def savefits(self,filename,bary=False):
'''
outputs a FITS file containing the histogram lightcurve
v1.0 Kieran O'Brien - Dec 2011
'''
# try:
if bary:
print 'saving barytime corrected lightcurve'
col1=pyfits.Column(name='BARYTIME',format='E', array=self.barytimes)
col2=pyfits.Column(name='COUNTS',format='E', array=self.obsheights)
cols=pyfits.ColDefs([col1,col2])
tbhdu=pyfits.new_table(cols)
hdu=pyfits.PrimaryHDU(0)
thdulist=pyfits.HDUList([hdu,tbhdu])
thdulist.writeto(filename)
else:
print 'saving uncorrected lightcurve'
col1=pyfits.Column(name='TIME',format='E', array=self.obstimes)
col2=pyfits.Column(name='COUNTS',format='E', array=self.obsheights)
cols=pyfits.ColDefs([col1,col2])
tbhdu=pyfits.new_table(cols)
hdu=pyfits.PrimaryHDU(0)
thdulist=pyfits.HDUList([hdu,tbhdu])
thdulist.writeto(filename)
# except:
# print 'ERROR: problem writing file'
return
def write(hdu, filename, quiet=False, clobber=True, shortdir=None):
'''Write a nice fits file. Filenames with .gz will be compressed using the system
gzip call. hdu can be either a column table list or a pyfits.bintable object.
it notifies the user what was written.
clobber=[True] -- Overwrite files by default
quiet=[False] -- Do not announce that we are writing a file. Why would you not?
shortdir=['/path/','<Dir>'] -- Shorten the filename that is printed out to the screen
'''
# Handle column lists and hdus
if isinstance(hdu, pyfits.hdu.table.BinTableHDU):
hdus = hdu
elif (isinstance(hdu, list) or isinstance(hdu, tuple)) and (isinstance(hdu[0], pyfits.Column)):
hdus = pyfits.new_table(pyfits.ColDefs(hdu))
elif isinstance(hdu, Cat):
hdus = pyfits.new_table(pyfits.ColDefs(hdu.columns))
else:
hdus = pyfits.HDUList(hdu)
# Save and compress if needed
outname = filename.replace('.gz','')
hdus.writeto(outname, clobber=clobber)
if '.gz' in filename:
subprocess.call(['gzip', '-f', outname])
# You should generally tell the user what was saved, but hey you can
# play with matches if you want.
if not quiet:
# print "Saved to: %s"%(filename)
if shortdir is not None:
splog('Saved to:', filename.replace(shortdir[0], shortdir[1]))
else:
splog('Saved to:', filename)
def pixelizeCatalog(infiles, config, force=False):
"""
Break catalog up into a set of healpix files.
"""
nside_catalog = config['coords']['nside_catalog']
nside_pixel = config['coords']['nside_pixel']
outdir = mkdir(config['catalog']['dirname'])
filenames = config.getFilenames()
for ii,infile in enumerate(infiles):
logger.info('(%i/%i) %s'%(ii+1, len(infiles), infile))
f = pyfits.open(infile)
data = f[1].data
header = f[1].header
logger.info("%i objects found"%len(data))
if not len(data): continue
glon,glat = cel2gal(data['RA'],data['DEC'])
catalog_pix = ang2pix(nside_catalog,glon,glat,coord='GAL')
pixel_pix = ang2pix(nside_pixel,glon,glat,coord='GAL')
names = [n.upper() for n in data.columns.names]
ra_idx = names.index('RA'); dec_idx = names.index('DEC')
idx = ra_idx if ra_idx > dec_idx else dec_idx
catalog_pix_name = 'PIX%i'%nside_catalog
pixel_pix_name = 'PIX%i'%nside_pixel
coldefs = pyfits.ColDefs(
[pyfits.Column(name='GLON',format='1D',array=glon),
pyfits.Column(name='GLAT',format='1D',array=glat),
pyfits.Column(name=catalog_pix_name,format='1J',array=catalog_pix),
pyfits.Column(name=pixel_pix_name ,format='1J',array=pixel_pix)]
)
hdu = pyfits.new_table(data.columns[:idx+1]+coldefs+data.columns[idx+1:])
table = hdu.data
for pix in numpy.unique(catalog_pix):
logger.debug("Processing pixel %s"%pix)
outfile = filenames.data['catalog'][pix]
if not os.path.exists(outfile):
logger.debug("Creating %s"%outfile)
names = [n.upper() for n in table.columns.names]
formats = table.columns.formats
columns = [pyfits.Column(n,f) for n,f in zip(names,formats)]
out = pyfits.HDUList([pyfits.PrimaryHDU(),pyfits.new_table(columns)])
out[1].header['NSIDE'] = nside_catalog
out[1].header['PIX'] = pix
out.writeto(outfile)
hdulist = pyfits.open(outfile,mode='update')
t1 = hdulist[1].data
# Could we speed up with sorting and indexing?
t2 = table[ table[catalog_pix_name] == pix ]
nrows1 = t1.shape[0]
nrows2 = t2.shape[0]
nrows = nrows1 + nrows2
out = pyfits.new_table(t1.columns, nrows=nrows)
for name in t1.columns.names:
out.data.field(name)[nrows1:]=t2.field(name)
hdulist[1] = out
logger.debug("Writing %s"%outfile)
hdulist.flush()
hdulist.close()
def make_irf_index(index_mapping, outfile):
if isinstance(index_mapping, dict):
evclass, evtype = read_mappings_from_dict(index_mapping)
else:
evclass, evtype = read_mappings(index_mapping)
output = pyfits.HDUList()
output.append(pyfits.PrimaryHDU())
evclass_cols = [
pyfits.Column('EVENT_CLASS', format='60A', unit=' ', array=evclass[0]),
pyfits.Column('BITPOSITION', format='1I', unit=' ', array=evclass[1]),
pyfits.Column('EVENT_TYPES', format='1J', unit=' ', array=evclass[2])
]
evclass_hdu = pyfits.new_table(evclass_cols)
evclass_hdu.name = "BITMASK_MAPPING"
output.append(evclass_hdu)
evtype_cols = [
pyfits.Column('EVENT_TYPE', format='60A', unit=' ', array=evtype[0]),
pyfits.Column('BITPOSITION', format='1I', unit=' ', array=evtype[1]),
pyfits.Column('EVENT_TYPE_PARTITION',
format='20A',
unit=' ',
array=evtype[2])
]
evtype_hdu = pyfits.new_table(evtype_cols)
evtype_hdu.name = "EVENT_TYPE_MAPPING"
output.append(evtype_hdu)
output.writeto(outfile, clobber=True)
def add_columns(filename, colnames, newarrays, formats):
# append new columns to an existing table
oldfile = filename + ".OLD"
try:
os.system('mv %s %s' % (filename, oldfile))
except:
os.system('rm %s' % oldfile)
os.system('mv %s %s' % (filename, oldfile))
# write the new columns to a temporary table
newcols = []
for i in range(len(colnames)):
newcols += [
pyfits.Column(name=colnames[i],
format=formats[i],
array=newarrays[i])
]
newcols = pyfits.ColDefs(newcols)
tbhdu = pyfits.new_table(newcols)
try:
tbhdu.writeto('temp.fits')
except:
os.system('rm temp.fits')
tbhdu.writeto('temp.fits')
# Now read in the old table and merge
h1 = pyfits.open(oldfile)
h2 = pyfits.open('temp.fits')
h = h1[1].columns + h2[1].columns # merge the columns
newhdu = pyfits.new_table(h)
newhdu.writeto(filename)
return 0
def writeSparseHealpixMap(pix, data_dict, nside, outfile,
distance_modulus_array = None,
coordsys = 'NULL', ordering = 'NULL',
header_dict = None):
"""
Sparse HEALPix maps are used to efficiently store maps of the sky by only
writing out the pixels that contain data.
