def run_pa(self,
input_image,
psf,
outwave,
boxwidth,
nspec,
fibers=None,
fibermap=None,
dumpfile=None,
maskFile=None,
usesigma=False,
quick_resolution=False):
from desispec.boxcar import do_boxcar
import desispec.psf
if fibermap['OBJTYPE'][0] == 'ARC':
psf = desispec.psf.PSF(psf)
flux, ivar, Rdata = do_boxcar(input_image,
psf,
outwave,
boxwidth=boxwidth,
nspec=nspec,
maskFile=maskFile,
usesigma=usesigma,
quick_resolution=quick_resolution)
#- write to a frame object
qndiag = 21
wsigma = None
if quick_resolution:
if hasattr(psf, 'wcoeff'):
wsigma = np.empty(flux.shape)
if isinstance(nspec, (tuple, list, np.ndarray)):
for i, s in enumerate(nspec):
#- GD: Need confirmation, but this appears to be missing.
wsigma[i] = psf.wdisp(
s, outwave) / psf.angstroms_per_pixel(s, outwave)
else:
for i in range(nspec):
wsigma[i] = psf.wdisp(
i, outwave) / psf.angstroms_per_pixel(i, outwave)
elif hasattr(psf, 'xsigma_boot'):
wsigma = np.tile(psf.xsigma_boot, (outwave.shape[0], 1))
frame = fr(outwave,
flux,
ivar,
resolution_data=Rdata,
fibers=fibers,
meta=input_image.meta,
fibermap=fibermap,
wsigma=wsigma,
ndiag=qndiag)
if dumpfile is not None:
night = frame.meta['NIGHT']
expid = frame.meta['EXPID']
io.write_frame(dumpfile, frame)
log.debug("Wrote intermediate file %s after %s" %
(dumpfile, self.name))
return frame
def run_pa(self,
input_image,
psf,
specmin,
nspec,
wave,
regularize=None,
ndecorr=True,
bundlesize=25,
wavesize=50,
outfile=None,
fibers=None,
fibermap=None):
import specter
from specter.extract import ex2d
from desispec.frame import Frame as fr
flux, ivar, Rdata = ex2d(input_image.pix,
input_image.ivar * (input_image.mask == 0),
psf,
specmin,
nspec,
wave,
regularize=regularize,
ndecorr=ndecorr,
bundlesize=bundlesize,
wavesize=wavesize)
#- Augment input image header for output
input_image.meta['NSPEC'] = (nspec, 'Number of spectra')
input_image.meta['WAVEMIN'] = (wave[0], 'First wavelength [Angstroms]')
input_image.meta['WAVEMAX'] = (wave[-1], 'Last wavelength [Angstroms]')
input_image.meta['WAVESTEP'] = (wave[1] - wave[0],
'Wavelength step size [Angstroms]')
input_image.meta['SPECTER'] = (specter.__version__,
'https://github.com/desihub/specter')
#input_image.meta['IN_PSF'] = (_trim(psf_file), 'Input spectral PSF')
#input_image.meta['IN_IMG'] = (_trim(input_file), 'Input image')
frame = fr(wave,
flux,
ivar,
resolution_data=Rdata,
fibers=fibers,
meta=input_image.meta,
fibermap=fibermap)
if outfile is not None: #- writing to a frame file if needed.
from desispec import io
io.write_frame(outfile, frame)
log.info("wrote frame output file %s" % outfile)
return frame
def run_pa(self, input_image, psf, outwave, boxwidth, nspec,fibers=None, fibermap=None,outfile=None):
from desispec.boxcar import do_boxcar
from desispec.frame import Frame as fr
flux,ivar,Rdata=do_boxcar(input_image, psf, outwave, boxwidth=boxwidth,
nspec=nspec)
#- write to a frame object
frame = fr(outwave, flux, ivar, resolution_data=Rdata,fibers=fibers, meta=input_image.meta, fibermap=fibermap)
if outfile is not None: #- writing to a frame file if needed.
from desispec import io
io.write_frame(outfile,frame)
log.info("wrote frame output file %s"%outfile)
return frame
def run_pa(self, input_image, psf, outwave, boxwidth, nspec,fibers=None, fibermap=None,dump=False,dumpfile=None):
from desispec.boxcar import do_boxcar
from desispec.frame import Frame as fr
flux,ivar,Rdata=do_boxcar(input_image, psf, outwave, boxwidth=boxwidth,
nspec=nspec)
#- write to a frame object
frame = fr(outwave, flux, ivar, resolution_data=Rdata,fibers=fibers, meta=input_image.meta, fibermap=fibermap)
if dump and dumpfile is not None:
from desispec import io
night = frame.meta['NIGHT']
expid = frame.meta['EXPID']
io.write_frame(dumpfile, frame)
log.info("Wrote intermediate file %s after %s"%(dumpfile,self.name))
return frame
def run_pa(self, input_image, psf, outwave, boxwidth, nspec,
fibers=None, fibermap=None,dump=False,dumpfile=None,
maskFile=None):
from desispec.boxcar import do_boxcar
from desispec.frame import Frame as fr
flux,ivar,Rdata=do_boxcar(input_image, psf, outwave, boxwidth=boxwidth,
nspec=nspec,maskFile=maskFile)
#- write to a frame object
frame = fr(outwave, flux, ivar, resolution_data=Rdata,fibers=fibers, meta=input_image.meta, fibermap=fibermap)
if dump and dumpfile is not None:
from desispec import io
night = frame.meta['NIGHT']
expid = frame.meta['EXPID']
io.write_frame(dumpfile, frame)
log.info("Wrote intermediate file %s after %s"%(dumpfile,self.name))
return frame
def run_pa(self,input_image,psf,specmin,nspec,wave,regularize=None,ndecorr=True,bundlesize=25,wavesize=50, outfile=None,fibers=None,fibermap=None):
import specter
from specter.extract import ex2d
from desispec.frame import Frame as fr
flux,ivar,Rdata=ex2d(input_image.pix,input_image.ivar*(input_image.mask==0),psf,specmin,nspec,wave,regularize=regularize,ndecorr=ndecorr,bundlesize=bundlesize,wavesize=wavesize)
#- Augment input image header for output
input_image.meta['NSPEC'] = (nspec, 'Number of spectra')
input_image.meta['WAVEMIN'] = (wave[0], 'First wavelength [Angstroms]')
input_image.meta['WAVEMAX'] = (wave[-1], 'Last wavelength [Angstroms]')
input_image.meta['WAVESTEP']= (wave[1]-wave[0], 'Wavelength step size [Angstroms]')
input_image.meta['SPECTER'] = (specter.__version__, 'https://github.com/desihub/specter')
#input_image.meta['IN_PSF'] = (_trim(psf_file), 'Input spectral PSF')
#input_image.meta['IN_IMG'] = (_trim(input_file), 'Input image')
frame = fr(wave, flux, ivar, resolution_data=Rdata,fibers=fibers, meta=input_image.meta, fibermap=fibermap)
if outfile is not None: #- writing to a frame file if needed.
from desispec import io
io.write_frame(outfile,frame)
log.info("wrote frame output file %s"%outfile)
return frame
