def __init__(self):
self.Q = EventQueue()
self.T = StatusStructure()
self.T1 = StatusStructure()
self.T2 = StatusStructure()
self.intersections = []
self.vertices = []
self.halfedges = []
self.faces = []
self.face1 = []
self.face2 = []
self.cycles = [CycleNode(cycle=None, inf_outer=True)]
class FindIntersections():
def __init__(self):
self.Q = EventQueue()
self.T = StatusStructure()
self.intersections = []
def find_intersections(self, lines):
for line in lines:
self.Q.insert_line(line)
while not self.Q.is_empty():
next_event = self.Q.pop_next_event()
self.handle_event_point(next_event)
def handle_event_point(self, p):
U_p = p.lines
L_p, C_p, L_C = self.T.find_segments_contain(p.point)
U_C = U_p + C_p
L_U_C = L_C + U_p
if len(L_U_C) > 1:
self.intersections.append(p.point)
for line in L_C:
self.T.delete(p.point, line)
self.T.insert(p.point, U_C)
self.T._print_name()
if len(U_C) == 0:
s_l = self.T.find_left_neighbor(p.point)
s_r = self.T.find_right_neighbor(p.point)
self.find_new_event(s_l, s_r, p.point)
else:
s_lm = self.T.find_leftmost(p.point)
s_l = self.T.find_left_neighbor(p.point)
self.find_new_event(s_lm, s_l, p.point)
s_rm = self.T.find_rightmost(p.point)
s_r = self.T.find_right_neighbor(p.point)
self.find_new_event(s_rm, s_r, p.point)
def find_new_event(self, s_l, s_r, p):
if s_l is None or s_r is None:
return
i = s_l.intersect(s_r)
if i is None:
return
x_i, y_i = i
x_p, y_p = p
if y_i < y_p or (y_i == y_p and x_i > x_p):
self.Q.insert(i)
class MapOverlay:
def __init__(self):
self.Q = EventQueue()
self.T = StatusStructure()
self.T1 = StatusStructure()
self.T2 = StatusStructure()
self.intersections = []
self.vertices = []
self.halfedges = []
self.faces = []
self.face1 = []
self.face2 = []
self.cycles = [CycleNode(cycle=None, inf_outer=True)]
def find_intersections(self, halfedges):
for he in halfedges:
self.Q.insert_he(he)
while not self.Q.is_empty():
next_event = self.Q.pop_next_event()
self.handle_event_point(next_event)
def handle_event_point(self, p):
def assign_pointer(hedges):
root = hedges[0]
sorted_hedges = []
dcel1_hedges = [hedge for hedge in hedges if hedge.belong_to == root.belong_to]
dcel2_hedges = [hedge for hedge in hedges if hedge.belong_to != root.belong_to]
i1 = i2 = 0
i = 1
while i < len(dcel2_hedges):
if root.clockwise_angle(dcel2_hedges[i]) < root.clockwise_angle(dcel2_hedges[i-1]):
break
i += 1
dcel2_hedges = dcel2_hedges[i:] + dcel2_hedges[:i]
while (i1 + i2) < len(hedges):
if i1 == len(dcel1_hedges):
sorted_hedges.extend(dcel2_hedges[i2:])
break
elif i2 == len(dcel2_hedges):
sorted_hedges.extend(dcel1_hedges[i1:])
break
if root.clockwise_angle(dcel1_hedges[i1]) < root.clockwise_angle(dcel2_hedges[i2]):
sorted_hedges.append(dcel1_hedges[i1])
i1 += 1
else:
sorted_hedges.append(dcel2_hedges[i2])
i2 += 1
for i in range(0, len(sorted_hedges)-1):
c_he = sorted_hedges[i]
n_he = sorted_hedges[i+1]
c_he.twin.set_next(n_he)
c_he = sorted_hedges[-1]
n_he = sorted_hedges[0]
c_he.twin.set_next(n_he)
U_p = p.segments_u
L_p, C_p, L_C = self.T.find_segments_contain(p.point)
U_C = U_p + C_p
L_U_C = L_C + U_p
if len(L_U_C) > 1:
self.intersections.append(p.point)
for segment in L_C:
self.T.delete(p.point, segment)
if segment.belong_to == 'dcel1' and p.point.belong_to == 'dcel1':
self.T1.delete(p.point, segment)
if segment.belong_to == 'dcel2' and p.point.belong_to == 'dcel2':
self.T2.delete(p.point, segment)
self.T.insert(p.point, U_C)
if p.point.belong_to == 'dcel1':
self.T1.insert(p.point, [s for s in U_C if s.belong_to == 'dcel1'])
if p.point.belong_to == 'dcel2':
self.T2.insert(p.point, [s for s in U_C if s.belong_to == 'dcel2'])
if not p.point.involves_both:
if p.point.belong_to == 'dcel1':
d2_left_he = self.T2.find_left_neighbor(p.point)
if d2_left_he is None:
p.point.face_contain = None
else:
p.point.face_contain = d2_left_he.halfedge.incident_face
else:
d1_left_he = self.T1.find_left_neighbor(p.point)
if d1_left_he is None:
p.point.face_contain = None
else:
p.point.face_contain = d1_left_he.halfedge.incident_face
if len(U_C) == 0:
s_l = self.T.find_left_neighbor(p.point)
s_r = self.T.find_right_neighbor(p.point)
self.find_new_event(s_l, s_r, p.point)
else:
s_lm = self.T.find_leftmost(p.point)
s_l = self.T.find_left_neighbor(p.point)