Three-dimensional data can be saved by supplying a distance modulus array
which is stored in a separate extension.
coordsys [gal, cel]
ordering [ring, nest]
"""
hdul = pyfits.HDUList()
# Pixel data extension
columns_array = [pyfits.Column(name = 'PIX',
format = 'K',
array = pix)]
for key in data_dict.keys():
if data_dict[key].shape[0] != len(pix):
logger.warning('First dimension of column %s (%i) does not match number of pixels (%i).'%(key,
data_dict[key].shape[0],
len(pix)))
if len(data_dict[key].shape) == 1:
columns_array.append(pyfits.Column(name = key,
format = 'E',
array = data_dict[key]))
elif len(data_dict[key].shape) == 2:
columns_array.append(pyfits.Column(name = key,
format = '%iE'%(data_dict[key].shape[1]),
array = data_dict[key]))
else:
logger.warning('Unexpected number of data dimensions for column %s.'%(key))
hdu_pix_data = pyfits.new_table(columns_array)
hdu_pix_data.header.update('NSIDE', nside)
hdu_pix_data.header.update('COORDSYS', coordsys.upper())
hdu_pix_data.header.update('ORDERING', ordering.upper())
hdu_pix_data.header.update(header_dict)
hdu_pix_data.name = 'PIX_DATA'
hdul.append(hdu_pix_data)
# Distance modulus extension
if distance_modulus_array is not None:
hdu_distance_modulus = pyfits.new_table([pyfits.Column(name = 'DISTANCE_MODULUS',
format = 'E',
array = distance_modulus_array)])
hdu_distance_modulus.name = 'DISTANCE_MODULUS'
hdul.append(hdu_distance_modulus)
hdul.writeto(outfile, clobber = True)
def main():
import glob
import numpy as np
import pyfits as pf
import matplotlib.pyplot as plt
dirlst = glob.glob('*cloud*')
dirlst.sort()
for dirname in dirlst:
print dirname
filelist = glob.glob(dirname+'/*.21')
filelist.sort()
hdu = pf.PrimaryHDU(np.arange(100))
hdulist = pf.HDUList([hdu])
for fname in filelist:
logg, partsize, temperature, metal, lam, flam = getDataCloudy(fname)
c1 = pf.Column(name='Wavelength',format='E',array=lam)
c2 = pf.Column(name='Flux',format='E',array=flam)
tbhdu = pf.new_table([c1,c2])
tbhdu.header.update('LOGG',logg)
tbhdu.header.update('TEMPERAT',temperature,'units K')
tbhdu.header.update('PARTSIZE',partsize,'units microns')
tbhdu.header.update('Z',metal)
hdulist.append(tbhdu)
hdulist.writeto(dirname+'.fits')
dirlst = glob.glob('clr*')
dirlst.sort()
for dirname in dirlst:
print dirname
filelist = glob.glob(dirname+'/*.clr')
filelist.sort()
hdu = pf.PrimaryHDU(np.arange(100))
hdulist = pf.HDUList([hdu])
for fname in filelist:
logg, temperature, eddy, metal, lam, flam = getDataClr(fname)
c1 = pf.Column(name='Wavelength',format='E',array=lam)
c2 = pf.Column(name='Flux',format='E',array=flam)
tbhdu = pf.new_table([c1,c2])
tbhdu.header.update('LOGG',logg)
tbhdu.header.update('TEMPERAT',temperature,'units K')
tbhdu.header.update('EDDYCOEF',eddy)
tbhdu.header.update('Z',metal)
hdulist.append(tbhdu)
hdulist.writeto(dirname+'.fits')
def testCombineCats(self):
normkeys = 'FLUX_APER1 FLUXERR_APER1 MAG_APER1 MAGERR_APER1 BLANK1 BLANK2'.split(
)
mastercols = [pyfits.Column(name = k,
format = 'E',
array = numpy.ones(30)) \
for k in normkeys]
mastercols[0] = pyfits.Column(name='FLUX_APER1',
format='E',
array=numpy.random.standard_normal(30))
zerokeys = 'MaxVal BackGr'.split()
for key in zerokeys:
mastercols.append(
pyfits.Column(name=key, format='E', array=numpy.zeros(30)))
mastercols.append(
pyfits.Column(name='IMAFLAGS_ISO',
format='J',
array=numpy.ones(30)))
cats = [ldac.LDACCat(pyfits.new_table(pyfits.ColDefs(mastercols)))]
for i in xrange(5):
cols = [pyfits.Column(name = k,
format = 'E',
array = numpy.random.standard_normal(30)) \
for k in normkeys]
cols[0] = pyfits.Column(name='FLUX_APER1',
format='E',
array=numpy.random.standard_normal(30))
for key in zerokeys:
cols.append(
pyfits.Column(name=key, format='E', array=numpy.zeros(30)))
cols.append(
pyfits.Column(name='IMAFLAGS_ISO',
format='E',
array=numpy.ones(30)))
cats.append(ldac.LDACCat(pyfits.new_table(pyfits.ColDefs(cols))))
keys = normkeys[2:] + zerokeys
keys.append('IMAFLAGS_ISO')
combinedcat = combineCats(cats, saturation=5)
self.assertEqual(type(combinedcat), type(cats[0]))
for key in keys:
self.assertTrue(key in combinedcat.keys())
self.assertTrue((combinedcat['BLANK1'] == 1).all())
self.assertTrue((combinedcat['BLANK2'] == 1).all())
self.assertTrue((combinedcat['MAG_APER1'] == 1).all())
self.assertTrue((combinedcat['MAGERR_APER1'] == 1).all())
self.assertTrue((combinedcat['FLUX_APER1-1'] != 1).all())
self.assertTrue((combinedcat['FLUXERR_APER1-1'] != 1).all())
def gen_UDFspec_fits(sourcefiles, outputdir, clobber=False, verbose=True):
"""
Load the 1D spectra from a set of source files, and save the indivdual spectra as
stand alone fits files (makes comparison plotting with MUSEWidePlots.plot_1DspecOverview() straight forward)
--- EXAMPLE OF USE ---
import MUSE_TDOSEvsUDF as mtu
sourcefiles = ['/Volumes/DATABCKUP1/UDFvsMUSEWide/udf10_c042_e031_withz_iter6/udf_udf10_00004.fits','/Volumes/DATABCKUP1/UDFvsMUSEWide/udf10_c042_e031_withz_iter6/udf_udf10_00006.fits','/Volumes/DATABCKUP1/UDFvsMUSEWide/udf10_c042_e031_withz_iter6/udf_udf10_00533.fits']
outputdir = '/Volumes/DATABCKUP1/UDFvsMUSEWide/udf10_c042_e031_withz_iter6_1Dspecs/'
mtu.gen_UDFspec_fits(sourcefiles,outputdir,clobber=False)
"""
if not os.path.isdir(outputdir):
sys.exit('Output directory specified (' + outputdir +
') does not appear to exist')
redshifts, specdic = mtu.load_sourcefile_spectra(sourcefiles,
verbose=verbose)
if verbose:
print(
' - Storing spectra extracted from source files to individual fits files'
)
for sourcefile in sourcefiles:
for spec in specdic[sourcefile].keys():
if spec.startswith('SPE_'):
specarr = specdic[sourcefile][spec]
fitsname = outputdir + sourcefile.split('/')[-1].replace(
'.fits', '_' + spec + '.fits')
if verbose: print(' Generating ' + fitsname)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
c1 = pyfits.Column(name='lambda',
format='D',
unit='ang',
array=specarr['lambda'])
c2 = pyfits.Column(name='flux',
format='D',
unit='1e-20 erg/ang/cm2/s',
array=specarr['flux'])
c3 = pyfits.Column(name='fluxerror',
format='D',
unit='1e-20 erg/ang/cm2/s',
array=specarr['fluxerror'])
coldefs = pyfits.ColDefs([c1, c2, c3])
tb = pyfits.new_table(coldefs) # creating default header
head = tb.header
tbHDU = pyfits.new_table(coldefs, header=head)
tbHDU.writeto(fitsname, clobber=clobber)
def add_bins(sname='final'):
p = pyfits.open(data_path+'gz2sample_%s_abs_regions.fits'%sname)
d = p['data'].data
redshift = d.field('redshift')
zmask = notNaN(redshift)
oldcols = p['data'].columns
bincols = {}
cols = []
for c in oldcols:
cols.append(pyfits.Column(name=c.name, format=c.format,
array=d.field(c.name)))
for k in bins.keys():
x = d.field(k)[zmask]
bin_min, bin_max, bin_step = bins[k]
xbin = N.zeros(redshift.shape, N.int) - 9999
xbinz = (N.floor((x - bin_min) / bin_step)).astype(N.int)
maxbin = int(round((bin_max - bin_min) / bin_step))
print k, maxbin
low = xbinz < 0
high = xbinz >= maxbin
xbinz[low] = -999
xbinz[high] = 999
xbin[zmask] = xbinz
name = ('%s_simple_bin'%k).upper()
cols.append(pyfits.Column(name=name,
format='I', array=xbin))
bin = N.arange(0, maxbin, 1)
min = bin * bin_step + bin_min
max = min + bin_step
center = min + 0.5*bin_step
bincols[k] = [pyfits.Column(name='bin', format='I', array=bin),
pyfits.Column(name='min', format='E', array=min),
pyfits.Column(name='max', format='E', array=max),
pyfits.Column(name='centre',
format='E', array=center)]
hdulist = pyfits.HDUList()
hdulist.append(pyfits.PrimaryHDU())
tbhdu=pyfits.new_table(cols)
tbhdu.name = 'data'
hdulist.append(tbhdu)
for k in bincols.keys():
c = bincols[k]
tbhdu=pyfits.new_table(c)
tbhdu.name = '%s_simple_bins'%k
hdulist.append(tbhdu)
outfile = data_path+'gz2sample_%s_abs_regions_bins.fits'%sname
file_exists = os.path.isfile(outfile)
if file_exists:
os.remove(outfile)
hdulist.writeto(outfile)
p.close()
def add_bins(sname='final'):
p = pyfits.open(data_path + 'gz2sample_%s_abs_regions.fits' % sname)
d = p['data'].data
redshift = d.field('redshift')
zmask = notNaN(redshift)
oldcols = p['data'].columns
bincols = {}
cols = []
for c in oldcols:
cols.append(
pyfits.Column(name=c.name, format=c.format, array=d.field(c.name)))
for k in bins.keys():
x = d.field(k)[zmask]
bin_min, bin_max, bin_step = bins[k]
xbin = N.zeros(redshift.shape, N.int) - 9999
xbinz = (N.floor((x - bin_min) / bin_step)).astype(N.int)
maxbin = int(round((bin_max - bin_min) / bin_step))
print k, maxbin
low = xbinz < 0
high = xbinz >= maxbin
xbinz[low] = -999
xbinz[high] = 999
xbin[zmask] = xbinz
name = ('%s_simple_bin' % k).upper()
cols.append(pyfits.Column(name=name, format='I', array=xbin))
bin = N.arange(0, maxbin, 1)
min = bin * bin_step + bin_min
max = min + bin_step
center = min + 0.5 * bin_step
bincols[k] = [
pyfits.Column(name='bin', format='I', array=bin),
pyfits.Column(name='min', format='E', array=min),
pyfits.Column(name='max', format='E', array=max),
pyfits.Column(name='centre', format='E', array=center)
]
hdulist = pyfits.HDUList()
hdulist.append(pyfits.PrimaryHDU())
tbhdu = pyfits.new_table(cols)
tbhdu.name = 'data'
hdulist.append(tbhdu)
for k in bincols.keys():
c = bincols[k]
tbhdu = pyfits.new_table(c)
tbhdu.name = '%s_simple_bins' % k
hdulist.append(tbhdu)
outfile = data_path + 'gz2sample_%s_abs_regions_bins.fits' % sname
file_exists = os.path.isfile(outfile)
if file_exists:
os.remove(outfile)
hdulist.writeto(outfile)
p.close()
def _defineVariables(self):
"""
Helper funtion to define pertinent variables from catalog data.
