def test_linearcoord():
coord1 = Coord([1, 2.5, 4, 5])
coord2 = Coord(np.array([1, 2.5, 4, 5]))
assert coord2 == coord1
coord3 = Coord(range(10))
coord4 = Coord(np.arange(10))
assert coord4 == coord3
coord5 = coord4.copy()
coord5 += 1
assert np.all(coord5.data == coord4.data + 1)
assert coord5 is not None
coord5.linear = True
coord6 = Coord(linear=True, offset=2.0, increment=2.0, size=10)
assert np.all(coord6.data == (coord4.data + 1.0) * 2.)
LinearCoord(offset=2.0, increment=2.0, size=10)
coord0 = LinearCoord.linspace(200.,
300.,
3,
labels=['cold', 'normal', 'hot'],
units="K",
title='temperature')
coord1 = LinearCoord.linspace(0.,
60.,
100,
labels=None,
units="minutes",
title='time-on-stream')
coord2 = LinearCoord.linspace(4000.,
1000.,
100,
labels=None,
units="cm^-1",
title='wavenumber')
assert coord0.size == 3
assert coord1.size == 100
assert coord2.size == 100
coordc = coord0.copy()
assert coord0 == coordc
coordc = coord1.copy()
assert coord1 == coordc
def test_coordset_copy(coord0, coord1):
coord2 = LinearCoord.linspace(200.,
300.,
3,
units="K",
title='temperature')
coordsa = CoordSet(coord0, coord1, coord2)
coordsb = coordsa.copy()
assert coordsa == coordsb
assert coordsa is not coordsb
assert coordsa(1) == coordsb(1)
assert coordsa(1).name == coordsb(1).name
# copy
coords = CoordSet(coord0, coord0.copy())
coords1 = coords[:]
assert coords is not coords1
import copy
coords2 = copy.deepcopy(coords)
assert coords == coords2
def _read_opus(*args, **kwargs):
debug_("Bruker OPUS import")
dataset, filename = args
content = kwargs.get("content", None)
if content:
fid = io.BytesIO(content)
else:
fid = open(filename, "rb")
opus_data = _read_data(fid)
# data
try:
npt = opus_data["AB Data Parameter"]["NPT"]
data = opus_data["AB"][:npt]
dataset.data = np.array(data[np.newaxis], dtype="float32")
except KeyError:
raise IOError(
f"{filename} is not an Absorbance spectrum. It cannot be read with the `read_opus` import method"
)
# todo: read background
# xaxis
fxv = opus_data["AB Data Parameter"]["FXV"]
lxv = opus_data["AB Data Parameter"]["LXV"]
# xdata = linspace(fxv, lxv, npt)
xaxis = LinearCoord.linspace(fxv, lxv, npt, title="wavenumbers", units="cm^-1")
# yaxis
name = opus_data["Sample"]["SNM"]
acqdate = opus_data["AB Data Parameter"]["DAT"]
acqtime = opus_data["AB Data Parameter"]["TIM"]
gmt_offset_hour = float(acqtime.split("GMT")[1].split(")")[0])
if len(acqdate.split("/")[0]) == 2:
date_time = datetime.strptime(
acqdate + "_" + acqtime.split()[0], "%d/%m/%Y_%H:%M:%S.%f"
)
elif len(acqdate.split("/")[0]) == 4:
date_time = datetime.strptime(
acqdate + "_" + acqtime.split()[0], "%Y/%m/%d_%H:%M:%S"
)
utc_dt = date_time - timedelta(hours=gmt_offset_hour)
utc_dt = utc_dt.replace(tzinfo=timezone.utc)
timestamp = utc_dt.timestamp()
yaxis = Coord(
[timestamp],
title="acquisition timestamp (GMT)",
units="s",
labels=([utc_dt], [name], [filename]),
)
# set dataset's Coordset
dataset.set_coordset(y=yaxis, x=xaxis)
dataset.units = "absorbance"
dataset.title = "absorbance"
# Set name, origin, description and history
dataset.name = filename.name
dataset.origin = "opus"
