def make_cube_from_images(flist, outf):
data = [np.copy(fits.getdata(f, ext=1)) for f in flist]
shape = np.max(np.array([d.shape for d in data]), axis=0)
for d in data:
d.resize(shape)
cube = Cube(data=np.dstack(data), copy=False)
cube.write(outf, savemask='nan')
def cont_sub(self, line, z, dv, ddv, savefile=None):
wv1, wv2, wv3, wv4 = interpWindow(line, z, dv, ddv)
mask_b = (self.wave >= wv1) & (self.wave <= wv2)
mask_r = (self.wave >= wv3) & (self.wave <= wv4)
mask_mid = (self.wave >= (wv1 - 200)) & (self.wave <= (wv4 + 200))
wavefit = np.concatenate((self.wave[mask_b], self.wave[mask_r]))
for y in range(0, self.ny):
for x in range(0, self.nx):
fluxfit = np.concatenate(
(self.data[mask_b, y, x], self.data[mask_r, y, x]))
z = np.polyfit(wavefit, fluxfit, 1)
p = np.poly1d(z)
linemodel = p(self.wave[mask_mid])
self.data[mask_mid, y, x] -= linemodel
if savefile is not None:
cubenew = Cube(data=self.data,
var=(self.err)**2,
data_header=self.dh,
wcs=self.wcs,
wave=self.wv)
cubenew.write(savefile, savemask='none')
def write(self, path=None, erase=False):
"""Save the current session in a folder that will have the name of the
ORIGIN object (self.name).
The ORIGIN.load(folder, newname=None) method will be used to load a
session. The parameter newname will let the user to load a session but
continue in a new one.
Parameters
----------
path : str
Path where the folder (self.name) will be stored.
erase : bool
Remove the folder if it exists.
"""
self._loginfo("Writing...")
# adapt session if path changes
if path is not None and path != self.path:
if not os.path.exists(path):
raise ValueError(f"path does not exist: {path}")
self.path = path
outpath = os.path.join(path, self.name)
# copy outpath to the new path
shutil.copytree(self.outpath, outpath)
self.outpath = outpath
self._setup_logfile(self.logger)
if erase:
shutil.rmtree(self.outpath)
os.makedirs(self.outpath, exist_ok=True)
# PSF
if isinstance(self.PSF, list):
for i, psf in enumerate(self.PSF):
cube = Cube(data=psf, mask=np.ma.nomask, copy=False)
cube.write(os.path.join(self.outpath,
"cube_psf_%02d.fits" % i))
else:
cube = Cube(data=self.PSF, mask=np.ma.nomask, copy=False)
cube.write(os.path.join(self.outpath, "cube_psf.fits"))
if self.wfields is not None:
for i, wfield in enumerate(self.wfields):
im = Image(data=wfield, mask=np.ma.nomask)
im.write(os.path.join(self.outpath, "wfield_%02d.fits" % i))
if self.ima_white is not None:
self.ima_white.write("%s/ima_white.fits" % self.outpath)
for step in self.steps.values():
step.dump(self.outpath)
# parameters in .yaml
with open(f"{self.outpath}/{self.name}.yaml", "w") as stream:
dump_yaml(self.param, stream)
# step3 - saving this manually for now
if self.nbAreas is not None:
if self.testO2 is not None:
for area in range(1, self.nbAreas + 1):
np.savetxt("%s/testO2_%d.txt" % (self.outpath, area),
self.testO2[area - 1])
if self.histO2 is not None:
for area in range(1, self.nbAreas + 1):
np.savetxt("%s/histO2_%d.txt" % (self.outpath, area),
self.histO2[area - 1])
if self.binO2 is not None:
for area in range(1, self.nbAreas + 1):
np.savetxt("%s/binO2_%d.txt" % (self.outpath, area),
self.binO2[area - 1])
self._loginfo("Current session saved in %s", self.outpath)
manager = mtp.Manager()
return_dict = manager.dict()
tstart = time.time()
#pool = Pool(processes=20)
#pool.map(dummy_function, range(c.shape[0]))
dummy_im = c[1,:,:].copy()
dummy_im.data.data[:,:] = 0
for i in range(0,c.shape[0]):
p = Process(target=rm_bg_multiproc, args=(i,c,dummy_im,return_dict))
p.start()
tend = time.time()
print('ellapsed time %s'%(tend-tstart))
c.unmask()
for k in range(c.shape[0]):
c.data.data[k,:,:] = c.data.data[k,:,:] - return_dict[k]
## Update Header
c.primary_header.add_comment('This cube has been median subtracted')
c.write(args.cube_out)
#if args.multip == 0:
# remove_bg(args.cube_in,args.mask,args.cube_out)
def rotate_cube_wcs(cube_name,
cube_folder="",
outwcs_folder=None,
rotangle=0.,
**kwargs):
"""Routine to remove potential Nan around an image and reconstruct
an optimal WCS reference image. The rotation angle is provided as a way
to optimise the extent of the output image, removing Nan along X and Y
at that angle.
