def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
if "FiberFlatFile" not in kwargs:
raise qlexceptions.ParameterException("Need Fiberflat file")
input_frame = args[0]
dump = False
dumpfile = None
if "DumpIntermediates" in kwargs:
dump = kwargs["DumpIntermediates"]
if dump: #- need a file to write
if "dumpfile" not in kwargs:
raise IOError("Need file to dump")
else:
dumpfile = kwargs["dumpfile"]
fiberflat = kwargs["FiberFlatFile"]
return self.run_pa(input_frame,
fiberflat,
dump=dump,
dumpfile=dumpfile)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
if not kwargs["PSFbootfile"]:
raise qlexceptions.ParameterException("Missing psfbootfile in the arguments")
if "PSFoutfile" not in kwargs:
raise qlexceptions.ParameterException("Missing psfoutfile in the arguments")
psfoutfile=kwargs["PSFoutfile"]
psfbootfile=kwargs["PSFbootfile"]
from desispec.psf import PSF
psfboot=PSF(psfbootfile)
domain=(psfboot.wmin,psfboot.wmax)
input_frame=args[0]
linelist=None
if "Linelist" in kwargs:
linelist=kwargs["Linelist"]
npoly=2
if "NPOLY" in kwargs:
npoly=kwargs["NPOLY"]
nbins=2
if "NBINS" in kwargs:
nbins=kwargs["NBINS"]
return self.run_pa(input_frame, psfbootfile, psfoutfile, linelist=linelist, npoly=npoly, nbins=nbins,domain=domain)
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
input_image = args[0]
camera = kwargs["camera"]
expid = kwargs["expid"]
paname = None
if "paname" in kwargs:
paname = kwargs["paname"]
amps = False
if "amps" in kwargs:
amps = kwargs["amps"]
url = None
if "url" in kwargs:
url = kwargs["url"]
if "qafig" in kwargs: qafig = kwargs["qafig"]
else: qafig = None
return self.run_qa(input_image,
camera,
expid,
paname=paname,
amps=amps,
url=url,
qafig=qafig)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
input_frame=args[0] #- this must be flat field applied before sky subtraction in the pipeline
if "SkyFile" in kwargs:
from desispec.io.sky import read_sky
skyfile=kwargs["SkyFile"] #- Read sky model file itself from an argument
log.info("Using given sky file %s for subtraction"%skyfile)
skymodel=read_sky(skyfile)
else:
if "Outskyfile" in kwargs:
outskyfile=kwargs["Outskyfile"]
else: outskyfile=None
log.info("No sky file given. Computing sky first")
from desispec.quicklook.quicksky import compute_sky
fibermap=input_frame.fibermap
skymodel=compute_sky(input_frame,fibermap)
if outskyfile is not None:
from desispec.io.sky import write_sky
log.info("writing an output sky model file %s "%outskyfile)
write_sky(outputfile,skymodel,input_frame.meta)
#- now do the subtraction
return self.run_pa(input_frame,skymodel)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
input_raw=args[0]
dump=False
dumpfile=None
if "DumpIntermediates" in kwargs:
dump=kwargs["DumpIntermediates"]
if dump: #- need a file to write
if "dumpfile" not in kwargs:
raise IOError("Need file to dump")
else: dumpfile=kwargs["dumpfile"]
if 'camera' not in kwargs:
raise qlexceptions.ParameterException("Need Camera to run preprocess on raw files")
else:
camera=kwargs["camera"]
if camera.upper() not in input_raw:
raise IOError('Camera {} not in raw input'.format(camera))
if "Bias" in kwargs:
bias=kwargs["Bias"]
else: bias=False
if "Pixflat" in kwargs:
pixflat=kwargs["Pixflat"]
else: pixflat=False
if "Mask" in kwargs:
mask=kwargs["Mask"]
else: mask=False
return self.run_pa(input_raw,camera,bias=bias,pixflat=pixflat,mask=mask,dump=dump,dumpfile=dumpfile)
