def test_extend_from_module(self):
# Custom unit is not known initially
with self.assertRaises(UnableToParseUnits):
unit_parser.parse_unit("custom_unit", suppress_unknown=False)
unit_parser.parser.extend(sample_units)
# Once parser is extended, the unit can be parsed
expected_unit = sample_units.custom_unit
self.assertEqual(unit_parser.parse_unit("custom_unit"), expected_unit)
self.assertEqual(unit_parser.parse_unit("cuwl"), expected_unit)
def volumetric_CV_flow_rate_to_volumetric_flow_rate(vol_cv_flow_rate,
column,
to_unit=None):
""" Convert a volumetric flow rate using the CV unit to a physical unit.
Parameters
----------
vol_cv_flow_rate : UnitScalar
Fow rate in column volume unit CV per unit time.
column : Column
Column object the flow happens in.
to_unit : str or Unit
Unit of the result flow rate.
Returns
-------
float
Flow rate in SI compatible unit.
"""
if to_unit is None:
to_unit = m**3 / second
elif isinstance(to_unit, basestring):
to_unit = unit_parser.parse_unit(to_unit)
si_flow_rate = vol_cv_flow_rate * column.volume
return chr_units.convert_units(si_flow_rate, tgt_unit=to_unit)
def test_strict_units_trait(self):
obj = UnitsStrict(units='km')
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'km')
obj.units = 'm/sec**2'
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'm/sec**2')
self.assertEqual(obj.units.derivation, (1, 0, -2, 0, 0, 0, 0))
self.assertRaises(TraitError, setattr, obj, 'units', 'invalid')
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'm/sec**2')
self.assertEqual(obj.units.derivation, (1, 0, -2, 0, 0, 0, 0))
units = unit_parser.parse_unit('g/cc')
self.assertFalse(units is None)
self.assertEqual(units.label, 'g/cc')
self.assertNotEqual(units.derivation, dimensionless.derivation)
obj.units = units
self.assertTrue(obj.units is units)
return
def test_strict_units_trait(self):
obj = UnitsStrict(units='km')
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'km')
obj.units = 'm/sec**2'
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'm/sec**2')
self.failUnlessEqual(obj.units.derivation, (1, 0, -2, 0, 0, 0, 0))
self.failUnlessRaises(TraitError, setattr, obj, 'units', 'invalid')
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'm/sec**2')
self.failUnlessEqual(obj.units.derivation, (1, 0, -2, 0, 0, 0, 0))
units = unit_parser.parse_unit('g/cc')
self.failIf(units is None)
self.failUnlessEqual(units.label, 'g/cc')
self.failIfEqual(units.derivation, dimensionless.derivation)
obj.units = units
self.failUnless(obj.units is units)
return
def test_parse_absorption_units(self):
# add custom units to the parser.
initialize_unit_parser()
# check we can parse based on the unit name
u1 = unit_parser.parse_unit('absorption_unit', suppress_unknown=False)
self.assertEqual(u1.label, 'absorption_unit')
# check we can parse based on the unit label
u2 = unit_parser.parse_unit('AU', suppress_unknown=False)
self.assertEqual(u2.label, 'AU')
# check the two units mean the same thing (except labels)
self.assertEqual(u1.derivation, u2.derivation)
self.assertEqual(u1.offset, u2.offset)
self.assertEqual(u1.value, u2.value)
def test_calculate_component_concentrations(self):
comp_absorb_data = {
"Acidic_1_Sim": self.data,
"Acidic_2_Sim": self.data,
"Native_Sim": self.data
}
comps = [Prod001_comp1, Prod001_comp2, Prod001_comp3]
product = Product(product_components=comps, **PRODUCT_DATA)
start_collect_idx, stop_collect_idx = 1, 3
comp_conc = calculate_component_concentrations(product,
comp_absorb_data,
start_collect_idx,
stop_collect_idx)
self.assertIsInstance(comp_conc, UnitArray)
self.assertEqual(comp_conc.units, unit_parser.parse_unit("g/liter"))
# All the same value since all the same XYdata
for concentration in comp_conc:
self.assertEqual(concentration, comp_conc[0])
def convert_units(unitted_data, tgt_unit, **kwargs):
""" Convert unitted data to the units specified by `tgt_unit`.
