def callScaFES(T_blood=T_blood):
global count
global params
count += 1
print()
print('##### ScaFES iteration: {} #####'.format(count))
case = params['NAME_CONFIGFILE_TEMPLATE'].split('.')[0]
case = case.split('_')[0]
params['NAME_CONFIGFILE'] = case + '-pymc-' + TESTED_VARIABLES + '.ini'
params['NAME_RESULTFILE'] = ''
config = configparser.ConfigParser()
config.optionxform = str
config.read(params['NAME_CONFIGFILE_TEMPLATE'])
# T_blood.
config['Brain']['T_BLOOD'] = str(T_blood)
config['Tumor']['T_BLOOD'] = str(T_blood)
with open(params['NAME_CONFIGFILE'], 'w') as configfile:
config.write(configfile)
# Call simulation.
parse_config_file(params)
check_variables(params)
calc_variables(params)
check_stability(params)
if params['USE_MRI_FILE'] == False:
create_region_file(params)
create_init_file(params)
set_environment_variables(params)
call_simulation(params, params['RUN_SCRIPT'])
if params['NAME_RESULTFILE'] != '':
# Compute temperatures of normal, tumor, vessel tisue.
temp = temperature_array_from_result(params['NAME_RESULTFILE'])
tumor = region_array_from_file(params['NAME_REGION_FILE'])
vessels = surface_vessels_array_from_file(
params['NAME_VESSELS_FILE'])
T_tumor, _, _, _ = calc_tumor_near_surface_temperatures(
temp, tumor)
if params['USE_VESSELS_SEGMENTATION'] == True:
temp = temp[-1, :, :]
T_vessel, _, _, _ = calc_vessels_temperatures(temp, vessels)
T_normal, _, _, _ = calc_non_vessels_temperatures(
temp, vessels)
else:
T_vessel = -1.0
T_normal = -1.0
else:
print('* ERROR: No result file written.')
print('Aborting.')
exit()
return [T_normal, T_tumor, T_vessel]
def main():
params = {'NAME_CONFIGFILE': ''}
params['NAME_RESULTFILE'] = ''
# Check if path to configfile is provided and if file exists.
if len(sys.argv) > 1:
if os.path.isfile(sys.argv[1]) == True:
params['NAME_CONFIGFILE'] = sys.argv[1]
run_script = 'RUN_WEAK_SCALINGTEST_HELPER.sh'
else:
print('* ERROR:', sys.argv[1], 'does not exist.')
if len(sys.argv) > 2:
if os.path.isfile(sys.argv[2]) == True:
run_script = sys.argv[2]
else:
print('* ERROR: Optional run script', sys.argv[2],
'does not exist.')
print('Aborting.')
exit()
else:
print('* ERROR: No command line argument for configfile provided.')
if params['NAME_CONFIGFILE'] == '':
print('Usage: python3', sys.argv[0],
'<PATH/TO/CONFIGFILE> [<PATH/TO/RUN/SCRIPT]')
print('Aborting.')
exit()
print('Start weak scaling test.')
parse_config_file(params)
parse_config_file_scaling(params)
check_variables(params)
check_variables_scaling(params)
print('Type of test: {0}.'.format(params['TEST']))
for factor in params['SCALING']:
calc_variables(params)
calc_variables_scaling(factor, params)
check_stability(params)
if params['CREATE_INITFILE'] == True:
create_init_file(params)
set_environment_variables(params)
set_environment_variables_scaling(params)
start_simulation(params, run_script)
if params['NAME_RESULTFILE'] != '' and params['SPACE_DIM'] == 3:
plot_surface(params['NAME_RESULTFILE'])
print()
print('Test finished.')
