def _run_continuous(self, version):
"""
Changed one session file:
- 012.txt resp & stdev changed from 0.0 to 0.1. Confirmed that this
session file causes the BMDS GUI to crash as well.
"""
output_folder = version.replace(".", "") + "_outputs"
input_path = os.path.join(BMDS_TEST_PATH, 'continuous', 'inputs')
output_path = os.path.join(BMDS_TEST_PATH, 'continuous', output_folder)
if os.path.exists(output_path):
shutil.rmtree(output_path)
os.makedirs(output_path)
wb, ws = self._create_xls_wb()
row = 0
# begin model runs
bmds = BMDS.versions[version]()
files = sorted(os.listdir(input_path))
for f in files:
fn = os.path.join(input_path, f)
dataset = self._load_continuous(fn)
endpoint_d = self._get_continuous_endpoint_d(dataset)
for setting in self.default_c_models:
# get default bmds settings
run_instance = bmds.models['C'][setting['model_name']]()
runnable = endpoint_d['numDG'] >= run_instance.minimum_DG
if runnable:
row += 1
logging.debug('Running {0}:{1}'.format(
f, setting['model_name']))
# change the poly degree for the multistage model
if setting['model_name'] == 'Polynomial':
setting['override'][
'degree_poly'] = endpoint_d['numDG'] - 1
if endpoint_d['dataset_increasing']:
setting['override']['restrict_polynomial'] = 1
else:
setting['override']['restrict_polynomial'] = -1
d_file = run_instance.dfile_print(endpoint_d)
model = BMD_model_run(model_name=run_instance.model_name)
results = model.execute_bmds(bmds,
run_instance,
d_file,
create_image=False)
file_identifier = f[:(len(f) - 4)]
model_name = setting['model_name']
self._print_individual_run(ws, results, file_identifier,
model_name, row, output_path,
d_file)
# save excel file
wb.save(os.path.join(output_path, 'outputs.xls'))
def _run_continuous(self, version):
"""
Changed one session file:
- 012.txt resp & stdev changed from 0.0 to 0.1. Confirmed that this
session file causes the BMDS GUI to crash as well.
"""
output_folder = version.replace(".", "") + "_outputs"
input_path = os.path.join(BMDS_TEST_PATH, 'continuous', 'inputs')
output_path = os.path.join(BMDS_TEST_PATH, 'continuous', output_folder)
if os.path.exists(output_path):
shutil.rmtree(output_path)
os.makedirs(output_path)
wb, ws = self._create_xls_wb()
row = 0
# begin model runs
bmds = BMDS.versions[version]()
files = sorted(os.listdir(input_path))
for f in files:
fn = os.path.join(input_path, f)
dataset = self._load_continuous(fn)
endpoint_d = self._get_continuous_endpoint_d(dataset)
for setting in self.default_c_models:
# get default bmds settings
run_instance = bmds.models['C'][setting['model_name']]()
runnable = endpoint_d['numDG'] >= run_instance.minimum_DG
if runnable:
row += 1
logging.debug('Running {0}:{1}'.format(f, setting['model_name']))
# change the poly degree for the multistage model
if setting['model_name'] == 'Polynomial':
setting['override']['degree_poly'] = endpoint_d['numDG'] - 1
if endpoint_d['dataset_increasing']:
setting['override']['restrict_polynomial'] = 1
else:
setting['override']['restrict_polynomial'] = -1
d_file = run_instance.dfile_print(endpoint_d)
model = BMD_model_run(model_name=run_instance.model_name)
results = model.execute_bmds(bmds,
run_instance,
d_file,
create_image=False)
file_identifier = f[:(len(f)-4)]
model_name = setting['model_name']
self._print_individual_run(ws, results, file_identifier,
model_name, row, output_path,
d_file)
# save excel file
wb.save(os.path.join(output_path, 'outputs.xls'))
def _run_dichotomous(self, version):
"""
One change made to input files: 038.dat, dropped highest dose. Confirmed
that this causes the standard BMDS models to hard-hang and therefore,
removed the high dose from this case which fixed modeling issue.
"""
output_folder = version.replace(".", "") + "_outputs"
input_path = os.path.join(BMDS_TEST_PATH, 'dichotomous', 'inputs')
output_path = os.path.join(BMDS_TEST_PATH, 'dichotomous',
output_folder)
if os.path.exists(output_path):
shutil.rmtree(output_path)
os.makedirs(output_path)
wb, ws = self._create_xls_wb()
row = 0
# begin model runs
bmds = BMDS.versions[version]()
files = sorted(os.listdir(input_path))
for f in files:
fn = os.path.join(input_path, f)
dataset = self._load_dichotomous(fn)
endpoint_d = self._get_dichotomous_endpoint_d(dataset)
for setting in self.default_d_models:
row += 1
# change the poly degree for the multistage model
if setting['model_name'] == 'Multistage':
setting['override']['degree_poly'] = len(dataset) - 1
# get default bmds settings
logging.debug('Running {0}:{1}'.format(f,
setting['model_name']))
run_instance = bmds.models['D'][setting['model_name']]()
d_file = run_instance.dfile_print(endpoint_d)
model = BMD_model_run(model_name=run_instance.model_name)
results = model.execute_bmds(bmds,
run_instance,
d_file,
create_image=False)
file_identifier = f[:(len(f) - 4)]
model_name = run_instance.model_name
self._print_individual_run(ws, results, file_identifier,
model_name, row, output_path,
d_file)
# save excel file
wb.save(os.path.join(output_path, 'outputs.xls'))
def _run_dichotomous(self, version):
"""
One change made to input files: 038.dat, dropped highest dose. Confirmed
that this causes the standard BMDS models to hard-hang and therefore,
removed the high dose from this case which fixed modeling issue.
"""
output_folder = version.replace(".", "") + "_outputs"
input_path = os.path.join(BMDS_TEST_PATH, 'dichotomous', 'inputs')
output_path = os.path.join(BMDS_TEST_PATH, 'dichotomous', output_folder)
if os.path.exists(output_path):
shutil.rmtree(output_path)
os.makedirs(output_path)
wb, ws = self._create_xls_wb()
row = 0
# begin model runs
bmds = BMDS.versions[version]()
files = sorted(os.listdir(input_path))
for f in files:
fn = os.path.join(input_path, f)
dataset = self._load_dichotomous(fn)
endpoint_d = self._get_dichotomous_endpoint_d(dataset)
for setting in self.default_d_models:
row += 1
# change the poly degree for the multistage model
if setting['model_name'] == 'Multistage':
setting['override']['degree_poly'] = len(dataset)-1
# get default bmds settings
logging.debug('Running {0}:{1}'.format(f, setting['model_name']))
run_instance = bmds.models['D'][setting['model_name']]()
d_file = run_instance.dfile_print(endpoint_d)
model = BMD_model_run(model_name=run_instance.model_name)
results = model.execute_bmds(bmds,
run_instance,
d_file,
create_image=False)
file_identifier = f[:(len(f)-4)]
model_name = run_instance.model_name
self._print_individual_run(
ws, results, file_identifier,
model_name, row, output_path, d_file)
# save excel file
wb.save(os.path.join(output_path, 'outputs.xls'))