self.find_new_event(s_lm, s_l, p.point)
s_rm = self.T.find_rightmost(p.point)
s_r = self.T.find_right_neighbor(p.point)
self.find_new_event(s_rm, s_r, p.point)
if p.point.involves_both:
assign_pointer(p.halfedges)
p.point.incident_edge = p.halfedges[0]
self.vertices.append(p.point)
p.point.left_hedge = s_l.halfedge if s_l is not None else None
def find_new_event(self, s_l, s_r, p):
def add_new_he(new_l, s_l, i):
h_newl = HalfEdge(origin=i)
h_sl = HalfEdge(origin=i)
h_newl.belong_to = new_l.belong_to
h_sl.belong_to = s_l.belong_to
h_newl.copy_next(s_l.halfedge)
h_sl.copy_next(s_l.halfedge.twin)
h_newl.set_twin(s_l.halfedge.twin)
h_sl.set_twin(s_l.halfedge)
new_l.set_halfedge(h_newl)
return h_sl, h_newl
if s_l is None or s_r is None:
return
i = s_l.intersect(s_r)
if i is None:
return
x_i, y_i = i.coordinates
x_p, y_p = p.coordinates
if y_i < y_p or (y_i == y_p and x_i > x_p):
segments=[]
he_w_origin_i = []
if s_l.lower_endpoint != i and s_l.upper_endpoint != i:
new_l = Segment(s_l.lower_endpoint, i)
new_l.belong_to = s_l.belong_to
s_l.lower_endpoint = i
segments.append(new_l)
h1, h2 = add_new_he(new_l, s_l, i)
he_w_origin_i.extend([h1, h2])
self.halfedges.extend([h1, h2])
if s_r.lower_endpoint != i and s_r.upper_endpoint != i:
new_r = Segment(s_r.lower_endpoint, i)
new_r.belong_to = s_r.belong_to
s_r.lower_endpoint = i
segments.append(new_r)
h1, h2 = add_new_he(new_r, s_r, i)
he_w_origin_i.extend([h1, h2])
self.halfedges.extend([h1, h2])
self.Q.insert(i, segments=segments, hedges=he_w_origin_i)
def plot(self, halfedges):
for he in halfedges:
x = he.origin
y = he.next.origin
if he.belong_to == he[0].belong_to:
plt.plot((x.coordinates[0], y.coordinates[0]), (x.coordinates[1], y.coordinates[1]), 'ro-')
else:
plt.plot((x.coordinates[0], y.coordinates[0]), (x.coordinates[1], y.coordinates[1]), 'bo-')
for point in self.intersections:
plt.plot(point.coordinates[0], point.coordinates[1], marker='x', markersize=10, color="blue")
plt.show()
def detect_cycle(self):
he_set = set(self.halfedges)
while len(he_set) != 0:
first_he = he_set.pop()
current_cycle = [first_he]
current_he = first_he
while current_he.next != first_he:
current_he = current_he.next
he_set.remove(current_he)
current_cycle.append(current_he)
self.cycles.append(CycleNode(current_cycle))
for cycle in self.cycles:
if cycle.is_inner_boundary:
left_hedge = cycle.find_leftmost_he().next.origin.left_hedge
outer_cycle = left_hedge.cycle if left_hedge is not None else self.cycles[0]
outer_cycle.links.append(cycle)
def compute_faces(self):
outer_cycles = [cycle for cycle in self.cycles if not cycle.is_inner_boundary]
for outer_cycle in outer_cycles:
face = Face()
face.outer_component = outer_cycle.cycle[0] if len(outer_cycle.cycle) != 0 else None
for inner_cycle in outer_cycle.links:
face.inner_components.append(inner_cycle.cycle[0])
face.cycle = outer_cycle
self.faces.append(face)
he_list = outer_cycle.cycle if len(outer_cycle.cycle) != 0 else outer_cycle.links[0].cycle
he_list.append(he_list[0])
for i in range(len(he_list) - 1):
prev_hedge = he_list[i]
current_hedge = he_list[i+1]
if current_hedge.origin.involves_both and prev_hedge.incident_face.belong_to != current_hedge.incident_face.belong_to:
f1 = prev_hedge.incident_face.name
f2 = current_hedge.incident_face.name
face.name = str(f1) + '.' + str(f2)
break
if face.name is None:
he = face.outer_component if face.outer_component is not None else face.inner_components[0]
v = he.origin
f1 = he.incident_face.name
if v.face_contain is None:
if v.belong_to == 'dcel1':
f2 = [f for f in self.face2 if f.outer_component is None][0].name
else:
f2 = [f for f in self.face1 if f.outer_component is None][0].name
else:
f2 = v.face_contain.name
face.name = str(f1) + '.' + str(f2)
outer_cycle = face.cycle
for hedge in outer_cycle.cycle:
hedge.incident_face = face
for inner_cycle in outer_cycle.links:
for hedge in inner_cycle.cycle:
hedge.incident_face = face
def get_dcel(self):
return DCEL(self.vertices, self.halfedges, self.faces)
def calculate(self, dcel1, dcel2, plot = False):
dcel1.set_name('dcel1')
dcel2.set_name('dcel2')
h = dcel1.halfedges + dcel2.halfedges
self.face1 = dcel1.faces
if self.face1[0].name is None:
for index, f in enumerate(self.face1):
f.name = 'f_'+str(index)
self.face2 = dcel2.faces
if self.face2[0].name is None:
for index, f in enumerate(self.face2):
f.name = 'g_'+str(index)
if plot:
_, ax = plt.subplots(nrows=1, ncols=3)
dcel1.plot_dcel(ax[0])
dcel2.plot_dcel(ax[1])
start_time = time.time()
self.halfedges = h
self.find_intersections(h)
print('Find intersection: ', time.time() - start_time)
self.detect_cycle()
print('Detect cycle: ', time.time() - start_time)
self.compute_faces()
print('Compute faces:', time.time() - start_time)
dcel = self.get_dcel()
total_time = time.time() - start_time
print('Finish:', total_time)
if plot:
dcel.plot_dcel(ax[2])
plt.show()
return dcel, total_time
def __init__(self):
self.pool = SampleTree()
self.eventQueue = EventQueue()
self.__resetCounts()
class Model(object):
def __init__(self):
self.pool = SampleTree()
self.eventQueue = EventQueue()
self.__resetCounts()
##################################################################
# there are five kinds of rates:
# N: (fixed) number of bases in the model
# rll: rate for dcj on the bases in the contig pool
# rld: rate for dcj where one break is in the pool
# and the other rate is in the garbage
# rdd: both in garbage
# fl: telomere loss modifier
# fg: telomere gain modifier
# pgain: dead gain probability
##################################################################
def setParameters(self, N, rll, rld = 0, rdd = 0, fl = 0, fg = 0,
pgain = 0):
self.eventQueue.reset()
self.N = N
self.fl = fl
self.fg = fg
self.pgain = pgain
if rll > 0:
self.eventQueue.addEventType(N * rll, self.__llEvent)
if rld > 0:
self.eventQueue.addEventType(N * rld, self.__ldEvent)
if rdd > 0:
self.eventQueue.addEventType(N * rdd, self.__ddEvent)
##################################################################
# intitialize the starting state
# the the contigs will all have the same sizes (modulo rounding)
# in order to satisfy the input parameters exactly
##################################################################
def setStartingState(self, garbageSize, numLinear, numCircular):
assert self.N > garbageSize + numLinear + numCircular
self.pool = SampleTree()
numGarbage = 0
if garbageSize > 0:
garbage = CircularContig(garbageSize)
garbage.setDead()
self.pool.insert(garbage, garbage.numBases())
numGarbage = 1
lrat = float(numLinear) / (numLinear + numCircular)
crat = float(numCircular) / (numLinear + numCircular)
linearBases = math.floor((self.N - garbageSize) * lrat)
circularBases = math.ceil((self.N - garbageSize) * crat)
assert linearBases + circularBases + garbageSize == self.N
if numLinear > 0:
linSize = math.floor(linearBases / numLinear)
extra = linearBases % numLinear
added = 0
for i in range(numLinear):
size = linSize
if i < extra:
size += 1
# plus 1 since number of adjacencies is 1 + number of bases
contig = LinearContig(size + 1)
self.pool.insert(contig, contig.numBases())
added += contig.size
assert added == linearBases + numLinear
assert self.pool.size() == numLinear + numGarbage
assert self.pool.weight() == linearBases + garbageSize
if numCircular > 0:
circSize = math.floor(circularBases / numCircular)
extra = circularBases % numCircular
added = 0
for i in range(numCircular):
size = circSize
if i < extra:
size += 1
contig = CircularContig(size)
self.pool.insert(contig, contig.numBases())
added += contig.size
assert added == circularBases
assert self.pool.size() == numLinear + numCircular + numGarbage
assert self.pool.weight() == circularBases + linearBases + \
garbageSize
##################################################################
# run the simulation for the specified time
##################################################################
def simulate(self, time):
self.eventQueue.begin()
self.__resetCounts()
while True:
nextEvent = self.eventQueue.next(time)
if nextEvent is not None:
nextEvent()
else:
break
##################################################################
# draw (and remove) two random adajcenies and their
# contigs from the pool (only if they are not dead)
##################################################################
def __drawSamples(self):
sampleNode1, offset1 = self.pool.uniformSample()
sampleNode2, offset2 = self.pool.uniformSample()
