def test_append_filehandle(self, tmpdir, mode):
"""
Test fits.append with a file handle argument.
"""
append_file = tmpdir.join('append.fits')
with append_file.open(mode) as handle:
fits.append(filename=handle, data=np.ones((4, 4)))
def export_to_fits(self, fitsfile='ModelSceneCube.fits'):
"""
Write model cube to a FITS file
"""
header = self.grid.wcs_info()
fits.writeto(fitsfile, np.rollaxis(self.int, 2), header, clobber=True)
fits.append(fitsfile, self.wave)
def export_to_fits(self, fitsfile='ModelDetectorCube'):
header = self.wcs_info()
slice_index = 0
for flux_plus_bg in self.flux_plus_bg_list:
fitsfile_slice = fitsfile + str(slice_index).strip() + '.fits'
fits.writeto(fitsfile_slice, np.rollaxis(flux_plus_bg, 2), header, clobber=True)
fits.append(fitsfile_slice, self.wave)
def save_reduced_data(input_file,sp,unc,wave=None):
print 'Saving extraction as %s'%(os.path.splitext(input_file)[0]+'_reduced.fits')
#load up file to grab header to append reduction information to
hdulist=loadfits(input_file)
head=hdulist[0].header
head['ORDERS'] = (sp.shape[1], 'Number of orders reduced')
#append header field 'how many orders',len(ord)
head['REDUTIME'] = (strftime("%c"), 'When reduced')
#append header field 'when reduced', time.strftime("%c")
head['comment'] = 'data saved as (ext,unc,wave) for each order'
if wave==None:
wave=np.arange(sp.shape[0])
data=[[]]*(sp.shape[1]+1)
for i in np.arange(sp.shape[1]):
data=np.vstack((sp[:,i],unc[:,i],wave[i,:][::-1]))
if i==0:
head['ORDER']=((i+1),'Order number')
pyfits.writeto(os.path.splitext(input_file)[0]+'_reduced.fits', data,head, clobber=True)
else:
head['ORDER']=((i+1),'Order number')
pyfits.append(os.path.splitext(input_file)[0]+'_reduced.fits', data,head)
#save file as original file + _reduced
#ie. if aug008811.fits was the file - this becomes
#aug008811_reduced.npy
hdulist.close()
def append_extension(filename, array):
"""Appends an extension to fits file.
"""
fits.append(filename, array)
print "\nFits extension appended"
def add_checksum(self):
"""Add checksums to `filepath`."""
output = "crds-" + str(uuid.uuid4()) + ".fits"
with fits_open(self.filepath, do_not_scale_image_data=True) as hdus:
for hdu in hdus:
fits.append(output, hdu.data, hdu.header, checksum=True)
os.remove(self.filepath)
os.rename(output, self.filepath)
def export_fits_prisim(self,fitsfile,pol_list,freq_list,scheme='RING',nside_out=None):
'''
export fits-file at channel chan and polarization pol
Args:
fitsfile, str, name of file to save .fits to
pol_list, list of labels of polarizations to write
chan_list, list of frequencies to write
'''
if nside_out is None:
nside_out=self.nside
pol_list=n.array(pol_list)
freq_list=n.array(freq_list)
pol_inds=[]
freq_inds=[]
for pol in pol_list:
assert pol in self.pols
pol_inds.append(n.where(n.array(self.pols)==pol)[0][0])
for freq in freq_list:
assert freq in self.fAxis
freq_inds.append(n.where(n.array(self.fAxis)==freq)[0][0])
data=self.data[:,freq_inds,:].reshape(-1,1)
theta_out,phi_out=hp.pix2ang(nside_out,n.arange(hp.nside2npix(nside_out)))
#freq_col=[fits.Column(name='Frequency [MHz]',format='D',array=n.array(freq_list))]
#freq_columns=fits.ColDefs(freq_col,ascii=False)
#freq_tbhdu = fits.BinTableHDU.from_columns(freq_col)
#freq_tbhdu = fits.BinTableHDU.from_columns(n.array(freq_list))
hduprimary=fits.PrimaryHDU()
hduprimary.header.set('EXTNAME','PRIMARY')
hduprimary.header.set('NEXTEN',2)
hduprimary.header.set('FITSTYPE','IMAGE')
hduprimary.header['NSIDE']=(nside_out,'NSIDE')
hduprimary.header['PIXAREA']=(hp.nside2pixarea(nside_out),'pixel solid angle (steradians)')
hduprimary.header['NEXTEN']=(2,'Number of extensions')
hduprimary.header['NPOL'] = (len(pol_inds), 'Number of polarizations')
hduprimary.header['SOURCE'] = ('HERA-CST', 'Source of data')
hdulist=[hduprimary]
fits.HDUList(hdulist).writeto(fitsfile,clobber=True)
for pol in pol_list:
#freq_tbhdu.header.set('EXTNAME','FREQS_{0}'.format(pol))
freq_tbhdu=fits.ImageHDU(freq_list,name='FREQS_{0}'.format(pol))
fits.append(fitsfile,freq_tbhdu.data,freq_tbhdu.header,verify=False)
data_interp=n.zeros((hp.nside2npix(nside_out),len(freq_inds)))
for polind,pol in zip(pol_inds,pol_list):
for fi,freqind in enumerate(freq_inds):
data=self.data[polind,freqind,:].flatten()
data_interp[:,fi]=hp.get_interp_val(data,theta_out,phi_out)
#if DEBUG:
# hp.mollview(data_interp[:,fi])
# plt.show()
imghdu = fits.ImageHDU(data_interp, name='BEAM_{0}'.format(pol))
imghdu.header['PIXTYPE'] = ('HEALPIX', 'Type of pixelization')
imghdu.header['ORDERING'] = (scheme, 'Pixel ordering scheme, either RING or NESTED')
imghdu.header['NSIDE'] = (nside_out, 'NSIDE parameter of HEALPIX')
imghdu.header['NPIX'] = (hp.nside2npix(nside_out), 'Number of HEALPIX pixels')
imghdu.header['FIRSTPIX'] = (0, 'First pixel # (0 based)')
imghdu.header['LASTPIX'] = (len(data_interp)-1, 'Last pixel # (0 based)')
fits.append(fitsfile,imghdu.data,imghdu.header,verify=False)
def remove_checksum(self):
"""Remove checksums from `filepath`."""
output = "crds-" + str(uuid.uuid4()) + ".fits"
with fits_open(self.filepath, checksum=False, do_not_scale_image_data=True) as hdus:
for hdu in hdus:
hdu.header.pop("CHECKSUM",None)
hdu.header.pop("DATASUM", None)
fits.append(output, hdu.data, hdu.header, checksum=False)
os.remove(self.filepath)
os.rename(output, self.filepath)
def writeFits(self, filename):
"""Write to FITS file
Parameters
----------
filename : `str`
Name of file to which to write.
"""
fits = astropy.io.fits.HDUList()
fits.append(astropy.io.fits.ImageHDU(self.vector))
with open(filename, "w") as fd:
fits.writeto(fd)
def write_hduL(fitsfn,hduL):
# If file doesn't exist, add the primary header
hdu_primary = hduL[0]
if os.path.exists(fitsfn) is False:
fits.append(fitsfn, hdu_primary.data, header=hdu_primary.header)
hduL = hduL[1:]
for hdu in hduL:
data = hdu.data
extname = hdu.header['EXTNAME']
header = hdu.header
try:
fits.update(fitsfn, data, extname, header=header)
except KeyError:
fits.append(fitsfn, data, header=header)
def _writeImpl(self, fits):
"""Implementation for writing to FITS file
Parameters
----------
fits : `astropy.io.fits.HDUList`
List of FITS HDUs. This has a Primary HDU already, the header of
which may be supplemented with additional keywords.
"""
from astropy.io.fits import BinTableHDU, Column
fits.append(BinTableHDU.from_columns([
Column("wavelength", "D", array=self.wavelength),
Column("flux", "D", array=self.flux),
Column("mask", "K", array=self.mask),
], header=astropyHeaderFromDict(self.flags.toFitsHeader()), name="FLUXTBL"))
self.target.toFits(fits)
def writeFits(self, filename):
"""Write to FITS file
This API is intended for use by the LSST data butler, which handles
translating the desired identity into a filename.
Parameters
----------
filename : `str`
Filename of FITS file.
"""
from astropy.io.fits import HDUList, PrimaryHDU
fits = HDUList()
fits.append(PrimaryHDU())
self._writeImpl(fits)
with open(filename, "w") as fd:
fits.writeto(fd)
def removerows(gal):
d = "/Data/vimos/cubes/"
f = glob.glob(d + gal + ".cube.combined.corr.fits")
p = pyfits.open(f[0])
data = p[0].data
header = p[0].header
data_new = data[:,0:40,0:40]
pyfits.writeto(d+gal+".cube.combined.corr.fits", data_new, header=header, clobber=True)
for ex in range(1, len(p)):
data_ex = p[ex].data
header_ex = p[ex].header
data_ex_new = data_ex[:,0:40,0:40]
pyfits.append(d+gal+".cube.combined.corr.fits",data_ex_new,header=header_ex)
p.close()
def do_analysis(i=0,n_ps_groupi=0,psloop1=False,pscomball=False,psloop2=False,minuit_new=False):
global emin,emax, eachps_dict, eachps_En_center
if method=='polychord':
polychord=True
else:
polychord=False
b.run_tag = run_tag_energy
tri = fa.make_triangle(b,run_tag_energy,edep=True,polychord=polychord,minuit_new=minuit_new)
tri.make_triangle()
if not minuit_new:
sle = fa.save_log_evidence(b,edep=True,polychord=polychord)
spect_dir = work_dir + 'data/spect/'
if not os.path.exists(spect_dir):
os.mkdir(spect_dir)
cs = fa.compute_spectra(b,run_tag_energy,f.CTB_en_bins[0],f.CTB_en_bins[-1],edep=True,plane_mask=plot_plane_mask,band_mask_range = [-plot_pmval,plot_pmval],lcut=plot_lcut,lmin=plot_lmin,lmax=plot_lmax,bcut=plot_bcut,bmin=plot_bmin,bmax=plot_bmax,mask_ring=plot_mask_ring,outer=plot_outer,inner=plot_inner,minuit_new = minuit_new,input_mask=force_ps_mask,the_input_mask=b.mask_total) # spectra over the whole energy range
cs.mask_total_dict['bubs']=np.logical_not(b.templates_dict_nested['bubs']['summed_templates_not_compressed'])
eachps_En_center = cs.En_center
if psloop1 or pscomball:
cs.make_norm_dict()
if psloop2 or pscomball:
cs.make_spectra_dict()
if pscomball:
cs.save_spectra_dict(spect_dir + save_spect_label,emin,emax,over_write= False)
cs.save_norm_dict(spect_dir + save_norm_label,emin,emax,over_write= False)
if psloop1:
# Create pslooptemp and psalltemp
pslooptempar = np.zeros(hp.nside2npix(nside))
if os.path.exists(ps_temp_dir + pslooptemp):
pslooptempar += fits.open(ps_temp_dir + pslooptemp)[0].data
for j in range(n_ps_groupi):
pstempj = b.templates_dict['ps_' + str(i*n_ps_run+j+1) + '-0'][0]
psnormj = cs.norm_dict['ps_' + str(i*n_ps_run+j+1) + '-0']
pswritej = pstempj*psnormj
pslooptempar += pswritej
fits.append(ps_temp_dir + psalltemp, pswritej)
fits.writeto(ps_temp_dir + pslooptemp,pslooptempar,clobber=True)
# Add norms to eachps_dict dictionary
if psloop2:
eachps_dict['ps_' + str(i+1)] = cs.spectra_dict['ps_' + str(i+1) + '-0']
def createVoronoiOutput(inputFile=datadir+cuberoot+'.fits',inputVoronoiFile=datadir+'voronoi_2d_binning_output.txt'):
cubefits = pyfits.open(inputFile)
cube = cubefits[0].data
hdr = cubefits[0].header
errors = cubefits[1].data
quality = cubefits[2].data
nframes = cubefits[3].data
cubeShape = (cube.shape[0],cube.shape[1],cube.shape[2])
yy, xx, binnum = np.loadtxt(inputVoronoiFile,unpack=True)
xx = xx.astype(int)
yy = yy.astype(int)
binnum = binnum.astype(int)
newCube = np.zeros(cubeShape, dtype=float)
newErr = np.zeros(cubeShape, dtype=float)
for nb in range(binnum.max()+1):
idx = np.where(binnum == nb)
nx = xx[idx]
ny = yy[idx]
nbins = len(idx[0])
tmpCube = np.sum(cube[nx,ny,:],axis=0)/nbins
tmpErr = np.sqrt(np.sum(errors[nx,ny,:]**2,axis=0))/nbins
newCube[nx,ny,:] = tmpCube
newErr[nx,ny,:] = tmpErr
#pdb.set_trace()
outfile = inputFile.replace('.fits','_vorcube.fits')
pyfits.writeto(outfile,newCube,header=hdr)
pyfits.append(outfile,newErr)
pyfits.append(outfile,quality)
pyfits.append(outfile,nframes)
def gen_superdark(inlist, fname='./Superdark.fits'):
'''
Generate a median image from a list of input image files.
The purpose of this script is to generate a "superdark";
a median dark multi-frame image to mimic the noise present
in NIRSpec-read images.
The median (average) calculation is done across the 3-frame
images expected from NIRSpec, and is more accurate as more
images are used.
Keyword arguments:
inlist -- The list of image files to be used for generating
the median image.
fname -- The name of the generated meadian image. Defaults
to 'Superdark'.
'''
stacked_darks = 0
# Read in the multiframe images and create a stack
for ii in xrange(len(inlist)):
fileBase = path.basename(inlist[ii])
print('(gen_superdark): Reading/processing {} ...'.format(fileBase))
stacked_darks = stacked_darks + fits.getdata(inlist[ii], 0)
# Create a superdark frame initiazed with zeros
superdark_frame = stacked_darks / len(inlist)
# Save the above information to a FITS file for later use
hdu = fits.PrimaryHDU()
print('(gen_superdark): Writing {} to file ...'.format(fname))
hdu.header.append('FILENAME', fname, '')
hdu.writeto(fname, clobber=True)
fits.append(fname, superdark_frame)
return superdark_frame
def save_filter(self, filename, clobber=False):
"""Save filter to file"""
hdu = fits.PrimaryHDU(self.filter, self.header)
hdu.writeto(filename, clobber=clobber)
fits.append(filename, self.approx, self.header)
fits.append(filename, self.filter + self.approx, self.header)
fits.append(filename, self.max_scale_image(), self.header)
def write_imgspec(flux, wave, loglam, objtype):
hdr = dict(FLUXUNIT='erg/s/cm^2/A')
if wave is None:
if loglam:
hdr['LOGLAM'] = loglam
hdr['CRVAL1'] = np.log10(wave1D[0])
hdr['CDELT1'] = np.log10(1+dwave/wave1D[0])
else:
if loglam is not None:
hdr['LOGLAM'] = loglam
hdr['CRVAL1'] = wave1D[0]
hdr['CDELT1'] = dwave
if type(objtype) == str:
hdr['OBJTYPE'] = objtype
filename = get_next_filename()
fits.writeto(filename, flux, header=hdr, clobber=True)
if wave is not None:
if loglam:
fits.append(filename, wave, extname='LOGLAM')
else:
fits.append(filename, wave, extname='WAVELENGTH')
if type(objtype) != str:
fits.append(filename, objtype, extname='TARGETINFO')
return filename
def writeFits(self, filename):
"""Write to FITS file
This API is intended for use by the LSST data butler, which handles
translating the desired identity into a filename.
Parameters
----------
filename : `str`
Filename of FITS file.
"""
self.validate()
import astropy.io.fits
fits = astropy.io.fits.HDUList()
header = self.metadata.copy()
header.update(self.flags.toFitsHeader())
fits.append(astropy.io.fits.PrimaryHDU(header=astropyHeaderFromDict(header)))
for attr in ("fiberId", "wavelength", "flux", "mask", "sky", "covar"):
hduName = attr.upper()
data = getattr(self, attr)
fits.append(astropy.io.fits.ImageHDU(data, name=hduName))
with open(filename, "w") as fd:
fits.writeto(fd)
def _writeImpl(self, fits):
"""Implementation for writing to FITS file
Parameters
----------
fits : `astropy.io.fits.HDUList`
List of FITS HDUs. This has a Primary HDU already, the header of
which may be supplemented with additional keywords.
"""
from astropy.io.fits import ImageHDU
super()._writeImpl(fits)
fits.append(ImageHDU(self.sky, name="SKY"))
self.observations.toFits(fits)
fits.append(ImageHDU(self.covar, name="COVAR"))
fits.append(ImageHDU(self.covar2, name="COVAR2"))
def write_flux_calibration(outfile, fluxcalib, header=None):
"""Writes flux calibration.
"""
hdr = fitsheader(header)
hdr['EXTNAME'] = ('FLUXCALIB', 'CHECK UNIT')
fits.writeto(outfile,fluxcalib.calib,header=hdr, clobber=True)
hdr['EXTNAME'] = ('IVAR', 'CHECK UNIT')
hdu = fits.ImageHDU(fluxcalib.ivar, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
hdr['EXTNAME'] = ('MASK', 'no dimension')
hdu = fits.ImageHDU(fluxcalib.mask, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
hdr['EXTNAME'] = ('WAVELENGTH', '[Angstroms]')
hdu = fits.ImageHDU(fluxcalib.wave, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
def test_append_filename(self):
"""
Test fits.append with a filename argument.
"""
data = np.arange(6)
testfile = self.temp('test_append_1.fits')
# Test case 1: creation of file
fits.append(testfile, data=data, checksum=True)
# Test case 2: append to existing file, with verify=True
# Also test that additional keyword can be passed to fitsopen
fits.append(testfile, data=data * 2, checksum=True, ignore_blank=True)
# Test case 3: append to existing file, with verify=False
fits.append(testfile, data=data * 3, checksum=True, verify=False)
with fits.open(testfile, checksum=True) as hdu1:
np.testing.assert_array_equal(hdu1[0].data, data)
np.testing.assert_array_equal(hdu1[1].data, data * 2)
np.testing.assert_array_equal(hdu1[2].data, data * 3)
def write_sky(outfile, skymodel, header=None):
"""Write sky model.
Args:
outfile : filename or (night, expid, camera) tuple
skymodel : SkyModel object, with the following attributes
wave : 1D wavelength in vacuum Angstroms
flux : 2D[nspec, nwave] sky flux
ivar : 2D inverse variance of sky flux
mask : 2D mask for sky flux
header : optional fits header data (fits.Header, dict, or list)
"""
outfile = makepath(outfile, 'sky')
#- Convert header to fits.Header if needed
if header is not None:
hdr = fitsheader(header)
else:
hdr = fitsheader(skymodel.header)
hdr['EXTNAME'] = ('SKY', 'no dimension')
fits.writeto(outfile, skymodel.flux,header=hdr, clobber=True)
hdr['EXTNAME'] = ('IVAR', 'no dimension')
hdu = fits.ImageHDU(skymodel.ivar, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
hdr['EXTNAME'] = ('MASK', 'no dimension')
hdu = fits.ImageHDU(skymodel.mask, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
hdr['EXTNAME'] = ('WAVELENGTH', '[Angstroms]')
hdu = fits.ImageHDU(skymodel.wave, header=hdr)
fits.append(outfile, hdu.data, header=hdu.header)
return outfile
### STITCH ALL THE ORDERS TOGETHER
wls, fluxes, sns = stitch(wlsol, spec, snr, cutoverlap='yes')
#step 4: save to a fits file
#write the primary data, and fill out the header
hdu = pyfits.PrimaryHDU()
hdu.writeto(filename_out, clobber=True)
#copy the target header
header = dataheader
header["EXTNAME"] = 'SPEC_STITCHED'
header.add_comment("This spectrum was created by combining the orders")
pyfits.update(filename_out, fluxes, header)
#add the rest of the extensions
header["EXTNAME"] = "WAVELENGTH"
pyfits.append(filename_out, wls, header)
###This one is new!
header["EXTNAME"] = "SNR"
pyfits.append(filename_out, sns, header)
print '*** File out ***'
print 'The divided spectra is being saved to ', filename_out
#step 5: plot
uncs = sns**-1
uncs_units = uncs * fluxes
plt.errorbar(wls, fluxes, yerr=uncs_units, marker='s')
plt.xlabel('Wavelength $\AA$')
plt.ylabel('Flux')
plt.ylim([-1.e6, 1.e6])
plt.xlim([19000, 25000])
def ex2d_patch(image, ivar, psf, specmin, nspec, wavelengths, xyrange=None,
full_output=False, regularize=0.0, ndecorr=False):
"""
2D PSF extraction of flux from image patch given pixel inverse variance.