Parameters
----------
unitted_data : UnitScalar or UnitArray
The data to be converted to `tgt_unit`
tgt_unit : scimath.unit or str
The target units for `unitted_data`.
kwargs : dict
Additional arguments that may be needed by custom converters for
special units.
Returns
-------
UnitScalar or UnitArray
The converted data.
"""
if isinstance(tgt_unit, basestring):
tgt_unit = unit_parser.parse_unit(tgt_unit)
if isinstance(unitted_data, UnitScalar):
unit_klass = UnitScalar
elif isinstance(unitted_data, UnitArray):
unit_klass = UnitArray
else:
msg = "The `unitted_data` argument must be an instance of either " \
"scimath's UnitScalar or UnitArray but got {}."
msg = msg.format(unitted_data.__class__.__name__)
logger.exception(msg)
raise ValueError(msg)
src_unit = unitted_data.units
if (src_unit.label, tgt_unit.label) in CUSTOM_UNITS_CONVERTERS:
converter = CUSTOM_UNITS_CONVERTERS[(src_unit.label, tgt_unit.label)]
unitted_data = converter(unitted_data, **kwargs)
return unit_klass(unitted_data, units=tgt_unit)
else:
data = np.array(unitted_data.tolist())
data = convert(data, src_unit, tgt_unit)
return unit_klass(data, units=tgt_unit)
def build_flow_rate_array(times, experiment, to_unit="liter/minute"):
""" Build array of flow rates in liter/min at each time of 'times' array.
Parameters
----------
times : numpy.array
Array of chromatogram times at which to extract the flow rates.
experiment : Experiment
Experiment to extract the flow rates from.
to_unit : str
Unit of the output.
Returns
-------
UnitArray
Array of flow rates at the times of the times array.
"""
method_steps = experiment.method.method_steps
step_boundary_times = experiment.method_step_boundary_times
flow_rates = ones(times.shape) * nan
for i, step in enumerate(method_steps):
step_start_time = step_boundary_times[i]
step_stop_time = step_boundary_times[i+1]
mask = (times >= step_start_time) & (times < step_stop_time)
if is_linear_flow_rate(step.flow_rate):
diam = experiment.column.column_type.diameter
flow_rate = linear_flow_rate_to_volumetric(step.flow_rate, diam,
to_unit=to_unit)
elif is_volumetric_flow_rate(step.flow_rate):
flow_rate = convert(step.flow_rate, from_unit=step.flow_rate.units,
to_unit=unit_parser.parse_unit(to_unit))
else:
flow_rate = volumetric_CV_flow_rate_to_volumetric_flow_rate(
step.flow_rate, experiment.column, to_unit=to_unit
)
flow_rates[mask] = float(flow_rate)
return UnitArray(flow_rates, units=to_unit)
def test_units_trait(self):
obj = UnitsNonStrict(units='km')
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'km')
obj.units = 'm/sec**2'
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'm/sec**2')
obj.units = 'invalid'
self.assertFalse(obj is None)
self.assertEqual(obj.units.label, 'invalid')
self.assertEqual(obj.units.derivation, dimensionless.derivation)
units = unit_parser.parse_unit('g/cc')
self.assertFalse(units is None)
self.assertEqual(units.label, 'g/cc')
self.assertNotEqual(units.derivation, dimensionless.derivation)
obj.units = units
self.assertTrue(obj.units is units)
return
def test_units_trait(self):
obj = UnitsNonStrict(units='km')
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'km')
obj.units = 'm/sec**2'
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'm/sec**2')
obj.units = 'invalid'
self.failIf(obj is None)
self.failUnlessEqual(obj.units.label, 'invalid')
self.failUnlessEqual(obj.units.derivation, dimensionless.derivation)
units = unit_parser.parse_unit('g/cc')
self.failIf(units is None)
self.failUnlessEqual(units.label, 'g/cc')
self.failIfEqual(units.derivation, dimensionless.derivation)
obj.units = units
self.failUnless(obj.units is units)
return
def compute_mass_from_abs_data(absorb_data, ext_coeff, experim, t_start=None,
t_stop=None, t_start_idx=None, t_stop_idx=None):
""" Compute total mass of a product component between start and stop times.
The total mass is computed by integrating the specified chromatogram,
between t_start and t_stop and using the specified extinction coefficient
and flow rate at each time.
