def ensure_dir_exists(cls, dir_location):
""" Helper function that will make directories if they don't exist.
Useful for temporary locations"""
if dir_location and not os.path.exists(dir_location):
from morphforge.core.mgrs.logmgr import LogMgr
LogMgr.info('Creating FS Location - ' + dir_location)
if not os.path.exists(dir_location):
os.makedirs(dir_location)
return cls.validate_exists(dir_location)
def Load(self, morphname, src, regionNames=None):
regionNames = regionNames if regionNames else self.defaultxyzXYZRegionNames
lines = [l.strip() for l in src.readlines()]
lines = [l for l in lines if l and l[0] != '#' and l[0] != ':']
# Check the header:
line1 = lines[0].translate(None, '\t ')
assert line1 == 'n,T,x,y,z,X,Y,Z,P'
line1 = lines[0].translate(None, '\t ')
assert line1 == 'n,T,x,y,z,X,Y,Z,P'
regionTypes = dict([(index, Region(name))
for index, name, in regionNames.iteritems()])
sections = []
for l in lines[1:]:
toks = l.split(',')
T = int(toks[1])
xyz = (float(toks[2]), float(toks[3]), float(toks[4]))
XYZ = (float(toks[5]), float(toks[6]), float(toks[7]))
centre = ((xyz[0] + XYZ[0]) / 2.0, (xyz[1] + XYZ[1]) / 2.0,
(xyz[2] + XYZ[2]) / 2.0)
rad = np.sqrt(sum([(xyz[i] - centre[i])**2.0 for i in [0, 1, 2]]))
if rad < 0.3:
rad = 0.3
if sections:
LogMgr.info("Loading ID: %d" % int(toks[0]))
newSect = sections[-1].create_distal_section(
regions=[regionTypes[T]],
x=centre[0],
y=centre[1],
z=centre[2],
r=rad)
else:
newSect = Section(regions=[regionTypes[T]],
x=centre[0],
y=centre[1],
z=centre[2],
r=rad)
sections.append(newSect)
# Create the Cell
c = MorphologyTree(name=morphname, root=sections[0], metadata={})
return c
def _run_spawn(self):
LogMgr.info("_run_spawn() [Pickling Sim]")
(bundle, resfilename) = MetaDataBundleBuilder.build_std_pickler(self)
(_bundlefname, sim_cmd) = bundle.write_to_file_and_get_exec_string()
# if Exists(resfilename):
# os.unlink(resfilename)
if not os.path.exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get("Neuron", "ld_library_path_suffix").split(":")
old_ld_path = os.environ.get("LD_LIBRARY_PATH", "")
os.environ["LD_LIBRARY_PATH"] = ":".join([old_ld_path] + ld_path_additions)
LogMgr.info("_run_spawn() [Spawning subprocess]")
ret_code = subprocess.call(sim_cmd, shell=True)
if ret_code != 1:
raise ValueError("Unable to simulate %s" % self.name)
LogMgr.info("_run_spawn() [Finished spawning subprocess]")
# Load back the results:
LogMgr.info("_run_spawn() [Loading results]")
print "_run_spawn() [Loading results from %s ]" % resfilename
self.result = SimulationResult.load_from_file(resfilename)
LogMgr.info("_run_spawn() [Finished loading results]")
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
# Save the simulation summary:
do_summary = False
if do_summary:
fname = "~/Desktop/pdfs/%s.pdf" % (self._sim_desc_str().replace(" ", ""))
summary = SimulationMRedoc.build(self)
summary.to_pdf(fname)
# And unlink the old files (so we don't go mad on disk space)
os.unlink(resfilename)
os.unlink(_bundlefname)
return self.result
def _run_spawn(self):
LogMgr.info('_run_spawn() [Pickling Sim]')
(bundle, resfilename) = MetaDataBundleBuilder.build_std_pickler(self)
(_bundlefname, sim_cmd) = bundle.write_to_file_and_get_exec_string()
# if Exists(resfilename):
# os.unlink(resfilename)
if not os.path.exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get('Neuron',
