def test_attrs_pre_eq_step(self):
self.assertEqual(self.model.name, 'Pre-Equilibration')
self.assertIsInstance(self.model.solutions, list)
expected_flow_rate = UnitScalar(200, units=cm_per_hr)
self.assertEqual(self.model.flow_rate, expected_flow_rate)
expected_volume = UnitScalar(1.5, units=column_volumes)
self.assertEqual(self.model.volume, expected_volume)
def _build_performance_data(self, perf_data, name):
"""
FIXME: Needed for the design space plot when we display
that information when changing the start and stop for taking the pool.
Probably need a Pool class that knows how to compute that data.
"""
if perf_data is None:
return
product = self.product
product_concentration = UnitScalar(perf_data["pool_concentration"],
units='g/L')
pool_volume = UnitScalar(perf_data["pool_volume"], units="CV")
pH = UnitScalar(perf_data["pH"], units="")
conductivity = UnitScalar(perf_data["conductivity"], units='mS/cm')
step_yield = UnitScalar(perf_data["step_yield"], units='%')
# Build product purity assay data based on product assays
prod_comp_assays = perf_data.pop('product_component_assay_dict')
product_assay_values = []
for assay_name in product.product_component_assays:
if assay_name == STRIP_COMP_NAME:
assay_fraction = 0.0
else:
assay_fraction = prod_comp_assays[assay_name]
product_assay_values.append(assay_fraction)
product_assay_values = UnitArray(product_assay_values, units='g/L')
# Build impurity assay data based on product impurity assays
impurity_comp_assays = perf_data.pop('impurity_assay_dict')
impurity_assay_values = []
for assay_name in product.impurity_assays:
impurity_assay_values.append(impurity_comp_assays[assay_name])
impurity_assay_values = UnitArray(impurity_assay_values, units="%")
pool = SolutionWithProduct(
name='{}_Pool'.format(name),
source="Experiment",
lot_id="unknown",
solution_type="Pool",
product=self.product,
product_concentration=product_concentration,
product_component_assay_values=product_assay_values,
impurity_assay_values=impurity_assay_values,
pH=pH,
conductivity=conductivity,
)
performance_data = PerformanceData(
name='{}_Performance_Data'.format(name),
pool_volume=pool_volume,
pool=pool,
step_yield=step_yield)
return performance_data
def test_offset_unit_computations():
""" Executing some basic computations with a basic custom unit with offset.
"""
my_u = unit(12, m.derivation, 14)
s1 = UnitScalar(3, units=my_u)
s2 = UnitScalar(5, units=my_u)
s3 = s1+s2
assert_equal(s3,UnitScalar(8, units=my_u))
def test_view_model_with_no_solution_step_and_no_ds(self):
# This situation can happen for now since the central pane views are
# not being passed a datasource. Remove test once datasource passed to
# central pane views.
data = {
'step_type': 'Gradient Elution',
'name': 'Gradient Elution',
'flow_rate': UnitScalar(100.0, units=cm_per_hr),
'volume': UnitScalar(8.4, units=column_volumes)
}
no_sol_step = MethodStep(**data)
self.model.method_steps.append(no_sol_step)
view = MethodModelView(model=self.model)
ui = view.edit_traits()
ui.dispose()
def _build_continuous_data(self, akta_fname, target_experiment=None):
""" Load all timeseries from AKTA file. These files typically contain a
time_** and a ** column. They are stored together in a XYData object.
Parameters
----------
akta_fname : str
Filename for AKTA file.
target_experiment : Experiment
Experimental method implemented to compare output data to method
data.
Returns
-------
continuous_data : dict
Dictionary of XYData with all timeseries contained.
akta_settings : dict
Settings to read the AKTA file. Contains the time shift if any, and
the regex used to select file columns for each dataset types.
