def main(self):
# Sort the data
msgs.bug("Files and folders should not be deleted -- there should be an option to overwrite files automatically if they already exist, or choose to rename them if necessary")
self._filesort = arsort.sort_data(self)
# Write out the details of the sorted files
if self._argflag['out']['sorted'] is not None: arsort.sort_write(self)
# Match Science frames to calibration frames
arsort.match_science(self)
# If the user is only debugging, then exit now
if self._argflag['run']['calcheck']:
msgs.info("Calibration check complete. Change the 'calcheck' flag to continue with data reduction")
sys.exit()
# Make directory structure for different objects
self._sci_targs = arsort.make_dirs(self)
# Store the name for the frames that have already been combined
done_bias, name_bias = [], []
done_flat, name_flat = [], []
done_arcs, name_arcs = [], []
# Reduce each science frame entirely before moving to the next one
sci = self._filesort['science']
sfx = self._spect["det"]["suffix"]
numsci = np.size(sci)
if numsci == 0:
msgs.bug("What to do if no science frames are input? The calibrations should still be processed.")
msgs.work("Maybe assume that each non-identical arc is a science frame, but force no science extraction")
msgs.error("No science frames are input!!")
numsci=1
self._argflag['run']['preponly'] = True # Prepare the calibration files, but don't do the science frame reduction
for sc in range(numsci):
###############
# First set the index for the science frame
scidx = self._spect['science']['index'][sc]
sciext_name_p, sciext_name_e = os.path.splitext(self._fitsdict['filename'][scidx[0]])
prefix = "{0:s}{1:s}".format(sciext_name_p,sfx)
###############
# Generate master bias frame
if self._argflag['reduce']['usebias'] in ['bias', 'dark']:
msgs.info("Preparing a master {0:s} frame".format(self._argflag['reduce']['usebias']))
if self._argflag['reduce']['usebias'] == 'bias':
# Get all of the bias frames for this science frame
ind = self._spect['bias']['index'][sc]
elif self._argflag['reduce']['usebias'] == 'dark':
# Get all of the dark frames for this science frame
ind = self._spect['dark']['index'][sc]
# Check if an *identical* master bias frame has already been produced
found = False
for gb in range(len(done_bias)):
if np.array_equal(ind, done_bias[gb]):
msgs.info("An identical master {0:s} frame already exists.".format(self._argflag['reduce']['usebias']))
msbias = arload.load_master(name_bias[gb], frametype=self._argflag['reduce']['usebias'])
found = True
break
if not found:
# Load the Bias/Dark frames
frames = arload.load_frames(self, ind, frametype=self._argflag['reduce']['usebias'], transpose=self._transpose)
msbias = arcomb.comb_frames(frames, spect=self._spect, frametype=self._argflag['reduce']['usebias'], **self._argflag['bias']['comb'])
# Derive a suitable name for the master bias frame
msbias_name = "{0:s}/{1:s}/msbias{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_bias))
# Send the data away to be saved
arsave.save_master(self, msbias, filename=msbias_name, frametype=self._argflag['reduce']['usebias'], ind=ind)
# Store the files used and the master bias name in case it can be used during the later reduction processes
done_bias.append(ind)
name_bias.append(msbias_name)
elif self._argflag['reduce']['usebias'] == 'overscan':
msbias = 'overscan'
elif self._argflag['reduce']['usebias'] == 'none':
msgs.info("Not performing a bias/dark subtraction")
msbias=None
else: # It must be the name of a file the user wishes to load
msbias_name = os.getcwd()+self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['usebias']
msbias = arload.load_master(self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['usebias'], frametype=None)
###############
# Generate a bad pixel mask
if self._argflag['reduce']['badpix']:
msgs.info("Preparing a bad pixel mask")
# Get all of the bias frames for this science frame
ind = self._spect['bias']['index'][sc]
# Load the Bias frames
frames = arload.load_frames(self, ind, frametype='bias', trim=False)
tbpix = arcomb.comb_frames(frames, spect=self._spect, frametype='bias', **self._argflag['bias']['comb'])
self._bpix = arproc.badpix(self,tbpix)
del tbpix
else:
msgs.info("Not preparing a bad pixel mask")
###############
# Estimate gain and readout noise for the amplifiers
msgs.work("Estimate Gain and Readout noise...")