# the offset is weighted based on the number of bases
# we want to translate this into number of edges (splitting)
# the probability between linear and telomere edges.
# so for linear contigs with zero offset, we flip a coin to
# move it to the other side.
if sampleNode1.data.isLinear() and offset1 == 0:
if random.random() < 0.5:
offset1 = sampleNode1.data.numBases()
if sampleNode2 is not sampleNode1 and sampleNode2.data.isLinear() and\
offset2 == 0:
if random.random() < 0.5:
offset2 = sampleNode2.data.numBases()
assert offset1 < sampleNode1.data.size
assert offset2 < sampleNode2.data.size
return (sampleNode1, offset1, sampleNode2, offset2)
##################################################################
#LIVE-LIVE event. Is normal DCJ operation between two live contigs
#unless the two breakpoints are identical or on telomeres, in which
#case fl and fg parameters are used to use fission operations to
#modifiy the number of telomeres
##################################################################
def __llEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
# draw (and remove) two random adajcenies and their
#contigs from the pool (only if they are not dead)
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# don't deal with dead contigs in this event
if c1.isDead() == True or c2.isDead() == True:
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
# case 1) gain of telomere
if sampleNode1 is sampleNode2 and offset1 == offset2:
return self.__llGain(c1, c2, offset1, offset2)
# case 2) loss of telomere
elif c1.isLinear() and c2.isLinear() and \
(offset1 == 0 or offset1 == c1.size - 1) and \
(offset2 == 0 or offset2 == c2.size - 1):
return self.__llLoss(c1, c2, offset1, offset2)
# case 3) no gain or loss
self.llCount += 1
forward = random.randint(0, 1) == 1
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, forward)
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
##################################################################
# Do the fission telomere gain operation (if fg check passes)
##################################################################
def __llGain(self, c1, c2, offset1, offset2):
# correct "not composite check below"
if c1.isCircular() or (offset1 != 0 and offset1 != c1.size - 1):
forward = self.fg > random.random()
if forward:
self.fgCount += 1
dcjResult = dcj(c1, offset1, c2, offset2, forward)
if c1.isCircular():
assert len(dcjResult) == 1 and dcjResult[0].isLinear()
else:
assert len(dcjResult) == 2 and dcjResult[0].isLinear() \
and dcjResult[1].isLinear()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
return
self.pool.insert(c1, c1.numBases())
if c2 is not c1:
self.pool.insert(c2, c2.numBases())
##################################################################
# Do the fission telomer loss operation (if fl check passes)
##################################################################
def __llLoss(self, c1, c2, offset1, offset2):
if c1 is c2:
forward = self.fl / 4.0 > random.random()
else:
forward = self.fl / 2.0 > random.random()
if forward:
c1 = c1.circularize()
if c1 is not c2:
c2 = c2.circularize()
dcjResult = dcj(c1, offset1, c2, offset2, forward)
self.flCount += 1
assert len(dcjResult) == 1
if c1 is not c2:
assert dcjResult[0].isLinear()
else:
assert dcjResult[0].isCircular()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
else:
self.pool.insert(c1, c1.numBases())
if c2 is not c1:
self.pool.insert(c2, c2.numBases())
##################################################################
#LIVE-DEAD (or DEAD-LIVE) event. One contig is alive and the
#other is the unique dead contig. This can result in a loss of
#live contigs and/or change in number of live bases
##################################################################
def __ldEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
# draw (and remove) two random adajcenies and their
#contigs from the pool (only if they are not dead)
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# only deal with live / dead contigs in this event
if (c1.isDead() == c2.isDead()):
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
# make sure c1 is alive and c2 is dead
if c1.isDead():
c1, c2 = c2, c1
offset1, offset2 = offset2, offset1
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, random.randint(0, 1) == 1)
deadIdx = 0;
if len(dcjResult) == 2 and \
random.randint(0, dcjResult[0].size + dcjResult[1].size) >= \
dcjResult[0].size:
deadIdx = 1
dcjResult[deadIdx].setDead(True)
if len(dcjResult) == 1:
self.ldLossCount += 1
else:
self.ldSwapCount += 1
# add the resulting contigs back to the pool
deadCount = 0
for res in dcjResult:
if res.isDead():
deadCount += 1
self.pool.insert(res, res.numBases())
assert deadCount == 1
##################################################################
#DEAD-DEAD event. The dead contig rearranges with itself. pgain
#is used to decide how oftern this oepration breaks off a new circular
#live chormosome
##################################################################
def __ddEvent(self):
if self.pool.size() == 0 or self.pool.weight() == 1:
return
sampleNode1, offset1, sampleNode2, offset2 = self.__drawSamples()
c1 = sampleNode1.data
c2 = sampleNode2.data
# only deal with dead / dead contigs in this event
if (c1.isDead() == False or c2.isDead() == False):
return
# only support single dead contig
assert c1 is c2
# don't know what to do here
if (offset1 == offset2):
return
self.pool.remove(sampleNode1)
if c1 is not c2:
self.pool.remove(sampleNode2)
#forward means do not cut
forward = random.random() > self.pgain
# do the dcj
dcjResult = dcj(c1, offset1, c2, offset2, forward)
deadIdx = 0;
if len(dcjResult) == 2 and \
random.randint(0, dcjResult[0].size + dcjResult[1].size) \
>= dcjResult[0].size:
deadIdx = 1
dcjResult[deadIdx].setDead(True)
if forward:
self.ddSwapCount += 1
assert len(dcjResult) == 1
else:
self.ddGainCount += 1
assert len(dcjResult) == 2
assert not dcjResult[0].isDead() or not dcjResult[1].isDead()
# add the resulting contigs back to the pool
for res in dcjResult:
self.pool.insert(res, res.numBases())