Args:
cube_name (str): input image name. No default.
cube_folder (str): input image folder ['']
outwcs_folder (str): folder where to write the output frame. Default is
None which means that it will use the folder of the input image.
rotangle (float): rotation angle in degrees [0]
**kwargs:
in_suffix (str): in suffix to remove from name ['prealign']
out_suffix (str): out suffix to add to name ['rotwcs']
margin_factor (float): factor to extend the image [1.1]
Returns:
"""
# Reading the input names and setting output folder
fullname = joinpath(cube_folder, cube_name)
cube_folder, cube_name = os.path.split(fullname)
if outwcs_folder is None:
outwcs_folder = cube_folder
# Suffix
in_suffix = kwargs.pop("in_suffix", "prealign")
out_suffix = kwargs.pop("out_suffix", "rotwcs")
# Get margin if needed
margin_factor = kwargs.pop("margin_factor", 1.1)
extend_fraction = np.maximum(0., (margin_factor - 1.))
upipe.print_info("Will use a {:5.2f}% extra margin".format(
extend_fraction * 100.))
# Opening the image via mpdaf
cubewcs = Cube(fullname)
imawcs = cubewcs.sum(axis=0)
extra_pixels = (np.array(imawcs.shape) * extend_fraction).astype(np.int)
# New dimensions and extend current image
new_dim = tuple(np.array(imawcs.shape).astype(np.int) + extra_pixels)
ima_ext = imawcs.regrid(newdim=new_dim,
refpos=imawcs.get_start(),
refpix=tuple(extra_pixels / 2.),
newinc=imawcs.get_step()[0] * 3600.)
# Copy and rotate WCS
new_wcs = copy.deepcopy(ima_ext.wcs)
upipe.print_info(
"Rotating spatial WCS of Cube by {} degrees".format(rotangle))
new_wcs.rotate(rotangle)
# New rotated image
ima_rot = Image(data=np.nan_to_num(ima_ext.data), wcs=new_wcs)
# Then resample the image using the initial one as your reference
ima_rot_resampled = ima_rot.align_with_image(ima_ext, flux=True)
# Crop NaN
ima_rot_resampled.crop()
# get the new header with wcs and rotate back
finalwcs = ima_rot_resampled.wcs
finalwcs.rotate(-rotangle)
# create the final image
data_cube_rot = np.repeat(ima_rot_resampled[np.newaxis, :, :].data,
cubewcs.shape[0],
axis=0)
final_rot_cube = Cube(data=data_cube_rot, wave=cubewcs.wave, wcs=finalwcs)
# Save image
if isinstance(in_suffix,
str) and in_suffix != "" and in_suffix in cube_name:
out_name = cube_name.replace(in_suffix, out_suffix)
else:
name, extension = os.path.splitext(cube_name)
if out_suffix != "":
out_suffix = "_{}".format(out_suffix)
out_name = "{0}{1}{2}".format(name, out_suffix, extension)
# write output
final_rot_cube.write(joinpath(outwcs_folder, out_name))
return outwcs_folder, out_name
def determine_best_astrometry(magecube_filename, musecube_filename, xypa_tuples,
chi2_wvrange, renorm_wvrange, plot_wvrange, plot=True):
"""Utility for determining the best astrometry for a MagE Cube based on a comparisom
with a reference MUSE Cube. It will use different (xc, yc, PA) positions taken from xypa_tuples
for a virtual MagE slit on a MUSE reference datacube and will determine the set that
has the minimum Chi2 within a spectral region. It will return a astropy.table.Table object
with the results.