Inputs:
image : 2D array of pixels
ivar : 2D array of inverse variance for the image
psf : PSF object
specmin : index of first spectrum to extract
nspec : number of spectra to extract
wavelengths : 1D array of wavelengths to extract
Optional Inputs:
xyrange = (xmin, xmax, ymin, ymax): treat image as a subimage
cutout of this region from the full image
full_output : if True, return a dictionary of outputs including
intermediate outputs such as the projection matrix.
ndecorr : if True, decorrelate the noise between fibers, at the
cost of residual signal correlations between fibers.
Returns (flux, ivar, R):
flux[nspec, nwave] = extracted resolution convolved flux
ivar[nspec, nwave] = inverse variance of flux
R : 2D resolution matrix to convert
"""
#- Range of image to consider
waverange = (wavelengths[0], wavelengths[-1])
specrange = (specmin, specmin+nspec)
if xyrange is None:
xmin, xmax, ymin, ymax = xyrange = psf.xyrange(specrange, waverange)
image = image[ymin:ymax, xmin:xmax]
ivar = ivar[ymin:ymax, xmin:xmax]
else:
xmin, xmax, ymin, ymax = xyrange
nx, ny = xmax-xmin, ymax-ymin
npix = nx*ny
nspec = specrange[1] - specrange[0]
nwave = len(wavelengths)
#- Solve AT W pix = (AT W A) flux
#- Projection matrix and inverse covariance
A = psf.projection_matrix(specrange, wavelengths, xyrange)
#- Pixel weights matrix
w = ivar.ravel()
W = spdiags(ivar.ravel(), 0, npix, npix)
#-----
#- Extend A with an optional regularization term to limit ringing.
#- If any flux bins don't contribute to these pixels,
#- also use this term to constrain those flux bins to 0.
#- Original: exclude flux bins with 0 pixels contributing
# ibad = (A.sum(axis=0).A == 0)[0]
#- Identify fluxes with very low weights of pixels contributing
fluxweight = W.dot(A).sum(axis=0).A[0]
minweight = 0.01*np.max(fluxweight)
ibad = fluxweight < minweight
#- Original version; doesn't work on older versions of scipy
# I = regularize*scipy.sparse.identity(nspec*nwave)
# I.data[0,ibad] = minweight - fluxweight[ibad]
#- Add regularization of low weight fluxes
Idiag = regularize*np.ones(nspec*nwave)
Idiag[ibad] = minweight - fluxweight[ibad]
I = scipy.sparse.identity(nspec*nwave)
I.setdiag(Idiag)
#- Only need to extend A if regularization is non-zero
if np.any(I.diagonal()):
pix = np.concatenate( (image.ravel(), np.zeros(nspec*nwave)) )
Ax = scipy.sparse.vstack( (A, I) )
wx = np.concatenate( (w, np.ones(nspec*nwave)) )
else:
pix = image.ravel()
Ax = A
wx = w
#- Inverse covariance
Wx = spdiags(wx, 0, len(wx), len(wx))
iCov = Ax.T.dot(Wx.dot(Ax))
#- Solve (image = A flux) weighted by Wx:
#- A^T W image = (A^T W A) flux = iCov flux
y = Ax.T.dot(Wx.dot(pix))
xflux = spsolve(iCov, y).reshape((nspec, nwave))
#- Solve for Resolution matrix
try:
if ndecorr:
R, fluxivar = resolution_from_icov(iCov)
else:
R, fluxivar = resolution_from_icov(iCov, decorr=[nwave for x in range(nspec)])
except np.linalg.linalg.LinAlgError, err:
outfile = 'LinAlgError_{}-{}_{}-{}.fits'.format(specrange[0], specrange[1], waverange[0], waverange[1])
print("ERROR: Linear Algebra didn't converge")
print("Dumping {} for debugging".format(outfile))
from astropy.io import fits
fits.writeto(outfile, image, clobber=True)
fits.append(outfile, ivar, name='IVAR')
fits.append(outfile, A.data, name='ADATA')
fits.append(outfile, A.indices, name='AINDICES')
fits.append(outfile, A.indptr, name='AINDPTR')
fits.append(outfile, iCov.toarray(), name='ICOV')
raise err
# Now, we construct an object that describes the data region and structure we
# want
cube = pf.h.covering_grid(int(level), # The level we are willing to extract to; higher
# levels than this will not contribute to the data!
# Now we set our spatial extent...
left_edge=[0.0, 0.0, 0.0],
right_edge=[1.0, 1.0, 1.0],
# How many dimensions along each axis
dims=DIMS,
# And any fields to preload (this is optional!)
fields=["Density"])
FlatFileName = tempdir+'/%s_flatrho_%04i.fits' %(name, num)
pyfits.writeto(FlatFileName, cube["Density"])
pyfits.append(FlatFileName, cube["x-velocity"])
pyfits.append(FlatFileName, cube["y-velocity"])
pyfits.append(FlatFileName, cube["z-velocity"])
#arg = 'caleb_flatrho_0025.fits/1/10'
#
subprocess.call('cp '+ppdir+'/dustkappa_silicate.inp '+tempdir)
subprocess.call('cp '+ppdir+'/molecule_13co.inp '+tempdir)
subprocess.call('cp '+ppdir+'/camera_wavelength_micron.inp '+tempdir)
Problem_setup(FlatFileName, face = face, dust_temp = 10.0)
command = ppdir+'radmc3d image npix '+str(DIMS[0])+' iline 1 widthkms 10 linenlam 500 loadlambda fluxcons inclline linelist nostar writepop doppcatch sizepc 10'
subprocess.call(command)
makefits()
#------------------------------------------------------------------------
# Open the input event file
hdu = fits.open(args.infile)
# HDU[0] is dummy, 1-4 are quadrants
# Create output file. Exit if it already exists
fits.writeto(args.outfile, hdu[0].data, hdu[0].header)
if args.verbose:
print("Wrote HDU 0")
for quad in np.arange(noe):
# Note that the output file needs quadrants from 0-3, but HDU extensions are 1-4
# Also process extension 5, which has veto spectrum
if args.verbose:
print("Processing quadrant {quad}/4 ".format(quad=quad + 1)),
data = hdu[quad + 1].data
if hdu[quad + 1].header['naxis2'] > 0:
timestamps = data['Time']
tmin = max([np.floor(min(timestamps)), args.tmin])
tmax = min([np.floor(max(timestamps)), args.tmax])
if args.verbose: print(tmin, tmax, args.tmin, args.tmax)
if args.verbose: sys.stdout.flush()
select = np.where((hdu[quad + 1].data['Time'] >= tmin)
& (hdu[quad + 1].data['Time'] <= tmax))
data = hdu[quad + 1].data[select]
fits.append(args.outfile, data,
header=hdu[quad + 1].header) #, verify=False)
#for ext in range(6, len(hdu)):
#fits.append(args.outfile, hdu[ext].data, hdu[ext].header)
def process_image(imfn,
ivarfn,
dqfn,
outfn=None,
clobber=False,
outdir=None,
verbose=False,
nproc=numpy.inf,
resume=False,
outmodelfn=None,
profile=False):
if profile:
import cProfile
import pstats
pr = cProfile.Profile()
pr.enable()
with fits.open(imfn) as hdulist:
extnames = [hdu.name for hdu in hdulist]
if 'PRIMARY' not in extnames:
raise ValueError('No PRIMARY header in file')
prihdr = fits.getheader(imfn, extname='PRIMARY')
if 'CENTRA' in prihdr:
bstarfn = os.path.join(os.environ['DECAM_DIR'], 'data',
'tyc2brighttrim.fits')
brightstars = fits.getdata(bstarfn)
from astropy.coordinates.angle_utilities import angular_separation
sep = angular_separation(numpy.radians(brightstars['ra']),
numpy.radians(brightstars['dec']),
numpy.radians(prihdr['CENTRA']),
numpy.radians(prihdr['CENTDEC']))
sep = numpy.degrees(sep)
m = sep < 3
brightstars = brightstars[m]
dmjd = prihdr['MJD-OBS'] - 51544.5 # J2000 MJD.
cosd = numpy.cos(
numpy.radians(numpy.clip(brightstars['dec'], -89.9999, 89.9999)))
brightstars['ra'] += dmjd * brightstars[
'pmra'] / 365.25 / cosd / 1000 / 60 / 60
brightstars[
'dec'] += dmjd * brightstars['pmde'] / 365.25 / 1000 / 60 / 60
else:
brightstars = None
filt = prihdr['filter']
if outfn is None or len(outfn) == 0:
outfn = os.path.splitext(os.path.basename(imfn))[0]
if outfn[-5:] == '.fits':
outfn = outfn[:-5]
outfn = outfn + '.cat.fits'
if outdir is not None:
outfn = os.path.join(outdir, outfn)
if not resume or not os.path.exists(outfn):
fits.writeto(outfn, None, prihdr, clobber=clobber)
extnamesdone = None
else:
hdulist = fits.open(outfn)
extnamesdone = []
for hdu in hdulist:
if hdu.name == 'PRIMARY':
continue
ext, exttype = hdu.name.split('_')
if exttype != 'CAT':
continue
extnamesdone.append(ext)
hdulist.close()
if outmodelfn and (not resume or not os.path.exists(outmodelfn)):
fits.writeto(outmodelfn, None, prihdr, clobber=clobber)
count = 0
fwhms = []
for name in extnames:
if name is 'PRIMARY':
continue
hdr = fits.getheader(imfn, extname=name)
if 'FWHM' in hdr:
fwhms.append(hdr['FWHM'])
fwhms = numpy.array(fwhms)
fwhms = fwhms[fwhms > 0]
for name in extnames:
if name is 'PRIMARY':
continue
if extnamesdone is not None and name in extnamesdone:
print('Skipping %s, extension %s; already done.' % (imfn, name))
continue
if verbose:
print('Fitting %s, extension %s.' % (imfn, name))
sys.stdout.flush()
im, wt, dq = read_data(imfn, ivarfn, dqfn, name)
hdr = fits.getheader(imfn, extname=name)
fwhm = hdr.get('FWHM', numpy.median(fwhms))
if fwhm <= 0.:
fwhm = 4.
fwhmmn, fwhmsd = numpy.mean(fwhms), numpy.std(fwhms)
if fwhmsd > 0.4:
fwhm = fwhmmn
psf = decam_psf(filt[0], fwhm)
wcs0 = wcs.WCS(hdr)
if brightstars is not None:
sep = angular_separation(numpy.radians(brightstars['ra']),
numpy.radians(brightstars['dec']),
numpy.radians(hdr['CENRA1']),
numpy.radians(hdr['CENDEC1']))
sep = numpy.degrees(sep)
m = sep < 0.2
# CCD is 4094 pix wide => everything is at most 0.15 deg
# from center
if numpy.any(m):
yb, xb = wcs0.all_world2pix(brightstars['ra'][m],
brightstars['dec'][m], 0)
vmag = brightstars['vtmag'][m]
# WCS module and I order x and y differently...
m = ((xb > 0) & (xb < im.shape[0] + 1) & (yb > 0) &
(yb < im.shape[1] + 1))
if numpy.any(m):
xb, yb = xb[m], yb[m]
vmag = vmag[m]
blist = [xb, yb, vmag]
else:
blist = None
else:
blist = None
else:
blist = None
if blist is not None:
# we did not enable this for first DECaPS v1
# dq = mask_very_bright_stars(dq, blist)
pass
# the actual fit
res = mosaic.fit_sections(im,
psf,
4,
2,
weight=wt,
dq=dq,
psfderiv=True,
refit_psf=True,
verbose=verbose,
blist=blist)
cat, modelim, skyim, psfs = res
if len(cat) > 0:
ra, dec = wcs0.all_pix2world(cat['y'], cat['x'], 0.)
else:
ra = numpy.zeros(0, dtype='f8')
dec = numpy.zeros(0, dtype='f8')
from matplotlib.mlab import rec_append_fields
decapsid = numpy.zeros(len(cat), dtype='i8')
decapsid[:] = (prihdr['EXPNUM'] * 2**32 * 2**7 +
hdr['CCDNUM'] * 2**32 +
numpy.arange(len(cat), dtype='i8'))
if verbose:
print('Writing %s %s, found %d sources.' % (outfn, name, len(cat)))
sys.stdout.flush()
hdr['EXTNAME'] = hdr['EXTNAME'] + '_HDR'
if numpy.any(wt > 0):
hdr['GAINCRWD'] = numpy.nanmedian((im * wt**2.)[wt > 0])
hdr['SKYCRWD'] = numpy.nanmedian(skyim[wt > 0])
else:
hdr['GAINCRWD'] = 4
hdr['SKYCRWD'] = 0
if len(cat) > 0:
hdr['FWHMCRWD'] = numpy.nanmedian(cat['fwhm'])
else:
hdr['FWHMCRWD'] = 0.0
gain = hdr['GAINCRWD'] * numpy.ones(len(cat), dtype='f4')
cat = rec_append_fields(cat, ['ra', 'dec', 'decapsid', 'gain'],
[ra, dec, decapsid, gain])
fits.append(outfn, numpy.zeros(0), hdr)
outpsfs = numpy.concatenate(
[tpsf.serialize(stampsz=19) for tpsf in psfs])
hdupsfs = fits.BinTableHDU(outpsfs)
hdupsfs.name = hdr['EXTNAME'][:-4] + '_PSF'
hducat = fits.BinTableHDU(cat)
hducat.name = hdr['EXTNAME'][:-4] + '_CAT'
hdulist = fits.open(outfn, mode='append')
hdulist.append(hdupsfs)
hdulist.append(hducat)
hdulist.close(closed=True)
if outmodelfn:
modhdulist = fits.open(outmodelfn, mode='append')
hdr['EXTNAME'] = hdr['EXTNAME'][:-4] + '_MOD'
# RICE should be significantly better here and supported in
# mrdfits?, but compression_type=RICE_1 seems to cause
# quantize_level to be ignored.
compkw = {
'compression_type': 'GZIP_1',
'quantize_method': 1,
'quantize_level': -4,
'tile_size': modelim.shape
}
modhdulist.append(fits.CompImageHDU(modelim, hdr, **compkw))
hdr['EXTNAME'] = hdr['EXTNAME'][:-4] + '_SKY'
modhdulist.append(fits.CompImageHDU(skyim, hdr, **compkw))
modhdulist.close(closed=True)
count += 1
if count > nproc:
break
if profile:
pr.disable()
pstats.Stats(pr).sort_stats('cumulative').print_stats(60)
def create_master_img(imglist,
imgtype='',
RON=0.,
gain=1.,
clip=5.,
with_errors=True,
asint=False,
savefiles=True,
scalable=False,
remove_outliers=True,
diffimg=False,
noneg=False,
timit=False):
"""
NOT CURRENTLY IN USE, BUT SNIPPETS FROM IT ARE USED IN VARIOUS CALIBRATION ROUTINES!!!!!
This routine co-adds spectra from a given input list. It can also remove cosmics etc. by replacing outlier pixels that deviate by more than a certain
number of sigmas from the median across all images with the mean pixel value of the remaining pixels.
NOTE: raw images are in units of ADU, but the processed master images are in units of electrons!!!
NOTE: if 'with_errors' is set to TRUE, then the error array is stored in the same FITS file as a second HDU
INPUT:
'imglist' : list of filenames of images to co-add
'imgtype' : ['bias' / 'dark' / 'white' / 'stellar'] are valid options
'RON' : read-out noise in electrons per pixel
'gain' : camera amplifier (inverse) gain in electrons per ADU
'clip' : threshold for outlier identification (in sigmas above/below median)
'with_errors' : boolean - do you want to save/return the estimated error-array as well?
'asint' : boolean - do you want the master image to be rounded to the nearest integer?
'savefiles' : boolean - do you want to save the master image as a FITS file?
'scalable' : boolean - do you want to make the master image scalable (ie normalize to t_exp = 1s)
'remove_outliers' : boolean - do you want to remove outlier pixels (eg cosmics) with the median of the remaining images?
'diffimg' : boolean - do you want to save the difference image to a fits file? only works if 'remove_outliers' is also set to TRUE
'noneg' : boolean - do you want to allow negative pixel values?
'timit' : boolean - measure time taken for completion of function?
OUTPUT:
'master' : the master image
"""
if timit:
start_time = time.time()
print('Creating master image from: ' + str(len(imglist)) + ' ' +
imgtype.upper() + ' images')
if savefiles or diffimg:
intstring = ''
outie_string = ''
noneg_string = ''
normstring = ''
while imgtype.lower() not in [
'white', 'w', 'dark', 'd', 'bias', 'b', 'stellar', 's'
]:
imgtype = raw_input(
"WARNING: Image type not specified! What kind of images are they? ['(b)ias' / '(d)ark' / '(w)hite' / '(s)tellar']"
)
if imgtype.lower() in ['b', 'bias']:
RON = 0.
#proceed if list is not empty
if len(imglist) > 0:
if with_errors:
allerr = []
if remove_outliers:
allimg = []
outie_string = '_outliers_removed'
for n, file in enumerate(imglist):
#img = gain * pyfits.getdata(file).T
img = gain * pyfits.getdata(file)
if with_errors:
err_img = np.sqrt(gain * img.astype(float) + RON * RON)
allerr.append(err_img)
if remove_outliers:
allimg.append(img)
if n == 0:
h = pyfits.getheader(file)
master = img.copy().astype(float)
if remove_outliers:
ny, nx = img.shape
master_outie_mask = np.zeros((ny, nx), dtype='int')
if diffimg:
diff = np.zeros((ny, nx), dtype='float')
else:
master += img
#add individual-image errors in quadrature
if with_errors:
err_master = np.sqrt(np.sum((np.array(allerr)**2), axis=0))
if remove_outliers:
medimg = np.median(np.array(allimg), axis=0)
#for bias and dark frames just use the median image; for whites use something more sophisticated
if imgtype[0] in ['b', 'd']:
#now set master image equal to median image
master = medimg
#estimate of the corresponding error array (estimate only!!!)
if with_errors:
err_master = err_master / len(imglist)
#do THIS for whites
else:
#make sure we do not have any negative pixels for the sqrt
medimgpos = medimg.copy()
medimgpos[medimg < 0] = 0.
med_sig_arr = np.sqrt(
RON * RON + gain * medimgpos
) #expected STDEV for the median image (from LB Eq 2.1)
# rms_arr = np.std(np.array(allimg),axis=0) #but in the very low SNR regime, this takes over, as med_sig_arr will just be RON, and flag a whole bunch of otherwise good pixels
# mydev = np.maximum(med_sig_arr,rms_arr)
# #check that the median pixel value does not deviate significantly from the minimum pixel value (unlikely!!!)
# minimg = np.amin(allimg,axis=0)
# min_sig_arr = np.sqrt(RON*RON + gain*minimg) #expected STDEV for the minimum image (from LB Eq 2.1)
# fu_mask = medimg - minimg > clip*min_sig_arr
for n, img in enumerate(allimg):
#outie_mask = np.abs(img - medimg) > clip*med_sig_arr
outie_mask = img - medimg > clip * med_sig_arr #do we only want HIGH outliers, ie cosmics?
#save info about which image contributes the outlier pixel using unique binary numbers technique
master_outie_mask += (outie_mask * 2**n).astype(int)
#see which image(s) produced the outlier(s) and replace outies by mean of pixel value from remaining images
n_outie = np.sum(master_outie_mask > 0)
print('Correcting ' + str(n_outie) + ' outliers...')