"""
self.objid = self.data.field(self.config['catalog']['objid_field'])
self.lon = self.data.field(self.config['catalog']['lon_field'])
self.lat = self.data.field(self.config['catalog']['lat_field'])
#if self.config['catalog']['coordsys'].lower() == 'cel' \
# and self.config['coords']['coordsys'].lower() == 'gal':
# logger.info('Converting catalog objects from CELESTIAL to GALACTIC cboordinates')
# self.lon, self.lat = ugali.utils.projector.celToGal(self.lon, self.lat)
#elif self.config['catalog']['coordsys'].lower() == 'gal' \
# and self.config['coords']['coordsys'].lower() == 'cel':
# logger.info('Converting catalog objects from GALACTIC to CELESTIAL coordinates')
# self.lon, self.lat = ugali.utils.projector.galToCel(self.lon, self.lat)
self.mag_1 = self.data.field(self.config['catalog']['mag_1_field'])
self.mag_err_1 = self.data.field(self.config['catalog']['mag_err_1_field'])
self.mag_2 = self.data.field(self.config['catalog']['mag_2_field'])
self.mag_err_2 = self.data.field(self.config['catalog']['mag_err_2_field'])
if self.config['catalog']['mc_source_id_field'] is not None:
if self.config['catalog']['mc_source_id_field'] in self.data.names:
self.mc_source_id = self.data.field(self.config['catalog']['mc_source_id_field'])
logger.info('Found %i MC source objects'%(numpy.sum(self.mc_source_id > 0)))
else:
#ADW: This is pretty kludgy, please fix... (FIXME)
columns_array = [pyfits.Column(name = self.config['catalog']['mc_source_id_field'],
format = 'I',
array = numpy.zeros(len(self.data)))]
hdu = pyfits.new_table(columns_array)
self.data = pyfits.new_table(pyfits.new_table(self.data.view(np.recarray)).columns + hdu.columns).data
self.mc_source_id = self.data.field(self.config['catalog']['mc_source_id_field'])
# should be @property
if self.config['catalog']['band_1_detection']:
self.mag = self.mag_1
self.mag_err = self.mag_err_1
else:
self.mag = self.mag_2
self.mag_err = self.mag_err_2
# should be @property
self.color = self.mag_1 - self.mag_2
self.color_err = numpy.sqrt(self.mag_err_1**2 + self.mag_err_2**2)
logger.info('Catalog contains %i objects'%(len(self.data)))
def testSaveOffsetsforSLR(self):
zplist = ldac.LDACCat(pyfits.new_table(pyfits.ColDefs([pyfits.Column(name = 'filter', format='20A',
array = self.filternames),
pyfits.Column(name = 'zeropoints', format='E',
array = self.orig_zps)])))
saveSlrZP(cluster = 'testcluster', offsetFile = self.offsetFile,
zplist = zplist, fluxtype = 'iso', myspec = 'custom',
photometry_db = self.db)
self.assertEquals(len(self.db.slr), 3)
self.assertEquals(sorted([slr.fitFilter for slr in self.db.slr]), sorted(self.slr_zps.keys()))
for slr in self.db.slr:
match = self.slr_zps[slr.fitFilter]
self.assertEquals(slr.cluster, 'testcluster')
self.assertEquals(slr.fitFilter, match.filter)
self.assertTrue(np.abs(slr.zp - match.zp) < 0.001)
self.assertTrue(np.abs(slr.zperr - match.zperr) < 0.001)
self.assertEquals(slr.fluxtype, 'iso')
self.assertEquals(slr.myspec, 'custom')
def hitrandom(n,NS,FS,scaledata,bp): #Randomly creates 1 or 2 hits per time step n = np.random.randint(1,3) detpow = np.random.uniform(20,100,n) meanpow = np.random.uniform(1,20,n) bzero3 = scaledata[0] bscale3 = scaledata[1] bzero4 = scaledata[2] bscale4 = scaledata[3] corchan = np.int16(np.array([i-bzero3 for i in np.random.randint(1,NS,size=n)])) finchan = np.int32(np.array([i-bzero4 for i in np.random.randint(1,FS,size=n)])) #ET Signal in a given beam beam = [0,1,2] if(bp in beam): detpow = np.append(detpow,1200.0) detpow = np.append(detpow,1300.0) meanpow = np.append(meanpow,10.0) meanpow = np.append(meanpow,10.0) corchan = np.append(corchan,np.int16(125-bzero3)) corchan = np.append(corchan,np.int16(225-bzero3)) finchan= np.append(finchan,np.int32(0-bzero4)) finchan= np.append(finchan,np.int32(0-bzero4)) c1 = pyfits.Column(name='DETPOW',format='1E',array=detpow) c2 = pyfits.Column(name='MEANPOW',format='1E',array=meanpow) #c3 = pyfits.Column(name='COARCHAN',format='1I',array=corchan,bzero=bzero3,bscale=bscale3) c3 = pyfits.Column(name='COARCHAN',format='1I',array=corchan) #c4 = pyfits.Column(name='FINECHAN',format='1J',array=finchan,bzero=bzero4,bscale=bscale4) c4 = pyfits.Column(name='FINECHAN',format='1J',array=finchan) tbhdu = pyfits.new_table([c1, c2, c3, c4]) return tbhdu
def write_cmd_file(near_targ, target):
'''
Takes the rec array of sources near target and the rec array of the target and produces a fits table.
'''
# Columns to be in the fits table: these data are for the nearby sources
c1 = pyfits.Column(name='HSTID', format='20A', array=near_targ['hstid'])
c2 = pyfits.Column(name='RA', format='F', array=near_targ['degra'])
c3 = pyfits.Column(name='DEC', format='F', array=near_targ['degdec'])
c4 = pyfits.Column(name='V', format='F', array=near_targ['v'])
c5 = pyfits.Column(name='VERR', format='F', array=near_targ['verr'])
c6 = pyfits.Column(name='BV', format='F', array=near_targ['bvcol'])
c7 = pyfits.Column(name='BVERR', format='F', array=near_targ['bvcolerr'])
c8 = pyfits.Column(name='VI', format='F', array=near_targ['vicol'])
c9 = pyfits.Column(name='VIERR', format='F', array=near_targ['vicolerr'])
# Make table
table_hdu = pyfits.new_table([c1, c2, c3, c4, c5, c6, c7, c8, c9])
# Updates header with contains the target's info
table_hdu.header.update(key='HSTID', value=target['hstid'])
table_hdu.header.update(key='LBTID', value=target['lbtid'])
table_hdu.header.update(key='RA', value=str(target['ra']))
table_hdu.header.update(key='DEC', value=str(target['dec']))
# Table data cannot be the Primary HDU, so we make an empty Primary HDU
phdu = pyfits.PrimaryHDU()
# Zeroth extension is empty, first extension contains the table
hdulist = pyfits.HDUList([phdu, table_hdu])
hdulist.writeto(target['lbtid'] + '.fits')
def Combine( flist , fout,
overwrite=0):
"Combines columns from various fits files"
"""flist needs to be of format ( (fname, col-prefix), ... ) """
tabins= [ (pyfits.open( x[0] )[1], x[1]) for x in flist ]
coldefs = []
for tab,prefix in tabins:
tabcds=tab.columns
print tabcds.formats
coldefs.extend( CopyColDefs( tab, prefix))
tabout= pyfits.new_table( coldefs , nrows=len(tabins[0][0].data))
for tab,prefix in tabins:
tabcds=tab.columns
for cname in tabcds.names:
tabout.data.field(prefix+cname)._copyFrom(tab.data.field(cname))
Write([pyfits.PrimaryHDU(), tabout],
fout,
overwrite=overwrite)
def save(self, pathname=None, sim_num=0, file_ext='fits', planet=None):
if not pathname: pathname = '.'