Parameters
----------
magecube : str
Filename of the MagE cube
musecube_filename : str
Filename of the MUSE reference cube
xyc_tuples: list of tuples
List of (xc, yc, PA) tuples
xc and yc are in units of MUSE pixels and
PA is in the position angle in degrees
chi2_wvrange : (float, float)
Wavelength range for performing the chi2 comparison. Ideally it has to be a small
region centred in a spectral feature (e.g. emission line)
renorm_wvrange : (float, float)
Wavelength range for performing the flux renormalization of MagE to MUSE. Ideally it
has to be a small region close to `chi2_range`.
plot_wvrange : (float, float)
Wavelength range for plotting. Must be larger than either renorm_range or chi2_range.
plot : bool
Whether to plot the iterations for visual inspection
Returns
-------
results : astropy.table.Table
Table with the results
"""
from PyMUSE import musecube as mc
import os
# load the cubes
musecube_pymuse = mc.MuseCube(musecube_filename)
musecube = Cube(musecube_filename)
magecube_orig = Cube(magecube_filename)
# create master subdir
master_dirname = magecube_filename.split('/')[-1].replace('.fits', '_astrometry_runs')
if not os.path.exists(master_dirname):
os.makedirs(master_dirname)
# define mage slit geometry
l=0.3*3*11
w=1.
n=11
pixscale = 0.2 # of MUSE datacube
# create a table to store the results
tab = Table()
# will create auxiliary cubes from MUSE to match geometry of mage
names = []
if 1: # left only for the indentantion
if 1: # left for the indentation
for tup in xypa_tuples:
xc, yc, pac = tup
rootname = '{:.1f}-{:.1f}-{:.1f}'.format(xc,yc,pac)
rootname = rootname.replace('.','p')
names += [rootname]
if not os.path.exists(master_dirname+'/'+rootname):
os.makedirs(master_dirname+'/'+rootname)
output = master_dirname + '/' + rootname + '/mage_slit_in_muse_{}.reg'.format(rootname)
ntr.create_regfile_nboxes_from_slit(output, (xc,yc), pac, l, w, n, pixscale)
# define name
newcube_name = master_dirname + '/' + rootname + '/magecube_from_muse_{}.fits'.format(rootname)
# check whether this cube already exists
if os.path.isfile(newcube_name):
print('File already exists, skiping: {}'.format(newcube_name.split('/')[-1]))
continue
else:
print('Writing file: {}'.format(newcube_name))
# create the data structure
nw, ny, nx = magecube_orig.shape
nw = musecube.shape[0] # replace mw with that of muse datacube
data = np.zeros(shape=(nw, ny, nx))
var = np.zeros_like(data)
# get the spectra from MUSE in the given region
for ii in range(n):
plt.figure(musecube_pymuse.n)
spec = musecube_pymuse.get_spec_from_ds9regfile(output, mode='sum', i=ii, frac=0.1, npix=0,
empirical_std=False, n_figure=None,
save=False, save_mask=False, plot=False)
# pymuse gets spectrum in vacuum, thus we will convert to air
# because the MUSEcube reduction is in air
# does not seem important, but I leave this here for transparency
spec.vactoair()
data[:, ny-ii-1, 0] = spec.flux
var[:, ny-ii-1, 0] = spec.sig**2
# import pdb; pdb.set_trace()
# redefine the structure
magecube_new = Cube(wcs=magecube_orig.wcs, wave=musecube.wave, data=data, var=var)
newcube_name = master_dirname + '/' + rootname + '/magecube_from_muse_{}.fits'.format(rootname)
magecube_new.write(newcube_name)
# plt.show()
tab['name'] = names
tab['xc'] = [float(name.split('-')[0].replace('p','.')) for name in tab['name']]
tab['yc'] = [float(name.split('-')[1].replace('p','.')) for name in tab['name']]
tab['PA'] = [float(name.split('-')[2].replace('p','.')) for name in tab['name']]
# now read the cubes and perform the chi2
chi2_spec = []
chi2_flux = []
fl_mage_11 = []
fl_muse_11 = []
for jj, name in enumerate(tab['name']):
newcube_name = master_dirname + '/' + name + '/magecube_from_muse_{}.fits'.format(name)
magecube1 = magecube_orig # MagE original
magecube2 = Cube(newcube_name) # from MUSE
chi2_s, chi2_f, fl_mage, fl_muse = compute_chi2_magecubes(magecube1, magecube2,
chi2_wvrange=chi2_wvrange,
renorm_wvrange=renorm_wvrange,
plot_wvrange=plot_wvrange, plot=plot,
text1= 'MagE', text2='MUSE')
print("{} [{}/{}]".format(name, jj + 1, len(tab)))
print(" Total Chi2_spec/DOF = {:.1f}".format(chi2_s))
print(" Total Chi2 flux/DOF = {:.1f}".format(chi2_f))
chi2_spec += [chi2_s]
chi2_flux += [chi2_f]
fl_mage_11 += [fl_mage]
fl_muse_11 += [fl_muse]
if plot:
fig = plt.gcf()
fig.suptitle(name)
tab['fl_muse_11'] = fl_muse_11
tab['fl_mage_11'] = fl_mage_11
tab['chi2_spec'] = chi2_spec
tab['chi2_flux'] = chi2_flux
return tab
def make_MagE_cube_v2(config_file, format='txt'):
"""A new version to create the MagE cubes, it uses MPDAF objects.
