def test_xarray_ufuncs_deprecation():
with pytest.warns(FutureWarning, match="xarray.ufuncs"):
xu.cos(xr.DataArray([0, 1]))
with pytest.warns(None) as record:
xu.angle(xr.DataArray([0, 1]))
assert len(record) == 0
def test_xarray_ufuncs_deprecation():
with pytest.warns(PendingDeprecationWarning, match='xarray.ufuncs'):
xu.cos(xr.DataArray([0, 1]))
with pytest.warns(None) as record:
xu.angle(xr.DataArray([0, 1]))
record = [el.message for el in record
if el.category == PendingDeprecationWarning]
assert len(record) == 0
def test_xarray_ufuncs_deprecation():
with pytest.warns(PendingDeprecationWarning, match='xarray.ufuncs'):
xu.cos(xr.DataArray([0, 1]))
with pytest.warns(None) as record:
xu.angle(xr.DataArray([0, 1]))
record = [el.message for el in record
if el.category == PendingDeprecationWarning]
assert len(record) == 0
def load_Bmns(
folder="./",
phasing=0.0,
slice=0,
cur_up=1.0,
cur_low=1.0,
cur_mid=None,
machine=None,
iplasma=None,
code="m3dc1",
ntor=None,
phase=False,
Jmn=False,
):
if machine is "diiid":
conv = 1.0
elif machine is "aug":
conv = -1.0
elif machine is "kstar":
conv = 1.0
if phase is not True:
phase = False
phasing = np.asarray(phasing)
if code is "all":
Bc1 = load_Bmns(
folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code="m3dc1",
ntor=ntor,
)
Bmars = load_Bmns(
folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code="mars",
ntor=ntor,
)
Bipec = load_Bmns(
folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code="ipec",
ntor=ntor,
)
return (Bc1, Bmars, Bipec)
elif code is "m3dc1":
if Jmn:
file_up = folder + "/jmn3_upper-" + str(slice) + ".cdf"
file_low = folder + "/jmn3_lower-" + str(slice) + ".cdf"
else:
file_up = folder + "/bmn_upper-" + str(slice) + ".cdf"
file_low = folder + "/bmn_lower-" + str(slice) + ".cdf"
ds_up = xr.open_dataset(file_up)
ds_low = xr.open_dataset(file_low)
ntor = ds_up.attrs["ntor"]
fac = geofac(machine=machine, ntor=ntor)
cur_up = fac * cur_up
cur_low = fac * cur_low
m = ds_up.m
try:
print("Using Bmn netCDF version " + str(ds_up.version))
Psi = ds_up.psi_norm
except AttributeError:
print("Using Bmn netCDF version 0")
Psi = ds_up.psi
Bup = ds_up.bmn_real.data + 1j * ds_up.bmn_imag.data
Blow = ds_low.bmn_real.data + 1j * ds_low.bmn_imag.data
if cur_mid is not None:
if Jmn:
file_mid = folder + "/jmn_middle-" + str(slice) + ".cdf"
else:
file_mid = folder + "/bmn_middle-" + str(slice) + ".cdf"
ds_mid = xr.open_dataset(file_mid)
cur_mid = fac * cur_mid
Bmid = ds_mid.bmn_real.data + 1j * ds_mid.bmn_imag.data
if (iplasma is not None) and (slice > 0):
if Jmn:
file_up = folder + "/jmn3_upper-0.cdf"
file_low = folder + "/jmn3_lower-0.cdf"
else:
file_up = folder + "/bmn_upper-0.cdf"
file_low = folder + "/bmn_lower-0.cdf"
ds_vu = xr.open_dataset(file_up)
ds_vl = xr.open_dataset(file_low)
