def worker_on_client(fn, pattern, o2params):
print 'detailedo2 on %s / %s' % (fn, pattern)
o2_refs = detailedo2.doit(fn, pattern, (o2params, o2params['name']))
if 0: #this is for data analysis on the clusters
for ref in o2_refs:
po2group = h5files.open(ref.fn)[ref.path]
detailedo2Analysis.WriteSamplesToDisk(po2group)
def worker_on_client(fn, pattern, o2params):
print 'detailedo2 on %s / %s' % (fn, pattern)
h5files.search_paths = [
dirname(fn)
] # so the plotting and measurement scripts can find the original tumor files using the stored basename alone
#no, this is not working!!!!, hand num_threads over to the cpp side
#num_threads = o2params.pop('num_threads')
#krebsutils.set_num_threads(num_threads)
o2_refs = detailedo2.doit(fn, pattern, (o2params, o2params['name']))
if 0: #this is for data analysis on the clusters
for ref in o2_refs:
po2group = h5files.open(ref.fn)[ref.path]
detailedo2Analysis.WriteSamplesToDisk(po2group)
h5files.closeall() # just to be sure
def worker_on_client(vessel_fn, tumor_parameters, o2_parameter_set_name,
num_threads):
krebsutils.set_num_threads(num_threads)
tumor_fn = tumor_parameters['fn_out']
tend = tumor_parameters['tend']
pattern1 = 'out0000'
pattern2 = 'out%04i' % int(round(tend / tumor_parameters['out_intervall']))
pattern = '|'.join([pattern1, pattern2])
print tumor_fn, pattern
#os.system("%s -s '%s'" % (krebsjobs.submitTumOnlyVessels.exe,dicttoinfo(tumor_parameters)))
os.system("%s -s '%s'" %
(krebs.tumors.run_faketum, dicttoinfo(tumor_parameters)))
o2_refs = detailedo2.doit(
tumor_fn, pattern,
(getattr(krebs.detailedo2Analysis.parameterSetsO2,
o2_parameter_set_name), o2_parameter_set_name))
for ref in o2_refs:
po2group = h5files.open(ref.fn)[ref.path]
krebs.analyzeTissueOxygenDetailed.WriteSamplesToDisk(po2group)
krebs.povrayRenderOxygenDetailed.doit(o2_refs[1].fn, o2_refs[1].path)
h5files.closeall()
def runDetailedO2(fn, pattern, o2params): print 'detailedo2 on %s / %s' % (fn, pattern) o2_refs = detailedo2.doit(fn, pattern, (o2params, o2params['name'])) h5files.closeall() # just to be sure return o2_refs[0]