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
input_frame = args[
0] #- frame object to calculate sky from. Should be fiber flat corrected
if "FiberMap" in kwargs:
fibermap = kwargs["FiberMap"]
else:
fibermap = None
if "Apply_resolution" in kwargs:
apply_resolution = kwargs["Apply_resolution"]
if "Outfile" not in kwargs:
raise qlexceptions.ParameterException(
"Need output file name to write skymodel")
outputfile = kwargs["Outfile"]
return self.run_pa(input_frame,
outputfile,
fibermap=fibermap,
apply_resolution=apply_resolution)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
if "PSFFile" not in kwargs:
raise qlexceptions.ParameterException("Need PSF File")
input_image=args[0]
psf=kwargs["PSFFile"]
boxwidth=kwargs["BoxWidth"]
nspec=kwargs["Nspec"]
if "Wavelength" not in kwargs:
wstart = np.ceil(psf.wmin)
wstop = np.floor(psf.wmax)
dw = 0.5
else:
wavelength=kwargs["Wavelength"]
if kwargs["Wavelength"] is not None: #- should be in wstart,wstop,dw format
wstart, wstop, dw = map(float, wavelength.split(','))
else:
wstart = np.ceil(psf.wmin)
wstop = np.floor(psf.wmax)
dw = 0.5
wave = np.arange(wstart, wstop+dw/2.0, dw)
if "Specmin" not in kwargs:
specmin=0
else:
specmin=kwargs["Specmin"]
if kwargs["Specmin"] is None:
specmin=0
if "Nspec" not in kwargs:
nspec = psf.nspec
else:
nspec=kwargs["Nspec"]
if nspec is None:
nspec=psf.nspec
specmax = specmin + nspec
camera = input_image.meta['CAMERA'].lower() #- b0, r1, .. z9
spectrograph = int(camera[1])
fibermin = spectrograph*500 + specmin
if "FiberMap" not in kwargs:
fibermap = None
fibers = np.arange(fibermin, fibermin+nspec, dtype='i4')
else:
fibermap=kwargs["FiberMap"]
fibermap = fibermap[fibermin:fibermin+nspec]
fibers = fibermap['FIBER']
if "Outfile" in kwargs:
outfile=kwargs["Outfile"]
else:
outfile=None
return self.run_pa(input_image,psf,wave,boxwidth,nspec,fibers=fibers,fibermap=fibermap,outfile=outfile)
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
return self.count_fibers(args[0])
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
input_frame = args[0]
camera = kwargs["camera"]
expid = kwargs["expid"]
wrange1 = None
wrange2 = None
if "wrange1" in kwargs:
wrange1 = kwargs["wrange1"]
if "wrange2" in kwargs:
wrange2 = kwargs["wrange2"]
if wrange1 == None:
if camera[0] == "b": wrange1 = "4000,4500"
if camera[0] == "r": wrange1 = "5950,6200"
if camera[0] == "z": wrange1 = "8120,8270"
if wrange2 == None:
if camera[0] == "b": wrange2 = "5250,5550"
if camera[0] == "r": wrange2 = "6990,7230"
if camera[0] == "z": wrange2 = "9110,9280"
paname = None
if "paname" in kwargs:
paname = kwargs["paname"]
amps = False
if "amps" in kwargs:
amps = kwargs["amps"]
psf = None
if "PSFFile" in kwargs:
psf = kwargs["PSFFile"]
url = None
if "url" in kwargs:
url = kwargs["url"]
if "qafig" in kwargs: qafig = kwargs["qafig"]
else: qafig = None
return self.run_qa(input_frame,
camera,
expid,
wrange1=wrange1,
wrange2=wrange2,
paname=paname,
amps=amps,
psf=psf,
url=url,
qafig=qafig)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
input_frame=args[0] #- frame object to calculate fiberflat from
if "outputFile" not in kwargs:
raise qlexceptions.ParameterException("Need output file name to write fiberflat File")
outputfile=kwargs["outputFile"]
return self.run_pa(input_frame,outputfile)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
