def test_custom_units(ureg, custom_ureg, sync_xdb):
"""dask _meta is a np.ndarray, but dask payload is a Quantity"""
import pint
a = xarray.DataArray(custom_ureg.Quantity([1], "test_unit"))
assert str(a.data.units) == "test_unit"
sync_xdb_custom = XarrayMongoDB(
sync_xdb.meta.database,
collection=sync_xdb.meta.name.split(".")[0],
ureg=custom_ureg,
embed_threshold_bytes=0,
)
_id, _ = sync_xdb_custom.put(a)
b = sync_xdb_custom.get(_id)
assert str(b.data.units) == "test_unit"
xarray.testing.assert_identical(a, b)
with pytest.raises(pint.UndefinedUnitError):
sync_xdb.get(_id)
pint.set_application_registry(custom_ureg)
try:
c = sync_xdb.get(_id)
assert str(c.data.units) == "test_unit"
xarray.testing.assert_identical(a, c)
finally:
pint.set_application_registry(ureg)
def custom_units(ureg, ureg_custom, xdb):
"""dask _meta is a np.ndarray, but dask payload is a Quantity
"""
import pint
a = xarray.DataArray(ureg_custom.Quantity(1, "test_unit"))
assert str(a.data.units) == "test_unit"
xdb_custom = XarrayMongoDB(
xdb.meta.database, collection=xdb.meta.name.split(".")[0], ureg=ureg_custom
)
_id, future = xdb_custom.put(a)
future.compute()
b = xdb_custom.get(_id)
assert str(b.data.compute().units) == "test_unit"
xarray.testing.assert_identical(a, b)
with pytest.raises(pint.UndefinedUnitError):
xdb.get(_id)
pint.set_application_registry(ureg_custom)
try:
c = xdb.get(_id)
assert str(c.data.compute().units) == "test_unit"
xarray.testing.assert_identical(a, c)
finally:
pint.set_application_registry(ureg)
def setUp(self):
super().setUp()
self.ureg_bak = get_application_registry()
self.ureg = UnitRegistry(None)
self.ureg.define("foo = []")
self.ureg.define("bar = foo / 2")
set_application_registry(self.ureg)
assert get_application_registry() is self.ureg
def ureg_custom_global():
import pint
ureg = pint.UnitRegistry()
ureg.define("test_unit = 123 kg")
prev = pint._APP_REGISTRY
pint.set_application_registry(ureg)
yield ureg
pint.set_application_registry(prev)
def test_update_saved_registries():
ureg1 = get_application_registry()
ureg2 = get_application_registry()
new = UnitRegistry()
new.define("foo = []")
set_application_registry(new)
assert ureg1.Unit("foo") == ureg2.Unit("foo")
def test_pickle(self):
import pickle
set_application_registry(self.ureg)
def pickle_test(q):
pq = pickle.loads(pickle.dumps(q))
np.testing.assert_array_equal(q.magnitude, pq.magnitude)
self.assertEqual(q.units, pq.units)
pickle_test([10,20]*self.ureg.m)
def class_tiny_app_registry():
ureg_bak = pint.get_application_registry()
ureg = pint.UnitRegistry(None)
ureg.define("foo = []")
ureg.define("bar = foo / 2")
pint.set_application_registry(ureg)
assert pint.get_application_registry() is ureg
yield ureg
pint.set_application_registry(ureg_bak)
def test_unit(self, protocol):
set_application_registry(self.ureg1)
u1 = Unit("bar")
set_application_registry(self.ureg2)
u2 = Unit("bar")
u3 = pickle.loads(pickle.dumps(u1, protocol))
assert u1.dimensionality == {"[dim1]": 1}
assert u2.dimensionality == {"[dim2]": 1}
assert u3.dimensionality == {"[dim2]": 1}
def test_quantity_2args(self, protocol):
set_application_registry(self.ureg1)
q1 = Quantity(1, "foo")
set_application_registry(self.ureg2)
q2 = Quantity(1, "foo")
q3 = pickle.loads(pickle.dumps(q1, protocol))
assert q1.dimensionality == {"[dim1]": 1}
assert q2.dimensionality == {"[dim2]": 1}
assert q3.dimensionality == {"[dim2]": 1}
assert q1.to("bar").magnitude == 2
assert q2.to("bar").magnitude == 3
assert q3.to("bar").magnitude == 3
def custom_ureg_global():
import pint
ureg = pint.UnitRegistry()
ureg.define("test_unit = 123 kg")
prev = pint.get_application_registry()
try:
# pint.__version__ > 0.18
prev = prev.get()
except AttributeError:
pass
pint.set_application_registry(ureg)
yield ureg
pint.set_application_registry(prev)
def getUnitRegistry(length="meter",
time="second",
substance="item",
volume=None,
other=()):
"""Return a pint.UnitRegistry made compatible with ecell4.
