def load_default_experiment_simulation(expt_id='Run_1'):
""" Load a default experiment and already run simulation.
DEPRECATED: use
kromatography.model.tests.sample_data_factories.make_sample_experiment2
instead.
"""
# Load the experiment
input_file = io_data_path('ChromExampleDataV2.xlsx')
study = load_exp_study_from_excel(input_file,
datasource=None,
allow_gui=False)
expt = study.search_experiment_by_name(expt_id)
# Build and load the simulation
sim = build_simulation_from_experiment(expt)
build_cadet_input(sim)
output_file = io_data_path('Chrom_Example_Run_1_cadet_simulation.h5')
update_simulation_results(sim, output_file)
return expt, sim
def create_cadet_file_for_sim(sim):
""" Create
Parameters
----------
sim : Simulation
Simulation for which to create the CADET file.
Returns
-------
str
File path created for the simulation.
"""
cadet_input = build_cadet_input(sim)
output_file = sim.cadet_filepath
write_to_h5(output_file, cadet_input, root='/input', overwrite=True)
return output_file
def write_sim_to_input_file_and_check(self, sim):
cadet_input = build_cadet_input(sim)
output_file = "test.h5"
with temp_fname(output_file):
write_to_h5(output_file,
cadet_input,
root='/input',
overwrite=True)
self.assertTrue(exists(output_file))
with h5py.File(F1NAME, "r") as h5:
self.assertEqual(h5.keys(), [u"input"])
expected = [
u'CHROMATOGRAPHY_TYPE', u'discretization', u'model',
u'sensitivity', u'solver'
]
self.assertEqual(set(h5[u"input"].keys()), set(expected))
data_found = read_from_h5(output_file)
return data_found
def setUpClass(cls):
input_file = io_data_path('ChromExampleDataV2.xlsx')
cls.study = load_study_from_excel(input_file, allow_gui=False)
# Building and running simulation for only 1 experiment
expt = cls.study.experiments[0]
output_file = "{}_{}_{}.h5".format(cls.study.name, expt.name,
'cadet_simulation')
output_file = string2filename(output_file)
sim = build_simulation_from_experiment(expt)
cls.study.simulations.append(sim)
# create the CADET inputs
cadet_input = build_cadet_input(sim)
# write the CADET inputs
write_to_h5(output_file, cadet_input, root='/input', overwrite=True)
# run simulation to generate outputs
run_cadet_simulator(output_file)
update_simulation_results(sim, output_file)
def test_build_simulation(self):
# Setup
self.sim_builder.column_name = 'CP_001'
self.sim_builder.method_name = 'Run_1'
self.sim_builder.first_simulated_step_name = 'Load'
self.sim_builder.last_simulated_step_name = 'Strip'
self.sim_builder.transport_model_name = DEFAULT_TRANSPORT_MODEL_NAME
self.sim_builder.binding_model_name = DEFAULT_BINDING_MODEL_NAME
sim = self.sim_builder.to_simulation()
self.assertIsInstance(sim, Simulation)
# init buffer:
self.assertEqual(self.sim_builder.initial_buffer_name, '')
exp1 = self.study.search_experiment_by_name("Run_1")
equil_buffer = exp1.method.method_steps[1].solutions[0].name
self.assertEqual(sim.method.initial_buffer.name, equil_buffer)
# the simulation has to be valid enough that it can be converted to a
# CADET input...
cadet_input = build_cadet_input(sim)
self.assertIsInstance(cadet_input, CADETInput)
def run_chromatography_simulation(input_file,
output_file=None,
expt_id="Run_1",
skip_cadet=False,
skip_plot=False,
skip_animation=False,
binding_model=None,
transport_model=None,
allow_gui=True):
""" Run chromatography simulation for the inputs given in `input_file`
and plot the results.
Parameters
----------
input_file : str (file path)
The file path for the excel file containing the experiment/simulation
input data.
output_file : str (file path)
The file path for the CADET output h5 file. If None, then a default
name is chosen based on the study and experiment ids.
expt_id : str
The name of the exeperiment to use for intializing the CADET
simulation. If None, the first experiment in the study is chosen.
skip_cadet : bool
If True, the CADET simulation is not run but instead the output
file is directly loaded (assuming one already exists). The main usecase
here is for testing.
skip_plot : bool
If True, the chromatogram plot is not generated. This is useful for
testing.
Returns
-------
study : Study
The Study instance containing the experiment and the simulation data.
"""
study = load_study_from_excel(input_file, allow_gui=allow_gui)
# lets just pick a single experiment
if expt_id is None:
expt = study.experiments[0]
else:
expt = study.search_experiment_by_name(expt_id)
logger.info('Running simulation for experiment : {!r}'.format(expt_id))
if output_file is None:
output_file = ("{}_{}_{}.h5".format(study.name, expt.name,
'cadet_simulation'))
output_file = string2filename(output_file)
# create a simulation object from an experiment
# FIXME: how to identify related expt and simulations !
sim = build_simulation_from_experiment(expt,
binding_model=binding_model,
transport_model=transport_model)
study.simulations.append(sim)
# create the CADET inputs
cadet_input = build_cadet_input(sim)
# NOTE: This is primarily used for testing/debugging workflow when the
# CADET simulation doesn't need to be run everytime.
if not skip_cadet:
# write the CADET inputs
write_to_h5(output_file, cadet_input, root='/input', overwrite=True)
logger.info("Output file {} was generated".format(output_file))
# run simulation to generate outputs
run_cadet_simulator(output_file)
update_simulation_results(sim, output_file)
if not skip_plot:
plot_chromatogram(expt, sim)
if not skip_animation:
column_animation(sim)
return study