def callScaFES(omega_brain=omega_brain,
omega_tumor=omega_tumor,
omega_vessel=omega_vessel,
T_blood=T_blood,
q_brain=q_brain,
q_tumor=q_tumor,
lambda_bt=lambda_bt,
rho_c_brain=rho_c_brain,
rho_c_tumor=rho_c_tumor,
h=h):
global count
global params
count += 1
print()
print('##### ScaFES iteration: {} #####'.format(count))
case = params['NAME_CONFIGFILE_TEMPLATE'].split('.')[0]
case = case.split('_')[0]
params['NAME_CONFIGFILE'] = case + '-pymc-' + TESTED_VARIABLES + '.ini'
params['NAME_RESULTFILE'] = ''
config = configparser.ConfigParser()
config.optionxform = str
config.read(params['NAME_CONFIGFILE_TEMPLATE'])
# Omega.
config['Brain']['OMEGA'] = str(omega_brain)
config['Tumor']['OMEGA'] = str(omega_tumor)
config['MRI']['USE_VESSELS_SEGMENTATION'] = 'True'
config['MRI']['VARIABLES_VESSELS'] = 'omega'
config['MRI']['VALUES_VESSELS'] = str(omega_vessel)
config['MRI']['VALUES_NON_VESSELS'] = str(omega_brain)
# T_blood.
config['Brain']['T_BLOOD'] = str(T_blood)
config['Tumor']['T_BLOOD'] = str(T_blood)
# Q.
config['Brain']['Q'] = str(q_brain)
config['Tumor']['Q'] = str(q_tumor)
# lambda.
config['Brain']['LAMBDA'] = str(lambda_bt)
config['Tumor']['LAMBDA'] = str(lambda_bt)
# rho * c.
config['Brain']['C'] = str(rho_c_brain)
config['Brain']['RHO'] = str(1000.0)
config['Tumor']['C'] = str(rho_c_tumor)
config['Tumor']['RHO'] = str(1000.0)
# h.
config['Parameters']['H'] = str(h)
with open(params['NAME_CONFIGFILE'], 'w') as configfile:
config.write(configfile)
# Call simulation.
parse_config_file(params)
check_variables(params)
calc_variables(params)
check_stability(params)
if params['USE_MRI_FILE'] == False:
create_region_file(params)
create_init_file(params)
set_environment_variables(params)
call_simulation(params, params['RUN_SCRIPT'])
if params['NAME_RESULTFILE'] != '':
# Compute temperatures of normal, tumor, vessel tisue.
temp = temperature_array_from_result(params['NAME_RESULTFILE'])
tumor = region_array_from_file(params['NAME_REGION_FILE'])
vessels = surface_vessels_array_from_file(
params['NAME_VESSELS_FILE'])
T_tumor, _, _, _ = calc_tumor_near_surface_temperatures(
temp, tumor)
if params['USE_VESSELS_SEGMENTATION'] == True:
temp = temp[-1, :, :]
T_vessel, _, _, _ = calc_vessels_temperatures(temp, vessels)
T_normal, _, _, _ = calc_non_vessels_temperatures(
temp, vessels)
else:
T_vessel = -1.0
T_normal = -1.0
else:
print('* ERROR: No result file written.')
print('Aborting.')
exit()
global dat_file_name
with open(dat_file_name, 'a') as backupfile:
backupfile.write(str(omega_brain) + '\t' \
+ str(omega_tumor) + '\t' \
+ str(omega_vessel) + '\t' \
+ str(T_blood) + '\t' \
+ str(q_brain) + '\t' \
+ str(q_tumor) + '\t' \
+ str(lambda_bt) + '\t' \
+ str(rho_c_brain) + '\t' \
+ str(rho_c_tumor) + '\t' \
+ str(h) + '\t' \
+ str(T_normal) + '\t' \
+ str(T_tumor) + '\t' \
+ str(T_vessel) + '\n')
if (count % 25 == 0):
searchpath = './' + params['NAME_EXECUTABLE'] + '-' + case + '-*.*'
log_files = glob.glob(searchpath)
for f in log_files:
os.remove(f)
return [T_normal, T_tumor, T_vessel]