def save_init_data(self, dirname):
data_utils.make_dir('optim_data/' + dirname)
for cell in self.cells:
data_utils.make_dir('optim_data/' + dirname + '/' + cell.bp_type)
cell.save_init_data('optim_data/' + dirname + '/' + cell.bp_type)
data_utils.save_var(self.rec_data,
file='optim_data/' + dirname +
'/init_rec_data.pkl')
def save_init_data(self, dirname):
''' Save pilot run, i.e. initial data.
'''
print('# Save init data to ' + dirname)
data_utils.make_dir(os.path.join('optim_data', dirname))
self.cell.save_init_data(os.path.join('optim_data', dirname))
data_utils.save_var(
self.rec_data,
os.path.join('optim_data', dirname, 'init_rec_data.pkl'))
def init_output_folder(self):
''' Create output folder.
'''
data_utils.make_dir('optim_data')
assert self.output_folder is not None
if os.path.exists(os.path.join('optim_data', self.output_folder)):
print('Output folder already exists.')
else:
data_utils.make_dir(os.path.join('optim_data', self.output_folder))
def gen_and_save_data(self,
method,
adaptive,
step_param,
pert_method,
pert_param='auto',
stim=None,
overwrite=False,
allowgenerror=False,
plot=False):
"""Generate data and save to file."""
folder, filename = self.get_data_folder_and_filename(
method, adaptive, step_param, pert_method, pert_param)
print('/'.join(filename.split('/')[2:]).rjust(60), end=' --> ')
data_utils.make_dir(folder)
if not os.path.isfile(filename):
data_loaded = 'file was not found.'
elif overwrite:
data_loaded = 'overwrite==True.'
else:
data_loaded = self.load_data_and_check(method=method,
adaptive=adaptive,
step_param=step_param,
pert_method=pert_method,
pert_param=pert_param,
stim=stim,
filename=filename)
if not isinstance(data_loaded, str):
print('Loaded data.')
return data_loaded
else:
print('Generate data because', data_loaded)
try:
data = self.gen_data(method=method,
adaptive=adaptive,
step_param=step_param,
pert_method=pert_method,
pert_param=pert_param,
plot=plot)
except KeyboardInterrupt:
raise KeyboardInterrupt()
except Exception:
if allowgenerror:
print('Data generation failed')
data = None
else:
traceback.print_exc()
raise
data_utils.save_var(data, filename)
return data
def savefig(filename, fig=None):
"""Save figure to file"""
assert "figures" not in filename
assert ".pdf" not in filename
assert ".png" not in filename
assert ".eps" not in filename
data_utils.make_dir("_figures")
data_utils.make_dir("../../_figures")
if fig is None: fig = plt.gcf()
fig.savefig(f"_figures/{filename}.pdf") # save in folder
fig.savefig(f"../../_figures/{filename}.pdf") # save in general folder
def __init__(
self, optim, prior, n_parallel=25, gen_minibatch=300,
samples_file=None, snpe_type='B', round_cl=1, scalar_loss=True,
post_as_truncated_normal=True,
samples_folder='samples', snpe_folder='snpe',
backups_folder='backups', retsim_folder='retsim',
):
''' Initialize DELFI wrapper.
Parameters:
post_as_truncated_normal : bool
Transform posteriors to truncated normal distributions.
'''
self.snpe_type = snpe_type
self.prior = prior
self.optim = optim
self.optim.n_parallel = n_parallel
self.scalar_loss = scalar_loss
self.gen_minibatch = gen_minibatch
self.round_cl = round_cl
# Make folders to store data.
self.general_folder = os.path.join('optim_data', self.optim.output_folder)
self.samples_folder = os.path.join(self.general_folder, samples_folder+'/')
self.snpe_folder = os.path.join(self.general_folder, snpe_folder+'/')
self.backups_folder = os.path.join(self.general_folder, backups_folder+'/')
self.retsim_folder = os.path.join(self.general_folder, retsim_folder+'/')
data_utils.make_dir(self.samples_folder)
data_utils.make_dir(self.snpe_folder)
data_utils.make_dir(self.backups_folder)
data_utils.make_dir(self.retsim_folder)
