def run_faketum_mts(configstring_file):
if qsub.is_client:
qsub.printClientInfo()
#moved to c++ side
# slurm_id = os.environ.get('SLURM_JOB_ID')
# if slurm_id:
# print("current slurm job id: %s" % slurm_id)
with open(configstring_file, 'r') as f:
configstring = f.read()
return tumor_cpp.run_faketum_mts_(configstring, False)
def worker_on_client(fn, grp_pattern, adaptionParams, num_threads):
print('Adaption on %s / %s / param: %s' % (fn, grp_pattern, adaptionParams['name']))
qsub.printClientInfo()
h5files.search_paths = [dirname(fn)] # so the plotting and measurement scripts can find the original tumor files using the stored basename alone
krebsutils.set_num_threads(num_threads)
#params['name'] = parameter_set_name
adaptionParams['adaption'].update(
vesselFileName = fn,
vesselGroupName = grp_pattern,
)
krebs.adaption.doit( adaptionParams)
def run_bulktissue_w_vessels(configstr):
if qsub.is_client:
qsub.printClientInfo()
return tumor_cpp.run_bulktissue_with_vessels_(configstr)
def rerun_faketum(filename_of_previous_run):
if qsub.is_client:
qsub.printClientInfo()
#with open(configstring_file, 'r') as f:
# configstring = f.read()
return tumor_cpp.run_faketum_(filename_of_previous_run, True)
def run_faketum(configstring_file):
if qsub.is_client:
qsub.printClientInfo()
with open(configstring_file, 'r') as f:
configstring = f.read()
return tumor_cpp.run_faketum_(configstring, False)
def rerun_faketum_mts(filename_of_previous_run):
if qsub.is_client:
qsub.printClientInfo()
return tumor_cpp.run_faketum_mts_(filename_of_previous_run, True)
def run_vesselgen_client(configstring_file, workdir, vesselfilename):
qsub.printClientInfo()
os.chdir(workdir)
with open(configstring_file, 'r') as f:
configstring = f.read()
krebsutils.run_vesselgen(configstring)