def __init__(self,
shared_mtg,
delta_t,
culm_density,
model_organs_inputs_df,
model_hiddenzones_inputs_df,
model_elements_inputs_df,
model_soils_inputs_df,
shared_axes_inputs_outputs_df,
shared_organs_inputs_outputs_df,
shared_hiddenzones_inputs_outputs_df,
shared_elements_inputs_outputs_df,
shared_soils_inputs_outputs_df,
update_parameters=None):
"""
:param openalea.mtg.mtg.MTG shared_mtg: The MTG shared between all models.
:param int delta_t: The delta between two runs, in seconds.
:param dict culm_density: The density of culm. One key per plant.
:param pandas.DataFrame model_organs_inputs_df: the inputs of the model at organs scale.
:param pandas.DataFrame model_hiddenzones_inputs_df: the inputs of the model at hiddenzones scale.
:param pandas.DataFrame model_elements_inputs_df: the inputs of the model at elements scale.
:param pandas.DataFrame model_soils_inputs_df: the inputs of the model at soils scale.
:param pandas.DataFrame shared_axes_inputs_outputs_df: the dataframe of inputs and outputs at axes scale shared between all models.
:param pandas.DataFrame shared_organs_inputs_outputs_df: the dataframe of inputs and outputs at organs scale shared between all models.
:param pandas.DataFrame shared_hiddenzones_inputs_outputs_df: the dataframe of inputs and outputs at hiddenzones scale shared between all models.
:param pandas.DataFrame shared_elements_inputs_outputs_df: the dataframe of inputs and outputs at elements scale shared between all models.
:param pandas.DataFrame shared_soils_inputs_outputs_df: the dataframe of inputs and outputs at soils scale shared between all models.
:param dict or None update_parameters: A dictionary with the parameters to update, should have the form {'Organ_label1': {'param1': value1, 'param2': value2}, ...}.
"""
self._shared_mtg = shared_mtg #: the MTG shared between all models
self._simulation = cnwheat_simulation.Simulation(
respiration_model=respiwheat_model,
delta_t=delta_t,
culm_density=culm_density)
self.population, self.soils = cnwheat_converter.from_dataframes(
model_organs_inputs_df, model_hiddenzones_inputs_df,
model_elements_inputs_df, model_soils_inputs_df)
self._update_parameters = update_parameters
self._simulation.initialize(self.population, self.soils)
self._update_shared_MTG()
self._shared_axes_inputs_outputs_df = shared_axes_inputs_outputs_df #: the dataframe at axes scale shared between all models
self._shared_organs_inputs_outputs_df = shared_organs_inputs_outputs_df #: the dataframe at organs scale shared between all models
self._shared_hiddenzones_inputs_outputs_df = shared_hiddenzones_inputs_outputs_df #: the dataframe at hiddenzones scale shared between all models
self._shared_elements_inputs_outputs_df = shared_elements_inputs_outputs_df #: the dataframe at elements scale shared between all models
self._shared_soils_inputs_outputs_df = shared_soils_inputs_outputs_df #: the dataframe at soils scale shared between all models
self._update_shared_dataframes(
cnwheat_organs_data_df=model_organs_inputs_df,
cnwheat_hiddenzones_data_df=model_hiddenzones_inputs_df,
cnwheat_elements_data_df=model_elements_inputs_df,
cnwheat_soils_data_df=model_soils_inputs_df)
def test_simulation_run(overwrite_desired_data=False):
"""Test the run of a simulation, without interpolation of the forcings."""