###############
# Generate a master arc frame
if self._argflag['reduce']['usearc'] in ['arc']:
msgs.info("Preparing a master arc frame")
ind = self._spect['arc']['index'][sc]
# Check if an *identical* master arc frame has already been produced
foundarc = False
for gb in range(len(done_arcs)):
if np.array_equal(ind, done_arcs[gb]):
msgs.info("An identical master arc frame already exists")
msarc = arload.load_master(name_arcs[gb], frametype='arc')
tltprefix = os.path.splitext(os.path.basename(msarc_name))[0]
msarc_name = name_arcs[gb]
foundarc = True
if not foundarc:
# Load the arc frames
frames = arload.load_frames(self, ind, frametype='arc', msbias=msbias)
if self._argflag['reduce']['arcmatch'] > 0.0:
sframes = arsort.match_frames(self, frames, self._argflag['reduce']['arcmatch'], frametype='arc', satlevel=self._spect['det']['saturation']*self._spect['det']['nonlinear'])
subframes = np.zeros((frames.shape[0], frames.shape[1], len(sframes)))
numarr = np.array([])
for i in range(len(sframes)):
numarr = np.append(numarr,sframes[i].shape[2])
msarc = arcomb.comb_frames(sframes[i], spect=self._spect, frametype='arc', **self._argflag['arc']['comb'])
msarc_name = "{0:s}/{1:s}/sub-msarc{2:s}_{3:03d}_{4:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_arcs),i)
# Send the data away to be saved
arsave.save_master(self, msarc, filename=msarc_name, frametype='arc', ind=ind)
subframes[:,:,i]=msarc.copy()
del sframes
# Combine all sub-frames
msarc = arcomb.comb_frames(subframes, spect=self._spect, frametype='arc', weights=numarr, **self._argflag['arc']['comb'])
del subframes
else:
msarc = arcomb.comb_frames(frames, spect=self._spect, frametype='arc', **self._argflag['arc']['comb'])
del frames
# Derive a suitable name for the master arc frame
msarc_name = "{0:s}/{1:s}/msarc{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_arcs))
tltprefix = os.path.splitext(os.path.basename(msarc_name))[0]
# Send the data away to be saved
arsave.save_master(self, msarc, filename=msarc_name, frametype='arc', ind=ind)
# Store the files used and the master bias name in case it can be used during the later reduction processes
done_arcs.append(ind)
name_arcs.append(msarc_name)
else:
msarc_name = self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['usearc']
tltprefix = os.path.splitext(os.path.basename(msarc_name))[0]
msarc=arload.load_master(msarc_name, frametype=None)
###############
# Determine the dispersion direction only on the first pass through
if (sc==0):
###############
# Guess dispersion direction
if self._argflag['trace']['disp']['direction'] is None:
self._dispaxis = artrace.dispdir(msarc, dispwin=self._argflag['trace']['disp']['window'], mode=0)
elif self._argflag['trace']['disp']['direction'] in [0,1]:
self._dispaxis = int(self._argflag['trace']['disp']['direction'])
else:
msgs.error("The argument for the dispersion direction (trace+disp+direction)"+msgs.newline()+
"must be either:"+msgs.newline()+" 0 if the dispersion axis is predominantly along a row"+msgs.newline()+
" 1 if the dispersion axis is predominantly along a column")
# Perform a check to warn the user if the longest axis is not equal to the dispersion direction
if (msarc.shape[0] > msarc.shape[1]):
if (self._dispaxis==1): msgs.warn("The dispersion axis is set to the shorter axis, is this correct?")
else:
if (self._dispaxis==0): msgs.warn("The dispersion axis is set to the shorter axis, is this correct?")