#loop over all outliers
for i, j in zip(
np.nonzero(master_outie_mask)[0],
np.nonzero(master_outie_mask)[1]):
#access binary numbers and retrieve component(s)
outnum = binary_indices(
master_outie_mask[i, j]
) #these are the indices (within allimg) of the images that contain outliers
dumix = np.arange(len(imglist))
#remove the images containing the outliers in order to compute mean from the remaining images
useix = np.delete(dumix, outnum)
if diffimg:
diff[i, j] = master[i, j] - (
len(outnum) *
np.mean(np.array([allimg[q][i, j]
for q in useix])) +
np.sum(np.array([allimg[q][i, j] for q in useix])))
#now replace value in master image by the sum of all pixel values in the unaffected pixels
#plus the number of affected images times the mean of the pixel values in the unaffected images
master[i, j] = len(outnum) * np.mean(
np.array([allimg[q][i, j] for q in useix])) + np.sum(
np.array([allimg[q][i, j] for q in useix]))
#once we have finished correcting the outliers, we want to "normalize" (ie divide by number of frames) the master image
master = master / len(imglist)
if with_errors:
err_master = err_master / len(imglist)
#if not remove outliers, still need to "normalize" (ie divide by number of frames)
else:
master = master / len(imglist)
if with_errors:
err_master = err_master / len(imglist)
if scalable:
texp = pyfits.getval(imglist[0], 'exptime')
master = master / texp
if with_errors:
err_master = err_master / texp
normstring = normstring + '_scalable'
if noneg:
master[master < 0] = 0.
noneg_string = '_noneg'
if asint:
master = np.round(master).astype(int)
if with_errors:
err_master = np.round(err_master).astype(int)
intstring = '_int'
if diffimg:
hdiff = h.copy()
dum = file.split('/')
path = file[:-len(dum[-1])]
hdiff[
'HISTORY'] = ' DIFFERENCE IMAGE - created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
hdiff['COMMENT'] = 'Results are in units of ELECTRONS'
pyfits.writeto(path + 'master_' + imgtype.lower() + normstring +
intstring + '_diffimg.fits',
diff,
hdiff,
clobber=True)
if savefiles:
dum = file.split('/')
path = file[:-len(dum[-1])]
# while imgtype.lower() not in ['white','dark','bias']:
# imgtype = raw_input("WARNING: Image type not specified! What kind of images are they ['white' / 'dark' / 'bias']: ")
h['HISTORY'] = ' MASTER ' + imgtype.upper(
) + ' - created ' + time.strftime("%Y-%m-%d %H:%M:%S",
time.gmtime()) + ' (GMT)'
hdiff['COMMENT'] = 'Results are in units of ELECTRONS'
pyfits.writeto(path + 'master_' + imgtype.lower() + normstring +
outie_string + intstring + noneg_string + '.fits',
master,
h,
clobber=True)
#save error array in second HDU
if with_errors:
h_err = h.copy()
h_err[
'LEGEND'] = 'estimated uncertainty in MASTER ' + imgtype.upper(
)
pyfits.append(path + 'master_' + imgtype.lower() + normstring +
outie_string + intstring + noneg_string +
'.fits',
err_master,
h_err,
clobber=True)
else:
print('WARNING: empty input list')
return
print('DONE!!!')
if timit:
print('Elapsed time: ' + str(np.round(time.time() - start_time, 2)) +
' seconds')
if with_errors:
return master, err_master
else:
return master
def lc_from_bulk_download(fits_path, target_list, fname_out, fname_targets,
fname_notes, path, fname_flagged,
custom_mask=[], apply_nan_mask=False):
'''This function opens each _lc.fits file in fits_path, masks flagged data
points from QUALITY and saves interpolated PDCSAP_FLUX, TIME and TICID to
fits file fname_out.
Parameters:
* fits_path : directory containing all light curve fits files
(ending with '/')
* target_list : returned by lc_by_camera_ccd()
* fname_out : name of fits file to save time, flux and ticids into
* fname_targets : saves ticid of every target saved
* fname_notes : saves the ticid of any target it fails on
* path : directory to save nan mask plots in
* fname_flagged : name of fits file to save flagged light curves
Returns:
* confirmation : boolean, returns False if failure
'''
import fnmatch
import gc
# >> get list of all light curve fits files
fnames_all = os.listdir(fits_path)
fnames = fnmatch.filter(fnames_all, '*fits*')
# >> find all light curves in a group
fnames_group = []
target_list = target_list[:,0]
for target in target_list:
try:
fname = list(filter(lambda x: str(int(target)) in x, fnames))[0]
fnames_group.append(fname)
except:
print('Missing ' + str(int(target)))
with open(fname_notes, 'a') as f:
f.write(str(int(target)) + '\n')
fnames = fnames_group
count = 0
ticid_list = []
intensity = []
for n in range(len(fnames)):
file = fnames[n]
print(count)
# >> open file
with fits.open(fits_path + file, memmap=False) as hdul:
hdu_data = hdul[1].data
# >> get time array (only for the first light curve)
if n == 0:
time = hdu_data['TIME']
# >> get flux array
i = hdu_data['PDCSAP_FLUX']
intensity.append(i)
# >> get quality mask
quality = hdu_data['QUALITY']
flagged_inds = np.nonzero(quality)
i[flagged_inds] = np.nan
# >> get ticid
ticid = hdul[1].header['TICID']
ticid_list.append(ticid)
with open(fname_targets, 'a') as f:
f.write(str(int(ticid)) + '\n')
# >> clear memory
del hdu_data
del hdul[1].data
del hdul[0].data
gc.collect()
count += 1
# >> interpolate and NaN mask
print('Interpolating...')
intensity = np.array(intensity)
ticid_list = np.array(ticid_list)
intensity_interp, time, ticid_interp, flagged, ticid_flagged = \
interpolate_all(intensity, time, ticid_list, custom_mask=custom_mask,
apply_nan_mask=apply_nan_mask)
# >> save time array, intensity array and ticids to fits file
print('Saving to fits file...')
hdr = fits.Header()
hdu = fits.PrimaryHDU(time, header=hdr)
hdu.writeto(fname_out)
fits.append(fname_out, intensity_interp)
fits.append(fname_out, ticid_interp)
# >> actually i'm going to save the raw intensities just in case
fits.append(fname_out, intensity)
# >> save flagged
if np.shape(flagged)[0] != 0:
hdr = fits.Header()
hdu = fits.PrimaryHDU(flagged, header=hdr)
hdu.writeto(fname_flagged)
fits.append(fname_flagged, ticid_flagged)
print("lc_from_bulk_download has finished running")
return time, intensity_interp, ticid_interp, flagged, ticid_flagged
def write_fits(filename, data, header, extension, extname, comm):
"""
Collectively write local arrays into a single FITS file.
Parameters
----------
filename : str
The FITS file name.
data : ndarray
The array to be written.
header : pyfits.Header
The data FITS header. None can be set, in which case a minimal FITS
header will be inferred from the data.
extension : boolean
If True, the data will be written as an extension to an already
existing FITS file.
extname : str
The FITS extension name. Use None to write the primary HDU.
comm : mpi4py.Comm
The MPI communicator of the local arrays. Use MPI.COMM_SELF if the data
are not meant to be combined into a global array. Make sure that the
MPI processes are not executing this routine with the same file name.
"""
# check if the file name is the same for all MPI jobs
files = comm.allgather(filename + str(extname))
all_equal = all(f == files[0] for f in files)
if comm.size > 1 and not all_equal:
raise ValueError('The file name is not the same for all MPI jobs.')
ndims = comm.allgather(data.ndim)
if any(n != ndims[0] for n in ndims):
raise ValueError("The arrays have an incompatible number of dimensions"
": '{0}'.".format(', '.join(str(n) for n in ndims)))
ndim = ndims[0]
shapes = comm.allgather(data.shape)
if any(s[1:] != shapes[0][1:] for s in shapes):
raise ValueError("The arrays have incompatible shapes: '{0}'.".format(
strshape(shapes)))
# get header
if header is None:
header = create_fitsheader_for(data, extname=extname)
else:
header = header.copy()
if extname is not None:
header['extname'] = extname
# we remove the file first to avoid an annoying pyfits informative message
if not extension:
if comm.rank == 0:
try:
os.remove(filename)
except OSError:
pass
# case without MPI communication
if comm.size == 1:
if not extension:
hdu = pyfits.PrimaryHDU(data, header)
hdu.writeto(filename, overwrite=True)
else:
pyfits.append(filename, data, header)
return
# get global/local parameters
nglobal = sum(s[0] for s in shapes)
s = split(nglobal, comm.size, comm.rank)
nlocal = s.stop - s.start
if data.shape[0] != nlocal:
raise ValueError(
"On rank {}, the local array shape '{}' is invalid. T"
"he first dimension does not match the expected local"
" number '{}' given the global number '{}'.{}".format(
comm.rank, data.shape, nlocal, nglobal,
'' if comm.rank > 0 else ' Shapes are: {}.'.format(shapes)))
# write FITS header
if comm.rank == 0:
header['NAXIS' + str(ndim)] = nglobal
shdu = pyfits.StreamingHDU(filename, header)
data_loc = shdu._datLoc
shdu.close()
else:
data_loc = None
data_loc = comm.bcast(data_loc)
# get a communicator excluding the processes which have no work to do
# (Create_subarray does not allow 0-sized subarrays)
chunk = product(data.shape[1:])
rank_nowork = min(comm.size, nglobal)
group = comm.Get_group()
group.Incl(list(range(rank_nowork)))
newcomm = comm.Create(group)
# collectively write data
if comm.rank < rank_nowork:
# mpi4py 1.2.2: pb with viewing data as big endian KeyError '>d'
if sys.byteorder == 'little' and data.dtype.byteorder == '=' or \
data.dtype.byteorder == '<':
data = data.byteswap()
data = data.newbyteorder('=')
mtype = DTYPE_MAP[data.dtype]
ftype = mtype.Create_subarray([nglobal * chunk], [nlocal * chunk],
[s.start * chunk])
ftype.Commit()
f = MPI.File.Open(newcomm,
filename,
amode=MPI.MODE_APPEND | MPI.MODE_WRONLY
| MPI.MODE_CREATE)
f.Set_view(data_loc, mtype, ftype, 'native', MPI.INFO_NULL)
f.Write_all(data)
f.Close()
ftype.Free()
newcomm.Free()
# pad FITS file with zeros
if comm.rank == 0:
datasize = nglobal * chunk * data.dtype.itemsize
BLOCK_SIZE = 2880
padding = BLOCK_SIZE - (datasize % BLOCK_SIZE)
with open(filename, 'a') as f:
if f.tell() - data_loc != datasize:
raise RuntimeError('Unexpected file size.')
f.write(padding * '\0')
comm.Barrier()
basedir,
uncompressed=args.uncompressed)
else:
print('No bright star catalog, not marking bright stars.')
res = process(im,
sqivar,
flag,
psf,
refit_psf=args.refit_psf,
verbose=args.verbose,
nx=4,
ny=4,
derivcentroids=True)
outfn = args.outfn[0]
x = (res[0])['x']
y = (res[0])['y']
wcs = wcs.WCS(hdr)
ra, dec = wcs.all_pix2world(y, x, 0)
import numpy.lib.recfunctions as rfn
cat = rfn.append_fields(res[0], ['ra', 'dec'], [ra, dec])
fits.writeto(outfn, cat)
fits.append(outfn, res[1])
fits.append(outfn, res[2])
psfext = numpy.array([tpsf(0, 0, stampsz=19) for tpsf in res[3]])
fits.append(outfn, psfext)
def fits_db(fits_address, model_db, ext_name='', header=None):
line_labels = model_db['inputs']['line_list']
params_traces = model_db['outputs']
sec_label = 'synthetic_fluxes' if ext_name == '' else f'{ext_name}_synthetic_fluxes'
# ---------------------------------- Input data
# Data
list_columns = []
for data_label, data_format in FITS_INPUTS_EXTENSION.items():
data_array = model_db['inputs'][data_label]
data_col = fits.Column(name=data_label, format=data_format, array=data_array)
list_columns.append(data_col)
# Header
hdr_dict = {}
for i_line, lineLabel in enumerate(line_labels):
hdr_dict[f'hierarch {lineLabel}'] = model_db['inputs']['line_fluxes'][i_line]
hdr_dict[f'hierarch {lineLabel}_err'] = model_db['inputs']['line_err'][i_line]
# User values:
for key, value in header.items():
if key not in ['logP_values', 'r_hat']:
hdr_dict[f'hierarch {key}'] = value
# Inputs extension
cols = fits.ColDefs(list_columns)
sec_label = 'inputs' if ext_name == '' else f'{ext_name}_inputs'
hdu_inputs = fits.BinTableHDU.from_columns(cols, name=sec_label, header=fits.Header(hdr_dict))
# ---------------------------------- Output data
params_list = model_db['inputs']['parameter_list']
param_matrix = np.array([params_traces[param] for param in params_list])
param_col = fits.Column(name='parameters_list', format=FITS_OUTPUTS_EXTENSION['parameter_list'], array=params_list)
param_val = fits.Column(name='parameters_fit', format='E', array=param_matrix.mean(axis=1))
param_err = fits.Column(name='parameters_err', format='E', array=param_matrix.std(axis=1))
list_columns = [param_col, param_val, param_err]
# Header
hdr_dict = {}
for i, param in enumerate(params_list):
param_trace = params_traces[param]
hdr_dict[f'hierarch {param}'] = np.mean(param_trace)
hdr_dict[f'hierarch {param}_err'] = np.std(param_trace)
for lineLabel in line_labels:
param_trace = params_traces[lineLabel]
hdr_dict[f'hierarch {lineLabel}'] = np.mean(param_trace)
hdr_dict[f'hierarch {lineLabel}_err'] = np.std(param_trace)
# # Data
# param_array = np.array(list(params_traces.keys()))
# paramMatrix = np.array([params_traces[param] for param in param_array])
#
# list_columns.append(fits.Column(name='parameter', format='20A', array=param_array))
# list_columns.append(fits.Column(name='mean', format='E', array=np.mean(paramMatrix, axis=0)))
# list_columns.append(fits.Column(name='std', format='E', array=np.std(paramMatrix, axis=0)))
# list_columns.append(fits.Column(name='median', format='E', array=np.median(paramMatrix, axis=0)))
# list_columns.append(fits.Column(name='p16th', format='E', array=np.percentile(paramMatrix, 16, axis=0)))
# list_columns.append(fits.Column(name='p84th', format='E', array=np.percentile(paramMatrix, 84, axis=0)))
cols = fits.ColDefs(list_columns)
sec_label = 'outputs' if ext_name == '' else f'{ext_name}_outputs'
hdu_outputs = fits.BinTableHDU.from_columns(cols, name=sec_label, header=fits.Header(hdr_dict))
# ---------------------------------- traces data
list_columns = []
# Data
for param, trace_array in params_traces.items():
col_trace = fits.Column(name=param, format='E', array=params_traces[param])
list_columns.append(col_trace)
cols = fits.ColDefs(list_columns)
# Header fitting properties
hdr_dict = {}
for stats_dict in ['logP_values', 'r_hat']:
for key, value in header[stats_dict].items():
hdr_dict[f'hierarch {key}_{stats_dict}'] = value
sec_label = 'traces' if ext_name == '' else f'{ext_name}_traces'
hdu_traces = fits.BinTableHDU.from_columns(cols, name=sec_label, header=fits.Header(hdr_dict))
# ---------------------------------- Save fits files
hdu_list = [hdu_inputs, hdu_outputs, hdu_traces]
if fits_address.is_file():
for hdu in hdu_list:
try:
fits.update(fits_address, data=hdu.data, header=hdu.header, extname=hdu.name, verify=True)
except KeyError:
fits.append(fits_address, data=hdu.data, header=hdu.header, extname=hdu.name)
else:
hdul = fits.HDUList([fits.PrimaryHDU()] + hdu_list)
hdul.writeto(fits_address, overwrite=True, output_verify='fix')
return
def keppixseries(infile, outfile, plotfile=None, plottype='global',
filterlc=False, function='boxcar', cutoff=1.0, overwrite=False,
verbose=False, logfile='keppixseries.log'):
"""
keppixseries -- individual time series photometry for all pixels within a
target mask
keppixseries plots a light curve for each individual pixel in a target
mask. Light curves are extracted from a target pixel file obtained from the
Kepler data archive at MAST. If required, the data can be fed through a
boxcar, gaussian or sinc function high bandpass filter in order to remove
low frequency signal from the data. keppixseries is a diagnostic tool for
identifying source contaminants in the background or foreground of the
target. It can be employed to identify pixels for inclusion or exclusion
when re-extracting a Kepler light curve from target pixel files.
Parameters
----------
infile : str
The name of a MAST standard format FITS file containing Kepler Target
Pixel data within the first data extension.
outfile : str
The name of the output FITS file. This file has two data extensions.
The first called 'PIXELSERIES' contains a table with columns of
barycenter-corrected time, barycenter time correction, cadence number,
cadence quality flag and a series of photometric light curves, one for
each pixel within the target mask. Each pixel is labeled COLx_ROWy,
where :math:`x` is the pixel column number and :math:`y` is the pixel
row number on the CCD module/output. The second extension contains the
mask definition map copied directly from the input target pixel file.
plotfile : str
Name of an optional diagnostic output plot file containing the results
of keppixseries. An example is provided in Figure 1. Typically this is
a PNG format file. If no diagnostic file is required, plotfile can be
'None'. The plot will be generated regardless of the value of this
field, but the plot will not be saved to a file if ``plotfile='None'``.
plottype : str
keppixseries can plot light curves of three types.
The choice is made using this argument. The options are:
* local - All individual pixel light curves are scaled separately to
provide the most dynamic range for each pixel.
* global - All pixel light curves are scaled between zero and the
maximum flux attained by the brightest pixel in the mask. This option
provides the relative contribution to the archived light curve by each
pixel.
* full - All pixels light curves are scaled between zero and the
maximum flux attained by that pixel. This provides the fraction of
variability within each individual pixel.
filterlc : bool
If True, the light curve for each pixel will be treated by a high
band-pass filter to remove long-term trends from e.g. differential
velocity aberration.
function : str
The functional form of the high pass-band filter:
* boxcar
* gauss
* sinc
cutoff : float
The frequency of the high pass-band cutoff in units of :math:`days^{-1}`.
overwrite : bool
Overwrite the output file?
verbose : bool
Print informative messages and warnings to the shell and logfile?
logfile = str
Name of the logfile containing error and warning messages.
