def allocfiles(self, **kwargs): # **kwargs override fname[k]
"""
Save version info and preallocate empty memory-mapped arrays on disk.
The arrays are taken from self.ftype, but may be overridden by
optional keyword arguments. For example, allocfiles(genotype=...) will
save the provided genotype as "genotype.npy" rather than allocate an
empty file of that name with dtype = ftype["genotype"].dtype.
"""
genotype = kwargs.pop("genotype", self.genotype)
shape = (len(genotype),) # must be tuple, or open_memmap creates broken file
np.save("index.npy", np.arange(len(genotype)))
for name, dtype in self.ftype.items():
fname = "%s.npy" % name
assert not os.path.exists(fname)
if name in kwargs:
np.save(fname, kwargs.pop(name))
else:
f = open_memmap(fname, mode="w+", dtype=dtype, shape=shape)
if name == "timing":
f[:] = nans_like(np.empty(dtype=dtype, shape=shape))
f["waiting"] = time()
f["attempts"] = 0
del f
assert not kwargs, "Unrecognized keyword argument(s) %s" % kwargs.keys()
def resume(self):
"""Prepare to rerun unfinished workpieces."""
timing = open_memmap("timing.npy")
indexbool = ~np.isfinite(timing["finished"])
if self.resumeconv:
c = np.load("convergence.npy").view(np.recarray)
indexbool = indexbool | ((c.intervals > 0) & (c.period == 0))
index = np.where(indexbool)[0]
if len(index) == 0:
raise Exception("No workpieces to resume")
np.save("index.npy", index)
timing[index]["waiting"] = time()
timing[index]["attempts"] += 1
del timing
def task(self, real_i):
"""
Map genotype i to parameter to steady state.
Input and output uses memmaps. To allow load balancing, the memmaps
have only a single element (one genotype, one parameter set, etc.).
In case of alternans, a list of (t, y, stats, integrals) is stored as e.g.
alternans/123.list.npy
To retrieve the list, use "L = np.load(filename).item()"
"""
m = Dotdict()
for name in self.ftype:
m[name] = open_memmap("%s.npy" % name, offset=real_i, shape=1)
i = 0
alog.debug("Workpiece: real_i=%s, i=%s", real_i, i)
m.timing[i]["attempts"] += 1
m.timing[i]["started"] = time()
try:
m.genotype[i] = gt = self.genotype[real_i]
m.parameter[i] = par = self.gt2par(gt)
li = self.li
with li.autorestore(_p=par):
# Compute quiescent state
with li.autorestore(stim_amplitude=0):
t, y, flag = li.integrate(t=[0, 1e6])
m.quiescent[i] = yq = y[-1:] # yq now has shape (1,)
# Run voltage stepping protocols
bp = li.bond_protocols()
p3, p5, p7 = [listify(bp[j].protocol) for j in 3, 5, 7]
p3[1][1] = -40, -20, 0, 20, 40
p5[1][1] = -40, -20, 0, 20, 40
p7[2][0] = 2, 127, 252, 377, 502
with li.autorestore(_y=yq):
L3 = li.vecvclamp(p3) # P1-P2 voltage stepping for i_Na
L5 = li.vecvclamp(p5) # P1-P2 voltage stepping for i_CaL
L7 = li.vecvclamp(p7) # Variable-gap protocol for i_CaL
d = OrderedDict() # to hold voltage-clamp phenotype characteristics
# Time constant of inactivation: -1/slope of ln(current) vs t after P1 peak
for curr, L in ("i_Na", L3), ("i_CaL", L5):
for v, tau in zip(*decayfits(L, 1, curr)):
sv = str(v).replace("-", "m") # avoid minus sign in field name
k = "%s_tau_%s" % (curr, sv)
d[k] = tau
# Michaelis-Menten half-saturation and asymptote of peak current vs gap duration
gaps, voltages = p7[2]
proto, traj = [np.array(j, dtype=object) for j in zip(*L7)]
# Vectorized voltage clamping returns a 1-d array.
# Dimensions should be (gap length, interpulse voltage, pulse index, last)
# where the last dimension has length 2 for proto (duration, voltage)
# and 4 for traj (t, y, dy, a).
for j in proto, traj:
j.shape = [len(gaps), len(voltages)] + list(j.shape[1:])
for j, v in enumerate(voltages):
imax, thalf = mmfits(zip(proto[:,j,:,:], traj[:,j,:,:]), k="i_CaL")
sv = str(v).replace("-", "m")
d["i_CaL_vg_max_" + sv] = imax
d["i_CaL_vg_thalf_" + sv] = thalf
# print " ".join(dict2rec(d).dtype.names) # for self.datatypes()
m.clamppheno[i] = dict2rec(d).view(np.recarray)
# Steady state under regular pacing
(period, intervals), steady = li.par2steady(y0=yq, reltol=self.reltol, max_nap=1000)
# # oldintervals will be nonzero if an earlier run failed to converge
# oldperiod, oldintervals = m.convergence[i]
# y0 = m.steady[i] if (self.resumeconv and oldintervals) else None
#
# # Run to convergence; steady is a list of (t, y, stats, integrals).
# # The cycle is aligned so that it starts with the highest Cai peak.
# (period, intervals), steady = self.par2steady(par, y0)
# intervals += oldintervals
m.convergence[i] = period, intervals
if period and (len(steady) > 1):
with write_if_not_exists("alternans/%s.list.npy" % real_i,
raise_if_exists=True) as f:
L = []
for t, y, stats, int_ in steady:
ix = thin(len(t), self.raw_nthin)
L.append((t[ix], y[ix], stats, int_))
np.save(f, L)
t, y, stats, _ = steady[-1]
m.steady[i] = y[0]
# Phenotypes for steady-state dynamics
aps = [(t, y, stats) for t, y, stats, int_ in steady[-self.raw_nap:]]
m.raw[i], m.ap_stats[i] = self.thin_aps(aps, self.raw_nthin, par)
# Ion-current phenotypes, also applied to other state variables.
# One table/ndarray per phenotype, one column per variable.
raw = m.raw[i]
currstats = np.concatenate([current_phenotypes_array(raw["t"], raw[k])
for k in raw.dtype.names if k != "t"])
for k in currstats.dtype.names:
m[k][i] = np.ascontiguousarray(currstats[k])
m.timing[i]["finished"] = time()
m.timing[i]["seconds"] = m.timing[i]["finished"] - m.timing[i]["started"]
except Exception, exc:
m.timing[i]["error"] = time()
alog.exception("Error processing item %s", i)