"""
from kromatography.ui.akta_file_setting_selector import \
AKTAFileSettingSelector
import_settings = {
"akta_fname": akta_fname,
"time_of_origin": UnitScalar(0., units="min")
}
settings_selector = AKTAFileSettingSelector(
akta_filepath=akta_fname, target_experiment=target_experiment)
if self.allow_akta_gui:
ui = settings_selector.edit_traits(kind="livemodal")
settings_selected = ui.result
if settings_selected:
# Optionally modify some parameters of the experiment method to
# reconcile mass balance discrepancies:
settings_selector.apply_strategy()
else:
settings_selected = True
if settings_selected:
import_settings["time_of_origin"] = \
settings_selector.time_of_origin
import_settings["col_name_patterns"] = \
settings_selector.col_name_patterns
continuous_data = continuous_data_from_akta(
import_settings, target_experiment)
else:
msg = "AKTA settings window cancelled: there won't be any " \
"continuous data loaded from {}".format(akta_fname)
logger.warning(msg)
continuous_data = {}
return continuous_data, import_settings
def dimensionless_test():
"""
Test the modification to the division, multiplication and pow
such that a dimensionless quantity formed by is indeed dimensionless
"""
a = UnitScalar(1.0, units='m')
b = UnitScalar(2.0, units='mm')
d = UnitScalar(2.0, units='m**(-1)')
c = a / b
e = b * d
f = UnitScalar(2.0, units=dimensionless)
g = f**2
assert_equal(c.units, dimensionless)
assert_equal(e.units, dimensionless)
assert_equal(g.units, dimensionless)
def _build_experiment_output(self, name, target_experiment=None):
""" Build the experiment results for a given experiment name.
Parameters
----------
name : str
Name of the experiment to extract the results from.
target_experiment : Experiment
Experiment implemented to compare output data to method data.
Returns
-------
ExperimentResults
Result object containing fraction data, and all continuous data. If
no data is specified, the returned Result object contains empty
dictionaries for the missing data (continuous and/or fraction).
"""
expt_data = self.excel_data['experiment_data'][name]
# initialize the continuous data from the AKTA files.
akta_fname = expt_data['continuous_data']
if akta_fname is not None:
# Assumes that the akta file path is relative to the Excel file:
dir_name = dirname(self.excel_reader.file_path)
akta_fname = join(dir_name, basename(akta_fname))
continuous_data, settings = self._build_continuous_data(
akta_fname, target_experiment)
else:
zero_min = UnitScalar(0., units="minute")
continuous_data = {}
settings = {"time_of_origin": zero_min, "holdup_volume": zero_min}
fraction_data = self._build_fraction_data(
expt_data['fraction_data'],
time_of_origin=settings["time_of_origin"],
target_experiment=target_experiment)
# Initialize the experiment performance results
raw_perf_data = expt_data['performance_parameter_data']
if raw_perf_data:
performance_data = self._build_performance_data(
raw_perf_data, name)
else:
performance_data = None
results = ExperimentResults(name=name,
fraction_data=fraction_data,
continuous_data=continuous_data,
performance_data=performance_data,
import_settings=settings)
return results
def _get_anion_concentration(self):
# Note that all ionic components are currently stored as
# `chemical_components`.
#: Pool instances from simulations will not have this
if self.chemical_component_concentrations is None:
return None
components = self.chemical_components
concentrations = self.chemical_component_concentrations
anion_concs = [
conc for comp, conc in zip(components, concentrations.tolist())
if comp.charge < 0
]
return UnitScalar(sum(anion_concs), units=concentrations.units)
def unit_array_units_converter(unit_array, new_units):
""" Convert a UnitArray from one set of units to another.
"""
if unit_array.units != new_units:
# Need conversion.
if isinstance(unit_array, ndarray) and unit_array.shape != ():
# this is an array
result = UnitArray(units.convert(unit_array.view(ndarray), unit_array.units,
new_units))
else:
# this is a scalar
result = UnitScalar(units.convert(unit_array.view(ndarray), unit_array.units,
new_units))
result.units = new_units
else:
# No conversion needed. Just return the unit_array.
result = unit_array
return result
def array_to_unit_array_converter(array, units):
""" Create a UnitArray with units='units' from the given 'array'.
"""
if array.shape == ():
return UnitScalar(array, units=units)
return UnitArray(array, units=units)
def scalar_to_unit_scalar_converter(x, units):
""" Create a UnitScalar with units='units' from the given scalar 'x'.
"""
return UnitScalar(x, units=units)
def _pH_default(self):
return UnitScalar(0.0, units="1")
def _conductivity_default(self):
return UnitScalar(0.0, units="mS/cm")
from kromatography.model.product import Product
from kromatography.model.product_component import ProductComponent
from kromatography.model.method_step import MethodStep
from kromatography.model.solution_with_product import SolutionWithProduct
from kromatography.utils.chromatography_units import (
column_volumes, cm_per_hr, extinction_coefficient_unit, fraction,
gram_per_liter, gram_per_milliliter, gram_per_mol, assay_unit,
kg_per_liter, mS_per_cm, milli_molar, milliliter, ml_per_min, molar)
from kromatography.model.factories.product import add_strip_to_product
RESIN_DATA = {
'lot_id': 'Lot123456',
'name': 'Fractogel-SO3 (M)',
'ligand': 'SO2',
'resin_type': 'CEX',
'average_bead_diameter': UnitScalar(65.0, units='um'),
'ligand_density': UnitScalar(75.0, units=milli_molar),
'settled_porosity': UnitScalar(0.42, units=fraction),
}
# Chemical components
COMPONENT_DATA = {
'name': 'Sodium',
'charge': UnitScalar(1, units='1'),
'pKa': UnitScalar(0.0, units='1')
}
COMPONENT2_DATA = {
'name': 'Chloride',
'charge': UnitScalar(-1, units='1'),
'pKa': UnitScalar(0.0, units='1')
def _build_fraction_data(self,
fraction_data,
time_of_origin=None,
target_experiment=None):
""" Convert fraction data from Excel fraction sheet into a fraction
data dictionary to describe ChromatographyResults.
