# filling cvArray
cvArray = zeros((arrSize,3))
for i in xrange(arrSize):
cvArray[i][0] = resArray[i]
# main loop
i = 1
for dir in dirList:
os.chdir(dir)
print " >> %s " % dir
j = 0
if arrSize == 1:
sim = "t%04dum" % resArray[arrIndex]
simPts = sim + "/" + sim + "_i.pts"
simAct = sim + "/" + "activation-thresh.dat"
cv = condVelocity(simPts, simAct)
cvArray[0][i] = cv
else:
for res in resArray:
sim = "t%04dum" % res
simPts = sim + "/" + sim + "_i.pts"
simAct = sim + "/" + "activation-thresh.dat"
if (os.path.isfile(simPts) != True):
print " error calculateCV: file %s not found" + simPts
exit(-1)
if (os.path.isfile(simAct) != True):
print " error calculateCV: file %s not found" + simAct
exit(-1)
def find_CV(avg_dx, vel, gil, gel, beta, model, sv_init, plugs, carpBinary, mesherBinary, carp_ver):
"""
Input: avg_dx - mesh resolution as a scalar or list
(list - Not implemented yet)
gil - intracellular conductivity along the cable
gel - extracellular conductivity along the cable
vel - desired conduction velocity
beta - surface-to-volume ratio
model - which ionic model to use
sv_init - file holding initial state vector
plugs - which plugins are used to augment the model
Output:
cv_measured in a 1cm long cable with avg_dx of resolution and using
the value of g_bulk as conductivity
"""
resList = [] # list of resolutions
cvList = [] # list of conduction velocities measured
if isinstance(avg_dx,list):
resList = avg_dx
elif isinstance(avg_dx,int) or isinstance(avg_dx,float):
resList.append(avg_dx)
# temporary files setttings
if os.name == 'posix':
temp_dir = os.environ.get("HOME")
temp_dir += '/tmp'
else:
temp_dir = ''
# settings
xsize = 1.0 # cm
mesh_temp = "mesh4exp"
mesh_name = "%s/mesh4exp" % (temp_dir)
mesh_file = "%s/expMesh.par" % (temp_dir)
carp_file = "%s/expParam.par" % (temp_dir)
out_dir = "%s/OUTPUT_DIR" % (temp_dir)
for res in resList:
yzsize = float(res/10000.) # convert to cm
tend = float(xsize/vel*10.) * 2 # cm*10/(mm/ms) +100%
# create mesh and cable
msh = MeshFile(mesh_name, size0=xsize, size1=yzsize,
size2=yzsize, element=1, resolution=res)
msh.write_to_file(mesh_file)
cab = CableTest(model, sv_init, plugs, gil, gel, beta, tend, carp_ver)
cab.write_to_file(carp_ver, carp_file)
# run MESHER
cmd = '%s +F %s' % (mesherBinary, mesh_file)
if DEBUG: print 'running %s' % cmd
run_command_line(cmd)
# run CARP
cmd = '%s +F %s -meshname %s -simID %s' % (carpBinary,
carp_file, mesh_name, out_dir)
if DEBUG: print 'running %s' % cmd
run_command_line(cmd)
# calculate CV
sim_pts = "%s/%s_i.pts" % (out_dir, mesh_temp)
sim_act = "%s/activation-thresh" % (out_dir)
condvel = condVelocity(sim_pts, sim_act, output=False)
cvList.append(condvel)
# clean temp files
if os.path.isdir(out_dir):
shutil.rmtree(out_dir)
if os.path.isfile(carp_file):
os.remove(carp_file)
if len(resList) == 1: return cvList[0]
return cvList