###############
# Change dispersion direction and files if necessary
# The code is programmed assuming dispaxis=0
if (self._dispaxis==1):
msgs.info("Transposing frames")
# Flip the transpose switch
self._transpose = True
# Transpose the master bias frame
msbias = msbias.T
arsave.save_master(self, msbias, filename=msbias_name, frametype=self._argflag['reduce']['usebias'], ind=ind)
# Transpose the master arc, and save it
msarc = msarc.T
arsave.save_master(self, msarc, filename=msarc_name, frametype='arc', ind=ind)
# Transpose the bad pixel mask
self._bpix = self._bpix.T
# Change the user-specified (x,y) pixel sizes
tmp = self._spect['det']['xgap']
self._spect['det']['xgap'] = self._spect['det']['ygap']
self._spect['det']['ygap'] = tmp
self._spect['det']['ysize'] = 1.0/self._spect['det']['ysize']
# Update the amplifier/data/overscan sections
for i in range(self._spect['det']['numamplifiers']):
# Flip the order of the sections
self._spect['det']['ampsec{0:02d}'.format(i+1)] = self._spect['det']['ampsec{0:02d}'.format(i+1)][::-1]
self._spect['det']['datasec{0:02d}'.format(i+1)] = self._spect['det']['datasec{0:02d}'.format(i+1)][::-1]
self._spect['det']['oscansec{0:02d}'.format(i+1)] = self._spect['det']['oscansec{0:02d}'.format(i+1)][::-1]
# Change the user-specified (x,y) pixel sizes
msgs.work("Transpose gain and readnoise frames")
# Set the new dispersion axis
self._dispaxis=0
###############
# Generate a master trace frame
if self._argflag['reduce']['usetrace'] in ['trace', 'blzflat']:
msgs.info("Preparing a master trace frame with {0:s}".format(self._argflag['reduce']['usetrace']))
if self._argflag['reduce']['usetrace'] == 'trace':
# Get all of the trace frames for this science frame
ind = self._spect['trace']['index'][sc]
elif self._argflag['reduce']['usetrace'] == 'blzflat':
# Get all of the blzflat frames for this science frame
ind = self._spect['blzflat']['index'][sc]
# Check if an *identical* master trace frame has already been produced
foundtrc = False
for gb in range(len(done_flat)):
if np.array_equal(ind, done_flat[gb]):
msgs.info("An identical master trace frame already exists")
mstrace_name = name_flat[gb]
mstrace = arload.load_master(name_flat[gb], frametype='trace')
trcprefix = os.path.splitext(os.path.basename(name_flat[gb]))[0]
foundtrc = True
break
if not foundtrc:
# Load the frames for tracing
frames = arload.load_frames(self, ind, frametype='trace', msbias=msbias, trim=self._argflag['reduce']['trim'], transpose=self._transpose)
if self._argflag['reduce']['flatmatch'] > 0.0:
sframes = arsort.match_frames(self, frames, self._argflag['reduce']['flatmatch'], frametype='trace', satlevel=self._spect['det']['saturation']*self._spect['det']['nonlinear'])
subframes = np.zeros((frames.shape[0], frames.shape[1], len(sframes)))
numarr = np.array([])
for i in range(len(sframes)):
numarr = np.append(numarr,sframes[i].shape[2])
mstrace = arcomb.comb_frames(sframes[i], spect=self._spect, frametype='trace', **self._argflag['trace']['comb'])
mstrace_name = "{0:s}/{1:s}/sub-msflat{2:s}_{3:03d}_{4:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_flat),i)
null = os.path.splitext(os.path.basename(mstrace_name))[0]
trcprefix = "{0:s}{1:s}".format(null,sfx)
# Send the data away to be saved
arsave.save_master(self, mstrace, filename=mstrace_name, frametype='trace', ind=ind)
subframes[:,:,i]=mstrace.copy()
del sframes
# Combine all sub-frames
mstrace = arcomb.comb_frames(subframes, spect=self._spect, frametype='trace', weights=numarr, **self._argflag['trace']['comb'])
del subframes
else:
mstrace = arcomb.comb_frames(frames, spect=self._spect, frametype='trace', **self._argflag['trace']['comb'])
del frames
# Derive a suitable name for the master trace frame
mstrace_name = "{0:s}/{1:s}/msflat{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_flat))
trcprefix = os.path.splitext(os.path.basename(mstrace_name))[0]
# Send the data away to be saved
arsave.save_master(self, mstrace, filename=mstrace_name, frametype='trace', ind=ind)
# Store the files used and the master bias name in case it can be used during the later reduction processes
done_flat.append(ind)
name_flat.append(mstrace_name)
elif self._argflag['reduce']['usetrace'] == 'science':
msgs.work("Tracing with a science frame is not implemented")
else: # It must be the name of a file the user wishes to load
mstrace_name = self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['usetrace']
mstrace=arload.load_master(mstrace_name, frametype=None)
trcprefix = os.path.splitext(os.path.basename(mstrace_name))[0]
###############
# Generate an array that provides the physical pixel locations on the detector
if self._argflag['reduce']['locations'] is None:
self._pixlocn = artrace.gen_pixloc(self,mstrace,gen=True)
elif self._argflag['reduce']['locations'] in ["mstrace"]:
self._pixlocn = arutils.gen_pixloc(self._spect,mstrace,gen=False)
else:
self._pixlocn = arload.load_master(self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['locations'], frametype=None)
###############
# Determine the location of and trace the orders for the trace frame
# if foundtrc:
# try:
# # Load the order locations from file
# self._lordloc, self._rordloc = arload.load_ordloc(mstrace_name)
# except:
# # If this fails, rederive the order locations
# self._lordloc, self._rordloc = artrace.trace_longslit(self, mstrace, prefix=prefix, trcprefix=trcprefix)
# # Save the traces
# arsave.save_ordloc(self, mstrace_name)
# else:
# # First time encountered this set of trace frames --> derive the order locations
# self._lordloc, self._rordloc = artrace.trace_longslit(self, mstrace, prefix=prefix, trcprefix=trcprefix)
# # Save the traces
# arsave.save_ordloc(self, mstrace_name)
# Take the edges of the (trimmed) data to be the order edges
self._lordloc = self._pixlocn[:,0,1].reshape((self._pixlocn.shape[0],1))
self._rordloc = self._pixlocn[:,-1,1].reshape((self._pixlocn.shape[0],1))
# Convert physical trace into a pixel trace
msgs.info("Converting physical trace locations to nearest pixel")
self._pixcen = artrace.phys_to_pix(0.5*(self._lordloc+self._rordloc), self._pixlocn, self._dispaxis, 1-self._dispaxis)
self._pixwid = (self._rordloc-self._lordloc).mean(0).astype(np.int)
self._lordpix = artrace.phys_to_pix(self._lordloc, self._pixlocn, self._dispaxis, 1-self._dispaxis)
self._rordpix = artrace.phys_to_pix(self._rordloc, self._pixlocn, self._dispaxis, 1-self._dispaxis)
###############
# Prepare the Flat-field frame
if self._argflag['reduce']['flatfield']:
###############
# Generate a master pixel flat frame
if self._argflag['reduce']['useflat'] in ['pixflat', 'blzflat']:
msgs.info("Preparing a master pixel flat frame with {0:s}".format(self._argflag['reduce']['useflat']))
if self._argflag['reduce']['useflat'] == 'pixflat':
# Get all of the pixel flat frames for this science frame
ind = self._spect['pixflat']['index'][sc]
elif self._argflag['reduce']['useflat'] == 'blzflat':
# Get all of the blzflat frames for this science frame
ind = self._spect['blzflat']['index'][sc]
# Check if an *identical* master pixel flat frame has already been produced
found = False
for gb in range(len(done_flat)):
if np.array_equal(ind, done_flat[gb]):
msgs.info("An identical master flat frame already exists")
mspixflat_name = name_flat[gb]
mspixflat = arload.load_master(mspixflat_name, frametype='pixel flat')
found = True
break
if not found:
# Load the frames for tracing
frames = arload.load_frames(self, ind, frametype='pixel flat', msbias=msbias)
if self._argflag['reduce']['flatmatch'] > 0.0:
sframes = arsort.match_frames(self, frames, self._argflag['reduce']['flatmatch'], frametype='pixel flat', satlevel=self._spect['det']['saturation']*self._spect['det']['nonlinear'])
subframes = np.zeros((frames.shape[0], frames.shape[1], len(sframes)))
numarr = np.array([])
for i in range(len(sframes)):
numarr = np.append(numarr,sframes[i].shape[2])
mspixflat = arcomb.comb_frames(sframes[i], spect=self._spect, frametype='pixel flat', **self._argflag['pixflat']['comb'])
mspixflat_name = "{0:s}/{1:s}/sub-msflat{2:s}_{3:03d}_{4:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_flat),i)
# Send the data away to be saved
arsave.save_master(self, mspixflat, filename=mspixflat_name, frametype='pixel flat', ind=ind)
subframes[:,:,i]=mspixflat.copy()
del sframes
# Combine all sub-frames
mspixflat = arcomb.comb_frames(subframes, spect=self._spect, frametype='pixel flat', weights=numarr, **self._argflag['pixflat']['comb'])
del subframes
else:
mspixflat = arcomb.comb_frames(frames, spect=self._spect, frametype='pixel flat', **self._argflag['pixflat']['comb'])
del frames
# Derive a suitable name for the master pixel flat frame
mspixflat_name = "{0:s}/{1:s}/msflat{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],sfx,len(done_flat))
# Send the data away to be saved
arsave.save_master(self, mspixflat, filename=mspixflat_name, frametype='pixel flat', ind=ind)
# Store the files used and the master bias name in case it can be used during the later reduction processes
done_flat.append(ind)
name_flat.append(mspixflat_name)
else: # It must be the name of a file the user wishes to load
mspixflat_name = self._argflag['run']['masterdir']+'/'+self._argflag['reduce']['usepixflat']
mspixflat=arload.load_master(mspixflat_name, frametype=None)
