def test_shape_error(self):
'''
Test for various shape errors
'''
mygridder = cygrid.WcsGrid(self.header)
mygridder.set_kernel(*self.kernel_args)
with pytest.raises(cygrid.ShapeError):
mygridder.grid(self.xcoords, self.ycoords[:, np.newaxis],
self.signal)
with pytest.raises(cygrid.ShapeError):
# this should not work, as the second call to grid has
# incompatible shape
mygridder.grid(self.xcoords, self.ycoords, self.signal)
mygridder.grid(self.xcoords, self.ycoords, self.signal[:,
np.newaxis])
# now test with user-provided data cube
dcube = np.zeros_like(self.test_maps[0, 0])
mygridder = cygrid.WcsGrid(self.header, datacube=dcube)
mygridder.set_kernel(*self.kernel_args)
with pytest.raises(cygrid.ShapeError):
mygridder.grid(self.xcoords, self.ycoords, self.signal[:,
np.newaxis])
def generate_cube(spectra, header, lightcone, outname=None):
# set up the gridder and kernel
gridder = cg.WcsGrid(header)
# set kernel
kernelsize_fwhm = header['BMAJ']
kernelsize_sigma = kernelsize_fwhm / 2.355
sphere_radius = 3. * kernelsize_sigma
gridder.set_kernel(
'gauss1d',
(kernelsize_sigma,),
sphere_radius,
kernelsize_sigma / 2.)
# grid and retrieve cube
gridder.grid(
lightcone['ra'].values,
lightcone['dec'].values,
spectra)
cube = gridder.get_datacube()
# write to disk
if outname is not None:
fits.writeto(outname, cube, header)
return cube
def test_gridding3d(self):
mygridder = cygrid.WcsGrid(self.header)
mygridder.set_kernel(*self.kernel_args)
mygridder.grid(self.xcoords, self.ycoords, self.signal2)
assert_allclose(mygridder.get_datacube(),
self.test_maps[0],
atol=1.e-6)
def test_gridding4d(self):
mygridder = cygrid.WcsGrid(self.header)
mygridder.set_kernel(*self.kernel_args)
mygridder.grid(self.xcoords, self.ycoords, self.signal3)
if False:
np.save('/tmp/cygrid_test_maps.npy', mygridder.get_datacube())
assert_allclose(mygridder.get_datacube(), self.test_maps, atol=1.e-6)
def test_c_contiguous(self):
'''
Cygrid should autocast to C-contiguous if necessary and raise
an error if user-provided datacube is not C-contiguous
'''
signal2_f_cont = np.require(self.signal2, self.signal2.dtype, 'F')
mygridder = cygrid.WcsGrid(self.header)
mygridder.set_kernel(*self.kernel_args)
mygridder.grid(self.xcoords, self.ycoords, signal2_f_cont)
assert_allclose(mygridder.get_datacube(),
self.test_maps[0],
atol=1.e-6)
dcube_f_cont = np.require(np.zeros_like(self.test_maps[0, 0]), 'F')
mygridder = cygrid.WcsGrid(self.header, datacube=dcube_f_cont)
mygridder.set_kernel(*self.kernel_args)
with pytest.raises(TypeError):
mygridder.grid(self.xcoords, self.ycoords, self.signal)
def test_dtype_warning(self):
'''
Test for dtype warning
In fact, at the moment there is only one possible warning, as
everything else should be properly casted, etc.
'''
dcube = np.zeros_like(self.test_maps[0, 0]) # float32
mygridder = cygrid.WcsGrid(self.header,
datacube=dcube,
dtype=np.float64)
mygridder.set_kernel(*self.kernel_args)
with pytest.warns(UserWarning):
mygridder.grid(self.xcoords, self.ycoords, self.signal)
def test_user_datacube_memorycell(self):
'''
If user provides a data cube, it must be made sure that cygrid
writes to the correct memory cell (even though, the
`get_unweighted_datacube` method can have a different object id
due to internal reshaping)
'''
dcube = np.zeros_like(self.test_maps[0, 0]) # float64
mygridder = cygrid.WcsGrid(self.header, datacube=dcube)
mygridder.set_kernel(*self.kernel_args)
mygridder.grid(self.xcoords, self.ycoords, self.signal)
assert_allclose(mygridder.get_datacube(),
self.test_maps[0, 0],
atol=1.e-6)
assert_allclose(mygridder.get_unweighted_datacube(), dcube, atol=1.e-6)
def test_byteorder_warning(self):
'''
Test for byteorder warning
Apparently astroquery.skyview can return wrong (non-native) byteorder.