if "FiberFlatFile" not in kwargs:
raise qlexceptions.ParameterException("Need Fiberflat file")
input_frame=args[0]
fiberflat=kwargs["FiberFlatFile"]
return self.run_pa(input_frame,fiberflat)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
if "SkyFile" not in kwargs:
raise qlexceptions.ParameterException("Need Skymodel file")
input_frame=args[0] #- this must be flat field applied before sky subtraction in the pipeline
skyfile=kwargs["SkyFile"] #- Read sky model file itself from an argument
from desispec.io.sky import read_sky
skymodel=read_sky(skyfile)
return self.run_pa(input_frame,skymodel)
def run(self,*args,**kwargs):
if len(args) == 0 :
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException("Incompatible input. Was expecting %s got %s"%(type(self.__inpType__),type(args[0])))
if "FiberFlatFile" not in kwargs: #- need this as fiberflat has to apply to frame first
raise qlexceptions.ParameterException("Need Fiberflat frame file")
input_frame=args[0] #- frame object to calculate sky from
if "FiberMap" in kwargs:
fibermap=kwargs["FiberMap"]
if "Outfile" not in kwargs:
raise qlexceptions.ParameterException("Need output file name to write skymodel")
fiberflat=kwargs["FiberFlatFile"]
outputfile=kwargs["Outfile"]
return self.run_pa(input_frame,fiberflat,outputfile)
def run(self, *args, **kwargs):
if len(args) == 0: #- args[0] should be the fiberflat image
raise qlexceptions.ParameterException("Missing input parameter")
if 'ArcLampImage' not in kwargs:
raise qlexceptions.ParameterException("Need ArcLampImage")
if "Deg" not in kwargs:
deg = 5 #- 5th order legendre polynomial
else:
deg = kwargs["Deg"]
flatimage = args[0]
arcimage = kwargs["ArcLampImage"]
outputfile = kwargs["outputFile"]
return self.run_pa(deg, flatimage, arcimage, outputfile)
def run(self, *args, **kwargs):
if 'ArcLampImage' not in kwargs:
raise qlexceptions.ParameterException("Need ArcLampImage")
if 'FlatImage' not in kwargs:
raise qlexceptions.ParameterException("Need FlatImage")
if 'outputFile' not in kwargs:
raise qlexceptions.ParameterException("Need outputFile")
if "Deg" not in kwargs:
deg = 5 #- 5th order legendre polynomial
else:
deg = kwargs["Deg"]
flatimage = kwargs["FlatImage"]
arcimage = kwargs["ArcLampImage"]
outputfile = kwargs["outputFile"]
return self.run_pa(deg, flatimage, arcimage, outputfile, args)
def _qaparams(self,qa):
params={}
if self.algorithms is not None:
for PA in self.palist:
if qa in self.qalist[PA]:
params[qa]=self.algorithms[PA]['QA'][qa]['PARAMS']
else:
# RK: Need to settle optimal error handling in cases like this.
raise qlexceptions.ParameterException("Run time PARAMs not provided for QA")
return params[qa]
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
if "PSFFile_sp" not in kwargs:
raise qlexceptions.ParameterException("Need PSF File")
from specter.psf import load_psf
input_image = args[0]
psffile = kwargs["PSFFile_sp"]
psf = load_psf(psffile)
if "Wavelength" not in kwargs:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.5
else:
wavelength = kwargs["Wavelength"]
if kwargs[
"Wavelength"] is not None: #- should be in wstart,wstop,dw format
wstart, wstop, dw = map(float, wavelength.split(','))
else:
wstart = np.ceil(psf.wmin_all)
wstop = np.floor(psf.wmax_all)
dw = 0.5
wave = np.arange(wstart, wstop + dw / 2.0, dw)
if "Specmin" not in kwargs:
specmin = 0
else:
specmin = kwargs["Specmin"]