It works for .fits 1-d spectra files stored in a directory with a specific
format. In particular:
XXX_yyy_??.txt
Errors are looked for in the same directory with *_sig.fits extension
Parameters
----------
config_file : str
Configuration file with important parameters. See mage.dump_config_make_MagE_cube()
format : str
Either 'fits' of 'txt'
Returns:
Cube fits files associated to each "XX_yyy"
"""
# read config_filename and add filename to params
f = open(config_file)
params = json.load(f)
params['config_filename'] = config_file
# reference files
reference_mage_file = params['reference_mage']
reference_muse_file = params['reference_muse']
# Add comment on how the header was created
comment = 'Cube created by pyntejos.mage.make_MagE_cube.py based on headers from {} and {}. Astrometry ' \
'and wavelength axis given by input configuration ' \
'file {}.'.format(reference_mage_file.split('/')[-1],reference_muse_file.split('/')[-1], params['config_filename'])
# Print message
print('')
print(comment.replace("Cube created", "MagE cube will be created"))
dirname = params['directory_mage']
# filenames = glob.glob(dirname+"/*syn_??.fits")
if format == 'txt':
rootname = params["rootname"]
print('rootname: '+rootname)
filenames = glob.glob(dirname+"/{}_??.txt".format(rootname))
# print(filenames)
elif format == 'fits':
raise NotImplementedError("Not properly implemented. It's almost there but depends on the file structures.")
if len(filenames) == 0:
raise ValueError("No files found matching the rootname: {}".format(rootname))
# sort them
filenames.sort()
# create the new datacube structure
# spec_ref = readspec(filenames[0])
nw, ny, nx = params['NAXIS3'], params['NAXIS2'], params['NAXIS1']
# get wavecoord
# hdr = spec_ref.header
# hdr['CUNIT1'] = 'Angstrom'
crpix = params['CRPIX3']
cdelt = params['CD3_3']
crval = params['CRVAL3']
wave = WaveCoord(hdr=None, crpix=crpix, cdelt=cdelt, crval=crval, cunit=u.AA, ctype='LINEAR', shape=None)
# wave = WaveCoord(hdr=hdr)
# get WCS
crpix_yx = params['CRPIX2'], params['CRPIX1'] # note y,x order
crval_decra = params['CRVAL2'], params['CRVAL1'] # ditto
cdelt_yx = params['PIXSCALE_Y'], -1*params['PIXSCALE_X'] # ditto (negative to decrease towards east)
PA = params['POS_ANGLE']
if PA == "None": # get angle from MagE reference header
print("No PA given in parameter file. Reding PA from MagE reference .fits header")
hdulist_mage = fits.open(params['reference_mage'])
PA = hdulist_mage[0].header['ROTANGLE'] - 44.5 # this is the current offset in angle
print("PA={}deg".format(PA))
shape = (ny, nx)
wcs = WCS(crpix=crpix_yx, crval=crval_decra, cdelt=cdelt_yx, deg=True, shape=shape, rot=-1*PA) # for some reason negative PA works
# redefine wcs to have CD matrix rather than PC matrix
if 1: #rot != 0:
hdr = wcs.to_header()
hdr.rename_keyword('PC1_1','CD1_1')
hdr.rename_keyword('PC2_1','CD2_1')
hdr.rename_keyword('PC1_2','CD1_2')
hdr.rename_keyword('PC2_2','CD2_2')
# hdr['CD1_1'] = hdr['PC1_1']
# hdr['CD2_1'] = hdr['PC2_1']
# hdr['CD1_2'] = hdr['PC1_2']
# hdr['CD2_2'] = hdr['PC2_2']
wcs = WCS(hdr=hdr)
# create data structures
data = np.zeros_like(np.ndarray(shape=(nw,ny,nx)))
var = np.zeros_like(data)
# read the files and fill the data cubes (cube and variance)
print("Reading files from directory {} ordered as:".format(dirname))
for ii,fname in enumerate(filenames):
fn = fname.split('/')[-1]
yspaxel = ny - ii # larger y will be the northern one
print("\t {}: {} --goes to--> spaxel (1,{})".format(ii + 1, fn, yspaxel))
# MAKE SURE THE SPECTRA IS PROPERLY SORTED
nfile = fn.split('.')[0].split('_')[-1]
nfile = int(nfile)
assert nfile == ii + 1, "The files in the directory are not sorted properly. Please check."