'''
dcube = np.zeros_like(self.test_maps[0, 0]) # float32
mygridder = cygrid.WcsGrid(self.header,
datacube=dcube,
dtype=np.float64)
mygridder.set_kernel(*self.kernel_args)
signal_swapped = self.signal.byteswap().newbyteorder()
with pytest.warns(UserWarning):
mygridder.grid(self.xcoords, self.ycoords, signal_swapped)
def main():
mapcenter = (0., 90.)
mapsize = (5., 5.) # degrees
beamsize_fwhm = 0.1 # degrees
pixsize = beamsize_fwhm / 4.
dnaxis1 = int(mapsize[0] / pixsize)
dnaxis2 = int(mapsize[1] / pixsize)
# define target grid (via fits header according to WCS convention)
projection = 'ZEA'
header = {
'NAXIS': 3,
'NAXIS1': dnaxis1,
'NAXIS2': dnaxis2,
'NAXIS3': 1, # need dummy spectral axis
'CTYPE1': 'GLON-{}'.format(projection),
'CTYPE2': 'GLAT-{}'.format(projection),
'CUNIT1': 'deg',
'CUNIT2': 'deg',
'CDELT1': -pixsize,
'CDELT2': pixsize,
'CRPIX1': dnaxis1 / 2.,
'CRPIX2': dnaxis2 / 2.,
'CRVAL1': mapcenter[0],
'CRVAL2': mapcenter[1],
}
my_wcs = wcs.WCS(header, naxis=[1, 2])
xpix, ypix = np.meshgrid(np.linspace(0, dnaxis1, 6 * dnaxis1 + 3),
np.linspace(0, dnaxis2, 6 * dnaxis2 + 3))
xcoords, ycoords = my_wcs.all_pix2world(xpix, ypix, 0)
xcoords, ycoords = xcoords.flatten(), ycoords.flatten()
signal = astro_signal(xcoords, ycoords, beamsize_fwhm)
signal = signal[:, np.newaxis] # need dummy spectral axis
header = pf.Header(header.items())
mygridder = cygrid.WcsGrid(header, dbg_messages=True)
kernelsize_fwhm = beamsize_fwhm / 2.
kernelsize_sigma = kernelsize_fwhm / 2.35
# mygridder.set_kernel(
# 'gauss1d',
# kernelsize_sigma,
# kernelsize_sigma * 3,
# kernelsize_sigma / 2.
# )
mygridder.set_kernel(
'gauss2d',
(kernelsize_sigma * 10, kernelsize_sigma, np.radians(45.)),
kernelsize_sigma * 10 * 3, # major axis is important here
kernelsize_sigma / 2. # minor axis is important here
)
mygridder.grid(xcoords, ycoords, signal)
data = mygridder.get_datacube()
pf.writeto('cygrid_demo_zea_elliptical.fits',
header=header,
data=data,
clobber=True)
do_plot(header, data, 'cygrid_demo_zea_elliptical.pdf', showplot=False)
def test_kernel_not_set_error(self):
mygridder = cygrid.WcsGrid(self.header)
with pytest.raises(RuntimeError):
mygridder.grid(self.xcoords, self.ycoords, self.signal)
def cygriddata(filelist,
cacheSpectra=False,
pixPerBeam=3.5,
templateHeader=None,
gridFunction=gg.jincGrid,
startChannel=1024,
endChannel=3072,
doBaseline=True,
baselineRegion=None,
blorder=1,
rebase=None,
rebaseorder=None,
beamSize=None,
OnlineDoppler=True,
flagRMS=False,
flagRipple=False,
flagSpike=False,
rmsThresh=1.25,
spikeThresh=10,
projection='TAN',
outdir=None,
outname=None,
dtype='float64',
**kwargs):
"""Gridding code for GBT spectral scan data produced by pipeline using CyGrid
Parameters
----------
filelist : list
List of FITS files to be gridded into an output
Keywords
--------
pixPerBeam : float
Number of pixels per beam FWHM
templateHeader : `Header` object
Template header used for spatial pixel grid.
gridFunction : function
Gridding function to be used. The default `jincGrid` is a
tapered circular Bessel function. The function has call
signature of func(xPixelCentre, yPixelCenter, xData, yData,
pixPerBeam)
startChannel : int
Starting channel for spectrum within the original spectral data.
endChannel : int
End channel for spectrum within the original spectral data
doBaseline : bool
Setting to True (default) performs per-scan baseline corrections.
baselineRegion : `numpy.slice` or list of `numpy.slice`
Regions in the original pixel data used for fitting the baseline.
blorder : int
Order of baseline. Defaults to 1 (linear)
rebase : bool
Setting to True (default is False) performs per-pixel
rebaselining of the resulting cube.
beamSize : float
Telescope beam size at this frequency measured in degrees.
