap")
for fitsname in fits_files:
t1=time.time()
fd = pf.open(idir+fitsname) # open the Fits file
fname = os.path.basename(fitsname)
if len(fd) == 0:
print fname," is EMPTY."
continue
phu = fd[0].header
inst = phu['instrume'] # instrument name for this image
if inst != 'NICI': #if not NICI, get the next filename
# print fname+' .. '+inst
fd.close()
continue
if len(fd) != 3:
line = ' Nici file '+fitsname+' does not have 2 extensions.'
print line
if log:
lg.write(line+'\n')
fd.close()
continue
nfiles += 1
im_ext1 = fd[1].data
hd1 = fd[1].header # reads extension header 1
im_ext2 = fd[2].data
hd2 = fd[2].header # reads extension header 1
shift_status1=-1
shift_status2=-1
# extension 1 and blue channel in
# extension 2.
# -1 if we do not have red channel
# 0 is all good
# 1 is shifted rows
if hd1.get('filter_b') == None and hd1.get('filter_r') != None:
shift_status1 = check_missing_rows (im_ext1,bad_r,log,lg)
if hd2.get('filter_b') != None and hd1.get('filter_r') == None:
shift_status2 = check_missing_rows (im_ext2,bad_b,log,lg)
devs = np.zeros(8, dtype=np.float32)
# Extracting the RMS of the
# 8x8-folded image sample. A high value may
# indicate readout noise problems
for sample in range(4):
x1 = 200+600*(sample % 2)
x2 = 263+600*(sample % 2)
y1 = 200+600*(sample/2)
y2 = 263+600*(sample/2)
devs[sample] = np.std(fold_88(im_ext1[x1:x2,y1:y2]))
for sample in range(4):
x1 = 200+600*(sample % 2)
x2 = 263+600*(sample % 2)
y1 = 200+600*(sample/2)
y2 = 263+600*(sample/2)
devs[sample+4] = np.std(fold_88(im_ext2[x1:x2,y1:y2]))
ncoadd_r = hd1['ncoadd_r']
ncoadd_b = hd2['ncoadd_b']
itime_r = hd1['itime_r']
crmode = phu.get('crmode')
if crmode == None:
line = 'Header keyword CRMODE not found in '+fname+' -skipped.'
print line
if log:
lg.write(line+'\n')
fd.close()
continue
# Start forming the output line.
obstype = str(phu.get('obstype'))
oclass = str(phu.get('obsclass'))
dichr = str(phu.get('dichroic')).lower()
#adi = ''
chan = ''
if 'mirror' in dichr:
chan = 'B'
if 'open' in dichr:
chan = 'R'
mask = phu.get('fpmw')
if 'clear' in mask.lower():
mask = '-NoMASK'
else:
mask = ''
tmp = obstype
if obstype == 'FLAT':
tmp = 'FLAT['+phu.get('gcalshut')+']'
# 1-Channel (ADI) (Dichroic is Mirror*(100% blue) or Open (100% red))
# 2-Channel (SDI or ASDI) (Dichroic is H-50/50*, H-CH4, H/K)
mode = "OTHER"
if (obstype == 'FLAT' or obstype == 'DARK'):
if chan:
mode = 'ADI-'+chan
else:
mode = 'SDI'
elif (oclass == 'science'):
if (crmode == 'FIXED'):
if chan:
mode = 'ADI-'+chan+mask
else:
mode = 'ASDI'+mask
elif (crmode == 'FOLLOW'):
if chan:
mode = 'Normal'+chan+mask
else:
mode = 'SDI'+mask
elif '-ENG' in phu.get('OBSID'):
mode = '* ENGINEERING DATA *'
else:
mode = '***WARNING***: Not ADI, SDI nor ASDI-- '+crmode+' '+dichr
line = ' '+str(phu.get('object'))+','+ oclass+','+tmp+','+mode
ti_coad = ' '+str(itime_r)+','+str(ncoadd_r)
dlab =' '+phu.get('DATALAB')
exp_time =' %.2f'%(itime_r*ncoadd_r/60.) # exposure time ... in minutes!