Examples
--------
.. code-block :: bash
$ keppixseries kplr008256049-2010174085026_lpd-targ.fits.gz keppixseries.fits
.. image:: ../_static/images/api/keppixseries.png
:align: center
"""
# log the call
hashline = '--------------------------------------------------------------'
kepmsg.log(logfile, hashline, verbose)
call = ('KEPPIXSERIES -- '
+ ' infile={}'.format(infile)
+ ' outfile={}'.format(outfile)
+ ' plotfile={}'.format(plotfile)
+ ' plottype={}'.format(plottype)
+ ' filterlc={}'.format(filterlc)
+ ' function={}'.format(function)
+ ' cutoff={}'.format(cutoff)
+ ' overwrite={}'.format(overwrite)
+ ' verbose={}'.format(verbose)
+ ' logfile={}'.format(logfile))
kepmsg.log(logfile, call+'\n', verbose)
# start time
kepmsg.clock('KEPPIXSERIES started at', logfile, verbose)
# overwrite output file
if overwrite:
kepio.overwrite(outfile, logfile, verbose)
if kepio.fileexists(outfile):
errmsg = ('ERROR -- KEPPIXSERIES: {} exists. Use --overwrite'
.format(outfile))
kepmsg.err(logfile, errmsg, verbose)
# open TPF FITS file
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, barytime = \
kepio.readTPF(infile, 'TIME', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, tcorr = \
kepio.readTPF(infile, 'TIMECORR', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, cadno = \
kepio.readTPF(infile, 'CADENCENO', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, fluxpixels = \
kepio.readTPF(infile, 'FLUX', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, errpixels = \
kepio.readTPF(infile, 'FLUX_ERR', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, qual = \
kepio.readTPF(infile, 'QUALITY', logfile, verbose)
# read mask defintion data from TPF file
maskimg, pixcoord1, pixcoord2 = kepio.readMaskDefinition(infile, logfile,
verbose)
# print target data
print('')
print(' KepID: {}'.format(kepid))
print(' RA (J2000): {}'.format(ra))
print('Dec (J2000): {}'.format(dec))
print(' KepMag: {}'.format(kepmag))
print(' SkyGroup: {}'.format(skygroup))
print(' Season: {}'.format(season))
print(' Channel: {}'.format(channel))
print(' Module: {}'.format(module))
print(' Output: {}'.format(output))
print('')
# how many quality = 0 rows?
npts = 0
nrows = len(fluxpixels)
for i in range(nrows):
if (qual[i] == 0 and np.isfinite(barytime[i])
and np.isfinite(fluxpixels[i, ydim * xdim // 2])):
npts += 1
time = np.empty((npts))
timecorr = np.empty((npts))
cadenceno = np.empty((npts))
quality = np.empty((npts))
pixseries = np.empty((ydim, xdim, npts))
errseries = np.empty((ydim, xdim, npts))
# construct output light curves
nptsx = 0
for i in tqdm(range(ydim)):
for j in range(xdim):
npts = 0
for k in range(nrows):
if (qual[k] == 0 and np.isfinite(barytime[k])
and np.isfinite(fluxpixels[k, int(ydim*xdim/2)])):
time[npts] = barytime[k]
timecorr[npts] = tcorr[k]
cadenceno[npts] = cadno[k]
quality[npts] = qual[k]
pixseries[i, j, npts] = fluxpixels[k, nptsx]
errseries[i, j, npts] = errpixels[k, nptsx]
npts += 1
nptsx += 1
# define data sampling
if filterlc:
tpf = pyfits.open(infile)
cadence = kepkey.cadence(tpf[1], infile, logfile, verbose)
tr = 1.0 / (cadence / 86400)
timescale = 1.0 / (cutoff / tr)
# define convolution function
if function == 'boxcar':
filtfunc = np.ones(int(np.ceil(timescale)))
elif function == 'gauss':
timescale /= 2
dx = np.ceil(timescale * 10 + 1)
filtfunc = filtfunc([1.0, dx / 2 - 1.0, timescale],
np.linspace(0, dx - 1, dx))
elif function == 'sinc':
dx = np.ceil(timescale * 12 + 1)
fx = np.linspace(0, dx - 1, dx)
fx = fx - dx / 2 + 0.5
fx /= timescale
filtfunc = np.sinc(fx)
filtfunc /= np.sum(filtfunc)
# pad time series at both ends with noise model
for i in range(ydim):
for j in range(xdim):
ave, sigma = (np.mean(pixseries[i, j, :len(filtfunc)]),
np.std(pixseries[i, j, :len(filtfunc)]))
padded = np.append(kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma), pixseries[i, j, :])
ave, sigma = (np.mean(pixseries[i, j, -len(filtfunc):]),
np.std(pixseries[i, j, -len(filtfunc):]))
padded = np.append(padded,
kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma))
# convolve data
convolved = np.convolve(padded, filtfunc, 'same')
# remove padding from the output array
outdata = convolved[len(filtfunc): -len(filtfunc)]
# subtract low frequencies
outmedian = np.median(outdata)
pixseries[i, j, :] = pixseries[i, j, :] - outdata + outmedian
# construct output file
if ydim * xdim < 1000:
instruct = pyfits.open(infile, 'readonly')
kepkey.history(call, instruct[0], outfile, logfile, verbose)
hdulist = pyfits.HDUList(instruct[0])
cols = []
cols.append(pyfits.Column(name='TIME', format='D',
unit='BJD - 2454833', disp='D12.7',
array=time))
cols.append(pyfits.Column(name='TIMECORR', format='E', unit='d',
disp='E13.6', array=timecorr))
cols.append(pyfits.Column(name='CADENCENO', format='J', disp='I10',
array=cadenceno))
cols.append(pyfits.Column(name='QUALITY', format='J', array=quality))
for i in range(ydim):
for j in range(xdim):
colname = 'COL{}_ROW{}'.format(i + column, j + row)
cols.append(pyfits.Column(name=colname, format='E',
disp='E13.6',
array=pixseries[i, j, :]))
hdu1 = pyfits.BinTableHDU.from_columns(pyfits.ColDefs(cols))
try:
hdu1.header['INHERIT'] = (True, 'inherit the primary header')
except:
pass
try:
hdu1.header['EXTNAME'] = ('PIXELSERIES', 'name of extension')
except:
pass
try:
hdu1.header['EXTVER' ] = (instruct[1].header['EXTVER'],
'extension version number (not format version)')
except:
pass
try:
hdu1.header['TELESCOP'] = (instruct[1].header['TELESCOP'],
'telescope')
except:
pass
try:
hdu1.header['INSTRUME'] = (instruct[1].header['INSTRUME'],
'detector type')
except:
pass
try:
hdu1.header['OBJECT' ] = (instruct[1].header['OBJECT'],
'string version of KEPLERID')
except:
pass
try:
hdu1.header['KEPLERID'] = (instruct[1].header['KEPLERID'],
'unique Kepler target identifier')
except:
pass
try:
hdu1.header['RADESYS'] = (instruct[1].header['RADESYS'],
'reference frame of celestial coordinates')
except:
pass
try:
hdu1.header['RA_OBJ' ] = (instruct[1].header['RA_OBJ'],
'[deg] right ascension from KIC')
except:
pass
try:
hdu1.header['DEC_OBJ'] = (instruct[1].header['DEC_OBJ'],
'[deg] declination from KIC')
except:
pass
try:
hdu1.header['EQUINOX'] = (instruct[1].header['EQUINOX'],
'equinox of celestial coordinate system')
except:
pass
try:
hdu1.header['TIMEREF'] = (instruct[1].header['TIMEREF'],
'barycentric correction applied to times')
except:
pass
try:
hdu1.header['TASSIGN'] = (instruct[1].header['TASSIGN'],
'where time is assigned')
except:
pass
try:
hdu1.header['TIMESYS'] = (instruct[1].header['TIMESYS'],
'time system is barycentric JD')
except:
pass
try:
hdu1.header['BJDREFI'] = (instruct[1].header['BJDREFI'],
'integer part of BJD reference date')
except:
pass
try:
hdu1.header['BJDREFF'] = (instruct[1].header['BJDREFF'],
'fraction of the day in BJD reference date')
except:
pass
try:
hdu1.header['TIMEUNIT'] = (instruct[1].header['TIMEUNIT'],
'time unit for TIME, TSTART and TSTOP')
except:
pass
try:
hdu1.header['TSTART'] = (instruct[1].header['TSTART'],
'observation start time in BJD-BJDREF')
except:
pass
try:
hdu1.header['TSTOP'] = (instruct[1].header['TSTOP'],
'observation stop time in BJD-BJDREF')
except:
pass
try:
hdu1.header['LC_START'] = (instruct[1].header['LC_START'],
'mid point of first cadence in MJD')
except:
pass
try:
hdu1.header['LC_END'] = (instruct[1].header['LC_END'],
'mid point of last cadence in MJD')
except:
pass
try:
hdu1.header['TELAPSE'] = (instruct[1].header['TELAPSE'],
'[d] TSTOP - TSTART')
except:
pass
try:
hdu1.header['LIVETIME'] = (instruct[1].header['LIVETIME'],
'[d] TELAPSE multiplied by DEADC')
except:
pass
try:
hdu1.header['EXPOSURE'] = (instruct[1].header['EXPOSURE'],
'[d] time on source')
except:
pass
try:
hdu1.header['DEADC'] = (instruct[1].header['DEADC'],
'deadtime correction')
except:
pass
try:
hdu1.header['TIMEPIXR'] = (instruct[1].header['TIMEPIXR'],
'bin time beginning=0 middle=0.5 end=1')
except:
pass
try:
hdu1.header['TIERRELA'] = (instruct[1].header['TIERRELA'],
'[d] relative time error')
except:
pass
try:
hdu1.header['TIERABSO'] = (instruct[1].header['TIERABSO'],
'[d] absolute time error')
except:
pass
try:
hdu1.header['INT_TIME'] = (instruct[1].header['INT_TIME'],
'[s] photon accumulation time per frame')
except:
pass
try:
hdu1.header['READTIME'] = (instruct[1].header['READTIME'],
'[s] readout time per frame')
except:
pass
try:
hdu1.header['FRAMETIM'] = (instruct[1].header['FRAMETIM'],
'[s] frame time (INT_TIME + READTIME)')
except:
pass
try:
hdu1.header['NUM_FRM'] = (instruct[1].header['NUM_FRM'],
'number of frames per time stamp')
except:
pass
try:
hdu1.header['TIMEDEL'] = (instruct[1].header['TIMEDEL'],
'[d] time resolution of data')
except:
pass
try:
hdu1.header['DATE-OBS'] = (instruct[1].header['DATE-OBS'],
'TSTART as UTC calendar date')
except:
pass
try:
hdu1.header['DATE-END'] = (instruct[1].header['DATE-END'],
'TSTOP as UTC calendar date')
except:
pass
try:
hdu1.header['BACKAPP'] = (instruct[1].header['BACKAPP'],
'background is subtracted')
except:
pass
try:
hdu1.header['DEADAPP'] = (instruct[1].header['DEADAPP'],
'deadtime applied')
except:
pass
try:
hdu1.header['VIGNAPP'] = (instruct[1].header['VIGNAPP'],
'vignetting or collimator correction applied')
except:
pass
try:
hdu1.header['GAIN'] = (instruct[1].header['GAIN'],
'[electrons/count] channel gain')
except:
pass
try:
hdu1.header['READNOIS'] = (instruct[1].header['READNOIS'],
'[electrons] read noise')
except:
pass
try:
hdu1.header['NREADOUT'] = (instruct[1].header['NREADOUT'],
'number of read per cadence')
except:
pass
try:
hdu1.header['TIMSLICE'] = (instruct[1].header['TIMSLICE'],
'time-slice readout sequence section')
except:
pass
try:
hdu1.header['MEANBLCK'] = (instruct[1].header['MEANBLCK'],
'[count] FSW mean black level')
except:
pass
hdulist.append(hdu1)
hdulist.writeto(outfile)
kepkey.new('EXTNAME', 'APERTURE', 'name of extension', instruct[2],
outfile, logfile, verbose)
pyfits.append(outfile, instruct[2].data, instruct[2].header)
instruct.close()
else:
warnmsg = ('WARNING -- KEPPIXSERIES: output FITS file requires > 999'
'columns. Non-compliant with FITS convention.')
kepmsg.warn(logfile, warnmsg)
# plot pixel array
fmin = 1.0e33
fmax = -1.033
plt.figure()
plt.clf()
dx = 0.93 / xdim
dy = 0.94 / ydim
ax = plt.axes([0.06, 0.05, 0.93, 0.94])
plt.gca().xaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
plt.gca().xaxis.set_major_locator(plt.MaxNLocator(integer=True))
plt.gca().yaxis.set_major_locator(plt.MaxNLocator(integer=True))
plt.xlim(np.min(pixcoord1) - 0.5, np.max(pixcoord1) + 0.5)
plt.ylim(np.min(pixcoord2) - 0.5, np.max(pixcoord2) + 0.5)
plt.xlabel('time', {'color' : 'k'})
plt.ylabel('arbitrary flux', {'color' : 'k'})
for i in range(ydim):
for j in range(xdim):
tmin = np.amin(time)
tmax = np.amax(time)
try:
np.isfinite(np.amin(pixseries[i, j, :]))
np.isfinite(np.amin(pixseries[i, j, :]))
fmin = np.amin(pixseries[i, j, :])
fmax = np.amax(pixseries[i, j, :])
except:
ugh = 1
xmin = tmin - (tmax - tmin) / 40
xmax = tmax + (tmax - tmin) / 40
ymin = fmin - (fmax - fmin) / 20
ymax = fmax + (fmax - fmin) / 20
if kepstat.bitInBitmap(maskimg[i, j], 2):
plt.axes([0.06 + float(j) * dx, 0.05 + i * dy, dx, dy],
facecolor='lightslategray')
elif maskimg[i, j] == 0:
plt.axes([0.06 + float(j) * dx, 0.05 + i * dy, dx, dy],
facecolor='black')
else:
plt.axes([0.06 + float(j) * dx, 0.05 + i * dy, dx, dy])
if j == int(xdim / 2) and i == 0:
plt.setp(plt.gca(), xticklabels=[], yticklabels=[])
elif j == 0 and i == int(ydim / 2):
plt.setp(plt.gca(), xticklabels=[], yticklabels=[])
else:
plt.setp(plt.gca(), xticklabels=[], yticklabels=[])
ptime = time * 1.0
ptime = np.insert(ptime, [0], ptime[0])
ptime = np.append(ptime, ptime[-1])
pflux = pixseries[i, j, :] * 1.0
pflux = np.insert(pflux, [0], -1000.0)
pflux = np.append(pflux, -1000.0)
plt.plot(time,pixseries[i, j, :], color='#0000ff', linestyle='-',
linewidth=0.5)
if not kepstat.bitInBitmap(maskimg[i, j], 2):
plt.fill(ptime, pflux, fc='lightslategray', linewidth=0.0,
alpha=1.0)
plt.fill(ptime, pflux, fc='#FFF380', linewidth=0.0,alpha=1.0)
if 'loc' in plottype:
plt.xlim(xmin, xmax)
plt.ylim(ymin, ymax)
if 'glob' in plottype:
plt.xlim(xmin, xmax)
plt.ylim(1.0e-10, np.nanmax(pixseries) * 1.05)
if 'full' in plottype:
plt.xlim(xmin, xmax)
plt.ylim(1.0e-10, ymax * 1.05)
# render plot
plt.show()
plt.savefig(plotfile)
# stop time
kepmsg.clock('KEPPIXSERIES ended at', logfile, verbose)
def split_fits(filename=None, split_dir='.', size_limit = 1024.0):
fits_list = []
filestat = os.stat(filename)
filesize = filestat.st_size/(1024.0**2)
if filesize <= size_limit:
logger.error("This file is only %f MB. It is smaller than our size limit %f MB, no split needed."%(filesize, size_limit))
return []
try:
bighdulist = pyfits.open(filename, memmap=True)
first_row = bighdulist[0]
header = first_row.header
except:
raise IOError("Error encountered when trying to open FITS file %s"%filename)
return []
fn = filename[filename.rfind('/')+1:filename.rfind('.fits')]
deltaf = header['DELTAF']
fftlen = header['NAXIS1']
fcntr = header['FCNTR']
frange = [fcntr - fftlen*deltaf/2, fcntr + fftlen*deltaf/2]
nfiles_min = int(math.ceil(filesize/size_limit))
new_width_max = fftlen/nfiles_min
new_width = 2**math.floor(np.log2(new_width_max))
nfiles = int(math.ceil(fftlen/new_width))
new_files = []
new_fcntrs = []
new_filenames = []
indices = []
new_primary_header = copy.deepcopy(header)
to_create = []
for i in range(0, nfiles):
new_filename = split_dir + '/' + fn + '_%d'%i + '.fits'
new_filenames.append(new_filename)
new_fcntr_tmp = frange[0] + deltaf * new_width * (i + 0.5)
new_fcntrs.append(new_fcntr_tmp)
new_primary_header['FCNTR'] = new_fcntr_tmp
ind = (i*new_width, min(fftlen, (i+1)*new_width))
indices.append(ind)
if os.path.isfile(new_filename):
logger.error("file %s already existed!"%new_filename)
to_create.append(False)
continue
to_create.append(True)
data = first_row.data[0][ind[0]:ind[1]]
prihdu = pyfits.PrimaryHDU(data, header = new_primary_header)
prihdu.writeto(new_filename)
logger.info("Created new file: %s"%new_filename)
for i, ohdu in enumerate(bighdulist[1:]):
logger.debug("Dealing with row %d"%i)
new_header = copy.deepcopy(ohdu.header)
for j, new_filename in enumerate(new_filenames):
if not to_create[j]:
continue
new_header['FCNTR'] = new_fcntrs[j]
ind = indices[j]
data = ohdu.data[0][ind[0]:ind[1]]
pyfits.append(new_filename, data, new_header)
##EE This, so that dedoppler is run in all the little new fits files
for new_filename in new_filenames:
fits_obj = FITS(new_filename)
fits_list.append(fits_obj)
return fits_list
def kepdiffim(infile, outfile, plotfile=None, imscale='logarithmic',
colmap='PuBu', filterlc=False, function='boxcar', cutoff=1.0,
overwrite=False, verbose=False, logfile='kepdiffim.log'):
"""
kepdiffim -- difference imaging of pixels within a target mask
kepdiffim plots the mean, standard deviation and chi distribution images
for the mask contained within a target pixel file. The standard deviation
on each pixel is defined as :math:`[flux - mean]^2 / [N - 1]`. The chi
distribution is :math:`\sqrt{[mean - flux] ^ 2 / sigma ^ 2}`. If required,
the data can be fed through a **boxcar**, **gaussian** or **sinc** function
high bandpass filter in order to remove low frequency signal from the data.
kepdiffim is a diagnostic tool for identifying source contaminants in the
background or foreground of the target. It can be employed to identify
pixels for inclusion or exclusion when re-extracting a Kepler light curve
from target pixel files.
Parameters
----------
infile : str
The name of a MAST standard format FITS file containing Kepler Target
Pixel data within the first data extension.
outfile : str
The name of the output FITS file. This file has four data extensions.
The first called 'FLUX' contains an image of the pixel-by-pixel
mean flux within target mask. The second contains the pixel variance
image of the mask pixels over time. The third contains the standard
deviation image, in this case the variance image is normalized to the
median 1-:math:`\sigma` error for each pixel. The fourth extension is
the pixel mask, as defined in the second extension of the target pixel
file.
plotfile : str
Name of an optional diagnostic output plot file containing the results
of kepdiffim. Typically this is a PNG format file. If no diagnostic
file is required, plotfile can be **None**. If **plotfile** is **None**
the plot will be generated but the plot will not be saved to a file.
imscale : str
**kepdiffim** can plot images with three choices of image scales. The
choice is made using this argument.
The options are:
* linear
* logarithmic
* squareroot
cmap : str
color intensity scheme for the image display.
filter : bool
If **filter** is **True**, the light curve for each pixel will be
treated by a high band-pass filter to remove long-term trends from
e. g. differential velocity aberration.
function : str
The functional form of the high pass-band filter. The options are:
* boxcar
* gauss
* sinc
cutoff : float [days]
The frequency of the high pass-band cutoff.
overwrite : bool
Overwrite the output file?
verbose : bool
Print informative messages and warnings to the shell and logfile?
logfile : str
Name of the logfile containing error and warning messages.