full_path = os.path.expanduser(os.path.join(pathname, str(sim_num), 'static'))
try:
os.makedirs(full_path)
except os.error:
pass
filename = os.path.join(full_path, self.opt.name)
if file_ext == 'fits':
prihdr = pyfits.Header()
prihdr['wavsol_0'] = (self.opt.ld().base[0], 'reference pixel wl')
prihdr['wavsol_1'] = (self.opt.ld().base[1], '')
prihdr['wavsol_2'] = (self.opt.ld().base[2], 'reference pixel')
prihdr['BUNITS'] = "{:>18s}".format(str(self.fp.units))
if planet:
prihdr['NAME'] = ("{:>18s}".format(planet.planet.name), '')
prihdr['T14'] = (float(planet.t14), str(planet.t14.units))
prihdr['PERIOD'] = (float(planet.planet.P),
str(planet.planet.P.units))
fp_hdu = pyfits.PrimaryHDU(self.fp, header=prihdr)
tb_hdu = pyfits.new_table(pyfits.ColDefs([
pyfits.Column(name='wl', format='E', array=self.wl_solution),
pyfits.Column(name='cr', format='E', array=self.planet.sed),
pyfits.Column(name='star', format='E', array=self.star.sed)]))
hdulist = pyfits.HDUList([fp_hdu, tb_hdu])
hdulist.writeto(filename + '.' + file_ext, clobber=True)
else:
exolib.exosim_error('channel.save - file format not supported')
def convertCosmos(inName, outName):
inFile = open(inName, "r")
table = asciitable.read(inFile, Reader=asciitable.FixedWidthTwoLine, delimiter='|', header_start=0,
data_start=4, data_end=-1)
schema = pyfits.ColDefs([column for column in MAPPING.values()])
outHdu = pyfits.new_table(schema, nrows=len(table))
outData = outHdu.data
for name, column in MAPPING.items():
outData.field(column.name)[:] = table.field(name)
for f in FILTERS:
mag = outData.field(f)
err = outData.field(f + "_err")
indices = numpy.where(numpy.logical_or(mag < 0, mag > 50))
mag[indices] = numpy.NAN
err[indices] = numpy.NAN
outHdu.writeto(outName, clobber=True)
print "Wrote %s" % outName
print "To create an astrometry.net catalogue, execute:"
outBase = outName.replace(".fits", "")
print "build-index -i %s -o %s_and_0.fits -I 77770 -P0 -n 100 -S r -L 20 -E -M -j 0.4" % (inName, outBase)
for i in range(1, 5):
print "build-index -1 %s_and_0.fits -o %s_and_%d.fits -I 7777%d -P%d -n 100 -S r -L 10 -E -M -j 0.4 &" % (outBase, outBase, i, i, i)
def run_treecorr(x, y, g1, g2):
"""Helper routine to take outputs of GalSim shear grid routine, and run treecorr on it."""
import pyfits
import os
import treecorr
# Use fits binary table for faster I/O.
assert x.shape == y.shape
assert x.shape == g1.shape
assert x.shape == g2.shape
x_col = pyfits.Column(name='x', format='1D', array=x.flatten() )
y_col = pyfits.Column(name='y', format='1D', array=y.flatten() )
g1_col = pyfits.Column(name='g1', format='1D', array=g1.flatten() )
g2_col = pyfits.Column(name='g2', format='1D', array=g2.flatten() )
cols = pyfits.ColDefs([x_col, y_col, g1_col, g2_col])
table = pyfits.new_table(cols)
phdu = pyfits.PrimaryHDU()
hdus = pyfits.HDUList([phdu,table])
hdus.writeto('temp.fits',clobber=True)
# Define the treecorr catalog object.
cat = treecorr.Catalog('temp.fits',x_units='degrees',y_units='degrees',
x_col='x',y_col='y',g1_col='g1',g2_col='g2')
# Define the corrfunc object
gg = treecorr.GGCorrelation(min_sep=min_sep, max_sep=max_sep, bin_size=0.1, sep_units='degrees')
# Actually calculate the correlation function.
gg.process(cat)
os.remove('temp.fits')
return gg
def seeingtable(sdb, mintime, maxtime):
#extract the seeing data from the sdb
sel_cmd='DateTime, Mass, Dimm'
tab_cmd='MassDimm'
log_cmd="DateTime>'%s' and DateTime<'%s'" % (mintime, maxtime)
see_rec=saltmysql.select(sdb, sel_cmd, tab_cmd, log_cmd)
if len(see_rec)<2: return None
stime_list=[]
mass_arr=np.zeros(len(see_rec))
dimm_arr=np.zeros(len(see_rec))
for i in range(len(see_rec)):
stime_list.append(see_rec[i][0])
mass_arr[i]=see_rec[i][1]
dimm_arr[i]=see_rec[i][2]
seecol=[]
seecol.append(pyfits.Column(name='Timestamp', format='20A', array=stime_list))
seecol.append(pyfits.Column(name='MASS', format='F', array=mass_arr ))
seecol.append(pyfits.Column(name='DIMM', format='F', array=dimm_arr ))
seetab= saltio.fitscolumns(seecol)
seehdu= pyfits.new_table(seetab)
seehdu.name='Seeing'
return seehdu
def guidertable(els, mintime, maxtime):
"""Extract the guider data from the els"""
#extract the guider data from the els
sel_cmd='_timestamp_, guidance_available, ee50, mag50'
tab_cmd='tpc_guidance_status__timestamp '
log_cmd="_timestamp_>'%s' and _timestamp_<'%s'" % (mintime, maxtime)
gui_rec=saltmysql.select(els, sel_cmd, tab_cmd, log_cmd)
if len(gui_rec)<2: return None
gtime_list=[]
ee50_arr=np.zeros(len(gui_rec))
mag50_arr=np.zeros(len(gui_rec))
avail_list=[]
for i in range(len(gui_rec)):
gtime_list.append(gui_rec[i][0])
ee50_arr[i]=gui_rec[i][2]
mag50_arr[i]=gui_rec[i][3]
avail_list.append(gui_rec[i][1])
avail_arr=(np.array(avail_list)=='T')
#write the results to a fits table
guicol=[]
guicol.append(pyfits.Column(name='Timestamp', format='20A', array=gtime_list))
guicol.append(pyfits.Column(name='Available', format='L', array=avail_arr ))
guicol.append(pyfits.Column(name='EE50', format='F', array=ee50_arr ))
guicol.append(pyfits.Column(name='mag50', format='F', array=mag50_arr ))
guitab= saltio.fitscolumns(guicol)
guihdu= pyfits.new_table(guitab)
guihdu.name='Guider'
return guihdu
def writeSpotFITS(spotDir, data):
phdu = pyfits.PrimaryHDU()
phdr = phdu.header
phdr.update('pixscale', 0.001, 'mm/pixel')
cols = []
cols.append(pyfits.Column(name='fiberIdx',
format='I',
array=data['fiberIdx']))
cols.append(pyfits.Column(name='wavelength',
format='D',
array=data['wavelength']))
cols.append(pyfits.Column(name='spot_xc',
format='D',
array=data['spot_xc']))
cols.append(pyfits.Column(name='spot_yc',
format='D',
array=data['spot_yc']))
spots = data['spot'][:]
spots.shape = (len(spots), 256*256)
cols.append(pyfits.Column(name='spot',
format='%dE' % (256*256),
dim='(256,256)',
array=spots))
colDefs = pyfits.ColDefs(cols)
thdu = pyfits.new_table(colDefs)
hdulist = pyfits.HDUList([phdu, thdu])
hdulist.writeto(os.path.join(spotDir, 'spots.fits'),
checksum=True, clobber=True)
def superaverage(self, weight='tintsys'):
"""
Average together all the scans in this supertable.