##################################################################
# all counters set to zero.
##################################################################
def __resetCounts(self):
self.llCount = 0
self.fgCount = 0
self.flCount = 0
self.ldLossCount = 0
self.ldSwapCount = 0
self.ddGainCount = 0
self.ddSwapCount = 0
def simulate(self):
t = 0
simulationTime = 10000
simulationLimit = 10000
arrivalDataRate = self.utilization / 0.00302 # = (6040 bits / 2e+6 bits/s) s |
lastDataPackageTime = 0
maxEventListSize = 1000
roundSize = 2000 # packages processed
transientPhaseSize = 2500 #packages processed
numberOfRounds = 10
totalSimulationsPackages = (numberOfRounds *
roundSize) + transientPhaseSize
consumedEvents = []
eventQueue = EventQueue()
voiceChannels = []
voiceQueue = []
dataQueue = []
servedPackages = 0
totalDataWaitingTimePerRound = [0] * numberOfRounds
WaitingTimeSamplePerRound = []
for i in range(numberOfRounds):
WaitingTimeSamplePerRound.append([])
totalDataProcessingTimePerRound = [0] * numberOfRounds
ProcessingTimeSamplePerRound = []
for i in range(numberOfRounds):
ProcessingTimeSamplePerRound.append([])
totalVoiceWaitingTimePerRound = [0] * numberOfRounds
VoiceWaitingTimeSamplePerRound = []
for i in range(numberOfRounds):
VoiceWaitingTimeSamplePerRound.append([])
X2PerRound = [
0.000256
] * numberOfRounds # voice package processing time is fixed due to voice package size being fixed
# T1 = W1 + X1 | T2 = W2 + X2
Nq1PerRound = [0] * numberOfRounds
Nq2PerRound = [0] * numberOfRounds
voicePackagesProcessedPerRound = [0] * numberOfRounds
dataPackagesProcessedPerRound = [0] * numberOfRounds
averageVoiceWaitingPerRound = []
averageDataWaitingPerRound = []
averageDataServingTimePerRound = []
transmissions = [{}] * (constants.VOICE_CHANNELS * numberOfRounds)
in_service_package = None
# Generating voice channels
for i in range(constants.VOICE_CHANNELS):
voiceChannels.append(VoiceChannel(i))
currentEvent = None
currentRound = -1
servedDataPackages = 0
while servedDataPackages < totalSimulationsPackages: #t < simulationTime and len(consumedEvents) < simulationLimit:
# print('Served packages: ' + str(servedPackages))
if servedDataPackages > transientPhaseSize:
# We're passed transient phase
if currentRound != (
(servedDataPackages - transientPhaseSize) // roundSize):
currentRound = (servedDataPackages -
transientPhaseSize) // roundSize
#print(currentRound)
#print(servedPackages)
#print(roundSize)
self.log(str(currentRound))
if currentRound >= 0 and ((
(servedDataPackages + 1) - transientPhaseSize) //
roundSize) > currentRound:
Nq1PerRound[currentRound] = len(dataQueue)
Nq2PerRound[currentRound] = len(voiceQueue)
self.log('Simulation time\t' + str(t) + 's\nEvent Queue Size:\t' +
str(eventQueue.length()))
if currentEvent is not None:
consumedEvents.append(currentEvent)
self.log('Event consumed\t' + str(currentEvent.type))
# treat evt
# if the event is a voice package arrival, the package is created and put in the
# voice package queue
if currentEvent.type == EventType.CREATE_VOICE_PACKAGE:
voiceQueue.append(
Package(PackageType.VOICE_PACKAGE, currentEvent.source,
t, currentEvent.transmission))
self.log('Voice Package from ' +
constants.PACKAGE_SOURCE[currentEvent.source] +
' queued')
# if the event type means a voice package should be moved from queue to processing
# the first package in the queue is removed and we create an event to finish serving it
elif currentEvent.type == EventType.VOICE_PACKAGE_PROCESSING:
in_service_package = voiceQueue.pop(0)
in_service_package.startServingTime = t
if currentRound >= 0:
totalVoiceWaitingTimePerRound[currentRound] += (
in_service_package.startServingTime -
in_service_package.arrivalTime)
VoiceWaitingTimeSamplePerRound[currentRound].append(
in_service_package.startServingTime -
in_service_package.arrivalTime)
# only for plot purpose
averageDataServingTimePerRound.append(
sum(totalDataProcessingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
averageVoiceWaitingPerRound.append(
