def griddata(pixPerBeam=3.0,
templateHeader=None,
gridFunction=jincGrid,
rootdir='/lustre/pipeline/scratch/GAS/',
region='NGC1333',
dirname='NGC1333_NH3_11',
startChannel=762, endChannel=3584,
doBaseline=True,
baselineRegion=[slice(762, 1024, 1), slice(3072, 3584, 1)],
blorder=1,
Sessions=None,
file_extension=None,
rebase=False, **kwargs):
if not Sessions:
filelist = glob.glob(rootdir + '/' + region + '/' + dirname + '/*fits')
if not file_extension:
file_extension = '_all'
history_message = 'Gridding of data using all sessions'
else:
filelist = []
for scan_i in Sessions:
filelist.extend(glob.glob(rootdir + '/' + region +
'/' + dirname + '/*_sess' +
str(scan_i) + '.fits'))
if isinstance(Sessions, list):
if not file_extension:
file_extension = '_sess{0}-sess{1}'.format(Sessions[0],
Sessions[-1])
if (Sessions[-1] + 1. - Sessions[0]) / len(Sessions) == 1.0:
history_message = 'Gridding of data using sessions' \
'between {0} and {1}'.format(Sessions[0], Sessions[-1])
else:
history_message = 'Gridding of data using sessions: '
for scan_i in Sessions:
history_message += '{0}, '.format(scan_i)
else:
if not file_extension:
file_extension = '_sess{0}'.format(Sessions)
history_message = 'Gridding of data using session'\
'{0}'.format(Sessions)
if len(filelist) == 0:
warnings.warn('There are no FITS files to process '
'in ' + rootdir + '/' + region + '/' + dirname)
return
# check that every file in the filelist is valid
# If not then remove it and send warning message
for file_i in filelist:
try:
fits.open(file_i)
except:
warnings.warn('file {0} is corrupted'.format(file_i))
filelist.remove(file_i)
# pull a test structure
s = fits.getdata(filelist[0])
c = 299792458.
nu0 = s[0]['RESTFREQ']
Data_Unit = s[0]['TUNIT7']
beamSize = 1.22 * (c / nu0 / 100.0) * 180 / np.pi # in degrees
naxis3 = len(s[0]['DATA'][startChannel:endChannel])
# Default behavior is to park the object velocity at
# the center channel in the VRAD-LSR frame
crval3 = s[0]['RESTFREQ'] * (1 - s[0]['VELOCITY'] / c)
crpix3 = s[0]['CRPIX1'] - startChannel
ctype3 = s[0]['CTYPE1']
cdelt3 = s[0]['CDELT1']
w = wcs.WCS(naxis=3)
w.wcs.restfrq = nu0
w.wcs.radesys = s[0]['RADESYS']
w.wcs.equinox = s[0]['EQUINOX']
# We are forcing this conversion to make nice cubes.
w.wcs.specsys = 'LSRK'
w.wcs.ssysobs = 'TOPOCENT'
if templateHeader is None:
wcsdict = autoHeader(filelist, beamSize=beamSize,
pixPerBeam=pixPerBeam)
w.wcs.crpix = [wcsdict['CRPIX1'], wcsdict['CRPIX2'], crpix3]
w.wcs.cdelt = np.array([wcsdict['CDELT1'], wcsdict['CDELT2'], cdelt3])
w.wcs.crval = [wcsdict['CRVAL1'], wcsdict['CRVAL2'], crval3]
w.wcs.ctype = [wcsdict['CTYPE1'], wcsdict['CTYPE2'], ctype3]
naxis2 = wcsdict['NAXIS2']
naxis1 = wcsdict['NAXIS1']
else:
w.wcs.crpix = [templateHeader['CRPIX1'],
templateHeader['CRPIX2'], crpix3]
w.wcs.cdelt = np.array([templateHeader['CDELT1'],
templateHeader['CDELT2'], cdelt3])
w.wcs.crval = [templateHeader['CRVAL1'],
templateHeader['CRVAL2'], crval3]
w.wcs.ctype = [templateHeader['CTYPE1'],
templateHeader['CTYPE2'], ctype3]
naxis2 = templateHeader['NAXIS2']
naxis1 = templateHeader['NAXIS1']
outCube = np.zeros((int(naxis3), int(naxis2), int(naxis1)))
outWts = np.zeros((int(naxis2), int(naxis1)))
xmat, ymat = np.meshgrid(np.arange(naxis1), np.arange(naxis2),
indexing='ij')
xmat = xmat.reshape(xmat.size)
ymat = ymat.reshape(ymat.size)
xmat = xmat.astype(np.int)
ymat = ymat.astype(np.int)
ctr = 0
for thisfile in filelist:
ctr += 1
s = fits.open(thisfile)
print("Now processing {0}".format(thisfile))
print("This is file {0} of {1}".format(ctr, len(filelist)))
nuindex = np.arange(len(s[1].data['DATA'][0]))
for spectrum in console.ProgressBar((s[1].data)):
# Generate Baseline regions
baselineIndex = np.concatenate([nuindex[ss]
for ss in baselineRegion])
specData = spectrum['DATA']
# baseline fit
if doBaseline & np.all(np.isfinite(specData)):
specData = baselineSpectrum(specData, order=blorder,
baselineIndex=baselineIndex)