TEST_DIR_PATH = 'simulation_run'
# Inputs of the test
INPUTS_DIRPATH = os.path.join(TEST_DIR_PATH, 'inputs')
ORGANS_INITIAL_STATE_FILENAME = 'organs_initial_state.csv'
HIDDENZONES_INITIAL_STATE_FILENAME = 'hiddenzones_initial_state.csv'
ELEMENTS_INITIAL_STATE_FILENAME = 'elements_initial_state.csv'
SOILS_INITIAL_STATE_FILENAME = 'soils_initial_state.csv'
ELEMENTS_PHOTOSYNTHESIS_FORCINGS_FILENAME = 'elements_photosynthesis_forcings.csv'
ROOTS_SENESCENCE_FORCINGS_FILENAME = 'roots_senescence_forcings.csv'
ELEMENTS_SENESCENCE_FORCINGS_FILENAME = 'elements_senescence_forcings.csv'
# Outputs of the test
OUTPUTS_DIRPATH = os.path.join(TEST_DIR_PATH, 'outputs')
DESIRED_AXES_OUTPUTS_FILENAME = 'desired_axes_outputs.csv'
DESIRED_ORGANS_OUTPUTS_FILENAME = 'desired_organs_outputs.csv'
DESIRED_HIDDENZONES_OUTPUTS_FILENAME = 'desired_hiddenzones_outputs.csv'
DESIRED_ELEMENTS_OUTPUTS_FILENAME = 'desired_elements_outputs.csv'
DESIRED_SOILS_OUTPUTS_FILENAME = 'desired_soils_outputs.csv'
ACTUAL_AXES_OUTPUTS_FILENAME = 'actual_axes_outputs.csv'
ACTUAL_ORGANS_OUTPUTS_FILENAME = 'actual_organs_outputs.csv'
ACTUAL_HIDDENZONES_OUTPUTS_FILENAME = 'actual_hiddenzones_outputs.csv'
ACTUAL_ELEMENTS_OUTPUTS_FILENAME = 'actual_elements_outputs.csv'
ACTUAL_SOILS_OUTPUTS_FILENAME = 'actual_soils_outputs.csv'
# Simulation parameters
START_TIME = 0
SIMULATION_LENGTH = 48
TIME_STEP = 1
CULM_DENSITY = {1: 410}
time_step_seconds = TIME_STEP * HOUR_TO_SECOND_CONVERSION_FACTOR
# Read the inputs from CSV files and create inputs dataframes
inputs_dataframes = {}
for inputs_filename in (ORGANS_INITIAL_STATE_FILENAME,
HIDDENZONES_INITIAL_STATE_FILENAME,
ELEMENTS_INITIAL_STATE_FILENAME,
SOILS_INITIAL_STATE_FILENAME):
inputs_dataframes[inputs_filename] = pd.read_csv(
os.path.join(INPUTS_DIRPATH, inputs_filename))
# Convert the inputs dataframes to a population of plants and a dictionary of soils
population, soils = cnwheat_converter.from_dataframes(
inputs_dataframes[ORGANS_INITIAL_STATE_FILENAME],
inputs_dataframes[HIDDENZONES_INITIAL_STATE_FILENAME],
inputs_dataframes[ELEMENTS_INITIAL_STATE_FILENAME],
inputs_dataframes[SOILS_INITIAL_STATE_FILENAME])
# Create the simulation
simulation_ = cnwheat_simulation.Simulation(
respiration_model=respiwheat_model,
delta_t=time_step_seconds,
culm_density=CULM_DENSITY)
# Initialize the simulation from the population of plants and the dictionary of soils created previously
simulation_.initialize(population, soils)
# Read photosynthesis and senescence forcings from CSV files, create dataframes, and group the dataframes by object index
photosynthesis_elements_data_filepath = os.path.join(
INPUTS_DIRPATH, ELEMENTS_PHOTOSYNTHESIS_FORCINGS_FILENAME)
photosynthesis_elements_data_df = pd.read_csv(
photosynthesis_elements_data_filepath)
photosynthesis_elements_data_grouped = photosynthesis_elements_data_df.groupby(
cnwheat_simulation.Simulation.ELEMENTS_T_INDEXES)
senescence_roots_data_filepath = os.path.join(
INPUTS_DIRPATH, ROOTS_SENESCENCE_FORCINGS_FILENAME)
senescence_roots_data_df = pd.read_csv(senescence_roots_data_filepath)
senescence_roots_data_grouped = senescence_roots_data_df.groupby(
cnwheat_simulation.Simulation.AXES_T_INDEXES)
senescence_elements_data_filepath = os.path.join(
INPUTS_DIRPATH, ELEMENTS_SENESCENCE_FORCINGS_FILENAME)
senescence_elements_data_df = pd.read_csv(
senescence_elements_data_filepath)
senescence_elements_data_grouped = senescence_elements_data_df.groupby(