sum(totalVoiceWaitingTimePerRound) /
(sum(voicePackagesProcessedPerRound) + 1))
averageDataWaitingPerRound.append(
sum(totalDataWaitingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
eventQueue.add(
Event(
t + (in_service_package.size /
float(constants.CHANNEL_SIZE)),
EventType.VOICE_PACKAGE_SERVED,
in_service_package.source,
in_service_package.transmission))
self.log(
'Voice Package from ' +
constants.PACKAGE_SOURCE[in_service_package.source] +
'is in the router')
# if the event is a voice package finishing being served we clear the router/server
elif currentEvent.type == EventType.VOICE_PACKAGE_SERVED:
self.log(
'Voice Package from ' +
constants.PACKAGE_SOURCE[in_service_package.source] +
' has finished serving')
if currentRound >= 0:
voicePackagesProcessedPerRound[currentRound] += 1
servedPackages += 1
if currentRound >= 0 and in_service_package.transmission in transmissions[
(in_service_package.source - 1) +
(currentRound * constants.VOICE_CHANNELS)].keys():
transmission = transmissions[
(in_service_package.source - 1) +
(currentRound * constants.VOICE_CHANNELS)][
in_service_package.transmission]
transmission.processedPackages += 1
if transmission.size < transmission.processedPackages:
transmission.endTime = t
in_service_package = None
# if the event is a data package arrival, the package is created and put in the
# data package queue
elif currentEvent.type == EventType.CREATE_DATA_PACKAGE:
dataQueue.append(
Package(PackageType.DATA_PACKAGE, currentEvent.source,
t, currentEvent.transmission))
self.log('Data Package from ' +
constants.PACKAGE_SOURCE[currentEvent.source] +
' with size ' +
str(dataQueue[len(dataQueue) - 1].size) +
' queued')
# here we also create the next data package
# if the event type means a data package should be moved from queue to processing
# the first package in the queue is removed and we create an event to finish serving it
elif currentEvent.type == EventType.DATA_PACKAGE_PROCESSING:
in_service_package = dataQueue.pop(0)
in_service_package.startServingTime = t
if currentRound >= 0:
totalDataWaitingTimePerRound[currentRound] += (
in_service_package.startServingTime -
in_service_package.arrivalTime)
WaitingTimeSamplePerRound[currentRound].append(
in_service_package.startServingTime -
in_service_package.arrivalTime)
# only for plot purpose
averageDataServingTimePerRound.append(
sum(totalDataProcessingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
averageVoiceWaitingPerRound.append(
sum(totalVoiceWaitingTimePerRound) /
(sum(voicePackagesProcessedPerRound) + 1))
averageDataWaitingPerRound.append(
sum(totalDataWaitingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
evt = Event(
t + (in_service_package.size /
float(constants.CHANNEL_SIZE)),
EventType.DATA_PACKAGE_SERVED,
in_service_package.source,
in_service_package.transmission)
if self.preemptive:
evt.package_reference = in_service_package
eventQueue.add(evt)
self.log(
'Data Package from ' +
constants.PACKAGE_SOURCE[in_service_package.source] +
' with size ' + str(in_service_package.size) +
' is in the router')
# if the event is a data package finishing being served we clear the router/server
elif currentEvent.type == EventType.DATA_PACKAGE_SERVED:
self.log(
'Data Package from ' +
constants.PACKAGE_SOURCE[in_service_package.source] +
' with size ' + str(in_service_package.size) +
' has finished serving')
in_service_package.endServingTime = t
if currentRound >= 0:
totalDataProcessingTimePerRound[currentRound] += (
in_service_package.endServingTime -
in_service_package.startServingTime)
dataPackagesProcessedPerRound[currentRound] += 1
ProcessingTimeSamplePerRound[currentRound].append(
in_service_package.endServingTime -
in_service_package.startServingTime)
# only for plot purpose
averageDataServingTimePerRound.append(
sum(totalDataProcessingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
averageVoiceWaitingPerRound.append(
sum(totalVoiceWaitingTimePerRound) /
(sum(voicePackagesProcessedPerRound) + 1))
averageDataWaitingPerRound.append(