Bup -= ds_vu.bmn_real.data
Bup -= 1j * ds_vu.bmn_imag.data
Blow -= ds_vl.bmn_real.data
Blow -= 1j * ds_vl.bmn_imag.data
if cur_mid is not None:
if Jmn:
file_mid = folder + "/jmn3_middle-0.cdf"
else:
file_mid = folder + "/bmn_middle-0.cdf"
ds_vm = xr.open_dataset(file_mid)
Bmid -= ds_vm.bmn_real.data
Bmid -= 1j * ds_vm.bmn_imag.data
q = ds_up.q.data
elif code is "mars":
file = folder + "/mars_bmn.nc"
dset = xr.open_dataset(file)
m = dset.m
Psi = dset.s ** 2.0
if slice is 0:
Bup = dset.vacuum_upper_real.data + 1j * dset.vacuum_upper_imag.data
Blow = dset.vacuum_lower_real.data + 1j * dset.vacuum_lower_imag.data
elif slice is 1:
Bup = dset.total_upper_real.data + 1j * dset.total_upper_imag.data
Blow = dset.total_lower_real.data + 1j * dset.total_lower_imag.data
if iplasma is not None:
Bup -= dset.vacuum_upper_real.data
Bup -= 1j * dset.vacuum_upper_imag.data
Blow -= dset.vacuum_lower_real.data
Blow -= 1j * dset.vacuum_lower_imag.data
else:
return NotImplemented
Psi1 = dset.q_s ** 2.0
q1 = dset.q
f = interp1d(Psi1, q1, bounds_error=False)
q = f(Psi)
# flip signs because theta is flipped
conv = -conv
m = -m
q = -q
elif code is "ipec":
if (slice == 0) or (iplasma is not None):
# get the vacuum field
base = folder + "ipec_vbnormal"
sr = 7
# skip this many rows
cr = 3
# column of real Bmn (zero-based)
ci = 4
# column of imaginary Bmn (zero-based)
(Pv, mv, Bvu, Bvl, qv) = B_ipec(base, sr, cr, ci)
if slice == 1:
# get the total field
base = folder + "ipec_xbnormal"
sr = 8
# skip this many rows
cr = 7
# column of real Bmn
ci = 8
# column of imaginary Bmn
(Pt, mt, Btu, Btl, qt) = B_ipec(base, sr, cr, ci)
if slice == 0:
# just the vacuum field
(Psi, m, Bup, Blow, q) = (Pv, mv, Bvu, Bvl, qv)
elif (slice == 1) and (iplasma is None):
# just the total field
(Psi, m, Bup, Blow, q) = (Pt, mt, Btu, Btl, qt)
else:
# we need to subtract the vacuum from the total field
Rv = RBS(Pv, mv, Bvu.real)
Iv = RBS(Pv, mv, Bvu.imag)
Bvu = Rv(Pt, mt) + 1j * Iv(Pt, mt)
Rv = RBS(Pv, mv, Bvl.real)
Iv = RBS(Pv, mv, Bvl.imag)
Bvl = Rv(Pt, mt) + 1j * Iv(Pt, mt)
(Psi, m, Bup, Blow, q) = (Pt, mt, Btu - Bvu, Btl - Bvl, qt)
conv = -conv
m = -m
q = -q
else:
return NotImplemented
# Quantities used for all code results
cur = xr.DataArray(np.cos(pi * phasing / 180.0) + conv * 1j * np.sin(pi * phasing / 180.0), {"phasing": phasing})
Bmn_up = cur_up * xr.DataArray(Bup, [("Psi", Psi), ("m", m)])
Bmn_low = cur_low * xr.DataArray(Blow, [("Psi", Psi), ("m", m)])
Bmn = cur * Bmn_up + Bmn_low
if cur_mid is not None:
cur2 = xr.DataArray(
np.cos(pi * phasing / 180.0) + conv * 1j * np.sin(pi * phasing / 180.0), {"phasing2": phasing}
)
Bmn_mid = cur_mid * xr.DataArray(Bmid, [("Psi", Psi), ("m", m)])
Bmn = Bmn + cur2 * Bmn_mid
if phase:
Bmn = xru.angle(Bmn, deg=True) % 360.0
else:
Bmn = np.abs(Bmn)
q = xr.DataArray(q, [("Psi", Psi)])