cnwheat_simulation.Simulation.ELEMENTS_T_INDEXES)
# Force the senescence and photosynthesis of the population
force_senescence_and_photosynthesis(0, population,
senescence_roots_data_grouped,
senescence_elements_data_grouped,
photosynthesis_elements_data_grouped)
# Reinitialize the simulation from forced population and soils
simulation_.initialize(population, soils)
# Define the time grid of the simulation
time_grid = range(START_TIME, SIMULATION_LENGTH + TIME_STEP, TIME_STEP)
# Create empty lists of dataframes to store the outputs at each step of the simulation
axes_outputs_df_list = []
organs_outputs_df_list = []
hiddenzones_outputs_df_list = []
elements_outputs_df_list = []
soils_outputs_df_list = []
for t in time_grid:
if t > 0:
# Run the model of CN exchanges ; the population is internally updated by the model
simulation_.run()
# Convert the model outputs to dataframes
_, axes_outputs_df, _, organs_outputs_df, hiddenzones_outputs_df, elements_outputs_df, soils_outputs_df = cnwheat_converter.to_dataframes(
simulation_.population, simulation_.soils)
# Append the outputs dataframes at current t to the global lists of dataframes
for df, list_ in ((axes_outputs_df, axes_outputs_df_list),
(organs_outputs_df, organs_outputs_df_list),
(hiddenzones_outputs_df,
hiddenzones_outputs_df_list),
(elements_outputs_df, elements_outputs_df_list),
(soils_outputs_df, soils_outputs_df_list)):
df.insert(0, 't', t)
list_.append(df)
if 0 < t < SIMULATION_LENGTH:
# Force the senescence and photosynthesis of the population
force_senescence_and_photosynthesis(
t, population, senescence_roots_data_grouped,
senescence_elements_data_grouped,
photosynthesis_elements_data_grouped)
# Reinitialize the simulation from forced population and soils
simulation_.initialize(population, soils)
# compare actual to desired outputs at each scale level (an exception is raised if the test failed)
for (outputs_df_list,
desired_outputs_filename,
actual_outputs_filename,
state_variables_names) \
in ((axes_outputs_df_list, DESIRED_AXES_OUTPUTS_FILENAME, ACTUAL_AXES_OUTPUTS_FILENAME,
cnwheat_simulation.Simulation.AXES_T_INDEXES + cnwheat_simulation.Simulation.AXES_STATE),
(organs_outputs_df_list, DESIRED_ORGANS_OUTPUTS_FILENAME, ACTUAL_ORGANS_OUTPUTS_FILENAME,
cnwheat_simulation.Simulation.ORGANS_T_INDEXES + cnwheat_simulation.Simulation.ORGANS_STATE),
(hiddenzones_outputs_df_list, DESIRED_HIDDENZONES_OUTPUTS_FILENAME,
ACTUAL_HIDDENZONES_OUTPUTS_FILENAME,
cnwheat_simulation.Simulation.HIDDENZONE_T_INDEXES + cnwheat_simulation.Simulation.HIDDENZONE_STATE),
(elements_outputs_df_list, DESIRED_ELEMENTS_OUTPUTS_FILENAME, ACTUAL_ELEMENTS_OUTPUTS_FILENAME,
cnwheat_simulation.Simulation.ELEMENTS_T_INDEXES + cnwheat_simulation.Simulation.ELEMENTS_STATE),
(soils_outputs_df_list, DESIRED_SOILS_OUTPUTS_FILENAME, ACTUAL_SOILS_OUTPUTS_FILENAME,
cnwheat_simulation.Simulation.SOILS_T_INDEXES + cnwheat_simulation.Simulation.SOILS_STATE)):
outputs_df = pd.concat(outputs_df_list, ignore_index=True)
outputs_df = outputs_df.loc[:,
state_variables_names] # compare only the values of the compartments
cnwheat_tools.compare_actual_to_desired(
OUTPUTS_DIRPATH,
outputs_df,
desired_outputs_filename,
actual_outputs_filename,
precision=PRECISION,
overwrite_desired_data=overwrite_desired_data)
def test_simulation_logging(overwrite_desired_data=False):
"""Test the logging of a simulation."""