Parameters
----------
length : str, optional
A default unit for '[length]'. 'meter' is its default.
time : str, optional
A default unit for '[time]'. 'second' is its default.
substance : str, optional
A default unit for '[substance]' (the number of molecules). 'item' is its default.
volume : str, optional
A default unit for '[volume]'. Its default is None, thus '[length]**3'.
other : tuple, optional
A list of user-defined default units other than the above.
Returns
-------
ureg : pint.UnitRegistry
"""
ureg = pint.UnitRegistry()
ureg.define('item = mole / avogadro_number')
assert ureg.Quantity(1, 'item').check('[substance]')
try:
ureg.molar
# except UndefinedUnitError:
except AttributeError:
# https://github.com/hgrecco/pint/blob/master/pint/default_en.txt#L75-L77
ureg.define('[concentration] = [substance] / [volume]')
ureg.define('molar = mol / (1e-3 * m ** 3) = M')
base_units = [
unit for unit in (length, time, substance, volume) if unit is not None
]
base_units.extend(other)
_ = ureg.System.from_lines(["@system local using international"] +
base_units, ureg.get_base_units)
ureg.default_system = 'local'
wrap_quantity(ureg.Quantity)
pint.set_application_registry(ureg) # for pickling
return ureg
def test_measurement_3args(self):
set_application_registry(self.ureg1)
m1 = Measurement(10, 1, "foo")
set_application_registry(self.ureg2)
m2 = Measurement(10, 1, "foo")
m3 = pickle.loads(pickle.dumps(m1))
assert m1.dimensionality == {"[dim1]": 1}
assert m2.dimensionality == {"[dim2]": 1}
self.assertEqual(m1.to("bar").value.magnitude, 20)
self.assertEqual(m2.to("bar").value.magnitude, 30)
self.assertEqual(m3.to("bar").value.magnitude, 30)
self.assertEqual(m1.to("bar").error.magnitude, 2)
self.assertEqual(m2.to("bar").error.magnitude, 3)
self.assertEqual(m3.to("bar").error.magnitude, 3)
def test_measurement_3args(self, protocol):
set_application_registry(self.ureg1)
m1 = Measurement(10, 1, "foo")
set_application_registry(self.ureg2)
m2 = Measurement(10, 1, "foo")
m3 = pickle.loads(pickle.dumps(m1, protocol))
assert m1.dimensionality == {"[dim1]": 1}
assert m2.dimensionality == {"[dim2]": 1}
assert m1.to("bar").value.magnitude == 20
assert m2.to("bar").value.magnitude == 30
assert m3.to("bar").value.magnitude == 30
assert m1.to("bar").error.magnitude == 2
assert m2.to("bar").error.magnitude == 3
assert m3.to("bar").error.magnitude == 3
def custom_registry(isolate_application_registry):
ureg = UnitRegistry(None)
ureg.define("foo = []")
ureg.define("bar = foo / 2")
set_application_registry(ureg)
"""
evaluator
A physical property evaluation toolkit from the Open Forcefield Consortium.
"""
import warnings
import pint
from ._version import get_versions
from .plugins import register_default_plugins, register_external_plugins
unit = pint.UnitRegistry()
unit.default_format = "~"
pint.set_application_registry(unit)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
pint.Quantity([])
# Load the default plugins
register_default_plugins()
