def basefit_auto(hdu, v, fitting_range=[-150, 150], degree=1,
smooth=11, mincount=21, nsig=1.3, convolve=5):
import numpy
import analyse
cube = hdu.data
nz, ny, nx = cube.shape
if hdu.header['_OBS-MOD']=='otf':
ccube = analyse.convolve(hdu, convolve)
else:
ccube = hdu
pass
spectra = ccube.data.T.reshape(nx*ny, nz)
fit_results = [basefit_auto_line(i, spec, v, fitting_range, degree, smooth, mincount, nsig) \
for i,spec in enumerate(spectra)]
fit_results = numpy.array(fit_results)
emission_flag = numpy.array(fit_results[:,1].reshape(nx, ny, nz).T, dtype=numpy.int16)
fitted = _basefit_flag(cube, emission_flag)
"""
import pyfits
cfitted = _basefit_flag(ccube.data, emission_flag)
cc = pyfits.PrimaryHDU(cfitted, hdu.header)
flag = pyfits.PrimaryHDU(emission_flag, hdu.header)
analyse.basefit_interactive(cc, flag)
"""
return fitted, emission_flag
def easy_analyse(fitspath, save=False, savepath='./'):
import analyse
print('make_cube: %s'%(fitspath.split('/')[-1]))
raw_data = analyse.loadfits(fitspath)
cw_data = analyse.makespec(raw_data)
fitted_data, flag = analyse.basefit(cw_data)
convolved_data = analyse.convolve(fitted_data, 2)
fitted_data, flag = analyse.basefit(convolved_data, 'auto')
savepath = savepath + fitspath.split('.fits')[0]
if save:
analyse.savefits(fitted_data, savepath+'.qlook.data.fits', clobber=True)
analyse.savefits(flag, savepath+'.qlook.flag.fits', clobber=True)
pass
raw_data.data = None
cw_data.data = None
del(raw_data)
del(cw_data)
return fitted_data
def easy_analyse(fitspath, output_dir, flag=None, plot=False, save=False):
import analyse
print('make_cube: %s'%(fitspath.split('/')[-1]))
raw_data = analyse.loadfits(fitspath)
cw_data = analyse.makespec(raw_data)
if flag is None:
fitted_data, flag = analyse.basefit(cw_data)
else:
flag = analyse.loadfits(flag)
fitted_data = analyse.basefit_flag(cw_data, None, flag)
pass
convolved_data = analyse.convolve(fitted_data, 2)
fitted_data = analyse.basefit_flag(convolved_data, None, flag)
ii = analyse.make_2d_map(fitted_data, flag)
rms = analyse.make_2d_map(fitted_data, flag, 'rms')
if save:
savepath = output_dir + fitspath.split('/')[-1].split('.fits')[0]
analyse.savefits(fitted_data, savepath+'.qlook.data.fits', clobber=True)
analyse.savefits(flag, savepath+'.qlook.flag.fits', clobber=True)
analyse.savefits(ii, savepath+'.qlook.ii.fits', clobber=True)
analyse.savefits(rms, savepath+'.qlook.rms.fits', clobber=True)
pass
if plot:
savepath = output_dir + fitspath.split('/')[-1].split('.fits')[0]
isotope = fitspath.split('_')[-2]
plot = analyse.custom_draw_map(figure=(8,8), xspacing=0.2, yspacing=0.2,
tick_labels_size=12, colorber_font_size=11, show=False)
plot(ii, title='mom0: '+isotope).save(savepath+'.qlook.ii.png')
plot(rms, title='rms: '+isotope).save(savepath+'.qlook.rms.png')
analyse.draw_otf_spectrum(fitted_data, figure=(12,5), title='spectra: '+isotope,
show=False).savefig(savepath+'.qlook.spectrum.png')
pass
raw_data.data = None
cw_data.data = None
return fitted_data, flag