if format=='fits':
try:
spec = readspec(fname)
if 0: # dummy
spec.flux = 1
spec.sig = 0
data[:,yspaxel-1,0] = spec.flux.value # position "01" is the most north, y increase to north
if np.isnan(spec.sig):
try:
spec_sig = readspec(fname.replace('flux','sigm'))
spec.sig = spec_sig.flux.value
except:
spec.sig = 0
var[:,yspaxel-1,0] = (spec.sig.value)**2
except:
print("Something is wrong with spectrum {}".format(fname.split('/')[-1]))
import pdb; pdb.set_trace()
raise ValueError("Something is wrong with spectrum {}".format(fname.split('/')[-1]))
elif format=='txt':
spec = read_single_mage_file(fname)
data[:, yspaxel - 1, 0] = spec.flux
var[:, yspaxel - 1, 0] = (spec.sig)**2
# import pdb;pdb.set_trace()
# create the Cube object
cube = Cube(data=data, var=var, wcs=wcs, wave=wave)
outputname = '{}_cube_{}.fits'.format(params['rootname'], params['datestamp'])
cube.write(outputname)
print('Wrote file: {}'.format(outputname))
# create white image
white = cube.sum(axis=0)
white.write(outputname.replace('cube', 'white'))
print('Wrote file: {}'.format(outputname.replace('cube', 'white')))
# import pdb; pdb.set_trace()
return cube
def determine_best_astrometry(magecube_filename,
musecube_filename,
xypa_tuples,
chi2_wvrange,
renorm_wvrange,
plot_wvrange,
plot=True):
"""Utility for determining the best astrometry for a MagE Cube based on a comparisom
with a reference MUSE Cube. It will use different (xc, yc, PA) positions taken from xypa_tuples
for a virtual MagE slit on a MUSE reference datacube and will determine the set that
has the minimum Chi2 within a spectral region. It will return a astropy.table.Table object
with the results.
Parameters
----------
magecube : str
Filename of the MagE cube
musecube_filename : str
Filename of the MUSE reference cube
xyc_tuples: list of tuples
List of (xc, yc, PA) tuples
xc and yc are in units of MUSE pixels and
PA is in the position angle in degrees
chi2_wvrange : (float, float)
Wavelength range for performing the chi2 comparison. Ideally it has to be a small
region centred in a spectral feature (e.g. emission line)
renorm_wvrange : (float, float)
Wavelength range for performing the flux renormalization of MagE to MUSE. Ideally it
has to be a small region close to `chi2_range`.
plot_wvrange : (float, float)
Wavelength range for plotting. Must be larger than either renorm_range or chi2_range.
plot : bool
Whether to plot the iterations for visual inspection
Returns
-------
results : astropy.table.Table
Table with the results
"""
from PyMUSE import musecube as mc
import os
# load the cubes
musecube_pymuse = mc.MuseCube(musecube_filename)
musecube = Cube(musecube_filename)
magecube_orig = Cube(magecube_filename)
# create master subdir
master_dirname = magecube_filename.split('/')[-1].replace(
'.fits', '_astrometry_runs')
if not os.path.exists(master_dirname):
os.makedirs(master_dirname)
# define mage slit geometry
l = 0.3 * 3 * 11
w = 1.