Parameters
----------
fraction_data : dict
Data loaded from Excel.
time_of_origin : UnitScalar [OPTIONAL]
User specified custom time shift to apply to the data, if the
experimental output wasn't recorded starting at the desired start.
"""
if fraction_data is None:
return {}
if time_of_origin is None:
time_of_origin = UnitScalar(0., units="minute")
# Faction times at which product is sampled and analyzed:
frac_time = []
# Component concentration at each fraction time:
frac_comp_conc = defaultdict(list)
# Total concentration of product, corrected from extinction at each
# fraction time:
frac_prod_absorbances = []
product = self.product
for fraction in fraction_data:
prod_comp_assays = fraction.pop('product_component_assay_dict')
# FIXME: read units instead of guessing
total_concentration = self._get_unitted_value(
'fraction_product_concentration',
fraction['total_concentration'])
conc_units = total_concentration.units
# To compute the product concentrations in the fraction,
# we must first compute the concentration of each product component
# then multiply each by their respective extinction coefficient
# finally sum these values together
# FIXME: Fraction component concentrations shoud be calculated in
# SolutionWithProduct. This is probably unnecessary --
# Look into later.
namespace = {}
namespace.update(prod_comp_assays)
namespace["product_concentration"] = float(total_concentration)
prod_comp_conc = [
eval(expression, namespace)
for expression in product.product_component_concentration_exps
]
frac_component_concs = UnitArray(prod_comp_conc, units=conc_units)
# Total concentration, corrected by the components' extinction coef
ext_coefs = [
comp.extinction_coefficient
for comp in product.product_components
]
ext_coef_array = unitted_list_to_array(ext_coefs)
# This converts the component concentration to absorption
frac_component_absorb = frac_component_concs * ext_coef_array
tot_prod_absorbance = sum(frac_component_absorb)
frac_prod_absorbances.append(tot_prod_absorbance)
frac_time.append(fraction['time'])
for ii, comp_name in enumerate(product.product_component_names):
frac_comp_conc[comp_name].append(frac_component_absorb[ii])
# Apply the user defined origin shift:
# Warning: this leads to all fraction XYData sharing the same array!
frac_time = np.array(frac_time, dtype='float64') - time_of_origin[()]
frac_prod_absorbances = np.array(frac_prod_absorbances,
dtype='float64')
fraction_outputs = {}
for key, data in frac_comp_conc.items():
fraction_outputs[key] = XYData(
name=key,
x_data=frac_time,
# FIXME: read units instead of guessing
x_metadata={
"time_of_origin": time_of_origin,
"units": "min"
},
y_data=data,
# FIXME: read units instead of guessing
y_metadata={
"Description":
"Absorbances for product "
"components {}".format(key),
"units":
"AU/cm"
},
)
fraction_outputs[FRACTION_TOTAL_DATA_KEY] = XYData(
name=FRACTION_TOTAL_DATA_KEY,
x_data=frac_time,
# FIXME: read units instead of guessing
x_metadata={
"time_of_origin": time_of_origin,
"units": "min"
},
y_data=frac_prod_absorbances,
# FIXME: read units instead of guessing
y_metadata={
"Description": "Sum of absorbances per unit path "
"length for all product components.",
"units": "AU/cm"
},
)
shift_fraction_data_by_holdup_vol(fraction_outputs, target_experiment)
return fraction_outputs
def test_construction_gradient_elution_step(self):
step = MethodStep(**GRADIENT_ELUTION_STEP)
self.assertEqual(step.name, 'Gradient Elution')
self.assertEqual(len(step.solutions), 2)
self.assertEqual(step.flow_rate, UnitScalar(100, units=cm_per_hr))
self.assertEqual(step.volume, UnitScalar(8.4, units=column_volumes))