# Now that the combined, master flat field frame is loaded...
# Normalize the flat field
mspixflatnrm, msblaze = arproc.flatnorm(self, mspixflat, overpix=0, fname=os.path.basename(os.path.splitext(mspixflat_name)[0]))
###############
# Derive the order tilts
if foundarc:
try:
# Load the order locations from file
self._tilts, self._satmask = arload.load_tilts(msarc_name)
except:
# If this fails, rederive the order tilts
self._tilts, self._satmask = artrace.model_tilt(self, msarc, prefix=prefix, trcprefix=trcprefix, tltprefix=tltprefix) # NOTE: self._tilts = tan(tilt angle), where "tilt angle" is the angle between (1) the line representing constant wavelength and (2) the column of pixels that is most closely parallel with the spatial direction of the slit.
# Save the traces
arsave.save_tilts(self, msarc_name)
else:
# First time encountered this set of arc frames --> derive the order tilts
self._tilts, self._satmask = artrace.model_tilt(self, msarc, prefix=prefix, trcprefix=trcprefix, tltprefix=tltprefix) # NOTE: self._tilts = tan(tilt angle), where "tilt angle" is the angle between (1) the line representing constant wavelength and (2) the column of pixels that is most closely parallel with the spatial direction of the slit.
# Save the tilts
msgs.error("OK?")
arsave.save_tilts(self, msarc_name)
###############
# Extract wavelength arrays and save the extracted lines
msarcext_name_p, msarcext_name_e = os.path.splitext(msarc_name)
msarcext_name = msarcext_name_p + "_ext1d" + msarcext_name_e
if self._argflag['arc']['load']['extracted'] == True:
if os.path.exists(msarcext_name):
self._arcext = arload.load_master(msarcext_name, frametype=None)
else:
msgs.warn("Master 1D arc extraction does not exist for file:"+msgs.newline()+msarc_name)
msgs.info("Reduction will continue by performing 1D arc extraction")
self._arcext, extprops = arextract.extract(self, msarc, mode='mean', frametype='arc')
arsave.save_master(self, self._arcext, filename=msarcext_name, frametype='1D arc extraction')
else:
self._arcext, extprops = arextract.extract(self, msarc, mode='mean', frametype='arc')
# Send the data away to be saved
arsave.save_master(self, self._arcext, filename=msarcext_name, frametype='1D arc extraction')
###############
# Perform wavelength calibration
if self._argflag['arc']['load']['calibrated'] == True:
if os.path.exists(somename):
self._waveids = arload.load_orderdetail(somename, frametype=None)
else:
msgs.warn("Master arc calibration does not exist for file:"+msgs.newline()+msarc_name)
msgs.info("Reduction will continue by calibrating 1D arc extraction")
self._waveids = ararc.calibrate(self)
arsave.save_orderdetail(self, filename=somename)
else:
msarc_id_p, msarc_id_e = os.path.splitext(msarc_name)
fname = msarc_id_p + "_id" + msarc_id_e
#pixels=arload.waveids(fname)
pixels=None
self._waveids = ararc.calibrate(self,msarc_name,pixtmp=pixels, prefix=prefix)
# Send the data away to be saved
msgs.work("Think about the best way to save the order location/tilt/calibration details")
msgs.bug("Order wavelength IDs not saved")
#arsave.save_orderdetail(self, filename=somename)
###############
# Perform a velocity correction
if self._argflag['reduce']['heliocorr'] == True:
if self._argflag['science']['load']['extracted'] == True:
msgs.warn("Heliocentric correction will not be applied if an extracted science frame exists, and is used")
msgs.work("Perform a full barycentric correction")
msgs.work("Include the facility to correct for gravitational redshifts and time delays (see Pulsar timing work)")
msgs.info("Performing a heliocentric correction")
# Load the header for the science frame
self._waveids = arvcorr.helio_corr(self, scidx[0])
else:
msgs.info("A heliocentric correction will not be performed")
###############
# Determine the wavelength scale (i.e. the wavelength of each pixel) to be used during the extraction
msgs.info("Generating the array of extraction wavelengths")
self._wavelength = arproc.get_wscale(self)
###############
# Check if the user only wants to prepare the calibrations
msgs.info("All calibration frames have been prepared")
if self._argflag['run']['preponly']:
msgs.info("If you would like to continue with the reduction,"+msgs.newline()+"disable the run+preponly command")
continue
###############
# Load the science frame and from this generate a Poisson error frame
sciframe = arload.load_frames(self, scidx, frametype='science', msbias=msbias)
sciframe = sciframe[:,:,0]
# Convert ADUs to electrons
sciframe *= self._spect['det']['gain']
varframe = arproc.variance_frame(slf, sciframe, scidx[0])
snframe = arproc.sn_frame(self, sciframe, scidx[0])
###############
# Subtract off the scattered light from the image
msgs.work("Scattered light subtraction is not yet implemented...")
"""
Do we want to do a scattered light subtraction? Probably not, since
these photons contribute to the noise (error) frame. If a scattered
light subtraction is implemented, make sure that the scattered light
frame is passed to the "arproc.error_frame" procedure below when
calculating the error frame.
"""
###############
# Flat field the science frame
if self._argflag['reduce']['flatfield']:
msgs.info("Flat fielding the science frame")
sciframe, errframe = arproc.flatfield(self, sciframe, mspixflatnrm, snframe=snframe)
else:
msgs.info("Not performing a flat field calibration")
errframe = np.zeros_like(sciframe)
wnz = np.where(snframe>0.0)
errframe[wnz] = sciframe[wnz]/snframe[wnz]
###############
# Flat field the science frame
if self._argflag['reduce']['bgsubtraction']:
msgs.info("Preparing a sky background frame from the science frame")
scibgsub, bgframe = arproc.background_subtraction(self, sciframe, errframe)
# Derive a suitable name for the master sky background frame
msbg_name = "{0:s}/{1:s}/{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],self._fitsdict['target'][scidx[0]],"sky")
# Send the data away to be saved
arsave.save_master(self, bgframe, filename=msbg_name, frametype='sky background', ind=ind)
# Derive a suitable name for the sky-subtracted science frame
msscibg_name = "{0:s}/{1:s}/{2:s}_{3:03d}.fits".format(os.getcwd(),self._argflag['run']['masterdir'],self._fitsdict['target'][scidx[0]],"skysub")
# Send the data away to be saved
arsave.save_master(self, scibgsub, filename=msscibg_name, frametype='sky subtracted science', ind=ind)
# msgs.error("There is a problem with the 2D spectrum fit - the mask flag (-999999.9) is not being correctly loaded in after being extracted."+
# "You either need to find a way to load this value correctly, or save the order width in the header. This affects line 150 or arextract")
#msgs.work("Temporary -- until extraction algorithm is improved")
#sciext1D, scierr1D, skyext1D, skyerr1D = arextract_temp.optimalextract(self, sciframe, prefix=prefix)
extdim = "ext1D"
sciext_name = "{0:s}/{1:s}/{2:s}/{3:s}_{4:s}.fits".format(os.getcwd(),self._argflag['run']['scidir'],self._fitsdict['target'][scidx[0]],prefix,extdim)
# Send the data away to be saved
arsave.save_extraction(self, sciext1D, scidx, scierr=scierr1D, filename=sciext_name, frametype='science extraction', wave=self._sciwav, sky=skyext1D, skyerr=skyerr1D)
msgs.work("Really need to work out the blaze/normalized flat when there are more than one amplifier")
msgs.error("Up to here")
continue
###############
# Extract and save the science frame
# DEPRECATED -> self._sciext, self._sciwav = arextract.extract(self, sciframe, mode=self._argflag["science"]["extraction"]["method"], frametype='science', wave=self._wavelength)
# msgs.error("Havn't completed this yet -- also need to calculate sciwav in arextract before returning")
# Derive a suitable name for the extracted science frame
if self._argflag["science"]["extraction"]["method"].lower() in ["2d"]:
extdim = "ext2D"
else:
extdim = "ext1D"
sciext_name = "{0:s}/{1:s}/{2:s}/{3:s}_{4:s}.fits".format(os.getcwd(),self._argflag['run']['scidir'],self._fitsdict['target'][scidx[0]],prefix,extdim)
if self._argflag['science']['load']['extracted'] == True:
if os.path.exists(sciext_name):
msgs.work("Loaded extraction arrays are sometimes off by the machine precision (1 part in 10^16)")
"""
This can be fixed by generating a wavelength scale using the pixsize from the header and finding the closest match to lambda_0.