n = 11
pixscale = 0.2 # of MUSE datacube
# create a table to store the results
tab = Table()
# will create auxiliary cubes from MUSE to match geometry of mage
names = []
if 1: # left only for the indentantion
if 1: # left for the indentation
for tup in xypa_tuples:
xc, yc, pac = tup
rootname = '{:.1f}-{:.1f}-{:.1f}'.format(xc, yc, pac)
rootname = rootname.replace('.', 'p')
names += [rootname]
if not os.path.exists(master_dirname + '/' + rootname):
os.makedirs(master_dirname + '/' + rootname)
output = master_dirname + '/' + rootname + '/mage_slit_in_muse_{}.reg'.format(
rootname)
ntr.create_regfile_nboxes_from_slit(output, (xc, yc), pac, l,
w, n, pixscale)
# define name
newcube_name = master_dirname + '/' + rootname + '/magecube_from_muse_{}.fits'.format(
rootname)
# check whether this cube already exists
if os.path.isfile(newcube_name):
print('File already exists, skiping: {}'.format(
newcube_name.split('/')[-1]))
continue
else:
print('Writing file: {}'.format(newcube_name))
# create the data structure
nw, ny, nx = magecube_orig.shape
nw = musecube.shape[0] # replace mw with that of muse datacube
data = np.zeros(shape=(nw, ny, nx))
var = np.zeros_like(data)
# get the spectra from MUSE in the given region
for ii in range(n):
plt.figure(musecube_pymuse.n)
spec = musecube_pymuse.get_spec_from_ds9regfile(
output,
mode='sum',
i=ii,
frac=0.1,
npix=0,
empirical_std=False,
n_figure=None,
save=False,
save_mask=False,
plot=False)
# pymuse gets spectrum in vacuum, thus we will convert to air
# because the MUSEcube reduction is in air
# does not seem important, but I leave this here for transparency
spec.vactoair()
data[:, ny - ii - 1, 0] = spec.flux
var[:, ny - ii - 1, 0] = spec.sig**2
# import pdb; pdb.set_trace()
# redefine the structure
magecube_new = Cube(wcs=magecube_orig.wcs,
wave=musecube.wave,
data=data,
var=var)
newcube_name = master_dirname + '/' + rootname + '/magecube_from_muse_{}.fits'.format(
rootname)
magecube_new.write(newcube_name)
# plt.show()
tab['name'] = names
tab['xc'] = [
float(name.split('-')[0].replace('p', '.')) for name in tab['name']
]
tab['yc'] = [
float(name.split('-')[1].replace('p', '.')) for name in tab['name']
]
tab['PA'] = [
float(name.split('-')[2].replace('p', '.')) for name in tab['name']
]
# now read the cubes and perform the chi2
chi2_spec = []
chi2_flux = []
fl_mage_11 = []
fl_muse_11 = []
for jj, name in enumerate(tab['name']):
newcube_name = master_dirname + '/' + name + '/magecube_from_muse_{}.fits'.format(
name)
magecube1 = magecube_orig # MagE original
magecube2 = Cube(newcube_name) # from MUSE
chi2_s, chi2_f, fl_mage, fl_muse = compute_chi2_magecubes(
magecube1,
magecube2,
chi2_wvrange=chi2_wvrange,
renorm_wvrange=renorm_wvrange,
plot_wvrange=plot_wvrange,
plot=plot,
text1='MagE',
text2='MUSE')
print("{} [{}/{}]".format(name, jj + 1, len(tab)))
print(" Total Chi2_spec/DOF = {:.1f}".format(chi2_s))
print(" Total Chi2 flux/DOF = {:.1f}".format(chi2_f))
chi2_spec += [chi2_s]
chi2_flux += [chi2_f]
fl_mage_11 += [fl_mage]
fl_muse_11 += [fl_muse]
if plot:
fig = plt.gcf()
fig.suptitle(name)
tab['fl_muse_11'] = fl_muse_11
tab['fl_mage_11'] = fl_mage_11
tab['chi2_spec'] = chi2_spec
tab['chi2_flux'] = chi2_flux
return tab
def make_MagE_cube_v2(config_file, format='txt'):
"""A new version to create the MagE cubes, it uses MPDAF objects.