Note
====
There is also a module function with this name which takes as its
arguments a sequence of supertables
@param weight : str::
same as the ASAP argument for 'average_time'
"""
mylogger.debug("Calling average_time for scan table")
new_scantable = self.average_time(weight=weight)
mylogger.debug("New scantable is %s", str(new_scantable))
if new_scantable:
new_head = self.header
new_cols = self.cols
new_hdu = pyfits.new_table(new_cols, header=new_head, nrows=1)
# assume that the scan header info for the average is mostly the
# same as for the first scan being averaged
ASAP_scan_numbers = list(self.getscannos())
mylogger.debug("ASAP scans: %s", str(ASAP_scan_numbers))
for column_index in range(len(new_cols)):
mylogger.debug("Processing column %d", column_index)
new_hdu.data.field(column_index)[0] = \
self.data.field(column_index)[0]
# some data have changed in the averaging
new_hdu.data.field('EXPOSURE')[0] = new_scantable.get_inttime(row=0)
new_hdu.data.field('TSYS')[0] = new_scantable.get_tsys()[0]
new_hdu.data.field('DATA')[0] = array(new_scantable[0])
return supertable(new_scantable, HDU=new_hdu)
else:
return None
def ascii2fits(asciifile,asciinames=True,skip_header=0,outpath=None,fitsformat='D',verbose=True):
"""
Convert ascii file into fits (see fits2ascii for the reverse command)
--- INPUT ---
asciifile Ascii file to convert
asciinames Do the ascii file contain the column names in the header?
skip_header The number of header lines to skip when reading the ascii file.
outpath Alternative destination for the resulting fits file.
--- EXAMPLE OF USE ---
import fits2ascii as f2a
outpath = '/Users/kschmidt/work/catalogs/'
catfile = '/Users/kschmidt/work/GitHub/GLASS/ROMAN_CATALOGS/A2744/A2744_CLUSTER.cat'
outputfile = f2a.ascii2fits(catfile,asciinames=True,skip_header=0,outpath=outpath,verbose=True)
"""
#-------------------------------------------------------------------------------------------------------------
if verbose: print ' - Reading ascii file ',asciifile
data = np.genfromtxt(asciifile,names=asciinames,skip_header=skip_header,comments='#',dtype=None)
keys = data.dtype.names
#-------------------------------------------------------------------------------------------------------------
if verbose: print ' - Initialize and fill dictionary with data'
datadic = {}
for kk in keys:
datadic[kk] = []
try:
lenarr = len(np.asarray(data[kk]))
datadic[kk] = np.asarray(data[kk])
except: # if only one row of data is to be written
datadic[kk] = np.asarray([data[kk]])
if verbose: print ' - found the columns '+','.join(keys)
if len(fitsformat) != len(keys):
fitsformat = np.asarray([fitsformat]*len(keys))
#-------------------------------------------------------------------------------------------------------------
# writing to fits table
tail = asciifile.split('.')[-1]# reomove extension
outputfile = asciifile.replace('.'+tail,'.fits')
if outpath != None:
outputfile = outpath+outputfile.split('/')[-1]
columndefs = []
for kk, key in enumerate(keys):
try:
columndefs.append(pyfits.Column(name=key , format=fitsformat[kk], array=datadic[key]))
except:
print ' ----ERROR---- in defining columns for fits file --> stopping with pdb.set_trace() to invest'
pdb.set_trace()
cols = pyfits.ColDefs(columndefs)
tbhdu = pyfits.new_table(cols) # creating table header
hdu = pyfits.PrimaryHDU() # creating primary (minimal) header
thdulist = pyfits.HDUList([hdu, tbhdu]) # combine primary and table header to hdulist
thdulist.writeto(outputfile,clobber=True) # write fits file (clobber=True overwrites excisting file)
#-------------------------------------------------------------------------------------------------------------
if verbose: print ' - Wrote the data to: ',outputfile
return outputfile
def createFitsTable(pathPriorFile, pathSaveFile):
c1 = Column(name='x', format='D')
c2 = Column(name='y', format='D')
c3 = Column(name='magnitude', format='D')
col_definitions = pyfits.ColDefs([c1, c2, c3])
x, y, m, r, f = np.loadtxt(pathPriorFile,
usecols=(0, 1, 2, 3, 6),
unpack=True)
sel = np.invert([((f == 0) & (r == 0)) | (m > 24.5)][0])
xsel = x[sel]
ysel = y[sel]
msel = m[sel]
image_hdu = pyfits.new_table(col_definitions, nrows=len(xsel))
# for c, tiled_position in enumerate(zip(xsel, ysel, msel)):
for index, (value1, value2, value3) in enumerate(zip(xsel, ysel, msel)):
image_hdu.data[index] = [((value1)), ((value2)), (value3)]
sys.stdout = open(os.devnull, "w")
image_hdu.writeto(pathSaveFile, clobber=True)
sys.stdout = sys.__stdout__
def cl2fits(cl, filename, lcut):
"""cl2fits(cl, filename, lcut)"""
table=[pyf.Column(name='TEMPERATURE',format='1D',array=cl[0:lcut+1])]
#print table
tbhdu=pyf.new_table(table)
tbhdu.writeto(filename, clobber=True)
def select_columns(tbhdu, *fieldnames):
"""
Select particular columns from given table
A new table with only the asked columns ('fieldnames')
is output.
Input:
- tbhdu : pyfits.open('data.fit')[?]
Table HDU, often "?" equals 1
- cols : str,
Comma separated list of variables to be read from 'hdulist'
Output:
-> (new) BinTableHDU, with just the selected fields
---
"""
coldefs = tbhdu.columns;
tbdata = tbhdu.data;
inds = [ tbdata.names.index(id.upper()) for id in fieldnames ];
cols = [];
for i in inds:
cols.append( pyfits.Column(name=coldefs[i].name, format=coldefs[i].format, array=tbdata.field(i)) );
coldefs = pyfits.ColDefs(cols);
return pyfits.new_table(coldefs);
def to_fits(self, filename, format=None, clobber=False, history=''):
if format is None:
format = healpix.default_fits_format_codes[self.get_dtype().type]
hdu0 = pyfits.PrimaryHDU()
col0 = pyfits.Column(name='signal', format=format, array=self.map.map)
col1 = pyfits.Column(name='weights', format=format, array=self.wgt.map)
col_inds = [
pyfits.Column(name='sp_index%d' % n, format=format, array=i.map)
for n, i in enumerate(self.ind)
]
cols = pyfits.ColDefs([col0, col1] + col_inds)
tbhdu = pyfits.new_table(cols)
self.map._set_fits_header(tbhdu.header)
hdulist = pyfits.HDUList([hdu0, tbhdu])
if history != '':
history = [h.strip() for h in history.split("\n")]
for line in history:
if len(line) > 1:
if line.startswith('#'):
for subline in img.word_wrap(line, 80, 0, 0,
'').split("\n"):
hdulist[0].header.add_history(subline)
else:
for subline in img.word_wrap(line, 70, 5, 10,
'#').split("\n"):
hdulist[0].header.add_history(subline)
hdulist.writeto(filename, clobber=clobber)
def extend_tbHDU(tbhdu_A, tbhdu_B):
"""
Extend first tbHDU with second entries
The output is a table (HDU) with column 'B' lines
extending 'A' entries. Column names on both input
table need to be the same.
Input:
- tbhdu_A : FITS binary table HDU
- tbhdu_B : FITS binary table HDU
Output:
- tbhdu : FITS binary table HDU
Result from extention, A+B
---
"""
Nrows_A = tbhdu_A.header['NAXIS2'];
Nrows_B = tbhdu_B.header['NAXIS2'];
Nrows = Nrows_A + Nrows_B;
new_tb = pyfits.new_table(tbhdu_A.columns,nrows=Nrows);
for name in tbhdu_A.columns.names:
new_tb.data.field(name)[Nrows_A:] = tbhdu_B.data.field(name);
return new_tb;
def new_HDU(self,scan_list):
"""
Make a new HDU from the ASAP scans in 'scan_list'
@param scan_list : list of ints::
the scans numbers used to select scans from the scantable
@return:
an SDFITS bintable HDU
"""
# The header and column definitions stay the same
new_head = self.header
new_cols = self.cols
num_rows = len(scan_list)
new_hdu = pyfits.new_table(new_cols, header=new_head, nrows=num_rows)
# Make sure that the new scan list is ordered
scan_list.sort()
old_scan_list = list(self.getscannos())
new_row_index = 0
for scan in scan_list:
old_scan_index = old_scan_list.index(scan)
for i in range(len(new_cols)):
new_hdu.data.field(i)[new_row_index] = \
self.data.field(i)[old_scan_index]
new_row_index += 1
return new_hdu
def write_fits(magpat, fits_output_file):
"""Save a magnification pattern to a FITS file.
The pattern itself is saved in the pimary HDU of the FITS file.
The coordinates of the source plane rectangle occupied by the
pattern are stored in the header fields
MAGPATX0, MAGPATY0, MAGPATX1, MAGPATY1
The lens list is stored in a binary table HDU named "LENSES".