if Jmn:
Bmns = xr.Dataset({"Jmn": Bmn, "q": q})
else:
Bmns = xr.Dataset({"Bmn": Bmn, "q": q})
Bmns.attrs["ntor"] = ntor
Bmns.attrs["phase"] = phase
return Bmns
def load_Bmns(folder='./',
phasing=0.,
slice=0,
cur_up=1.,
cur_low=1.,
cur_mid=None,
probeg_up=False,
probeg_low=False,
probeg_mid=False,
machine=None,
iplasma=None,
code='m3dc1',
ntor=None,
phase=False,
Jmn=False):
if machine is 'diiid':
conv = 1.0
elif machine is 'aug':
conv = -1.0
elif machine is 'kstar':
conv = 1.0
if phase is not True:
phase = False
phasing = np.asarray(phasing)
if code is 'all':
Bc1 = load_Bmns(folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code='m3dc1',
ntor=ntor)
Bmars = load_Bmns(folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code='mars',
ntor=ntor)
Bipec = load_Bmns(folder=folder,
phasing=phasing,
slice=slice,
cur_up=cur_up,
cur_low=cur_low,
machine=machine,
iplasma=iplasma,
code='ipec',
ntor=ntor)
return (Bc1, Bmars, Bipec)
elif code is 'm3dc1':
if Jmn:
file_up = folder + '/jmn3_upper-' + str(slice) + '.cdf'
file_low = folder + '/jmn3_lower-' + str(slice) + '.cdf'
else:
file_up = folder + '/bmn_upper-' + str(slice) + '.cdf'
file_low = folder + '/bmn_lower-' + str(slice) + '.cdf'
ds_up = xr.open_dataset(file_up)
ds_low = xr.open_dataset(file_low)
ntor = ds_up.attrs['ntor']
if probeg_up:
fac = 2.
else:
fac = geofac(machine=machine, ntor=ntor)
cur_up = fac * cur_up
if probeg_low:
fac = 2.
else:
fac = geofac(machine=machine, ntor=ntor)
cur_low = fac * cur_low
m = ds_up.m
try:
print("Using Bmn netCDF version " + str(ds_up.version))
Psi = ds_up.psi_norm
except AttributeError:
print("Using Bmn netCDF version 0")
Psi = ds_up.psi
Bup = ds_up.bmn_real.data + 1j * ds_up.bmn_imag.data
Blow = ds_low.bmn_real.data + 1j * ds_low.bmn_imag.data
if cur_mid is not None:
if Jmn:
file_mid = folder + '/jmn_middle-' + str(slice) + '.cdf'
else:
file_mid = folder + '/bmn_middle-' + str(slice) + '.cdf'
ds_mid = xr.open_dataset(file_mid)
if probeg_mid:
fac = 2.
else:
fac = geofac(machine=machine, ntor=ntor)
cur_mid = fac * cur_mid
Bmid = ds_mid.bmn_real.data + 1j * ds_mid.bmn_imag.data
if (iplasma is not None) and (slice > 0):
if Jmn:
file_up = folder + '/jmn3_upper-0.cdf'
file_low = folder + '/jmn3_lower-0.cdf'
else:
file_up = folder + '/bmn_upper-0.cdf'
file_low = folder + '/bmn_lower-0.cdf'
ds_vu = xr.open_dataset(file_up)
ds_vl = xr.open_dataset(file_low)
Bup -= ds_vu.bmn_real.data
Bup -= 1j * ds_vu.bmn_imag.data
Blow -= ds_vl.bmn_real.data
Blow -= 1j * ds_vl.bmn_imag.data
if cur_mid is not None:
if Jmn:
file_mid = folder + '/jmn3_middle-0.cdf'
else:
file_mid = folder + '/bmn_middle-0.cdf'
ds_vm = xr.open_dataset(file_mid)
Bmid -= ds_vm.bmn_real.data
Bmid -= 1j * ds_vm.bmn_imag.data
q = ds_up.q.data
elif code is 'mars':
file = folder + '/mars_bmn.nc'