Examples
--------
.. code-block:: bash
$ kepdiffim kplr011390659-2010355172524_lpd-targ.fits.gz kepdiffim.fits
--filter --function boxcar --cutoff 0.1 --plotfile kepdiffim.png
--cmap YlOrBr --imscale linear --verbose
.. image:: ../_static/images/api/kepdiffim.png
:align: center
"""
# log the call
hashline = '--------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = ('KEPDIFFIM -- '
+ ' infile={}'.format(infile)
+ ' outfile={}'.format(outfile)
+ ' plotfile={}'.format(plotfile)
+ ' imscale={}'.format(imscale)
+ ' cmap={}'.format(colmap)
+ ' filterlc={}'.format(filterlc)
+ ' function={}'.format(function)
+ ' cutoff={}'.format(cutoff)
+ ' overwrite={}'.format(overwrite)
+ ' verbose={}'.format(verbose)
+ ' logfile={}'.format(logfile))
kepmsg.log(logfile, call+'\n', verbose)
# start time
kepmsg.clock('KEPDIFFIM started at: ', logfile, verbose)
# overwrite output file
if overwrite:
kepio.overwrite(outfile, logfile, verbose)
if kepio.fileexists(outfile):
errmsg = 'ERROR -- KEPDIFFIM: {} exists. Use --overwrite'.format(outfile)
kepmsg.err(logfile, errmsg, verbose)
# open TPF FITS file
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, barytime = \
kepio.readTPF(infile, 'TIME', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, tcorr = \
kepio.readTPF(infile, 'TIMECORR', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, cadno = \
kepio.readTPF(infile, 'CADENCENO',logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, fluxpixels = \
kepio.readTPF(infile, 'FLUX', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, errpixels = \
kepio.readTPF(infile, 'FLUX_ERR', logfile, verbose)
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, qual = \
kepio.readTPF(infile, 'QUALITY', logfile, verbose)
# read mask defintion data from TPF file
maskimg, pixcoord1, pixcoord2 = kepio.readMaskDefinition(infile, logfile,
verbose)
# print target data
print('')
print(' KepID: %s' % kepid)
print(' RA (J2000): %s' % ra)
print('Dec (J2000): %s' % dec)
print(' KepMag: %s' % kepmag)
print(' SkyGroup: %2s' % skygroup)
print(' Season: %2s' % str(season))
print(' Channel: %2s' % channel)
print(' Module: %2s' % module)
print(' Output: %1s' % output)
print('')
# how many quality = 0 rows?
npts = 0
nrows = len(fluxpixels)
for i in range(nrows):
if (qual[i] == 0 and np.isfinite(barytime[i])
and np.isfinite(fluxpixels[i, int(ydim * xdim / 2)])):
npts += 1
time = np.empty((npts))
timecorr = np.empty((npts))
cadenceno = np.empty((npts))
quality = np.empty((npts))
pixseries = np.empty((ydim * xdim, npts))
errseries = np.empty((ydim * xdim, npts))
# construct output light curves
nptsx = 0
for i in range(ydim*xdim):
npts = 0
for k in range(nrows):
if (qual[k] == 0
and np.isfinite(barytime[k])
and np.isfinite(fluxpixels[k, int(ydim * xdim / 2)])):
time[npts] = barytime[k]
timecorr[npts] = tcorr[k]
cadenceno[npts] = cadno[k]
quality[npts] = qual[k]
pixseries[i, npts] = fluxpixels[k, nptsx]
errseries[i, npts] = errpixels[k, nptsx]
npts += 1
nptsx += 1
# define data sampling
if filterlc:
tpf = pyfits.open(infile)
cadence = kepkey.cadence(tpf[1], infile, logfile, verbose)
tr = 1.0 / (cadence / 86400)
timescale = 1.0 / (cutoff / tr)
# define convolution function
if function == 'boxcar':
filtfunc = np.ones(int(np.ceil(timescale)))
elif function == 'gauss':
timescale /= 2
dx = np.ceil(timescale * 10 + 1)
filtfunc = kepfunc.gauss()
filtfunc = filtfunc([1.0, dx / 2 - 1.0, timescale],
linspace(0, dx - 1, dx))
elif function == 'sinc':
dx = np.ceil(timescale * 12 + 1)
fx = linspace(0, dx - 1, dx)
fx = fx - dx / 2 + 0.5
fx /= timescale
filtfunc = np.sinc(fx)
filtfunc /= np.sum(filtfunc)
# pad time series at both ends with noise model
for i in range(ydim * xdim):
ave, sigma = (np.mean(pixseries[i, :len(filtfunc)]),
np.std(pixseries[i, :len(filtfunc)]))
padded = np.append(kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma), pixseries[i, :])
ave, sigma = (np.mean(pixseries[i, -len(filtfunc):]),
np.std(pixseries[i, -len(filtfunc):]))
padded = np.append(padded,
kepstat.randarray(np.ones(len(filtfunc)) * ave,
np.ones(len(filtfunc)) * sigma))
# convolve data
convolved = np.convolve(padded,filtfunc,'same')
# remove padding from the output array
outdata = convolved[len(filtfunc):-len(filtfunc)]
# subtract low frequencies
outmedian = np.nanmedian(outdata)
pixseries[i, :] = pixseries[i, :] - outdata + outmedian
# sum pixels over cadence
nptsx = 0
nrows = len(fluxpixels)
pixsum = np.zeros((ydim*xdim))
errsum = np.zeros((ydim*xdim))
for i in range(npts):
if quality[i] == 0:
pixsum += pixseries[:, i]
errsum += errseries[:, i] **2
nptsx += 1
pixsum /= nptsx
errsum = np.sqrt(errsum) / nptsx
# calculate standard deviation pixels
pixvar = np.zeros((ydim*xdim))
for i in range(npts):
if quality[i] == 0:
pixvar += (pixsum - pixseries[:,i] / errseries[:,i])**2
pixvar = np.sqrt(pixvar)
# median pixel errors
errmed = np.empty((ydim*xdim))
for i in range(ydim*xdim):
errmed[i] = np.median(errseries[:,i])
# calculate chi distribution pixels
pixdev = np.zeros((ydim*xdim))
for i in range(npts):
if quality[i] == 0:
pixdev += ((pixsum - pixseries[:,i]) / pixsum)**2
pixdev = np.sqrt(pixdev)
# image scale and intensity limits
pixsum_pl, zminsum, zmaxsum = kepplot.intScale1D(pixsum, imscale)
pixvar_pl, zminvar, zmaxvar = kepplot.intScale1D(pixvar, imscale)
pixdev_pl, zmindev, zmaxdev = kepplot.intScale1D(pixdev, imscale)
# construct output summed image
imgsum = np.empty((ydim, xdim))
imgvar = np.empty((ydim, xdim))
imgdev = np.empty((ydim, xdim))
imgsum_pl = np.empty((ydim, xdim))
imgvar_pl = np.empty((ydim, xdim))
imgdev_pl = np.empty((ydim, xdim))
n = 0
for i in range(ydim):
for j in range(xdim):
imgsum[i, j] = pixsum[n]
imgvar[i, j] = pixvar[n]
imgdev[i, j] = pixdev[n]
imgsum_pl[i, j] = pixsum_pl[n]
imgvar_pl[i, j] = pixvar_pl[n]
imgdev_pl[i, j] = pixdev_pl[n]
n += 1
# construct output file
instruct = pyfits.open(infile)
kepkey.history(call, instruct[0], outfile, logfile, verbose)
hdulist = pyfits.HDUList(instruct[0])
hdulist.writeto(outfile)
kepkey.new('EXTNAME', 'FLUX', 'name of extension', instruct[2], outfile,
logfile, verbose)
pyfits.append(outfile, imgsum, instruct[2].header)
kepkey.new('EXTNAME', 'CHI', 'name of extension', instruct[2], outfile,
logfile, verbose)
pyfits.append(outfile, imgvar, instruct[2].header)
kepkey.new('EXTNAME', 'STDDEV', 'name of extension', instruct[2], outfile,
logfile, verbose)
pyfits.append(outfile, imgdev, instruct[2].header)
kepkey.new('EXTNAME', 'APERTURE', 'name of extension', instruct[2], outfile,
logfile, verbose)
pyfits.append(outfile, instruct[2].data,instruct[2].header)
instruct.close()
# pixel limits of the subimage
ymin = row
ymax = ymin + ydim
xmin = column
xmax = xmin + xdim
# plot limits for summed image
ymin = float(ymin) - 0.5
ymax = float(ymax) - 0.5
xmin = float(xmin) - 0.5
xmax = float(xmax) - 0.5
# plot style
plotimage(imgsum_pl, imgvar_pl, imgdev_pl, zminsum, zminvar, zmindev,
zmaxsum, zmaxvar, zmaxdev, xmin, xmax, ymin, ymax, colmap,
plotfile)
# stop time
kepmsg.clock('KEPDIFFIM ended at: ',logfile,verbose)
def ex2d_patch(image,
ivar,
psf,
specmin,
nspec,
wavelengths,
xyrange=None,
full_output=False,
regularize=0.0,
ndecorr=False):
"""
2D PSF extraction of flux from image patch given pixel inverse variance.
Inputs:
image : 2D array of pixels
ivar : 2D array of inverse variance for the image
psf : PSF object
specmin : index of first spectrum to extract
nspec : number of spectra to extract
wavelengths : 1D array of wavelengths to extract
Optional Inputs:
xyrange = (xmin, xmax, ymin, ymax): treat image as a subimage
cutout of this region from the full image
full_output : if True, return a dictionary of outputs including
intermediate outputs such as the projection matrix.
ndecorr : if True, decorrelate the noise between fibers, at the
cost of residual signal correlations between fibers.
Returns (flux, ivar, R):
flux[nspec, nwave] = extracted resolution convolved flux
ivar[nspec, nwave] = inverse variance of flux
R : 2D resolution matrix to convert
"""
#- Range of image to consider
waverange = (wavelengths[0], wavelengths[-1])
specrange = (specmin, specmin + nspec)
if xyrange is None:
xmin, xmax, ymin, ymax = xyrange = psf.xyrange(specrange, waverange)
image = image[ymin:ymax, xmin:xmax]
ivar = ivar[ymin:ymax, xmin:xmax]
else:
xmin, xmax, ymin, ymax = xyrange
nx, ny = xmax - xmin, ymax - ymin
npix = nx * ny
nspec = specrange[1] - specrange[0]
nwave = len(wavelengths)
#- Solve AT W pix = (AT W A) flux
#- Projection matrix and inverse covariance
A = psf.projection_matrix(specrange, wavelengths, xyrange)
#- Pixel weights matrix
w = ivar.ravel()
W = spdiags(ivar.ravel(), 0, npix, npix)
#-----
#- Extend A with an optional regularization term to limit ringing.
#- If any flux bins don't contribute to these pixels,
#- also use this term to constrain those flux bins to 0.
#- Original: exclude flux bins with 0 pixels contributing
# ibad = (A.sum(axis=0).A == 0)[0]
#- Identify fluxes with very low weights of pixels contributing
fluxweight = W.dot(A).sum(axis=0).A[0]
minweight = 0.01 * np.max(fluxweight)
ibad = fluxweight < minweight
#- Original version; doesn't work on older versions of scipy
# I = regularize*scipy.sparse.identity(nspec*nwave)
# I.data[0,ibad] = minweight - fluxweight[ibad]
#- Add regularization of low weight fluxes
Idiag = regularize * np.ones(nspec * nwave)
Idiag[ibad] = minweight - fluxweight[ibad]
I = scipy.sparse.identity(nspec * nwave)
I.setdiag(Idiag)
#- Only need to extend A if regularization is non-zero
if np.any(I.diagonal()):
pix = np.concatenate((image.ravel(), np.zeros(nspec * nwave)))
Ax = scipy.sparse.vstack((A, I))
wx = np.concatenate((w, np.ones(nspec * nwave)))
else:
pix = image.ravel()
Ax = A
wx = w
#- Inverse covariance
Wx = spdiags(wx, 0, len(wx), len(wx))
iCov = Ax.T.dot(Wx.dot(Ax))
#- Solve (image = A flux) weighted by Wx:
#- A^T W image = (A^T W A) flux = iCov flux
y = Ax.T.dot(Wx.dot(pix))
xflux = spsolve(iCov, y).reshape((nspec, nwave))
#- TODO: could check for outliers, remask and re-extract
#- Be careful in case masking blocks off all inputs to a flux bin and
#- thus creates a singular array. May need to keep regularization piece.
# model = A.dot(xflux.ravel())
# chi = (image.ravel() - model) * np.sqrt(ivar.ravel())
# good = np.abs(chi)<5
# ...
#- Solve for Resolution matrix
try:
if ndecorr:
R, fluxivar = resolution_from_icov(iCov)
else:
R, fluxivar = resolution_from_icov(
iCov, decorr=[nwave for x in range(nspec)])
except np.linalg.linalg.LinAlgError as err:
outfile = 'LinAlgError_{}-{}_{}-{}.fits'.format(
specrange[0], specrange[1], waverange[0], waverange[1])
print("ERROR: Linear Algebra didn't converge")
print("Dumping {} for debugging".format(outfile))
from astropy.io import fits
fits.writeto(outfile, image, clobber=True)
fits.append(outfile, ivar, name='IVAR')
fits.append(outfile, A.data, name='ADATA')
fits.append(outfile, A.indices, name='AINDICES')
fits.append(outfile, A.indptr, name='AINDPTR')
fits.append(outfile, iCov.toarray(), name='ICOV')
raise err
#- Convolve with Resolution matrix to decorrelate errors
fluxivar = fluxivar.reshape((nspec, nwave))
rflux = R.dot(xflux.ravel()).reshape(xflux.shape)
if full_output:
results = dict(flux=rflux,
ivar=fluxivar,
R=R,
xflux=xflux,
A=A,
iCov=iCov)
results['options'] = dict(specmin=specmin,
nspec=nspec,
wavelengths=wavelengths,
xyrange=xyrange,
regularize=regularize,
ndecorr=ndecorr)
return results
else:
return rflux, fluxivar, R
def main(specpath, tblpath, obj_ind, outfile, *normto):
tbl = fits.getdata(tblpath, ext=1)
#input arrays
masklist = tbl['maskname'][obj_ind]
idlist = tbl['id'][obj_ind]
zarray = tbl['z_mosfire'][obj_ind]
ha6565_lum = tbl['ha6565_lum'][obj_ind]
hb4863_lum = tbl['hb4863_lum'][obj_ind]
luvcorr = tbl['luv'][obj_ind]
ha6565_abs_flux = tbl['ha6565_abs_flux'][obj_ind]
hb4863_abs_flux = tbl['hb4863_abs_flux'][obj_ind]
ha6565_lum_err = tbl['ha6565_lum_err'][obj_ind]
hb4863_lum_err = tbl['hb4863_lum_err'][obj_ind]
idliststr = [str(e) for e in idlist]
specfile = specpath + masklist.strip() + '.*.' + idliststr + '.ell.1d.fits'
#counting the number of files
speccount = 0
for i, f in enumerate(specfile):
filelisttemp = glob(f)
for n in filelisttemp:
speccount += 1
#making a list of file paths
filelist = ['' for i in range(speccount)]
zlist = np.zeros(speccount)
halumlist = np.zeros(speccount)
hblumlist = np.zeros(speccount)
uvlumlist = np.zeros(speccount)
ha6565_abs_fluxlist = np.zeros(speccount)
hb4863_abs_fluxlist = np.zeros(speccount)
specind = 0
for i, f in enumerate(specfile):
filelisttemp = glob(f)
for n in filelisttemp:
filelist[specind] = n
zlist[specind] = zarray[i]
halumlist[specind] = ha6565_lum[i]
hblumlist[specind] = hb4863_lum[i]
uvlumlist[specind] = luvcorr[i]
ha6565_abs_fluxlist[specind] = ha6565_abs_flux[i]
hb4863_abs_fluxlist[specind] = hb4863_abs_flux[i]
specind += 1
import sys
if sys.argv[5] == 'Ha':
norm = 1. / halumlist
normbalm = 1. / ha6565_lum
if sys.argv[5] == 'Hb':
norm = 1. / hblumlist
normbalm = 1. / hb4863_lum
if sys.argv[5] == 'UV':
norm = 1. / uvlumlist
normbalm = 1. / luvcorr
if sys.argv[5] == 'none':
norm = np.ones(len(halumlist))
normbalm = np.ones(len(ha6565_lum))
if ((sys.argv[5] != 'Ha') & (sys.argv[5] != 'Hb') & (sys.argv[5] != 'UV') &
(sys.argv[5] != 'none')):
print(
'normto keyword should be set to one of these: "Ha","Hb","UV", or "none" '
)
#make a grid of wavelength with the desired resolution
wavemin = 3250
wavemax = 10000
delwave = 0.5 #in AA
gridwl = np.arange(wavemin, wavemax, delwave)
nwave = len(gridwl)
specall = np.zeros((nwave, speccount))
specerrall = np.zeros((nwave, speccount))
t0 = time.time()
print('# Stacking ', speccount, ' spectra of ', len(idlist), ' objects')
for i, specfile in enumerate(filelist):
header, spec, specerr, specwl = read_spec(specfile)
#cut the bad beginning and end of the spectra
goodpix = removebad(spec)
spec = spec[goodpix]
specerr = specerr[goodpix]
specwl = specwl[goodpix]
ldist = cosmo.luminosity_distance(zlist[i]).to(u.cm)
lspec = 1e-40 * ldist * ldist * 4 * np.pi * (1 + zlist[i]) * spec
lspecerr = 1e-40 * ldist * ldist * 4 * np.pi * (1 + zlist[i]) * specerr
lspec = lspec * norm[i]
lspecerr = lspecerr * norm[i]
#calculate rest-frame wavelength
specwl /= 1. + zlist[i]
#interpolate to the new wavelength grid
UNDEF = -999.
gridspec = np.interp(gridwl, specwl, lspec, left=UNDEF, right=UNDEF)
gridspecerr = np.interp(gridwl,
specwl,
lspecerr,
left=UNDEF,
right=UNDEF)
#take into account the resampling for the error spectrum
errfac = np.sqrt(header['CDELT1'] / (1. + zlist[i]) / delwave)
gridspecerr = gridspecerr * errfac
#remove sky lines (remove those with error > 3. * median(err))
mederr = np.median(gridspecerr[gridspecerr > 0.])
keep = (np.abs(gridspecerr) < mederr * 3.)
gridspec[keep == False] = UNDEF
#pdb.set_trace()
#assign the spetra and error spectra to arrays:
specall[:, i] = gridspec
specerrall[:, i] = gridspecerr
#declare arrays
wt_avg = np.zeros(nwave)
nwt_avg = np.zeros(nwave)
med = np.zeros(nwave)
clip_avg = np.zeros(nwave)
wt_err = np.zeros(nwave)
disp = np.zeros(nwave)
z = np.zeros(nwave)
num = np.zeros(nwave)
#stacking
for j in range(nwave):
speccol = specall[j, :]
specerrcol = specerrall[j, :]
good = np.where(speccol != UNDEF)
ngood = len(speccol[good])
if ngood == 0: continue
if ngood == 1:
speccol = speccol[good]
specerrcol = specerrcol[good]
zcol = zlist[good]
weight = 1 / (specerrcol * specerrcol)
wt_avg[j] = np.nansum(speccol * weight) / np.nansum(weight)
nwt_avg[j] = np.nanmean(speccol)
med[j] = speccol
wt_err[j] = np.sqrt(1. / np.nansum(weight))
disp[j] = 0.
z[j] = zcol.mean()
num[j] = ngood
if ngood > 1:
speccol = speccol[good]
specerrcol = specerrcol[good]
zcol = zlist[good]
weight = 1 / (specerrcol * specerrcol)
wt_avg[j] = np.nansum(speccol * weight) / np.nansum(weight)
nwt_avg[j] = np.nanmean(speccol)
med[j] = np.nanmedian(speccol)
clip_avg[j] = clip(speccol, 3., .01)
wt_err[j] = np.sqrt(1. / np.nansum(weight))
disp[j] = np.nanstd(speccol)
z[j] = zcol.mean()
num[j] = ngood
#Measure weighted average Balmer absorption
ldistarr = cosmo.luminosity_distance(zarray).to(u.cm)
goodha = np.where((ha6565_abs_flux != -999.) & (ha6565_lum_err != 0.)
& (np.isfinite(ha6565_abs_flux)))
n1 = len(ha6565_lum_err[goodha])
goodhb = np.where((hb4863_abs_flux != -999.)