Parameters:
magpat magnification pattern to save
fits_output_file
file name of the output file
"""
img_hdu = pyfits.PrimaryHDU(magpat)
region = magpat.region
img_hdu.header.update("ctype1", " ")
img_hdu.header.update("crpix1", 0.5)
img_hdu.header.update("crval1", region.x)
img_hdu.header.update("cdelt1", region.width / magpat.params.xpixels)
img_hdu.header.update("ctype2", " ")
img_hdu.header.update("crpix2", 0.5)
img_hdu.header.update("crval2", region.y)
img_hdu.header.update("cdelt2", region.height / magpat.params.ypixels)
for s in ["x0", "y0", "x1", "y1"]:
img_hdu.header.update("magpat" + s, getattr(region, s))
lens_hdu = pyfits.new_table(magpat.lenses)
lens_hdu.name = "lenses"
pyfits.HDUList([img_hdu, lens_hdu]).writeto(fits_output_file, clobber=True)
utils.logger.info("Wrote magnification pattern to %s", fits_output_file)
def mwrfits(filename, data, hdu=1, colnames=None, keys=None):
"""Write columns to a fits file in a table extension.
Input:
- filename: the fits file name
- data: a list of 1D arrays to write in the table
Parameters:
- hdu: header where to write the data. Default: 1
- colnames: the column names
- keys: a dictionary with keywords to write in the header
"""
# Check the inputs
if colnames is not None:
if len(colnames) != len(data):
raise ValueError("colnames and data must the same length")
else:
colnames = [""] * len(data)
cols = []
for line in xrange(len(data)):
cols.append(pyf.Column(name=colnames[line], format=getformat(data[line]), array=data[line]))
coldefs = pyf.ColDefs(cols)
tbhdu = pyf.new_table(coldefs)
if type(keys) is dict:
for k, v in keys.items():
tbhdu.header.update(k, v)
# write the file
tbhdu.writeto(filename, clobber=True)
def Select(dirin, filein , selfn, dirout,
overwrite=False):
"Select a subsample from ma table "
"""
If overwrite is False, will skip existing files in destination
directory.
"""
mask=[ selfn(row) for row in pyfits.open(filein)[1].data ]
mind=[ x for x,f in enumerate (mask) if f]
nrows=len(mind)
print "Selected %i rows." % nrows
fitsel=re.compile(".*fits?")
flist = [ fnamein for fnamein in os.listdir(dirin) if fitsel.match(fnamein) ]
for fnamein in flist:
foutname=os.path.join(dirout,fnamein)
if os.access(foutname, os.F_OK) and (not overwrite):
print "Skipping %s as it already exists" % fnamein
else:
fin=pyfits.open(os.path.join(dirin,fnamein))
newtab=pyfits.new_table( fin[1].columns , nrows= nrows)
for cname in fin[1].columns.names:
newtab.data.field(cname)._copyFrom( fin[1].data.field(cname)[ mind] )
Write([pyfits.PrimaryHDU(), newtab],
foutname,
overwrite=1)
def subsetSchlafly(inName, outName):
inFile = pyfits.open(inName)
inData = inFile[1].data
schema = pyfits.ColDefs([pyfits.Column(name="id", format="K"),
pyfits.Column(name="ra", format="D"),
pyfits.Column(name="dec", format="D")] +
[pyfits.Column(name=name, format="E") for name in FILTERS] +
[pyfits.Column(name=name + "_err", format="E") for name in FILTERS] +
[pyfits.Column(name=name + "_stdev", format="E") for name in FILTERS]
)
outHdu = pyfits.new_table(schema, nrows=len(inData))
outData = outHdu.data
outData.ident = inData.obj_id
outData.ra = inData.ra
outData.dec = inData.dec
for i, f in enumerate(FILTERS):
# Some of the below (e.g., "mean") are functions in the pyfits.FITS_rec class,
# so we need to access them differently than just grabbing an attribute.
mean = outData.field(f)
err = outData.field(f + "_err")
stdev = outData.field(f + "_stdev")
mean[:] = inData.field("mean")[:,i]
err[:] = inData.field("err")[:,i]
stdev[:] = inData.field("stdev")[:,i]
outHdu.writeto(outName, clobber=True)
print "Wrote %s" % outName
inFile.close()
def RepTable ( tabin ,
rowmask=None ,
colsel=None,
keycopylist = ["dz"]
):
"Replicate a fits table"
if rowmask ==None:
rowmask = numpy.ones(len(tabin.data),
numpy.bool)
nrowsout=sum(rowmask)
tabout=pyfits.new_table( CopyColDefs(tabin),
nrows=nrowsout)
for k in keycopylist:
if k in tabin.header.keys():
tabout.header.update ( k , tabin.header[k] )
if colsel == None:
colsel = tabin.columns.names
if nrowsout > 0 :
for cname in colsel:
tabout.data[cname]=tabin.data.field(cname)[ rowmask]
return tabout
def writeCandidates(self, filename=None):
if filename is None: filename = self.candfile
threshold = self.config['search']['cand_threshold']
select = (self.assocs['CUT'] == 0)
select &= (self.assocs['TS'] > threshold)
#select &= (self.assocs['ASSOC2']=='')
self.candidates = self.assocs[select]
# ADW: View as a recarray or selection doesn't work.
# Why? I don't know, and I'm slightly terrified...
hdu = pyfits.new_table(self.candidates.view(np.recarray))
logger.info("Writing %s..." % filename)
hdu.writeto(filename, clobber=True)
# Dump to txt file
if which('fdump'):
txtfile = filename.replace('.fits', '.txt')
columns = ['NAME', 'TS', 'GLON', 'GLAT', 'DISTANCE', 'MASS']
cmd = 'fdump %(infile)s %(outfile)s columns="%(columns)s" rows="-" prhead="no" showcol="yes" clobber="yes" pagewidth="256" fldsep=" " showrow="no"' % (
dict(infile=filename,
outfile=txtfile,
columns=','.join(columns)))
print cmd
subprocess.call(cmd, shell=True)
def parsePDZ(cls, pdzfile, sourcefile):
'''parses text output from ZEBRA'''
input = open(pdzfile)
source = ldac.openObjectFile(sourcefile)
minPDZ, maxPDZ, pdzstep = 0.0, 4.005, 0.005
pdzs = []
for line in input.readlines():
if re.match('^#', line):
continue
tokens = line.split()
pdz = map(float, tokens)
pdzs.append(pdz)
nobjects = len(pdzs)
npdzs = len(np.arange(minPDZ, maxPDZ, pdzstep))
ids = source['SeqNr']
cols = [pyfits.Column(name = 'SeqNr', format = 'J', array = ids),
pyfits.Column(name = 'pdz', format = '%dE' % npdzs, array = np.array(pdzs))]
pdzs = ldac.LDACCat(pyfits.new_table(pyfits.ColDefs(cols)))
pdzs.hdu.header.update('MINPDZ', minPDZ)
pdzs.hdu.header.update('MAXPDZ', maxPDZ)
pdzs.hdu.header.update('PDZSTEP', pdzstep)
return cls(pdzs)
def sex2fits(c, fitsname, booleancols=[]):
""" usage: sex2fits(c, fitsname, booleancols=[])
c -- input sextutils.sextractor catalog instance
fitsname -- output file name of the binary FITS table
booleancols -- column names that should be converted to boolean values"""
fitscols = []
# construct all the columns
for i in range(len(c._d)):
colname = c._colnames[i]
coltype = c._type[colname]
colfmt = colformats[coltype]
if coltype == 's':
slen = c._fmt[colname][1:-1] # length of string
colfmt = slen + colfmt
colarray = c.__getattribute__(colname)
# catch the Boolean array of 0 or 1
if colname in booleancols:
colfmt = 'L'
colarray = where(colarray == 0, False,
True) # convert to boolean array
col = pyfits.Column(name=colname, format=colfmt, array=colarray)
fitscols += [col]
# create table header unit
cols = pyfits.ColDefs(fitscols)
tbhdu = pyfits.new_table(cols)
hdu = pyfits.PrimaryHDU(array(
[])) # create a primary HDU with an empty list
thdulist = pyfits.HDUList([hdu, tbhdu])
thdulist.writeto(fitsname)
return 0
def saveClass(out,filename):
"""
NAME:
saveClass
PURPOSE:
save the classifications
INPUT:
out - listof varClass objects key, qsologlike, starloglike)
filename - name of the file that the output will be saved to
OUTPUT:
(none)
HISTORY:
2011-01-30 - Written - Bovy (NYU)
"""
key= [re.split(r'.fit',o.key)[0] for o in out]
lenkey= [len(k) for k in key]
#Prepare columns
cols= []
colkey= pyfits.Column(name='key',format=str(max(lenkey))+'A',array=key)
cols.append(colkey)
colqso= pyfits.Column(name='qsologlike',format='E',
array=[o.qsologlike for o in out])
cols.append(colqso)
colstar= pyfits.Column(name='starloglike',format='E',
array=[o.starloglike for o in out])
cols.append(colstar)
colrrlyrae= pyfits.Column(name='rrlyraeloglike',format='E',
array=[o.rrlyraeloglike for o in out])
cols.append(colrrlyrae)
#Save
columns= pyfits.ColDefs(cols)
tbhdu= pyfits.new_table(columns)
tbhdu.writeto(filename)
return None
def change_column_names(filename, old_colnames, new_colnames):
"""
Change the name of a column.
