def get_simulation_data_atn_csv_format(file_object):
"""
Given an ATN CSV file,
return a tuple (node_config, node_config_attributes, biomass_data).
node_config_attributes is a dictionary with the node config parameters (as
returned by nodeConfigToParams()).
biomass_data is a DataFrame whose columns are node IDs and whose index is the timeteps of the simulation.
"""
node_config_attributes = None
biomass_data = pd.DataFrame()
reader = csv.reader(file_object)
reader.__next__() # Skip the header row
for row in reader:
if len(row) == 0 or row[0] == '':
# Blank line: end of biomass data
break
node_id = int(row[0].split('.')[1])
biomass_data[node_id] = [float(x) for x in row[1:]]
# The next row should have the node config
row = reader.__next__()
node_config_str = row[0].split(': ')[1]
node_config = parse_node_config(node_config_str)
node_config_attributes = node_config_to_params(node_config)
return node_config, node_config_attributes, biomass_data
def get_simulation_data_hdf5(filename):
""" Read ATN simulation data from an HDF5 file produced by WoB Server.
Parameters
----------
filename : str
The name of the HDF5 file
Returns
-------
(node_config : str, node_config_attributes : dict, biomass_data : pd.DataFrame)
- node_config is the node configuration string
- node_config_attributes is the corresponding output of node_config_to_params()
- DataFrame columns are node IDs and whose index is the timeteps of the simulation.
"""
with h5py.File(filename, 'r') as f:
biomass_data = pd.DataFrame(f['biomass'][:, :], columns=list(f['node_ids']))
node_config_str = f.attrs['node_config'].decode('utf-8')
node_config = parse_node_config(node_config_str)
node_config_attributes = node_config_to_params(node_config)
return node_config, node_config_attributes, biomass_data
if not os.path.isdir(args.set_directory):
print("Error: set directory {} does not exist".format(args.set_directory), file=sys.stderr)
sys.exit(1)
if not os.path.isdir(args.data_directory):
print("Error: data directory {} does not exist".format(args.data_directory), file=sys.stderr)
sys.exit(1)
set_directory = os.path.normpath(args.set_directory)
data_directory = os.path.normpath(args.data_directory)
# Read the first nodeconfig from the nodeconfig file in the set directory
nodeconfig_filename = os.path.join(set_directory, 'nodeconfigs.{}.txt'.format(os.path.basename(set_directory)))
try:
nodeconfig_file = open(nodeconfig_filename)
except IOError:
print("Error: could not read node config file {}".format(nodeconfig_filename), file=sys.stderr)
sys.exit(1)
nodeconfig_str = nodeconfig_file.readline()
nodeconfig_file.close()
nodeconfig = parse_node_config(nodeconfig_str)
# Determine the number of species and food web ID
node_ids = [node['nodeId'] for node in nodeconfig]
node_ids.sort()
num_species = len(node_ids)
food_web_id = '-'.join(map(str, node_ids))
# Do the move
new_set_directory = os.path.join(data_directory, '{}-species'.format(num_species), food_web_id, set_directory)
print("Moving {} to {}".format(set_directory, new_set_directory))
os.renames(set_directory, new_set_directory)
def node_ids_from_node_config(node_config):
nodes = nodeconfigs.parse_node_config(node_config)
node_ids = [node['nodeId'] for node in nodes]
node_ids.sort()
return node_ids
set_directory = os.path.normpath(args.set_directory)
data_directory = os.path.normpath(args.data_directory)
# Read the first nodeconfig from the nodeconfig file in the set directory
nodeconfig_filename = os.path.join(
set_directory,
'nodeconfigs.{}.txt'.format(os.path.basename(set_directory)))
try:
nodeconfig_file = open(nodeconfig_filename)
except IOError:
print("Error: could not read node config file {}".format(
nodeconfig_filename),
file=sys.stderr)
sys.exit(1)
nodeconfig_str = nodeconfig_file.readline()
nodeconfig_file.close()
nodeconfig = parse_node_config(nodeconfig_str)
# Determine the number of species and food web ID
node_ids = [node['nodeId'] for node in nodeconfig]
node_ids.sort()
num_species = len(node_ids)
food_web_id = '-'.join(map(str, node_ids))
# Do the move
new_set_directory = os.path.join(data_directory,
'{}-species'.format(num_species), food_web_id,
set_directory)
print("Moving {} to {}".format(set_directory, new_set_directory))
os.renames(set_directory, new_set_directory)