def test_save(filepath):
hdu = fits.open(filepath)
cube = hdu[0].data
hdu.close()
params_ami = {
"peakmethod": 'fft',
"bs_multi_tri": False,
"maskname": "g7",
"fw_splodge": 0.7,
}
bs = amical.extract_bs(cube,
filepath,
targetname='test',
**params_ami,
display=False)
cal = amical.calibrate(bs, bs)
assert isinstance(cal, munch.Munch)
dic, savefile = amical.save(cal, oifits_file='test.oifits', fake_obj=True)
v2 = dic['OI_VIS2']['VIS2DATA']
cp = dic['OI_T3']['T3PHI']
assert isinstance(dic, dict)
assert isinstance(savefile, str)
assert (isinstance(v2, np.ndarray))
assert (isinstance(cp, np.ndarray))
assert (len(v2) == 21)
assert (len(cp) == 35)
def _extract_bs_ifile(f, args, ami_param):
"""Extract the bispectrum on individial file (f) and save them as hdf5."""
hdu = fits.open(f)
cube = hdu[0].data
hdu.close()
# Extract the bispectrum
bs = amical.extract_bs(cube, f, **ami_param, save_to=args.save_to)
bs_file = os.path.join(args.outdir, Path(f).stem + "_bispectrum")
amical.save_bs_hdf5(bs, bs_file)
return 0
def example_cal_fft(global_datadir):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bs = amical.extract_bs(
cube,
fits_file,
targetname="test",
bs_multi_tri=False,
maskname="g7",
fw_splodge=0.7,
display=False,
peakmethod="fft",
)
return amical.calibrate(bs, bs)
def test_cal_phscorr(global_datadir):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bs = amical.extract_bs(
cube,
fits_file,
targetname="test",
bs_multi_tri=False,
maskname="g7",
fw_splodge=0.7,
display=False,
peakmethod="fft",
)
cal = amical.calibrate(bs, bs, apply_atmcorr=True)
assert isinstance(cal, munch.Munch)
def test_extract(peakmethod, global_datadir):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bs = amical.extract_bs(
cube,
fits_file,
targetname="test",
bs_multi_tri=False,
maskname="g7",
fw_splodge=0.7,
display=False,
peakmethod=peakmethod,
)
bs_keys = list(bs.keys())
assert isinstance(bs, munch.Munch)
assert len(bs_keys) == 13
def test_show(filepath):
hdu = fits.open(filepath)
cube = hdu[0].data
hdu.close()
params_ami = {
"peakmethod": 'fft',
"bs_multi_tri": False,
"maskname": "g7",
"fw_splodge": 0.7,
}
bs = amical.extract_bs(cube,
filepath,
targetname='test',
**params_ami,
display=False)
cal = amical.calibrate(bs, bs)
amical.show(cal)
def example_bss(global_datadir):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bss = {}
for peakmethod in peakmethods:
bss[peakmethod] = amical.extract_bs(
cube,
fits_file,
targetname='test',
bs_multi_tri=False,
maskname="g7",
fw_splodge=0.7,
display=False,
peakmethod=peakmethod
)
return bss
def test_extraction(filepath):
hdu = fits.open(filepath)
cube = hdu[0].data
hdu.close()
method = ['fft', 'gauss', 'square']
for m in method:
params_ami = {
"peakmethod": m,
"bs_multi_tri": False,
"maskname": "g7",
"fw_splodge": 0.7,
}
bs = amical.extract_bs(cube,
filepath,
targetname='test',
**params_ami,
display=False)
assert isinstance(bs, munch.Munch)
def test_extract_multitri(global_datadir, tmp_path):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bs = amical.extract_bs(
cube,
fits_file,
targetname="test",
bs_multi_tri=True,
maskname="g7",
fw_splodge=0.7,
display=True,
expert_plot=True,
naive_err=True,
verbose=True,
save_to=str(tmp_path),
peakmethod="fft",
)
bs_keys = list(bs.keys())
assert isinstance(bs, munch.Munch)
assert len(bs_keys) == 13
def test_quiet_mode(global_datadir, capsys):
fits_file = global_datadir / "test.fits"
with fits.open(fits_file) as fh:
cube = fh[0].data
bs = amical.extract_bs(
cube,
fits_file,
targetname="test",
bs_multi_tri=False,
maskname="g7",
fw_splodge=0.7,
display=False,
peakmethod="fft",
verbose=False,
)
captured = capsys.readouterr()
bs_keys = list(bs.keys())
assert isinstance(bs, munch.Munch)
assert len(bs_keys) == 13
assert captured.out == ""
assert captured.err == ""
# Check example_SPHERE.py for more details.
# ----------------------------------
# AMI parameters (refer to the docstrings of `extract_bs` for details)
params_ami = {
"peakmethod": "fft",
"bs_multi_tri": False,
"maskname": "g7",
"fw_splodge": 0.7,
}
# Extract raw complex observables for the target and the calibrator:
# It's the core of the pipeline (amical/mf_pipeline/bispect.py)
bs_t = amical.extract_bs(cube_t,
file_t,
targetname="fakebinary",
**params_ami,
display=True)
bs_c = amical.extract_bs(cube_c,
file_c,
targetname="fakepsf",
**params_ami,
display=False)
# Calibrate the raw data to get calibrated V2 and CP.
# bs_c can be a single calibrator result or a list of calibrators.
# (see amical/calibration.py for details).
cal = amical.calibrate(bs_t, bs_c)
# Display and save the results as oifits
amical.show(cal)
cube_c = amical.select_clean_data(file_c, clip=True,
**clean_param, display=True)
# AMI parameters (refer to the docstrings of `extract_bs` for details)
params_ami = {"peakmethod": 'fft',
"bs_multi_tri": False,
"maskname": "g7",
"fw_splodge": 0.7,
"filtname": 'K1'
}
# # Extract raw complex observables for the target and the calibrator:
# # It's the core of the pipeline (amical/mf_pipeline/bispect.py)
bs_t = amical.extract_bs(cube_t, file_t, targetname='HD142527',
**params_ami, display=True)
bs_c = amical.extract_bs(cube_c, file_c, targetname='HD142695',
**params_ami, display=False)
# (from amical.tools import check_seeing_cond, plot_seeing_cond)
# In case of multiple files for a same target, you can
# check the seeing condition and select only the good ones.
# cond_t = check_seeing_cond([bs_t])
# cond_c = check_seeing_cond([bs_c])
# plot_seeing_cond([cond_t, cond_c], lim_seeing=1)
# Calibrate the raw data to get get calibrated V2 and CP
# bs_c can be a single calibrator result or a list of calibrator.
# (see amical/core.py for details).
cal = amical.calibrate(bs_t, bs_c)