& (np.isfinite(hb4863_abs_flux)))
n2 = len(hb4863_abs_flux[goodhb])
print('# Number of objs with Balmer absorption of two lines: ', n1,
' and ', n2)
lhaabs = 1e-40 * ldistarr * ldistarr * 4 * np.pi * ha6565_abs_flux * normbalm
lhbabs = 1e-40 * ldistarr * ldistarr * 4 * np.pi * hb4863_abs_flux * normbalm
habalm = (np.ma.masked_invalid(
lhaabs[goodha] /
(ha6565_lum_err[goodha] * ha6565_lum_err[goodha])).sum() /
np.ma.masked_invalid(
1 / (ha6565_lum_err[goodha] * ha6565_lum_err[goodha])).sum())
hbbalm = (np.ma.masked_invalid(
lhbabs[goodhb] /
(hb4863_lum_err[goodhb] * hb4863_lum_err[goodhb])).sum() /
np.ma.masked_invalid(
1 / (hb4863_lum_err[goodhb] * hb4863_lum_err[goodhb])).sum())
#defining the columns for the output
#wt_avg_col=fits.Column(name='wt_avg',format='D',array=wt_avg)
#nwt_avg_col=fits.Column(name='nwt_avg',format='D',array=nwt_avg)
#med_col=fits.Column(name='med',format='D',array=med)
#wt_err_col=fits.Column(name='wt_err',format='D',array=wt_err)
#disp_col=fits.Column(name='disp',format='D',array=disp)
#z_col=fits.Column(name='z',format='D',array=z)
#num_col=fits.Column(name='num',format='D',array=num)
#cols = fits.ColDefs([wt_avg_col,nwt_avg_col,med_col,wt_err_col,disp_col,z_col,num_col])
#define the output file
#out = fits.BinTableHDU.from_columns(cols)
out = fits.PrimaryHDU()
hdr = out.header
#making the header of the output file
out.header['UNITS'] = '1.d40 erg/s/A'
out.header['CTYPE1'] = 'LINEAR'
out.header['CRPIX1'] = 1.0
out.header['CRVAL1'] = wavemin
out.header['CDELT1'] = delwave
out.header['CD1_1'] = delwave
out.header['haabs'] = habalm.value
out.header['hbabs'] = hbbalm.value
out.header['uvcor'] = np.median(uvlumlist)
out.header['uvcorerr'] = uvlumlist.std() / len(uvlumlist)
out.header['COMMENT'] = 'Ext 1: weighted average'
out.header['COMMENT'] = 'Ext 2: error'
out.header['COMMENT'] = 'Ext 3: unweighted average'
out.header['COMMENT'] = 'Ext 4: median'
out.header['COMMENT'] = 'Ext 5: 3sigma-clipped average'
out.header['COMMENT'] = 'Ext 6: standard deviation in each wavelength bin'
out.header[
'COMMENT'] = 'Ext 7: average redshift of objs contributing to each wavelength bin'
out.header['COMMENT'] = 'Ext 8: number of objs in each wavelength bin'
for i in range(len(idlist)):
hdrspecname = masklist[i] + '_' + str(idlist[i])
out.header['COMMENT'] = hdrspecname
#Writing the output
#out.writeto('test_py.fits', clobber=True)
outname = outfile
out.writeto(outname, clobber=True)
hdr['OBJ'] = 'wt_avg'
fits.append(outname, wt_avg, hdr)
hdr['OBJ'] = 'wt_err'
fits.append(outname, wt_err, hdr)
hdr['OBJ'] = 'nwt_avg'
fits.append(outname, nwt_avg, hdr)
hdr['OBJ'] = 'med'
fits.append(outname, med, hdr)
hdr['OBJ'] = 'clip_avg'
fits.append(outname, clip_avg, hdr)
hdr['OBJ'] = 'disp'
fits.append(outname, disp, hdr)
hdr['OBJ'] = 'z'
fits.append(outname, z, hdr)
hdr['OBJ'] = 'num'
fits.append(outname, num, hdr)
print('# Stacking took: {0:3.2f}'.format((time.time() - t0) / 60.),
' min.')
def lc_from_target_list(yourpath, targetList, fname_time_intensities_raw,
fname_targets, fname_notes, path='./',
custom_mask=[], apply_nan_mask=False):
""" runs getting the files and data for all targets on the list
then appends the time & intensity arrays and the TIC number into text files
that can later be accessed
modified [lcg 07092020]
"""
intensity = []
ticids = []
for n in range(len(targetList)): #for each item on the list
if n == 0: #for the first target only do you need to get the time index
target = targetList[n][0] #get that target number
time1, i1, tic = get_lc_file_and_data(yourpath, target) #grab that data
if type(i1) == np.ndarray: #if the data IS data
intensity.append(i1)
ticids.append(tic)
else: #if the data is NOT a data
print("First target failed, no time index was saved")
with open(fname_notes, 'a') as file_object:
file_object.write("\n")
file_object.write(str(int(target)))
else: #only saving the light curve into the fits file because it's all you need
target = targetList[n][0] #get that target number
time1, i1, tic = get_lc_file_and_data(yourpath, target)
if type(i1) == np.ndarray:
intensity.append(i1)
ticids.append(tic)
else: #IF THE DATA IS NOT DATA
print("File failed to return targets")
with open(fname_notes, 'a') as file_object:
file_object.write("\n")
file_object.write(str(int(target)))
#if n %10 == 0: #every 50, print how many have been done
print(str(n), "completed")
intensity = np.array(intensity)
ticids = np.array(ticids)
# >> interpolate and nan mask
print('Interpolating and applying nan mask')
intensity_interp, time, ticids, flagged, ticid_flagged = \
interpolate_all(intensity, time1, ticids, custom_mask=custom_mask,
apply_nan_mask=apply_nan_mask)
print('Saving to fits file')
# i_interp = np.array(i_interp)
hdr = fits.Header() # >> make the header
hdu = fits.PrimaryHDU(time, header=hdr)
hdu.writeto(fname_time_intensities_raw)
fits.append(fname_time_intensities_raw, intensity_interp)
fits.append(fname_time_intensities_raw, ticids)
# >> actually i'm going to save the raw intensities just in case
fits.append(fname_time_intensities_raw, intensity)
# with open(fname_time_intensities_raw, 'rb+') as f:
# # >> don't want to save 2x data we need to, so only save interpolated
# # fits.append(fname_time_intensities_raw, intensity)
# fits.append(fname_time_intensities_raw, i_interp)
# fits.append(fname_time_intensities_raw, ticids)
confirmation = "lc_from_target_list has finished running"
return confirmation
'SPECTER_DIR'] + "/data/bigboss/designs/20120827difdet/bbpsf-I.fits" outfile = os.environ['SPECTER_DIR'] + "/test/data/psf-spot.fits" fx = fits.open(infile) x, xhdr = fx[0].data, fx[0].header y, yhdr = fx[1].data, fx[1].header w, whdr = fx[2].data, fx[2].header spots, spotshdr = fx[3].data, fx[3].header spotx, spotxhdr = fx[4].data, fx[4].header spoty, spotyhdr = fx[5].data, fx[5].header fiberpos, fposhdr = fx[6].data, fx[6].header spotpos, sposhdr = fx[7].data, fx[7].header spotwave, swavehdr = fx[8].data, fx[8].header throughput, thruhdr = fx[9].data, fx[9].header fits.writeto(outfile, x[:, 0::10], header=xhdr, clobber=True) fits.append(outfile, y[:, 0::10], header=yhdr) fits.append(outfile, w[:, 0::10], header=whdr) fits.append(outfile, spots[0::5, 0::5, :, :], header=spotshdr) fits.append(outfile, spotx[0::5, 0::5], header=spotxhdr) fits.append(outfile, spoty[0::5, 0::5], header=spotyhdr) fits.append(outfile, fiberpos, header=fposhdr) fits.append(outfile, spotpos[0::5], header=sposhdr) fits.append(outfile, spotwave[0::5], header=swavehdr) fits.append(outfile, throughput, header=thruhdr)
def targetwise_lc(yourpath, target_list, fname_time_intensities,fname_notes):
""" runs getting the files and data for all targets on the list
then appends the time & intensity arrays and the TIC number into text files
that can later be accessed
parameters:
* yourpath = folder into which things will get saved
* target_list = list of ticids, as integers
* fname_time_intensities = direct path to the file to save into
* fname_notes = direct path to file to save TICIDS of targets that
return no data into
returns: list of ticids as an array
requires: get_lc_file_and_data(), interpolate_lc()
modified [lcg 07112020]
"""
ticids = []
for n in range(len(target_list)): #for each item on the list
if n == 0: #for the first target only do you need to get the time index
target = target_list[0] #get that target number
time1, i1, tic = get_lc_file_and_data(yourpath, target) #grab that data
if type(i1) == np.ndarray: #if the data IS data
i_interp, flag = interpolate_lc(i1, time1, flux_err=False, interp_tol=20./(24*60),
num_sigma=10, DEBUG_INTERP=False,
output_dir=yourpath, prefix='')
TI = [time1, i1]
TI_array = np.asarray(TI)
hdr = fits.Header() # >> make the header
hdu = fits.PrimaryHDU(TI_array, header=hdr)
hdu.writeto(fname_time_intensities)
ticids.append(tic)
else: #if the data is NOT a data
print("First target failed, no time index was saved")
with open(fname_notes, 'a') as file_object:
file_object.write("\n")
file_object.write(str(int(target)))
else:
target = target_list[n] #get that target number
time1, i1, tic = get_lc_file_and_data(yourpath, target) #grab that data
if type(i1) == np.ndarray: #if the data IS data
i_interp, flag = interpolate_lc(i1, time1, flux_err=False, interp_tol=20./(24*60),
num_sigma=10, DEBUG_INTERP=False,
output_dir=yourpath, prefix='')
TI = [time1, i1]
TI_array = np.asarray(TI)
fits.append(fname_time_intensities, TI_array)
ticids.append(tic)
else: #if the data is NOT a data
print("Target failed to return a light curve")
with open(fname_notes, 'a') as file_object:
file_object.write("\n")
file_object.write(str(int(target)))
print(n, " completed")
fits.append(fname_time_intensities, np.asarray(ticids))
print("lc_from_target_list has finished running")
return np.asarray(ticids)
def createVoronoiInput(cubeFile=None):
# makes a version of the median flux map that is all positive, and a
# version of the error array that is directly scaled from this new
# flux map and the SNR map created empirically (via ifu.map_snr)
if cubeFile:
cubefits = pyfits.open(cubeFile)
else:
cubefits = pyfits.open(datadir + cuberoot + '.fits')
cube = cubefits[0].data
hdr = cubefits[0].header
errors = cubefits[1].data
quality = cubefits[2].data
#nframes = cubefits[3].data
#snrimg = pyfits.getdata(datadir + cuberoot + '_snr.fits')
if cubeFile:
#snrimg = pyfits.getdata(cubeFile.replace('_bulgesub.fits','_snr.fits'))
snrimg = pyfits.getdata(cubeFile.replace('.fits','_snr.fits'))
else:
snrimg = pyfits.getdata(datadir+'m31_all_scalederr_cleanhdr_snr.fits')
xx = np.arange(cube.shape[0])
yy = np.arange(cube.shape[1])
imgShape = (cube.shape[0],cube.shape[1])
cubeVor = np.zeros(imgShape, dtype=float)
errVor = np.zeros(imgShape, dtype=float)
for nx in xx:
for ny in yy:
tmpcube = cube[nx,ny,:]
# add a constant to the spectrum to make it above 0
#print "old cube mean is %f " % tmpcube.mean()
#minFlux = tmpcube.mean() - (1.0 * tmpcube.std())
#print "minflux is %f" % minFlux
#tmpcube += np.abs(minFlux)
#print "new cube mean is %f " % tmpcube.mean()
tmpcubeavg = tmpcube.mean()
tmpcubeavg = np.median(tmpcube)
tmpsnr = np.abs(snrimg[ny,nx])
#tmpsnr = np.abs(snrimg[nx,ny])
# calc errors for tessellation based on the empirical
# S/N already calculated
tmperr = tmpcubeavg/tmpsnr
cubeVor[nx,ny] = tmpcubeavg
errVor[nx,ny] = tmperr
#if ny==71:
# print 'ny = 71'
# if nx==28:
# pdb.set_trace()
# change NaN to 0
errVor = np.nan_to_num(errVor)
if cubeFile:
outfile = cubeFile.replace('.fits','_vor.fits')
else:
outfile = datadir + cuberoot + '_vor.fits'
pyfits.writeto(outfile, cubeVor, header=hdr)
pyfits.append(outfile, errVor)
##
print('Writing meta to %s' % meta_name)
meta.write(meta_name, format='ascii', overwrite=True)
##
print('Writing spectra to %s' % infile)
meta.write(meta_name, format='ascii', overwrite=True)
##
hdr = fits.Header()
hdr['EXTNAME'] = 'WAVELENGTH'
hdr['BUNIT'] = 'Angstrom'
fits.writeto(infile, wave, header=hdr, overwrite=True)
hdr['EXTNAME'] = 'FLUX'
hdr['BUNIT'] = '10^-17 erg/(s*cm^2*Angstrom)' # Satisifes FITS standard AND Astropy-compatible.
fits.append(infile, flux, header=hdr)
hdr['EXTNAME'] = 'REDSHIFTS'
hdr['BUNIT'] = 'DIMENSIONLESS' # Satisifes FITS standard AND Astropy-compatible.
fits.append(infile, redshifts, header=hdr)
hdr['EXTNAME'] = 'MAGNITUDES'
hdr['BUNIT'] = 'DIMENSIONLESS' # Satisifes FITS standard AND Astropy-compatible.
fits.append(infile, magnitudes, header=hdr)
print('\n\nDone.\n\n')
print(files)
elif '.' not in a and '106' in a:
files.append(findfiles(html + '/' + a))
print(files)
return files
fits = []
tbl = []
dir = findfiles(
'https://irsa.ipac.caltech.edu/ibe/data/wise/allsky/4band_p1bm_frm/6a/02206a'
)
print('dir: ', dir[0])
for i in dir[0]:
if '.fits' in i:
fits.append(i)
elif '.tbl' in i:
tbl.append(i)
print('fits files: ', fits)
print('tbl files: ', tbl)
with open('fits_files.csv', 'w') as csvFile:
for name in fits:
csvFile.write(name)
csvFile.write('\n')
csvFile.close()
with open('tbl_files.csv', 'w') as csvFile:
for name in tbl:
csvFile.write(name)
default=numpy.inf,
help='pixel brightness limit for saturation')
args = parser.parse_args()
imagefn = args.imagefn[0]
ivarfn = args.ivarfn[0]
flagfn = args.flagfn[0]
if getattr(args, 'psffn', None):
# stamp = numpy.clip(fits.getdata(args.psffn), 1e-10, numpy.inf)
stamp = fits.getdata(args.psffn)
stamp[stamp < 0] = 0.
stamp = stamp / numpy.sum(stamp)
psf = psfmod.SimplePSF(stamp)
from functools import partial
psf.fitfun = partial(psfmod.wise_psf_fit, fname=args.psffn)
else:
print('using moffat')
psf = psfmod.SimplePSF(psfmod.moffat_psf(2.5, beta=2.5)[0])
res = process(imagefn,
ivarfn,
flagfn,
psf,
refit_psf=args.refit_psf,
verbose=args.verbose,
nx=4,
ny=4,
satlimit=args.satlimit)
outfn = args.outfn[0]
fits.writeto(outfn, res[0])
fits.append(outfn, res[1])
fits.append(outfn, res[2])
def process_whites(white_list,
MB=None,
ronmask=None,
MD=None,
gain=None,
P_id=None,
scalable=False,
fancy=False,
remove_bg=True,
clip=5.,
savefile=True,
saveall=False,
diffimg=False,
path=None,
debug_level=0,
timit=False):
"""
This routine processes all whites from a given list of files. It corrects the orientation of the image and crops the overscan regions,
and subtracts both the MASTER BIAS frame [in ADU], and the MASTER DARK frame [in e-] from every image before combining them to create a MASTER WHITE frame.
NOTE: the input image has units of ADU, but the output image has units of electrons!!!
INPUT:
'white_list' : list of filenames of raw white images (incl. directories)
'MB' : the master bias frame (bias only, excluding OS levels) [ADU]
'ronmask' : the read-noise mask (or frame) [e-]
'MD' : the master dark frame [e-]
'gain' : the gains for each quadrant [e-/ADU]
'P_id' : order tracing dictionary (only needed if remove_bg is set to TRUE)
'scalable' : boolean - do you want to normalize the dark current to an exposure time of 1s? (ie do you want to make it "scalable"?)
'fancy' : boolean - do you want to use the 'fancy' method for creating the master white frame? (otherwise a simple median image will be used)
'remove_bg' : boolean - do you want to remove the background from the output master white?
'clip' : number of 'expected-noise sigmas' a pixel has to deviate from the median pixel value across all images to be considered an outlier when using the 'fancy' method
'savefile' : boolean - do you want to save the master white frame as a FITS file?
'saveall' : boolean - do you want to save all individual bias- & dark-corrected images as well?
'diffimg' : boolean - do you want to save the difference image (ie containing the outliers)? only used if 'fancy' is set to TRUE
'path' : path to the output file directory (only needed if savefile is set to TRUE)
'debug_level' : for debugging...
'timit' : boolean - do you want to measure execution run time?
OUTPUT:
'master' : the master white image [e-] (also has been brought to 'correct' orientation, overscan regions cropped, and (if desired) bg-corrected)
'err_master' : the corresponding uncertainty array [e-]
"""
if timit:
start_time = time.time()
if debug_level >= 1:
print('Creating master white frame from ' + str(len(white_list)) +
' fibre flats...')
# if INPUT arrays are not given, read them from default files
if path is None:
print('WARNING: output file directory not provided!!!')
print('Using same directory as input file...')
dum = white_list[0].split('/')
path = white_list[0][0:-len(dum[-1])]
date = path.split('/')[-2]
if MB is None:
# no need to fix orientation, this is already a processed file [ADU]
# MB = pyfits.getdata(path+'master_bias.fits')
MB = pyfits.getdata(path + date + '_median_bias.fits')
if ronmask is None:
# no need to fix orientation, this is already a processed file [e-]
ronmask = pyfits.getdata(path + date + '_read_noise_mask.fits')
if MD is None:
if scalable:
# no need to fix orientation, this is already a processed file [e-]
MD = pyfits.getdata(path + date + '_master_dark_scalable.fits', 0)
# err_MD = pyfits.getdata(path+'master_dark_scalable.fits', 1)
else:
# no need to fix orientation, this is already a processed file [e-]
texp = pyfits.getval(white_list[0])
MD = pyfits.getdata(
path + date + '_master_dark_t' + str(int(np.round(texp, 0))) +
'.fits', 0)
# err_MD = pyfits.getdata(path+'master_dark_t'+str(int(np.round(texp,0)))+'.fits', 1)
# prepare arrays
allimg = []
allerr = []
# loop over all files in "white_list"; correct for bias and darks on the fly
for n, fn in enumerate(sorted(white_list)):
if debug_level >= 1:
print('Now processing file ' + str(n + 1) + '/' +
str(len(white_list)) + ' (' + fn + ')')
# call routine that does all the bias and dark correction stuff and converts from ADU to e-
if scalable:
# if the darks have a different exposure time than the whites, then we need to re-scale the master dark
texp = pyfits.getval(white_list[0], 'ELAPSED')
img = correct_for_bias_and_dark_from_filename(
fn,
MB,
MD * texp,
gain=gain,
scalable=scalable,
savefile=saveall,
path=path,
timit=timit
) #these are now bias- & dark-corrected images; units are e-
else:
img = correct_for_bias_and_dark_from_filename(
fn,
MB,
MD,
gain=gain,
scalable=scalable,
savefile=saveall,
path=path,
timit=timit
) # these are now bias- & dark-corrected images; units are e-
if debug_level >= 2:
print('min(img) = ' + str(np.min(img)))
allimg.append(img)
# err_img = np.sqrt(img + ronmask*ronmask) # [e-]
# TEMPFIX: (how should I be doing this properly???)
err_img = np.sqrt(np.clip(img, 0, None) + ronmask * ronmask) # [e-]
allerr.append(err_img)
# list of individual exposure times for all whites (should all be the same, but just in case...)
texp_list = [pyfits.getval(file, 'ELAPSED') for file in white_list]
# scale to the median exposure time
tscale = np.array(texp_list) / np.median(texp_list)
#########################################################################
### now we do essentially what "CREATE_MASTER_IMG" does for whites... ###
#########################################################################
# add individual-image errors in quadrature (need it either way, not only for fancy method)
err_summed = np.sqrt(np.sum((np.array(allerr)**2), axis=0))
# # get plain median image
# medimg = np.median(np.array(allimg), axis=0)
# take median after scaling to median exposure time
medimg = np.median(np.array(allimg) / tscale.reshape(len(allimg), 1, 1),
axis=0)
if fancy:
# need to create a co-added frame if we want to do outlier rejection the fancy way
summed = np.sum((np.array(allimg)), axis=0)
if diffimg:
diff = np.zeros(summed.shape)
master_outie_mask = np.zeros(summed.shape, dtype='int')
# make sure we do not have any negative pixels for the sqrt
medimgpos = medimg.copy()
medimgpos[medimgpos < 0] = 0.
med_sig_arr = np.sqrt(
medimgpos + ronmask * ronmask
) # expected STDEV for the median image (from LB Eq 2.1); still in ADUs
for n, img in enumerate(allimg):
# outie_mask = np.abs(img - medimg) > clip*med_sig_arr
outie_mask = (
img - medimg
) > clip * med_sig_arr # do we only want HIGH outliers, ie cosmics?