TEST_DIR_PATH = 'simulation_logging'
# Inputs of the test
INPUTS_DIRPATH = os.path.join(TEST_DIR_PATH, 'inputs')
ORGANS_INITIAL_STATE_FILENAME = 'organs_initial_state.csv'
HIDDENZONES_INITIAL_STATE_FILENAME = 'hiddenzones_initial_state.csv'
ELEMENTS_INITIAL_STATE_FILENAME = 'elements_initial_state.csv'
SOILS_INITIAL_STATE_FILENAME = 'soils_initial_state.csv'
ELEMENTS_PHOTOSYNTHESIS_FORCINGS_FILENAME = 'elements_photosynthesis_forcings.csv'
ROOTS_SENESCENCE_FORCINGS_FILENAME = 'roots_senescence_forcings.csv'
ELEMENTS_SENESCENCE_FORCINGS_FILENAME = 'elements_senescence_forcings.csv'
# Outputs of the test
LOGS_DIRPATH = os.path.join(TEST_DIR_PATH, 'logs')
DESIRED_AXES_COMPARTMENTS_FILENAME = 'desired_axes_compartments.csv'
DESIRED_ORGANS_COMPARTMENTS_FILENAME = 'desired_organs_compartments.csv'
DESIRED_HIDDENZONES_COMPARTMENTS_FILENAME = 'desired_hiddenzones_compartments.csv'
DESIRED_ELEMENTS_COMPARTMENTS_FILENAME = 'desired_elements_compartments.csv'
DESIRED_SOILS_COMPARTMENTS_FILENAME = 'desired_soils_compartments.csv'
DESIRED_AXES_DERIVATIVES_FILENAME = 'desired_axes_derivatives.csv'
DESIRED_ORGANS_DERIVATIVES_FILENAME = 'desired_organs_derivatives.csv'
DESIRED_HIDDENZONES_DERIVATIVES_FILENAME = 'desired_hiddenzones_derivatives.csv'
DESIRED_ELEMENTS_DERIVATIVES_FILENAME = 'desired_elements_derivatives.csv'
DESIRED_SOILS_DERIVATIVES_FILENAME = 'desired_soils_derivatives.csv'
ACTUAL_AXES_COMPARTMENTS_FILENAME = 'actual_axes_compartments.csv'
ACTUAL_ORGANS_COMPARTMENTS_FILENAME = 'actual_organs_compartments.csv'
ACTUAL_HIDDENZONES_COMPARTMENTS_FILENAME = 'actual_hiddenzones_compartments.csv'
ACTUAL_ELEMENTS_COMPARTMENTS_FILENAME = 'actual_elements_compartments.csv'
ACTUAL_SOILS_COMPARTMENTS_FILENAME = 'actual_soils_compartments.csv'
ACTUAL_AXES_DERIVATIVES_FILENAME = 'actual_axes_derivatives.csv'
ACTUAL_ORGANS_DERIVATIVES_FILENAME = 'actual_organs_derivatives.csv'
ACTUAL_HIDDENZONES_DERIVATIVES_FILENAME = 'actual_hiddenzones_derivatives.csv'
ACTUAL_ELEMENTS_DERIVATIVES_FILENAME = 'actual_elements_derivatives.csv'
ACTUAL_SOILS_DERIVATIVES_FILENAME = 'actual_soils_derivatives.csv'
# Config file path for logging
LOGGING_CONFIG_FILEPATH = os.path.join(TEST_DIR_PATH, 'logging.json')
# Simulation parameters
START_TIME = 0
SIMULATION_LENGTH = 5
TIME_STEP = 1
CULM_DENSITY = {1: 410}
time_step_seconds = TIME_STEP * HOUR_TO_SECOND_CONVERSION_FACTOR
# Remove actual logs files
for logs_file in glob.glob(os.path.join(LOGS_DIRPATH, "actual*.csv")):
os.remove(logs_file)
# Setup the logging (without removing the desired logs since we need them for the comparison test)
cnwheat_tools.setup_logging(config_filepath=LOGGING_CONFIG_FILEPATH,
level=logging.DEBUG,
log_model=True,
log_compartments=True,
log_derivatives=True,
remove_old_logs=False)
# Read the inputs from CSV files and create inputs dataframes
inputs_dataframes = {}
for inputs_filename in (ORGANS_INITIAL_STATE_FILENAME,
HIDDENZONES_INITIAL_STATE_FILENAME,
ELEMENTS_INITIAL_STATE_FILENAME,
SOILS_INITIAL_STATE_FILENAME):
inputs_dataframes[inputs_filename] = pd.read_csv(
os.path.join(INPUTS_DIRPATH, inputs_filename))