sum(totalDataWaitingTimePerRound) /
(sum(dataPackagesProcessedPerRound) + 1))
servedPackages += 1
servedDataPackages += 1
in_service_package = None
# Note: altough voice and data events could be treated together, the separation will make
# things easier to track and change for the preemptive scenario
if self.preemptive:
if len(
voiceQueue
) > 0 and in_service_package is not None and in_service_package.type == PackageType.DATA_PACKAGE:
totalDataProcessingTimePerRound[currentRound] += (
t - in_service_package.startServingTime)
ProcessingTimeSamplePerRound[currentRound].append(
t - in_service_package.startServingTime)
pkg = Package(PackageType.DATA_PACKAGE, 0, t + 0.000256, 0)
pkg.size = in_service_package.size # - (( t - in_service_package.startServingTime ) * constants.CHANNEL_SIZE)
dataQueue.insert(0, pkg)
eventQueue.remove_with_package(in_service_package)
in_service_package = None
if pkg.size < 0:
print("ERROR SIZE")
# if there's no package being processed
if in_service_package is None:
# we check if there's any voice packages waiting to be processed
if len(voiceQueue) > 0:
eventQueue.add(
Event(t, EventType.VOICE_PACKAGE_PROCESSING,
voiceQueue[0].source,
voiceQueue[0].transmission))
# in case there's no voice package to be processed we check if there's any data package
# to process
# Note: this is due to the fact voice packages have the priority
elif len(dataQueue) > 0:
eventQueue.add(
Event(t, EventType.DATA_PACKAGE_PROCESSING, 0, 0))
# Generate voice arrivals
self.log('==================================')
for i in range(len(voiceChannels)):
if t >= voiceChannels[
i].nextTransmission: # and eventQueue.length() < maxEventListSize:
evtTimes = voiceChannels[i].getEventTimes(t)[1:]
transmissionId = 0
if currentRound >= 0 and len(evtTimes) > 0:
transmission = Transmission(evtTimes[0], 0,
(len(evtTimes) - 1), 0)
transmissionId = len(
transmissions[i +
(currentRound *
constants.VOICE_CHANNELS)].keys())
transmissions[i +
(currentRound * constants.VOICE_CHANNELS
)][transmissionId] = transmission
for evtTime in evtTimes:
evt = Event(evtTime + t,
EventType.CREATE_VOICE_PACKAGE, i + 1,
transmissionId)
# self.log('Voice evt added in ' + str(evt.eventTime) + 's', 0.005)
eventQueue.add(evt)
self.log('==================================')
# Generate data arrivals
if t >= lastDataPackageTime:
evtTime = lastDataPackageTime + np.random.exponential(
1 / arrivalDataRate)
eventQueue.add(
Event(evtTime, EventType.CREATE_DATA_PACKAGE, 0, 0))
lastDataPackageTime = evtTime
self.log('Data evt added in ' + str(evtTime) + 's')
#print('Data evt added in ' + str(evtTime) + 's')
# self.log('---------')
# for i in range(eventQueue.length()):
# self.log(str(eventQueue.get(i).type) + ' ' + str(eventQueue.get(i).eventTime))
# self.log('---------')
# getting next event in simulation time and setting simulation time to event's time
currentEvent = eventQueue.pop()
# self.log('--------- next event ---------')
# self.log(str(currentEvent.type) + ' ' + str(currentEvent.eventTime))
# self.log('---------')
t = currentEvent.eventTime
# GENERATE STATISTICS
finalW1 = 0
finalStdW1 = 0
finalW2 = 0
finalStdW2 = 0
finalX1 = 0
finalStdX1 = 0
finalX2 = 0
finalStdX2 = 0
finalT1 = 0
finalStdT1 = 0
finalT2 = 0
finalStdT2 = 0
finalNq1 = 0
finalStdNq1 = 0
finalNq2 = 0
finalStdNq2 = 0
delta = 0
if (self.PLOT):
if (not (os.path.exists("images"))):
os.mkdir("images")
plt.plot(averageDataWaitingPerRound)
plt.ylabel('E[W1]')
plt.ylabel('Pacotes servidos')
plt.title("V.A. W1 com valor rho1 = " + str(self.utilization))
plt.xlim(xmax=servedPackages)
plt.savefig('images/W1-' + str(self.utilization) + '.png')
plt.clf()
plt.plot(averageDataServingTimePerRound)
plt.ylabel('E[X1]')
plt.ylabel('Pacotes servidos')
plt.title("V.A. X1 com valor rho1 = " + str(self.utilization))
plt.xlim(xmax=servedPackages)
plt.savefig('images/X1-' + str(self.utilization) + '.png')
plt.clf()
plt.plot(averageVoiceWaitingPerRound)
plt.ylabel('E[W2]')
plt.ylabel('Pacotes servidos')