'ld_library_path_suffix').split(':')
old_ld_path = os.environ.get('LD_LIBRARY_PATH', '')
os.environ['LD_LIBRARY_PATH'] = ':'.join([old_ld_path] +
ld_path_additions)
LogMgr.info('_run_spawn() [Spawning subprocess]')
ret_code = subprocess.call(sim_cmd, shell=True)
if ret_code != 1:
raise ValueError('Unable to simulate %s' % self.name)
LogMgr.info('_run_spawn() [Finished spawning subprocess]')
# Load back the results:
LogMgr.info('_run_spawn() [Loading results]')
self.result = SimulationResult.load_from_file(resfilename)
LogMgr.info('_run_spawn() [Finished loading results]')
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
# Save the simulation summary:
do_summary = False
if do_summary:
fname = '~/Desktop/pdfs/%s.pdf' % (self._sim_desc_str().replace(
' ', ''))
summary = SimulationMRedoc.build(self)
summary.to_pdf(fname)
return self.result
def Load(self, morphname, src, regionNames=None):
assert False, 'Do not use this module ~ currently in development'
regionNames = regionNames if regionNames else self.defaultxyzXYZRegionNames
lines = [l.strip() for l in src.readlines()]
lines = [l for l in lines if l and l[0] != '#' and l[0] != ':']
# Check the header:
line1 = lines[0].translate(None, '\t ')
assert line1 == 'n,T,x,y,z,X,Y,Z,P'
line1 = lines[0].translate(None, '\t ')
assert line1 == 'n,T,x,y,z,X,Y,Z,P'
regionTypes = dict([(index, Region(name)) for index, name, in regionNames.iteritems() ])
sections = []
for l in lines[1:]:
toks = l.split(',')
T = int(toks[1])
xyz = (float(toks[2]), float(toks[3]), float(toks[4]))
XYZ = (float(toks[5]), float(toks[6]), float(toks[7]))
centre = ((xyz[0] + XYZ[0]) / 2.0, (xyz[1] + XYZ[1]) / 2.0, (xyz[2] + XYZ[2]) / 2.0)
rad = np.sqrt(sum([(xyz[i] - centre[i]) ** 2.0 for i in [0, 1, 2]]))
if rad < 0.3:
rad = 0.3
if sections:
LogMgr.info("Loading ID: %d" % int(toks[0]))
newSect = sections[-1].create_distal_section(regions=[regionTypes[T]], x=centre[0], y=centre[1], z=centre[2], r=rad)
else:
newSect = Section (regions=[regionTypes[T]], x=centre[0], y=centre[1], z=centre[2], r=rad)
sections.append(newSect)
# Create the Cell
c = MorphologyTree(name=morphname, root=sections[0],
metadata={})
return c
def _RunSpawn(self):
LogMgr.info("_RunSpawn() [Pickling Sim]")
b, resfilename = MetaDataBundleBuilder.buildStdPickler(self)
bundlefilename, simCmd = b.writeToFileAndGetExecString()
#if Exists(resfilename):
# os.unlink(resfilename)
if not Exists(resfilename):
# Setup the LD_LIBRARY PATH:
# It may be nessesary to add the following to .mfrc
# ld_library_path_suffix = /home/michael/hw/morphforge/src/morphforgecontrib/neuron_gsl/cpp
ld_path_additions = RCMgr.get("Neuron","ld_library_path_suffix").split(":")
old_ld_path = os.environ.get('LD_LIBRARY_PATH','')
os.environ['LD_LIBRARY_PATH'] = ":".join( [old_ld_path] + ld_path_additions )
LogMgr.info("_RunSpawn() [Spawning subprocess]")
retCode = ExecCommandGetRetCode(simCmd)
if retCode != 1: raise ValueError("Unable to simulate %s" % self.name)
LogMgr.info("_RunSpawn() [Finished spawning subprocess]")
# Load back the results:
LogMgr.info("_RunSpawn() [Loading results]")
self.result = SimulationResult.loadFromFile(resfilename)
LogMgr.info("_RunSpawn() [Finished loading results]")
# We have to do this so that the simulation object
# within the result is correct!!
self.result.simulation = self
return self.result