# This part takes the TOPOCENTRIC frequency that is at
# CRPIX1 (i.e., CRVAL1) and calculates the what frequency
# that would have in the LSRK frame with freqShiftValue.
# This then compares to the desired frequency CRVAL3.
DeltaNu = freqShiftValue(spectrum['CRVAL1'],
-spectrum['VFRAME']) - crval3
DeltaChan = DeltaNu / cdelt3
specData = channelShift(specData, -DeltaChan)
outslice = (specData)[startChannel:endChannel]
spectrum_wt = np.isfinite(outslice).astype(np.float)
outslice = np.nan_to_num(outslice)
xpoints, ypoints, zpoints = w.wcs_world2pix(spectrum['CRVAL2'],
spectrum['CRVAL3'],
spectrum['CRVAL1'], 0)
tsys = spectrum['TSYS']
if (tsys > 10) and (xpoints > 0) and (xpoints < naxis1) \
and (ypoints > 0) and (ypoints < naxis2):
pixelWeight, Index = gridFunction(xmat, ymat,
xpoints, ypoints,
pixPerBeam=pixPerBeam)
vector = np.outer(outslice * spectrum_wt,
pixelWeight / tsys**2)
wts = pixelWeight / tsys**2
outCube[:, ymat[Index], xmat[Index]] += vector
outWts[ymat[Index], xmat[Index]] += wts
# Temporarily do a file write for every batch of scans.
outWtsTemp = np.copy(outWts)
outWtsTemp.shape = (1,) + outWtsTemp.shape
outCubeTemp = np.copy(outCube)
outCubeTemp /= outWtsTemp
hdr = fits.Header(w.to_header())
hdr = addHeader_nonStd(hdr, beamSize, Data_Unit)
#
hdu = fits.PrimaryHDU(outCubeTemp, header=hdr)
hdu.writeto(dirname + file_extension + '.fits', clobber=True)
outWts.shape = (1,) + outWts.shape
outCube /= outWts
# Create basic fits header from WCS structure
hdr = fits.Header(w.to_header())
# Add non standard fits keyword
hdr = addHeader_nonStd(hdr, beamSize, Data_Unit)
# Adds history message
hdr.add_history(history_message)
hdr.add_history('Using GAS pipeline version {0}'.format(__version__))
hdu = fits.PrimaryHDU(outCube, header=hdr)
hdu.writeto(dirname + file_extension + '.fits', clobber=True)
w2 = w.dropaxis(2)
hdr2 = fits.Header(w2.to_header())
hdu2 = fits.PrimaryHDU(outWts, header=hdr2)
hdu2.writeto(dirname + file_extension + '_wts.fits', clobber=True)
if rebase:
if 'NH3_11' in dirname:
baseline.rebaseline(dirname + file_extension + '.fits',
windowFunction=baseline.ammoniaWindow,
line='oneone', **kwargs)
if 'NH3_22' in dirname:
winfunc = baseline.ammoniaWindow
baseline.rebaseline(dirname + file_extension + '.fits',
windowFunction=baseline.ammoniaWindow,
line='twotwo', **kwargs)
if 'NH3_33' in dirname:
baseline.rebaseline(dirname + file_extension + '.fits',
winfunc = baseline.ammoniaWindow,
line='threethree', **kwargs)
else:
baseline.rebaseline(dirname + file_extension + '.fits',
windowFunction=baseline.tightWindow,
**kwargs)
hdr = addHeader_nonStd(hdr, beamSize, Data_Unit)
#
hdu = fits.PrimaryHDU(outCubeTemp, header=hdr)
hdu.writeto(dirname + file_extension + '.fits', clobber=True)
outWts.shape = (1,) + outWts.shape
outCube /= outWts
# Create basic fits header from WCS structure
hdr = fits.Header(w.to_header())
# Add non standard fits keyword
hdr = addHeader_nonStd(hdr, beamSize, Data_Unit)
# Adds history message
hdr.add_history(history_message)
hdr.add_history('Using GAS pipeline version {0}'.format(__version__))
hdu = fits.PrimaryHDU(outCube, header=hdr)
hdu.writeto(dirname + file_extension + '.fits', clobber=True)
w2 = w.dropaxis(2)
hdr2 = fits.Header(w2.to_header())
hdu2 = fits.PrimaryHDU(outWts, header=hdr2)
hdu2.writeto(dirname + file_extension + '_wts.fits', clobber=True)
if rebase:
if 'NH3' in dirname:
winfunc = baseline.ammoniaWindow
else:
winfunc = baseline.tightWindow
baseline.rebaseline(dirname + file_extension + '.fits',
windowFunction = winfunc)
