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'))
def test_run_Continuous_231(self):
"""
Test suite for standard Continuous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 1 SD BMR. Note that in the polynomial case, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_c)
run_suite = (
{
'type': 'Linear',
'fn': '2-continuous-tc-LinearCV-1SD.out'
},
{
'type': 'Polynomial',
'fn': '2-continuous-tc-Poly4CV-1SD.out',
'override': {
'degree_poly': 4,
'restrict_polynomial': 1
},
'override_text': ['Degree of Polynomial = 4']
},
{
'type': 'Power',
'fn': '2-continuous-tc-PowerCV-1SD.out'
},
{
'type': 'Hill',
'fn': '2-continuous-tc-HillCV-1SD.out'
},
{
'type': 'Exponential-M2',
'fn': '2-continuous-tc-M2M2ExpCV-1SD.out'
},
{
'type': 'Exponential-M3',
'fn': '2-continuous-tc-M3M3ExpCV-1SD.out'
},
{
'type': 'Exponential-M4',
'fn': '2-continuous-tc-M4M4ExpCV-1SD.out'
},
{
'type': 'Exponential-M5',
'fn': '2-continuous-tc-M5M5ExpCV-1SD.out'
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['C'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'],
self.bmr_c)
m = BMD_model_run(model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_continuous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# with open(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w') as f:
# f.write('\n'.join(output_text))
# with open(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w') as f:
# f.write('\n'.join(gold_standard))
self.assertTrue(output_text == gold_standard)
def test_run_Dichotomous_231(self):
"""
Test suite for standard Dichotomous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 10% BMR check. Note that in a few multistage cases, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_d)
run_suite = (
{
'type': 'Logistic',
'fn': '1-dichotomous-tc-Logistic-10%.out'
},
{
'type': 'LogLogistic',
'fn': '1-dichotomous-tc-LogLogistic-10%.out'
},
{
'type': 'Weibull',
'fn': '1-dichotomous-tc-Weibull-10%.out'
},
{
'type': 'Probit',
'fn': '1-dichotomous-tc-Probit-10%.out'
},
{
'type': 'LogProbit',
'fn': '1-dichotomous-tc-LogProbit-10%.out'
},
{
'type': 'Gamma',
'fn': '1-dichotomous-tc-Gamma-10%.out'
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi1-10%.out',
'override': {
'degree_poly': 1
},
'override_text': ['Degree of Polynomial = 1']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi2-10%.out',
'override': {
'degree_poly': 2
}, # todo: these lines shouldn't be required, think parent class needs to update child class
'override_text': ['Degree of Polynomial = 2']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi3-10%.out',
'override': {
'degree_poly': 3
},
'override_text': ['Degree of Polynomial = 3']
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['D'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'],
self.bmr_d)
m = BMD_model_run(model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_dichotomous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# f = file(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w')
# f.write('\n'.join(output_text))
# f.close()
# f = file(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w')
# f.write('\n'.join(gold_standard))
# f.close()
self.assertTrue(output_text == gold_standard)
def test_run_Continuous_231(self):
"""
Test suite for standard Continuous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 1 SD BMR. Note that in the polynomial case, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_c)
run_suite = (
{
'type': 'Linear',
'fn': '2-continuous-tc-LinearCV-1SD.out'
},
{
'type': 'Polynomial',
'fn': '2-continuous-tc-Poly4CV-1SD.out',
'override': {
'degree_poly': 4,
'restrict_polynomial': 1
},
'override_text': ['Degree of Polynomial = 4']
},
{
'type': 'Power',
'fn': '2-continuous-tc-PowerCV-1SD.out'
},
{
'type': 'Hill',
'fn': '2-continuous-tc-HillCV-1SD.out'
},
{
'type': 'Exponential-M2',
'fn': '2-continuous-tc-M2M2ExpCV-1SD.out'
},
{
'type': 'Exponential-M3',
'fn': '2-continuous-tc-M3M3ExpCV-1SD.out'
},
{
'type': 'Exponential-M4',
'fn': '2-continuous-tc-M4M4ExpCV-1SD.out'
},
{
'type': 'Exponential-M5',
'fn': '2-continuous-tc-M5M5ExpCV-1SD.out'
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['C'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'], self.bmr_c)
m = BMD_model_run(
model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_continuous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# with open(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w') as f:
# f.write('\n'.join(output_text))
# with open(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w') as f:
# f.write('\n'.join(gold_standard))
self.assertTrue(output_text == gold_standard)
def test_run_Dichotomous_231(self):
"""
Test suite for standard Dichotomous 2.3.1. models. This test contains
basic models, with very minimal modifications. It also assumes the
standard 10% BMR check. Note that in a few multistage cases, the
degree_poly value is overridden from the default.
"""
session = BMD_session(BMDS_version='2.31', bmrs=self.bmr_d)
run_suite = (
{
'type': 'Logistic',
'fn': '1-dichotomous-tc-Logistic-10%.out'
},
{
'type': 'LogLogistic',
'fn': '1-dichotomous-tc-LogLogistic-10%.out'
},
{
'type': 'Weibull',
'fn': '1-dichotomous-tc-Weibull-10%.out'
},
{
'type': 'Probit',
'fn': '1-dichotomous-tc-Probit-10%.out'
},
{
'type': 'LogProbit',
'fn': '1-dichotomous-tc-LogProbit-10%.out'
},
{
'type': 'Gamma',
'fn': '1-dichotomous-tc-Gamma-10%.out'
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi1-10%.out',
'override': {'degree_poly': 1},
'override_text': ['Degree of Polynomial = 1']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi2-10%.out',
'override': {'degree_poly': 2}, # todo: these lines shouldn't be required, think parent class needs to update child class
'override_text': ['Degree of Polynomial = 2']
},
{
'type': 'Multistage',
'fn': '1-dichotomous-tc-Multi3-10%.out',
'override': {'degree_poly': 3},
'override_text': ['Degree of Polynomial = 3']
},
)
for run in run_suite:
logging.debug('Testing ' + run['fn'])
m_run = self.v.models['D'][run['type']]()
if 'override' in run:
m_run.update_model(run['override'], run['override_text'], self.bmr_d)
m = BMD_model_run(
model_name=run['type'],
BMD_session=session,
option_override={},
option_override_text=[""])
m.run_model(self.v, m_run, self.dataset_dichotomous)
output_text = m.output_text.splitlines()[10:]
fn = os.path.join(BMDS_TEST_PATH, run['fn'])
gold_standard = self.import_bmds_output_file(fn)
# f = file(os.path.join(BMDS_TEST_PATH, 'test_output.txt'), 'w')
# f.write('\n'.join(output_text))
# f.close()
# f = file(os.path.join(BMDS_TEST_PATH, 'gold_standard.txt'), 'w')
# f.write('\n'.join(gold_standard))
# f.close()
self.assertTrue(output_text == gold_standard)