# save info about which image contributes the outlier pixel using unique binary numbers technique
master_outie_mask += (outie_mask * 2**n).astype(int)
# see which image(s) produced the outlier(s) and replace outies by mean of pixel value from remaining images
n_outie = np.sum(master_outie_mask > 0)
print('Correcting ' + str(n_outie) + ' outliers...')
# loop over all outliers
for i, j in zip(
np.nonzero(master_outie_mask)[0],
np.nonzero(master_outie_mask)[1]):
# access binary numbers and retrieve component(s)
outnum = binary_indices(
master_outie_mask[i, j]
) # these are the indices (within allimg) of the images that contain outliers
dumix = np.arange(len(white_list))
# remove the images containing the outliers in order to compute mean from the remaining images
useix = np.delete(dumix, outnum)
if diffimg:
diff[i, j] = summed[i, j] - (len(outnum) * np.mean(
np.array([allimg[q][i, j] for q in useix])) + np.sum(
np.array([allimg[q][i, j] for q in useix])))
# now replace value in master image by the sum of all pixel values in the unaffected pixels
# plus the number of affected images times the mean of the pixel values in the unaffected images
summed[i, j] = len(outnum) * np.mean(
np.array([allimg[q][i, j] for q in useix])) + np.sum(
np.array([allimg[q][i, j] for q in useix]))
# once we have finished correcting the outliers, we want to "normalize" (ie divide by number of frames) the master image and the corresponding error array
master = summed / len(white_list)
err_master = err_summed / len(white_list)
else:
# ie not fancy, just take the median image to remove outliers
# now set master image equal to median image
master = medimg.copy()
nw = len(white_list) # number of whites
# # estimate of the corresponding error array (estimate only!!!)
# err_master = err_summed / nw # I don't know WTF I was thinking here...
# if roughly Gaussian distribution of values: error of median ~= 1.253*error of mean
# err_master = 1.253 * np.std(allimg, axis=0) / np.sqrt(nw-1) # normally it would be sigma/sqrt(n), but np.std is dividing by sqrt(n), not by sqrt(n-1)
# need to rescale by exp time here, too
if nw == 1:
err_master = allerr[0]
else:
err_master = 1.253 * np.std(
np.array(allimg) / tscale.reshape(len(allimg), 1, 1), axis=0
) / np.sqrt(
nw - 1
) # normally it would be sigma/sqrt(n), but np.std is dividing by sqrt(n), not by sqrt(n-1)
# err_master = np.sqrt( np.sum( (np.array(allimg) - np.mean(np.array(allimg), axis=0))**2 / (nw*(nw-1)) , axis=0) ) # that is equivalent, but slower
# now subtract background (errors remain unchanged)
if remove_bg:
# identify and extract background
bg = extract_background_pid(master,
P_id,
slit_height=30,
exclude_top_and_bottom=True,
timit=timit)
# fit background
bg_coeffs, bg_img = fit_background(bg,
clip=10,
return_full=True,
timit=timit)
# subtract background
master = master - bg_img
# now save master white to file
if savefile:
outfn = path + date + '_master_white.fits'
pyfits.writeto(outfn, np.float32(master), overwrite=True)
pyfits.setval(outfn,
'HISTORY',
value=' MASTER WHITE frame - created ' +
time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime()) +
' (GMT)')
# pyfits.setval(outfn, 'EXPTIME', value=texp, comment='exposure time [s]')
pyfits.setval(outfn, 'UNITS', value='ELECTRONS')
if fancy:
pyfits.setval(
outfn,
'METHOD',
value='fancy',
comment='method to create master white & remove outliers')
else:
pyfits.setval(
outfn,
'METHOD',
value='median',
comment='method to create master white & remove outliers')
h = pyfits.getheader(outfn)
h_err = h.copy()
h_err[
'HISTORY'] = 'estimated uncertainty in MASTER WHITE frame - created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
pyfits.append(outfn, np.float32(err_master), h_err, overwrite=True)
# also save the difference image if desired
if diffimg:
hdiff = h.copy()
hdiff[
'HISTORY'] = ' MASTER WHITE DIFFERENCE IMAGE - created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
pyfits.writeto(path + date + '_master_white_diffimg.fits',
diff,
hdiff,
overwrite=True)
if timit:
print('Total time elapsed: ' +
str(np.round(time.time() - start_time, 1)) + ' seconds')
return master, err_master
Squeeze a DESI GAUSS-HERMITE PSF into something smaller for testing.
Also works for GAUSS-HERMITE2
"""
import sys
import numpy as np
from astropy.io import fits
from astropy.table import Table
infile, outfile = sys.argv
fx = fits.open(infile)
hdr = fx[0].header.copy()
fits.writeto(outfile, np.zeros(0), header=hdr)
hdr = fx[1].header.copy()
nspec = 25
hdr['FIBERMAX'] = nspec-1
data = fx[1].data
tx = Table()
tx['PARAM'] = data['PARAM']
tx['WAVEMIN'] = data['WAVEMIN']
tx['WAVEMAX'] = data['WAVEMAX']
if 'NCOEFF' in data.dtype.names:
tx['NCOEFF'] = data['NCOEFF']
tx['COEFF'] = data['COEFF'][:, 0:nspec, :]
fits.append(outfile, np.array(tx), header=hdr)
def feature_gen_from_lc_fits(path, sector, feature_version=0):
"""Given a path to a folder containing ALL the light curve metafiles
for a sector, produces the feature vector metafile for each group and then
one main feature vector metafile containing ALL the features in [0] and the
TICIDS in [1].
Parameters:
* folderpath to where the light curve metafiles are saved
*must end in a backslash
* sector number
* what version of features you want generated (default is 0)
modified [lcg 07112020]"""
import datetime
from datetime import datetime
now = datetime.now()
dt_string = now.strftime("%d/%m/%Y %H:%M:%S")
print("Starting Feature Generation at", dt_string)
ticids_all = [10]
ticids_all = np.asarray(ticids_all)
sector = sector
for n in range(1, 5):
camera = int(n)
for m in range(1, 5):
ccd = int(m)
file_label = "Sector" + str(sector) + "Cam" + str(
camera) + "CCD" + str(ccd)
folderpath = path + "/" + file_label + "/"
t, i1, targets = load_group_from_fits(folderpath, sector, camera,
ccd)
ticids_all = np.concatenate((ticids_all, targets))
i2, t2 = nan_mask(i1,
t,
flux_err=False,
DEBUG=False,
debug_ind=1042,
ticid=False,
output_dir=folderpath,
prefix='',
tol1=0.05,
tol2=0.1)
i3 = normalize(i2, axis=1)
now = datetime.now()
dt_string = now.strftime("%d/%m/%Y %H:%M:%S")
print("Starting feature vectors for camera ", camera, "ccd ", ccd,
"at ", dt_string)
create_save_featvec(folderpath,
t2,
i3,
file_label,
version=0,
save=True)
ticids_all = ticids_all[1:]
feats_all = np.zeros((2, 16))
#make main listing
for n in range(1, 5):
camera = int(n)
for m in range(1, 5):
ccd = int(m)
file_label = "Sector" + str(sector) + "Cam" + str(
camera) + "CCD" + str(ccd)
folderpath = path + "/" + file_label + "/"
f = fits.open(folderpath + file_label + "_features.fits",
memmap=False)
feats = f[0].data
feats_all = np.concatenate((feats_all, feats))
f.close()
#print(n,m)
feats_all = feats_all[2:]
hdr = fits.Header() # >> make the header
hdr["Sector"] = sector
hdr["Version"] = feature_version
hdr["Date"] = str(datetime.now())
#hdr["Creator"] = "L. Gordon"
hdu = fits.PrimaryHDU(feats_all, header=hdr)
hdu.writeto(folderpath + "Sector" + str(sector) + "_features_v" +
str(feature_version) + "_all.fits")
fits.append(
folderpath + "Sector" + str(sector) + "_features_v" +
str(feature_version) + "_all.fits", ticids_all)
return feats_all, ticids_all
from astropy.io import fits
msName = 'HDFC0155MFSC_CAL_vis.ms'
x=fits.getdata(msName[:-3]+'_'+str(0)+'.fits',0)
header_primary = fits.getheader(msName[:-3]+'_'+str(0)+'.fits')
fits.writeto('HDFC0155_cube.fits', x, header_primary)
for i in range(1,8):
x=fits.getdata(msName[:-3]+'_'+str(i)+'.fits',0)
header_primary = fits.getheader(msName[:-3]+'_'+str(i)+'.fits')
fits.append('HDFC0155_cube.fits', x, header_primary)
print fits.info("HDFC0155_cube.fits")
def remove_cosmics(img,
ronmask,
obsname,
path,
Flim=3.0,
siglim=5.0,
maxiter=20,
savemask=True,
savefile=False,
save_err=False,
verbose=False,
timit=False):
"""
Top-level wrapper function for the cosmic-ray cleaning of an image.
INPUT:
'img' : input image (2-dim numpy array)
'ronmask' : read-out noise mask (or ron-image really...) from "make_master_bias_and_ronmask"
'obsname' : the obsname in "obsname.fits"
'path' : the directory of the files
'Flim' : lower threshold for the identification of a pixel as a cosmic ray when using L+/F (ie Laplacian image divided by fine-structure image) (= lbarplus/F2 in the implementation below)
'siglim' : sigma threshold for identification as cosmic in S_prime
'maxiter' : maximum number of iterations
'savemask' : boolean - do you want to save the cosmic-ray mask?
'savefile' : boolean - do you want to save the cosmic-ray corrected image?
'save_err' : boolean - do you want to save the corresponding error array as well? (remains unchanged though)
'verbose' : boolean - for user information / debugging...
'timit' : boolean - do you want to measure execution run time?
OUTPUT:
'cleaned' : the cosmic-ray corrected image
"""
if timit:
start_time = time.time()
if verbose:
print('Cleaning cosmic rays...')
#some preparations
global_mask = np.cast['bool'](np.zeros(img.shape))
n_cosmics = 0
niter = 0
n_new = 0
cleaned = img.copy()
#remove cosmics iteratively
while ((niter == 0) or n_new > 0) and (niter < maxiter):
print('Now running iteration ' + str(niter + 1) + '...')
#go and identify cosmics
mask = identify_cosmics(cleaned,
ronmask,
Flim=Flim,
siglim=siglim,
verbose=verbose,
timit=timit)
n_new = np.sum(mask)
#add to global mask
global_mask = np.logical_or(global_mask, mask)
n_cosmics += n_new
#n_global = np.sum(global_mask) #should be equal to n_cosmics!!!!! if they're not, this means that some of the "cleaned" cosmics from a previous round are identified as cosmics again!!! well, they're not...
#now go and clean these newly found cosmics
cleaned = clean_cosmics(cleaned, mask, verbose=verbose, timit=timit)
niter += 1
#save cosmic-ray mask
if savemask:
outfn = path + obsname + '_CR_mask.fits'
#get header from the BIAS- & DARK-subtracted image if it exits; otherwise from the original image FITS file
try:
h = pyfits.getheader(path + obsname + '_BD.fits')
except:
h = pyfits.getheader(path + obsname + '.fits')
h['HISTORY'] = ' (boolean) COSMIC-RAY MASK- created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
pyfits.writeto(outfn, global_mask.astype(int), h, clobber=True)
#save cosmic-ray corrected image
if savefile:
outfn = path + obsname + '_BD_CR.fits'
#get header from the BIAS- & DARK-subtracted images if they exit; otherwise from the original image FITS file
try:
h = pyfits.getheader(path + obsname + '_BD.fits')
except:
h = pyfits.getheader(path + obsname + '.fits')
h['UNITS'] = 'ELECTRONS'
h['HISTORY'] = ' COSMIC-RAY corrected image - created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
pyfits.writeto(outfn, cleaned, h, clobber=True)
#also save the error array if desired
if save_err:
try:
err = pyfits.getdata(path + obsname + '_BD.fits', 1)
h_err = h.copy()
h_err[
'HISTORY'] = 'estimated uncertainty in COSMIC-RAY corrected image - created ' + time.strftime(
"%Y-%m-%d %H:%M:%S", time.gmtime()) + ' (GMT)'
pyfits.append(outfn, err, h_err, clobber=True)
except:
print(
'WARNING: error array not found - cannot save error array')
if verbose:
print('Done!')
if timit:
print('Total time elapsed: ' +
str(np.round(time.time() - start_time, 1)) + ' seconds')
return cleaned
def main(massfunction = 0, starformationhistory = 0, A_v = 10.0, sfr = .01, apera = 24000,\
maxage = 2000000., distance = 8.0, appendix='default', quiet=0, precise=0):
"""main(massfunction = 0, starformationhistory = 0, A_v = 10.0, sfr = .01, apera = 24000,\
maxage = 2000000., distance = 8.0, appendix='default', quiet=0, precise=0)
Creates a sample of stars
Parameters
----------
massfunction distribution:
relatively in mass, with lower and upper restriction, see also what the distribution must provide
starformation history distribution:
relatively in age, with lower and upper restriction, see also what the distribution must provide
A_v float:
value for the visual extinction
sfr float:
average star formation rate in M_sun/year (only if precise = True)
apera float:
used aperture size for selecting the fluxes of the protostars
maxage float:
age of the star formation site, sfr is assumed to be constant
distance float:
distance to the simulated starformation site
appendix String:
sets the outputfilename, default is the starting time (via time.time())
quiet boolean:
if true (=1) suppresses all standard output
precise boolean:
if true (=1) sample single star till expected mass reached based on the
integrated starformationhistory times the starformationrate
else sfr is the number of expected stars and the starformationrate is
calculated by the cumulated mass divided by the formation time
The distributions must provide an object which has the following members:
float cdf(float x) returns the integrated distribution up to x, is used to calculate
the expected mass
float _upperbound returns the upper limit of the distribution, is used to calculate
the expected mass
float[] sample(int n) returns an array of n floats, sampled from the distribution
float mean() returns the mean value of the distribution
Returns
----------
returns a fits file in the out-folder, either using the appendix as filename or the time of the
starting of the script in order to prevent overwriting existing files
In the header of the fits-file are the values: A_v, sfr, apera, maxage and distance recorded
In the data part are the age, mass, modelnumber and the uncorrected and corrected fluxes
"""
if quiet:
output_stream = StringIO()
else:
output_stream = sys.stdout
t0 = time()
if appendix=='default': # making sure not to overwrite former output
appendix=t0 # by using the starting time as an unique id
#parameter settings
k_v = 211.4 # opacity in v_band in cm^2/g
# wavelength of the corresponding filterband in microns
wavelength = [1.235, 1.662, 2.159, 3.550, 4.493, 5.731, 7.872, 23.68, 71.42, 155.9]
models = ['2H', '2J', '2K', 'I1', 'I2', 'I3', 'I4', 'M1', 'M2', 'M3']
if massfunction == 0 and starformationhistory == 0:
# star mass function
kroupa = np.vectorize(functions.kroupa)
massfunction = dist.Distribution(kroupa, .1, 50.)
#star formation history
constant_sfr = np.vectorize(functions.constant_sfr)
starformationhistory = dist.Distribution(constant_sfr, 1000., maxage)
cumass = 0. #sampled mass
stars = [] #storing for the sample
sfh = starformationhistory
t1 = time() #startup completed
if precise:
n = 0
exmass = sfh.cdf()(sfh._upperbound)*sfr #expected mass formed
while cumass < exmass:
mass, age = massfunction.sample(), sfh.sample()
cumass = cumass + mass
stars.append([n, age, mass])
if n % 10000 == 0:
print (n, cumass, file=output_stream) #reporting progress
n = n+1
else:
n = sfr
mass, age = massfunction.sample(n), sfh.sample(n)
cumass = np.sum(mass)
exmass = n * massfunction.mean()
stars = [[i, age[i], mass[i]] for i in range(n)]
sfr = cumass/(sfh._upperbound-sfh._lowerbound) #average star formation rate
print ('number of sampled stars: %s' %n , file=output_stream)
print ('mass of sampled stars: %s' % cumass , file=output_stream)
print ('mean mass: %s' % (cumass/n), file=output_stream)
print ('expected mass of stars: %s' % exmass , file=output_stream)
t2 = time() # sampleing completed
# python code for model contact
#initial parameters
model = [ fits.open('models/%s.fits' % mod) for mod in models ] # fits-data for the model
param = fits.open('models/parameters.fits.gz') # modelparameter
app_num = [ np.interp(apera, model[i][2].data.field(0), range(model[i][2].data.field(0).size)) for i in range(len(models)) ]
# sampling viewing angle
angle = np.random.random_integers(0,9,len(stars))
#reading model grid
mass = param[1].data['MASSC'][::10]
age = param[1].data['TIME'][::10]
grid = np.vstack([age, mass]).transpose()
#converting to logspace
stars = np.asarray(stars)
grid = np.log10(grid)
stars[:,1:] = np.log10(stars[:,1:])
output = stars.tolist() #creating output
#normalizing for nearest neighbor search
grid[0,:] = grid[0,:]/(grid[0,:].max() - grid[0,:].min())
grid[1,:] = grid[1,:]/(grid[1,:].max() - grid[1,:].min())
stars[1,:] = stars[1,:]/(grid[0,:].max() - grid[0,:].min())
stars[2,:] = stars[2,:]/(grid[1,:].max() - grid[1,:].min())
t3 = time() #model data load complete
tree = scipy.spatial.cKDTree(grid,leafsize=10) #search tree
matches = [tree.query(star[1:] , k=1)[1] for star in stars] #saves matches with (dist, index)
t4 = time() #matching sample to data complete
# extracting fluxes
fluxes = [0 for j in range(len(models)) ]
indices = 10*np.asarray(matches) + angle
for j in range(len(models)):
fluxes[j] = model[j][1].data[indices]['TOTAL_FLUX'][:,app_num[j]]
# applying extinction
extinction = np.loadtxt('models/extinction_law.ascii')
k_lambda = np.interp(wavelength, extinction[:,0], extinction[:,1])
correctionfactor = 10.**(-.4 * A_v * k_lambda / k_v)
newfluxes = [0 for j in range(len(models)) ]
for j in range(len(models)):
newfluxes[j] = np.asarray(fluxes[j]) * correctionfactor[j] * (1./distance)**2
t5 = time() #extracting fluxes complete
# saving data
fluxes = np.asarray(fluxes)
newfluxes = np.asarray(newfluxes)
output = np.vstack([np.asarray(output).transpose(), matches, fluxes, newfluxes]).transpose()
# create table
# data table
t = Table()
t.add_column(Column(name='age', data=output[:,1]))
t.add_column(Column(name='mass', data=output[:,2]))
t.add_column(Column(name='model', data=output[:,3]))
for i in range(len(models)):
t.add_column(Column(name='%s' % models[i], data=output[:,4+i]))
for i in range(len(models)):
t.add_column(Column(name='c%s' % models[i], data=output[:,4+len(models)+i]))
# head table
header = Table()
header.add_column(Column(name='AV', data = [A_v]))
header.add_column(Column(name='SFR', data = [sfr]))
header.add_column(Column(name='APPERA', data = [apera]) )
header.add_column(Column(name='MAXAGE', data = [maxage]))
header.add_column(Column(name='DIST', data = [distance]))
fits.writeto('out/%s' % appendix, np.array(t), clobber=True)
fits.append('out/%s' % appendix, np.array(header), clobber=True)
t6 = time() #saving complete
# timing possibility for optimization efforts
print( 'starting script at %f' %(t0), file=output_stream)
print( 'initializing %f' %(t1-t0), file=output_stream)
print( "sampleing %f" %(t2-t1), file=output_stream)
print( "model data load %f" %(t3-t2), file=output_stream)
print( "matching model %f" %(t4-t3), file=output_stream)
print( "extracting fluxes %f" %(t5-t4), file=output_stream)
print( "saving %f" %(t6-t5), file=output_stream)
print( "________________________", file=output_stream)
print( "total runtime %f" %(t6-t0), file=output_stream)
print( "finishing script %f" %t6, file=output_stream)
#main(sfr = .08) # for testing purposes and directly called from bash
def _check_hdu_list(self, cutout_dimensions, hdu_list):
has_match = False
pixel_matches_left = len(cutout_dimensions)
for curr_extension_idx, hdu in enumerate(hdu_list):
# If we encounter a PrimaryHDU, write it at the top and continue.
if isinstance(hdu, PrimaryHDU) and hdu.data is None:
logger.debug('Appending Primary from index {}'.format(
curr_extension_idx))
fits.append(filename=self.output_writer,
header=hdu.header,
data=None,
overwrite=False,
output_verify='silentfix',
checksum='remove')
elif hdu.is_image:
header = hdu.header
ext_name = header.get('EXTNAME')
ext_ver = header.get('EXTVER', 0)
curr_ext_name_ver = None
if ext_name is not None:
curr_ext_name_ver = (ext_name, ext_ver)
try:
if isinstance(cutout_dimensions[0], PixelCutoutHDU):
for cutout_dimension in cutout_dimensions:
if self._is_extension_requested(
curr_extension_idx, curr_ext_name_ver,
cutout_dimension):
logger.debug(
'*** Extension {} does match ({} | {})'.
format(cutout_dimension.get_extension(),
curr_extension_idx,
curr_ext_name_ver))
pixel_matches_left -= 1
self._pixel_cutout(header, hdu.data,
cutout_dimension)
has_match = True
if pixel_matches_left == 0:
return has_match
else:
logger.debug('Handling WCS transform.')
