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)
SOILS_INDEX_COLUMNS = ['t', 'plant', 'axis']
# Define culm density (culm m-2)
DENSITY = 410.
NPLANTS = 1
CULM_DENSITY = {i: DENSITY / NPLANTS for i in range(1, NPLANTS + 1)}
INPUTS_OUTPUTS_PRECISION = 5 # 10
LOGGING_CONFIG_FILEPATH = os.path.join('logging.json')
LOGGING_LEVEL = logging.INFO # can be one of: DEBUG, INFO, WARNING, ERROR, CRITICAL
cnwheat_tools.setup_logging(LOGGING_CONFIG_FILEPATH,
LOGGING_LEVEL,
log_model=False,
log_compartments=False,
log_derivatives=False)
def calculate_PARa_from_df(g,
Eabs_df,
PARi,
multiple_sources=False,
ratio_diffus_PAR=None):
"""
Compute PARa from an input dataframe having Eabs values.
"""
Eabs_df_grouped = Eabs_df.groupby(['plant', 'metamer', 'organ'])
ELEMENTS_STATE)].dropna().to_dict()
element.__dict__.update(
photosynthesis_elements_data_to_use)
if RUN_SIMU:
print('Prepare the simulation...')
time_step_seconds = TIME_STEP * HOUR_TO_SECOND_CONVERSION_FACTOR
if LOG_EXECUTION:
# Setup the logging
cnwheat_tools.setup_logging(config_filepath=LOGGING_CONFIG_FILEPATH,
level=logging.DEBUG,
log_model=True,
log_compartments=True,
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],