Pyfits does not really provide a convenient function to do this, so I'll have to
create a new table based on the old table, just use a different column name.
"""
os.system('mv %s %s.copy' % (filename, filename))
c = pyfits.open(filename + ".copy")
tbhdu = c[1]
ncol = len(tbhdu.data.columns)
newcols = []
for i in range(ncol):
colname = tbhdu.data.columns[i].name
colfmt = tbhdu.data.formats[i]
colarr = tbhdu.data.field(colname)
for j in range(len(old_colnames)):
if tbhdu.data.columns[i].name == old_colnames[j]:
colname = new_colnames[j]
break
#print colname
newcols += [pyfits.Column(name=colname, format=colfmt, array=colarr)]
newcols = pyfits.ColDefs(newcols)
#print newcols
newhdu = pyfits.new_table(newcols)
newhdu.writeto(filename)
c.close()
os.system('rm %s.copy' % filename)
def mwrfits(filename,data,hdu=1,colnames=None,keys=None):
"""Write columns to a fits file in a table extension.
Parameters
----------
filename : str
The fits file name
data : list of 1D arrays
A list of 1D arrays to write in the table
hdu : int, optional
The header where to write the data. Default: 1
colnames : list of str
The column names
keys : dict-like
A dictionary with keywords to write in the header
"""
# Check the inputs
if colnames is not None:
if len(colnames) != len(data):
raise ValueError("colnames and data must the same length")
else:
colnames = ['']*len(data)
cols=[]
for line in xrange(len(data)):
cols.append(pf.Column(name=colnames[line],
format=getformat(data[line]),
array=data[line]))
tbhdu = pf.new_table(cols)
if type(keys) is dict:
for k,v in keys.items():
tbhdu.header.update(k,v)
# write the file
tbhdu.writeto(filename,clobber=True)
def write_cl(filename, cl, dtype=np.float64):
"""Writes Cl into an healpix file, as IDL cl2fits.
Parameters
----------
filename : str
the fits file name
cl : array
the cl array to write to file, currently TT only
"""
# check the dtype and convert it
fitsformat = getformat(dtype)
column_names = ['TEMPERATURE','GRADIENT','CURL','G-T','C-T','C-G']
if isinstance(cl, list):
cols = [pf.Column(name=column_name,
format='%s'%fitsformat,
array=column_cl) for column_name, column_cl in zip(column_names[:len(cl)], cl)]
else: # we write only one TT
cols = [pf.Column(name='TEMPERATURE',
format='%s'%fitsformat,
array=cl)]
tbhdu = pf.new_table(cols)
# add needed keywords
tbhdu.header.update('CREATOR','healpy')
tbhdu.writeto(filename,clobber=True)
def export_dpc_balm_to_fits(objprefix, fitsfname):
import pyfits
import piolib
ix = piolib.ReadVECTObject(objprefix + '_idx', "PIOINT", "")
re = piolib.ReadVECTObject(objprefix + '_re', "PIOFLOAT", "")
im = piolib.ReadVECTObject(objprefix + '_im', "PIOFLOAT", "")
l = np.floor(np.sqrt(ix - 1))
m = ix - l * l - l - 1
lmax = np.int(np.max(l))
mmax = np.int(np.max(m))
hdu = pyfits.new_table([
pyfits.Column(name='INDEX', format=r'1J', array=ix),
pyfits.Column(name='REAL', format=r'1D', array=re),
pyfits.Column(name='IMAG', format=r'1D', array=im)
])
hdu.header.update('MAX-LPOL', lmax, "Maximum L multipole order")
hdu.header.update('MAX-MPOL', mmax, "Maximum M multipole degree")
hdu.header.update('SOURCE', objprefix)
hdu.name = 'ALM'
hdu.writeto(fitsfname)
def beam_to_fits(filename, beam):
import pyfits
cols = pyfits.ColDefs([
pyfits.Column(name='beam', format='D16.8', array=beam)], tbtype='TableHDU')
tab = pyfits.new_table(cols, tbtype='TableHDU')
hdulist = pyfits.HDUList([pyfits.PrimaryHDU(), tab])
hdulist.writeto(filename)
def sort_by_column(tbhdu,fieldname):
"""
Sort a FITS table HDU by the its "fieldname" column in increasing order.
Inputs:
- tbhdu: FITS table HDU
- fieldname <str> : field name of the column to sort
Output:
- new tbhdu with data sorted according to 'fieldname' column
"""
from operator import itemgetter, attrgetter
coldefs = tbhdu.columns
tbdata = tbhdu.data
index = tbdata.names.index(fieldname)
sorted_data = np.transpose(sorted(tbdata,key=itemgetter(index)))
cols = [];
for i in xrange(len(coldefs.names)):
cols.append( pyfits.Column(name=coldefs[i].name, format=coldefs[i].format, array=sorted_data[i]) );
coldefs = pyfits.ColDefs(cols);
return pyfits.new_table(coldefs);
def convert_to_pogson(p):
import pyfits, scipy
cols = []
for col in p.columns:
if col.name[0:7] == 'psfFlux':
array = -2.5 * scipy.log10(p.data.field(col.name)) + 22.5
cols.append(
pyfits.Column(name=col.name.replace('psfFlux', 'psfPog'),
format=col.format,
array=array))
cols.append(col)
hdu = pyfits.PrimaryHDU()
hdulist = pyfits.HDUList([hdu])
print cols
tbhu = pyfits.new_table(cols)
#hdulist.append(tbhu)
#hdulist[1].header.update('EXTNAME','STDTAB')
#outcat = '/tmp/test' #path + 'PHOTOMETRY/' + type + '.cat'
#os.system('rm ' + f + '.tab')
#hdulist.writeto(f + '.tab')
return tbhu
def writeFits (taustar, transmission, filename) :
tauCol = pyfits.Column (name='tau', format = 'E', array = taustar)
transmissionCol = pyfits.Column (name='transmission', format='E',
array=transmission)
columns = pyfits.ColDefs ([tauCol, transmissionCol])
tableHDU = pyfits.new_table (columns)
tableHDU.writeto (filename)
def convert(self, inName, outName):
"""Convert input data to the format to be processed by astrometry.net"""
if os.path.exists(outName):
print "Output file %s exists; not clobbering" % outName
return
inFile = pyfits.open(inName)
inData = inFile[1].data
print "Read %d rows from %s" % (len(inData), inName)
# Filter the data and get the columns we want
columns = self.filter(inData)
if not "ra" in self.schema or not "dec" in self.schema:
raise RuntimeError("Don't have 'ra' and 'dec' columns in schema")
size = None
for col in self.schema:
if not col in columns:
raise RuntimeError("Schema column %s was not present after filtering" % col)
if size is None:
size = len(columns[col])
elif len(columns[col]) != size:
raise RuntimeError("Size mismatch for column %s: %d vs %d" % (col, len(columns[col], size)))
# Write it all out
schema = pyfits.ColDefs([pyfits.Column(name=col, format=self.schema[col]) for col in self.schema])
outHdu = pyfits.new_table(schema, nrows=size)
outData = outHdu.data
for col in self.schema:
outData.field(col)[:] = columns[col]
outHdu.writeto(outName, clobber=True)
print "Wrote %d rows as %s" % (size, outName)
inFile.close()
def mwrfits(filename,data,hdu=1,colnames=None,keys=None):
"""Write columns to a fits file in a table extension.
Parameters
----------
filename : str
The fits file name
data : list of 1D arrays
A list of 1D arrays to write in the table
hdu : int, optional
The header where to write the data. Default: 1
colnames : list of str
The column names
keys : dict-like
A dictionary with keywords to write in the header
"""
# Check the inputs
if colnames is not None:
if len(colnames) != len(data):
raise ValueError("colnames and data must the same length")
else:
colnames = ['']*len(data)
cols=[]
for line in xrange(len(data)):
cols.append(pf.Column(name=colnames[line],
format=getformat(data[line]),
array=data[line]))
tbhdu = pf.new_table(cols)
if type(keys) is dict:
for k,v in keys.items():
tbhdu.header.update(k,v)
# write the file
tbhdu.writeto(filename,clobber=True)
def write_fits(magpat, fits_output_file):
"""Save a magnification pattern to a FITS file.
The pattern itself is saved in the pimary HDU of the FITS file.
The coordinates of the source plane rectangle occupied by the
pattern are stored in the header fields
MAGPATX0, MAGPATY0, MAGPATX1, MAGPATY1
The lens list is stored in a binary table HDU named "LENSES".