# Handle WCS transform.
transform = Transform()
transformed_cutout_dimension = \
transform.world_to_pixels(cutout_dimensions, header)
logger.debug('Transformed {} into {}'.format(
cutout_dimensions, transformed_cutout_dimension))
self._pixel_cutout(header, hdu.data,
transformed_cutout_dimension)
has_match = True
except NoContentError:
# Skip for now as we're iterating the loop.
logger.debug('No overlap with extension {}'.format(
curr_extension_idx))
logger.debug('Finished extension {}'.format(curr_extension_idx))
logger.debug('Has match in list? -- {}'.format(has_match))
return has_match
inv_sq_root_nuisance = 0
white_covar = 0
Un = 0
Dn = 0
ortho_r = 0
Ln = 0
Ln_minus = 0
Pn = 0
vv = 0
Rq = 0
Rq_nuisance = 0
pyfits.append(
'ilc_weights_' + output_suffix + "_" + str(j).strip() + '.fits',
w_target)
w_target = 0
############################################################################ ############################################################################
##### Apply GNILC weights to wavelet maps
print "Applying the GNILC weights to the observed wavelet maps."
for i in range(0, nf):
pyfits.append('wavelet_gnilc_target_' + str(i).strip() + '.fits',
bands[:, 0:relevant_band_max[i] + 1])
for j in range(0, nbands): # loop over needlet bands
def fitting_ve(name):
image_path = name
if not os.path.exists(image_path):
print("{}/{} could not be found: {}".format(i + 1, N, image_path))
keep[i] = False
# We only store flux,ivar,inf_flux,parameters,parameters_new,parameters_sim,ve(n*3)(include ve, ve_new,ve_sim)
try:
image = fits.open(image_path, ignore_missing_end=True)
dat = Table.read(image_path)
flux = image[1].data
flux_err = image[2].data
flux = np.atleast_2d(flux)
flux_err = np.atleast_2d(flux_err)
except IOError:
print("opts. This one fail")
em =0
else:
em =1
badpix = get_pixmask(flux, flux_err)
ivar = 1.0 / flux_err ** 2
error = flux_err
# badpix is a array and the length is 8575
flux = np.array(flux, dtype=np.float64)
ivar = np.array(ivar, dtype=np.float64)
flux[badpix] = np.median(flux)
ivar[badpix] = 0.0
flux = np.array(flux)
ivar = np.array(ivar)
# normalize flux:
# value
tr_ID = image_path
test_labels_all_i = np.array([5000, 1, 1])
ds = dataset.Dataset(wl, tr_ID, flux, ivar,
test_labels_all_i, tr_ID, flux, ivar)
ds.ranges = [[371, 3192], [3697, 5997], [6461, 8255]]
# set sudo-continuous spectrum
pseudo_tr_flux, pseudo_tr_ivar = ds.continuum_normalize_training_q \
(q=0.90, delta_lambda=50)
# set mask
contmask = ds.make_contmask(pseudo_tr_flux, pseudo_tr_ivar, frac=0.07)
# get continuous mask
ds.set_continuum(contmask)
# fit the normalized-spectrum in the continuous region
cont = ds.fit_continuum(3, "sinusoid")
# Obtain the normalized flux
norm_tr_flux, norm_tr_ivar, norm_test_flux, norm_test_ivar = \
ds.continuum_normalize(cont)
norm_tr_flux = np.atleast_2d(norm_tr_flux)
if len(norm_tr_flux[:,0])<3:
em=0
else:
nothing=1
# infer labels
# inf_labels = model.fit(norm_tr_flux, norm_tr_ivar)
# Use inferred labels from the combined spectra:
inf_labels = model.fit(norm_tr_flux, norm_tr_ivar)
# only use the inf labels from the combined spectra
com = len(inf_labels[:, 0])
inf_labels_com = inf_labels[0, :]
inf_labels = []
for z in range(0, com):
inf_labels.append(inf_labels_com)
inf_labels = np.array(inf_labels)
v = model.vectorizer.get_label_vector(inf_labels)
inf_flux = np.dot(v, model.theta.T)
opt_flux, parameters = model.fitting_spectrum_parameters_single \
(norm_tr_flux, norm_tr_ivar, inf_flux)
# calculate chi-squared!
chi_inf = (norm_tr_flux-inf_flux)**2*norm_tr_ivar
chi_inf = np.sum(chi_inf,axis=1)
chi_mix = (norm_tr_flux-opt_flux)**2*norm_tr_ivar
chi_mix = np.sum(chi_mix,axis=1)
ve = (parameters[:, 2] - parameters[:, 0]) / (parameters[:, 0] + parameters[:, 1] + parameters[:, 2]) * 4144.68
ve_un = model.uncertainty
# old
a0 = parameters
a1 = ve
a2 = ve_un
# covariance matrix for abc
a3 = model.un_cov
# spectra
a4 = norm_tr_flux
a5 = norm_tr_ivar
a6 = inf_flux
a7 = opt_flux
# inf_labels are from the
a8 = inf_labels
a9 = chi_inf
a10 = chi_mix
# VHELIO
a11 = np.array(dat[0]["VHELIO"])
# Fiber
a12 = np.array(dat[0]["FIBER"])
# Files
# BJD
RA = image[0].header["RA"]
DEC = image[0].header["DEC"]
SNR = image[0].header["SNR"]
MJD = dat[0]["MJD"]
c = SkyCoord(RA, DEC, frame='icrs', unit='deg')
BJD = MJD2BJD(MJD, c)
a13 = np.array(BJD)
# calculate chi-squared:
try:
# save them
# pay attention to the fits file saving
path_fits_i = image_path.replace("/Volumes/Data_2TB/Data/DR13_rc/apStar-r6-",
"/Users/caojunzhi/Desktop/Data/dr13_red_clump/")
print("saving files" + path_fits_i)
hdu = fits.PrimaryHDU(data=a0)
hdu.header[
'COMMENT'] = "Simple orange juice"
# add header info
hdu.header['SNR'] = SNR
hdu.header['RA'] = RA
hdu.header['DEC'] = DEC
hdu.writeto(path_fits_i, clobber=True)
ts.append(path_fits_i, a1)
ts.append(path_fits_i, a2)
ts.append(path_fits_i, a3)
ts.append(path_fits_i, a4)
ts.append(path_fits_i, a5)
ts.append(path_fits_i, a6)
ts.append(path_fits_i, a7)
ts.append(path_fits_i, a8)
ts.append(path_fits_i, a9)
ts.append(path_fits_i, a10)
ts.append(path_fits_i, a11)
ts.append(path_fits_i, a12)
ts.append(path_fits_i, a13)
except OSError:
print("fail")
em=0
return em
def table_model(modelname, userparfile, specfile, outfile, clobber=False):
# Create Xspec/Sherpa style table model
#
# :rtype: None, <outfile> fits file created.
#
# :param modelname: name of the table model displayed in Xspec/Sherpa
# :param userparfile: file with user keywords for the table model
# :specfile: file with grid of energy spectra, 1st column: energy grid
# in keV; consecutive columns: model spectra
# :param outfile: name of the output fits file
# :param clobber: T/F, if T outfile will be overwritten
#
# Tmp file 'tmp_tabmod.fits' created and removed.
# ----------- READ IN USER INPUT --------------------
if os.path.isfile(outfile) and not clobber:
raise NameError("Output file " + outfile + " exists and clobber set to false\n")
userdict = read_userparams(userparfile)
# Convert userdict['value'] into a list of tuples; one tuple
# for each model parameter
# value_not_padded: used in get_paramval to calculate array with
# combinations of model parameters
idx = 0
value_not_padded = []
for item in userdict["numbvals"]:
value_not_padded.append(tuple(userdict["value"][idx : idx + item]))
idx += item
# value_padded: format required for col10 of the fits file
value_padded = []
maxnum = max(userdict["numbvals"])
for val in value_not_padded:
if len(val) != maxnum:
n = maxnum - len(val)
value_padded.append(val + (0.0,) * n)
else:
value_padded.append(val)
# model energy grid (bin edges!)
energy = np.loadtxt(specfile)[:, 0] # energy in keV
energ_lo = energy[:-1]
energ_hi = energy[1:]
paramval = get_paramval(value_not_padded)
# list of tuples with spectra
input_spectra = read_input_spectra(specfile, userdict["numbvals"])
# ----------- END ---------------------------------
# initialize fits file by creating user parameters extension
col1 = fits.Column(name="NAME", format="12A", array=userdict["name"])
col2 = fits.Column(name="METHOD", format="J", array=userdict["method"])
col3 = fits.Column(name="INITIAL", format="E", array=userdict["initial"])
col4 = fits.Column(name="DELTA", format="E", array=userdict["delta"])
col5 = fits.Column(name="MINIMUM", format="E", array=userdict["minimum"])
col6 = fits.Column(name="BOTTOM", format="E", array=userdict["bottom"])
col7 = fits.Column(name="TOP", format="E", array=userdict["top"])
col8 = fits.Column(name="MAXIMUM", format="E", array=userdict["maximum"])
col9 = fits.Column(name="NUMBVALS", format="J", array=userdict["numbvals"])
col10 = fits.Column(name="VALUE", format=np.str(np.max(userdict["numbvals"])) + "E", array=value_padded)
cols = fits.ColDefs([col1, col2, col3, col4, col5, col6, col7, col8, col9, col10])
tbhdu = fits.BinTableHDU.from_columns(cols)
# update header of user parameters extension
nintparm = len(userdict["numbvals"])
tbhdr = tbhdu.header
tbhdr.set("EXTNAME", "PARAMETERS", "name of this binary table extension")
tbhdr.set("HDUCLASS", "OGIP", "format conforms to OGIP standard")
tbhdr.set("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC")
tbhdr.set("HDUCLAS2", "PARAMETERS", "extension containing parameter info")
tbhdr.set("HDUVERS1", "1.0.0", "version of format")
tbhdr.set("NINTPARM", nintparm, "Number of interpolation parameters")
tbhdr.set("NADDPARM", 0, "Number of additional parameters")
if os.path.isfile("tmp_tabmod.fits"):
os.remove("tmp_tabmod.fits")
tbhdu.writeto("tmp_tabmod.fits")
# update primary header
hdulist = fits.open("tmp_tabmod.fits")
prihdr = hdulist[0].header
prihdr["bitpix"] = 16
prihdr.set("modlname", modelname, "model name")
prihdr.set("modlunit", "photons/cm^2/s", "model units")
prihdr.set("redshift", True, "If true then redshift will be included as a par")
prihdr.set("addmodel", userdict["addmodel"], "If true then this is an additive table model")
prihdr.set("hduclass", "OGIP", "format conforms to OGIP standard")
prihdr.set("hduclas1", "XSPEC TABLE MODEL", "model spectra for XSPEC")
prihdr.set("hduvers1", "1.0.0", "version of format")
if os.path.isfile(outfile):
os.remove(outfile)
hdulist.writeto(outfile)
hdulist.close()
os.remove("tmp_tabmod.fits")
# append extension energies and update its header
col1 = fits.Column(name="ENERG_LO", format="E", array=energ_lo, unit="keV")
col2 = fits.Column(name="ENERG_HI", format="E", array=energ_hi, unit="keV")
cols = fits.ColDefs([col1, col2])
tbhdu_energies = fits.BinTableHDU.from_columns(cols)
hdr = tbhdu_energies.header
hdr.set("EXTNAME", "ENERGIES", "name of this binary table extension")
hdr.set("HDUCLASS", "OGIP", "format conforms to OGIP standard")
hdr.set("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC")
hdr.set("HDUCLAS2", "ENERGIES", "extension containing energy bins info")
hdr.set("HDUVERS1", "1.0.0", "version of format")
fits.append(outfile, tbhdu_energies.data, hdr)
# append extension spectra and update its header
col1 = fits.Column(name="PARAMVAL", format=np.str(nintparm) + "E", array=paramval)
col2 = fits.Column(name="INTPSPEC", format=np.str(len(energ_lo)) + "E", array=input_spectra, unit="photons/cm^2/s")
cols = fits.ColDefs([col1, col2])
tbhdu_spectra = fits.BinTableHDU.from_columns(cols)
hdr = tbhdu_spectra.header
hdr.set("EXTNAME", "SPECTRA", "name of this binary table extension")
hdr.set("HDUCLASS", "OGIP", "format conforms to OGIP standard")
hdr.set("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC")
hdr.set("HDUCLAS2", "MODEL SPECTRA", "extension containing model spectra")
hdr.set("HDUVERS1", "1.0.0", "version of format")
fits.append(outfile, tbhdu_spectra.data, hdr)
return
Version : $Rev: 514 $
Last Update: $Date: 2015-10-16 10:30:00 +0530 (Fri, 16 Oct 2015) $
""")
parser.add_argument("infile",
help="Input Detector Plane Histogram (DPH) file name",
type=str)
parser.add_argument("relqefile",
nargs="?",
default="relativeQE.fits",
help="Input relative qe file name",
type=str)
parser.add_argument("outfile",
nargs="?",
default="output.dph",
help="Output Detector Plane Histrogram file name",
type=str)
args = parser.parse_args()
warnings.simplefilter(action="ignore", category=RuntimeWarning)
#------------------------------------------------------------------------------
dphhdu = fits.open(args.infile)
qehdu = fits.open(args.relqefile)
fits.writeto(args.outfile, dphhdu[0].data, dphhdu[0].header)
for hdunum in range(1, 5):
dph = dphhdu[hdunum].data
qe = qehdu[hdunum].data
dph = dph / qe
dph_ = np.where(np.isnan(dph), 0, dph)
fits.append(args.outfile, dph_, dphhdu[hdunum].header)
#outhdu.writeto(args.outfile);
night = args[0]
expid = int(args[1])
#- Make sure we have what we need as input
assert 'DESI_SPECTRO_SIM' in os.environ
assert 'PIXPROD' in os.environ
if isinstance(expid, str):
expid = int(expid)
#- Where are the input files?
simpath = os.path.join(os.getenv('DESI_SPECTRO_SIM'),
os.getenv('PIXPROD'), night)
opts.inspec = '{}/simspec-{:08d}.fits'.format(simpath, expid)
stdfiber, wave, flux = get_simstds(opts.inspec, opts.spectroid)
if opts.outfile is None:
assert 'DESI_SPECTRO_REDUX' in os.environ
assert 'PRODNAME' in os.environ
outdir = os.path.join(os.getenv('DESI_SPECTRO_REDUX'),
os.getenv('PRODNAME'), 'exposures', night,
'{:08d}'.format(expid))
opts.outfile = '{}/stdflux-sp{}-{:08d}.fits'.format(
outdir, opts.spectroid, expid)
print opts.outfile
fits.writeto(opts.outfile, flux, clobber=True)
fits.append(opts.outfile, wave)
fits.append(opts.outfile, stdfiber)
def run_ppxf(flux, ivar, mask, wave, specres, flux_hdr, outname, redshift, verbose=True):
dx = flux_hdr['CD1_1'] * 3600. # deg to arcsec
dy = flux_hdr['CD2_2'] * 3600. # deg to arcsec
ppxf_obj=ppxf_wrap(redshift, wave, specres)
nx, ny, _ = flux.shape
velarr=np.zeros((nx,ny))
sigarr=np.zeros((nx,ny))
medsnarr=np.zeros((nx,ny))
flagarr=np.zeros((nx,ny),dtype=np.int16) #define flag array
do_not_use = (mask & 2**10) > 0
flux_masked=np.ma.array(flux, mask=do_not_use)
flux_median=np.median(flux_masked, axis=2)
nflux=np.sum(flux_median>0)
print('Start kinematic measurement')
t_start=perf_counter()
if verbose:
print("%2s %2s %10s %10s %5s %11s %4s" % ('i', 'j', 'Velocity', 'Dispersion', 'Chi2', 'Median S/N','t'))
count=0
for j in range(ny):
for i in range(nx):
t = perf_counter()
if flux_median[j,i] > 0:
ppxf_obj.flux=flux[j,i]
ppxf_obj.ivar=ivar[j,i]
ppxf_obj.mask=((mask[j,i] & 2**10) == 0)
res, medsn=ppxf_obj.run()
if not res:
continue
velarr[j,i]=res.sol[0]
sigarr[j,i]=res.sol[1]
medsnarr[j,i]=medsn
flagarr[j,i]=1
count+=1
if verbose:
print("%02d %02d %10.3f %10.3f %5.2f %11.1f %4.1f" % (i, j, res.sol[0], res.sol[1], res.chi2, medsn, perf_counter()-t))
else:
if count==1:
t1=perf_counter()
if count==int(nflux*0.1):
remain_time=(nflux-int(nflux*0.1))*(perf_counter()-t1)/int(nflux*0.1)*1.1
print('remaining time to finish kinematic measurement (approx.): '+('%d' % int(remain_time))+' sec')
print('End measurement')
print('Elapsed time: '+str(int(perf_counter()-t_start))+' sec')
print('Save velocity measurement data in to FITS file: ', outname)
hdu = fits.PrimaryHDU()
hdu.writeto(outname, overwrite=True)
fits.append(outname, velarr)
fits.append(outname, sigarr)
fits.append(outname, medsnarr)
fits.append(outname, flagarr.astype(np.int16))
append_file=fits.open(outname, mode='update')
extnames=['STELLAR_VEL','STELLAR_SIGMA','MEDSN','FLAG']
for k in range(4):
hdr=append_file[k+1].header
hdr['EXTNAME']=extnames[k]
hdr['CD1_1']=dx/3600
hdr['CD2_2']=dy/3600
append_file.close()
#import h5py
name = sys.argv[1]
num = float(sys.argv[2])
path=sys.argv[4]
fn = path+"/DD%04i/DD%04i" % (num, num) # parameter file to load
print(fn)
pf = load(fn) # load data
# This is the resolution we will extract at
DIMS = int(sys.argv[3])
# Now, we construct an object that describes the data region and structure we
# want
cube = pf.h.covering_grid(0, # The level we are willing to extract to; higher
left_edge=[0.0, 0.0, 0.0],
right_edge=[1.0, 1.0, 1.0],
dims=[DIMS,DIMS,DIMS],
fields=["Density"])
#print cube
pyfits.writeto('%s_flatrho_%04i.fits' %(name, num), cube["Density"])
pyfits.append('%s_flatrho_%04i.fits' %(name, num), cube["x-velocity"])
pyfits.append('%s_flatrho_%04i.fits' %(name, num), cube["y-velocity"])
pyfits.append('%s_flatrho_%04i.fits' %(name, num), cube["z-velocity"])
def _saveCube(self, total_cube, name):
fits_file_name = os.path.join(Caliball._storageFolder(), name)
pyfits.writeto(fits_file_name, total_cube.data)
pyfits.append(fits_file_name, total_cube.mask.astype(int))