def check(self, delay):
all_negative = (delay <= self.max_delay).all()
all_positive = (delay >= self.min_delay).all(
) # If the delay is too small , we have to throw an error
if not (all_negative and all_positive):
raise errors.ConnectionError(
"delay (%s) is out of range [%s,%s]" %
(delay, common.get_min_delay(), common.get_max_delay()))
return delay
def connect(self, projection):
"""Connect-up a Projection."""
# Timers
global rank
timer0 = 0.0
timer1 = 0.0
timer2 = 0.0
timer3 = 0.0
timer4 = 0.0
# Recuperate variables #
n = self.n
dist_factor = self.dist_factor
noise_factor = self.noise_factor
# Do some checking #
assert dist_factor >= 0
assert noise_factor >= 0
if isinstance(n, int):
assert n >= 0
else:
raise Exception("n must be an integer.")
# Get posts and pres #
listPostIDs = projection.post.local_cells
listPreIDs = projection.pre.all_cells
countPost = len(listPostIDs)
countPre = len(listPreIDs)
listPreIndexes = numpy.arange(countPre)
listPostIndexes = map(projection.post.id_to_index, listPostIDs)
# Prepare all distances #
allDistances = self.space.distances(projection.post.positions, projection.pre.positions)
# Get weights #
weights = numpy.empty(n)
weights[:] = self.weights
is_conductance = common.is_conductance(projection.post[listPostIndexes[0]])
weights = common.check_weight(weights, projection.synapse_type, is_conductance)
for i in xrange(len(listPostIDs)):
currentPostIndex = listPostIndexes[i]
currentPostID = listPostIDs[i]
#currentPostIDAsList = [currentPostID]
# Pick n neurons at random in pre population
myTimer = time.time()
chosenPresIndexes = list(numpy.random.permutation(numpy.arange(countPre))[0:n])
chosenPresIDs = list(projection.pre[chosenPresIndexes].all_cells)
#if rank==0:
# print(chosenPresIDs)
#chosenPresIDs = chosenPresIDs.tolist()
timer0 += time.time() - myTimer
# Get distances
myTimer = time.time()
#distances = allDistances[currentPostIndex,chosenPresIndexes]
distances = allDistances[currentPostIndex, chosenPresIndexes]
timer1 += time.time() - myTimer
# Generate gamme noise
noise = numpy.random.gamma(1.0, noise_factor, n)
# Create delays with distance and noise
myTimer = time.time()
delays = dist_factor * distances * (1.0 + noise)
timer2 += time.time() - myTimer
#delays[:] = 1.0
# Check for small and big delays
myTimer = time.time()
delaysClipped = numpy.clip(delays, common.get_min_delay(), common.get_max_delay())
howManyClipped = len((delays != delaysClipped).nonzero()[0])
if (howManyClipped > 1):
print("Warning: %d of %d delays were cliped because they were either bigger than the max delay or lower than the min delay." % (howManyClipped, n))
delaysClipped = delaysClipped.tolist()
timer3 += time.time() - myTimer
# Connect everything up
yTimer = time.time()
projection._convergent_connect(chosenPresIDs, currentPostID, weights, delaysClipped)
timer4 += time.time() - myTimer
# Print timings
if rank == 0:
print("\033[2;46m" + ("Timer 0: %5.4f seconds" % timer0).ljust(60) + "\033[m")
print("\033[2;46m" + ("Timer 1: %5.4f seconds" % timer1).ljust(60) + "\033[m")
print("\033[2;46m" + ("Timer 2: %5.4f seconds" % timer2).ljust(60) + "\033[m")
print("\033[2;46m" + ("Timer 3: %5.4f seconds" % timer3).ljust(60) + "\033[m")
print("\033[2;46m" + ("Timer 4: %5.4f seconds" % timer4).ljust(60) + "\033[m")
def check(self, delay):
all_negative = (delay<=self.max_delay).all()
all_positive = (delay>=self.min_delay).all()# If the delay is too small , we have to throw an error
if not (all_negative and all_positive):
raise errors.ConnectionError("delay (%s) is out of range [%s,%s]" % (delay, common.get_min_delay(), common.get_max_delay()))
return delay
def __init__(self, source, local_mask, safe=True):
ConnectionAttributeGenerator.__init__(self, source, local_mask, safe)
self.min_delay = common.get_min_delay()
self.max_delay = common.get_max_delay()
def __init__(self, source, local_mask, safe=True):
ConnectionAttributeGenerator.__init__(self, source, local_mask, safe)
self.min_delay = common.get_min_delay()
self.max_delay = common.get_max_delay()