It works for .fits 1-d spectra files stored in a directory with a specific
format. In particular:
XXX_yyy_??.txt
Where XXX -> Name of object
yyy -> ['flx', 'nor', syn']
?? -> ['01', '02', ..., '11']
Each individual file must contain its error array
Parameters
----------
config_file : str
Configuration file with important parameters. See mage.dump_config_make_MagE_cube()
for an example
format : str
Only '.txt' format is allowed. The convention is set by N.Tejos and S.Lopez
northernmost_ypixel : str
What is the Northernmost spaxel, either '11' or '1'
Returns:
Cube fits files associated to each "XX_yyy" object
It writes the .fits to disk
"""
# read config_filename and add filename to params
f = open(config_file)
params = json.load(f)
params['config_filename'] = config_file
# reference files
reference_mage_file = params['reference_mage']
reference_muse_file = params['reference_muse']
# Add comment on how the header was created
comment = 'Cube created by pyntejos.mage.make_MagE_cube.py based on headers from {} and {}. Astrometry ' \
'and wavelength axis given by input configuration ' \
'file {}.'.format(reference_mage_file.split('/')[-1],reference_muse_file.split('/')[-1], params['config_filename'])
# Print message
print('')
print(comment.replace("Cube created", "MagE cube will be created"))
dirname = params['directory_mage']
rootname = params['rootname']
# filenames = glob.glob(dirname+"/*syn_??.fits")
print('rootname: ' + rootname)
if format == 'txt':
# import pdb; pdb.set_trace()
filenames = glob.glob(dirname + "/{}_??.txt".format(rootname))
print('This format is deprecated. Please use .fits instead.')
# print(filenames)
#elif format == 'fits':
# filenames = glob.glob(dirname + "/{}_flux_??.fits".format(rootname))
else:
#raise ValueError('Only implemented for .txt or .fits files.')
raise ValueError(
'Only implemented for .txt files (with a special format convention).'
)
if len(filenames) == 0:
raise ValueError(
"No files found matching the rootname: {}".format(rootname))
# sort them
filenames.sort()
# the structure must be consistent with that specified by the user in the config file
nw, ny, nx = params['NAXIS3'], params['NAXIS2'], params['NAXIS1']
# get wavecoord
# hdr = spec_ref.header
# hdr['CUNIT1'] = 'Angstrom'
crpix = params['CRPIX3']
cdelt = params['CDELT3']
crval = params['CRVAL3']
wave = WaveCoord(hdr=None,
crpix=crpix,
cdelt=cdelt,
crval=crval,
cunit=u.AA,
ctype='LINEAR',
shape=None)
# wave = WaveCoord(hdr=hdr)
# get WCS
crpix_yx = params['CRPIX2'], params['CRPIX1'] # note y,x order
crval_decra = params['CRVAL2'], params['CRVAL1'] # ditto
cdelt_yx = params['PIXSCALE_Y'], -1 * params[
'PIXSCALE_X'] # ditto (negative to decrease towards east)
PA = params['POS_ANGLE']
if PA == "None": # get angle from MagE reference header
print(
"No PA given in parameter file. Reading PA from MagE reference .fits header"
)
hdulist_mage = fits.open(params['reference_mage'])
PA = hdulist_mage[0].header[
'ROTANGLE'] - 44.5 # this is the current offset in angle
print("\tPA={}deg".format(PA))
shape = (ny, nx)
wcs = WCS(crpix=crpix_yx,
crval=crval_decra,
cdelt=cdelt_yx,
deg=True,
shape=shape,
rot=-1 * PA) # for some reason negative PA works
# redefine wcs to have CD matrix rather than PC matrix
if 1: #rot != 0:
hdr = wcs.to_header()
hdr.rename_keyword('PC1_1', 'CD1_1')
hdr.rename_keyword('PC2_1', 'CD2_1')
hdr.rename_keyword('PC1_2', 'CD1_2')
hdr.rename_keyword('PC2_2', 'CD2_2')
# hdr['CD1_1'] = hdr['PC1_1']
# hdr['CD2_1'] = hdr['PC2_1']
# hdr['CD1_2'] = hdr['PC1_2']
# hdr['CD2_2'] = hdr['PC2_2']
wcs = WCS(hdr=hdr)
# create data structures
data = np.zeros_like(np.ndarray(shape=(nw, ny, nx)))
var = np.zeros_like(data)
# read the files and fill the data cubes (cube and variance)
print("Reading files from directory {} ordered as:".format(dirname))
print('Northernmost position is {}'.format(
params['northernmost_position']))
for ii, fname in enumerate(filenames):
fn = fname.split('/')[-1]
if params['northernmost_position'] == '11':
yspaxel = ny - ii # larger y will be the northern one
elif params['northernmost_position'] == '01':
yspaxel = ii + 1
else:
raise ValueError(
'`northernmost_position` must be either `11` or `01` (str) in the configuration file.'