Parameters
----------
absorb_data : XYData
Data (fraction or continuous) to integrate to compute the contained
mass.
ext_coeff : UnitScalar
Extinction coefficient to use to convert the absorbance to a product
concentration.
experim : Experiment
Experiment from which to extract the method (and therefore flow rate)
information and the system's path length.
t_start : UnitScalar
Time at which to start integrating, in minutes. Leave as None to use
the t_start_idx to specify the time range to integrate.
t_stop : UnitScalar
Time at which to stop integrating, in minutes. Leave as None to use
the t_stop_idx to specify the time range to integrate.
t_start_idx : Int or None
Index in the x_data to start integrating at (inclusive).
t_stop_idx : Int or None
Index in the x_data to stop integrating at (exclusive). Leave as None
to go all the way to the end.
Returns
-------
UnitScalar
Product mass, in grams, estimated to elute between t_start and t_stop.
"""
all_x_data = absorb_data.x_data
all_y_data = absorb_data.y_data
# Convert time inputs into minutes:
data_time_unit = unit_parser.parse_unit(absorb_data.x_metadata["units"])
all_x_data = convert(all_x_data, from_unit=data_time_unit, to_unit=minute)
if t_start is not None and t_stop is not None:
t_start = convert_units(t_start, tgt_unit=minute)
t_stop = convert_units(t_stop, tgt_unit=minute)
t_start_idx = searchsorted(all_x_data, t_start)
t_stop_idx = searchsorted(all_x_data, t_stop)
if t_start_idx == t_stop_idx:
msg = "Unable to compute the integral of the provided because" \
"t_start too close to t_stop."
logger.warning(msg)
return UnitScalar(0., units="gram")
collect_idx = slice(t_start_idx, t_stop_idx)
times = all_x_data[collect_idx]
absorbances = all_y_data[collect_idx]
#: Extract the flow rate from the experiment method:
flow_rates = build_flow_rate_array(times, experim, to_unit="liter/minute")
missing_flow_rates = where(isnan(flow_rates))[0]
if len(missing_flow_rates) > 0:
msg = "The time range requested to integrate results goes beyond the "\
"known method steps, and will need to be cropped by {} values." \
" Cropped values are {}.".format(len(missing_flow_rates),
missing_flow_rates)
logger.warning(msg)
t_stop_idx = missing_flow_rates[0]
collect_idx = slice(t_start_idx, t_stop_idx)
times = all_x_data[collect_idx]
absorbances = all_y_data[collect_idx]
flow_rates = flow_rates[collect_idx]
# Turn absorbances into AU/cm
path_length = convert_units(experim.system.abs_path_length, "cm")[()]
data_absorb_unit = unit_parser.parse_unit(absorb_data.y_metadata["units"])
absorbances_au = convert(absorbances, from_unit=data_absorb_unit,
to_unit=absorption_unit)
# Compute masses in grams
masses = (absorbances_au*array(flow_rates)) / (path_length*ext_coeff[()])
total_mass = trapz(masses, times)
return UnitScalar(total_mass, units="gram")
def units_compatible(u0, u1):
return (unit_parser.parse_unit(u0).derivation ==
unit_parser.parse_unit(u1).derivation)
def unit_string_is_valid(units):
return unit_parser.parse_unit(units).valid
def __parse_expr(self, node):
"""
helper function for get_variable that recursively evaluates the AST tree
based on: https://stackoverflow.com/a/9558001.