cenwave =' %.3f'%(float(phu.get('WAVELENG'))/10000.) # Central wavelenght in microns
filter_r = ' %10.10s'%phu.get('FILTER_R')
filter_b = ' %10.10s'%phu.get('FILTER_B')
mindevs = ' (%8.2f,'%min(devs)
maxdevs = '%8.2f)'%max(devs)
medext1 = ' [%8.2f,'%np.median(im_ext1)
medext2 = '%8.2f]'%np.median(im_ext2)
longl = fname+dlab+exp_time+cenwave+filter_r+filter_b+mindevs+maxdevs+medext1+medext2+line+ti_coad
if 'ENGINE' in mode:
print longl
if log:
lg.write(longl+'\n')
continue
# hh = 'MIN-MAX rms 8x8 boxes: (min - max) MEDIAN: [ext1,ext2],(OBJECT),'\
# '(OBSCLASS),(OBSTYPE),(CRMODE),(DICHROIC),(FPMW),(ITIME),(NCOADD)'
# Don't print until core2halo value is defined below.
# print longl
if lists:
if (obstype == 'FLAT' or obstype == 'DARK'):
if chan:
flis_1.write(fname+'\n')
else:
flis_2.write(fname+'\n')
elif oclass == 'science':
md = mode.lower()
if 'mask' in md:
slis_other.write(fname+'\n')
elif 'adi' in md:
slis_adi.write(fname+'\n')
elif 'asdi' in md:
slis_asdi.write(fname+'\n')
elif 'sdi' in md:
slis_sdi.write(fname+'\n')
else:
slis_other.write(fname+'\n')
# extast,hd1,astr ;extract the astrometric structure (astr) from the
# first extension header
# cd=astr.cd ;extract the CD matrix from the astrometric structure,
# this matrix defines scale/rotation/shear
ra_pointing = hd1['crval1'] # pointing RA from astrometry
dec_pointing = hd1['crval2'] # pointing DEC
st = np.asfarray(phu['st'].split(':'))
st = dmstod(phu['st']) # sidereal time
HA = st - ra_pointing/15. # defining the hour angle
harr = HA + np.asfarray([0,-1/60.])
para_angle = parangle(harr, dec_pointing, -30.240750)
# computing the paralactic angle. -30.240750 is the
# latitude of Cerro Pachon
obs_time = (dmstod(phu['LT'])*60.+720) % 1440
# here time is expressed in minutes after noon
angular_rate = para_angle[0] - para_angle[1]
# computing the rate of change of the paralactic angle
current_angle = para_angle[0]
astrom_angular_rate = (current_angle - previous_angle)/ \
(obs_time - previous_time)
# angle change as found by taking the difference in
# angle between this frame and the previous one
telescope_offset = np.sqrt( ((ra_pointing - previous_ra)*\
math.cos(np.radians(dec_pointing)))**2+\
(dec_pointing - previous_dec)**2 )
if (crmode == 'FIXED') and (previous_mode == 'FIXED'):
# we are in ADI mode
if (abs(angular_rate - astrom_angular_rate) > 1/10.) \
and (telescope_offset < 1E-3) and \
((obs_time - previous_time) < 3*exp_time):
print '---------- !!!!!!!! ---------------'
print 'Expected angular rate : '+str(angular_rate)+\
' deg/minute'
print 'Astrometric angular rate : '+\
str(astrom_angular_rate)+' deg/minute'
# CROP THE FRAMES and get core2halo ratios
crop1=0; crop2=0; c2h_1=-1; c2h_2=-1
if full:
out_ext1 = rebin(im_ext1,256,256)
out_ext2 = rebin(im_ext2,256,256)
else:
Ndev = lambda im : (np.amax(im) - np.median(im))/robust_sigma(im)
tmp = rebin(im_ext1,32,32)
if Ndev(tmp) > 50:
# We might have a peak:
crop1 = 1
c2h_1,x,y = peak2halo('',image=im_ext1)
if x-128 < 0 or x+128 > 1024 or y-128 < 0 or y+128 > 1024:
out_ext1 = rebin(im_ext1,256,256)
crop1 = 0
else:
#shift frame to center
out_ext1 = im_ext1[y-128:y+128,x-128:x+128]
else:
out_ext1 = rebin(im_ext1,256,256)
tmp = rebin(im_ext2,32,32)
if Ndev(tmp) > 50:
# We might have a peak:
crop2 = 1
c2h_2,x,y = peak2halo('',image=im_ext2)
if x-128 < 0 or x+128 > 1024 or y-128 < 0 or y+128 > 1024:
out_ext2 = rebin(im_ext2,256,256)
crop2 = 0
else:
#shift frame to center
out_ext2 = im_ext2[y-128:y+128,x-128:x+128]
else:
out_ext2 = rebin(im_ext2,256,256)
if 1: # Do not process if there is no red flux
a = out_ext1/ncoadd_r
saturated_1 = a > saturate
saturated_1[0:20,0:140] = 0
sat_red = np.sum(saturated_1)
#IDL out_ext1>=out_ext1[ (sort(out_ext1))[.01*n_elements(out_ext1)]]
szx1 = np.size(out_ext1)
sout = np.sort(out_ext1.ravel())
limit = sout[.01*szx1]
xmin = sout[0]; xmax= sout[np.size(sout)-1]
out_ext1 = np.clip(out_ext1, limit, xmax)
# we put lower and upper limits and the 1% and
# 99.5% (OR NCOADD*3500) of the image
#IDL out_ext1<=( out_ext1[ (sort(out_ext1))[.995*n_elements(out_ext1)]]
# < (sxpar(hd1,'ncoadd_r')*saturate) )
szx1 = np.size(out_ext1)
if sout[.995*szx1] < ncoadd_r*saturate:
limit = ncoadd_r*saturate
else:
limit = sout[.995*szx1]
out_ext1 = np.clip(out_ext1, xmin, limit)
if 1:
a = out_ext2/ncoadd_b
saturated_2 = nd.rotate(a > saturate,5,reshape=False)
saturated_2[0:20,0:140] = 0
sat_blue = np.sum(saturated_2)
szx2 = np.size(out_ext2)
sout = np.sort(out_ext2.ravel())
limit = sout[.01*szx2]
xmin = sout[0]; xmax= sout[np.size(sout)-1]
out_ext2 = np.clip(out_ext2, limit, xmax)
# we put lower and upper limits and the 1% and
# 99.5% (OR NCOADD*3500) of the image
#IDL: out_ext2<=( out_ext2[ (sort(out_ext2))[.995*n_elements(out_ext2)]]
# < (sxpar(hd2,'ncoadd_b')*saturate) )
szx2 = np.size(out_ext2)
if sout[.995*szx2] < ncoadd_b*saturate:
limit = ncoadd_b*saturate
else:
limit = sout[.995*szx2]
out_ext2 = np.clip(out_ext2, xmin, limit)
out = np.zeros((256,512),dtype=np.float32)
#create the image that will receive the frames to display
out[:,:256] = ((out_ext1 - np.amin(out_ext1)) / \
(np.amax(out_ext1) - np.amin(out_ext1)))[::-1,:]
a = out_ext2 - np.amin(out_ext2)
b = np.amax(out_ext2) - np.amin(out_ext2)
out[:,256:] = nd.rotate( (a/b), 5, reshape=False)[::-1,::-1]
#extract the root name of the file.
name_out = os.path.splitext(os.path.basename(fname))[0]
name_out += '['+('full','crop')[crop1]+'/'+('full','crop')[crop2]+']'
# Form the text to overlay onto the lower left of the output array.
rgba, depth1 = parser.to_rgba(name_out, color='gray', fontsize=10, dpi=200)
c = rgba[::2,::2,3]
far = np.asarray(c,dtype=np.float32)
stx = np.shape(far)
out[:stx[0],:stx[1]] = far[::-1,:]/256
if not full:
if sat_red != 0:
tmp1=out[:,:256]
tmp1[np.where(saturated_1)] = np.nan
out[:,:256]=tmp1
if not full:
if sat_blue != 0:
tmp2=out[:,256:]
tmp2[np.where(saturated_2)] = np.nan
out[:,256:]=tmp2
if nodisplay == False:
ndis.display(out,z1=-1,z2=1,zscale=False)
#ds9.view(out)
cube[nfiles-1,:,:] = out[::-1,:]
# Now print
if oclass == 'science':
if chan == 'red': c2h_2=-1
if chan == 'blue': c2h_1=-1
if c2h_1 > 0 and c2h_2 > 0:
longl += ',['+'%.2f,%.2f' % (c2h_1,c2h_2)+']'
elif c2h_1*c2h_2 == 1: # both -1
longl += ',[,]'
elif c2h_1 > 0:
longl += ',['+'%.2f,' % (c2h_1)+']'
else:
longl += ',['+',%.2f' % (c2h_2)+']'
if sat_red or sat_blue:
longl += ' Saturated('+str(sat_red)+','+str(sat_blue)+')'
print longl
if log:
lg.write(longl+'\n')
previous_angle=current_angle
#keep track of some variables for next iteration
previous_time =obs_time
previous_ra =ra_pointing
previous_dec =dec_pointing
previous_mode =crmode
fd.close()
if log:
lg.close()
if lists:
flis_1.close()
flis_2.close()
slis_adi.close()
slis_sdi.close()
slis_asdi.close()
slis_other.close()
if (nfiles > 0):
pf.writeto(odir+froot+'_cube.fits',cube[:nfiles,::-1,:], clobber=True)
# write the output cube with cropped/binned images
else:
print 'No NICI files found for the specified input: ',inputs
return