plt.title("V.A. W2 com valor rho1 = " + str(self.utilization))
plt.xlim(xmax=servedPackages)
plt.savefig('images/W2-' + str(self.utilization) + '.png')
plt.clf()
stdW1perRound = []
stdW2perRound = []
stdX1perRound = []
stdX2perRound = []
stdT1perRound = []
stdT2perRound = []
stdNq1perRound = []
stdNq2perRound = []
for i in range(numberOfRounds):
W1 = totalDataWaitingTimePerRound[
i] / dataPackagesProcessedPerRound[i]
X1 = totalDataProcessingTimePerRound[
i] / dataPackagesProcessedPerRound[i]
T1 = X1 + W1
stdT1perRound.append(T1)
W2 = totalVoiceWaitingTimePerRound[
i] / voicePackagesProcessedPerRound[i]
X2 = X2PerRound[i]
T2 = X2 + W2
stdT2perRound.append(T2)
#print('Round ' + str(i) + ':\nW1: ' + str(W1) + '\tX1: ' + str(X1) + '\tT1: ' + str(T1))
#print('W2: ' + str(W2) + '\tX2: ' + str(X2) + '\tT2: ' + str(T2) + '\n')
dt = 0
dt2 = 0
dts = [0] * constants.VOICE_CHANNELS
for j in range(len(transmissions) // constants.VOICE_CHANNELS):
for k in transmissions[j +
(i * constants.VOICE_CHANNELS)].keys():
transmission = transmissions[
j + (i * constants.VOICE_CHANNELS)].get(k)
if transmission.endTime > 0:
dt += (
(transmission.endTime - transmission.startTime) /
(len(transmissions[j +
(i * constants.VOICE_CHANNELS)])
- 1))
dts[j] = dt
for j in range(len(transmissions) // constants.VOICE_CHANNELS):
for k in transmissions[j +
(i * constants.VOICE_CHANNELS)].keys():
transmission = transmissions[
j + (i * constants.VOICE_CHANNELS)].get(k)
if transmission.endTime > 0:
dt2 += (
((transmission.endTime - transmission.startTime) -
dts[j])**2) / (len(transmissions[
j + (i * constants.VOICE_CHANNELS)]) - 1)
finalW1 += W1 / numberOfRounds
stdW1perRound.append(std(WaitingTimeSamplePerRound[i]))
finalW2 += W2 / numberOfRounds
stdW2perRound.append(std(VoiceWaitingTimeSamplePerRound[i]))
finalX1 += X1 / numberOfRounds
stdX1perRound.append(std(ProcessingTimeSamplePerRound[i]))
finalX2 += X2 / numberOfRounds
finalT1 += T1 / numberOfRounds
finalT2 += T2 / numberOfRounds
finalNq1 += dataPackagesProcessedPerRound[i] / numberOfRounds
finalNq2 += voicePackagesProcessedPerRound[i] / numberOfRounds
dt /= (constants.M1 * numberOfRounds)
dt2 /= (constants.M2 / (constants.M3 * self.utilization) *
numberOfRounds)
finalNq1 = arrivalDataRate * finalW1
finalNq2 = constants.VOICE_PACKAGE_ARRIVAL_RATE * finalW2
finalStdW1 = std(stdW1perRound)
finalStdW2 = std(stdW2perRound)
finalStdX1 = std(stdX1perRound)
finalStdX2 = std(X2PerRound)
finalStdNq1 = std(dataPackagesProcessedPerRound)
finalStdNq2 = std(voicePackagesProcessedPerRound)
finalStdT1 = std(stdT1perRound)
finalStdT2 = std(stdT2perRound)
print('E[W1]: ' + str(finalW1))
print('Std[W1]: ' + str(finalStdW1))
print('IC para W1: ' +
str(stats.norm.interval(0.9, loc=finalW1, scale=finalStdW1)))
print('E[W2]: ' + str(finalW2))
print('Std[W2]: ' + str(finalStdW2))
print('IC para W2: ' +
str(stats.norm.interval(0.9, loc=finalW2, scale=finalStdW2)))
print('E[X1]: ' + str(finalX1))
print('Std[X1]: ' + str(finalStdX1))
print('IC para X1: ' +
str(stats.norm.interval(0.9, loc=finalX1, scale=finalStdX1)))
print('E[X2]: ' + str(finalX2))
print('Std[X2]: ' + str(finalStdX2))
print('IC para X2: ' +
str(stats.norm.interval(0.9, loc=finalX2, scale=finalStdX2)))
print('E[T1]: ' + str(finalT1))
print('Std[T1]: ' + str(finalStdT1))
print('IC para T1: ' +
str(stats.norm.interval(0.9, loc=finalT1, scale=finalStdT1)))
print('E[T2]: ' + str(finalT2))
print('Std[T2]: ' + str(finalStdT2))
print('IC para T2: ' +
str(stats.norm.interval(0.9, loc=finalT2, scale=finalStdT2)))
print('E[Nq1]: ' + str(finalNq1))
print('Std[Nq1]: ' + str(finalStdNq1))
print('IC para Nq1: ' +
str(stats.norm.interval(0.9, loc=finalNq1, scale=finalStdNq1)))
print('E[Nq2]: ' + str(finalNq2))
print('Std[Nq2]: ' + str(finalStdNq2))
print('IC para Nq2: ' +
str(stats.norm.interval(0.9, loc=finalNq2, scale=finalStdNq2)))
print('E[Delta]: ' + str(dt))
print('V[Delta]: ' + str(dt2))
def __init__(self):
self.Q = EventQueue()
self.T = StatusStructure()
self.intersections = []