# Convert the inputs dataframes to a population of plants and a dictionary of soils
population, soils = cnwheat_converter.from_dataframes(
inputs_dataframes[ORGANS_INITIAL_STATE_FILENAME],
inputs_dataframes[HIDDENZONES_INITIAL_STATE_FILENAME],
inputs_dataframes[ELEMENTS_INITIAL_STATE_FILENAME],
inputs_dataframes[SOILS_INITIAL_STATE_FILENAME])
# Create the simulation
simulation_ = cnwheat_simulation.Simulation(
respiration_model=respiwheat_model,
delta_t=time_step_seconds,
culm_density=CULM_DENSITY)
# Initialize the simulation from the population of plants and the dictionary of soils created previously
simulation_.initialize(population, soils)
# Read photosynthesis and senescence forcings from CSV files, create dataframes, and group the dataframes by object index
photosynthesis_elements_data_filepath = os.path.join(
INPUTS_DIRPATH, ELEMENTS_PHOTOSYNTHESIS_FORCINGS_FILENAME)
photosynthesis_elements_data_df = pd.read_csv(
photosynthesis_elements_data_filepath)
photosynthesis_elements_data_grouped = photosynthesis_elements_data_df.groupby(
cnwheat_simulation.Simulation.ELEMENTS_T_INDEXES)
senescence_roots_data_filepath = os.path.join(
INPUTS_DIRPATH, ROOTS_SENESCENCE_FORCINGS_FILENAME)
senescence_roots_data_df = pd.read_csv(senescence_roots_data_filepath)
senescence_roots_data_grouped = senescence_roots_data_df.groupby(
cnwheat_simulation.Simulation.AXES_T_INDEXES)
senescence_elements_data_filepath = os.path.join(
INPUTS_DIRPATH, ELEMENTS_SENESCENCE_FORCINGS_FILENAME)
senescence_elements_data_df = pd.read_csv(
senescence_elements_data_filepath)
senescence_elements_data_grouped = senescence_elements_data_df.groupby(
cnwheat_simulation.Simulation.ELEMENTS_T_INDEXES)
# Force the senescence and photosynthesis of the population
force_senescence_and_photosynthesis(0, population,
senescence_roots_data_grouped,
senescence_elements_data_grouped,
photosynthesis_elements_data_grouped)
# Reinitialize the simulation from forced population and soils
simulation_.initialize(population, soils)
# Define the time grid of the simulation
time_grid = range(START_TIME, SIMULATION_LENGTH + TIME_STEP, TIME_STEP)
# Create empty lists of dataframes to store the outputs at each step of the simulation
axes_outputs_df_list = []
organs_outputs_df_list = []
hiddenzones_outputs_df_list = []
elements_outputs_df_list = []
soils_outputs_df_list = []
for t in time_grid:
if t > 0:
# Run the model of CN exchanges ; the population is internally updated by the model
simulation_.run()
# Convert the model outputs to dataframes
_, axes_outputs_df, _, organs_outputs_df, hiddenzones_outputs_df, elements_outputs_df, soils_outputs_df = cnwheat_converter.to_dataframes(
simulation_.population, simulation_.soils)
# Append the outputs dataframes at current t to the global lists of dataframes
for df, list_ in ((axes_outputs_df, axes_outputs_df_list),
(organs_outputs_df, organs_outputs_df_list),
(hiddenzones_outputs_df,
hiddenzones_outputs_df_list),
(elements_outputs_df, elements_outputs_df_list),
(soils_outputs_df, soils_outputs_df_list)):
df.insert(0, 't', t)
list_.append(df)
if 0 < t < SIMULATION_LENGTH:
# Force the senescence and photosynthesis of the population
force_senescence_and_photosynthesis(