OnlineDopper : bool
Setting to True (default) assumes that the Doppler corrections
in the data are corrected during a telescope scan. Setting to
False assumes that the Doppler correction is updated at the
end of a scan and linearly interpolates between scan ends.
flagRMS : bool
Setting to True (default = False) flags spectra with rms
values >rmsThresh x higher than prediction from the radiometer
formula. This rms determination assumes that channels are not
strongly correlated
rmsThresh : float
Threshold for scan flagging based on rms. Default = 1.5
flagRipple : bool
Setting to True (default = False) flags spectra with structure
in the line that is 2x higher than the rms prediction of the
radiometer formula. Note that these estimators are outlier
robust.
flagSpike : bool
Setting to True (default = False) flags regions in spectra
that show jumps of > 5 times the typical pixel to pixel fluctuation.
outdir : str
Output directory name. Defaults to current working directory.
outname : str
Output directory file name. Defaults to object name in the
original spectra.
Returns
-------
None
"""
if outdir is None:
outdir = os.getcwd()
if baselineRegion is None:
baselineRegion = [slice(1024, 1536, 1), slice(2560, 3072, 1)]
if len(filelist) == 0:
warnings.warn('There are no FITS files to process ')
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
hdulist = fits.open(filelist[0])
s = hdulist[1].data
# Constants block
sqrt2 = np.sqrt(2)
mad2rms = 1.4826
prefac = mad2rms / sqrt2
c = 299792458.
nu0 = s[0]['RESTFREQ']
Data_Unit = s[0]['TUNIT7']
if outname is None:
outname = s[0]['OBJECT']
# New Beam size measurements use 1.18 vs. 1.22 based on GBT Memo 296.
if beamSize is None:
beamSize = 1.18 * (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
# We are forcing this conversion to make nice cubes.
w.wcs.specsys = 'LSRK'
w.wcs.ssysobs = 'TOPOCENT'
if templateHeader is None:
wcsdict = gg.autoHeader(filelist,
beamSize=beamSize,
pixPerBeam=pixPerBeam,
projection=projection)
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']
w.wcs.radesys = s[0]['RADESYS']
w.wcs.equinox = s[0]['EQUINOX']
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']
w.wcs.radesys = templateHeader['RADESYS']
w.wcs.equinox = templateHeader['EQUINOX']
pixPerBeam = np.abs(beamSize / w.pixel_scale_matrix[1, 1])
if pixPerBeam < 3.5:
warnings.warn('Template header requests {0}'.format(pixPerBeam) +
' pixels per beam.')
if (((w.wcs.ctype[0]).split('-'))[0] !=
((s[0]['CTYPE1']).split('-'))[0]):
warnings.warn('Spectral data not in same frame as template header')
eulerFlag = True
# outCube = np.zeros((int(naxis3), int(naxis2), int(naxis1)),dtype=dtype)
# outWts = np.zeros((int(naxis2), int(naxis1)),dtype=dtype)
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
speclist = []
lonlist = []
latlist = []
for thisfile in filelist:
ctr += 1
cachefile = thisfile.replace('.fits', '_speccache.npz')
if cacheSpectra and os.path.isfile(cachefile):
npzfile = np.load(cachefile)
speclist += npzfile['speclist'].tolist()
lonlist += npzfile['lonlist'].tolist()
latlist += npzfile['latlist'].tolist()
else:
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]))
if not OnlineDoppler:
vframe = gg.VframeInterpolator(s[1].data)
else:
vframe = s[1].data['VFRAME']
flagct = 0
if eulerFlag:
if 'GLON' in s[1].data['CTYPE2'][0]:
inframe = 'galactic'
elif 'RA' in s[1].data['CTYPE2'][0]:
inframe = 'fk5'
else:
raise NotImplementedError
if 'GLON' in w.wcs.ctype[0]:
outframe = 'galactic'
elif 'RA' in w.wcs.ctype[0]:
outframe = 'fk5'
else:
raise NotImplementedError
coords = SkyCoord(s[1].data['CRVAL2'],
s[1].data['CRVAL3'],
unit=(u.deg, u.deg),
frame=inframe)
coords_xform = coords.transform_to(outframe)