# Save retsim files and check parameters.
if self.optim.cell is not None:
self.optim.copy_retsim_files(
cell=self.optim.cell, retsim_folder=self.retsim_folder
)
self.optim.check_parameter_files(
cell=self.optim.cell, params=self.optim.params, folder=self.general_folder
)
# Define file for samples.
self.update_samples_file(samples_file)
self.post_as_truncated_normal = post_as_truncated_normal
if self.post_as_truncated_normal:
self.trunc_lower = self.prior.lower
self.trunc_upper = self.prior.upper
else:
self.trunc_lower = None
self.trunc_upper = None
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--mode',
choices={'train', 'chat'},
default='train',
help="mode. if not specified, it's in the train mode")
args = parser.parse_args()
if not os.path.isdir(config.PROCESSED_PATH):
data_utils.prepare_raw_data()
data_utils.process_data()
print('Data ready!')
data_utils.make_dir(config.CPT_PATH)
if args.mode == 'train':
train()
elif args.mode == 'chat':
chat()
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--mode",
choices={"train", "chat"},
default="train",
help="mode. if not specified, it's in the train mode")
args = parser.parse_args()
if not os.path.exists(os.path.join(config.DATA_PATH, "test_ids.dec")):
data_utils.process_data()
print("Data ready!")
# create checkpoints folder if there isn't one already
data_utils.make_dir(config.CPT_PATH)
if args.mode == "train":
train()
elif args.mode == "chat":
chat()
def __init__(self, params, output_folder, EDL_phase_total,
V_amps, absZ_est, verbose=True, p_unit={}, reset=True):
assert isinstance(p_unit, dict)
self.output_folder = output_folder
self.params = params
self.p_unit = p_unit
self.EDL_phase_total = EDL_phase_total
self.V_amps = V_amps
self.absZ_est = absZ_est
data_utils.make_dir('optim_data/' + output_folder)
self.folder_i = 'COMSOL2python_interface/COMSOL_input/'
self.folder_o = 'COMSOL2python_interface/COMSOL_output/'
data_utils.make_dir(self.folder_i)
data_utils.make_dir(self.folder_o)
if reset: self.reset_and_wait_for_COMSOL()
def find_and_replace_in_files(inputfiles, input_folder, outputfiles,
output_folder, params):
''' Find params in given files and replace them with new params.
Save updated files to given output folder.
'''
found_params = {}
data_utils.make_dir(output_folder)
data_utils.clean_folder(output_folder)
for inputfile, outputfile in zip(inputfiles, outputfiles):
inputfilepath = os.path.join(input_folder, inputfile)
assert os.path.isfile(
inputfilepath), 'Input file not found: ' + inputfilepath
with open(inputfilepath, 'r') as f:
lines = f.readlines()
# Replace optimized params.
for p_name, p_value in params.items():
found_param = False
for idx, line in enumerate(lines):
if p_name in line:
found_param = True
for i in np.flip(np.arange(15)):
if p_name.ljust(i) in line:
line = line.replace(
p_name.ljust(i),
"{:.5g}".format(p_value).ljust(i - 1) + " ")
lines[idx] = line
lines[idx] = lines[idx].replace('\t', ' ')
if found_param: found_params[p_name] = p_value
# Write file.
outputfilepath = os.path.join(output_folder, outputfile)
print()
print('saveing updated version of (1) to (2)')
print('\t(1)', inputfilepath)
print('\t(2)', outputfilepath)
print()
with open(outputfilepath, 'w+') as f:
for line in lines:
f.write(line)
print()
print('The following params were (not) found:')
max_len_p_name = np.max([len(p_name) for p_name in params.keys()])
for p_name, p_value in params.items():
if p_name not in found_params.keys():
print('\t WARNING: Have not found \t' +
p_name.ljust(max_len_p_name) +
' = {:.5g} \t Please replace manually.'.format(p_value))
else:
print('\t Found \t' + p_name.ljust(max_len_p_name) +
' = {:.5g}'.format(p_value))
def save_acc_sols_to_file(self):
"""Save acc sols in folder"""
folder = f'{self.base_folder}'
if self.subfoldername is not None: folder += f'/{self.subfoldername}'
data_utils.make_dir(folder)
data_utils.save_var(self.acc_sols, f"{folder}/acc_sols.pkl")