)
print("\t {}: {} --goes to--> spaxel (1,{}) ; i.e. y_python={}".format(
ii + 1, fn, yspaxel, yspaxel - 1))
# MAKE SURE THE SPECTRA IS PROPERLY SORTED
nfile = fn.split('.')[0].split('_')[-1]
nfile = int(nfile)
assert nfile == ii + 1, "The files in the directory are not sorted properly. Please check."
'''
if format=='fits':
spec = readspec(fname)
if 0: # dummy
spec.flux = 1
spec.sig = 0
if spec.sig_is_set:
flux_aux = spec.flux.value
sigm_aux = spec.sig.value
else: # get the sigma values from another file
try:
# import pdb; pdb.set_trace()
sigma_file = fname.replace('flux', 'sigm')
spec_sig = readspec(sigma_file)
spec.sig = spec_sig.flux
except:
print("No sigma spectrum was found in the directory with the right name: {}".format(sigma_file))
spec.sig = 0
flux_aux = spec.flux.value
sigm_aux = spec.sig.value
data[:, yspaxel-1, 0] = flux_aux
var[:, yspaxel-1, 0] = (sigm_aux) ** 2
print("Reading {}, storing it into y={}".format(fname, yspaxel-1))
'''
if format == 'txt':
spec = read_single_mage_file(fname)
data[:, yspaxel - 1, 0] = spec.flux
var[:, yspaxel - 1, 0] = (spec.sig)**2
# import pdb;pdb.set_trace()
# create the Cube object
cube = Cube(data=data, var=var, wcs=wcs, wave=wave)
outputname = '{}_cube_{}.fits'.format(params['rootname'],
params['datestamp'])
cube.write(outputname)
print('Wrote file: {}'.format(outputname))
# create white image
white = cube.sum(axis=0)
white.write(outputname.replace('cube', 'white'))
print('Wrote file: {}'.format(outputname.replace('cube', 'white')))
# import pdb; pdb.set_trace()
return cube
def create_reference_cube(self,
lambdamin=4700,
lambdamax=9400,
step=1.25,
outcube_name=None,
filter_for_nan=False,
**kwargs):
"""Create a reference cube using an input one, and overiding
the lambda part, to get a new WCS
Args:
lambdamin:
lambdamax:
step:
outcube_name:
filter_for_nan:
**kwargs:
Returns:
"""
# Separate folder and name of file
cube_folder, cube_name = os.path.split(self.filename)
# Creating the outcube filename
if outcube_name is None:
prefix = kwargs.pop(
"prefix", "l{0:4d}l{1:4d}_".format(np.int(lambdamin),
np.int(lambdamax)))
outcube_name = "{0}{1}".format(prefix, cube_name)
# Range of lambd and number of spectral pixels
range_lambda = lambdamax - lambdamin
npix_spec = np.int(range_lambda // step + 1.0)
# if filter_nan remove the Nan
if filter_for_nan:
ind = np.indices(self.data[0].shape)
selgood = np.any(~np.isnan(self.data), axis=0)
if self._debug:
upipe.print_debug(
"Xmin={0} Xmax={1} / Ymin={2} Ymax={3}".format(
np.min(ind[0][selgood]), np.max(ind[0][selgood]),
np.min(ind[1][selgood]), np.max(ind[1][selgood])))
subcube = self[:,
np.min(ind[0][selgood]):np.max(ind[0][selgood]),
np.min(ind[1][selgood]):np.max(ind[1][selgood])]
else:
subcube = self
# Create the WCS which we need for the output cube
wcs_header = subcube.get_wcs_header()
wcs1 = subcube.wcs
wave1 = WaveCoord(cdelt=step,
crval=lambdamin,
ctype=wcs_header['CTYPE3'],
crpix=1.0,
shape=npix_spec)
# Create a fake dataset with int to be faster
cube_data = np.ones((npix_spec, wcs1.naxis2, wcs1.naxis1),
dtype=np.uint8)
cube = Cube(data=cube_data, wcs=wcs1, wave=wave1)
# Write the output
cube.write(joinpath(cube_folder, outcube_name))
# just provide the output name by folder+name
return cube_folder, outcube_name