"""
if node is None:
return None
elif isinstance(node, ast.Num):
return node.n
elif isinstance(node, ast.Str):
return node.s
elif isinstance(node, ast.Constant):
return node.val
# look for name in variable dictionary
elif isinstance(node, ast.Name):
# check if it is a unit
val = unit_parser.parse_unit(node.id)
if val.is_valid():
return convert(1, val, self._clk)
#check if it is a variable
val = self.__vars_dict.get(node.id, None)
return val
# define binary operators (+,-,*,/)
elif isinstance(node, ast.BinOp):
lhs = self.__parse_expr(node.left)
rhs = self.__parse_expr(node.right)
op = ast_ops_dict[type(node.op)]
if isinstance(lhs, np.ndarray) or isinstance(rhs, np.ndarray):
if not isinstance(lhs, np.ndarray):
if np.issubdtype(rhs.dtype, np.integer):
lhs = rhs.dtype.type(round(lhs))
else:
lhs = rhs.dtype.type(lhs)
if not isinstance(rhs, np.ndarray):
if np.issubdtype(lhs.dtype, np.integer):
rhs = lhs.dtype.type(round(rhs))
else:
rhs = lhs.dtype.type(rhs)
out = op(lhs, rhs)
self.__proc_list.append((op, (lhs, rhs, out)))
self.__proc_strs.append("Binary operator: " + op.__name__)
return out
return op(lhs, rhs)
# define unary operators (-)
elif isinstance(node, ast.UnaryOp):
operand = self.__parse_expr(node.operand)
op = ast_ops_dict[type(node.op)]
out = op(operand)
# if we have a np array, add to processor list
if isinstance(out, np.ndarray):
self.__proc_list.append((op, (operand, out)))
self.__proc_strs.append("Unary operator: " + op.__name__)
return out
elif isinstance(node, ast.Subscript):
# print(ast.dump(node))
val = self.__parse_expr(node.value)
if isinstance(node.slice, ast.Index):
if isinstance(val, np.ndarray):
return val[..., self.__parse_expr(node.slice.value)]
else:
return val[self.__parse_expr(node.slice.value)]
elif isinstance(node.slice, ast.Slice):
if isinstance(val, np.ndarray):
return val[...,
slice(self.__parse_expr(node.slice.lower),
self.__parse_expr(node.slice.upper),
self.__parse_expr(node.slice.step))]
else:
print(self.__parse_expr(node.slice.upper))
return val[slice(self.__parse_expr(node.slice.upper),
self.__parse_expr(node.slice.lower),
self.__parse_expr(node.slice.step))]
elif isinstance(node.slice, ast.ExtSlice):
slices = tuple(node.slice.dims)
for i, sl in enumerate(slices):
if isinstance(sl, ast.index):
slices[i] = self.__parse_expr(sl.value)
else:
slices[i] = slice(self.__parse_expr(sl.upper),
self.__parse_expr(sl.lower),
self.__parse_expr(sl.step))
return val[..., slices]
# for name.attribute
elif isinstance(node, ast.Attribute):
val = self.__parse_expr(node.value)
# get shape with buffer_len dimension removed
if node.attr == 'shape' and isinstance(val, np.ndarray):
return val.shape[1:]
# for func([args])
elif isinstance(node, ast.Call):
func = node.func.id
# get length of 1D array variable
if func == "len" and len(node.args) == 1 and isinstance(
node.args[0], ast.Name):
var = self.__parse_expr(node.args[0])
if isinstance(var, np.ndarray) and len(var.shape) == 2:
return var.shape[1]
else:
raise ValueError("len(): " + node.args[0].id +
"has wrong number of dims")
elif func == "round" and len(node.args) == 1:
var = self.__parse_expr(node.args[0])
return int(round(var))
# if this is a valid call to construct a new array, do so; otherwise raise an exception
else:
if len(node.args) == 2:
shape = self.__parse_expr(node.args[0])
if isinstance(shape, (int, np.int32, np.int64)):
shape = (self._block_width, shape)
elif isinstance(shape, tuple):
shape = (self._block_width, ) + shape
else:
raise ValueError(
"Do not recognize call to " + func +
" with arguments of types " +
str([arg.__dict__ for arg in node.args]))
try:
dtype = np.dtype(node.args[1].id)
except:
raise ValueError(
"Do not recognize call to " + func +
" with arguments of types " +
str([arg.__dict__ for arg in node.args]))
if func in self.__vars_dict:
var = self.__vars_dict[func]
if not var.shape == shape and var.dtype == dtype:
raise ValueError("Requested shape and type for " +
func +
" do not match existing values")
return var
else:
var = np.zeros(shape, dtype, 'F')
self.__vars_dict[func] = var
self.__print(
2, 'Added variable ' + func + ' with shape ' +
str(tuple(shape)) + ' and type ' + str(dtype))
return var
else:
raise ValueError(
"Do not recognize call to " + func +
" with arguments " +
str([str(arg.__dict__) for arg in node.args]))
raise ValueError("Cannot parse AST nodes of type " +
str(node.__dict__))
def units_compatible(u0, u1):
return (unit_parser.parse_unit(u0).derivation == unit_parser.parse_unit(
u1).derivation)
def unit_string_is_valid(units):
return unit_parser.parse_unit(units).valid