"""
self._sciext, self._sciwav, extprops = arload.load_extraction(sciext_name, frametype="Science", wave=True)
else:
msgs.warn("A file containing the science extraction does not exist for file:"+msgs.newline()+sciext_name)
msgs.info("Reduction will continue by performing science extraction")
self._sciext, extprops, self._sciwav = arextract.extract(self, sciframe, error=errframe, mode=self._argflag["science"]["extraction"]["method"], frametype='Science', wave=self._wavelength)
# Send the data away to be saved
arsave.save_extraction(self, self._sciext, scidx, filename=sciext_name, frametype='science extraction', wave=self._sciwav, extprops=extprops)
else:
self._sciext, extprops, self._sciwav = arextract.extract(self, sciframe, error=errframe, mode=self._argflag["science"]["extraction"]["method"], frametype='Science', wave=self._wavelength)
# Send the data away to be saved
arsave.save_extraction(self, self._sciext, scidx, filename=sciext_name, frametype='science extraction', wave=self._sciwav, extprops=extprops)
###############
# Continue with the next science target if the user only wanted a 1D extraction
if self._argflag["science"]["extraction"]["method"].lower() not in ["2d"]:
continue
###############
# Otherwise, fit the 2D extracted science frame, and save the results
msgs.work("The error frame is currently not self-consistently extracted from the science frame"+msgs.newline()+
"Instead, an error frame is generated from the extracted science frame")
#scierr = arproc.error_frame_postext(self, self._sciext, scidx[0])
sciext1D, scierr1D, skyext1D, skyerr1D = arextract.fit_spec2D(self, self._sciext, extprops, prefix=prefix)
extdim = "ext1D"
sciext_name = "{0:s}/{1:s}/{2:s}/{3:s}_{4:s}.fits".format(os.getcwd(),self._argflag['run']['scidir'],self._fitsdict['target'][scidx[0]],prefix,extdim)
# Send the data away to be saved
arsave.save_extraction(self, sciext1D, scidx, scierr=scierr1D, filename=sciext_name, frametype='science extraction', wave=self._sciwav, sky=skyext1D, skyerr=skyerr1D)
# Transform the wavelength scale onto the 2D master flat-field frame with the user-specified pixel velocity size.
# Extract orders from master flat-field.
# Normalise the orders in the flat-field (i.e. go back to the 2D flat-field frame and for each wavelength bin, divide all pixels in this bin by the value derived in the previous step (times the fraction of this pixel in the appropriate wavelength bin).
# Divide the science frame by the normalised flat-field frame.
# Transform the wavelength scale onto the 2D science frame, and extract the data.
#
##############################################
#$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
if __name__ == "__main__":
debug = True
if debug:
argflag = arload.optarg(sys.argv, last_updated)
ClassMain(argflag)
else:
try:
argflag = arload.optarg(sys.argv, last_updated)
ClassMain(argflag)
except Exception:
# There is a bug in the code, print the file and line number of the error.
et, ev, tb = sys.exc_info()
while tb:
co = tb.tb_frame.f_code
filename = str(co.co_filename)
line_no = str(traceback.tb_lineno(tb))
tb = tb.tb_next
filename=filename.split('/')[-1]
msgs.bug("There appears to be a bug on Line "+line_no+" of "+filename+" with error:"+msgs.newline()+str(ev)+msgs.newline()+"---> please contact the author")