dataset.description = "Dataset from opus files. \n"
dataset.history = str(datetime.now(timezone.utc)) + ": import from opus files \n"
dataset._date = datetime.now(timezone.utc)
dataset._modified = dataset.date
return dataset
def _read_opus(*args, **kwargs):
debug_('Bruker OPUS import')
dataset, filename = args
content = kwargs.get('content', None)
if content:
fid = io.BytesIO(content)
else:
fid = open(filename, 'rb')
opus_data = _read_data(fid)
# data
try:
npt = opus_data['AB Data Parameter']['NPT']
data = opus_data["AB"][:npt]
dataset.data = np.array(data[np.newaxis], dtype='float32')
except KeyError:
raise IOError(
f"{filename} is not an Absorbance spectrum. It cannot be read with the `read_opus` import method"
)
# xaxis
fxv = opus_data['AB Data Parameter']['FXV']
lxv = opus_data['AB Data Parameter']['LXV']
# xdata = linspace(fxv, lxv, npt)
xaxis = LinearCoord.linspace(fxv,
lxv,
npt,
title='wavenumbers',
units='cm^-1')
# yaxis
name = opus_data["Sample"]['SNM']
acqdate = opus_data["AB Data Parameter"]["DAT"]
acqtime = opus_data["AB Data Parameter"]["TIM"]
gmt_offset_hour = float(acqtime.split('GMT')[1].split(')')[0])
date_time = datetime.strptime(acqdate + '_' + acqtime.split()[0],
'%d/%m/%Y_%H:%M:%S.%f')
utc_dt = date_time - timedelta(hours=gmt_offset_hour)
utc_dt = utc_dt.replace(tzinfo=timezone.utc)
timestamp = utc_dt.timestamp()
yaxis = Coord([timestamp],
title='acquisition timestamp (GMT)',
units='s',
labels=([utc_dt], [name]))
# set dataset's Coordset
dataset.set_coordset(y=yaxis, x=xaxis)
dataset.units = 'absorbance'
dataset.title = 'absorbance'
# Set name, origin, description and history
dataset.name = filename.name
dataset.origin = "opus"
dataset.description = 'Dataset from opus files. \n'
dataset.history = str(datetime.now(
timezone.utc)) + ': import from opus files \n'
dataset._date = datetime.now(timezone.utc)
dataset._modified = dataset.date
return dataset
def test_linearcoord():
coord1 = Coord([1, 2.5, 4, 5])
coord2 = Coord(np.array([1, 2.5, 4, 5]))
assert coord2 == coord1
coord3 = Coord(range(10))
coord4 = Coord(np.arange(10))
assert coord4 == coord3
coord5 = coord4.copy()
coord5 += 1
assert np.all(coord5.data == coord4.data + 1)
assert coord5 is not None
coord5.linear = True
coord6 = Coord(linear=True, offset=2.0, increment=2.0, size=10)
assert np.all(coord6.data == (coord4.data + 1.0) * 2.0)
LinearCoord(offset=2.0, increment=2.0, size=10)
coord0 = LinearCoord.linspace(
200.0,
300.0,
3,
labels=["cold", "normal", "hot"],
units="K",
title="temperature",
)
coord1 = LinearCoord.linspace(0.0,
60.0,
100,
labels=None,
units="minutes",
title="time-on-stream")
coord2 = LinearCoord.linspace(4000.0,
1000.0,
100,
labels=None,
units="cm^-1",
title="wavenumber")
assert coord0.size == 3
assert coord1.size == 100
assert coord2.size == 100
coordc = coord0.copy()
assert coord0 == coordc
coordc = coord1.copy()
assert coord1 == coordc
assert_approx_equal(coord1.spacing.m, 0.606060606)
assert coord1.author is None
assert not coord1.history
assert not coord1.descendant
assert coord2.descendant
assert coord1.is_1d
assert coord0.transpose() == coord0