Parameters:
magpat magnification pattern to save
fits_output_file
file name of the output file
"""
img_hdu = pyfits.PrimaryHDU(magpat)
region = magpat.region
img_hdu.header.update("ctype1", " ")
img_hdu.header.update("crpix1", 0.5)
img_hdu.header.update("crval1", region.x)
img_hdu.header.update("cdelt1", region.width / magpat.params.xpixels)
img_hdu.header.update("ctype2", " ")
img_hdu.header.update("crpix2", 0.5)
img_hdu.header.update("crval2", region.y)
img_hdu.header.update("cdelt2", region.height / magpat.params.ypixels)
for s in ["x0", "y0", "x1", "y1"]:
img_hdu.header.update("magpat" + s, getattr(region, s))
lens_hdu = pyfits.new_table(magpat.lenses)
lens_hdu.name = "lenses"
pyfits.HDUList([img_hdu, lens_hdu]).writeto(fits_output_file, clobber=True)
utils.logger.info("Wrote magnification pattern to %s", fits_output_file)
def run_treecorr(x, y, g1, g2):
"""Helper routine to take outputs of GalSim shear grid routine, and run treecorr on it."""
import pyfits
import os
import treecorr
# Use fits binary table for faster I/O.
assert x.shape == y.shape
assert x.shape == g1.shape
assert x.shape == g2.shape
x_col = pyfits.Column(name='x', format='1D', array=x.flatten())
y_col = pyfits.Column(name='y', format='1D', array=y.flatten())
g1_col = pyfits.Column(name='g1', format='1D', array=g1.flatten())
g2_col = pyfits.Column(name='g2', format='1D', array=g2.flatten())
cols = pyfits.ColDefs([x_col, y_col, g1_col, g2_col])
table = pyfits.new_table(cols)
phdu = pyfits.PrimaryHDU()
hdus = pyfits.HDUList([phdu, table])
hdus.writeto('temp.fits', clobber=True)
# Define the treecorr catalog object.
cat = treecorr.Catalog('temp.fits',
x_units='degrees',
y_units='degrees',
x_col='x',
y_col='y',
g1_col='g1',
g2_col='g2')
# Define the corrfunc object
gg = treecorr.GGCorrelation(min_sep=min_sep,
max_sep=max_sep,
bin_size=0.1,
sep_units='degrees')
# Actually calculate the correlation function.
gg.process(cat)
os.remove('temp.fits')
return gg
def merge_tables(table1, table2, newtabname, mode='left'):
""" usage: merge_tables(table1, table2, newtabname, mode='left')
table1, table2 are two fits tables (Ftable instances) to be merged.
mode:
'left': only merge columns that are in table1; ignore other columns in table2.
'right': only merge columns that are in table2; ignore other columns in table1.
"""
columns = []
if mode == 'left':
for i in range(len(table1.Columns)):
col = table1.Columns[i]
if col in table2.Columns: # if col is also in table2
a1 = table1.__getitem__(col)
a2 = table2.__getitem__(col)
a_all = concatenate([a1, a2])
fmt = table1.d.formats[i]
columns += [pyfits.Column(name=col, format=fmt, array=a_all)]
elif mode == 'right':
for i in range(len(table2.Columns)):
col = table2.Columns[i]
if col in table1.Columns: # if col is also in table1
a2 = table2.__getitem__(col)
a1 = table1.__getitem__(col)
a_all = concatenate([a1, a2])
fmt = table2.d.formats[i]
columns += [pyfits.Column(name=col, format=fmt, array=a_all)]
cols = pyfits.ColDefs(columns)
tbhdu = pyfits.new_table(cols)
tbhdu.writeto(newtabname)
def write_cmd_file(near_targ, target): ''' Takes the rec array of sources near target and the rec array of the target and produces a fits table. ''' # Columns to be in the fits table: these data are for the nearby sources c1 = pyfits.Column(name='HSTID', format='20A', array=near_targ['hstid']) c2 = pyfits.Column(name='RA', format='F', array=near_targ['degra']) c3 = pyfits.Column(name='DEC', format='F', array=near_targ['degdec']) c4 = pyfits.Column(name='V', format='F', array=near_targ['v']) c5 = pyfits.Column(name='VERR', format='F', array=near_targ['verr']) c6 = pyfits.Column(name='BV', format='F', array=near_targ['bvcol']) c7 = pyfits.Column(name='BVERR', format='F', array=near_targ['bvcolerr']) c8 = pyfits.Column(name='VI', format='F', array=near_targ['vicol']) c9 = pyfits.Column(name='VIERR', format='F', array=near_targ['vicolerr']) # Make table table_hdu = pyfits.new_table([c1, c2, c3, c4, c5, c6, c7, c8, c9]) # Updates header with contains the target's info table_hdu.header.update(key='HSTID', value=target['hstid']) table_hdu.header.update(key='LBTID', value=target['lbtid']) table_hdu.header.update(key='RA', value=str(target['ra'])) table_hdu.header.update(key='DEC', value=str(target['dec'])) # Table data cannot be the Primary HDU, so we make an empty Primary HDU phdu = pyfits.PrimaryHDU() # Zeroth extension is empty, first extension contains the table hdulist = pyfits.HDUList([phdu, table_hdu]) hdulist.writeto(target['lbtid']+'.fits')
def makeHDU(config,mag_1,mag_err_1,mag_2,mag_err_2,lon,lat,mc_source_id):
"""
Create a catalog fits file object based on input data.
ADW: This should be combined with the write_membership function of loglike.
"""
if config['catalog']['coordsys'].lower() == 'cel' \
and config['coords']['coordsys'].lower() == 'gal':
lon, lat = ugali.utils.projector.gal2cel(lon, lat)
elif config['catalog']['coordsys'].lower() == 'gal' \
and config['coords']['coordsys'].lower() == 'cel':
lon, lat = ugali.utils.projector.cel2gal(lon, lat)
columns = [
pyfits.Column(name=config['catalog']['objid_field'],
format = 'D',array = np.arange(len(lon))),
pyfits.Column(name=config['catalog']['lon_field'],
format = 'D',array = lon),
pyfits.Column(name = config['catalog']['lat_field'],
format = 'D',array = lat),
pyfits.Column(name = config['catalog']['mag_1_field'],
format = 'E',array = mag_1),
pyfits.Column(name = config['catalog']['mag_err_1_field'],
format = 'E',array = mag_err_1),
pyfits.Column(name = config['catalog']['mag_2_field'],
format = 'E',array = mag_2),
pyfits.Column(name = config['catalog']['mag_err_2_field'],
format = 'E',array = mag_err_2),
pyfits.Column(name = config['catalog']['mc_source_id_field'],
format = 'I',array = mc_source_id),
]
hdu = pyfits.new_table(columns)
return hdu
def addPDvals(filename,pdfile,extnam,prefix,tstart):
if (os.path.getsize(filename) < 35000000):
print "File %s appears to be bogus." % filename
return 0
hdulist = pf.open(filename, mode='update')
tmdata = numpy.zeros((3000), dtype=numpy.float64)
pddata = numpy.zeros((3000), dtype=numpy.float64)
# fpd = open("%s/pd-values-for-seq-%d-exp-%d" % (cdir,seq,i),"r");
fpd = open(pdfile,"r");
ival = 0
for line in fpd:
tokens = str.split(line)
pdval = float(tokens[1])
pdtime = float(tokens[0])
print "time = %10.4e , pdval = %10.4e" % (pdtime,pdval)
pddata[ival] = pdval
tmdata[ival] = pdtime
ival = ival + 1
fpd.close()
# hdulist.append(pf.BinTableHDU(data=(tmdata,pddata)))
c1 = pf.Column(name="%s_MEAS_TIMES" % prefix, format='D', array=tmdata)
c2 = pf.Column(name="%s_A_CURRENT" % prefix, format="D", array=pddata)
table_hdu = pf.new_table([c1, c2])
hdulist.append(table_hdu)
for seg in hdulist :
hdr=seg.header
hdr.update("EXTNAME", extnam)
hdr.update("TSTART", tstart)
hdulist.close()
def write(self, file_name) :
"""Write stored data to file.
Take all the data stored in the Writer (from added DataBlocks) and
write it to a fits file with the passed file name.
"""
# Add the data
Col = pyfits.Column(name='DATA', format=self.data_format,
array=self.data)
columns = [Col,]
# Add all the other stored fields.
for field_name in self.field.iterkeys() :
Col = pyfits.Column(name=field_name,
format=self.formats[field_name],
array=self.field[field_name])
columns.append(Col)
coldefs = pyfits.ColDefs(columns)
# Creat fits header data units, one for the table and the mandatory
# primary.
tbhdu = pyfits.new_table(coldefs)
prihdu = pyfits.PrimaryHDU()
# Add the write history.
fname_abbr = ku.abbreviate_file_path(file_name)
self.history.add('Written to file.', ('File name: ' + fname_abbr,))
# Add the history to the header.
bf.write_history_header(prihdu.header, self.history)
# Combine the HDUs and write to file.
hdulist = pyfits.HDUList([prihdu, tbhdu])
hdulist.writeto(file_name, clobber=True)
if self.feedback > 0 :
print 'Wrote data to file: ' + fname_abbr