# Load in any found external plugins.
register_external_plugins()
# Handle versioneer
versions = get_versions()
__version__ = versions["version"]
__git_revision__ = versions["full-revisionid"]
del get_versions, versions
from pint import UnitRegistry, set_application_registry __author__ = 'Anubhav Jain <*****@*****.**>, Saurabh Bajaj <*****@*****.**>' ureg = UnitRegistry() Q_ = ureg.Quantity set_application_registry(ureg)
def tearDown(self):
set_application_registry(self.ureg_bak)
Example scripts are available at https://github.com/PrincetonUniversity/PsyNeuLink/tree/master/Scripts If you have trouble installing PsyNeuLink, run into any bugs, or have suggestions for development, please contact [email protected]. """ import logging as _logging import numpy as _numpy import pint as _pint # pint requires a package-specific unit registry, and to use it as # needed in psyneulink, it has to come before imports. This is the # reason for skipping E402 below _unit_registry = _pint.get_application_registry() _pint.set_application_registry(_unit_registry) _unit_registry.precision = 8 # TODO: remove when floating point issues resolved # starred imports to allow user imports from top level from . import core # noqa: E402 from . import library # noqa: E402 from ._version import get_versions # noqa: E402 from .core import * # noqa: E402 from .library import * # noqa: E402 _pnl_global_names = [ 'primary_registries', 'System', 'Process', '_unit_registry',
from functools import wraps
import numpy as np
from .. import ditParams
try:
import pint
ureg = pint.UnitRegistry()
ureg.define('nat = {} * bit'.format(np.log2(np.e)))
ureg.define('dit = {} * bit'.format(np.log2(10)))
pint.set_application_registry(ureg)
def unitful(f):
"""
Add units to the functions return value.
Parameters
----------
f : func
The function to wrap.
Returns
-------
wrapper : func
A function which optionally adds units to return values.
U_.define("absolute_transmittance = 1.")
U_.define("absorbance = 1. = a.u.")
U_.define("Kubelka_Munk = 1. = K.M.")
U_.define("ppm = 1. = ppm")
U_.define(UnitDefinition("percent", "pct", (), ScaleConverter(1 / 100.0)))
U_.define(
UnitDefinition("weight_percent", "wt_pct", (),
ScaleConverter(1 / 100.0)))
U_.default_format = "~P"
Q_ = U_.Quantity
Q_.default_format = "~P"
set_application_registry(U_)
del UnitRegistry # to avoid importing it
else:
warn("Unit registry was already set up. Bypassed the new loading")
U_.enable_contexts("spectroscopy", "boltzmann", "chemistry")
# Context for NMR
# ------------------------------------------------------------------
def set_nmr_context(larmor):
"""
Set a NMR context relative to the given Larmor frequency.
Parameters
def ureg():
ureg = pint.UnitRegistry()
pint.set_application_registry(ureg)
return ureg
(pd.refDensity * pd.refGravity * pd.refLength**3).to_base_units() /
(pd.refViscosity * pd.refDiffusivity).to_base_units()).magnitude
# In[37]:
#print the timescale
s2myr = (1. * ur.megayear).to_base_units().magnitude
if uw.mpi.size == 1:
print('Dimensionless time to Myr conversion is {}'.format(
Kt.to_base_units().magnitude / s2myr))
# In[38]:
#*************CHECKPOINT-BLOCK**************#
pint.set_application_registry(ur) #https://github.com/hgrecco/pint/issues/146
#if this is a restart, attempt to read in saved dicts.
if cp.restart and md.restartParams:
#try:
with open(os.path.join(cp.loadpath, 'pd.pkl'), 'rb') as fp:
pd = pickle.load(fp)
with open(os.path.join(cp.loadpath, 'md.pkl'), 'rb') as fp:
md = pickle.load(fp)
#and check if additional command line args are also being provided
utils.easy_args(sysArgs, pd)
utils.easy_args(sysArgs, md)
#create dimensionless versions of the parameter dictionaries
npd = params.build_nondim_dict(pd, sca)
def tearDown(self):
super(TestCustomApplicationRegistry, self).tearDown()
set_application_registry(self.ureg_bak)
def tearDown(self):
super().tearDown()
set_application_registry(self.ureg_bak)
>>> v
<Quantity(10.0, 'millimeter / second')>
"""
__test__ = {"Q": Q_.__doc__} # enable doctest checking.
U_ = WELDX_UNIT_REGISTRY.Unit
U_.__name__ = "U_"
U_.__module__ = "pint.unit" # skipcq: PYL-W0212
U_.__doc__ = """For details on working with quantities and units, please see the
`pint documentation <https://pint.readthedocs.io/>`_
"""
# set default units
_DEFAULT_LEN_UNIT = WELDX_UNIT_REGISTRY.millimeters
_DEFAULT_ANG_UNIT = WELDX_UNIT_REGISTRY.rad
# set default unit registry for pint-xarray
pint.set_application_registry(WELDX_UNIT_REGISTRY)
pint_xarray.unit_registry = WELDX_UNIT_REGISTRY
__all__ = (
"META_ATTR",
"USER_ATTR",
"WELDX_PATH",
"WELDX_QUANTITY",
"WELDX_UNIT_REGISTRY",
"Q_",
"U_",
"UNITS_KEY",
)