if outframe == 'fk5':
longCoord = coords_xform.ra.deg
latCoord = coords_xform.dec.deg
elif outframe == 'galactic':
longCoord = coords_xform.l.deg
latCoord = coords_xform.b.deg
else:
longCoord = s[1].data['CRVAL2'],
latCoord = s[1].data['CRVAL3']
lonlist += [longCoord]
latlist += [latCoord]
for idx, spectrum in enumerate(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 = gg.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 = gg.freqShiftValue(spectrum['CRVAL1'],
-vframe[idx]) - crval3
DeltaChan = DeltaNu / cdelt3
specData = gg.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(longCoord[idx],
# latCoord[idx],
# spectrum['CRVAL1'], 0)
tsys = spectrum['TSYS']
if flagSpike:
jumps = (outslice - np.roll(outslice, -1))
noise = gg.mad1d(jumps) * 2**(-0.5)
spikemask = (np.abs(jumps) < spikeThresh * noise)
spikemask = spikemask * np.roll(spikemask, 1)
spectrum_wt *= spikemask
if flagRMS:
radiometer_rms = tsys / np.sqrt(
np.abs(spectrum['CDELT1']) * spectrum['EXPOSURE'])
scan_rms = prefac * np.median(
np.abs(outslice[0:-2] - outslice[2:]))
if scan_rms > rmsThresh * radiometer_rms:
tsys = 0 # Blank spectrum
if flagRipple:
scan_rms = prefac * np.median(
np.abs(outslice[0:-2] - outslice[2:]))
ripple = prefac * sqrt2 * np.median(np.abs(outslice))
if ripple > 2 * scan_rms:
tsys = 0 # Blank spectrum
if tsys == 0:
flagct += 1
speclist += [outslice]
# if (tsys > 10) and (xpoints > 0) and (xpoints < naxis1) \
# and (ypoints > 0) and (ypoints < naxis2):
# pixelWeight, Index = gridFunction(xmat, ymat,
# xpoints, ypoints,
# 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
print("Percentage of flagged scans: {0:4.2f}".format(100 * flagct /
float(idx)))
# Temporarily do a file write for every batch of scans.
if cacheSpectra:
np.savez(thisfile.replace('.fits', '_speccache.npz'),
lonlist=lonlist,
latlist=latlist,
speclist=speclist)
try:
lonlist = np.squeeze(np.stack(lonlist))
latlist = np.squeeze(np.stack(latlist))
speclist = np.squeeze(np.stack(speclist))
except ValueError:
lonlist = np.squeeze(np.hstack(lonlist))
latlist = np.squeeze(np.hstack(latlist))
speclist = np.squeeze(np.stack(speclist))
# DO THE GRIDDING
hdr = w.to_header()
hdr['NAXIS1'] = naxis1
hdr['NAXIS2'] = naxis2
hdr['NAXIS3'] = 10
gridder = cygrid.WcsGrid(hdr)
gridder.set_kernel('gauss1d', (beamSize / 2.355 / 2),
2 * (beamSize / 2.355), beamSize / 2 / 2.355)
gridder.grid(lonlist, latlist, speclist, dtype=dtype)
hdr = fits.Header(w.to_header())
s = fits.open(thisfile)
hdr = gg.addHeader_nonStd(hdr, beamSize, s[1].data[0])
hdr.add_history('Using GBTPIPE gridder version {0}'.format(__version__))
hdu = fits.PrimaryHDU(gridder.get_datacube(), header=hdr)
hdu.writeto(outdir + '/' + outname + '.fits', clobber=True)
# outWts.shape = (1,) + outWts.shape
# outCube /= outWts
# hdu = fits.PrimaryHDU(outCube, header=hdr)
# w2 = w.dropaxis(2)
# hdr2 = fits.Header(w2.to_header())
# hdu2 = fits.PrimaryHDU(outWts, header=hdr2)
# hdu2.writeto(outdir + '/' + outname + '_wts.fits', clobber=True)
if rebase:
if rebaseorder is None:
rebaseorder = blorder
if 'NH3_11' in outname:
Baseline.rebaseline(outdir + '/' + outname + '.fits',
windowFunction=Baseline.ammoniaWindow,
line='oneone',
blorder=rebaseorder,
**kwargs)
elif 'NH3_22' in outname:
Baseline.rebaseline(outdir + '/' + outname + '.fits',
windowFunction=Baseline.ammoniaWindow,
line='twotwo',
blorder=rebaseorder,
**kwargs)
elif 'NH3_33' in outname:
Baseline.rebaseline(outdir + '/' + outname + '.fits',
winfunc=Baseline.ammoniaWindow,
blorder=rebaseorder,
line='threethree',
**kwargs)
else:
Baseline.rebaseline(outdir + '/' + outname + '.fits',
blorder=rebaseorder,
windowFunction=Baseline.tightWindow,
**kwargs)