def _get_md5_of_morphology(m):
# assert False # Is this Cruft?? Added Jan 2011
treemd5 = _get_md5_of_section(m._dummysection)
name_md5 = StrUtils.get_hash_md5(m.name)
assert not m.metadata
regions_md5 = ','.join([_get_md5_of_region(region) for region in m.get_regions()])
return StrUtils.get_hash_md5(treemd5 + name_md5 + regions_md5)
def _get_md5_of_section(s):
# assert False # Is this Cruft?? Added Jan 2011
section_string = '%2.2f %2.2f %2.2f %2.2f '
regions_string = (_get_md5_of_region(s.region) if s.region else '')
children_string = ','.join([_get_md5_of_section(s) for s in s.children])
id_string = ('' if not s.idtag else StrUtils.get_hash_md5(s.idtag))
return StrUtils.get_hash_md5(section_string + regions_string + children_string + id_string)
def _get_md5_of_morphology(m):
# assert False # Is this Cruft?? Added Jan 2011
treemd5 = _get_md5_of_section(m._dummysection)
name_md5 = StrUtils.get_hash_md5(m.name)
assert not m.metadata
regions_md5 = ','.join(
[_get_md5_of_region(region) for region in m.get_regions()])
return StrUtils.get_hash_md5(treemd5 + name_md5 + regions_md5)
def _get_md5_of_section(s):
# assert False # Is this Cruft?? Added Jan 2011
section_string = '%2.2f %2.2f %2.2f %2.2f '
regions_string = (_get_md5_of_region(s.region) if s.region else '')
children_string = ','.join([_get_md5_of_section(s) for s in s.children])
id_string = ('' if not s.idtag else StrUtils.get_hash_md5(s.idtag))
return StrUtils.get_hash_md5(section_string + regions_string +
children_string + id_string)
def test1(self):
swcSrc = """
1 0 1.0 2.0 3.0 4.0 -1
2 0 5.0 6.0 7.0 8.0 1
"""
swcOut = MorphologyArray.fromSWC(StringIO(swcSrc)).to_tree().toSWCStr()
print "*", StrUtils.strip_comments_and_blank_lines(swcSrc), "*"
print "*", StrUtils.strip_comments_and_blank_lines(swcOut), "*"
assert StrUtils.strip_comments_and_blank_lines(swcSrc) == StrUtils.strip_comments_and_blank_lines(swcOut)
m=MorphologyArray.fromSWC(StringIO(swcSrc))
s = m.toSWC()
print s
def get_temporary_filename(cls, suffix='', filedirectory=None):
rnd_string = "%f%d%s" % (time.time(), random.randint(0, 32000), socket.gethostname())
from morphforge.core.misc import StrUtils
filename = 'tmp_%s%s' % (StrUtils.get_hash_md5(rnd_string), suffix)
filedirectory = filedirectory if filedirectory else cls.get_tmp_path()
return Join(filedirectory, filename)
def get_temporary_filename(cls, suffix='', filedirectory=None):
rnd_string = "%f%d%s" % (time.time(), random.randint(
0, 32000), socket.gethostname())
from morphforge.core.misc import StrUtils
filename = 'tmp_%s%s' % (StrUtils.get_hash_md5(rnd_string), suffix)
filedirectory = filedirectory if filedirectory else cls.get_tmp_path()
return Join(filedirectory, filename)
def prepare_sim_bundle(cls, sim):
simstring = cPickle.dumps(sim)
simmd5sum = StrUtils.get_hash_md5(simstring)
simloc = LocMgr.get_simulation_tmp_dir() + simmd5sum[0:2]
simloc = LocMgr.ensure_dir_exists(simloc)
simfilename = Join(simloc, simmd5sum + cls.simsuffix)
FileIO.write_to_file(txt=simstring, filename=simfilename)
bundle = SimMetaDataBundle(sim)
return bundle
def prepare_sim_bundle(cls, sim):
simstring = cPickle.dumps(sim)
simmd5sum = StrUtils.get_hash_md5(simstring)
simloc = LocMgr.get_simulation_tmp_dir() + simmd5sum[0:2]
simloc = LocMgr.ensure_dir_exists(simloc)
simfilename = Join(simloc, simmd5sum + cls.simsuffix)
FileIO.write_to_file(txt=simstring, filename=simfilename)
bundle = SimMetaDataBundle(sim)
return bundle
def get_neuron_suffix(self):
# Cache the result: (We shouldn't have to do this, but there is a bug
# with EqnSetChlNeuron::getModFileChangeble(), which is not returning the same thing
# on each call for some reason.
if self.cachedNeuronSuffix is None:
# We take the hash off the parameters that will change the mod-file.
# This means we don't duplicate millions of mod-files
mod_file_changeables = self.get_mod_file_changeables()
mod_file_changeables[None] = str(type(mod_file_changeables).__str__), str(self.__class__.__name__)
md5 = StrUtils.get_hash_md5(pickle.dumps(sorted(tuple(mod_file_changeables.iteritems()))))
self.cachedNeuronSuffix = 'MIKETMP%sChl' % md5
return self.cachedNeuronSuffix
def get_neuron_suffix(self):
# Cache the result: (We shouldn't have to do this, but there is a bug
# with EqnSetChlNeuron::getModFileChangeble(), which is not returning the same thing
# on each call for some reason.
if self.cachedNeuronSuffix is None:
# We take the hash off the parameters that will change the mod-file.
# This means we don't duplicate millions of mod-files
# print 'At get_neuron_suffix'
mod_file_changeables = self.get_mod_file_changeables()
mod_file_changeables[None] = str(type(mod_file_changeables).__str__)
md5 = StrUtils.get_hash_md5(pickle.dumps(mod_file_changeables))
self.cachedNeuronSuffix = 'MIKETMP%sChl' % md5
return self.cachedNeuronSuffix
def __init__(self, sim):
super(SimMetaDataBundleBase, self).__init__()
self.sim = sim
self.simmd5sum = StrUtils.get_hash_md5(cPickle.dumps(sim))
self.postsimulationactions = []
def _get_md5_of_region(r):
# assert False # Is this Cruft?? Added Jan 2011
return StrUtils.get_hash_md5(r.name)
def get_md5_hash(self):
return StrUtils.get_hash_md5(self.modtxt)
def __init__(self, sim):
super(SimMetaDataBundleBase, self).__init__()
self.sim = sim
self.simmd5sum = StrUtils.get_hash_md5(cPickle.dumps(sim))
self.postsimulationactions = []
def get_md5_hash(self):
return StrUtils.get_hash_md5(self.modtxt)
def _get_md5_of_region(r):
# assert False # Is this Cruft?? Added Jan 2011
return StrUtils.get_hash_md5(r.name)