t, population, senescence_roots_data_grouped,
senescence_elements_data_grouped,
photosynthesis_elements_data_grouped)
# Reinitialize the simulation from forced population and soils
simulation_.initialize(population, soils)
# compare actual to desired logs at each scale level (an exception is raised if the test failed)
# Compartments logs
for (desired_compartments_filename,
actual_compartments_filename) \
in ((DESIRED_AXES_COMPARTMENTS_FILENAME, ACTUAL_AXES_COMPARTMENTS_FILENAME),
(DESIRED_ORGANS_COMPARTMENTS_FILENAME, ACTUAL_ORGANS_COMPARTMENTS_FILENAME),
(DESIRED_HIDDENZONES_COMPARTMENTS_FILENAME, ACTUAL_HIDDENZONES_COMPARTMENTS_FILENAME),
(DESIRED_ELEMENTS_COMPARTMENTS_FILENAME, ACTUAL_ELEMENTS_COMPARTMENTS_FILENAME),
(DESIRED_SOILS_COMPARTMENTS_FILENAME, ACTUAL_SOILS_COMPARTMENTS_FILENAME)):
try:
actual_compartments_df = pd.read_csv(
os.path.join(LOGS_DIRPATH, actual_compartments_filename))
except pd.errors.EmptyDataError:
continue # This file is empty: ignore it.
cnwheat_tools.compare_actual_to_desired(
LOGS_DIRPATH,
actual_compartments_df,
desired_compartments_filename,
precision=PRECISION,
overwrite_desired_data=overwrite_desired_data)
# Derivatives logs
for (desired_derivatives_filename,
actual_derivatives_filename) \
in ((DESIRED_AXES_DERIVATIVES_FILENAME, ACTUAL_AXES_DERIVATIVES_FILENAME),
(DESIRED_ORGANS_DERIVATIVES_FILENAME, ACTUAL_ORGANS_DERIVATIVES_FILENAME),
(DESIRED_HIDDENZONES_DERIVATIVES_FILENAME, ACTUAL_HIDDENZONES_DERIVATIVES_FILENAME),
(DESIRED_ELEMENTS_DERIVATIVES_FILENAME, ACTUAL_ELEMENTS_DERIVATIVES_FILENAME),
(DESIRED_SOILS_DERIVATIVES_FILENAME, ACTUAL_SOILS_DERIVATIVES_FILENAME)):
try:
actual_derivatives_df = pd.read_csv(
os.path.join(LOGS_DIRPATH, actual_derivatives_filename))
except pd.errors.EmptyDataError:
continue # This file is empty: ignore it.
cnwheat_tools.compare_actual_to_desired(
LOGS_DIRPATH,
actual_derivatives_df,
desired_derivatives_filename,
precision=PRECISION,
overwrite_desired_data=overwrite_desired_data)
log_derivatives=True,
remove_old_logs=True)
# Read the inputs from CSV files and create inputs dataframes
inputs_dataframes = {}
for inputs_filename in (ORGANS_INITIAL_STATE_FILENAME,
HIDDENZONES_INITIAL_STATE_FILENAME,
ELEMENTS_INITIAL_STATE_FILENAME,
SOILS_INITIAL_STATE_FILENAME):
inputs_dataframes[inputs_filename] = pd.read_csv(
os.path.join(INPUTS_DIRPATH, inputs_filename))
# Convert the inputs dataframes to a population of plants and a dictionary of soils
population, soils = cnwheat_converter.from_dataframes(
inputs_dataframes[ORGANS_INITIAL_STATE_FILENAME],
inputs_dataframes[HIDDENZONES_INITIAL_STATE_FILENAME],
inputs_dataframes[ELEMENTS_INITIAL_STATE_FILENAME],
inputs_dataframes[SOILS_INITIAL_STATE_FILENAME])
# Set simulation parameters for interpolation
if INTERPOLATE_FORCINGS:
senescence_forcings_delta_t = time_step_seconds
photosynthesis_forcings_delta_t = time_step_seconds
else:
senescence_forcings_delta_t = None
photosynthesis_forcings_delta_t = None
# Create the simulation
simulation_ = cnwheat_simulation.Simulation(
respiration_model=respiwheat_model,
delta_t=time_step_seconds,