if kwargs["Specmin"] is None:
specmin = 0
if "Nspec" not in kwargs:
nspec = psf.nspec
else:
nspec = kwargs["Nspec"]
if nspec is None:
nspec = psf.nspec
specmax = specmin + nspec
camera = input_image.meta['CAMERA'].lower() #- b0, r1, .. z9
spectrograph = int(camera[1])
fibermin = spectrograph * 500 + specmin
if "FiberMap" not in kwargs:
fibermap = None
fibers = np.arange(fibermin, fibermin + nspec, dtype='i4')
else:
fibermap = kwargs["FiberMap"]
fibermap = fibermap[fibermin:fibermin + nspec]
fibers = fibermap['FIBER']
if "Regularize" in kwargs:
regularize = kwargs["Regularize"]
else:
regularize = False
if "ndecorr" in kwargs:
ndecorr = ndecorr
else:
ndecorr = True
bundlesize = 25 #- hard coded
if "Outfile" in kwargs:
outfile = kwargs["Outfile"]
else:
outfile = None
if "Nwavestep" in kwargs:
wavesize = kwargs["Nwavestep"]
else:
wavesize = 50
return self.run_pa(input_image,
psf,
specmin,
nspec,
wave,
regularize=regularize,
ndecorr=ndecorr,
bundlesize=bundlesize,
wavesize=wavesize,
outfile=outfile,
fibers=fibers,
fibermap=fibermap)
def run(self, *args, **kwargs):
if len(args) == 0:
raise qlexceptions.ParameterException("Missing input parameter")
if not self.is_compatible(type(args[0])):
raise qlexceptions.ParameterException(
"Incompatible input. Was expecting %s got %s" %
(type(self.__inpType__), type(args[0])))
if "PSFFile" not in kwargs:
raise qlexceptions.ParameterException("Need PSF File")
input_image = args[0]
dumpfile = None
if "dumpfile" in kwargs:
dumpfile = kwargs["dumpfile"]
psf = kwargs["PSFFile"]
boxwidth = kwargs["BoxWidth"]
nspec = kwargs["Nspec"]
quickRes = kwargs[
"QuickResolution"] if "QuickResolution" in kwargs else False
if "usesigma" in kwargs:
usesigma = kwargs["usesigma"]
else:
usesigma = False
if "Wavelength" not in kwargs:
wstart = np.ceil(psf.wmin)
wstop = np.floor(psf.wmax)
dw = 0.5
else:
wavelength = kwargs["Wavelength"]
if kwargs[
"Wavelength"] is not None: #- should be in wstart,wstop,dw format
wstart, wstop, dw = [float(w) for w in wavelength]
else:
wstart = np.ceil(psf.wmin)
wstop = np.floor(psf.wmax)
dw = 0.5
wave = np.arange(wstart, wstop + dw / 2.0, dw)
if "Specmin" not in kwargs:
specmin = 0
else:
specmin = kwargs["Specmin"]
if kwargs["Specmin"] is None:
specmin = 0
if "Nspec" not in kwargs:
nspec = psf.nspec
else:
nspec = kwargs["Nspec"]
if nspec is None:
nspec = psf.nspec
specmax = specmin + nspec
camera = input_image.meta['CAMERA'].lower() #- b0, r1, .. z9
spectrograph = int(camera[1])
fibermin = spectrograph * 500 + specmin
if "FiberMap" not in kwargs:
fibermap = None
fibers = np.arange(fibermin, fibermin + nspec, dtype='i4')
else:
fibermap = kwargs["FiberMap"]
fibermap = fibermap[fibermin:fibermin + nspec]
fibers = fibermap['FIBER']
if "Outfile" in kwargs:
outfile = kwargs["Outfile"]
else:
outfile = None
maskFile = None
if "MaskFile" in kwargs:
maskFile = kwargs['MaskFile']
#- Add some header keys relevant for this extraction
input_image.meta['NSPEC'] = (nspec, 'Number of spectra')
input_image.meta['WAVEMIN'] = (wstart, 'First wavelength [Angstroms]')
input_image.meta['WAVEMAX'] = (wstop, 'Last wavelength [Angstroms]')
input_image.meta['WAVESTEP'] = (dw, 'Wavelength step size [Angstroms]')
return self.run_pa(input_image,
psf,
wave,
boxwidth,
nspec,
fibers=fibers,
fibermap=fibermap,
dumpfile=dumpfile,
maskFile=maskFile,
usesigma=usesigma,
quick_resolution=quickRes)