dset = xr.open_dataset(file)
m = dset.m
Psi = dset.s**2.0
if slice is 0:
Bup = dset.vacuum_upper_real.data + 1j * dset.vacuum_upper_imag.data
Blow = dset.vacuum_lower_real.data + 1j * dset.vacuum_lower_imag.data
elif slice is 1:
Bup = dset.total_upper_real.data + 1j * dset.total_upper_imag.data
Blow = dset.total_lower_real.data + 1j * dset.total_lower_imag.data
if (iplasma is not None):
Bup -= dset.vacuum_upper_real.data
Bup -= 1j * dset.vacuum_upper_imag.data
Blow -= dset.vacuum_lower_real.data
Blow -= 1j * dset.vacuum_lower_imag.data
else:
return NotImplemented
Psi1 = dset.q_s**2.0
q1 = dset.q
f = interp1d(Psi1, q1, bounds_error=False)
q = f(Psi)
# flip signs because theta is flipped
conv = -conv
m = -m
q = -q
elif code is 'ipec':
if (slice == 0) or (iplasma is not None):
# get the vacuum field
base = folder + 'ipec_vbnormal'
sr = 7
# skip this many rows
cr = 3
# column of real Bmn (zero-based)
ci = 4
# column of imaginary Bmn (zero-based)
(Pv, mv, Bvu, Bvl, qv) = B_ipec(base, sr, cr, ci)
if slice == 1:
# get the total field
base = folder + 'ipec_xbnormal'
sr = 8
# skip this many rows
cr = 7
# column of real Bmn
ci = 8
# column of imaginary Bmn
(Pt, mt, Btu, Btl, qt) = B_ipec(base, sr, cr, ci)
if slice == 0:
# just the vacuum field
(Psi, m, Bup, Blow, q) = (Pv, mv, Bvu, Bvl, qv)
elif (slice == 1) and (iplasma is None):
# just the total field
(Psi, m, Bup, Blow, q) = (Pt, mt, Btu, Btl, qt)
else:
# we need to subtract the vacuum from the total field
Rv = RBS(Pv, mv, Bvu.real)
Iv = RBS(Pv, mv, Bvu.imag)
Bvu = Rv(Pt, mt) + 1j * Iv(Pt, mt)
Rv = RBS(Pv, mv, Bvl.real)
Iv = RBS(Pv, mv, Bvl.imag)
Bvl = Rv(Pt, mt) + 1j * Iv(Pt, mt)
(Psi, m, Bup, Blow, q) = (Pt, mt, Btu - Bvu, Btl - Bvl, qt)
conv = -conv
m = -m
q = -q
else:
return NotImplemented
# Quantities used for all code results
cur = xr.DataArray(np.cos(pi * phasing / 180.) +
conv * 1j * np.sin(pi * phasing / 180.),
coords=[('phasing', phasing)])
Bmn_up = cur_up * xr.DataArray(Bup, coords=[('Psi', Psi), ('m', m)])
Bmn_low = cur_low * xr.DataArray(Blow, coords=[('Psi', Psi), ('m', m)])
Bmn = cur * Bmn_up + Bmn_low
if cur_mid is not None:
cur2 = xr.DataArray(np.cos(pi * phasing / 180.) +
conv * 1j * np.sin(pi * phasing / 180.),
coords=[('phasing2', phasing)])
Bmn_mid = cur_mid * xr.DataArray(Bmid, coords=[('Psi', Psi), ('m', m)])
Bmn = Bmn + cur2 * Bmn_mid
if phase:
Bmn = xru.angle(Bmn, deg=True) % 360.
else:
Bmn = np.abs(Bmn)
q = xr.DataArray(q, coords=[('Psi', Psi)])
if Jmn:
Bmns = xr.Dataset({'Jmn': Bmn, 'q': q})
else:
Bmns = xr.Dataset({'Bmn': Bmn, 'q': q})
Bmns.attrs['ntor'] = ntor
Bmns.attrs['phase'] = phase
return Bmns
def test_xarray_ufuncs_deprecation():
with pytest.warns(FutureWarning, match="xarray.ufuncs"):
xu.cos(xr.DataArray([0, 1]))
with assert_no_warnings():
xu.angle(xr.DataArray([0, 1]))
